# | 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 "ConjugateMinimizer.hpp" |
14 | + | #include "OOPSEMinimizer.hpp" |
15 | ||
16 | #ifdef IS_MPI | |
17 | #include "mpiBASS.h" | |
# | Line 20 | Line 24 | |
24 | #define NVT_ENS 1 | |
25 | #define NPTi_ENS 2 | |
26 | #define NPTf_ENS 3 | |
27 | < | #define NPTim_ENS 4 |
24 | < | #define NPTfm_ENS 5 |
25 | < | #define NVEZCONS_ENS 6 |
26 | < | #define NVTZCONS_ENS 7 |
27 | < | #define NPTiZCONS_ENS 8 |
28 | < | #define NPTfZCONS_ENS 9 |
29 | < | #define NPTimZCONS_ENS 10 |
30 | < | #define NPTfmZCONS_ENS 11 |
27 | > | #define NPTxyz_ENS 4 |
28 | ||
32 | – | #define FF_DUFF 0 |
33 | – | #define FF_LJ 1 |
34 | – | #define FF_EAM 2 |
29 | ||
30 | + | #define FF_DUFF 0 |
31 | + | #define FF_LJ 1 |
32 | + | #define FF_EAM 2 |
33 | + | #define FF_H2O 3 |
34 | + | |
35 | using namespace std; | |
36 | ||
37 | + | /** |
38 | + | * Check whether dividend is divisble by divisor or not |
39 | + | */ |
40 | + | bool isDivisible(double dividend, double divisor){ |
41 | + | double tolerance = 0.000001; |
42 | + | double quotient; |
43 | + | double diff; |
44 | + | int intQuotient; |
45 | + | |
46 | + | quotient = dividend / divisor; |
47 | + | |
48 | + | if (quotient < 0) |
49 | + | quotient = -quotient; |
50 | + | |
51 | + | intQuotient = int (quotient + tolerance); |
52 | + | |
53 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
54 | + | |
55 | + | if (diff <= tolerance) |
56 | + | return true; |
57 | + | else |
58 | + | return false; |
59 | + | } |
60 | + | |
61 | SimSetup::SimSetup(){ | |
62 | ||
63 | + | initSuspend = false; |
64 | isInfoArray = 0; | |
65 | nInfo = 1; | |
66 | < | |
66 | > | |
67 | stamps = new MakeStamps(); | |
68 | globals = new Globals(); | |
69 | < | |
70 | < | |
69 | > | |
70 | > | |
71 | #ifdef IS_MPI | |
72 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
72 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
73 | MPIcheckPoint(); | |
74 | #endif // IS_MPI | |
75 | } | |
# | Line 55 | Line 79 | SimSetup::~SimSetup(){ | |
79 | delete globals; | |
80 | } | |
81 | ||
82 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
83 | < | info = the_info; |
84 | < | nInfo = theNinfo; |
85 | < | isInfoArray = 1; |
86 | < | } |
82 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
83 | > | info = the_info; |
84 | > | nInfo = theNinfo; |
85 | > | isInfoArray = 1; |
86 | > | initSuspend = true; |
87 | > | } |
88 | ||
89 | ||
90 | < | void SimSetup::parseFile( char* fileName ){ |
66 | < | |
90 | > | void SimSetup::parseFile(char* fileName){ |
91 | #ifdef IS_MPI | |
92 | < | if( worldRank == 0 ){ |
92 | > | if (worldRank == 0){ |
93 | #endif // is_mpi | |
94 | < | |
94 | > | |
95 | inFileName = fileName; | |
96 | < | set_interface_stamps( stamps, globals ); |
97 | < | |
96 | > | set_interface_stamps(stamps, globals); |
97 | > | |
98 | #ifdef IS_MPI | |
99 | mpiEventInit(); | |
100 | #endif | |
101 | ||
102 | < | yacc_BASS( fileName ); |
102 | > | yacc_BASS(fileName); |
103 | ||
104 | #ifdef IS_MPI | |
105 | throwMPIEvent(NULL); | |
106 | } | |
107 | < | else receiveParse(); |
107 | > | else{ |
108 | > | receiveParse(); |
109 | > | } |
110 | #endif | |
111 | ||
112 | } | |
113 | ||
114 | #ifdef IS_MPI | |
115 | void SimSetup::receiveParse(void){ | |
116 | < | |
117 | < | set_interface_stamps( stamps, globals ); |
118 | < | mpiEventInit(); |
119 | < | MPIcheckPoint(); |
94 | < | mpiEventLoop(); |
95 | < | |
116 | > | set_interface_stamps(stamps, globals); |
117 | > | mpiEventInit(); |
118 | > | MPIcheckPoint(); |
119 | > | mpiEventLoop(); |
120 | } | |
121 | ||
122 | #endif // is_mpi | |
123 | ||
124 | < | void SimSetup::createSim( void ){ |
124 | > | void SimSetup::createSim(void){ |
125 | ||
102 | – | int i, j, k, globalAtomIndex; |
103 | – | |
126 | // gather all of the information from the Bass file | |
127 | < | |
127 | > | |
128 | gatherInfo(); | |
129 | ||
130 | // creation of complex system objects | |
# | Line 110 | Line 132 | void SimSetup::createSim( void ){ | |
132 | sysObjectsCreation(); | |
133 | ||
134 | // check on the post processing info | |
135 | < | |
135 | > | |
136 | finalInfoCheck(); | |
137 | ||
138 | // initialize the system coordinates | |
139 | ||
140 | < | initSystemCoords(); |
141 | < | |
140 | > | if ( !initSuspend ){ |
141 | > | initSystemCoords(); |
142 | ||
143 | + | if( !(globals->getUseInitTime()) ) |
144 | + | info[0].currentTime = 0.0; |
145 | + | } |
146 | + | |
147 | // make the output filenames | |
148 | ||
149 | makeOutNames(); | |
150 | < | |
151 | < | // make the integrator |
150 | > | |
151 | > | if (globals->haveMinimizer()) |
152 | > | // make minimizer |
153 | > | makeMinimizer(); |
154 | > | else |
155 | > | // make the integrator |
156 | > | makeIntegrator(); |
157 | ||
127 | – | makeIntegrator(); |
128 | – | |
158 | #ifdef IS_MPI | |
159 | mpiSim->mpiRefresh(); | |
160 | #endif | |
# | Line 133 | Line 162 | void SimSetup::createSim( void ){ | |
162 | // initialize the Fortran | |
163 | ||
164 | initFortran(); | |
136 | – | |
137 | – | |
138 | – | |
165 | } | |
166 | ||
167 | ||
168 | < | void SimSetup::makeMolecules( void ){ |
169 | < | |
170 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
168 | > | void SimSetup::makeMolecules(void){ |
169 | > | int i, j, k; |
170 | > | int exI, exJ, exK, exL, slI, slJ; |
171 | > | int tempI, tempJ, tempK, tempL; |
172 | > | int molI; |
173 | > | int stampID, atomOffset, rbOffset; |
174 | molInit molInfo; | |
175 | DirectionalAtom* dAtom; | |
176 | + | RigidBody* myRB; |
177 | + | StuntDouble* mySD; |
178 | LinkedAssign* extras; | |
179 | LinkedAssign* current_extra; | |
180 | AtomStamp* currentAtom; | |
181 | BondStamp* currentBond; | |
182 | BendStamp* currentBend; | |
183 | TorsionStamp* currentTorsion; | |
184 | + | RigidBodyStamp* currentRigidBody; |
185 | ||
186 | bond_pair* theBonds; | |
187 | bend_set* theBends; | |
188 | torsion_set* theTorsions; | |
189 | ||
190 | < | |
190 | > | set<int> skipList; |
191 | > | |
192 | > | double phi, theta, psi; |
193 | > | |
194 | //init the forceField paramters | |
195 | ||
196 | the_ff->readParams(); | |
197 | ||
163 | – | |
198 | // init the atoms | |
199 | ||
200 | < | double ux, uy, uz, u, uSqr; |
167 | < | |
168 | < | atomOffset = 0; |
169 | < | excludeOffset = 0; |
170 | < | for(i=0; i<info->n_mol; i++){ |
171 | < | |
172 | < | stampID = the_molecules[i].getStampID(); |
200 | > | int nMembers, nNew, rb1, rb2; |
201 | ||
202 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
203 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
176 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 | < | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 | < | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
202 | > | for (k = 0; k < nInfo; k++){ |
203 | > | the_ff->setSimInfo(&(info[k])); |
204 | ||
205 | < | molInfo.myAtoms = &the_atoms[atomOffset]; |
181 | < | molInfo.myExcludes = &the_excludes[excludeOffset]; |
182 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
183 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
184 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
205 | > | atomOffset = 0; |
206 | ||
207 | < | theBonds = new bond_pair[molInfo.nBonds]; |
208 | < | theBends = new bend_set[molInfo.nBends]; |
209 | < | theTorsions = new torsion_set[molInfo.nTorsions]; |
210 | < | |
211 | < | // make the Atoms |
212 | < | |
213 | < | for(j=0; j<molInfo.nAtoms; j++){ |
207 | > | for (i = 0; i < info[k].n_mol; i++){ |
208 | > | stampID = info[k].molecules[i].getStampID(); |
209 | > | |
210 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
211 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
212 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
213 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
214 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
215 | ||
216 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 | < | if( currentAtom->haveOrientation() ){ |
196 | < | |
197 | < | dAtom = new DirectionalAtom(j + atomOffset); |
198 | < | info->n_oriented++; |
199 | < | molInfo.myAtoms[j] = dAtom; |
200 | < | |
201 | < | ux = currentAtom->getOrntX(); |
202 | < | uy = currentAtom->getOrntY(); |
203 | < | uz = currentAtom->getOrntZ(); |
204 | < | |
205 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 | < | |
207 | < | u = sqrt( uSqr ); |
208 | < | ux = ux / u; |
209 | < | uy = uy / u; |
210 | < | uz = uz / u; |
211 | < | |
212 | < | dAtom->setSUx( ux ); |
213 | < | dAtom->setSUy( uy ); |
214 | < | dAtom->setSUz( uz ); |
215 | < | } |
216 | < | else{ |
217 | < | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
218 | < | } |
219 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 | < | |
221 | < | #ifdef IS_MPI |
222 | < | |
223 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 | < | |
225 | < | #endif // is_mpi |
226 | < | } |
227 | < | |
228 | < | // make the bonds |
229 | < | for(j=0; j<molInfo.nBonds; j++){ |
230 | < | |
231 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
232 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
233 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
216 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
217 | ||
218 | < | exI = theBonds[j].a; |
219 | < | exJ = theBonds[j].b; |
218 | > | if (molInfo.nBonds > 0) |
219 | > | molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
220 | > | else |
221 | > | molInfo.myBonds = NULL; |
222 | ||
223 | < | // exclude_I must always be the smaller of the pair |
224 | < | if( exI > exJ ){ |
225 | < | tempEx = exI; |
226 | < | exI = exJ; |
242 | < | exJ = tempEx; |
243 | < | } |
244 | < | #ifdef IS_MPI |
245 | < | tempEx = exI; |
246 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
247 | < | tempEx = exJ; |
248 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
249 | < | |
250 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
251 | < | #else // isn't MPI |
223 | > | if (molInfo.nBends > 0) |
224 | > | molInfo.myBends = new (Bend *) [molInfo.nBends]; |
225 | > | else |
226 | > | molInfo.myBends = NULL; |
227 | ||
228 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
229 | < | #endif //is_mpi |
230 | < | } |
231 | < | excludeOffset += molInfo.nBonds; |
228 | > | if (molInfo.nTorsions > 0) |
229 | > | molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
230 | > | else |
231 | > | molInfo.myTorsions = NULL; |
232 | ||
233 | < | //make the bends |
234 | < | for(j=0; j<molInfo.nBends; j++){ |
233 | > | theBonds = new bond_pair[molInfo.nBonds]; |
234 | > | theBends = new bend_set[molInfo.nBends]; |
235 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
236 | ||
237 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
238 | < | theBends[j].a = currentBend->getA() + atomOffset; |
239 | < | theBends[j].b = currentBend->getB() + atomOffset; |
240 | < | theBends[j].c = currentBend->getC() + atomOffset; |
241 | < | |
242 | < | if( currentBend->haveExtras() ){ |
243 | < | |
244 | < | extras = currentBend->getExtras(); |
245 | < | current_extra = extras; |
246 | < | |
247 | < | while( current_extra != NULL ){ |
248 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
249 | < | |
250 | < | switch( current_extra->getType() ){ |
251 | < | |
252 | < | case 0: |
253 | < | theBends[j].ghost = |
254 | < | current_extra->getInt() + atomOffset; |
255 | < | theBends[j].isGhost = 1; |
256 | < | break; |
257 | < | |
258 | < | case 1: |
259 | < | theBends[j].ghost = |
260 | < | (int)current_extra->getDouble() + atomOffset; |
261 | < | theBends[j].isGhost = 1; |
262 | < | break; |
263 | < | |
264 | < | default: |
265 | < | sprintf( painCave.errMsg, |
266 | < | "SimSetup Error: ghostVectorSource was neither a " |
267 | < | "double nor an int.\n" |
268 | < | "-->Bend[%d] in %s\n", |
269 | < | j, comp_stamps[stampID]->getID() ); |
270 | < | painCave.isFatal = 1; |
271 | < | simError(); |
272 | < | } |
273 | < | } |
274 | < | |
275 | < | else{ |
276 | < | |
277 | < | sprintf( painCave.errMsg, |
278 | < | "SimSetup Error: unhandled bend assignment:\n" |
279 | < | " -->%s in Bend[%d] in %s\n", |
280 | < | current_extra->getlhs(), |
281 | < | j, comp_stamps[stampID]->getID() ); |
282 | < | painCave.isFatal = 1; |
283 | < | simError(); |
284 | < | } |
285 | < | |
286 | < | current_extra = current_extra->getNext(); |
287 | < | } |
237 | > | // make the Atoms |
238 | > | |
239 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
240 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
241 | > | |
242 | > | if (currentAtom->haveOrientation()){ |
243 | > | dAtom = new DirectionalAtom((j + atomOffset), |
244 | > | info[k].getConfiguration()); |
245 | > | info[k].n_oriented++; |
246 | > | molInfo.myAtoms[j] = dAtom; |
247 | > | |
248 | > | // Directional Atoms have standard unit vectors which are oriented |
249 | > | // in space using the three Euler angles. We assume the standard |
250 | > | // unit vector was originally along the z axis below. |
251 | > | |
252 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
253 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
254 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
255 | > | |
256 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
257 | > | |
258 | > | } |
259 | > | else{ |
260 | > | |
261 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
262 | > | } |
263 | > | |
264 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
265 | > | |
266 | > | #ifdef IS_MPI |
267 | > | |
268 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
269 | > | |
270 | > | #endif // is_mpi |
271 | > | } |
272 | > | |
273 | > | // make the bonds |
274 | > | for (j = 0; j < molInfo.nBonds; j++){ |
275 | > | currentBond = comp_stamps[stampID]->getBond(j); |
276 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
277 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
278 | > | |
279 | > | tempI = theBonds[j].a; |
280 | > | tempJ = theBonds[j].b; |
281 | > | |
282 | > | #ifdef IS_MPI |
283 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
284 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
285 | > | #else |
286 | > | exI = tempI + 1; |
287 | > | exJ = tempJ + 1; |
288 | > | #endif |
289 | > | |
290 | > | info[k].excludes->addPair(exI, exJ); |
291 | } | |
292 | < | |
293 | < | if( !theBends[j].isGhost ){ |
294 | < | |
295 | < | exI = theBends[j].a; |
296 | < | exJ = theBends[j].c; |
297 | < | } |
298 | < | else{ |
299 | < | |
300 | < | exI = theBends[j].a; |
301 | < | exJ = theBends[j].b; |
302 | < | } |
303 | < | |
304 | < | // exclude_I must always be the smaller of the pair |
305 | < | if( exI > exJ ){ |
306 | < | tempEx = exI; |
307 | < | exI = exJ; |
308 | < | exJ = tempEx; |
309 | < | } |
292 | > | |
293 | > | //make the bends |
294 | > | for (j = 0; j < molInfo.nBends; j++){ |
295 | > | currentBend = comp_stamps[stampID]->getBend(j); |
296 | > | theBends[j].a = currentBend->getA() + atomOffset; |
297 | > | theBends[j].b = currentBend->getB() + atomOffset; |
298 | > | theBends[j].c = currentBend->getC() + atomOffset; |
299 | > | |
300 | > | if (currentBend->haveExtras()){ |
301 | > | extras = currentBend->getExtras(); |
302 | > | current_extra = extras; |
303 | > | |
304 | > | while (current_extra != NULL){ |
305 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
306 | > | switch (current_extra->getType()){ |
307 | > | case 0: |
308 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
309 | > | theBends[j].isGhost = 1; |
310 | > | break; |
311 | > | |
312 | > | case 1: |
313 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
314 | > | atomOffset; |
315 | > | theBends[j].isGhost = 1; |
316 | > | break; |
317 | > | |
318 | > | default: |
319 | > | sprintf(painCave.errMsg, |
320 | > | "SimSetup Error: ghostVectorSource was neither a " |
321 | > | "double nor an int.\n" |
322 | > | "-->Bend[%d] in %s\n", |
323 | > | j, comp_stamps[stampID]->getID()); |
324 | > | painCave.isFatal = 1; |
325 | > | simError(); |
326 | > | } |
327 | > | } |
328 | > | else{ |
329 | > | sprintf(painCave.errMsg, |
330 | > | "SimSetup Error: unhandled bend assignment:\n" |
331 | > | " -->%s in Bend[%d] in %s\n", |
332 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
333 | > | painCave.isFatal = 1; |
334 | > | simError(); |
335 | > | } |
336 | > | |
337 | > | current_extra = current_extra->getNext(); |
338 | > | } |
339 | > | } |
340 | > | |
341 | > | if (theBends[j].isGhost) { |
342 | > | |
343 | > | tempI = theBends[j].a; |
344 | > | tempJ = theBends[j].b; |
345 | > | |
346 | #ifdef IS_MPI | |
347 | < | tempEx = exI; |
348 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
349 | < | tempEx = exJ; |
350 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
351 | < | |
352 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
353 | < | #else // isn't MPI |
339 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
340 | < | #endif //is_mpi |
341 | < | } |
342 | < | excludeOffset += molInfo.nBends; |
347 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
348 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
349 | > | #else |
350 | > | exI = tempI + 1; |
351 | > | exJ = tempJ + 1; |
352 | > | #endif |
353 | > | info[k].excludes->addPair(exI, exJ); |
354 | ||
355 | < | for(j=0; j<molInfo.nTorsions; j++){ |
345 | < | |
346 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
347 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
348 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
349 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
350 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
351 | < | |
352 | < | exI = theTorsions[j].a; |
353 | < | exJ = theTorsions[j].d; |
355 | > | } else { |
356 | ||
357 | < | // exclude_I must always be the smaller of the pair |
358 | < | if( exI > exJ ){ |
359 | < | tempEx = exI; |
360 | < | exI = exJ; |
361 | < | exJ = tempEx; |
357 | > | tempI = theBends[j].a; |
358 | > | tempJ = theBends[j].b; |
359 | > | tempK = theBends[j].c; |
360 | > | |
361 | > | #ifdef IS_MPI |
362 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
363 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
364 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
365 | > | #else |
366 | > | exI = tempI + 1; |
367 | > | exJ = tempJ + 1; |
368 | > | exK = tempK + 1; |
369 | > | #endif |
370 | > | |
371 | > | info[k].excludes->addPair(exI, exK); |
372 | > | info[k].excludes->addPair(exI, exJ); |
373 | > | info[k].excludes->addPair(exJ, exK); |
374 | > | } |
375 | } | |
376 | + | |
377 | + | for (j = 0; j < molInfo.nTorsions; j++){ |
378 | + | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
379 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
380 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
381 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
382 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
383 | + | |
384 | + | tempI = theTorsions[j].a; |
385 | + | tempJ = theTorsions[j].b; |
386 | + | tempK = theTorsions[j].c; |
387 | + | tempL = theTorsions[j].d; |
388 | + | |
389 | #ifdef IS_MPI | |
390 | < | tempEx = exI; |
391 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
392 | < | tempEx = exJ; |
393 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
394 | < | |
395 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
396 | < | #else // isn't MPI |
397 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
398 | < | #endif //is_mpi |
399 | < | } |
372 | < | excludeOffset += molInfo.nTorsions; |
390 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
391 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
392 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
393 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
394 | > | #else |
395 | > | exI = tempI + 1; |
396 | > | exJ = tempJ + 1; |
397 | > | exK = tempK + 1; |
398 | > | exL = tempL + 1; |
399 | > | #endif |
400 | ||
401 | < | |
402 | < | // send the arrays off to the forceField for init. |
401 | > | info[k].excludes->addPair(exI, exJ); |
402 | > | info[k].excludes->addPair(exI, exK); |
403 | > | info[k].excludes->addPair(exI, exL); |
404 | > | info[k].excludes->addPair(exJ, exK); |
405 | > | info[k].excludes->addPair(exJ, exL); |
406 | > | info[k].excludes->addPair(exK, exL); |
407 | > | } |
408 | ||
409 | < | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
378 | < | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
379 | < | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
380 | < | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
409 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
410 | ||
411 | + | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
412 | + | nMembers = currentRigidBody->getNMembers(); |
413 | ||
414 | < | the_molecules[i].initialize( molInfo ); |
414 | > | // Create the Rigid Body: |
415 | ||
416 | + | myRB = new RigidBody(); |
417 | + | |
418 | + | for (rb1 = 0; rb1 < nMembers; rb1++) { |
419 | ||
420 | < | atomOffset += molInfo.nAtoms; |
421 | < | delete[] theBonds; |
422 | < | delete[] theBends; |
423 | < | delete[] theTorsions; |
420 | > | // molI is atom numbering inside this molecule |
421 | > | molI = currentRigidBody->getMember(rb1); |
422 | > | |
423 | > | // tempI is atom numbering on local processor |
424 | > | tempI = molI + atomOffset; |
425 | > | |
426 | > | // currentAtom is the AtomStamp (which we need for |
427 | > | // rigid body reference positions) |
428 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
429 | > | |
430 | > | // When we add to the rigid body, add the atom itself and |
431 | > | // the stamp info: |
432 | > | |
433 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
434 | > | |
435 | > | // Add this atom to the Skip List for the integrators |
436 | > | #ifdef IS_MPI |
437 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
438 | > | #else |
439 | > | slI = tempI; |
440 | > | #endif |
441 | > | skipList.insert(slI); |
442 | > | |
443 | > | } |
444 | > | |
445 | > | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
446 | > | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
447 | > | |
448 | > | tempI = currentRigidBody->getMember(rb1); |
449 | > | tempJ = currentRigidBody->getMember(rb2); |
450 | > | |
451 | > | // Some explanation is required here. |
452 | > | // Fortran indexing starts at 1, while c indexing starts at 0 |
453 | > | // Also, in parallel computations, the GlobalIndex is |
454 | > | // used for the exclude list: |
455 | > | |
456 | > | #ifdef IS_MPI |
457 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
458 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
459 | > | #else |
460 | > | exI = tempI + 1; |
461 | > | exJ = tempJ + 1; |
462 | > | #endif |
463 | > | |
464 | > | info[k].excludes->addPair(exI, exJ); |
465 | > | |
466 | > | } |
467 | > | } |
468 | > | |
469 | > | molInfo.myRigidBodies.push_back(myRB); |
470 | > | info[k].rigidBodies.push_back(myRB); |
471 | > | } |
472 | > | |
473 | > | |
474 | > | // After this is all set up, scan through the atoms to |
475 | > | // see if they can be added to the integrableObjects: |
476 | > | |
477 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
478 | > | |
479 | > | #ifdef IS_MPI |
480 | > | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
481 | > | #else |
482 | > | slJ = j+atomOffset; |
483 | > | #endif |
484 | > | |
485 | > | // if they aren't on the skip list, then they can be integrated |
486 | > | |
487 | > | if (skipList.find(slJ) == skipList.end()) { |
488 | > | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
489 | > | info[k].integrableObjects.push_back(mySD); |
490 | > | molInfo.myIntegrableObjects.push_back(mySD); |
491 | > | } |
492 | > | } |
493 | > | |
494 | > | // all rigid bodies are integrated: |
495 | > | |
496 | > | for (j = 0; j < molInfo.nRigidBodies; j++) { |
497 | > | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
498 | > | info[k].integrableObjects.push_back(mySD); |
499 | > | molInfo.myIntegrableObjects.push_back(mySD); |
500 | > | } |
501 | > | |
502 | > | |
503 | > | // send the arrays off to the forceField for init. |
504 | > | |
505 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
506 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
507 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
508 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
509 | > | theTorsions); |
510 | > | |
511 | > | info[k].molecules[i].initialize(molInfo); |
512 | > | |
513 | > | |
514 | > | atomOffset += molInfo.nAtoms; |
515 | > | delete[] theBonds; |
516 | > | delete[] theBends; |
517 | > | delete[] theTorsions; |
518 | > | } |
519 | } | |
520 | ||
521 | #ifdef IS_MPI | |
522 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
522 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
523 | MPIcheckPoint(); | |
524 | #endif // is_mpi | |
525 | ||
526 | // clean up the forcefield | |
398 | – | the_ff->calcRcut(); |
399 | – | the_ff->cleanMe(); |
527 | ||
528 | < | } |
528 | > | if (!globals->haveLJrcut()){ |
529 | ||
530 | < | void SimSetup::initFromBass( void ){ |
530 | > | the_ff->calcRcut(); |
531 | ||
532 | + | } else { |
533 | + | |
534 | + | the_ff->setRcut( globals->getLJrcut() ); |
535 | + | } |
536 | + | |
537 | + | the_ff->cleanMe(); |
538 | + | } |
539 | + | |
540 | + | void SimSetup::initFromBass(void){ |
541 | int i, j, k; | |
542 | int n_cells; | |
543 | double cellx, celly, cellz; | |
# | Line 410 | Line 546 | void SimSetup::initFromBass( void ){ | |
546 | int n_extra; | |
547 | int have_extra, done; | |
548 | ||
549 | < | temp1 = (double)tot_nmol / 4.0; |
550 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
551 | < | temp3 = ceil( temp2 ); |
549 | > | double vel[3]; |
550 | > | vel[0] = 0.0; |
551 | > | vel[1] = 0.0; |
552 | > | vel[2] = 0.0; |
553 | ||
554 | < | have_extra =0; |
555 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
556 | < | have_extra =1; |
554 | > | temp1 = (double) tot_nmol / 4.0; |
555 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
556 | > | temp3 = ceil(temp2); |
557 | ||
558 | < | n_cells = (int)temp3 - 1; |
559 | < | cellx = info->boxL[0] / temp3; |
560 | < | celly = info->boxL[1] / temp3; |
561 | < | cellz = info->boxL[2] / temp3; |
425 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
426 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
427 | < | n_per_extra = (int)ceil( temp1 ); |
558 | > | have_extra = 0; |
559 | > | if (temp2 < temp3){ |
560 | > | // we have a non-complete lattice |
561 | > | have_extra = 1; |
562 | ||
563 | < | if( n_per_extra > 4){ |
564 | < | sprintf( painCave.errMsg, |
565 | < | "SimSetup error. There has been an error in constructing" |
566 | < | " the non-complete lattice.\n" ); |
563 | > | n_cells = (int) temp3 - 1; |
564 | > | cellx = info[0].boxL[0] / temp3; |
565 | > | celly = info[0].boxL[1] / temp3; |
566 | > | cellz = info[0].boxL[2] / temp3; |
567 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
568 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
569 | > | n_per_extra = (int) ceil(temp1); |
570 | > | |
571 | > | if (n_per_extra > 4){ |
572 | > | sprintf(painCave.errMsg, |
573 | > | "SimSetup error. There has been an error in constructing" |
574 | > | " the non-complete lattice.\n"); |
575 | painCave.isFatal = 1; | |
576 | simError(); | |
577 | } | |
578 | } | |
579 | else{ | |
580 | < | n_cells = (int)temp3; |
581 | < | cellx = info->boxL[0] / temp3; |
582 | < | celly = info->boxL[1] / temp3; |
583 | < | cellz = info->boxL[2] / temp3; |
580 | > | n_cells = (int) temp3; |
581 | > | cellx = info[0].boxL[0] / temp3; |
582 | > | celly = info[0].boxL[1] / temp3; |
583 | > | cellz = info[0].boxL[2] / temp3; |
584 | } | |
585 | ||
586 | current_mol = 0; | |
# | Line 446 | Line 588 | void SimSetup::initFromBass( void ){ | |
588 | current_comp = 0; | |
589 | current_atom_ndx = 0; | |
590 | ||
591 | < | for( i=0; i < n_cells ; i++ ){ |
592 | < | for( j=0; j < n_cells; j++ ){ |
593 | < | for( k=0; k < n_cells; k++ ){ |
591 | > | for (i = 0; i < n_cells ; i++){ |
592 | > | for (j = 0; j < n_cells; j++){ |
593 | > | for (k = 0; k < n_cells; k++){ |
594 | > | makeElement(i * cellx, j * celly, k * cellz); |
595 | ||
596 | < | makeElement( i * cellx, |
454 | < | j * celly, |
455 | < | k * cellz ); |
596 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
597 | ||
598 | < | makeElement( i * cellx + 0.5 * cellx, |
458 | < | j * celly + 0.5 * celly, |
459 | < | k * cellz ); |
598 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
599 | ||
600 | < | makeElement( i * cellx, |
462 | < | j * celly + 0.5 * celly, |
463 | < | k * cellz + 0.5 * cellz ); |
464 | < | |
465 | < | makeElement( i * cellx + 0.5 * cellx, |
466 | < | j * celly, |
467 | < | k * cellz + 0.5 * cellz ); |
600 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
601 | } | |
602 | } | |
603 | } | |
604 | ||
605 | < | if( have_extra ){ |
605 | > | if (have_extra){ |
606 | done = 0; | |
607 | ||
608 | int start_ndx; | |
609 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
610 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
609 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
610 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
611 | > | if (i < n_cells){ |
612 | > | if (j < n_cells){ |
613 | > | start_ndx = n_cells; |
614 | > | } |
615 | > | else |
616 | > | start_ndx = 0; |
617 | > | } |
618 | > | else |
619 | > | start_ndx = 0; |
620 | ||
621 | < | if( i < n_cells ){ |
621 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
622 | > | makeElement(i * cellx, j * celly, k * cellz); |
623 | > | done = (current_mol >= tot_nmol); |
624 | ||
625 | < | if( j < n_cells ){ |
626 | < | start_ndx = n_cells; |
627 | < | } |
628 | < | else start_ndx = 0; |
629 | < | } |
486 | < | else start_ndx = 0; |
625 | > | if (!done && n_per_extra > 1){ |
626 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
627 | > | k * cellz); |
628 | > | done = (current_mol >= tot_nmol); |
629 | > | } |
630 | ||
631 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
631 | > | if (!done && n_per_extra > 2){ |
632 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
633 | > | k * cellz + 0.5 * cellz); |
634 | > | done = (current_mol >= tot_nmol); |
635 | > | } |
636 | ||
637 | < | makeElement( i * cellx, |
638 | < | j * celly, |
639 | < | k * cellz ); |
640 | < | done = ( current_mol >= tot_nmol ); |
641 | < | |
642 | < | if( !done && n_per_extra > 1 ){ |
496 | < | makeElement( i * cellx + 0.5 * cellx, |
497 | < | j * celly + 0.5 * celly, |
498 | < | k * cellz ); |
499 | < | done = ( current_mol >= tot_nmol ); |
500 | < | } |
501 | < | |
502 | < | if( !done && n_per_extra > 2){ |
503 | < | makeElement( i * cellx, |
504 | < | j * celly + 0.5 * celly, |
505 | < | k * cellz + 0.5 * cellz ); |
506 | < | done = ( current_mol >= tot_nmol ); |
507 | < | } |
508 | < | |
509 | < | if( !done && n_per_extra > 3){ |
510 | < | makeElement( i * cellx + 0.5 * cellx, |
511 | < | j * celly, |
512 | < | k * cellz + 0.5 * cellz ); |
513 | < | done = ( current_mol >= tot_nmol ); |
514 | < | } |
515 | < | } |
637 | > | if (!done && n_per_extra > 3){ |
638 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
639 | > | k * cellz + 0.5 * cellz); |
640 | > | done = (current_mol >= tot_nmol); |
641 | > | } |
642 | > | } |
643 | } | |
644 | } | |
645 | } | |
646 | ||
647 | < | |
648 | < | for( i=0; i<info->n_atoms; i++ ){ |
522 | < | info->atoms[i]->set_vx( 0.0 ); |
523 | < | info->atoms[i]->set_vy( 0.0 ); |
524 | < | info->atoms[i]->set_vz( 0.0 ); |
647 | > | for (i = 0; i < info[0].n_atoms; i++){ |
648 | > | info[0].atoms[i]->setVel(vel); |
649 | } | |
650 | } | |
651 | ||
652 | < | void SimSetup::makeElement( double x, double y, double z ){ |
529 | < | |
652 | > | void SimSetup::makeElement(double x, double y, double z){ |
653 | int k; | |
654 | AtomStamp* current_atom; | |
655 | DirectionalAtom* dAtom; | |
656 | double rotMat[3][3]; | |
657 | + | double pos[3]; |
658 | ||
659 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
660 | < | |
661 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
662 | < | if( !current_atom->havePosition() ){ |
663 | < | sprintf( painCave.errMsg, |
664 | < | "SimSetup:initFromBass error.\n" |
665 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
666 | < | "\tThe initialization routine is unable to give a start" |
667 | < | " position.\n", |
544 | < | comp_stamps[current_comp]->getID(), |
545 | < | current_atom->getType() ); |
659 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
660 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
661 | > | if (!current_atom->havePosition()){ |
662 | > | sprintf(painCave.errMsg, |
663 | > | "SimSetup:initFromBass error.\n" |
664 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
665 | > | "\tThe initialization routine is unable to give a start" |
666 | > | " position.\n", |
667 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
668 | painCave.isFatal = 1; | |
669 | simError(); | |
670 | } | |
671 | ||
672 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
673 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
674 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
672 | > | pos[0] = x + current_atom->getPosX(); |
673 | > | pos[1] = y + current_atom->getPosY(); |
674 | > | pos[2] = z + current_atom->getPosZ(); |
675 | ||
676 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
676 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
677 | ||
678 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
678 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
679 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
680 | ||
681 | rotMat[0][0] = 1.0; | |
682 | rotMat[0][1] = 0.0; | |
# | Line 567 | Line 690 | void SimSetup::makeElement( double x, double y, double | |
690 | rotMat[2][1] = 0.0; | |
691 | rotMat[2][2] = 1.0; | |
692 | ||
693 | < | dAtom->setA( rotMat ); |
693 | > | dAtom->setA(rotMat); |
694 | } | |
695 | ||
696 | current_atom_ndx++; | |
# | Line 576 | Line 699 | void SimSetup::makeElement( double x, double y, double | |
699 | current_mol++; | |
700 | current_comp_mol++; | |
701 | ||
702 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
580 | < | |
702 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
703 | current_comp_mol = 0; | |
704 | current_comp++; | |
705 | } | |
706 | } | |
707 | ||
708 | ||
709 | < | void SimSetup::gatherInfo( void ){ |
710 | < | int i,j,k; |
709 | > | void SimSetup::gatherInfo(void){ |
710 | > | int i; |
711 | ||
712 | ensembleCase = -1; | |
713 | ffCase = -1; | |
714 | ||
593 | – | // get the stamps and globals; |
594 | – | stamps = stamps; |
595 | – | globals = globals; |
596 | – | |
715 | // set the easy ones first | |
716 | < | info->target_temp = globals->getTargetTemp(); |
717 | < | info->dt = globals->getDt(); |
718 | < | info->run_time = globals->getRunTime(); |
716 | > | |
717 | > | for (i = 0; i < nInfo; i++){ |
718 | > | info[i].target_temp = globals->getTargetTemp(); |
719 | > | info[i].dt = globals->getDt(); |
720 | > | info[i].run_time = globals->getRunTime(); |
721 | > | } |
722 | n_components = globals->getNComponents(); | |
723 | ||
724 | ||
725 | // get the forceField | |
726 | ||
727 | < | strcpy( force_field, globals->getForceField() ); |
727 | > | strcpy(force_field, globals->getForceField()); |
728 | ||
729 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
730 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
731 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
729 | > | if (!strcasecmp(force_field, "DUFF")){ |
730 | > | ffCase = FF_DUFF; |
731 | > | } |
732 | > | else if (!strcasecmp(force_field, "LJ")){ |
733 | > | ffCase = FF_LJ; |
734 | > | } |
735 | > | else if (!strcasecmp(force_field, "EAM")){ |
736 | > | ffCase = FF_EAM; |
737 | > | } |
738 | > | else if (!strcasecmp(force_field, "WATER")){ |
739 | > | ffCase = FF_H2O; |
740 | > | } |
741 | else{ | |
742 | < | sprintf( painCave.errMsg, |
743 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
744 | < | force_field ); |
745 | < | painCave.isFatal = 1; |
616 | < | simError(); |
742 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
743 | > | force_field); |
744 | > | painCave.isFatal = 1; |
745 | > | simError(); |
746 | } | |
747 | ||
748 | < | // get the ensemble |
748 | > | // get the ensemble |
749 | ||
750 | < | strcpy( ensemble, globals->getEnsemble() ); |
750 | > | strcpy(ensemble, globals->getEnsemble()); |
751 | ||
752 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
753 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
754 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
752 | > | if (!strcasecmp(ensemble, "NVE")){ |
753 | > | ensembleCase = NVE_ENS; |
754 | > | } |
755 | > | else if (!strcasecmp(ensemble, "NVT")){ |
756 | > | ensembleCase = NVT_ENS; |
757 | > | } |
758 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
759 | ensembleCase = NPTi_ENS; | |
760 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
761 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
762 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
763 | < | |
764 | < | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
765 | < | else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
766 | < | else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) |
634 | < | ensembleCase = NPTiZCONS_ENS; |
635 | < | else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; |
636 | < | else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
637 | < | else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; |
638 | < | |
760 | > | } |
761 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
762 | > | ensembleCase = NPTf_ENS; |
763 | > | } |
764 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
765 | > | ensembleCase = NPTxyz_ENS; |
766 | > | } |
767 | else{ | |
768 | < | sprintf( painCave.errMsg, |
769 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
770 | < | "reverting to NVE for this simulation.\n", |
771 | < | ensemble ); |
772 | < | painCave.isFatal = 0; |
773 | < | simError(); |
774 | < | strcpy( ensemble, "NVE" ); |
775 | < | ensembleCase = NVE_ENS; |
768 | > | sprintf(painCave.errMsg, |
769 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
770 | > | "\treverting to NVE for this simulation.\n", |
771 | > | ensemble); |
772 | > | painCave.isFatal = 0; |
773 | > | simError(); |
774 | > | strcpy(ensemble, "NVE"); |
775 | > | ensembleCase = NVE_ENS; |
776 | } | |
649 | – | strcpy( info->ensemble, ensemble ); |
777 | ||
778 | < | // get the mixing rule |
778 | > | for (i = 0; i < nInfo; i++){ |
779 | > | strcpy(info[i].ensemble, ensemble); |
780 | ||
781 | < | strcpy( info->mixingRule, globals->getMixingRule() ); |
782 | < | info->usePBC = globals->getPBC(); |
783 | < | |
784 | < | |
781 | > | // get the mixing rule |
782 | > | |
783 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
784 | > | info[i].usePBC = globals->getPBC(); |
785 | > | } |
786 | > | |
787 | // get the components and calculate the tot_nMol and indvidual n_mol | |
788 | < | |
788 | > | |
789 | the_components = globals->getComponents(); | |
790 | components_nmol = new int[n_components]; | |
791 | ||
792 | ||
793 | < | if( !globals->haveNMol() ){ |
793 | > | if (!globals->haveNMol()){ |
794 | // we don't have the total number of molecules, so we assume it is | |
795 | // given in each component | |
796 | ||
797 | tot_nmol = 0; | |
798 | < | for( i=0; i<n_components; i++ ){ |
799 | < | |
800 | < | if( !the_components[i]->haveNMol() ){ |
801 | < | // we have a problem |
802 | < | sprintf( painCave.errMsg, |
803 | < | "SimSetup Error. No global NMol or component NMol" |
804 | < | " given. Cannot calculate the number of atoms.\n" ); |
805 | < | painCave.isFatal = 1; |
676 | < | simError(); |
798 | > | for (i = 0; i < n_components; i++){ |
799 | > | if (!the_components[i]->haveNMol()){ |
800 | > | // we have a problem |
801 | > | sprintf(painCave.errMsg, |
802 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
803 | > | "\tCannot calculate the number of atoms.\n"); |
804 | > | painCave.isFatal = 1; |
805 | > | simError(); |
806 | } | |
807 | ||
808 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 681 | Line 810 | void SimSetup::gatherInfo( void ){ | |
810 | } | |
811 | } | |
812 | else{ | |
813 | < | sprintf( painCave.errMsg, |
814 | < | "SimSetup error.\n" |
815 | < | "\tSorry, the ability to specify total" |
816 | < | " nMols and then give molfractions in the components\n" |
817 | < | "\tis not currently supported." |
818 | < | " Please give nMol in the components.\n" ); |
813 | > | sprintf(painCave.errMsg, |
814 | > | "SimSetup error.\n" |
815 | > | "\tSorry, the ability to specify total" |
816 | > | " nMols and then give molfractions in the components\n" |
817 | > | "\tis not currently supported." |
818 | > | " Please give nMol in the components.\n"); |
819 | painCave.isFatal = 1; | |
820 | simError(); | |
821 | } | |
822 | ||
823 | < | // set the status, sample, and thermal kick times |
824 | < | |
825 | < | if( globals->haveSampleTime() ){ |
826 | < | info->sampleTime = globals->getSampleTime(); |
827 | < | info->statusTime = info->sampleTime; |
828 | < | info->thermalTime = info->sampleTime; |
823 | > | //check whether sample time, status time, thermal time and reset time are divisble by dt |
824 | > | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
825 | > | sprintf(painCave.errMsg, |
826 | > | "Sample time is not divisible by dt.\n" |
827 | > | "\tThis will result in samples that are not uniformly\n" |
828 | > | "\tdistributed in time. If this is a problem, change\n" |
829 | > | "\tyour sampleTime variable.\n"); |
830 | > | painCave.isFatal = 0; |
831 | > | simError(); |
832 | } | |
701 | – | else{ |
702 | – | info->sampleTime = globals->getRunTime(); |
703 | – | info->statusTime = info->sampleTime; |
704 | – | info->thermalTime = info->sampleTime; |
705 | – | } |
833 | ||
834 | < | if( globals->haveStatusTime() ){ |
835 | < | info->statusTime = globals->getStatusTime(); |
834 | > | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
835 | > | sprintf(painCave.errMsg, |
836 | > | "Status time is not divisible by dt.\n" |
837 | > | "\tThis will result in status reports that are not uniformly\n" |
838 | > | "\tdistributed in time. If this is a problem, change \n" |
839 | > | "\tyour statusTime variable.\n"); |
840 | > | painCave.isFatal = 0; |
841 | > | simError(); |
842 | } | |
843 | ||
844 | < | if( globals->haveThermalTime() ){ |
845 | < | info->thermalTime = globals->getThermalTime(); |
846 | < | } |
844 | > | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
845 | > | sprintf(painCave.errMsg, |
846 | > | "Thermal time is not divisible by dt.\n" |
847 | > | "\tThis will result in thermalizations that are not uniformly\n" |
848 | > | "\tdistributed in time. If this is a problem, change \n" |
849 | > | "\tyour thermalTime variable.\n"); |
850 | > | painCave.isFatal = 0; |
851 | > | simError(); |
852 | > | } |
853 | ||
854 | < | // check for the temperature set flag |
855 | < | |
856 | < | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
854 | > | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
855 | > | sprintf(painCave.errMsg, |
856 | > | "Reset time is not divisible by dt.\n" |
857 | > | "\tThis will result in integrator resets that are not uniformly\n" |
858 | > | "\tdistributed in time. If this is a problem, change\n" |
859 | > | "\tyour resetTime variable.\n"); |
860 | > | painCave.isFatal = 0; |
861 | > | simError(); |
862 | > | } |
863 | ||
864 | < | // get some of the tricky things that may still be in the globals |
864 | > | // set the status, sample, and thermal kick times |
865 | ||
866 | < | double boxVector[3]; |
867 | < | if( globals->haveBox() ){ |
868 | < | boxVector[0] = globals->getBox(); |
869 | < | boxVector[1] = globals->getBox(); |
870 | < | boxVector[2] = globals->getBox(); |
871 | < | |
872 | < | info->setBox( boxVector ); |
873 | < | } |
874 | < | else if( globals->haveDensity() ){ |
866 | > | for (i = 0; i < nInfo; i++){ |
867 | > | if (globals->haveSampleTime()){ |
868 | > | info[i].sampleTime = globals->getSampleTime(); |
869 | > | info[i].statusTime = info[i].sampleTime; |
870 | > | info[i].thermalTime = info[i].sampleTime; |
871 | > | } |
872 | > | else{ |
873 | > | info[i].sampleTime = globals->getRunTime(); |
874 | > | info[i].statusTime = info[i].sampleTime; |
875 | > | info[i].thermalTime = info[i].sampleTime; |
876 | > | } |
877 | ||
878 | < | double vol; |
879 | < | vol = (double)tot_nmol / globals->getDensity(); |
733 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
734 | < | boxVector[1] = boxVector[0]; |
735 | < | boxVector[2] = boxVector[0]; |
736 | < | |
737 | < | info->setBox( boxVector ); |
738 | < | } |
739 | < | else{ |
740 | < | if( !globals->haveBoxX() ){ |
741 | < | sprintf( painCave.errMsg, |
742 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
743 | < | painCave.isFatal = 1; |
744 | < | simError(); |
878 | > | if (globals->haveStatusTime()){ |
879 | > | info[i].statusTime = globals->getStatusTime(); |
880 | } | |
746 | – | boxVector[0] = globals->getBoxX(); |
881 | ||
882 | < | if( !globals->haveBoxY() ){ |
883 | < | sprintf( painCave.errMsg, |
750 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
751 | < | painCave.isFatal = 1; |
752 | < | simError(); |
882 | > | if (globals->haveThermalTime()){ |
883 | > | info[i].thermalTime = globals->getThermalTime(); |
884 | } | |
754 | – | boxVector[1] = globals->getBoxY(); |
885 | ||
886 | < | if( !globals->haveBoxZ() ){ |
887 | < | sprintf( painCave.errMsg, |
888 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
889 | < | painCave.isFatal = 1; |
760 | < | simError(); |
886 | > | info[i].resetIntegrator = 0; |
887 | > | if( globals->haveResetTime() ){ |
888 | > | info[i].resetTime = globals->getResetTime(); |
889 | > | info[i].resetIntegrator = 1; |
890 | } | |
762 | – | boxVector[2] = globals->getBoxZ(); |
891 | ||
892 | < | info->setBox( boxVector ); |
892 | > | // check for the temperature set flag |
893 | > | |
894 | > | if (globals->haveTempSet()) |
895 | > | info[i].setTemp = globals->getTempSet(); |
896 | > | |
897 | > | // check for the extended State init |
898 | > | |
899 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
900 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
901 | > | |
902 | } | |
903 | + | |
904 | + | //setup seed for random number generator |
905 | + | int seedValue; |
906 | ||
907 | + | if (globals->haveSeed()){ |
908 | + | seedValue = globals->getSeed(); |
909 | ||
910 | + | if(seedValue / 1E9 == 0){ |
911 | + | sprintf(painCave.errMsg, |
912 | + | "Seed for sprng library should contain at least 9 digits\n" |
913 | + | "OOPSE will generate a seed for user\n"); |
914 | + | painCave.isFatal = 0; |
915 | + | simError(); |
916 | + | |
917 | + | //using seed generated by system instead of invalid seed set by user |
918 | + | #ifndef IS_MPI |
919 | + | seedValue = make_sprng_seed(); |
920 | + | #else |
921 | + | if (worldRank == 0){ |
922 | + | seedValue = make_sprng_seed(); |
923 | + | } |
924 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
925 | + | #endif |
926 | + | } |
927 | + | }//end of if branch of globals->haveSeed() |
928 | + | else{ |
929 | ||
930 | + | #ifndef IS_MPI |
931 | + | seedValue = make_sprng_seed(); |
932 | + | #else |
933 | + | if (worldRank == 0){ |
934 | + | seedValue = make_sprng_seed(); |
935 | + | } |
936 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
937 | + | #endif |
938 | + | }//end of globals->haveSeed() |
939 | + | |
940 | + | for (int i = 0; i < nInfo; i++){ |
941 | + | info[i].setSeed(seedValue); |
942 | + | } |
943 | + | |
944 | #ifdef IS_MPI | |
945 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
945 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
946 | MPIcheckPoint(); | |
947 | #endif // is_mpi | |
773 | – | |
948 | } | |
949 | ||
950 | ||
951 | < | void SimSetup::finalInfoCheck( void ){ |
951 | > | void SimSetup::finalInfoCheck(void){ |
952 | int index; | |
953 | int usesDipoles; | |
954 | < | |
954 | > | int i; |
955 | ||
956 | < | // check electrostatic parameters |
957 | < | |
958 | < | index = 0; |
959 | < | usesDipoles = 0; |
960 | < | while( (index < info->n_atoms) && !usesDipoles ){ |
961 | < | usesDipoles = ((info->atoms)[index])->hasDipole(); |
962 | < | index++; |
963 | < | } |
964 | < | |
956 | > | for (i = 0; i < nInfo; i++){ |
957 | > | // check electrostatic parameters |
958 | > | |
959 | > | index = 0; |
960 | > | usesDipoles = 0; |
961 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
962 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
963 | > | index++; |
964 | > | } |
965 | > | |
966 | #ifdef IS_MPI | |
967 | < | int myUse = usesDipoles; |
968 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
967 | > | int myUse = usesDipoles; |
968 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
969 | #endif //is_mpi | |
970 | ||
971 | < | double theEcr, theEst; |
971 | > | double theEcr, theEst; |
972 | ||
973 | < | if (globals->getUseRF() ) { |
974 | < | info->useReactionField = 1; |
800 | < | |
801 | < | if( !globals->haveECR() ){ |
802 | < | sprintf( painCave.errMsg, |
803 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
804 | < | "box length for the electrostaticCutoffRadius.\n" |
805 | < | "I hope you have a very fast processor!\n"); |
806 | < | painCave.isFatal = 0; |
807 | < | simError(); |
808 | < | double smallest; |
809 | < | smallest = info->boxL[0]; |
810 | < | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
811 | < | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
812 | < | theEcr = 0.5 * smallest; |
813 | < | } else { |
814 | < | theEcr = globals->getECR(); |
815 | < | } |
973 | > | if (globals->getUseRF()){ |
974 | > | info[i].useReactionField = 1; |
975 | ||
976 | < | if( !globals->haveEST() ){ |
977 | < | sprintf( painCave.errMsg, |
978 | < | "SimSetup Warning: using default value of 0.05 * the " |
979 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
980 | < | ); |
981 | < | painCave.isFatal = 0; |
982 | < | simError(); |
983 | < | theEst = 0.05 * theEcr; |
825 | < | } else { |
826 | < | theEst= globals->getEST(); |
827 | < | } |
828 | < | |
829 | < | info->setEcr( theEcr, theEst ); |
830 | < | |
831 | < | if(!globals->haveDielectric() ){ |
832 | < | sprintf( painCave.errMsg, |
833 | < | "SimSetup Error: You are trying to use Reaction Field without" |
834 | < | "setting a dielectric constant!\n" |
835 | < | ); |
836 | < | painCave.isFatal = 1; |
837 | < | simError(); |
838 | < | } |
839 | < | info->dielectric = globals->getDielectric(); |
840 | < | } |
841 | < | else { |
842 | < | if (usesDipoles) { |
843 | < | |
844 | < | if( !globals->haveECR() ){ |
845 | < | sprintf( painCave.errMsg, |
846 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
847 | < | "box length for the electrostaticCutoffRadius.\n" |
848 | < | "I hope you have a very fast processor!\n"); |
849 | < | painCave.isFatal = 0; |
850 | < | simError(); |
851 | < | double smallest; |
852 | < | smallest = info->boxL[0]; |
853 | < | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
854 | < | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
855 | < | theEcr = 0.5 * smallest; |
856 | < | } else { |
857 | < | theEcr = globals->getECR(); |
976 | > | if (!globals->haveECR()){ |
977 | > | sprintf(painCave.errMsg, |
978 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
979 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
980 | > | "\tfor the electrostaticCutoffRadius.\n"); |
981 | > | painCave.isFatal = 0; |
982 | > | simError(); |
983 | > | theEcr = 15.0; |
984 | } | |
985 | < | |
986 | < | if( !globals->haveEST() ){ |
861 | < | sprintf( painCave.errMsg, |
862 | < | "SimSetup Warning: using default value of 0.05 * the " |
863 | < | "electrostaticCutoffRadius for the " |
864 | < | "electrostaticSkinThickness\n" |
865 | < | ); |
866 | < | painCave.isFatal = 0; |
867 | < | simError(); |
868 | < | theEst = 0.05 * theEcr; |
869 | < | } else { |
870 | < | theEst= globals->getEST(); |
985 | > | else{ |
986 | > | theEcr = globals->getECR(); |
987 | } | |
988 | ||
989 | < | info->setEcr( theEcr, theEst ); |
990 | < | } |
991 | < | } |
989 | > | if (!globals->haveEST()){ |
990 | > | sprintf(painCave.errMsg, |
991 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
992 | > | "\tOOPSE will use a default value of\n" |
993 | > | "\t0.05 * electrostaticCutoffRadius\n" |
994 | > | "\tfor the electrostaticSkinThickness\n"); |
995 | > | painCave.isFatal = 0; |
996 | > | simError(); |
997 | > | theEst = 0.05 * theEcr; |
998 | > | } |
999 | > | else{ |
1000 | > | theEst = globals->getEST(); |
1001 | > | } |
1002 | ||
1003 | + | info[i].setDefaultEcr(theEcr, theEst); |
1004 | + | |
1005 | + | if (!globals->haveDielectric()){ |
1006 | + | sprintf(painCave.errMsg, |
1007 | + | "SimSetup Error: No Dielectric constant was set.\n" |
1008 | + | "\tYou are trying to use Reaction Field without" |
1009 | + | "\tsetting a dielectric constant!\n"); |
1010 | + | painCave.isFatal = 1; |
1011 | + | simError(); |
1012 | + | } |
1013 | + | info[i].dielectric = globals->getDielectric(); |
1014 | + | } |
1015 | + | else{ |
1016 | + | if (usesDipoles){ |
1017 | + | if (!globals->haveECR()){ |
1018 | + | sprintf(painCave.errMsg, |
1019 | + | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
1020 | + | "\tOOPSE will use a default value of 15.0 angstroms" |
1021 | + | "\tfor the electrostaticCutoffRadius.\n"); |
1022 | + | painCave.isFatal = 0; |
1023 | + | simError(); |
1024 | + | theEcr = 15.0; |
1025 | + | } |
1026 | + | else{ |
1027 | + | theEcr = globals->getECR(); |
1028 | + | } |
1029 | + | |
1030 | + | if (!globals->haveEST()){ |
1031 | + | sprintf(painCave.errMsg, |
1032 | + | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
1033 | + | "\tOOPSE will use a default value of\n" |
1034 | + | "\t0.05 * electrostaticCutoffRadius\n" |
1035 | + | "\tfor the electrostaticSkinThickness\n"); |
1036 | + | painCave.isFatal = 0; |
1037 | + | simError(); |
1038 | + | theEst = 0.05 * theEcr; |
1039 | + | } |
1040 | + | else{ |
1041 | + | theEst = globals->getEST(); |
1042 | + | } |
1043 | + | |
1044 | + | info[i].setDefaultEcr(theEcr, theEst); |
1045 | + | } |
1046 | + | } |
1047 | + | } |
1048 | #ifdef IS_MPI | |
1049 | < | strcpy( checkPointMsg, "post processing checks out" ); |
1049 | > | strcpy(checkPointMsg, "post processing checks out"); |
1050 | MPIcheckPoint(); | |
1051 | #endif // is_mpi | |
881 | – | |
1052 | } | |
1053 | + | |
1054 | + | void SimSetup::initSystemCoords(void){ |
1055 | + | int i; |
1056 | ||
1057 | < | void SimSetup::initSystemCoords( void ){ |
1057 | > | char* inName; |
1058 | ||
1059 | < | if( globals->haveInitialConfig() ){ |
1060 | < | |
1061 | < | InitializeFromFile* fileInit; |
1059 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1060 | > | |
1061 | > | for (i = 0; i < info[0].n_atoms; i++) |
1062 | > | info[0].atoms[i]->setCoords(); |
1063 | > | |
1064 | > | if (globals->haveInitialConfig()){ |
1065 | > | InitializeFromFile* fileInit; |
1066 | #ifdef IS_MPI // is_mpi | |
1067 | < | if( worldRank == 0 ){ |
1067 | > | if (worldRank == 0){ |
1068 | #endif //is_mpi | |
1069 | < | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
1069 | > | inName = globals->getInitialConfig(); |
1070 | > | fileInit = new InitializeFromFile(inName); |
1071 | #ifdef IS_MPI | |
1072 | < | }else fileInit = new InitializeFromFile( NULL ); |
1072 | > | } |
1073 | > | else |
1074 | > | fileInit = new InitializeFromFile(NULL); |
1075 | #endif | |
1076 | < | fileInit->readInit( info ); // default velocities on |
1076 | > | fileInit->readInit(info); // default velocities on |
1077 | ||
1078 | < | delete fileInit; |
1079 | < | } |
1080 | < | else{ |
1078 | > | delete fileInit; |
1079 | > | } |
1080 | > | else{ |
1081 | > | |
1082 | > | // no init from bass |
1083 | > | |
1084 | > | sprintf(painCave.errMsg, |
1085 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1086 | > | painCave.isFatal = 1;; |
1087 | > | simError(); |
1088 | > | |
1089 | > | } |
1090 | ||
902 | – | #ifdef IS_MPI |
903 | – | |
904 | – | // no init from bass |
905 | – | |
906 | – | sprintf( painCave.errMsg, |
907 | – | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
908 | – | painCave.isFatal; |
909 | – | simError(); |
910 | – | |
911 | – | #else |
912 | – | |
913 | – | initFromBass(); |
914 | – | |
915 | – | |
916 | – | #endif |
917 | – | } |
918 | – | |
1091 | #ifdef IS_MPI | |
1092 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1092 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1093 | MPIcheckPoint(); | |
1094 | #endif // is_mpi | |
923 | – | |
1095 | } | |
1096 | ||
1097 | ||
1098 | < | void SimSetup::makeOutNames( void ){ |
1098 | > | void SimSetup::makeOutNames(void){ |
1099 | > | int k; |
1100 | ||
1101 | + | |
1102 | + | for (k = 0; k < nInfo; k++){ |
1103 | #ifdef IS_MPI | |
1104 | < | if( worldRank == 0 ){ |
1104 | > | if (worldRank == 0){ |
1105 | #endif // is_mpi | |
1106 | < | |
1107 | < | if( globals->haveFinalConfig() ){ |
1108 | < | strcpy( info->finalName, globals->getFinalConfig() ); |
935 | < | } |
936 | < | else{ |
937 | < | strcpy( info->finalName, inFileName ); |
938 | < | char* endTest; |
939 | < | int nameLength = strlen( info->finalName ); |
940 | < | endTest = &(info->finalName[nameLength - 5]); |
941 | < | if( !strcmp( endTest, ".bass" ) ){ |
942 | < | strcpy( endTest, ".eor" ); |
1106 | > | |
1107 | > | if (globals->haveFinalConfig()){ |
1108 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1109 | } | |
944 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
945 | – | strcpy( endTest, ".eor" ); |
946 | – | } |
1110 | else{ | |
1111 | < | endTest = &(info->finalName[nameLength - 4]); |
1112 | < | if( !strcmp( endTest, ".bss" ) ){ |
1113 | < | strcpy( endTest, ".eor" ); |
1114 | < | } |
1115 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1116 | < | strcpy( endTest, ".eor" ); |
1117 | < | } |
1118 | < | else{ |
1119 | < | strcat( info->finalName, ".eor" ); |
1120 | < | } |
1111 | > | strcpy(info[k].finalName, inFileName); |
1112 | > | char* endTest; |
1113 | > | int nameLength = strlen(info[k].finalName); |
1114 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1115 | > | if (!strcmp(endTest, ".bass")){ |
1116 | > | strcpy(endTest, ".eor"); |
1117 | > | } |
1118 | > | else if (!strcmp(endTest, ".BASS")){ |
1119 | > | strcpy(endTest, ".eor"); |
1120 | > | } |
1121 | > | else{ |
1122 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1123 | > | if (!strcmp(endTest, ".bss")){ |
1124 | > | strcpy(endTest, ".eor"); |
1125 | > | } |
1126 | > | else if (!strcmp(endTest, ".mdl")){ |
1127 | > | strcpy(endTest, ".eor"); |
1128 | > | } |
1129 | > | else{ |
1130 | > | strcat(info[k].finalName, ".eor"); |
1131 | > | } |
1132 | > | } |
1133 | } | |
1134 | < | } |
1135 | < | |
1136 | < | // make the sample and status out names |
1137 | < | |
1138 | < | strcpy( info->sampleName, inFileName ); |
1139 | < | char* endTest; |
1140 | < | int nameLength = strlen( info->sampleName ); |
1141 | < | endTest = &(info->sampleName[nameLength - 5]); |
1142 | < | if( !strcmp( endTest, ".bass" ) ){ |
968 | < | strcpy( endTest, ".dump" ); |
969 | < | } |
970 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
971 | < | strcpy( endTest, ".dump" ); |
972 | < | } |
973 | < | else{ |
974 | < | endTest = &(info->sampleName[nameLength - 4]); |
975 | < | if( !strcmp( endTest, ".bss" ) ){ |
976 | < | strcpy( endTest, ".dump" ); |
1134 | > | |
1135 | > | // make the sample and status out names |
1136 | > | |
1137 | > | strcpy(info[k].sampleName, inFileName); |
1138 | > | char* endTest; |
1139 | > | int nameLength = strlen(info[k].sampleName); |
1140 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
1141 | > | if (!strcmp(endTest, ".bass")){ |
1142 | > | strcpy(endTest, ".dump"); |
1143 | } | |
1144 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1145 | < | strcpy( endTest, ".dump" ); |
1144 | > | else if (!strcmp(endTest, ".BASS")){ |
1145 | > | strcpy(endTest, ".dump"); |
1146 | } | |
1147 | else{ | |
1148 | < | strcat( info->sampleName, ".dump" ); |
1148 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1149 | > | if (!strcmp(endTest, ".bss")){ |
1150 | > | strcpy(endTest, ".dump"); |
1151 | > | } |
1152 | > | else if (!strcmp(endTest, ".mdl")){ |
1153 | > | strcpy(endTest, ".dump"); |
1154 | > | } |
1155 | > | else{ |
1156 | > | strcat(info[k].sampleName, ".dump"); |
1157 | > | } |
1158 | } | |
1159 | < | } |
1160 | < | |
1161 | < | strcpy( info->statusName, inFileName ); |
1162 | < | nameLength = strlen( info->statusName ); |
1163 | < | endTest = &(info->statusName[nameLength - 5]); |
1164 | < | if( !strcmp( endTest, ".bass" ) ){ |
990 | < | strcpy( endTest, ".stat" ); |
991 | < | } |
992 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
993 | < | strcpy( endTest, ".stat" ); |
994 | < | } |
995 | < | else{ |
996 | < | endTest = &(info->statusName[nameLength - 4]); |
997 | < | if( !strcmp( endTest, ".bss" ) ){ |
998 | < | strcpy( endTest, ".stat" ); |
1159 | > | |
1160 | > | strcpy(info[k].statusName, inFileName); |
1161 | > | nameLength = strlen(info[k].statusName); |
1162 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1163 | > | if (!strcmp(endTest, ".bass")){ |
1164 | > | strcpy(endTest, ".stat"); |
1165 | } | |
1166 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1167 | < | strcpy( endTest, ".stat" ); |
1166 | > | else if (!strcmp(endTest, ".BASS")){ |
1167 | > | strcpy(endTest, ".stat"); |
1168 | } | |
1169 | else{ | |
1170 | < | strcat( info->statusName, ".stat" ); |
1170 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1171 | > | if (!strcmp(endTest, ".bss")){ |
1172 | > | strcpy(endTest, ".stat"); |
1173 | > | } |
1174 | > | else if (!strcmp(endTest, ".mdl")){ |
1175 | > | strcpy(endTest, ".stat"); |
1176 | > | } |
1177 | > | else{ |
1178 | > | strcat(info[k].statusName, ".stat"); |
1179 | > | } |
1180 | } | |
1181 | < | } |
1007 | < | |
1181 | > | |
1182 | #ifdef IS_MPI | |
1009 | – | } |
1010 | – | #endif // is_mpi |
1183 | ||
1184 | + | } |
1185 | + | #endif // is_mpi |
1186 | + | } |
1187 | } | |
1188 | ||
1189 | ||
1190 | < | void SimSetup::sysObjectsCreation( void ){ |
1190 | > | void SimSetup::sysObjectsCreation(void){ |
1191 | > | int i, k; |
1192 | ||
1017 | – | int i; |
1018 | – | |
1193 | // create the forceField | |
1194 | ||
1195 | createFF(); | |
# | Line 1030 | Line 1204 | void SimSetup::sysObjectsCreation( void ){ | |
1204 | ||
1205 | #ifdef IS_MPI | |
1206 | // divide the molecules among the processors | |
1207 | < | |
1207 | > | |
1208 | mpiMolDivide(); | |
1209 | #endif //is_mpi | |
1210 | < | |
1210 | > | |
1211 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1212 | < | |
1212 | > | |
1213 | makeSysArrays(); | |
1214 | ||
1215 | // make and initialize the molecules (all but atomic coordinates) | |
1216 | < | |
1216 | > | |
1217 | makeMolecules(); | |
1044 | – | info->identArray = new int[info->n_atoms]; |
1045 | – | for(i=0; i<info->n_atoms; i++){ |
1046 | – | info->identArray[i] = the_atoms[i]->getIdent(); |
1047 | – | } |
1048 | – | |
1218 | ||
1219 | < | |
1219 | > | for (k = 0; k < nInfo; k++){ |
1220 | > | info[k].identArray = new int[info[k].n_atoms]; |
1221 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1222 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1223 | > | } |
1224 | > | } |
1225 | } | |
1226 | ||
1227 | ||
1228 | < | void SimSetup::createFF( void ){ |
1228 | > | void SimSetup::createFF(void){ |
1229 | > | switch (ffCase){ |
1230 | > | case FF_DUFF: |
1231 | > | the_ff = new DUFF(); |
1232 | > | break; |
1233 | ||
1234 | < | switch( ffCase ){ |
1234 | > | case FF_LJ: |
1235 | > | the_ff = new LJFF(); |
1236 | > | break; |
1237 | ||
1238 | < | case FF_DUFF: |
1239 | < | the_ff = new DUFF(); |
1240 | < | break; |
1238 | > | case FF_EAM: |
1239 | > | the_ff = new EAM_FF(); |
1240 | > | break; |
1241 | ||
1242 | < | case FF_LJ: |
1243 | < | the_ff = new LJFF(); |
1244 | < | break; |
1242 | > | case FF_H2O: |
1243 | > | the_ff = new WATER(); |
1244 | > | break; |
1245 | ||
1246 | < | case FF_EAM: |
1247 | < | the_ff = new EAM_FF(); |
1248 | < | break; |
1249 | < | |
1250 | < | default: |
1071 | < | sprintf( painCave.errMsg, |
1072 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1073 | < | painCave.isFatal = 1; |
1074 | < | simError(); |
1246 | > | default: |
1247 | > | sprintf(painCave.errMsg, |
1248 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1249 | > | painCave.isFatal = 1; |
1250 | > | simError(); |
1251 | } | |
1252 | ||
1253 | #ifdef IS_MPI | |
1254 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1254 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1255 | MPIcheckPoint(); | |
1256 | #endif // is_mpi | |
1081 | – | |
1257 | } | |
1258 | ||
1259 | ||
1260 | < | void SimSetup::compList( void ){ |
1086 | < | |
1260 | > | void SimSetup::compList(void){ |
1261 | int i; | |
1262 | + | char* id; |
1263 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1264 | + | LinkedMolStamp* currentStamp = NULL; |
1265 | + | comp_stamps = new MoleculeStamp * [n_components]; |
1266 | ||
1089 | – | comp_stamps = new MoleculeStamp*[n_components]; |
1090 | – | |
1267 | // make an array of molecule stamps that match the components used. | |
1268 | // also extract the used stamps out into a separate linked list | |
1269 | ||
1270 | < | info->nComponents = n_components; |
1271 | < | info->componentsNmol = components_nmol; |
1272 | < | info->compStamps = comp_stamps; |
1273 | < | info->headStamp = new LinkedMolStamp(); |
1274 | < | |
1275 | < | char* id; |
1100 | < | LinkedMolStamp* headStamp = info->headStamp; |
1101 | < | LinkedMolStamp* currentStamp = NULL; |
1102 | < | for( i=0; i<n_components; i++ ){ |
1270 | > | for (i = 0; i < nInfo; i++){ |
1271 | > | info[i].nComponents = n_components; |
1272 | > | info[i].componentsNmol = components_nmol; |
1273 | > | info[i].compStamps = comp_stamps; |
1274 | > | info[i].headStamp = headStamp; |
1275 | > | } |
1276 | ||
1277 | + | |
1278 | + | for (i = 0; i < n_components; i++){ |
1279 | id = the_components[i]->getType(); | |
1280 | comp_stamps[i] = NULL; | |
1281 | < | |
1281 | > | |
1282 | // check to make sure the component isn't already in the list | |
1283 | ||
1284 | < | comp_stamps[i] = headStamp->match( id ); |
1285 | < | if( comp_stamps[i] == NULL ){ |
1111 | < | |
1284 | > | comp_stamps[i] = headStamp->match(id); |
1285 | > | if (comp_stamps[i] == NULL){ |
1286 | // extract the component from the list; | |
1287 | < | |
1288 | < | currentStamp = stamps->extractMolStamp( id ); |
1289 | < | if( currentStamp == NULL ){ |
1290 | < | sprintf( painCave.errMsg, |
1291 | < | "SimSetup error: Component \"%s\" was not found in the " |
1292 | < | "list of declared molecules\n", |
1293 | < | id ); |
1294 | < | painCave.isFatal = 1; |
1295 | < | simError(); |
1287 | > | |
1288 | > | currentStamp = stamps->extractMolStamp(id); |
1289 | > | if (currentStamp == NULL){ |
1290 | > | sprintf(painCave.errMsg, |
1291 | > | "SimSetup error: Component \"%s\" was not found in the " |
1292 | > | "list of declared molecules\n", |
1293 | > | id); |
1294 | > | painCave.isFatal = 1; |
1295 | > | simError(); |
1296 | } | |
1297 | < | |
1298 | < | headStamp->add( currentStamp ); |
1299 | < | comp_stamps[i] = headStamp->match( id ); |
1297 | > | |
1298 | > | headStamp->add(currentStamp); |
1299 | > | comp_stamps[i] = headStamp->match(id); |
1300 | } | |
1301 | } | |
1302 | ||
1303 | #ifdef IS_MPI | |
1304 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1304 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1305 | MPIcheckPoint(); | |
1306 | #endif // is_mpi | |
1133 | – | |
1134 | – | |
1307 | } | |
1308 | ||
1309 | < | void SimSetup::calcSysValues( void ){ |
1310 | < | int i, j, k; |
1309 | > | void SimSetup::calcSysValues(void){ |
1310 | > | int i; |
1311 | ||
1312 | + | int* molMembershipArray; |
1313 | ||
1314 | tot_atoms = 0; | |
1315 | tot_bonds = 0; | |
1316 | tot_bends = 0; | |
1317 | tot_torsions = 0; | |
1318 | < | for( i=0; i<n_components; i++ ){ |
1319 | < | |
1320 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1321 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1322 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1318 | > | tot_rigid = 0; |
1319 | > | for (i = 0; i < n_components; i++){ |
1320 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1321 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1322 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1323 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1324 | + | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1325 | } | |
1326 | < | |
1326 | > | |
1327 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1328 | + | molMembershipArray = new int[tot_atoms]; |
1329 | ||
1330 | < | info->n_atoms = tot_atoms; |
1331 | < | info->n_bonds = tot_bonds; |
1332 | < | info->n_bends = tot_bends; |
1333 | < | info->n_torsions = tot_torsions; |
1334 | < | info->n_SRI = tot_SRI; |
1335 | < | info->n_mol = tot_nmol; |
1336 | < | |
1162 | < | info->molMembershipArray = new int[tot_atoms]; |
1163 | < | } |
1330 | > | for (i = 0; i < nInfo; i++){ |
1331 | > | info[i].n_atoms = tot_atoms; |
1332 | > | info[i].n_bonds = tot_bonds; |
1333 | > | info[i].n_bends = tot_bends; |
1334 | > | info[i].n_torsions = tot_torsions; |
1335 | > | info[i].n_SRI = tot_SRI; |
1336 | > | info[i].n_mol = tot_nmol; |
1337 | ||
1338 | + | info[i].molMembershipArray = molMembershipArray; |
1339 | + | } |
1340 | + | } |
1341 | ||
1342 | #ifdef IS_MPI | |
1343 | ||
1344 | < | void SimSetup::mpiMolDivide( void ){ |
1169 | < | |
1344 | > | void SimSetup::mpiMolDivide(void){ |
1345 | int i, j, k; | |
1346 | int localMol, allMol; | |
1347 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1348 | + | int local_rigid; |
1349 | ||
1350 | < | mpiSim = new mpiSimulation( info ); |
1351 | < | |
1350 | > | mpiSim = new mpiSimulation(info); |
1351 | > | |
1352 | globalIndex = mpiSim->divideLabor(); | |
1353 | ||
1354 | // set up the local variables | |
1355 | < | |
1355 | > | |
1356 | mol2proc = mpiSim->getMolToProcMap(); | |
1357 | molCompType = mpiSim->getMolComponentType(); | |
1358 | < | |
1358 | > | |
1359 | allMol = 0; | |
1360 | localMol = 0; | |
1361 | local_atoms = 0; | |
1362 | local_bonds = 0; | |
1363 | local_bends = 0; | |
1364 | local_torsions = 0; | |
1365 | + | local_rigid = 0; |
1366 | globalAtomIndex = 0; | |
1367 | ||
1368 | < | |
1369 | < | for( i=0; i<n_components; i++ ){ |
1370 | < | |
1371 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1372 | < | |
1373 | < | if( mol2proc[allMol] == worldRank ){ |
1374 | < | |
1375 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1376 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1200 | < | local_bends += comp_stamps[i]->getNBends(); |
1201 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1202 | < | localMol++; |
1368 | > | for (i = 0; i < n_components; i++){ |
1369 | > | for (j = 0; j < components_nmol[i]; j++){ |
1370 | > | if (mol2proc[allMol] == worldRank){ |
1371 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1372 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1373 | > | local_bends += comp_stamps[i]->getNBends(); |
1374 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1375 | > | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1376 | > | localMol++; |
1377 | } | |
1378 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1379 | < | info->molMembershipArray[globalAtomIndex] = allMol; |
1378 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1379 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1380 | globalAtomIndex++; | |
1381 | } | |
1382 | ||
1383 | < | allMol++; |
1383 | > | allMol++; |
1384 | } | |
1385 | } | |
1386 | local_SRI = local_bonds + local_bends + local_torsions; | |
1387 | + | |
1388 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1389 | ||
1390 | < | info->n_atoms = mpiSim->getMyNlocal(); |
1391 | < | |
1392 | < | if( local_atoms != info->n_atoms ){ |
1393 | < | sprintf( painCave.errMsg, |
1394 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1395 | < | " localAtom (%d) are not equal.\n", |
1220 | < | info->n_atoms, |
1221 | < | local_atoms ); |
1390 | > | |
1391 | > | if (local_atoms != info[0].n_atoms){ |
1392 | > | sprintf(painCave.errMsg, |
1393 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1394 | > | "\tlocalAtom (%d) are not equal.\n", |
1395 | > | info[0].n_atoms, local_atoms); |
1396 | painCave.isFatal = 1; | |
1397 | simError(); | |
1398 | } | |
1399 | ||
1400 | < | info->n_bonds = local_bonds; |
1401 | < | info->n_bends = local_bends; |
1402 | < | info->n_torsions = local_torsions; |
1403 | < | info->n_SRI = local_SRI; |
1404 | < | info->n_mol = localMol; |
1400 | > | info[0].n_bonds = local_bonds; |
1401 | > | info[0].n_bends = local_bends; |
1402 | > | info[0].n_torsions = local_torsions; |
1403 | > | info[0].n_SRI = local_SRI; |
1404 | > | info[0].n_mol = localMol; |
1405 | ||
1406 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1406 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1407 | MPIcheckPoint(); | |
1408 | } | |
1409 | < | |
1409 | > | |
1410 | #endif // is_mpi | |
1411 | ||
1412 | ||
1413 | < | void SimSetup::makeSysArrays( void ){ |
1414 | < | int i, j, k; |
1413 | > | void SimSetup::makeSysArrays(void){ |
1414 | > | |
1415 | > | #ifndef IS_MPI |
1416 | > | int k, j; |
1417 | > | #endif // is_mpi |
1418 | > | int i, l; |
1419 | ||
1420 | + | Atom** the_atoms; |
1421 | + | Molecule* the_molecules; |
1422 | ||
1423 | < | // create the atom and short range interaction arrays |
1423 | > | for (l = 0; l < nInfo; l++){ |
1424 | > | // create the atom and short range interaction arrays |
1425 | ||
1426 | < | Atom::createArrays(info->n_atoms); |
1427 | < | the_atoms = new Atom*[info->n_atoms]; |
1428 | < | the_molecules = new Molecule[info->n_mol]; |
1248 | < | int molIndex; |
1426 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1427 | > | the_molecules = new Molecule[info[l].n_mol]; |
1428 | > | int molIndex; |
1429 | ||
1430 | < | // initialize the molecule's stampID's |
1430 | > | // initialize the molecule's stampID's |
1431 | ||
1432 | #ifdef IS_MPI | |
1253 | – | |
1433 | ||
1434 | < | molIndex = 0; |
1435 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1436 | < | |
1437 | < | if(mol2proc[i] == worldRank ){ |
1438 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1439 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1440 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1441 | < | molIndex++; |
1434 | > | |
1435 | > | molIndex = 0; |
1436 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1437 | > | if (mol2proc[i] == worldRank){ |
1438 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1439 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1440 | > | the_molecules[molIndex].setGlobalIndex(i); |
1441 | > | molIndex++; |
1442 | > | } |
1443 | } | |
1264 | – | } |
1444 | ||
1445 | #else // is_mpi | |
1446 | < | |
1447 | < | molIndex = 0; |
1448 | < | globalAtomIndex = 0; |
1449 | < | for(i=0; i<n_components; i++){ |
1450 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1451 | < | the_molecules[molIndex].setStampID( i ); |
1452 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1453 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1454 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1455 | < | info->molMembershipArray[globalAtomIndex] = molIndex; |
1456 | < | globalAtomIndex++; |
1446 | > | |
1447 | > | molIndex = 0; |
1448 | > | globalAtomIndex = 0; |
1449 | > | for (i = 0; i < n_components; i++){ |
1450 | > | for (j = 0; j < components_nmol[i]; j++){ |
1451 | > | the_molecules[molIndex].setStampID(i); |
1452 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1453 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1454 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1455 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1456 | > | globalAtomIndex++; |
1457 | > | } |
1458 | > | molIndex++; |
1459 | } | |
1279 | – | molIndex++; |
1460 | } | |
1281 | – | } |
1282 | – | |
1461 | ||
1462 | + | |
1463 | #endif // is_mpi | |
1464 | ||
1465 | < | |
1466 | < | if( info->n_SRI ){ |
1465 | > | info[l].globalExcludes = new int; |
1466 | > | info[l].globalExcludes[0] = 0; |
1467 | ||
1468 | < | Exclude::createArray(info->n_SRI); |
1290 | < | the_excludes = new Exclude*[info->n_SRI]; |
1291 | < | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1292 | < | info->globalExcludes = new int; |
1293 | < | info->n_exclude = info->n_SRI; |
1294 | < | } |
1295 | < | else{ |
1296 | < | |
1297 | < | Exclude::createArray( 1 ); |
1298 | < | the_excludes = new Exclude*; |
1299 | < | the_excludes[0] = new Exclude(0); |
1300 | < | the_excludes[0]->setPair( 0,0 ); |
1301 | < | info->globalExcludes = new int; |
1302 | < | info->globalExcludes[0] = 0; |
1303 | < | info->n_exclude = 0; |
1304 | < | } |
1468 | > | // set the arrays into the SimInfo object |
1469 | ||
1470 | < | // set the arrays into the SimInfo object |
1471 | < | |
1472 | < | info->atoms = the_atoms; |
1309 | < | info->molecules = the_molecules; |
1310 | < | info->nGlobalExcludes = 0; |
1311 | < | info->excludes = the_excludes; |
1470 | > | info[l].atoms = the_atoms; |
1471 | > | info[l].molecules = the_molecules; |
1472 | > | info[l].nGlobalExcludes = 0; |
1473 | ||
1474 | < | the_ff->setSimInfo( info ); |
1475 | < | |
1474 | > | the_ff->setSimInfo(info); |
1475 | > | } |
1476 | } | |
1477 | ||
1478 | < | void SimSetup::makeIntegrator( void ){ |
1478 | > | void SimSetup::makeIntegrator(void){ |
1479 | > | int k; |
1480 | ||
1481 | < | NVT<RealIntegrator>* myNVT = NULL; |
1482 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1483 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1484 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1485 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1324 | < | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1325 | < | ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1326 | < | ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1327 | < | ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1328 | < | ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1329 | < | ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1330 | < | |
1331 | < | cerr << "setting integrator" <<endl; |
1481 | > | NVE<RealIntegrator>* myNVE = NULL; |
1482 | > | NVT<RealIntegrator>* myNVT = NULL; |
1483 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1484 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1485 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1486 | ||
1487 | < | switch( ensembleCase ){ |
1487 | > | for (k = 0; k < nInfo; k++){ |
1488 | > | switch (ensembleCase){ |
1489 | > | case NVE_ENS: |
1490 | > | if (globals->haveZconstraints()){ |
1491 | > | setupZConstraint(info[k]); |
1492 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1493 | > | } |
1494 | > | else{ |
1495 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1496 | > | } |
1497 | > | |
1498 | > | info->the_integrator = myNVE; |
1499 | > | break; |
1500 | ||
1501 | < | case NVE_ENS: |
1502 | < | new NVE<RealIntegrator>( info, the_ff ); |
1503 | < | break; |
1501 | > | case NVT_ENS: |
1502 | > | if (globals->haveZconstraints()){ |
1503 | > | setupZConstraint(info[k]); |
1504 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1505 | > | } |
1506 | > | else |
1507 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1508 | ||
1509 | < | case NVT_ENS: |
1340 | < | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1341 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1509 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1510 | ||
1511 | < | if (globals->haveTauThermostat()) |
1512 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1511 | > | if (globals->haveTauThermostat()) |
1512 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1513 | > | else{ |
1514 | > | sprintf(painCave.errMsg, |
1515 | > | "SimSetup error: If you use the NVT\n" |
1516 | > | "\tensemble, you must set tauThermostat.\n"); |
1517 | > | painCave.isFatal = 1; |
1518 | > | simError(); |
1519 | > | } |
1520 | ||
1521 | < | else { |
1522 | < | sprintf( painCave.errMsg, |
1348 | < | "SimSetup error: If you use the NVT\n" |
1349 | < | " ensemble, you must set tauThermostat.\n"); |
1350 | < | painCave.isFatal = 1; |
1351 | < | simError(); |
1352 | < | } |
1353 | < | break; |
1521 | > | info->the_integrator = myNVT; |
1522 | > | break; |
1523 | ||
1524 | < | case NPTi_ENS: |
1525 | < | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1526 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1524 | > | case NPTi_ENS: |
1525 | > | if (globals->haveZconstraints()){ |
1526 | > | setupZConstraint(info[k]); |
1527 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1528 | > | } |
1529 | > | else |
1530 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1531 | ||
1532 | < | if (globals->haveTargetPressure()) |
1360 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1361 | < | else { |
1362 | < | sprintf( painCave.errMsg, |
1363 | < | "SimSetup error: If you use a constant pressure\n" |
1364 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1365 | < | painCave.isFatal = 1; |
1366 | < | simError(); |
1367 | < | } |
1368 | < | |
1369 | < | if( globals->haveTauThermostat() ) |
1370 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1371 | < | else{ |
1372 | < | sprintf( painCave.errMsg, |
1373 | < | "SimSetup error: If you use an NPT\n" |
1374 | < | " ensemble, you must set tauThermostat.\n"); |
1375 | < | painCave.isFatal = 1; |
1376 | < | simError(); |
1377 | < | } |
1532 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1533 | ||
1534 | < | if( globals->haveTauBarostat() ) |
1535 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1536 | < | else{ |
1537 | < | sprintf( painCave.errMsg, |
1538 | < | "SimSetup error: If you use an NPT\n" |
1539 | < | " ensemble, you must set tauBarostat.\n"); |
1540 | < | painCave.isFatal = 1; |
1541 | < | simError(); |
1542 | < | } |
1388 | < | break; |
1534 | > | if (globals->haveTargetPressure()) |
1535 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1536 | > | else{ |
1537 | > | sprintf(painCave.errMsg, |
1538 | > | "SimSetup error: If you use a constant pressure\n" |
1539 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1540 | > | painCave.isFatal = 1; |
1541 | > | simError(); |
1542 | > | } |
1543 | ||
1544 | < | case NPTf_ENS: |
1545 | < | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1546 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1544 | > | if (globals->haveTauThermostat()) |
1545 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1546 | > | else{ |
1547 | > | sprintf(painCave.errMsg, |
1548 | > | "SimSetup error: If you use an NPT\n" |
1549 | > | "\tensemble, you must set tauThermostat.\n"); |
1550 | > | painCave.isFatal = 1; |
1551 | > | simError(); |
1552 | > | } |
1553 | ||
1554 | < | if (globals->haveTargetPressure()) |
1555 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1556 | < | else { |
1557 | < | sprintf( painCave.errMsg, |
1558 | < | "SimSetup error: If you use a constant pressure\n" |
1559 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1560 | < | painCave.isFatal = 1; |
1561 | < | simError(); |
1562 | < | } |
1554 | > | if (globals->haveTauBarostat()) |
1555 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1556 | > | else{ |
1557 | > | sprintf(painCave.errMsg, |
1558 | > | "SimSetup error: If you use an NPT\n" |
1559 | > | "\tensemble, you must set tauBarostat.\n"); |
1560 | > | painCave.isFatal = 1; |
1561 | > | simError(); |
1562 | > | } |
1563 | ||
1564 | < | if( globals->haveTauThermostat() ) |
1565 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1406 | < | else{ |
1407 | < | sprintf( painCave.errMsg, |
1408 | < | "SimSetup error: If you use an NPT\n" |
1409 | < | " ensemble, you must set tauThermostat.\n"); |
1410 | < | painCave.isFatal = 1; |
1411 | < | simError(); |
1412 | < | } |
1564 | > | info->the_integrator = myNPTi; |
1565 | > | break; |
1566 | ||
1567 | < | if( globals->haveTauBarostat() ) |
1568 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1569 | < | else{ |
1570 | < | sprintf( painCave.errMsg, |
1571 | < | "SimSetup error: If you use an NPT\n" |
1572 | < | " ensemble, you must set tauBarostat.\n"); |
1573 | < | painCave.isFatal = 1; |
1421 | < | simError(); |
1422 | < | } |
1423 | < | break; |
1424 | < | |
1425 | < | case NPTim_ENS: |
1426 | < | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1427 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1567 | > | case NPTf_ENS: |
1568 | > | if (globals->haveZconstraints()){ |
1569 | > | setupZConstraint(info[k]); |
1570 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1571 | > | } |
1572 | > | else |
1573 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1574 | ||
1575 | < | if (globals->haveTargetPressure()) |
1430 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1431 | < | else { |
1432 | < | sprintf( painCave.errMsg, |
1433 | < | "SimSetup error: If you use a constant pressure\n" |
1434 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1435 | < | painCave.isFatal = 1; |
1436 | < | simError(); |
1437 | < | } |
1438 | < | |
1439 | < | if( globals->haveTauThermostat() ) |
1440 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1441 | < | else{ |
1442 | < | sprintf( painCave.errMsg, |
1443 | < | "SimSetup error: If you use an NPT\n" |
1444 | < | " ensemble, you must set tauThermostat.\n"); |
1445 | < | painCave.isFatal = 1; |
1446 | < | simError(); |
1447 | < | } |
1575 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1576 | ||
1577 | < | if( globals->haveTauBarostat() ) |
1578 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1579 | < | else{ |
1580 | < | sprintf( painCave.errMsg, |
1581 | < | "SimSetup error: If you use an NPT\n" |
1582 | < | " ensemble, you must set tauBarostat.\n"); |
1583 | < | painCave.isFatal = 1; |
1584 | < | simError(); |
1585 | < | } |
1458 | < | break; |
1577 | > | if (globals->haveTargetPressure()) |
1578 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1579 | > | else{ |
1580 | > | sprintf(painCave.errMsg, |
1581 | > | "SimSetup error: If you use a constant pressure\n" |
1582 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1583 | > | painCave.isFatal = 1; |
1584 | > | simError(); |
1585 | > | } |
1586 | ||
1587 | < | case NPTfm_ENS: |
1588 | < | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1462 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1587 | > | if (globals->haveTauThermostat()) |
1588 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1589 | ||
1590 | < | if (globals->haveTargetPressure()) |
1591 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1592 | < | else { |
1593 | < | sprintf( painCave.errMsg, |
1594 | < | "SimSetup error: If you use a constant pressure\n" |
1595 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1596 | < | painCave.isFatal = 1; |
1471 | < | simError(); |
1472 | < | } |
1473 | < | |
1474 | < | if( globals->haveTauThermostat() ) |
1475 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1476 | < | else{ |
1477 | < | sprintf( painCave.errMsg, |
1478 | < | "SimSetup error: If you use an NPT\n" |
1479 | < | " ensemble, you must set tauThermostat.\n"); |
1480 | < | painCave.isFatal = 1; |
1481 | < | simError(); |
1482 | < | } |
1590 | > | else{ |
1591 | > | sprintf(painCave.errMsg, |
1592 | > | "SimSetup error: If you use an NPT\n" |
1593 | > | "\tensemble, you must set tauThermostat.\n"); |
1594 | > | painCave.isFatal = 1; |
1595 | > | simError(); |
1596 | > | } |
1597 | ||
1598 | < | if( globals->haveTauBarostat() ) |
1599 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1486 | < | else{ |
1487 | < | sprintf( painCave.errMsg, |
1488 | < | "SimSetup error: If you use an NPT\n" |
1489 | < | " ensemble, you must set tauBarostat.\n"); |
1490 | < | painCave.isFatal = 1; |
1491 | < | simError(); |
1492 | < | } |
1493 | < | break; |
1494 | < | |
1495 | < | case NVEZCONS_ENS: |
1598 | > | if (globals->haveTauBarostat()) |
1599 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1600 | ||
1601 | + | else{ |
1602 | + | sprintf(painCave.errMsg, |
1603 | + | "SimSetup error: If you use an NPT\n" |
1604 | + | "\tensemble, you must set tauBarostat.\n"); |
1605 | + | painCave.isFatal = 1; |
1606 | + | simError(); |
1607 | + | } |
1608 | ||
1609 | < | //setup index of z-constraint molecules, z-constraint sampel time |
1610 | < | //and z-constraint force output name. These parameter should be known |
1500 | < | //before constructing the z-constraint integrator |
1501 | < | setupZConstraint(); |
1502 | < | |
1503 | < | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1504 | < | |
1505 | < | break; |
1506 | < | |
1507 | < | |
1508 | < | case NVTZCONS_ENS: |
1509 | < | |
1510 | < | setupZConstraint(); |
1511 | < | |
1512 | < | myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
1513 | < | myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1609 | > | info->the_integrator = myNPTf; |
1610 | > | break; |
1611 | ||
1612 | < | if (globals->haveTauThermostat()) |
1613 | < | myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1612 | > | case NPTxyz_ENS: |
1613 | > | if (globals->haveZconstraints()){ |
1614 | > | setupZConstraint(info[k]); |
1615 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1616 | > | } |
1617 | > | else |
1618 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1619 | ||
1620 | < | else { |
1519 | < | sprintf( painCave.errMsg, |
1520 | < | "SimSetup error: If you use the NVT\n" |
1521 | < | " ensemble, you must set tauThermostat.\n"); |
1522 | < | painCave.isFatal = 1; |
1523 | < | simError(); |
1524 | < | } |
1525 | < | break; |
1526 | < | |
1527 | < | case NPTiZCONS_ENS: |
1528 | < | |
1529 | < | setupZConstraint(); |
1530 | < | |
1531 | < | myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
1532 | < | myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1620 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1621 | ||
1622 | < | if (globals->haveTargetPressure()) |
1623 | < | myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1624 | < | else { |
1625 | < | sprintf( painCave.errMsg, |
1626 | < | "SimSetup error: If you use a constant pressure\n" |
1627 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1628 | < | painCave.isFatal = 1; |
1629 | < | simError(); |
1630 | < | } |
1543 | < | |
1544 | < | if( globals->haveTauThermostat() ) |
1545 | < | myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1546 | < | else{ |
1547 | < | sprintf( painCave.errMsg, |
1548 | < | "SimSetup error: If you use an NPT\n" |
1549 | < | " ensemble, you must set tauThermostat.\n"); |
1550 | < | painCave.isFatal = 1; |
1551 | < | simError(); |
1552 | < | } |
1622 | > | if (globals->haveTargetPressure()) |
1623 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1624 | > | else{ |
1625 | > | sprintf(painCave.errMsg, |
1626 | > | "SimSetup error: If you use a constant pressure\n" |
1627 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1628 | > | painCave.isFatal = 1; |
1629 | > | simError(); |
1630 | > | } |
1631 | ||
1632 | < | if( globals->haveTauBarostat() ) |
1633 | < | myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1634 | < | else{ |
1635 | < | sprintf( painCave.errMsg, |
1636 | < | "SimSetup error: If you use an NPT\n" |
1637 | < | " ensemble, you must set tauBarostat.\n"); |
1638 | < | painCave.isFatal = 1; |
1639 | < | simError(); |
1640 | < | } |
1563 | < | |
1564 | < | break; |
1565 | < | |
1566 | < | case NPTfZCONS_ENS: |
1567 | < | |
1568 | < | setupZConstraint(); |
1569 | < | |
1570 | < | myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
1571 | < | myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1572 | < | |
1573 | < | if (globals->haveTargetPressure()) |
1574 | < | myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1575 | < | else { |
1576 | < | sprintf( painCave.errMsg, |
1577 | < | "SimSetup error: If you use a constant pressure\n" |
1578 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1579 | < | painCave.isFatal = 1; |
1580 | < | simError(); |
1581 | < | } |
1632 | > | if (globals->haveTauThermostat()) |
1633 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1634 | > | else{ |
1635 | > | sprintf(painCave.errMsg, |
1636 | > | "SimSetup error: If you use an NPT\n" |
1637 | > | "\tensemble, you must set tauThermostat.\n"); |
1638 | > | painCave.isFatal = 1; |
1639 | > | simError(); |
1640 | > | } |
1641 | ||
1642 | < | if( globals->haveTauThermostat() ) |
1643 | < | myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1644 | < | else{ |
1645 | < | sprintf( painCave.errMsg, |
1646 | < | "SimSetup error: If you use an NPT\n" |
1647 | < | " ensemble, you must set tauThermostat.\n"); |
1648 | < | painCave.isFatal = 1; |
1649 | < | simError(); |
1650 | < | } |
1642 | > | if (globals->haveTauBarostat()) |
1643 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1644 | > | else{ |
1645 | > | sprintf(painCave.errMsg, |
1646 | > | "SimSetup error: If you use an NPT\n" |
1647 | > | "\tensemble, you must set tauBarostat.\n"); |
1648 | > | painCave.isFatal = 1; |
1649 | > | simError(); |
1650 | > | } |
1651 | ||
1652 | < | if( globals->haveTauBarostat() ) |
1653 | < | myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1595 | < | else{ |
1596 | < | sprintf( painCave.errMsg, |
1597 | < | "SimSetup error: If you use an NPT\n" |
1598 | < | " ensemble, you must set tauBarostat.\n"); |
1599 | < | painCave.isFatal = 1; |
1600 | < | simError(); |
1601 | < | } |
1602 | < | |
1603 | < | break; |
1604 | < | |
1605 | < | case NPTimZCONS_ENS: |
1606 | < | |
1607 | < | setupZConstraint(); |
1608 | < | |
1609 | < | myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
1610 | < | myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1652 | > | info->the_integrator = myNPTxyz; |
1653 | > | break; |
1654 | ||
1655 | < | if (globals->haveTargetPressure()) |
1656 | < | myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1657 | < | else { |
1658 | < | sprintf( painCave.errMsg, |
1659 | < | "SimSetup error: If you use a constant pressure\n" |
1617 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1618 | < | painCave.isFatal = 1; |
1619 | < | simError(); |
1655 | > | default: |
1656 | > | sprintf(painCave.errMsg, |
1657 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1658 | > | painCave.isFatal = 1; |
1659 | > | simError(); |
1660 | } | |
1621 | – | |
1622 | – | if( globals->haveTauThermostat() ) |
1623 | – | myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1624 | – | else{ |
1625 | – | sprintf( painCave.errMsg, |
1626 | – | "SimSetup error: If you use an NPT\n" |
1627 | – | " ensemble, you must set tauThermostat.\n"); |
1628 | – | painCave.isFatal = 1; |
1629 | – | simError(); |
1630 | – | } |
1631 | – | |
1632 | – | if( globals->haveTauBarostat() ) |
1633 | – | myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1634 | – | else{ |
1635 | – | sprintf( painCave.errMsg, |
1636 | – | "SimSetup error: If you use an NPT\n" |
1637 | – | " ensemble, you must set tauBarostat.\n"); |
1638 | – | painCave.isFatal = 1; |
1639 | – | simError(); |
1640 | – | } |
1641 | – | |
1642 | – | break; |
1643 | – | |
1644 | – | case NPTfmZCONS_ENS: |
1645 | – | |
1646 | – | setupZConstraint(); |
1647 | – | |
1648 | – | myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
1649 | – | myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1650 | – | |
1651 | – | if (globals->haveTargetPressure()) |
1652 | – | myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1653 | – | else { |
1654 | – | sprintf( painCave.errMsg, |
1655 | – | "SimSetup error: If you use a constant pressure\n" |
1656 | – | " ensemble, you must set targetPressure in the BASS file.\n"); |
1657 | – | painCave.isFatal = 1; |
1658 | – | simError(); |
1659 | – | } |
1660 | – | |
1661 | – | if( globals->haveTauThermostat() ) |
1662 | – | myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1663 | – | else{ |
1664 | – | sprintf( painCave.errMsg, |
1665 | – | "SimSetup error: If you use an NPT\n" |
1666 | – | " ensemble, you must set tauThermostat.\n"); |
1667 | – | painCave.isFatal = 1; |
1668 | – | simError(); |
1669 | – | } |
1670 | – | |
1671 | – | if( globals->haveTauBarostat() ) |
1672 | – | myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1673 | – | else{ |
1674 | – | sprintf( painCave.errMsg, |
1675 | – | "SimSetup error: If you use an NPT\n" |
1676 | – | " ensemble, you must set tauBarostat.\n"); |
1677 | – | painCave.isFatal = 1; |
1678 | – | simError(); |
1679 | – | } |
1680 | – | break; |
1681 | – | |
1682 | – | |
1683 | – | |
1684 | – | default: |
1685 | – | sprintf( painCave.errMsg, |
1686 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1687 | – | painCave.isFatal = 1; |
1688 | – | simError(); |
1661 | } | |
1690 | – | |
1662 | } | |
1663 | ||
1664 | < | void SimSetup::initFortran( void ){ |
1664 | > | void SimSetup::initFortran(void){ |
1665 | > | info[0].refreshSim(); |
1666 | ||
1667 | < | info->refreshSim(); |
1668 | < | |
1697 | < | if( !strcmp( info->mixingRule, "standard") ){ |
1698 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1667 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1668 | > | the_ff->initForceField(LB_MIXING_RULE); |
1669 | } | |
1670 | < | else if( !strcmp( info->mixingRule, "explicit") ){ |
1671 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1670 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1671 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1672 | } | |
1673 | else{ | |
1674 | < | sprintf( painCave.errMsg, |
1675 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1706 | < | info->mixingRule ); |
1674 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1675 | > | info[0].mixingRule); |
1676 | painCave.isFatal = 1; | |
1677 | simError(); | |
1678 | } | |
1679 | ||
1680 | ||
1681 | #ifdef IS_MPI | |
1682 | < | strcpy( checkPointMsg, |
1714 | < | "Successfully intialized the mixingRule for Fortran." ); |
1682 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1683 | MPIcheckPoint(); | |
1684 | #endif // is_mpi | |
1717 | – | |
1685 | } | |
1686 | ||
1687 | < | void SimSetup::setupZConstraint() |
1688 | < | { |
1689 | < | if(globals->haveZConsTime()){ |
1690 | < | |
1691 | < | //add sample time of z-constraint into SimInfo's property list |
1692 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1693 | < | zconsTimeProp->setID("zconstime"); |
1694 | < | zconsTimeProp->setData(globals->getZConsTime()); |
1695 | < | info->addProperty(zconsTimeProp); |
1687 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1688 | > | int nZConstraints; |
1689 | > | ZconStamp** zconStamp; |
1690 | > | |
1691 | > | if (globals->haveZconstraintTime()){ |
1692 | > | //add sample time of z-constraint into SimInfo's property list |
1693 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1694 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1695 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1696 | > | theInfo.addProperty(zconsTimeProp); |
1697 | } | |
1698 | else{ | |
1699 | < | sprintf( painCave.errMsg, |
1700 | < | "ZConstraint error: If you use an ZConstraint\n" |
1701 | < | " , you must set sample time.\n"); |
1699 | > | sprintf(painCave.errMsg, |
1700 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1701 | > | "\tyou must set zconsTime.\n"); |
1702 | painCave.isFatal = 1; | |
1703 | + | simError(); |
1704 | + | } |
1705 | + | |
1706 | + | //push zconsTol into siminfo, if user does not specify |
1707 | + | //value for zconsTol, a default value will be used |
1708 | + | DoubleData* zconsTol = new DoubleData(); |
1709 | + | zconsTol->setID(ZCONSTOL_ID); |
1710 | + | if (globals->haveZconsTol()){ |
1711 | + | zconsTol->setData(globals->getZconsTol()); |
1712 | + | } |
1713 | + | else{ |
1714 | + | double defaultZConsTol = 0.01; |
1715 | + | sprintf(painCave.errMsg, |
1716 | + | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1717 | + | "\tOOPSE will use a default value of %f.\n" |
1718 | + | "\tTo set the tolerance, use the zconsTol variable.\n", |
1719 | + | defaultZConsTol); |
1720 | + | painCave.isFatal = 0; |
1721 | simError(); | |
1722 | + | |
1723 | + | zconsTol->setData(defaultZConsTol); |
1724 | } | |
1725 | < | |
1726 | < | if(globals->haveIndexOfAllZConsMols()){ |
1727 | < | |
1728 | < | //add index of z-constraint molecules into SimInfo's property list |
1729 | < | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1730 | < | |
1731 | < | //sort the index |
1732 | < | sort(tempIndex.begin(), tempIndex.end()); |
1745 | < | |
1746 | < | IndexData* zconsIndex = new IndexData(); |
1747 | < | zconsIndex->setID("zconsindex"); |
1748 | < | zconsIndex->setIndexData(tempIndex); |
1749 | < | info->addProperty(zconsIndex); |
1725 | > | theInfo.addProperty(zconsTol); |
1726 | > | |
1727 | > | //set Force Subtraction Policy |
1728 | > | StringData* zconsForcePolicy = new StringData(); |
1729 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1730 | > | |
1731 | > | if (globals->haveZconsForcePolicy()){ |
1732 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1733 | } | |
1734 | else{ | |
1735 | < | sprintf( painCave.errMsg, |
1736 | < | "SimSetup error: If you use an ZConstraint\n" |
1737 | < | " , you must set index of z-constraint molecules.\n"); |
1738 | < | painCave.isFatal = 1; |
1739 | < | simError(); |
1740 | < | |
1735 | > | sprintf(painCave.errMsg, |
1736 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1737 | > | "\tOOPSE will use PolicyByMass.\n" |
1738 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1739 | > | painCave.isFatal = 0; |
1740 | > | simError(); |
1741 | > | zconsForcePolicy->setData("BYMASS"); |
1742 | } | |
1743 | ||
1744 | + | theInfo.addProperty(zconsForcePolicy); |
1745 | + | |
1746 | + | //set zcons gap |
1747 | + | DoubleData* zconsGap = new DoubleData(); |
1748 | + | zconsGap->setID(ZCONSGAP_ID); |
1749 | + | |
1750 | + | if (globals->haveZConsGap()){ |
1751 | + | zconsGap->setData(globals->getZconsGap()); |
1752 | + | theInfo.addProperty(zconsGap); |
1753 | + | } |
1754 | + | |
1755 | + | //set zcons fixtime |
1756 | + | DoubleData* zconsFixtime = new DoubleData(); |
1757 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1758 | + | |
1759 | + | if (globals->haveZConsFixTime()){ |
1760 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
1761 | + | theInfo.addProperty(zconsFixtime); |
1762 | + | } |
1763 | + | |
1764 | + | //set zconsUsingSMD |
1765 | + | IntData* zconsUsingSMD = new IntData(); |
1766 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1767 | + | |
1768 | + | if (globals->haveZConsUsingSMD()){ |
1769 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1770 | + | theInfo.addProperty(zconsUsingSMD); |
1771 | + | } |
1772 | + | |
1773 | //Determine the name of ouput file and add it into SimInfo's property list | |
1774 | //Be careful, do not use inFileName, since it is a pointer which | |
1775 | //point to a string at master node, and slave nodes do not contain that string | |
1776 | < | |
1777 | < | string zconsOutput(info->finalName); |
1778 | < | |
1776 | > | |
1777 | > | string zconsOutput(theInfo.finalName); |
1778 | > | |
1779 | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; | |
1780 | < | |
1780 | > | |
1781 | StringData* zconsFilename = new StringData(); | |
1782 | < | zconsFilename->setID("zconsfilename"); |
1782 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1783 | zconsFilename->setData(zconsOutput); | |
1784 | ||
1785 | < | info->addProperty(zconsFilename); |
1785 | > | theInfo.addProperty(zconsFilename); |
1786 | ||
1787 | + | //setup index, pos and other parameters of z-constraint molecules |
1788 | + | nZConstraints = globals->getNzConstraints(); |
1789 | + | theInfo.nZconstraints = nZConstraints; |
1790 | + | |
1791 | + | zconStamp = globals->getZconStamp(); |
1792 | + | ZConsParaItem tempParaItem; |
1793 | + | |
1794 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1795 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1796 | + | |
1797 | + | for (int i = 0; i < nZConstraints; i++){ |
1798 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1799 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1800 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1801 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1802 | + | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1803 | + | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1804 | + | zconsParaData->addItem(tempParaItem); |
1805 | + | } |
1806 | + | |
1807 | + | //check the uniqueness of index |
1808 | + | if(!zconsParaData->isIndexUnique()){ |
1809 | + | sprintf(painCave.errMsg, |
1810 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1811 | + | painCave.isFatal = 1; |
1812 | + | simError(); |
1813 | + | } |
1814 | + | |
1815 | + | //sort the parameters by index of molecules |
1816 | + | zconsParaData->sortByIndex(); |
1817 | + | |
1818 | + | //push data into siminfo, therefore, we can retrieve later |
1819 | + | theInfo.addProperty(zconsParaData); |
1820 | } | |
1821 | + | |
1822 | + | void SimSetup::makeMinimizer(){ |
1823 | + | |
1824 | + | OOPSEMinimizer* myOOPSEMinimizer; |
1825 | + | MinimizerParameterSet* param; |
1826 | + | char minimizerName[100]; |
1827 | + | |
1828 | + | for (int i = 0; i < nInfo; i++){ |
1829 | + | |
1830 | + | //prepare parameter set for minimizer |
1831 | + | param = new MinimizerParameterSet(); |
1832 | + | param->setDefaultParameter(); |
1833 | + | |
1834 | + | if (globals->haveMinimizer()){ |
1835 | + | param->setFTol(globals->getMinFTol()); |
1836 | + | } |
1837 | + | |
1838 | + | if (globals->haveMinGTol()){ |
1839 | + | param->setGTol(globals->getMinGTol()); |
1840 | + | } |
1841 | + | |
1842 | + | if (globals->haveMinMaxIter()){ |
1843 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1844 | + | } |
1845 | + | |
1846 | + | if (globals->haveMinWriteFrq()){ |
1847 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1848 | + | } |
1849 | + | |
1850 | + | if (globals->haveMinWriteFrq()){ |
1851 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
1852 | + | } |
1853 | + | |
1854 | + | if (globals->haveMinStepSize()){ |
1855 | + | param->setStepSize(globals->getMinStepSize()); |
1856 | + | } |
1857 | + | |
1858 | + | if (globals->haveMinLSMaxIter()){ |
1859 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1860 | + | } |
1861 | + | |
1862 | + | if (globals->haveMinLSTol()){ |
1863 | + | param->setLineSearchTol(globals->getMinLSTol()); |
1864 | + | } |
1865 | + | |
1866 | + | strcpy(minimizerName, globals->getMinimizer()); |
1867 | + | |
1868 | + | if (!strcasecmp(minimizerName, "CG")){ |
1869 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1870 | + | } |
1871 | + | else if (!strcasecmp(minimizerName, "SD")){ |
1872 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1873 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1874 | + | } |
1875 | + | else{ |
1876 | + | sprintf(painCave.errMsg, |
1877 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1878 | + | painCave.isFatal = 0; |
1879 | + | simError(); |
1880 | + | |
1881 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1882 | + | } |
1883 | + | info[i].the_integrator = myOOPSEMinimizer; |
1884 | + | |
1885 | + | //store the minimizer into simInfo |
1886 | + | info[i].the_minimizer = myOOPSEMinimizer; |
1887 | + | info[i].has_minimizer = true; |
1888 | + | } |
1889 | + | |
1890 | + | } |
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