# | 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" | |
# | Line 21 | Line 21 | |
21 | #define NVT_ENS 1 | |
22 | #define NPTi_ENS 2 | |
23 | #define NPTf_ENS 3 | |
24 | < | #define NPTim_ENS 4 |
25 | < | #define NPTfm_ENS 5 |
24 | > | #define NPTxyz_ENS 4 |
25 | ||
26 | + | |
27 | #define FF_DUFF 0 | |
28 | #define FF_LJ 1 | |
29 | #define FF_EAM 2 | |
# | Line 32 | Line 32 | SimSetup::SimSetup(){ | |
32 | ||
33 | SimSetup::SimSetup(){ | |
34 | ||
35 | + | initSuspend = false; |
36 | isInfoArray = 0; | |
37 | nInfo = 1; | |
38 | < | |
38 | > | |
39 | stamps = new MakeStamps(); | |
40 | globals = new Globals(); | |
41 | < | |
42 | < | |
41 | > | |
42 | > | |
43 | #ifdef IS_MPI | |
44 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
44 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
45 | MPIcheckPoint(); | |
46 | #endif // IS_MPI | |
47 | } | |
# | Line 50 | Line 51 | SimSetup::~SimSetup(){ | |
51 | delete globals; | |
52 | } | |
53 | ||
54 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 | < | info = the_info; |
56 | < | nInfo = theNinfo; |
57 | < | isInfoArray = 1; |
54 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
55 | > | info = the_info; |
56 | > | nInfo = theNinfo; |
57 | > | isInfoArray = 1; |
58 | > | initSuspend = true; |
59 | } | |
60 | ||
61 | ||
62 | < | void SimSetup::parseFile( char* fileName ){ |
61 | < | |
62 | > | void SimSetup::parseFile(char* fileName){ |
63 | #ifdef IS_MPI | |
64 | < | if( worldRank == 0 ){ |
64 | > | if (worldRank == 0){ |
65 | #endif // is_mpi | |
66 | < | |
66 | > | |
67 | inFileName = fileName; | |
68 | < | set_interface_stamps( stamps, globals ); |
69 | < | |
68 | > | set_interface_stamps(stamps, globals); |
69 | > | |
70 | #ifdef IS_MPI | |
71 | mpiEventInit(); | |
72 | #endif | |
73 | ||
74 | < | yacc_BASS( fileName ); |
74 | > | yacc_BASS(fileName); |
75 | ||
76 | #ifdef IS_MPI | |
77 | throwMPIEvent(NULL); | |
78 | } | |
79 | < | else receiveParse(); |
79 | > | else{ |
80 | > | receiveParse(); |
81 | > | } |
82 | #endif | |
83 | ||
84 | } | |
85 | ||
86 | #ifdef IS_MPI | |
87 | void SimSetup::receiveParse(void){ | |
88 | < | |
89 | < | set_interface_stamps( stamps, globals ); |
90 | < | mpiEventInit(); |
91 | < | MPIcheckPoint(); |
89 | < | mpiEventLoop(); |
90 | < | |
88 | > | set_interface_stamps(stamps, globals); |
89 | > | mpiEventInit(); |
90 | > | MPIcheckPoint(); |
91 | > | mpiEventLoop(); |
92 | } | |
93 | ||
94 | #endif // is_mpi | |
95 | ||
96 | void SimSetup::createSim(void){ | |
97 | ||
97 | – | int i, j, k, globalAtomIndex; |
98 | – | |
98 | // gather all of the information from the Bass file | |
99 | ||
100 | gatherInfo(); | |
# | Line 104 | Line 103 | void SimSetup::createSim(void){ | |
103 | ||
104 | sysObjectsCreation(); | |
105 | ||
106 | < | // check on the post processing info |
106 | > | // initialize the system coordinates |
107 | ||
108 | < | finalInfoCheck(); |
108 | > | if ( !initSuspend ){ |
109 | > | initSystemCoords(); |
110 | ||
111 | < | // initialize the system coordinates |
111 | > | if( !(globals->getUseInitTime()) ) |
112 | > | info[0].currentTime = 0.0; |
113 | > | } |
114 | ||
115 | < | if( !isInfoArray ) initSystemCoords(); |
115 | > | // check on the post processing info |
116 | ||
117 | + | finalInfoCheck(); |
118 | + | |
119 | // make the output filenames | |
120 | ||
121 | makeOutNames(); | |
122 | < | |
122 | > | |
123 | // make the integrator | |
124 | < | |
124 | > | |
125 | makeIntegrator(); | |
126 | < | |
126 | > | |
127 | #ifdef IS_MPI | |
128 | mpiSim->mpiRefresh(); | |
129 | #endif | |
# | Line 127 | Line 131 | void SimSetup::createSim(void){ | |
131 | // initialize the Fortran | |
132 | ||
133 | initFortran(); | |
130 | – | |
131 | – | |
132 | – | |
134 | } | |
135 | ||
136 | ||
137 | < | void SimSetup::makeMolecules( void ){ |
138 | < | |
138 | < | int k,l; |
137 | > | void SimSetup::makeMolecules(void){ |
138 | > | int k; |
139 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
140 | molInit molInfo; | |
141 | DirectionalAtom* dAtom; | |
# | Line 150 | Line 150 | void SimSetup::makeMolecules( void ){ | |
150 | bend_set* theBends; | |
151 | torsion_set* theTorsions; | |
152 | ||
153 | < | |
153 | > | |
154 | //init the forceField paramters | |
155 | ||
156 | the_ff->readParams(); | |
157 | ||
158 | < | |
158 | > | |
159 | // init the atoms | |
160 | ||
161 | double ux, uy, uz, u, uSqr; | |
162 | – | |
163 | – | for(k=0; k<nInfo; k++){ |
164 | – | |
165 | – | the_ff->setSimInfo( &(info[k]) ); |
162 | ||
163 | + | for (k = 0; k < nInfo; k++){ |
164 | + | the_ff->setSimInfo(&(info[k])); |
165 | + | |
166 | atomOffset = 0; | |
167 | excludeOffset = 0; | |
168 | < | for(i=0; i<info[k].n_mol; i++){ |
170 | < | |
168 | > | for (i = 0; i < info[k].n_mol; i++){ |
169 | stampID = info[k].molecules[i].getStampID(); | |
170 | ||
171 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
172 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
173 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
171 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
172 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
173 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
174 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
175 | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; | |
176 | < | |
176 | > | |
177 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
178 | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); | |
179 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
180 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
181 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
179 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
180 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
181 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
182 | ||
183 | theBonds = new bond_pair[molInfo.nBonds]; | |
184 | theBends = new bend_set[molInfo.nBends]; | |
185 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
186 | < | |
187 | < | // make the Atoms |
188 | < | |
189 | < | for(j=0; j<molInfo.nAtoms; j++){ |
190 | < | |
191 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
192 | < | if( currentAtom->haveOrientation() ){ |
193 | < | |
194 | < | dAtom = new DirectionalAtom( (j + atomOffset), |
195 | < | info[k].getConfiguration() ); |
196 | < | info[k].n_oriented++; |
197 | < | molInfo.myAtoms[j] = dAtom; |
198 | < | |
199 | < | ux = currentAtom->getOrntX(); |
200 | < | uy = currentAtom->getOrntY(); |
201 | < | uz = currentAtom->getOrntZ(); |
202 | < | |
203 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
204 | < | |
205 | < | u = sqrt( uSqr ); |
206 | < | ux = ux / u; |
207 | < | uy = uy / u; |
208 | < | uz = uz / u; |
209 | < | |
210 | < | dAtom->setSUx( ux ); |
211 | < | dAtom->setSUy( uy ); |
212 | < | dAtom->setSUz( uz ); |
213 | < | } |
214 | < | else{ |
215 | < | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
216 | < | info[k].getConfiguration() ); |
217 | < | } |
220 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 | < | |
186 | > | |
187 | > | // make the Atoms |
188 | > | |
189 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
190 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
191 | > | if (currentAtom->haveOrientation()){ |
192 | > | dAtom = new DirectionalAtom((j + atomOffset), |
193 | > | info[k].getConfiguration()); |
194 | > | info[k].n_oriented++; |
195 | > | molInfo.myAtoms[j] = dAtom; |
196 | > | |
197 | > | ux = currentAtom->getOrntX(); |
198 | > | uy = currentAtom->getOrntY(); |
199 | > | uz = currentAtom->getOrntZ(); |
200 | > | |
201 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
202 | > | |
203 | > | u = sqrt(uSqr); |
204 | > | ux = ux / u; |
205 | > | uy = uy / u; |
206 | > | uz = uz / u; |
207 | > | |
208 | > | dAtom->setSUx(ux); |
209 | > | dAtom->setSUy(uy); |
210 | > | dAtom->setSUz(uz); |
211 | > | } |
212 | > | else{ |
213 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
214 | > | info[k].getConfiguration()); |
215 | > | } |
216 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
217 | > | |
218 | #ifdef IS_MPI | |
219 | < | |
220 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
221 | < | |
219 | > | |
220 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
221 | > | |
222 | #endif // is_mpi | |
223 | } | |
224 | < | |
225 | < | // make the bonds |
226 | < | for(j=0; j<molInfo.nBonds; j++){ |
227 | < | |
228 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
229 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
230 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
231 | < | |
232 | < | exI = theBonds[j].a; |
233 | < | exJ = theBonds[j].b; |
234 | < | |
235 | < | // exclude_I must always be the smaller of the pair |
236 | < | if( exI > exJ ){ |
237 | < | tempEx = exI; |
238 | < | exI = exJ; |
239 | < | exJ = tempEx; |
244 | < | } |
224 | > | |
225 | > | // make the bonds |
226 | > | for (j = 0; j < molInfo.nBonds; j++){ |
227 | > | currentBond = comp_stamps[stampID]->getBond(j); |
228 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
229 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
230 | > | |
231 | > | exI = theBonds[j].a; |
232 | > | exJ = theBonds[j].b; |
233 | > | |
234 | > | // exclude_I must always be the smaller of the pair |
235 | > | if (exI > exJ){ |
236 | > | tempEx = exI; |
237 | > | exI = exJ; |
238 | > | exJ = tempEx; |
239 | > | } |
240 | #ifdef IS_MPI | |
241 | < | tempEx = exI; |
242 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
243 | < | tempEx = exJ; |
244 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
245 | < | |
246 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
241 | > | tempEx = exI; |
242 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
243 | > | tempEx = exJ; |
244 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
245 | > | |
246 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
247 | #else // isn't MPI | |
248 | < | |
249 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
248 | > | |
249 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
250 | #endif //is_mpi | |
251 | } | |
252 | excludeOffset += molInfo.nBonds; | |
253 | < | |
253 | > | |
254 | //make the bends | |
255 | < | for(j=0; j<molInfo.nBends; j++){ |
256 | < | |
257 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
258 | < | theBends[j].a = currentBend->getA() + atomOffset; |
259 | < | theBends[j].b = currentBend->getB() + atomOffset; |
260 | < | theBends[j].c = currentBend->getC() + atomOffset; |
261 | < | |
262 | < | if( currentBend->haveExtras() ){ |
263 | < | |
264 | < | extras = currentBend->getExtras(); |
265 | < | current_extra = extras; |
266 | < | |
267 | < | while( current_extra != NULL ){ |
268 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
269 | < | |
270 | < | switch( current_extra->getType() ){ |
271 | < | |
272 | < | case 0: |
273 | < | theBends[j].ghost = |
274 | < | current_extra->getInt() + atomOffset; |
275 | < | theBends[j].isGhost = 1; |
276 | < | break; |
277 | < | |
278 | < | case 1: |
279 | < | theBends[j].ghost = |
280 | < | (int)current_extra->getDouble() + atomOffset; |
281 | < | theBends[j].isGhost = 1; |
282 | < | break; |
283 | < | |
284 | < | default: |
285 | < | sprintf( painCave.errMsg, |
286 | < | "SimSetup Error: ghostVectorSource was neither a " |
287 | < | "double nor an int.\n" |
288 | < | "-->Bend[%d] in %s\n", |
289 | < | j, comp_stamps[stampID]->getID() ); |
290 | < | painCave.isFatal = 1; |
291 | < | simError(); |
255 | > | for (j = 0; j < molInfo.nBends; j++){ |
256 | > | currentBend = comp_stamps[stampID]->getBend(j); |
257 | > | theBends[j].a = currentBend->getA() + atomOffset; |
258 | > | theBends[j].b = currentBend->getB() + atomOffset; |
259 | > | theBends[j].c = currentBend->getC() + atomOffset; |
260 | > | |
261 | > | if (currentBend->haveExtras()){ |
262 | > | extras = currentBend->getExtras(); |
263 | > | current_extra = extras; |
264 | > | |
265 | > | while (current_extra != NULL){ |
266 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
267 | > | switch (current_extra->getType()){ |
268 | > | case 0: |
269 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
270 | > | theBends[j].isGhost = 1; |
271 | > | break; |
272 | > | |
273 | > | case 1: |
274 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
275 | > | atomOffset; |
276 | > | theBends[j].isGhost = 1; |
277 | > | break; |
278 | > | |
279 | > | default: |
280 | > | sprintf(painCave.errMsg, |
281 | > | "SimSetup Error: ghostVectorSource was neither a " |
282 | > | "double nor an int.\n" |
283 | > | "-->Bend[%d] in %s\n", |
284 | > | j, comp_stamps[stampID]->getID()); |
285 | > | painCave.isFatal = 1; |
286 | > | simError(); |
287 | > | } |
288 | > | } |
289 | > | else{ |
290 | > | sprintf(painCave.errMsg, |
291 | > | "SimSetup Error: unhandled bend assignment:\n" |
292 | > | " -->%s in Bend[%d] in %s\n", |
293 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
294 | > | painCave.isFatal = 1; |
295 | > | simError(); |
296 | > | } |
297 | > | |
298 | > | current_extra = current_extra->getNext(); |
299 | > | } |
300 | } | |
301 | < | } |
302 | < | |
303 | < | else{ |
304 | < | |
305 | < | sprintf( painCave.errMsg, |
306 | < | "SimSetup Error: unhandled bend assignment:\n" |
307 | < | " -->%s in Bend[%d] in %s\n", |
308 | < | current_extra->getlhs(), |
309 | < | j, comp_stamps[stampID]->getID() ); |
310 | < | painCave.isFatal = 1; |
311 | < | simError(); |
312 | < | } |
313 | < | |
314 | < | current_extra = current_extra->getNext(); |
315 | < | } |
316 | < | } |
314 | < | |
315 | < | if( !theBends[j].isGhost ){ |
316 | < | |
317 | < | exI = theBends[j].a; |
318 | < | exJ = theBends[j].c; |
319 | < | } |
320 | < | else{ |
321 | < | |
322 | < | exI = theBends[j].a; |
323 | < | exJ = theBends[j].b; |
324 | < | } |
325 | < | |
326 | < | // exclude_I must always be the smaller of the pair |
327 | < | if( exI > exJ ){ |
328 | < | tempEx = exI; |
329 | < | exI = exJ; |
330 | < | exJ = tempEx; |
331 | < | } |
301 | > | |
302 | > | if (!theBends[j].isGhost){ |
303 | > | exI = theBends[j].a; |
304 | > | exJ = theBends[j].c; |
305 | > | } |
306 | > | else{ |
307 | > | exI = theBends[j].a; |
308 | > | exJ = theBends[j].b; |
309 | > | } |
310 | > | |
311 | > | // exclude_I must always be the smaller of the pair |
312 | > | if (exI > exJ){ |
313 | > | tempEx = exI; |
314 | > | exI = exJ; |
315 | > | exJ = tempEx; |
316 | > | } |
317 | #ifdef IS_MPI | |
318 | < | tempEx = exI; |
319 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
320 | < | tempEx = exJ; |
321 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
322 | < | |
323 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
318 | > | tempEx = exI; |
319 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
320 | > | tempEx = exJ; |
321 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
322 | > | |
323 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
324 | #else // isn't MPI | |
325 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
325 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
326 | #endif //is_mpi | |
327 | } | |
328 | excludeOffset += molInfo.nBends; | |
329 | < | |
330 | < | for(j=0; j<molInfo.nTorsions; j++){ |
331 | < | |
332 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
333 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
334 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
335 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
336 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
337 | < | |
338 | < | exI = theTorsions[j].a; |
339 | < | exJ = theTorsions[j].d; |
340 | < | |
341 | < | // exclude_I must always be the smaller of the pair |
342 | < | if( exI > exJ ){ |
343 | < | tempEx = exI; |
344 | < | exI = exJ; |
345 | < | exJ = tempEx; |
361 | < | } |
329 | > | |
330 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
331 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
332 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
333 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
334 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
335 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
336 | > | |
337 | > | exI = theTorsions[j].a; |
338 | > | exJ = theTorsions[j].d; |
339 | > | |
340 | > | // exclude_I must always be the smaller of the pair |
341 | > | if (exI > exJ){ |
342 | > | tempEx = exI; |
343 | > | exI = exJ; |
344 | > | exJ = tempEx; |
345 | > | } |
346 | #ifdef IS_MPI | |
347 | < | tempEx = exI; |
348 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
349 | < | tempEx = exJ; |
350 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
351 | < | |
352 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 | > | tempEx = exI; |
348 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
349 | > | tempEx = exJ; |
350 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
351 | > | |
352 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
353 | #else // isn't MPI | |
354 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
354 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
355 | #endif //is_mpi | |
356 | } | |
357 | excludeOffset += molInfo.nTorsions; | |
358 | < | |
359 | < | |
358 | > | |
359 | > | |
360 | // send the arrays off to the forceField for init. | |
377 | – | |
378 | – | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 | – | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 | – | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 | – | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 | – | |
383 | – | |
384 | – | info[k].molecules[i].initialize( molInfo ); |
361 | ||
362 | < | |
362 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
363 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
364 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
365 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
366 | > | theTorsions); |
367 | > | |
368 | > | |
369 | > | info[k].molecules[i].initialize(molInfo); |
370 | > | |
371 | > | |
372 | atomOffset += molInfo.nAtoms; | |
373 | delete[] theBonds; | |
374 | delete[] theBends; | |
375 | delete[] theTorsions; | |
376 | } | |
377 | } | |
378 | < | |
378 | > | |
379 | #ifdef IS_MPI | |
380 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
380 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
381 | MPIcheckPoint(); | |
382 | #endif // is_mpi | |
383 | < | |
383 | > | |
384 | // clean up the forcefield | |
385 | ||
386 | the_ff->calcRcut(); | |
387 | the_ff->cleanMe(); | |
403 | – | |
388 | } | |
389 | ||
390 | < | void SimSetup::initFromBass( void ){ |
407 | < | |
390 | > | void SimSetup::initFromBass(void){ |
391 | int i, j, k; | |
392 | int n_cells; | |
393 | double cellx, celly, cellz; | |
# | Line 418 | Line 401 | void SimSetup::initFromBass( void ){ | |
401 | vel[1] = 0.0; | |
402 | vel[2] = 0.0; | |
403 | ||
404 | < | temp1 = (double)tot_nmol / 4.0; |
405 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
406 | < | temp3 = ceil( temp2 ); |
404 | > | temp1 = (double) tot_nmol / 4.0; |
405 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
406 | > | temp3 = ceil(temp2); |
407 | ||
408 | < | have_extra =0; |
409 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
410 | < | have_extra =1; |
408 | > | have_extra = 0; |
409 | > | if (temp2 < temp3){ |
410 | > | // we have a non-complete lattice |
411 | > | have_extra = 1; |
412 | ||
413 | < | n_cells = (int)temp3 - 1; |
413 | > | n_cells = (int) temp3 - 1; |
414 | cellx = info[0].boxL[0] / temp3; | |
415 | celly = info[0].boxL[1] / temp3; | |
416 | cellz = info[0].boxL[2] / temp3; | |
417 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
418 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
419 | < | n_per_extra = (int)ceil( temp1 ); |
417 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
418 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
419 | > | n_per_extra = (int) ceil(temp1); |
420 | ||
421 | < | if( n_per_extra > 4){ |
422 | < | sprintf( painCave.errMsg, |
423 | < | "SimSetup error. There has been an error in constructing" |
424 | < | " the non-complete lattice.\n" ); |
421 | > | if (n_per_extra > 4){ |
422 | > | sprintf(painCave.errMsg, |
423 | > | "SimSetup error. There has been an error in constructing" |
424 | > | " the non-complete lattice.\n"); |
425 | painCave.isFatal = 1; | |
426 | simError(); | |
427 | } | |
428 | } | |
429 | else{ | |
430 | < | n_cells = (int)temp3; |
430 | > | n_cells = (int) temp3; |
431 | cellx = info[0].boxL[0] / temp3; | |
432 | celly = info[0].boxL[1] / temp3; | |
433 | cellz = info[0].boxL[2] / temp3; | |
# | Line 454 | Line 438 | void SimSetup::initFromBass( void ){ | |
438 | current_comp = 0; | |
439 | current_atom_ndx = 0; | |
440 | ||
441 | < | for( i=0; i < n_cells ; i++ ){ |
442 | < | for( j=0; j < n_cells; j++ ){ |
443 | < | for( k=0; k < n_cells; k++ ){ |
441 | > | for (i = 0; i < n_cells ; i++){ |
442 | > | for (j = 0; j < n_cells; j++){ |
443 | > | for (k = 0; k < n_cells; k++){ |
444 | > | makeElement(i * cellx, j * celly, k * cellz); |
445 | ||
446 | < | makeElement( i * cellx, |
462 | < | j * celly, |
463 | < | k * cellz ); |
446 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
447 | ||
448 | < | makeElement( i * cellx + 0.5 * cellx, |
466 | < | j * celly + 0.5 * celly, |
467 | < | k * cellz ); |
448 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
449 | ||
450 | < | makeElement( i * cellx, |
470 | < | j * celly + 0.5 * celly, |
471 | < | k * cellz + 0.5 * cellz ); |
472 | < | |
473 | < | makeElement( i * cellx + 0.5 * cellx, |
474 | < | j * celly, |
475 | < | k * cellz + 0.5 * cellz ); |
450 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
451 | } | |
452 | } | |
453 | } | |
454 | ||
455 | < | if( have_extra ){ |
455 | > | if (have_extra){ |
456 | done = 0; | |
457 | ||
458 | int start_ndx; | |
459 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
460 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
459 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
460 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
461 | > | if (i < n_cells){ |
462 | > | if (j < n_cells){ |
463 | > | start_ndx = n_cells; |
464 | > | } |
465 | > | else |
466 | > | start_ndx = 0; |
467 | > | } |
468 | > | else |
469 | > | start_ndx = 0; |
470 | ||
471 | < | if( i < n_cells ){ |
471 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
472 | > | makeElement(i * cellx, j * celly, k * cellz); |
473 | > | done = (current_mol >= tot_nmol); |
474 | ||
475 | < | if( j < n_cells ){ |
476 | < | start_ndx = n_cells; |
477 | < | } |
478 | < | else start_ndx = 0; |
479 | < | } |
494 | < | else start_ndx = 0; |
495 | < | |
496 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
475 | > | if (!done && n_per_extra > 1){ |
476 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
477 | > | k * cellz); |
478 | > | done = (current_mol >= tot_nmol); |
479 | > | } |
480 | ||
481 | < | makeElement( i * cellx, |
482 | < | j * celly, |
483 | < | k * cellz ); |
484 | < | done = ( current_mol >= tot_nmol ); |
481 | > | if (!done && n_per_extra > 2){ |
482 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
483 | > | k * cellz + 0.5 * cellz); |
484 | > | done = (current_mol >= tot_nmol); |
485 | > | } |
486 | ||
487 | < | if( !done && n_per_extra > 1 ){ |
488 | < | makeElement( i * cellx + 0.5 * cellx, |
489 | < | j * celly + 0.5 * celly, |
490 | < | k * cellz ); |
491 | < | done = ( current_mol >= tot_nmol ); |
492 | < | } |
509 | < | |
510 | < | if( !done && n_per_extra > 2){ |
511 | < | makeElement( i * cellx, |
512 | < | j * celly + 0.5 * celly, |
513 | < | k * cellz + 0.5 * cellz ); |
514 | < | done = ( current_mol >= tot_nmol ); |
515 | < | } |
516 | < | |
517 | < | if( !done && n_per_extra > 3){ |
518 | < | makeElement( i * cellx + 0.5 * cellx, |
519 | < | j * celly, |
520 | < | k * cellz + 0.5 * cellz ); |
521 | < | done = ( current_mol >= tot_nmol ); |
522 | < | } |
523 | < | } |
487 | > | if (!done && n_per_extra > 3){ |
488 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
489 | > | k * cellz + 0.5 * cellz); |
490 | > | done = (current_mol >= tot_nmol); |
491 | > | } |
492 | > | } |
493 | } | |
494 | } | |
495 | } | |
496 | ||
497 | < | for( i=0; i<info[0].n_atoms; i++ ){ |
498 | < | info[0].atoms[i]->setVel( vel ); |
497 | > | for (i = 0; i < info[0].n_atoms; i++){ |
498 | > | info[0].atoms[i]->setVel(vel); |
499 | } | |
500 | } | |
501 | ||
502 | < | void SimSetup::makeElement( double x, double y, double z ){ |
534 | < | |
502 | > | void SimSetup::makeElement(double x, double y, double z){ |
503 | int k; | |
504 | AtomStamp* current_atom; | |
505 | DirectionalAtom* dAtom; | |
506 | double rotMat[3][3]; | |
507 | double pos[3]; | |
508 | ||
509 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
510 | < | |
511 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
512 | < | if( !current_atom->havePosition() ){ |
513 | < | sprintf( painCave.errMsg, |
514 | < | "SimSetup:initFromBass error.\n" |
515 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
516 | < | "\tThe initialization routine is unable to give a start" |
517 | < | " position.\n", |
550 | < | comp_stamps[current_comp]->getID(), |
551 | < | current_atom->getType() ); |
509 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
510 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
511 | > | if (!current_atom->havePosition()){ |
512 | > | sprintf(painCave.errMsg, |
513 | > | "SimSetup:initFromBass error.\n" |
514 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
515 | > | "\tThe initialization routine is unable to give a start" |
516 | > | " position.\n", |
517 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
518 | painCave.isFatal = 1; | |
519 | simError(); | |
520 | } | |
521 | < | |
521 | > | |
522 | pos[0] = x + current_atom->getPosX(); | |
523 | pos[1] = y + current_atom->getPosY(); | |
524 | pos[2] = z + current_atom->getPosZ(); | |
559 | – | |
560 | – | info[0].atoms[current_atom_ndx]->setPos( pos ); |
525 | ||
526 | < | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
526 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
527 | ||
528 | < | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
528 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
529 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
530 | ||
531 | rotMat[0][0] = 1.0; | |
532 | rotMat[0][1] = 0.0; | |
# | Line 575 | Line 540 | void SimSetup::makeElement( double x, double y, double | |
540 | rotMat[2][1] = 0.0; | |
541 | rotMat[2][2] = 1.0; | |
542 | ||
543 | < | dAtom->setA( rotMat ); |
543 | > | dAtom->setA(rotMat); |
544 | } | |
545 | ||
546 | current_atom_ndx++; | |
# | Line 584 | Line 549 | void SimSetup::makeElement( double x, double y, double | |
549 | current_mol++; | |
550 | current_comp_mol++; | |
551 | ||
552 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
588 | < | |
552 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
553 | current_comp_mol = 0; | |
554 | current_comp++; | |
555 | } | |
556 | } | |
557 | ||
558 | ||
559 | < | void SimSetup::gatherInfo( void ){ |
560 | < | int i,j,k; |
559 | > | void SimSetup::gatherInfo(void){ |
560 | > | int i; |
561 | ||
562 | ensembleCase = -1; | |
563 | ffCase = -1; | |
564 | ||
565 | // set the easy ones first | |
566 | ||
567 | < | for( i=0; i<nInfo; i++){ |
567 | > | for (i = 0; i < nInfo; i++){ |
568 | info[i].target_temp = globals->getTargetTemp(); | |
569 | info[i].dt = globals->getDt(); | |
570 | info[i].run_time = globals->getRunTime(); | |
# | Line 610 | Line 574 | void SimSetup::gatherInfo( void ){ | |
574 | ||
575 | // get the forceField | |
576 | ||
577 | < | strcpy( force_field, globals->getForceField() ); |
577 | > | strcpy(force_field, globals->getForceField()); |
578 | ||
579 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
580 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
581 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
579 | > | if (!strcasecmp(force_field, "DUFF")){ |
580 | > | ffCase = FF_DUFF; |
581 | > | } |
582 | > | else if (!strcasecmp(force_field, "LJ")){ |
583 | > | ffCase = FF_LJ; |
584 | > | } |
585 | > | else if (!strcasecmp(force_field, "EAM")){ |
586 | > | ffCase = FF_EAM; |
587 | > | } |
588 | else{ | |
589 | < | sprintf( painCave.errMsg, |
590 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
591 | < | force_field ); |
592 | < | painCave.isFatal = 1; |
623 | < | simError(); |
589 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
590 | > | force_field); |
591 | > | painCave.isFatal = 1; |
592 | > | simError(); |
593 | } | |
594 | ||
595 | < | // get the ensemble |
595 | > | // get the ensemble |
596 | ||
597 | < | strcpy( ensemble, globals->getEnsemble() ); |
597 | > | strcpy(ensemble, globals->getEnsemble()); |
598 | ||
599 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
600 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
601 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
599 | > | if (!strcasecmp(ensemble, "NVE")){ |
600 | > | ensembleCase = NVE_ENS; |
601 | > | } |
602 | > | else if (!strcasecmp(ensemble, "NVT")){ |
603 | > | ensembleCase = NVT_ENS; |
604 | > | } |
605 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
606 | ensembleCase = NPTi_ENS; | |
607 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
608 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
609 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
607 | > | } |
608 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
609 | > | ensembleCase = NPTf_ENS; |
610 | > | } |
611 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
612 | > | ensembleCase = NPTxyz_ENS; |
613 | > | } |
614 | else{ | |
615 | < | sprintf( painCave.errMsg, |
616 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
617 | < | "reverting to NVE for this simulation.\n", |
618 | < | ensemble ); |
619 | < | painCave.isFatal = 0; |
620 | < | simError(); |
621 | < | strcpy( ensemble, "NVE" ); |
622 | < | ensembleCase = NVE_ENS; |
615 | > | sprintf(painCave.errMsg, |
616 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
617 | > | "reverting to NVE for this simulation.\n", |
618 | > | ensemble); |
619 | > | painCave.isFatal = 0; |
620 | > | simError(); |
621 | > | strcpy(ensemble, "NVE"); |
622 | > | ensembleCase = NVE_ENS; |
623 | } | |
647 | – | |
648 | – | for(i=0; i<nInfo; i++){ |
649 | – | |
650 | – | strcpy( info[i].ensemble, ensemble ); |
624 | ||
625 | + | for (i = 0; i < nInfo; i++){ |
626 | + | strcpy(info[i].ensemble, ensemble); |
627 | + | |
628 | // get the mixing rule | |
629 | ||
630 | < | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
630 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
631 | info[i].usePBC = globals->getPBC(); | |
632 | } | |
633 | < | |
633 | > | |
634 | // get the components and calculate the tot_nMol and indvidual n_mol | |
635 | < | |
635 | > | |
636 | the_components = globals->getComponents(); | |
637 | components_nmol = new int[n_components]; | |
638 | ||
639 | ||
640 | < | if( !globals->haveNMol() ){ |
640 | > | if (!globals->haveNMol()){ |
641 | // we don't have the total number of molecules, so we assume it is | |
642 | // given in each component | |
643 | ||
644 | tot_nmol = 0; | |
645 | < | for( i=0; i<n_components; i++ ){ |
646 | < | |
647 | < | if( !the_components[i]->haveNMol() ){ |
648 | < | // we have a problem |
649 | < | sprintf( painCave.errMsg, |
650 | < | "SimSetup Error. No global NMol or component NMol" |
651 | < | " given. Cannot calculate the number of atoms.\n" ); |
652 | < | painCave.isFatal = 1; |
677 | < | simError(); |
645 | > | for (i = 0; i < n_components; i++){ |
646 | > | if (!the_components[i]->haveNMol()){ |
647 | > | // we have a problem |
648 | > | sprintf(painCave.errMsg, |
649 | > | "SimSetup Error. No global NMol or component NMol" |
650 | > | " given. Cannot calculate the number of atoms.\n"); |
651 | > | painCave.isFatal = 1; |
652 | > | simError(); |
653 | } | |
654 | ||
655 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 682 | Line 657 | void SimSetup::gatherInfo( void ){ | |
657 | } | |
658 | } | |
659 | else{ | |
660 | < | sprintf( painCave.errMsg, |
661 | < | "SimSetup error.\n" |
662 | < | "\tSorry, the ability to specify total" |
663 | < | " nMols and then give molfractions in the components\n" |
664 | < | "\tis not currently supported." |
665 | < | " Please give nMol in the components.\n" ); |
660 | > | sprintf(painCave.errMsg, |
661 | > | "SimSetup error.\n" |
662 | > | "\tSorry, the ability to specify total" |
663 | > | " nMols and then give molfractions in the components\n" |
664 | > | "\tis not currently supported." |
665 | > | " Please give nMol in the components.\n"); |
666 | painCave.isFatal = 1; | |
667 | simError(); | |
668 | } | |
669 | ||
670 | // set the status, sample, and thermal kick times | |
696 | – | |
697 | – | for(i=0; i<nInfo; i++){ |
671 | ||
672 | < | if( globals->haveSampleTime() ){ |
672 | > | for (i = 0; i < nInfo; i++){ |
673 | > | if (globals->haveSampleTime()){ |
674 | info[i].sampleTime = globals->getSampleTime(); | |
675 | info[i].statusTime = info[i].sampleTime; | |
676 | info[i].thermalTime = info[i].sampleTime; | |
# | Line 706 | Line 680 | void SimSetup::gatherInfo( void ){ | |
680 | info[i].statusTime = info[i].sampleTime; | |
681 | info[i].thermalTime = info[i].sampleTime; | |
682 | } | |
683 | < | |
684 | < | if( globals->haveStatusTime() ){ |
683 | > | |
684 | > | if (globals->haveStatusTime()){ |
685 | info[i].statusTime = globals->getStatusTime(); | |
686 | } | |
687 | < | |
688 | < | if( globals->haveThermalTime() ){ |
687 | > | |
688 | > | if (globals->haveThermalTime()){ |
689 | info[i].thermalTime = globals->getThermalTime(); | |
690 | } | |
691 | ||
692 | + | info[i].resetIntegrator = 0; |
693 | + | if( globals->haveResetTime() ){ |
694 | + | info[i].resetTime = globals->getResetTime(); |
695 | + | info[i].resetIntegrator = 1; |
696 | + | } |
697 | + | |
698 | // check for the temperature set flag | |
699 | + | |
700 | + | if (globals->haveTempSet()) |
701 | + | info[i].setTemp = globals->getTempSet(); |
702 | ||
703 | < | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
703 | > | // check for the extended State init |
704 | > | |
705 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
706 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
707 | ||
722 | – | // get some of the tricky things that may still be in the globals |
723 | – | |
724 | – | double boxVector[3]; |
725 | – | if( globals->haveBox() ){ |
726 | – | boxVector[0] = globals->getBox(); |
727 | – | boxVector[1] = globals->getBox(); |
728 | – | boxVector[2] = globals->getBox(); |
729 | – | |
730 | – | info[i].setBox( boxVector ); |
731 | – | } |
732 | – | else if( globals->haveDensity() ){ |
733 | – | |
734 | – | double vol; |
735 | – | vol = (double)tot_nmol / globals->getDensity(); |
736 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 | – | boxVector[1] = boxVector[0]; |
738 | – | boxVector[2] = boxVector[0]; |
739 | – | |
740 | – | info[i].setBox( boxVector ); |
708 | } | |
709 | < | else{ |
710 | < | if( !globals->haveBoxX() ){ |
711 | < | sprintf( painCave.errMsg, |
712 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
713 | < | painCave.isFatal = 1; |
714 | < | simError(); |
709 | > | |
710 | > | //setup seed for random number generator |
711 | > | int seedValue; |
712 | > | |
713 | > | if (globals->haveSeed()){ |
714 | > | seedValue = globals->getSeed(); |
715 | > | |
716 | > | if(seedValue / 1E9 == 0){ |
717 | > | sprintf(painCave.errMsg, |
718 | > | "Seed for sprng library should contain at least 9 digits\n" |
719 | > | "OOPSE will generate a seed for user\n"); |
720 | > | painCave.isFatal = 0; |
721 | > | simError(); |
722 | > | |
723 | > | //using seed generated by system instead of invalid seed set by user |
724 | > | #ifndef IS_MPI |
725 | > | seedValue = make_sprng_seed(); |
726 | > | #else |
727 | > | if (worldRank == 0){ |
728 | > | seedValue = make_sprng_seed(); |
729 | } | |
730 | < | boxVector[0] = globals->getBoxX(); |
731 | < | |
751 | < | if( !globals->haveBoxY() ){ |
752 | < | sprintf( painCave.errMsg, |
753 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
754 | < | painCave.isFatal = 1; |
755 | < | simError(); |
756 | < | } |
757 | < | boxVector[1] = globals->getBoxY(); |
758 | < | |
759 | < | if( !globals->haveBoxZ() ){ |
760 | < | sprintf( painCave.errMsg, |
761 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
762 | < | painCave.isFatal = 1; |
763 | < | simError(); |
764 | < | } |
765 | < | boxVector[2] = globals->getBoxZ(); |
766 | < | |
767 | < | info[i].setBox( boxVector ); |
730 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
731 | > | #endif |
732 | } | |
733 | + | }//end of if branch of globals->haveSeed() |
734 | + | else{ |
735 | + | |
736 | + | #ifndef IS_MPI |
737 | + | seedValue = make_sprng_seed(); |
738 | + | #else |
739 | + | if (worldRank == 0){ |
740 | + | seedValue = make_sprng_seed(); |
741 | + | } |
742 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
743 | + | #endif |
744 | + | }//end of globals->haveSeed() |
745 | ||
746 | + | for (int i = 0; i < nInfo; i++){ |
747 | + | info[i].setSeed(seedValue); |
748 | } | |
749 | < | |
749 | > | |
750 | #ifdef IS_MPI | |
751 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
751 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
752 | MPIcheckPoint(); | |
753 | #endif // is_mpi | |
776 | – | |
754 | } | |
755 | ||
756 | ||
757 | < | void SimSetup::finalInfoCheck( void ){ |
757 | > | void SimSetup::finalInfoCheck(void){ |
758 | int index; | |
759 | int usesDipoles; | |
760 | int i; | |
761 | ||
762 | < | for(i=0; i<nInfo; i++){ |
762 | > | for (i = 0; i < nInfo; i++){ |
763 | // check electrostatic parameters | |
764 | < | |
764 | > | |
765 | index = 0; | |
766 | usesDipoles = 0; | |
767 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
767 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
768 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
769 | index++; | |
770 | } | |
771 | < | |
771 | > | |
772 | #ifdef IS_MPI | |
773 | int myUse = usesDipoles; | |
774 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
774 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
775 | #endif //is_mpi | |
776 | < | |
776 | > | |
777 | double theEcr, theEst; | |
778 | < | |
779 | < | if (globals->getUseRF() ) { |
778 | > | |
779 | > | if (globals->getUseRF()){ |
780 | info[i].useReactionField = 1; | |
781 | < | |
782 | < | if( !globals->haveECR() ){ |
783 | < | sprintf( painCave.errMsg, |
784 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
785 | < | "box length for the electrostaticCutoffRadius.\n" |
786 | < | "I hope you have a very fast processor!\n"); |
787 | < | painCave.isFatal = 0; |
788 | < | simError(); |
789 | < | double smallest; |
790 | < | smallest = info[i].boxL[0]; |
791 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
792 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
793 | < | theEcr = 0.5 * smallest; |
794 | < | } else { |
795 | < | theEcr = globals->getECR(); |
781 | > | |
782 | > | if (!globals->haveECR()){ |
783 | > | sprintf(painCave.errMsg, |
784 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
785 | > | "box length for the electrostaticCutoffRadius.\n" |
786 | > | "I hope you have a very fast processor!\n"); |
787 | > | painCave.isFatal = 0; |
788 | > | simError(); |
789 | > | double smallest; |
790 | > | smallest = info[i].boxL[0]; |
791 | > | if (info[i].boxL[1] <= smallest) |
792 | > | smallest = info[i].boxL[1]; |
793 | > | if (info[i].boxL[2] <= smallest) |
794 | > | smallest = info[i].boxL[2]; |
795 | > | theEcr = 0.5 * smallest; |
796 | } | |
797 | < | |
798 | < | if( !globals->haveEST() ){ |
822 | < | sprintf( painCave.errMsg, |
823 | < | "SimSetup Warning: using default value of 0.05 * the " |
824 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 | < | ); |
826 | < | painCave.isFatal = 0; |
827 | < | simError(); |
828 | < | theEst = 0.05 * theEcr; |
829 | < | } else { |
830 | < | theEst= globals->getEST(); |
797 | > | else{ |
798 | > | theEcr = globals->getECR(); |
799 | } | |
800 | < | |
801 | < | info[i].setEcr( theEcr, theEst ); |
802 | < | |
803 | < | if(!globals->haveDielectric() ){ |
804 | < | sprintf( painCave.errMsg, |
805 | < | "SimSetup Error: You are trying to use Reaction Field without" |
806 | < | "setting a dielectric constant!\n" |
807 | < | ); |
840 | < | painCave.isFatal = 1; |
841 | < | simError(); |
800 | > | |
801 | > | if (!globals->haveEST()){ |
802 | > | sprintf(painCave.errMsg, |
803 | > | "SimSetup Warning: using default value of 0.05 * the " |
804 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
805 | > | painCave.isFatal = 0; |
806 | > | simError(); |
807 | > | theEst = 0.05 * theEcr; |
808 | } | |
809 | < | info[i].dielectric = globals->getDielectric(); |
810 | < | } |
845 | < | else { |
846 | < | if (usesDipoles) { |
847 | < | |
848 | < | if( !globals->haveECR() ){ |
849 | < | sprintf( painCave.errMsg, |
850 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
851 | < | "box length for the electrostaticCutoffRadius.\n" |
852 | < | "I hope you have a very fast processor!\n"); |
853 | < | painCave.isFatal = 0; |
854 | < | simError(); |
855 | < | double smallest; |
856 | < | smallest = info[i].boxL[0]; |
857 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 | < | theEcr = 0.5 * smallest; |
860 | < | } else { |
861 | < | theEcr = globals->getECR(); |
862 | < | } |
863 | < | |
864 | < | if( !globals->haveEST() ){ |
865 | < | sprintf( painCave.errMsg, |
866 | < | "SimSetup Warning: using default value of 0.05 * the " |
867 | < | "electrostaticCutoffRadius for the " |
868 | < | "electrostaticSkinThickness\n" |
869 | < | ); |
870 | < | painCave.isFatal = 0; |
871 | < | simError(); |
872 | < | theEst = 0.05 * theEcr; |
873 | < | } else { |
874 | < | theEst= globals->getEST(); |
875 | < | } |
876 | < | |
877 | < | info[i].setEcr( theEcr, theEst ); |
809 | > | else{ |
810 | > | theEst = globals->getEST(); |
811 | } | |
812 | < | } |
812 | > | |
813 | > | info[i].setDefaultEcr(theEcr, theEst); |
814 | > | |
815 | > | if (!globals->haveDielectric()){ |
816 | > | sprintf(painCave.errMsg, |
817 | > | "SimSetup Error: You are trying to use Reaction Field without" |
818 | > | "setting a dielectric constant!\n"); |
819 | > | painCave.isFatal = 1; |
820 | > | simError(); |
821 | > | } |
822 | > | info[i].dielectric = globals->getDielectric(); |
823 | > | } |
824 | > | else{ |
825 | > | if (usesDipoles){ |
826 | > | if (!globals->haveECR()){ |
827 | > | sprintf(painCave.errMsg, |
828 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
829 | > | "box length for the electrostaticCutoffRadius.\n" |
830 | > | "I hope you have a very fast processor!\n"); |
831 | > | painCave.isFatal = 0; |
832 | > | simError(); |
833 | > | double smallest; |
834 | > | smallest = info[i].boxL[0]; |
835 | > | if (info[i].boxL[1] <= smallest) |
836 | > | smallest = info[i].boxL[1]; |
837 | > | if (info[i].boxL[2] <= smallest) |
838 | > | smallest = info[i].boxL[2]; |
839 | > | theEcr = 0.5 * smallest; |
840 | > | } |
841 | > | else{ |
842 | > | theEcr = globals->getECR(); |
843 | > | } |
844 | > | |
845 | > | if (!globals->haveEST()){ |
846 | > | sprintf(painCave.errMsg, |
847 | > | "SimSetup Warning: using default value of 0.05 * the " |
848 | > | "electrostaticCutoffRadius for the " |
849 | > | "electrostaticSkinThickness\n"); |
850 | > | painCave.isFatal = 0; |
851 | > | simError(); |
852 | > | theEst = 0.05 * theEcr; |
853 | > | } |
854 | > | else{ |
855 | > | theEst = globals->getEST(); |
856 | > | } |
857 | > | |
858 | > | info[i].setDefaultEcr(theEcr, theEst); |
859 | > | } |
860 | > | } |
861 | > | |
862 | > | if( !initSuspend ) |
863 | > | info[i].checkCutOffs(); |
864 | } | |
865 | ||
866 | #ifdef IS_MPI | |
867 | < | strcpy( checkPointMsg, "post processing checks out" ); |
867 | > | strcpy(checkPointMsg, "post processing checks out"); |
868 | MPIcheckPoint(); | |
869 | #endif // is_mpi | |
886 | – | |
870 | } | |
871 | ||
872 | < | void SimSetup::initSystemCoords( void ){ |
872 | > | void SimSetup::initSystemCoords(void){ |
873 | int i; | |
874 | < | |
874 | > | |
875 | char* inName; | |
876 | ||
877 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
877 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
878 | ||
879 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
880 | < | |
881 | < | if( globals->haveInitialConfig() ){ |
882 | < | |
879 | > | for (i = 0; i < info[0].n_atoms; i++) |
880 | > | info[0].atoms[i]->setCoords(); |
881 | > | |
882 | > | if (globals->haveInitialConfig()){ |
883 | InitializeFromFile* fileInit; | |
884 | #ifdef IS_MPI // is_mpi | |
885 | < | if( worldRank == 0 ){ |
885 | > | if (worldRank == 0){ |
886 | #endif //is_mpi | |
887 | inName = globals->getInitialConfig(); | |
888 | < | double* tempDouble = new double[1000000]; |
906 | < | fileInit = new InitializeFromFile( inName ); |
888 | > | fileInit = new InitializeFromFile(inName); |
889 | #ifdef IS_MPI | |
890 | < | }else fileInit = new InitializeFromFile( NULL ); |
890 | > | } |
891 | > | else |
892 | > | fileInit = new InitializeFromFile(NULL); |
893 | #endif | |
894 | < | fileInit->readInit( info ); // default velocities on |
895 | < | |
894 | > | fileInit->readInit(info); // default velocities on |
895 | > | |
896 | delete fileInit; | |
897 | } | |
898 | else{ | |
915 | – | |
899 | #ifdef IS_MPI | |
900 | < | |
900 | > | |
901 | // no init from bass | |
902 | < | |
903 | < | sprintf( painCave.errMsg, |
904 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
905 | < | painCave.isFatal; |
902 | > | |
903 | > | sprintf(painCave.errMsg, |
904 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
905 | > | painCave.isFatal = 1;; |
906 | simError(); | |
907 | < | |
907 | > | |
908 | #else | |
909 | < | |
909 | > | |
910 | initFromBass(); | |
911 | < | |
912 | < | |
911 | > | |
912 | > | |
913 | #endif | |
914 | } | |
915 | < | |
915 | > | |
916 | #ifdef IS_MPI | |
917 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
917 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
918 | MPIcheckPoint(); | |
919 | #endif // is_mpi | |
937 | – | |
920 | } | |
921 | ||
922 | ||
923 | < | void SimSetup::makeOutNames( void ){ |
942 | < | |
923 | > | void SimSetup::makeOutNames(void){ |
924 | int k; | |
925 | ||
945 | – | |
946 | – | for(k=0; k<nInfo; k++){ |
926 | ||
927 | + | for (k = 0; k < nInfo; k++){ |
928 | #ifdef IS_MPI | |
929 | < | if( worldRank == 0 ){ |
929 | > | if (worldRank == 0){ |
930 | #endif // is_mpi | |
931 | < | |
932 | < | if( globals->haveFinalConfig() ){ |
933 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
931 | > | |
932 | > | if (globals->haveFinalConfig()){ |
933 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
934 | } | |
935 | else{ | |
936 | < | strcpy( info[k].finalName, inFileName ); |
937 | < | char* endTest; |
938 | < | int nameLength = strlen( info[k].finalName ); |
939 | < | endTest = &(info[k].finalName[nameLength - 5]); |
940 | < | if( !strcmp( endTest, ".bass" ) ){ |
941 | < | strcpy( endTest, ".eor" ); |
942 | < | } |
943 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
944 | < | strcpy( endTest, ".eor" ); |
945 | < | } |
946 | < | else{ |
947 | < | endTest = &(info[k].finalName[nameLength - 4]); |
948 | < | if( !strcmp( endTest, ".bss" ) ){ |
949 | < | strcpy( endTest, ".eor" ); |
950 | < | } |
951 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
952 | < | strcpy( endTest, ".eor" ); |
953 | < | } |
954 | < | else{ |
955 | < | strcat( info[k].finalName, ".eor" ); |
956 | < | } |
957 | < | } |
936 | > | strcpy(info[k].finalName, inFileName); |
937 | > | char* endTest; |
938 | > | int nameLength = strlen(info[k].finalName); |
939 | > | endTest = &(info[k].finalName[nameLength - 5]); |
940 | > | if (!strcmp(endTest, ".bass")){ |
941 | > | strcpy(endTest, ".eor"); |
942 | > | } |
943 | > | else if (!strcmp(endTest, ".BASS")){ |
944 | > | strcpy(endTest, ".eor"); |
945 | > | } |
946 | > | else{ |
947 | > | endTest = &(info[k].finalName[nameLength - 4]); |
948 | > | if (!strcmp(endTest, ".bss")){ |
949 | > | strcpy(endTest, ".eor"); |
950 | > | } |
951 | > | else if (!strcmp(endTest, ".mdl")){ |
952 | > | strcpy(endTest, ".eor"); |
953 | > | } |
954 | > | else{ |
955 | > | strcat(info[k].finalName, ".eor"); |
956 | > | } |
957 | > | } |
958 | } | |
959 | < | |
959 | > | |
960 | // make the sample and status out names | |
961 | < | |
962 | < | strcpy( info[k].sampleName, inFileName ); |
961 | > | |
962 | > | strcpy(info[k].sampleName, inFileName); |
963 | char* endTest; | |
964 | < | int nameLength = strlen( info[k].sampleName ); |
964 | > | int nameLength = strlen(info[k].sampleName); |
965 | endTest = &(info[k].sampleName[nameLength - 5]); | |
966 | < | if( !strcmp( endTest, ".bass" ) ){ |
967 | < | strcpy( endTest, ".dump" ); |
966 | > | if (!strcmp(endTest, ".bass")){ |
967 | > | strcpy(endTest, ".dump"); |
968 | } | |
969 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
970 | < | strcpy( endTest, ".dump" ); |
969 | > | else if (!strcmp(endTest, ".BASS")){ |
970 | > | strcpy(endTest, ".dump"); |
971 | } | |
972 | else{ | |
973 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
974 | < | if( !strcmp( endTest, ".bss" ) ){ |
975 | < | strcpy( endTest, ".dump" ); |
976 | < | } |
977 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
978 | < | strcpy( endTest, ".dump" ); |
979 | < | } |
980 | < | else{ |
981 | < | strcat( info[k].sampleName, ".dump" ); |
982 | < | } |
973 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
974 | > | if (!strcmp(endTest, ".bss")){ |
975 | > | strcpy(endTest, ".dump"); |
976 | > | } |
977 | > | else if (!strcmp(endTest, ".mdl")){ |
978 | > | strcpy(endTest, ".dump"); |
979 | > | } |
980 | > | else{ |
981 | > | strcat(info[k].sampleName, ".dump"); |
982 | > | } |
983 | } | |
984 | < | |
985 | < | strcpy( info[k].statusName, inFileName ); |
986 | < | nameLength = strlen( info[k].statusName ); |
984 | > | |
985 | > | strcpy(info[k].statusName, inFileName); |
986 | > | nameLength = strlen(info[k].statusName); |
987 | endTest = &(info[k].statusName[nameLength - 5]); | |
988 | < | if( !strcmp( endTest, ".bass" ) ){ |
989 | < | strcpy( endTest, ".stat" ); |
988 | > | if (!strcmp(endTest, ".bass")){ |
989 | > | strcpy(endTest, ".stat"); |
990 | } | |
991 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
992 | < | strcpy( endTest, ".stat" ); |
991 | > | else if (!strcmp(endTest, ".BASS")){ |
992 | > | strcpy(endTest, ".stat"); |
993 | } | |
994 | else{ | |
995 | < | endTest = &(info[k].statusName[nameLength - 4]); |
996 | < | if( !strcmp( endTest, ".bss" ) ){ |
997 | < | strcpy( endTest, ".stat" ); |
998 | < | } |
999 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1000 | < | strcpy( endTest, ".stat" ); |
1001 | < | } |
1002 | < | else{ |
1003 | < | strcat( info[k].statusName, ".stat" ); |
1004 | < | } |
995 | > | endTest = &(info[k].statusName[nameLength - 4]); |
996 | > | if (!strcmp(endTest, ".bss")){ |
997 | > | strcpy(endTest, ".stat"); |
998 | > | } |
999 | > | else if (!strcmp(endTest, ".mdl")){ |
1000 | > | strcpy(endTest, ".stat"); |
1001 | > | } |
1002 | > | else{ |
1003 | > | strcat(info[k].statusName, ".stat"); |
1004 | > | } |
1005 | } | |
1006 | < | |
1006 | > | |
1007 | #ifdef IS_MPI | |
1008 | + | |
1009 | } | |
1010 | #endif // is_mpi | |
1011 | } | |
1012 | } | |
1013 | ||
1014 | ||
1015 | < | void SimSetup::sysObjectsCreation( void ){ |
1016 | < | |
1017 | < | int i,k; |
1037 | < | |
1015 | > | void SimSetup::sysObjectsCreation(void){ |
1016 | > | int i, k; |
1017 | > | |
1018 | // create the forceField | |
1019 | ||
1020 | createFF(); | |
# | Line 1049 | Line 1029 | void SimSetup::sysObjectsCreation( void ){ | |
1029 | ||
1030 | #ifdef IS_MPI | |
1031 | // divide the molecules among the processors | |
1032 | < | |
1032 | > | |
1033 | mpiMolDivide(); | |
1034 | #endif //is_mpi | |
1035 | < | |
1035 | > | |
1036 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1037 | < | |
1037 | > | |
1038 | makeSysArrays(); | |
1039 | ||
1040 | // make and initialize the molecules (all but atomic coordinates) | |
1041 | < | |
1041 | > | |
1042 | makeMolecules(); | |
1043 | < | |
1044 | < | for(k=0; k<nInfo; k++){ |
1043 | > | |
1044 | > | for (k = 0; k < nInfo; k++){ |
1045 | info[k].identArray = new int[info[k].n_atoms]; | |
1046 | < | for(i=0; i<info[k].n_atoms; i++){ |
1046 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1047 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1048 | } | |
1049 | } | |
1050 | } | |
1051 | ||
1052 | ||
1053 | < | void SimSetup::createFF( void ){ |
1053 | > | void SimSetup::createFF(void){ |
1054 | > | switch (ffCase){ |
1055 | > | case FF_DUFF: |
1056 | > | the_ff = new DUFF(); |
1057 | > | break; |
1058 | ||
1059 | < | switch( ffCase ){ |
1059 | > | case FF_LJ: |
1060 | > | the_ff = new LJFF(); |
1061 | > | break; |
1062 | ||
1063 | < | case FF_DUFF: |
1064 | < | the_ff = new DUFF(); |
1065 | < | break; |
1063 | > | case FF_EAM: |
1064 | > | the_ff = new EAM_FF(); |
1065 | > | break; |
1066 | ||
1067 | < | case FF_LJ: |
1068 | < | the_ff = new LJFF(); |
1069 | < | break; |
1070 | < | |
1071 | < | case FF_EAM: |
1086 | < | the_ff = new EAM_FF(); |
1087 | < | break; |
1088 | < | |
1089 | < | default: |
1090 | < | sprintf( painCave.errMsg, |
1091 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 | < | painCave.isFatal = 1; |
1093 | < | simError(); |
1067 | > | default: |
1068 | > | sprintf(painCave.errMsg, |
1069 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1070 | > | painCave.isFatal = 1; |
1071 | > | simError(); |
1072 | } | |
1073 | ||
1074 | #ifdef IS_MPI | |
1075 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1075 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1076 | MPIcheckPoint(); | |
1077 | #endif // is_mpi | |
1100 | – | |
1078 | } | |
1079 | ||
1080 | ||
1081 | < | void SimSetup::compList( void ){ |
1105 | < | |
1081 | > | void SimSetup::compList(void){ |
1082 | int i; | |
1083 | char* id; | |
1084 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1085 | LinkedMolStamp* currentStamp = NULL; | |
1086 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1087 | < | |
1086 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1087 | > | |
1088 | // make an array of molecule stamps that match the components used. | |
1089 | // also extract the used stamps out into a separate linked list | |
1090 | < | |
1091 | < | for(i=0; i<nInfo; i++){ |
1090 | > | |
1091 | > | for (i = 0; i < nInfo; i++){ |
1092 | info[i].nComponents = n_components; | |
1093 | info[i].componentsNmol = components_nmol; | |
1094 | info[i].compStamps = comp_stamps; | |
1095 | info[i].headStamp = headStamp; | |
1096 | } | |
1121 | – | |
1097 | ||
1098 | < | for( i=0; i<n_components; i++ ){ |
1099 | < | |
1098 | > | |
1099 | > | for (i = 0; i < n_components; i++){ |
1100 | id = the_components[i]->getType(); | |
1101 | comp_stamps[i] = NULL; | |
1102 | < | |
1102 | > | |
1103 | // check to make sure the component isn't already in the list | |
1104 | ||
1105 | < | comp_stamps[i] = headStamp->match( id ); |
1106 | < | if( comp_stamps[i] == NULL ){ |
1132 | < | |
1105 | > | comp_stamps[i] = headStamp->match(id); |
1106 | > | if (comp_stamps[i] == NULL){ |
1107 | // extract the component from the list; | |
1108 | < | |
1109 | < | currentStamp = stamps->extractMolStamp( id ); |
1110 | < | if( currentStamp == NULL ){ |
1111 | < | sprintf( painCave.errMsg, |
1112 | < | "SimSetup error: Component \"%s\" was not found in the " |
1113 | < | "list of declared molecules\n", |
1114 | < | id ); |
1115 | < | painCave.isFatal = 1; |
1116 | < | simError(); |
1108 | > | |
1109 | > | currentStamp = stamps->extractMolStamp(id); |
1110 | > | if (currentStamp == NULL){ |
1111 | > | sprintf(painCave.errMsg, |
1112 | > | "SimSetup error: Component \"%s\" was not found in the " |
1113 | > | "list of declared molecules\n", |
1114 | > | id); |
1115 | > | painCave.isFatal = 1; |
1116 | > | simError(); |
1117 | } | |
1118 | < | |
1119 | < | headStamp->add( currentStamp ); |
1120 | < | comp_stamps[i] = headStamp->match( id ); |
1118 | > | |
1119 | > | headStamp->add(currentStamp); |
1120 | > | comp_stamps[i] = headStamp->match(id); |
1121 | } | |
1122 | } | |
1123 | ||
1124 | #ifdef IS_MPI | |
1125 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1125 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1126 | MPIcheckPoint(); | |
1127 | #endif // is_mpi | |
1128 | + | } |
1129 | ||
1130 | + | void SimSetup::calcSysValues(void){ |
1131 | + | int i; |
1132 | ||
1133 | < | } |
1133 | > | int* molMembershipArray; |
1134 | ||
1158 | – | void SimSetup::calcSysValues( void ){ |
1159 | – | int i, j, k; |
1160 | – | |
1161 | – | int *molMembershipArray; |
1162 | – | |
1135 | tot_atoms = 0; | |
1136 | tot_bonds = 0; | |
1137 | tot_bends = 0; | |
1138 | tot_torsions = 0; | |
1139 | < | for( i=0; i<n_components; i++ ){ |
1140 | < | |
1141 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1142 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1171 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1139 | > | for (i = 0; i < n_components; i++){ |
1140 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1141 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1142 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1143 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1144 | } | |
1145 | < | |
1145 | > | |
1146 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1147 | molMembershipArray = new int[tot_atoms]; | |
1148 | < | |
1149 | < | for(i=0; i<nInfo; i++){ |
1148 | > | |
1149 | > | for (i = 0; i < nInfo; i++){ |
1150 | info[i].n_atoms = tot_atoms; | |
1151 | info[i].n_bonds = tot_bonds; | |
1152 | info[i].n_bends = tot_bends; | |
1153 | info[i].n_torsions = tot_torsions; | |
1154 | info[i].n_SRI = tot_SRI; | |
1155 | info[i].n_mol = tot_nmol; | |
1156 | < | |
1156 | > | |
1157 | info[i].molMembershipArray = molMembershipArray; | |
1158 | < | } |
1158 | > | } |
1159 | } | |
1160 | ||
1161 | #ifdef IS_MPI | |
1162 | ||
1163 | < | void SimSetup::mpiMolDivide( void ){ |
1193 | < | |
1163 | > | void SimSetup::mpiMolDivide(void){ |
1164 | int i, j, k; | |
1165 | int localMol, allMol; | |
1166 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1167 | ||
1168 | < | mpiSim = new mpiSimulation( info ); |
1169 | < | |
1168 | > | mpiSim = new mpiSimulation(info); |
1169 | > | |
1170 | globalIndex = mpiSim->divideLabor(); | |
1171 | ||
1172 | // set up the local variables | |
1173 | < | |
1173 | > | |
1174 | mol2proc = mpiSim->getMolToProcMap(); | |
1175 | molCompType = mpiSim->getMolComponentType(); | |
1176 | < | |
1176 | > | |
1177 | allMol = 0; | |
1178 | localMol = 0; | |
1179 | local_atoms = 0; | |
# | Line 1213 | Line 1183 | void SimSetup::mpiMolDivide( void ){ | |
1183 | globalAtomIndex = 0; | |
1184 | ||
1185 | ||
1186 | < | for( i=0; i<n_components; i++ ){ |
1187 | < | |
1188 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1189 | < | |
1190 | < | if( mol2proc[allMol] == worldRank ){ |
1191 | < | |
1192 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1193 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1224 | < | local_bends += comp_stamps[i]->getNBends(); |
1225 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1226 | < | localMol++; |
1186 | > | for (i = 0; i < n_components; i++){ |
1187 | > | for (j = 0; j < components_nmol[i]; j++){ |
1188 | > | if (mol2proc[allMol] == worldRank){ |
1189 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1190 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1191 | > | local_bends += comp_stamps[i]->getNBends(); |
1192 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1193 | > | localMol++; |
1194 | } | |
1195 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1195 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1196 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
1197 | globalAtomIndex++; | |
1198 | } | |
1199 | ||
1200 | < | allMol++; |
1200 | > | allMol++; |
1201 | } | |
1202 | } | |
1203 | local_SRI = local_bonds + local_bends + local_torsions; | |
1204 | < | |
1204 | > | |
1205 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1206 | < | |
1207 | < | if( local_atoms != info[0].n_atoms ){ |
1208 | < | sprintf( painCave.errMsg, |
1209 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1210 | < | " localAtom (%d) are not equal.\n", |
1211 | < | info[0].n_atoms, |
1245 | < | local_atoms ); |
1206 | > | |
1207 | > | if (local_atoms != info[0].n_atoms){ |
1208 | > | sprintf(painCave.errMsg, |
1209 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1210 | > | " localAtom (%d) are not equal.\n", |
1211 | > | info[0].n_atoms, local_atoms); |
1212 | painCave.isFatal = 1; | |
1213 | simError(); | |
1214 | } | |
# | Line 1253 | Line 1219 | void SimSetup::mpiMolDivide( void ){ | |
1219 | info[0].n_SRI = local_SRI; | |
1220 | info[0].n_mol = localMol; | |
1221 | ||
1222 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1222 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1223 | MPIcheckPoint(); | |
1224 | } | |
1225 | < | |
1225 | > | |
1226 | #endif // is_mpi | |
1227 | ||
1228 | ||
1229 | < | void SimSetup::makeSysArrays( void ){ |
1230 | < | int i, j, k, l; |
1229 | > | void SimSetup::makeSysArrays(void){ |
1230 | > | |
1231 | > | #ifndef IS_MPI |
1232 | > | int k, j; |
1233 | > | #endif // is_mpi |
1234 | > | int i, l; |
1235 | ||
1236 | Atom** the_atoms; | |
1237 | Molecule* the_molecules; | |
1238 | Exclude** the_excludes; | |
1239 | ||
1240 | < | |
1241 | < | for(l=0; l<nInfo; l++){ |
1272 | < | |
1240 | > | |
1241 | > | for (l = 0; l < nInfo; l++){ |
1242 | // create the atom and short range interaction arrays | |
1243 | < | |
1244 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1243 | > | |
1244 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1245 | the_molecules = new Molecule[info[l].n_mol]; | |
1246 | int molIndex; | |
1247 | ||
1248 | // initialize the molecule's stampID's | |
1249 | < | |
1249 | > | |
1250 | #ifdef IS_MPI | |
1251 | < | |
1252 | < | |
1251 | > | |
1252 | > | |
1253 | molIndex = 0; | |
1254 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1255 | < | |
1256 | < | if(mol2proc[i] == worldRank ){ |
1257 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1258 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1259 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1291 | < | molIndex++; |
1254 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1255 | > | if (mol2proc[i] == worldRank){ |
1256 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1257 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1258 | > | the_molecules[molIndex].setGlobalIndex(i); |
1259 | > | molIndex++; |
1260 | } | |
1261 | } | |
1262 | < | |
1262 | > | |
1263 | #else // is_mpi | |
1264 | < | |
1264 | > | |
1265 | molIndex = 0; | |
1266 | globalAtomIndex = 0; | |
1267 | < | for(i=0; i<n_components; i++){ |
1268 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1269 | < | the_molecules[molIndex].setStampID( i ); |
1270 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1271 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1272 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1273 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1274 | < | globalAtomIndex++; |
1275 | < | } |
1276 | < | molIndex++; |
1267 | > | for (i = 0; i < n_components; i++){ |
1268 | > | for (j = 0; j < components_nmol[i]; j++){ |
1269 | > | the_molecules[molIndex].setStampID(i); |
1270 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1271 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1272 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1273 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1274 | > | globalAtomIndex++; |
1275 | > | } |
1276 | > | molIndex++; |
1277 | } | |
1278 | } | |
1279 | < | |
1280 | < | |
1279 | > | |
1280 | > | |
1281 | #endif // is_mpi | |
1282 | ||
1283 | ||
1284 | < | if( info[l].n_SRI ){ |
1317 | < | |
1284 | > | if (info[l].n_SRI){ |
1285 | Exclude::createArray(info[l].n_SRI); | |
1286 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1287 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1288 | < | the_excludes[ex] = new Exclude(ex); |
1286 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1287 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1288 | > | the_excludes[ex] = new Exclude(ex); |
1289 | } | |
1290 | info[l].globalExcludes = new int; | |
1291 | info[l].n_exclude = info[l].n_SRI; | |
1292 | } | |
1293 | else{ | |
1294 | < | |
1295 | < | Exclude::createArray( 1 ); |
1329 | < | the_excludes = new Exclude*; |
1294 | > | Exclude::createArray(1); |
1295 | > | the_excludes = new Exclude * ; |
1296 | the_excludes[0] = new Exclude(0); | |
1297 | < | the_excludes[0]->setPair( 0,0 ); |
1297 | > | the_excludes[0]->setPair(0, 0); |
1298 | info[l].globalExcludes = new int; | |
1299 | info[l].globalExcludes[0] = 0; | |
1300 | info[l].n_exclude = 0; | |
# | Line 1341 | Line 1307 | void SimSetup::makeSysArrays( void ){ | |
1307 | info[l].nGlobalExcludes = 0; | |
1308 | info[l].excludes = the_excludes; | |
1309 | ||
1310 | < | the_ff->setSimInfo( info ); |
1345 | < | |
1310 | > | the_ff->setSimInfo(info); |
1311 | } | |
1312 | } | |
1313 | ||
1314 | < | void SimSetup::makeIntegrator( void ){ |
1350 | < | |
1314 | > | void SimSetup::makeIntegrator(void){ |
1315 | int k; | |
1316 | ||
1317 | < | NVT<RealIntegrator>* myNVT = NULL; |
1318 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1319 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1320 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1321 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1322 | < | |
1323 | < | for(k=0; k<nInfo; k++){ |
1324 | < | |
1325 | < | switch( ensembleCase ){ |
1326 | < | |
1327 | < | case NVE_ENS: |
1328 | < | if (globals->haveZconstraints()){ |
1329 | < | setupZConstraint(info[k]); |
1330 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1331 | < | } |
1317 | > | NVE<RealIntegrator>* myNVE = NULL; |
1318 | > | NVT<RealIntegrator>* myNVT = NULL; |
1319 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1320 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1321 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1322 | > | |
1323 | > | for (k = 0; k < nInfo; k++){ |
1324 | > | switch (ensembleCase){ |
1325 | > | case NVE_ENS: |
1326 | > | if (globals->haveZconstraints()){ |
1327 | > | setupZConstraint(info[k]); |
1328 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1329 | > | } |
1330 | > | else{ |
1331 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1332 | > | } |
1333 | > | |
1334 | > | info->the_integrator = myNVE; |
1335 | > | break; |
1336 | ||
1337 | < | else |
1338 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1339 | < | break; |
1340 | < | |
1341 | < | case NVT_ENS: |
1342 | < | if (globals->haveZconstraints()){ |
1343 | < | setupZConstraint(info[k]); |
1376 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 | < | } |
1378 | < | else |
1379 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1337 | > | case NVT_ENS: |
1338 | > | if (globals->haveZconstraints()){ |
1339 | > | setupZConstraint(info[k]); |
1340 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1341 | > | } |
1342 | > | else |
1343 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1344 | ||
1345 | myNVT->setTargetTemp(globals->getTargetTemp()); | |
1346 | < | |
1347 | < | if (globals->haveTauThermostat()) |
1346 | > | |
1347 | > | if (globals->haveTauThermostat()) |
1348 | myNVT->setTauThermostat(globals->getTauThermostat()); | |
1349 | < | |
1350 | < | else { |
1351 | < | sprintf( painCave.errMsg, |
1352 | < | "SimSetup error: If you use the NVT\n" |
1389 | < | " ensemble, you must set tauThermostat.\n"); |
1349 | > | else{ |
1350 | > | sprintf(painCave.errMsg, |
1351 | > | "SimSetup error: If you use the NVT\n" |
1352 | > | " ensemble, you must set tauThermostat.\n"); |
1353 | painCave.isFatal = 1; | |
1354 | simError(); | |
1355 | } | |
1356 | + | |
1357 | + | info->the_integrator = myNVT; |
1358 | break; | |
1394 | – | |
1395 | – | case NPTi_ENS: |
1396 | – | if (globals->haveZconstraints()){ |
1397 | – | setupZConstraint(info[k]); |
1398 | – | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 | – | } |
1400 | – | else |
1401 | – | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1359 | ||
1360 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1361 | < | |
1362 | < | if (globals->haveTargetPressure()) |
1363 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1364 | < | else { |
1365 | < | sprintf( painCave.errMsg, |
1366 | < | "SimSetup error: If you use a constant pressure\n" |
1410 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1411 | < | painCave.isFatal = 1; |
1412 | < | simError(); |
1413 | < | } |
1414 | < | |
1415 | < | if( globals->haveTauThermostat() ) |
1416 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 | < | else{ |
1418 | < | sprintf( painCave.errMsg, |
1419 | < | "SimSetup error: If you use an NPT\n" |
1420 | < | " ensemble, you must set tauThermostat.\n"); |
1421 | < | painCave.isFatal = 1; |
1422 | < | simError(); |
1423 | < | } |
1424 | < | |
1425 | < | if( globals->haveTauBarostat() ) |
1426 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 | < | else{ |
1428 | < | sprintf( painCave.errMsg, |
1429 | < | "SimSetup error: If you use an NPT\n" |
1430 | < | " ensemble, you must set tauBarostat.\n"); |
1431 | < | painCave.isFatal = 1; |
1432 | < | simError(); |
1433 | < | } |
1434 | < | break; |
1435 | < | |
1436 | < | case NPTf_ENS: |
1437 | < | if (globals->haveZconstraints()){ |
1438 | < | setupZConstraint(info[k]); |
1439 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 | < | } |
1441 | < | else |
1442 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1360 | > | case NPTi_ENS: |
1361 | > | if (globals->haveZconstraints()){ |
1362 | > | setupZConstraint(info[k]); |
1363 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1364 | > | } |
1365 | > | else |
1366 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1367 | ||
1368 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1445 | < | |
1446 | < | if (globals->haveTargetPressure()) |
1447 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 | < | else { |
1449 | < | sprintf( painCave.errMsg, |
1450 | < | "SimSetup error: If you use a constant pressure\n" |
1451 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1452 | < | painCave.isFatal = 1; |
1453 | < | simError(); |
1454 | < | } |
1455 | < | |
1456 | < | if( globals->haveTauThermostat() ) |
1457 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 | < | else{ |
1459 | < | sprintf( painCave.errMsg, |
1460 | < | "SimSetup error: If you use an NPT\n" |
1461 | < | " ensemble, you must set tauThermostat.\n"); |
1462 | < | painCave.isFatal = 1; |
1463 | < | simError(); |
1464 | < | } |
1465 | < | |
1466 | < | if( globals->haveTauBarostat() ) |
1467 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 | < | else{ |
1469 | < | sprintf( painCave.errMsg, |
1470 | < | "SimSetup error: If you use an NPT\n" |
1471 | < | " ensemble, you must set tauBarostat.\n"); |
1472 | < | painCave.isFatal = 1; |
1473 | < | simError(); |
1474 | < | } |
1475 | < | break; |
1476 | < | |
1477 | < | case NPTim_ENS: |
1478 | < | if (globals->haveZconstraints()){ |
1479 | < | setupZConstraint(info[k]); |
1480 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 | < | } |
1482 | < | else |
1483 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1368 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1369 | ||
1370 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1371 | < | |
1372 | < | if (globals->haveTargetPressure()) |
1373 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1489 | < | else { |
1490 | < | sprintf( painCave.errMsg, |
1370 | > | if (globals->haveTargetPressure()) |
1371 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1372 | > | else{ |
1373 | > | sprintf(painCave.errMsg, |
1374 | "SimSetup error: If you use a constant pressure\n" | |
1375 | " ensemble, you must set targetPressure in the BASS file.\n"); | |
1376 | < | painCave.isFatal = 1; |
1377 | < | simError(); |
1378 | < | } |
1379 | < | |
1380 | < | if( globals->haveTauThermostat() ) |
1381 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1382 | < | else{ |
1383 | < | sprintf( painCave.errMsg, |
1376 | > | painCave.isFatal = 1; |
1377 | > | simError(); |
1378 | > | } |
1379 | > | |
1380 | > | if (globals->haveTauThermostat()) |
1381 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1382 | > | else{ |
1383 | > | sprintf(painCave.errMsg, |
1384 | "SimSetup error: If you use an NPT\n" | |
1385 | " ensemble, you must set tauThermostat.\n"); | |
1386 | < | painCave.isFatal = 1; |
1387 | < | simError(); |
1388 | < | } |
1506 | < | |
1507 | < | if( globals->haveTauBarostat() ) |
1508 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 | < | else{ |
1510 | < | sprintf( painCave.errMsg, |
1511 | < | "SimSetup error: If you use an NPT\n" |
1512 | < | " ensemble, you must set tauBarostat.\n"); |
1513 | < | painCave.isFatal = 1; |
1514 | < | simError(); |
1515 | < | } |
1516 | < | break; |
1517 | < | |
1518 | < | case NPTfm_ENS: |
1519 | < | if (globals->haveZconstraints()){ |
1520 | < | setupZConstraint(info[k]); |
1521 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 | < | } |
1523 | < | else |
1524 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1386 | > | painCave.isFatal = 1; |
1387 | > | simError(); |
1388 | > | } |
1389 | ||
1390 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1391 | < | |
1392 | < | if (globals->haveTargetPressure()) |
1393 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1530 | < | else { |
1531 | < | sprintf( painCave.errMsg, |
1532 | < | "SimSetup error: If you use a constant pressure\n" |
1533 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1534 | < | painCave.isFatal = 1; |
1535 | < | simError(); |
1536 | < | } |
1537 | < | |
1538 | < | if( globals->haveTauThermostat() ) |
1539 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1540 | < | else{ |
1541 | < | sprintf( painCave.errMsg, |
1390 | > | if (globals->haveTauBarostat()) |
1391 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1392 | > | else{ |
1393 | > | sprintf(painCave.errMsg, |
1394 | "SimSetup error: If you use an NPT\n" | |
1395 | < | " ensemble, you must set tauThermostat.\n"); |
1396 | < | painCave.isFatal = 1; |
1397 | < | simError(); |
1398 | < | } |
1395 | > | " ensemble, you must set tauBarostat.\n"); |
1396 | > | painCave.isFatal = 1; |
1397 | > | simError(); |
1398 | > | } |
1399 | ||
1400 | < | if( globals->haveTauBarostat() ) |
1401 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1402 | < | else{ |
1403 | < | sprintf( painCave.errMsg, |
1400 | > | info->the_integrator = myNPTi; |
1401 | > | break; |
1402 | > | |
1403 | > | case NPTf_ENS: |
1404 | > | if (globals->haveZconstraints()){ |
1405 | > | setupZConstraint(info[k]); |
1406 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1407 | > | } |
1408 | > | else |
1409 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1410 | > | |
1411 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1412 | > | |
1413 | > | if (globals->haveTargetPressure()) |
1414 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1415 | > | else{ |
1416 | > | sprintf(painCave.errMsg, |
1417 | > | "SimSetup error: If you use a constant pressure\n" |
1418 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1419 | > | painCave.isFatal = 1; |
1420 | > | simError(); |
1421 | > | } |
1422 | > | |
1423 | > | if (globals->haveTauThermostat()) |
1424 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1425 | > | |
1426 | > | else{ |
1427 | > | sprintf(painCave.errMsg, |
1428 | "SimSetup error: If you use an NPT\n" | |
1429 | + | " ensemble, you must set tauThermostat.\n"); |
1430 | + | painCave.isFatal = 1; |
1431 | + | simError(); |
1432 | + | } |
1433 | + | |
1434 | + | if (globals->haveTauBarostat()) |
1435 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1436 | + | |
1437 | + | else{ |
1438 | + | sprintf(painCave.errMsg, |
1439 | + | "SimSetup error: If you use an NPT\n" |
1440 | " ensemble, you must set tauBarostat.\n"); | |
1441 | + | painCave.isFatal = 1; |
1442 | + | simError(); |
1443 | + | } |
1444 | + | |
1445 | + | info->the_integrator = myNPTf; |
1446 | + | break; |
1447 | + | |
1448 | + | case NPTxyz_ENS: |
1449 | + | if (globals->haveZconstraints()){ |
1450 | + | setupZConstraint(info[k]); |
1451 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1452 | + | } |
1453 | + | else |
1454 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1455 | + | |
1456 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1457 | + | |
1458 | + | if (globals->haveTargetPressure()) |
1459 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1460 | + | else{ |
1461 | + | sprintf(painCave.errMsg, |
1462 | + | "SimSetup error: If you use a constant pressure\n" |
1463 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1464 | + | painCave.isFatal = 1; |
1465 | + | simError(); |
1466 | + | } |
1467 | + | |
1468 | + | if (globals->haveTauThermostat()) |
1469 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1470 | + | else{ |
1471 | + | sprintf(painCave.errMsg, |
1472 | + | "SimSetup error: If you use an NPT\n" |
1473 | + | " ensemble, you must set tauThermostat.\n"); |
1474 | + | painCave.isFatal = 1; |
1475 | + | simError(); |
1476 | + | } |
1477 | + | |
1478 | + | if (globals->haveTauBarostat()) |
1479 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1480 | + | else{ |
1481 | + | sprintf(painCave.errMsg, |
1482 | + | "SimSetup error: If you use an NPT\n" |
1483 | + | " ensemble, you must set tauBarostat.\n"); |
1484 | + | painCave.isFatal = 1; |
1485 | + | simError(); |
1486 | + | } |
1487 | + | |
1488 | + | info->the_integrator = myNPTxyz; |
1489 | + | break; |
1490 | + | |
1491 | + | default: |
1492 | + | sprintf(painCave.errMsg, |
1493 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1494 | painCave.isFatal = 1; | |
1495 | simError(); | |
1556 | – | } |
1557 | – | break; |
1558 | – | |
1559 | – | default: |
1560 | – | sprintf( painCave.errMsg, |
1561 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1562 | – | painCave.isFatal = 1; |
1563 | – | simError(); |
1496 | } | |
1497 | } | |
1498 | } | |
1499 | ||
1500 | < | void SimSetup::initFortran( void ){ |
1569 | < | |
1500 | > | void SimSetup::initFortran(void){ |
1501 | info[0].refreshSim(); | |
1502 | < | |
1503 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1504 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1502 | > | |
1503 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1504 | > | the_ff->initForceField(LB_MIXING_RULE); |
1505 | } | |
1506 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1507 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1506 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1507 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1508 | } | |
1509 | else{ | |
1510 | < | sprintf( painCave.errMsg, |
1511 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 | < | info[0].mixingRule ); |
1510 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1511 | > | info[0].mixingRule); |
1512 | painCave.isFatal = 1; | |
1513 | simError(); | |
1514 | } | |
1515 | ||
1516 | ||
1517 | #ifdef IS_MPI | |
1518 | < | strcpy( checkPointMsg, |
1589 | < | "Successfully intialized the mixingRule for Fortran." ); |
1518 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1519 | MPIcheckPoint(); | |
1520 | #endif // is_mpi | |
1592 | – | |
1521 | } | |
1522 | ||
1523 | < | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 | < | { |
1523 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1524 | int nZConstraints; | |
1525 | ZconStamp** zconStamp; | |
1526 | ||
1527 | < | if(globals->haveZconstraintTime()){ |
1601 | < | |
1527 | > | if (globals->haveZconstraintTime()){ |
1528 | //add sample time of z-constraint into SimInfo's property list | |
1529 | DoubleData* zconsTimeProp = new DoubleData(); | |
1530 | zconsTimeProp->setID(ZCONSTIME_ID); | |
# | Line 1606 | Line 1532 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1532 | theInfo.addProperty(zconsTimeProp); | |
1533 | } | |
1534 | else{ | |
1535 | < | sprintf( painCave.errMsg, |
1536 | < | "ZConstraint error: If you use an ZConstraint\n" |
1537 | < | " , you must set sample time.\n"); |
1535 | > | sprintf(painCave.errMsg, |
1536 | > | "ZConstraint error: If you use an ZConstraint\n" |
1537 | > | " , you must set sample time.\n"); |
1538 | painCave.isFatal = 1; | |
1539 | < | simError(); |
1539 | > | simError(); |
1540 | } | |
1541 | ||
1542 | //push zconsTol into siminfo, if user does not specify | |
1543 | //value for zconsTol, a default value will be used | |
1544 | DoubleData* zconsTol = new DoubleData(); | |
1545 | zconsTol->setID(ZCONSTOL_ID); | |
1546 | < | if(globals->haveZconsTol()){ |
1546 | > | if (globals->haveZconsTol()){ |
1547 | zconsTol->setData(globals->getZconsTol()); | |
1548 | } | |
1549 | else{ | |
1550 | < | double defaultZConsTol = 0.01; |
1551 | < | sprintf( painCave.errMsg, |
1552 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1553 | < | " , default value %f is used.\n", defaultZConsTol); |
1550 | > | double defaultZConsTol = 0.01; |
1551 | > | sprintf(painCave.errMsg, |
1552 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1553 | > | " , default value %f is used.\n", |
1554 | > | defaultZConsTol); |
1555 | painCave.isFatal = 0; | |
1556 | simError(); | |
1557 | ||
# | Line 1632 | Line 1559 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1559 | } | |
1560 | theInfo.addProperty(zconsTol); | |
1561 | ||
1562 | < | //set Force Substraction Policy |
1563 | < | StringData* zconsForcePolicy = new StringData(); |
1562 | > | //set Force Subtraction Policy |
1563 | > | StringData* zconsForcePolicy = new StringData(); |
1564 | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); | |
1565 | < | |
1566 | < | if(globals->haveZconsForcePolicy()){ |
1565 | > | |
1566 | > | if (globals->haveZconsForcePolicy()){ |
1567 | zconsForcePolicy->setData(globals->getZconsForcePolicy()); | |
1568 | < | } |
1568 | > | } |
1569 | else{ | |
1570 | < | sprintf( painCave.errMsg, |
1571 | < | "ZConstraint Warning: User does not set force substraction policy, " |
1572 | < | "average force substraction policy is used\n"); |
1573 | < | painCave.isFatal = 0; |
1574 | < | simError(); |
1575 | < | zconsForcePolicy->setData("BYNUMBER"); |
1570 | > | sprintf(painCave.errMsg, |
1571 | > | "ZConstraint Warning: User does not set force Subtraction policy, " |
1572 | > | "PolicyByMass is used\n"); |
1573 | > | painCave.isFatal = 0; |
1574 | > | simError(); |
1575 | > | zconsForcePolicy->setData("BYMASS"); |
1576 | } | |
1577 | < | |
1578 | < | theInfo.addProperty(zconsForcePolicy); |
1579 | < | |
1577 | > | |
1578 | > | theInfo.addProperty(zconsForcePolicy); |
1579 | > | |
1580 | //Determine the name of ouput file and add it into SimInfo's property list | |
1581 | //Be careful, do not use inFileName, since it is a pointer which | |
1582 | //point to a string at master node, and slave nodes do not contain that string | |
1583 | < | |
1583 | > | |
1584 | string zconsOutput(theInfo.finalName); | |
1585 | < | |
1585 | > | |
1586 | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; | |
1587 | < | |
1587 | > | |
1588 | StringData* zconsFilename = new StringData(); | |
1589 | zconsFilename->setID(ZCONSFILENAME_ID); | |
1590 | zconsFilename->setData(zconsOutput); | |
1591 | < | |
1591 | > | |
1592 | theInfo.addProperty(zconsFilename); | |
1593 | < | |
1593 | > | |
1594 | //setup index, pos and other parameters of z-constraint molecules | |
1595 | nZConstraints = globals->getNzConstraints(); | |
1596 | theInfo.nZconstraints = nZConstraints; | |
# | Line 1673 | Line 1600 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1600 | ||
1601 | ZConsParaData* zconsParaData = new ZConsParaData(); | |
1602 | zconsParaData->setID(ZCONSPARADATA_ID); | |
1603 | < | |
1604 | < | for(int i = 0; i < nZConstraints; i++){ |
1603 | > | |
1604 | > | for (int i = 0; i < nZConstraints; i++){ |
1605 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
1606 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1607 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
# | Line 1683 | Line 1610 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1610 | zconsParaData->addItem(tempParaItem); | |
1611 | } | |
1612 | ||
1613 | + | //check the uniqueness of index |
1614 | + | if(!zconsParaData->isIndexUnique()){ |
1615 | + | sprintf(painCave.errMsg, |
1616 | + | "ZConstraint Error: molIndex is not unique\n"); |
1617 | + | painCave.isFatal = 1; |
1618 | + | simError(); |
1619 | + | } |
1620 | + | |
1621 | //sort the parameters by index of molecules | |
1622 | zconsParaData->sortByIndex(); | |
1623 | ||
1624 | //push data into siminfo, therefore, we can retrieve later | |
1625 | theInfo.addProperty(zconsParaData); | |
1691 | – | |
1626 | } |
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