# | 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" | |
# | Line 20 | Line 21 | |
21 | #define NVT_ENS 1 | |
22 | #define NPTi_ENS 2 | |
23 | #define NPTf_ENS 3 | |
24 | < | #define NPTim_ENS 4 |
24 | < | #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 31 | 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 49 | 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 ){ |
60 | < | |
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(); |
88 | < | mpiEventLoop(); |
89 | < | |
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 | ||
96 | – | int i, j, k, globalAtomIndex; |
97 | – | |
98 | // gather all of the information from the Bass file | |
99 | < | |
99 | > | |
100 | gatherInfo(); | |
101 | ||
102 | // creation of complex system objects | |
# | Line 104 | Line 104 | void SimSetup::createSim(void){ | |
104 | sysObjectsCreation(); | |
105 | ||
106 | // check on the post processing info | |
107 | < | |
107 | > | |
108 | finalInfoCheck(); | |
109 | ||
110 | // initialize the system coordinates | |
111 | ||
112 | < | if( !isInfoArray ) initSystemCoords(); |
112 | > | if ( !initSuspend ){ |
113 | > | initSystemCoords(); |
114 | ||
115 | + | if( !(globals->getUseInitTime()) ) |
116 | + | info[0].currentTime = 0.0; |
117 | + | } |
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 126 | Line 131 | void SimSetup::createSim(void){ | |
131 | // initialize the Fortran | |
132 | ||
133 | initFortran(); | |
129 | – | |
130 | – | |
131 | – | |
134 | } | |
135 | ||
136 | ||
137 | < | void SimSetup::makeMolecules( void ){ |
138 | < | |
137 | < | 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 149 | 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; | |
161 | – | |
162 | – | for(k=0; k<nInfo; k++){ |
163 | – | |
164 | – | 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++){ |
169 | < | |
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 | < | |
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 | < | } |
219 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 | < | |
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; |
243 | < | } |
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(); |
292 | < | } |
293 | < | } |
294 | < | |
295 | < | else{ |
296 | < | |
297 | < | sprintf( painCave.errMsg, |
298 | < | "SimSetup Error: unhandled bend assignment:\n" |
299 | < | " -->%s in Bend[%d] in %s\n", |
300 | < | current_extra->getlhs(), |
301 | < | j, comp_stamps[stampID]->getID() ); |
302 | < | painCave.isFatal = 1; |
303 | < | simError(); |
304 | < | } |
305 | < | |
306 | < | current_extra = current_extra->getNext(); |
307 | < | } |
308 | < | } |
309 | < | |
310 | < | if( !theBends[j].isGhost ){ |
311 | < | |
312 | < | exI = theBends[j].a; |
313 | < | exJ = theBends[j].c; |
314 | < | } |
315 | < | else{ |
316 | < | |
321 | < | exI = theBends[j].a; |
322 | < | exJ = theBends[j].b; |
323 | < | } |
324 | < | |
325 | < | // exclude_I must always be the smaller of the pair |
326 | < | if( exI > exJ ){ |
327 | < | tempEx = exI; |
328 | < | exI = exJ; |
329 | < | exJ = tempEx; |
330 | < | } |
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 | > | 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; |
360 | < | } |
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. | |
376 | – | |
377 | – | 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 ); |
381 | – | |
382 | – | |
383 | – | 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(); | |
402 | – | |
388 | } | |
389 | ||
390 | < | void SimSetup::initFromBass( void ){ |
406 | < | |
390 | > | void SimSetup::initFromBass(void){ |
391 | int i, j, k; | |
392 | int n_cells; | |
393 | double cellx, celly, cellz; | |
# | Line 417 | 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 453 | 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, |
461 | < | j * celly, |
462 | < | k * cellz ); |
446 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
447 | ||
448 | < | makeElement( i * cellx + 0.5 * cellx, |
465 | < | j * celly + 0.5 * celly, |
466 | < | k * cellz ); |
448 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
449 | ||
450 | < | makeElement( i * cellx, |
469 | < | j * celly + 0.5 * celly, |
470 | < | k * cellz + 0.5 * cellz ); |
471 | < | |
472 | < | makeElement( i * cellx + 0.5 * cellx, |
473 | < | j * celly, |
474 | < | 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 | < | } |
493 | < | else start_ndx = 0; |
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 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
482 | < | |
483 | < | makeElement( i * cellx, |
484 | < | j * celly, |
485 | < | k * cellz ); |
500 | < | 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 | < | } |
508 | < | |
509 | < | if( !done && n_per_extra > 2){ |
510 | < | makeElement( i * cellx, |
511 | < | j * celly + 0.5 * celly, |
512 | < | k * cellz + 0.5 * cellz ); |
513 | < | done = ( current_mol >= tot_nmol ); |
514 | < | } |
515 | < | |
516 | < | if( !done && n_per_extra > 3){ |
517 | < | makeElement( i * cellx + 0.5 * cellx, |
518 | < | j * celly, |
519 | < | k * cellz + 0.5 * cellz ); |
520 | < | done = ( current_mol >= tot_nmol ); |
521 | < | } |
522 | < | } |
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 ){ |
533 | < | |
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", |
549 | < | comp_stamps[current_comp]->getID(), |
550 | < | 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(); | |
558 | – | |
559 | – | 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 574 | 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 583 | 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] ){ |
587 | < | |
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 609 | 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; |
622 | < | 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 | } | |
646 | – | |
647 | – | for(i=0; i<nInfo; i++){ |
648 | – | |
649 | – | 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; |
676 | < | 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 681 | 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 | |
695 | – | |
696 | – | 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 705 | 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() ) info[i].setTemp = globals->getTempSet(); |
701 | < | |
700 | > | if (globals->haveTempSet()) |
701 | > | info[i].setTemp = globals->getTempSet(); |
702 | > | |
703 | // get some of the tricky things that may still be in the globals | |
704 | < | |
704 | > | |
705 | double boxVector[3]; | |
706 | < | if( globals->haveBox() ){ |
706 | > | if (globals->haveBox()){ |
707 | boxVector[0] = globals->getBox(); | |
708 | boxVector[1] = globals->getBox(); | |
709 | boxVector[2] = globals->getBox(); | |
710 | < | |
711 | < | info[i].setBox( boxVector ); |
710 | > | |
711 | > | info[i].setBox(boxVector); |
712 | } | |
713 | < | else if( globals->haveDensity() ){ |
732 | < | |
713 | > | else if (globals->haveDensity()){ |
714 | double vol; | |
715 | < | vol = (double)tot_nmol / globals->getDensity(); |
716 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
715 | > | vol = (double) tot_nmol / globals->getDensity(); |
716 | > | boxVector[0] = pow(vol, (1.0 / 3.0)); |
717 | boxVector[1] = boxVector[0]; | |
718 | boxVector[2] = boxVector[0]; | |
719 | < | |
720 | < | info[i].setBox( boxVector ); |
721 | < | } |
719 | > | |
720 | > | info[i].setBox(boxVector); |
721 | > | } |
722 | else{ | |
723 | < | if( !globals->haveBoxX() ){ |
724 | < | sprintf( painCave.errMsg, |
725 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
726 | < | painCave.isFatal = 1; |
727 | < | simError(); |
723 | > | if (!globals->haveBoxX()){ |
724 | > | sprintf(painCave.errMsg, |
725 | > | "SimSetup error, no periodic BoxX size given.\n"); |
726 | > | painCave.isFatal = 1; |
727 | > | simError(); |
728 | } | |
729 | boxVector[0] = globals->getBoxX(); | |
730 | < | |
731 | < | if( !globals->haveBoxY() ){ |
732 | < | sprintf( painCave.errMsg, |
733 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
734 | < | painCave.isFatal = 1; |
735 | < | simError(); |
730 | > | |
731 | > | if (!globals->haveBoxY()){ |
732 | > | sprintf(painCave.errMsg, |
733 | > | "SimSetup error, no periodic BoxY size given.\n"); |
734 | > | painCave.isFatal = 1; |
735 | > | simError(); |
736 | } | |
737 | boxVector[1] = globals->getBoxY(); | |
738 | < | |
739 | < | if( !globals->haveBoxZ() ){ |
740 | < | sprintf( painCave.errMsg, |
741 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
742 | < | painCave.isFatal = 1; |
743 | < | simError(); |
738 | > | |
739 | > | if (!globals->haveBoxZ()){ |
740 | > | sprintf(painCave.errMsg, |
741 | > | "SimSetup error, no periodic BoxZ size given.\n"); |
742 | > | painCave.isFatal = 1; |
743 | > | simError(); |
744 | } | |
745 | boxVector[2] = globals->getBoxZ(); | |
765 | – | |
766 | – | info[i].setBox( boxVector ); |
767 | – | } |
746 | ||
747 | + | info[i].setBox(boxVector); |
748 | + | } |
749 | } | |
750 | + | |
751 | + | //setup seed for random number generator |
752 | + | int seedValue; |
753 | + | |
754 | + | if (globals->haveSeed()){ |
755 | + | seedValue = globals->getSeed(); |
756 | + | |
757 | + | if(seedValue / 1E9 == 0){ |
758 | + | sprintf(painCave.errMsg, |
759 | + | "Seed for sprng library should contain at least 9 digits\n" |
760 | + | "OOPSE will generate a seed for user\n"); |
761 | + | painCave.isFatal = 0; |
762 | + | simError(); |
763 | + | |
764 | + | //using seed generated by system instead of invalid seed set by user |
765 | + | #ifndef IS_MPI |
766 | + | seedValue = make_sprng_seed(); |
767 | + | #else |
768 | + | if (worldRank == 0){ |
769 | + | seedValue = make_sprng_seed(); |
770 | + | } |
771 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
772 | + | #endif |
773 | + | } |
774 | + | }//end of if branch of globals->haveSeed() |
775 | + | else{ |
776 | ||
777 | + | #ifndef IS_MPI |
778 | + | seedValue = make_sprng_seed(); |
779 | + | #else |
780 | + | if (worldRank == 0){ |
781 | + | seedValue = make_sprng_seed(); |
782 | + | } |
783 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
784 | + | #endif |
785 | + | }//end of globals->haveSeed() |
786 | + | |
787 | + | for (int i = 0; i < nInfo; i++){ |
788 | + | info[i].setSeed(seedValue); |
789 | + | } |
790 | + | |
791 | #ifdef IS_MPI | |
792 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
792 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
793 | MPIcheckPoint(); | |
794 | #endif // is_mpi | |
775 | – | |
795 | } | |
796 | ||
797 | ||
798 | < | void SimSetup::finalInfoCheck( void ){ |
798 | > | void SimSetup::finalInfoCheck(void){ |
799 | int index; | |
800 | int usesDipoles; | |
801 | int i; | |
802 | ||
803 | < | for(i=0; i<nInfo; i++){ |
803 | > | for (i = 0; i < nInfo; i++){ |
804 | // check electrostatic parameters | |
805 | < | |
805 | > | |
806 | index = 0; | |
807 | usesDipoles = 0; | |
808 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
808 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
809 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
810 | index++; | |
811 | } | |
812 | < | |
812 | > | |
813 | #ifdef IS_MPI | |
814 | int myUse = usesDipoles; | |
815 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
815 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
816 | #endif //is_mpi | |
817 | < | |
817 | > | |
818 | double theEcr, theEst; | |
819 | < | |
820 | < | if (globals->getUseRF() ) { |
819 | > | |
820 | > | if (globals->getUseRF()){ |
821 | info[i].useReactionField = 1; | |
822 | < | |
823 | < | if( !globals->haveECR() ){ |
824 | < | sprintf( painCave.errMsg, |
825 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
826 | < | "box length for the electrostaticCutoffRadius.\n" |
827 | < | "I hope you have a very fast processor!\n"); |
828 | < | painCave.isFatal = 0; |
829 | < | simError(); |
830 | < | double smallest; |
831 | < | smallest = info[i].boxL[0]; |
832 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
833 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
834 | < | theEcr = 0.5 * smallest; |
835 | < | } else { |
836 | < | theEcr = globals->getECR(); |
822 | > | |
823 | > | if (!globals->haveECR()){ |
824 | > | sprintf(painCave.errMsg, |
825 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
826 | > | "box length for the electrostaticCutoffRadius.\n" |
827 | > | "I hope you have a very fast processor!\n"); |
828 | > | painCave.isFatal = 0; |
829 | > | simError(); |
830 | > | double smallest; |
831 | > | smallest = info[i].boxL[0]; |
832 | > | if (info[i].boxL[1] <= smallest) |
833 | > | smallest = info[i].boxL[1]; |
834 | > | if (info[i].boxL[2] <= smallest) |
835 | > | smallest = info[i].boxL[2]; |
836 | > | theEcr = 0.5 * smallest; |
837 | } | |
838 | < | |
839 | < | if( !globals->haveEST() ){ |
821 | < | sprintf( painCave.errMsg, |
822 | < | "SimSetup Warning: using default value of 0.05 * the " |
823 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
824 | < | ); |
825 | < | painCave.isFatal = 0; |
826 | < | simError(); |
827 | < | theEst = 0.05 * theEcr; |
828 | < | } else { |
829 | < | theEst= globals->getEST(); |
838 | > | else{ |
839 | > | theEcr = globals->getECR(); |
840 | } | |
841 | < | |
842 | < | info[i].setEcr( theEcr, theEst ); |
843 | < | |
844 | < | if(!globals->haveDielectric() ){ |
845 | < | sprintf( painCave.errMsg, |
846 | < | "SimSetup Error: You are trying to use Reaction Field without" |
847 | < | "setting a dielectric constant!\n" |
848 | < | ); |
839 | < | painCave.isFatal = 1; |
840 | < | simError(); |
841 | > | |
842 | > | if (!globals->haveEST()){ |
843 | > | sprintf(painCave.errMsg, |
844 | > | "SimSetup Warning: using default value of 0.05 * the " |
845 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
846 | > | painCave.isFatal = 0; |
847 | > | simError(); |
848 | > | theEst = 0.05 * theEcr; |
849 | } | |
850 | < | info[i].dielectric = globals->getDielectric(); |
851 | < | } |
844 | < | else { |
845 | < | if (usesDipoles) { |
846 | < | |
847 | < | if( !globals->haveECR() ){ |
848 | < | sprintf( painCave.errMsg, |
849 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
850 | < | "box length for the electrostaticCutoffRadius.\n" |
851 | < | "I hope you have a very fast processor!\n"); |
852 | < | painCave.isFatal = 0; |
853 | < | simError(); |
854 | < | double smallest; |
855 | < | smallest = info[i].boxL[0]; |
856 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
857 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
858 | < | theEcr = 0.5 * smallest; |
859 | < | } else { |
860 | < | theEcr = globals->getECR(); |
861 | < | } |
862 | < | |
863 | < | if( !globals->haveEST() ){ |
864 | < | sprintf( painCave.errMsg, |
865 | < | "SimSetup Warning: using default value of 0.05 * the " |
866 | < | "electrostaticCutoffRadius for the " |
867 | < | "electrostaticSkinThickness\n" |
868 | < | ); |
869 | < | painCave.isFatal = 0; |
870 | < | simError(); |
871 | < | theEst = 0.05 * theEcr; |
872 | < | } else { |
873 | < | theEst= globals->getEST(); |
874 | < | } |
875 | < | |
876 | < | info[i].setEcr( theEcr, theEst ); |
850 | > | else{ |
851 | > | theEst = globals->getEST(); |
852 | } | |
878 | – | } |
879 | – | } |
853 | ||
854 | < | #ifdef IS_MPI |
882 | < | strcpy( checkPointMsg, "post processing checks out" ); |
883 | < | MPIcheckPoint(); |
884 | < | #endif // is_mpi |
854 | > | info[i].setEcr(theEcr, theEst); |
855 | ||
856 | < | } |
856 | > | if (!globals->haveDielectric()){ |
857 | > | sprintf(painCave.errMsg, |
858 | > | "SimSetup Error: You are trying to use Reaction Field without" |
859 | > | "setting a dielectric constant!\n"); |
860 | > | painCave.isFatal = 1; |
861 | > | simError(); |
862 | > | } |
863 | > | info[i].dielectric = globals->getDielectric(); |
864 | > | } |
865 | > | else{ |
866 | > | if (usesDipoles){ |
867 | > | if (!globals->haveECR()){ |
868 | > | sprintf(painCave.errMsg, |
869 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
870 | > | "box length for the electrostaticCutoffRadius.\n" |
871 | > | "I hope you have a very fast processor!\n"); |
872 | > | painCave.isFatal = 0; |
873 | > | simError(); |
874 | > | double smallest; |
875 | > | smallest = info[i].boxL[0]; |
876 | > | if (info[i].boxL[1] <= smallest) |
877 | > | smallest = info[i].boxL[1]; |
878 | > | if (info[i].boxL[2] <= smallest) |
879 | > | smallest = info[i].boxL[2]; |
880 | > | theEcr = 0.5 * smallest; |
881 | > | } |
882 | > | else{ |
883 | > | theEcr = globals->getECR(); |
884 | > | } |
885 | ||
886 | < | void SimSetup::initSystemCoords( void ){ |
887 | < | int i; |
888 | < | |
889 | < | std::cerr << "Setting atom Coords\n"; |
890 | < | |
891 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
892 | < | |
893 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
894 | < | |
895 | < | if( globals->haveInitialConfig() ){ |
896 | < | |
886 | > | if (!globals->haveEST()){ |
887 | > | sprintf(painCave.errMsg, |
888 | > | "SimSetup Warning: using default value of 0.05 * the " |
889 | > | "electrostaticCutoffRadius for the " |
890 | > | "electrostaticSkinThickness\n"); |
891 | > | painCave.isFatal = 0; |
892 | > | simError(); |
893 | > | theEst = 0.05 * theEcr; |
894 | > | } |
895 | > | else{ |
896 | > | theEst = globals->getEST(); |
897 | > | } |
898 | > | |
899 | > | info[i].setEcr(theEcr, theEst); |
900 | > | } |
901 | > | } |
902 | > | } |
903 | > | |
904 | > | #ifdef IS_MPI |
905 | > | strcpy(checkPointMsg, "post processing checks out"); |
906 | > | MPIcheckPoint(); |
907 | > | #endif // is_mpi |
908 | > | } |
909 | > | |
910 | > | void SimSetup::initSystemCoords(void){ |
911 | > | int i; |
912 | > | |
913 | > | char* inName; |
914 | > | |
915 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
916 | > | |
917 | > | for (i = 0; i < info[0].n_atoms; i++) |
918 | > | info[0].atoms[i]->setCoords(); |
919 | > | |
920 | > | if (globals->haveInitialConfig()){ |
921 | InitializeFromFile* fileInit; | |
922 | #ifdef IS_MPI // is_mpi | |
923 | < | if( worldRank == 0 ){ |
923 | > | if (worldRank == 0){ |
924 | #endif //is_mpi | |
925 | < | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
925 | > | inName = globals->getInitialConfig(); |
926 | > | fileInit = new InitializeFromFile(inName); |
927 | #ifdef IS_MPI | |
928 | < | }else fileInit = new InitializeFromFile( NULL ); |
928 | > | } |
929 | > | else |
930 | > | fileInit = new InitializeFromFile(NULL); |
931 | #endif | |
932 | < | fileInit->readInit( info ); // default velocities on |
933 | < | |
932 | > | fileInit->readInit(info); // default velocities on |
933 | > | |
934 | delete fileInit; | |
935 | } | |
936 | else{ | |
912 | – | |
937 | #ifdef IS_MPI | |
938 | < | |
938 | > | |
939 | // no init from bass | |
940 | < | |
941 | < | sprintf( painCave.errMsg, |
942 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
943 | < | painCave.isFatal; |
940 | > | |
941 | > | sprintf(painCave.errMsg, |
942 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
943 | > | painCave.isFatal = 1;; |
944 | simError(); | |
945 | < | |
945 | > | |
946 | #else | |
947 | < | |
947 | > | |
948 | initFromBass(); | |
949 | < | |
950 | < | |
949 | > | |
950 | > | |
951 | #endif | |
952 | } | |
953 | < | |
953 | > | |
954 | #ifdef IS_MPI | |
955 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
955 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
956 | MPIcheckPoint(); | |
957 | #endif // is_mpi | |
934 | – | |
958 | } | |
959 | ||
960 | ||
961 | < | void SimSetup::makeOutNames( void ){ |
939 | < | |
961 | > | void SimSetup::makeOutNames(void){ |
962 | int k; | |
963 | ||
942 | – | |
943 | – | for(k=0; k<nInfo; k++){ |
964 | ||
965 | + | for (k = 0; k < nInfo; k++){ |
966 | #ifdef IS_MPI | |
967 | < | if( worldRank == 0 ){ |
967 | > | if (worldRank == 0){ |
968 | #endif // is_mpi | |
969 | < | |
970 | < | if( globals->haveFinalConfig() ){ |
971 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
969 | > | |
970 | > | if (globals->haveFinalConfig()){ |
971 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
972 | } | |
973 | else{ | |
974 | < | strcpy( info[k].finalName, inFileName ); |
975 | < | char* endTest; |
976 | < | int nameLength = strlen( info[k].finalName ); |
977 | < | endTest = &(info[k].finalName[nameLength - 5]); |
978 | < | if( !strcmp( endTest, ".bass" ) ){ |
979 | < | strcpy( endTest, ".eor" ); |
980 | < | } |
981 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
982 | < | strcpy( endTest, ".eor" ); |
983 | < | } |
984 | < | else{ |
985 | < | endTest = &(info[k].finalName[nameLength - 4]); |
986 | < | if( !strcmp( endTest, ".bss" ) ){ |
987 | < | strcpy( endTest, ".eor" ); |
988 | < | } |
989 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
990 | < | strcpy( endTest, ".eor" ); |
991 | < | } |
992 | < | else{ |
993 | < | strcat( info[k].finalName, ".eor" ); |
994 | < | } |
995 | < | } |
974 | > | strcpy(info[k].finalName, inFileName); |
975 | > | char* endTest; |
976 | > | int nameLength = strlen(info[k].finalName); |
977 | > | endTest = &(info[k].finalName[nameLength - 5]); |
978 | > | if (!strcmp(endTest, ".bass")){ |
979 | > | strcpy(endTest, ".eor"); |
980 | > | } |
981 | > | else if (!strcmp(endTest, ".BASS")){ |
982 | > | strcpy(endTest, ".eor"); |
983 | > | } |
984 | > | else{ |
985 | > | endTest = &(info[k].finalName[nameLength - 4]); |
986 | > | if (!strcmp(endTest, ".bss")){ |
987 | > | strcpy(endTest, ".eor"); |
988 | > | } |
989 | > | else if (!strcmp(endTest, ".mdl")){ |
990 | > | strcpy(endTest, ".eor"); |
991 | > | } |
992 | > | else{ |
993 | > | strcat(info[k].finalName, ".eor"); |
994 | > | } |
995 | > | } |
996 | } | |
997 | < | |
997 | > | |
998 | // make the sample and status out names | |
999 | < | |
1000 | < | strcpy( info[k].sampleName, inFileName ); |
999 | > | |
1000 | > | strcpy(info[k].sampleName, inFileName); |
1001 | char* endTest; | |
1002 | < | int nameLength = strlen( info[k].sampleName ); |
1002 | > | int nameLength = strlen(info[k].sampleName); |
1003 | endTest = &(info[k].sampleName[nameLength - 5]); | |
1004 | < | if( !strcmp( endTest, ".bass" ) ){ |
1005 | < | strcpy( endTest, ".dump" ); |
1004 | > | if (!strcmp(endTest, ".bass")){ |
1005 | > | strcpy(endTest, ".dump"); |
1006 | } | |
1007 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1008 | < | strcpy( endTest, ".dump" ); |
1007 | > | else if (!strcmp(endTest, ".BASS")){ |
1008 | > | strcpy(endTest, ".dump"); |
1009 | } | |
1010 | else{ | |
1011 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1012 | < | if( !strcmp( endTest, ".bss" ) ){ |
1013 | < | strcpy( endTest, ".dump" ); |
1014 | < | } |
1015 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1016 | < | strcpy( endTest, ".dump" ); |
1017 | < | } |
1018 | < | else{ |
1019 | < | strcat( info[k].sampleName, ".dump" ); |
1020 | < | } |
1011 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1012 | > | if (!strcmp(endTest, ".bss")){ |
1013 | > | strcpy(endTest, ".dump"); |
1014 | > | } |
1015 | > | else if (!strcmp(endTest, ".mdl")){ |
1016 | > | strcpy(endTest, ".dump"); |
1017 | > | } |
1018 | > | else{ |
1019 | > | strcat(info[k].sampleName, ".dump"); |
1020 | > | } |
1021 | } | |
1022 | < | |
1023 | < | strcpy( info[k].statusName, inFileName ); |
1024 | < | nameLength = strlen( info[k].statusName ); |
1022 | > | |
1023 | > | strcpy(info[k].statusName, inFileName); |
1024 | > | nameLength = strlen(info[k].statusName); |
1025 | endTest = &(info[k].statusName[nameLength - 5]); | |
1026 | < | if( !strcmp( endTest, ".bass" ) ){ |
1027 | < | strcpy( endTest, ".stat" ); |
1026 | > | if (!strcmp(endTest, ".bass")){ |
1027 | > | strcpy(endTest, ".stat"); |
1028 | } | |
1029 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1030 | < | strcpy( endTest, ".stat" ); |
1029 | > | else if (!strcmp(endTest, ".BASS")){ |
1030 | > | strcpy(endTest, ".stat"); |
1031 | } | |
1032 | else{ | |
1033 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1034 | < | if( !strcmp( endTest, ".bss" ) ){ |
1035 | < | strcpy( endTest, ".stat" ); |
1036 | < | } |
1037 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1038 | < | strcpy( endTest, ".stat" ); |
1039 | < | } |
1040 | < | else{ |
1041 | < | strcat( info[k].statusName, ".stat" ); |
1042 | < | } |
1033 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1034 | > | if (!strcmp(endTest, ".bss")){ |
1035 | > | strcpy(endTest, ".stat"); |
1036 | > | } |
1037 | > | else if (!strcmp(endTest, ".mdl")){ |
1038 | > | strcpy(endTest, ".stat"); |
1039 | > | } |
1040 | > | else{ |
1041 | > | strcat(info[k].statusName, ".stat"); |
1042 | > | } |
1043 | } | |
1044 | < | |
1044 | > | |
1045 | #ifdef IS_MPI | |
1046 | + | |
1047 | } | |
1048 | #endif // is_mpi | |
1049 | } | |
1050 | } | |
1051 | ||
1052 | ||
1053 | < | void SimSetup::sysObjectsCreation( void ){ |
1054 | < | |
1055 | < | int i,k; |
1034 | < | |
1053 | > | void SimSetup::sysObjectsCreation(void){ |
1054 | > | int i, k; |
1055 | > | |
1056 | // create the forceField | |
1057 | < | |
1057 | > | |
1058 | createFF(); | |
1059 | ||
1060 | // extract componentList | |
# | Line 1046 | Line 1067 | void SimSetup::sysObjectsCreation( void ){ | |
1067 | ||
1068 | #ifdef IS_MPI | |
1069 | // divide the molecules among the processors | |
1070 | < | |
1070 | > | |
1071 | mpiMolDivide(); | |
1072 | #endif //is_mpi | |
1073 | < | |
1073 | > | |
1074 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1075 | < | |
1075 | > | |
1076 | makeSysArrays(); | |
1077 | ||
1078 | // make and initialize the molecules (all but atomic coordinates) | |
1079 | < | |
1079 | > | |
1080 | makeMolecules(); | |
1081 | < | |
1082 | < | for(k=0; k<nInfo; k++){ |
1081 | > | |
1082 | > | for (k = 0; k < nInfo; k++){ |
1083 | info[k].identArray = new int[info[k].n_atoms]; | |
1084 | < | for(i=0; i<info[k].n_atoms; i++){ |
1084 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1085 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1086 | } | |
1087 | } | |
1088 | } | |
1089 | ||
1090 | ||
1091 | < | void SimSetup::createFF( void ){ |
1091 | > | void SimSetup::createFF(void){ |
1092 | > | switch (ffCase){ |
1093 | > | case FF_DUFF: |
1094 | > | the_ff = new DUFF(); |
1095 | > | break; |
1096 | ||
1097 | < | switch( ffCase ){ |
1097 | > | case FF_LJ: |
1098 | > | the_ff = new LJFF(); |
1099 | > | break; |
1100 | ||
1101 | < | case FF_DUFF: |
1102 | < | the_ff = new DUFF(); |
1103 | < | break; |
1101 | > | case FF_EAM: |
1102 | > | the_ff = new EAM_FF(); |
1103 | > | break; |
1104 | ||
1105 | < | case FF_LJ: |
1106 | < | the_ff = new LJFF(); |
1107 | < | break; |
1108 | < | |
1109 | < | case FF_EAM: |
1083 | < | the_ff = new EAM_FF(); |
1084 | < | break; |
1085 | < | |
1086 | < | default: |
1087 | < | sprintf( painCave.errMsg, |
1088 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1089 | < | painCave.isFatal = 1; |
1090 | < | simError(); |
1105 | > | default: |
1106 | > | sprintf(painCave.errMsg, |
1107 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1108 | > | painCave.isFatal = 1; |
1109 | > | simError(); |
1110 | } | |
1111 | ||
1112 | #ifdef IS_MPI | |
1113 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1113 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1114 | MPIcheckPoint(); | |
1115 | #endif // is_mpi | |
1097 | – | |
1116 | } | |
1117 | ||
1118 | ||
1119 | < | void SimSetup::compList( void ){ |
1102 | < | |
1119 | > | void SimSetup::compList(void){ |
1120 | int i; | |
1121 | char* id; | |
1122 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1123 | LinkedMolStamp* currentStamp = NULL; | |
1124 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1125 | < | |
1124 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1125 | > | |
1126 | // make an array of molecule stamps that match the components used. | |
1127 | // also extract the used stamps out into a separate linked list | |
1128 | < | |
1129 | < | for(i=0; i<nInfo; i++){ |
1128 | > | |
1129 | > | for (i = 0; i < nInfo; i++){ |
1130 | info[i].nComponents = n_components; | |
1131 | info[i].componentsNmol = components_nmol; | |
1132 | info[i].compStamps = comp_stamps; | |
1133 | info[i].headStamp = headStamp; | |
1134 | } | |
1118 | – | |
1135 | ||
1120 | – | for( i=0; i<n_components; i++ ){ |
1136 | ||
1137 | + | for (i = 0; i < n_components; i++){ |
1138 | id = the_components[i]->getType(); | |
1139 | comp_stamps[i] = NULL; | |
1140 | < | |
1140 | > | |
1141 | // check to make sure the component isn't already in the list | |
1142 | ||
1143 | < | comp_stamps[i] = headStamp->match( id ); |
1144 | < | if( comp_stamps[i] == NULL ){ |
1129 | < | |
1143 | > | comp_stamps[i] = headStamp->match(id); |
1144 | > | if (comp_stamps[i] == NULL){ |
1145 | // extract the component from the list; | |
1146 | < | |
1147 | < | currentStamp = stamps->extractMolStamp( id ); |
1148 | < | if( currentStamp == NULL ){ |
1149 | < | sprintf( painCave.errMsg, |
1150 | < | "SimSetup error: Component \"%s\" was not found in the " |
1151 | < | "list of declared molecules\n", |
1152 | < | id ); |
1153 | < | painCave.isFatal = 1; |
1154 | < | simError(); |
1146 | > | |
1147 | > | currentStamp = stamps->extractMolStamp(id); |
1148 | > | if (currentStamp == NULL){ |
1149 | > | sprintf(painCave.errMsg, |
1150 | > | "SimSetup error: Component \"%s\" was not found in the " |
1151 | > | "list of declared molecules\n", |
1152 | > | id); |
1153 | > | painCave.isFatal = 1; |
1154 | > | simError(); |
1155 | } | |
1156 | < | |
1157 | < | headStamp->add( currentStamp ); |
1158 | < | comp_stamps[i] = headStamp->match( id ); |
1156 | > | |
1157 | > | headStamp->add(currentStamp); |
1158 | > | comp_stamps[i] = headStamp->match(id); |
1159 | } | |
1160 | } | |
1161 | ||
1162 | #ifdef IS_MPI | |
1163 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1163 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1164 | MPIcheckPoint(); | |
1165 | #endif // is_mpi | |
1166 | + | } |
1167 | ||
1168 | + | void SimSetup::calcSysValues(void){ |
1169 | + | int i; |
1170 | ||
1171 | < | } |
1171 | > | int* molMembershipArray; |
1172 | ||
1155 | – | void SimSetup::calcSysValues( void ){ |
1156 | – | int i, j, k; |
1157 | – | |
1158 | – | int *molMembershipArray; |
1159 | – | |
1173 | tot_atoms = 0; | |
1174 | tot_bonds = 0; | |
1175 | tot_bends = 0; | |
1176 | tot_torsions = 0; | |
1177 | < | for( i=0; i<n_components; i++ ){ |
1178 | < | |
1179 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1180 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1168 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1177 | > | for (i = 0; i < n_components; i++){ |
1178 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1179 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1180 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1181 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1182 | } | |
1183 | < | |
1183 | > | |
1184 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1185 | molMembershipArray = new int[tot_atoms]; | |
1186 | < | |
1187 | < | for(i=0; i<nInfo; i++){ |
1186 | > | |
1187 | > | for (i = 0; i < nInfo; i++){ |
1188 | info[i].n_atoms = tot_atoms; | |
1189 | info[i].n_bonds = tot_bonds; | |
1190 | info[i].n_bends = tot_bends; | |
1191 | info[i].n_torsions = tot_torsions; | |
1192 | info[i].n_SRI = tot_SRI; | |
1193 | info[i].n_mol = tot_nmol; | |
1194 | < | |
1194 | > | |
1195 | info[i].molMembershipArray = molMembershipArray; | |
1196 | < | } |
1196 | > | } |
1197 | } | |
1198 | ||
1199 | #ifdef IS_MPI | |
1200 | ||
1201 | < | void SimSetup::mpiMolDivide( void ){ |
1190 | < | |
1201 | > | void SimSetup::mpiMolDivide(void){ |
1202 | int i, j, k; | |
1203 | int localMol, allMol; | |
1204 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1205 | ||
1206 | < | mpiSim = new mpiSimulation( info ); |
1207 | < | |
1206 | > | mpiSim = new mpiSimulation(info); |
1207 | > | |
1208 | globalIndex = mpiSim->divideLabor(); | |
1209 | ||
1210 | // set up the local variables | |
1211 | < | |
1211 | > | |
1212 | mol2proc = mpiSim->getMolToProcMap(); | |
1213 | molCompType = mpiSim->getMolComponentType(); | |
1214 | < | |
1214 | > | |
1215 | allMol = 0; | |
1216 | localMol = 0; | |
1217 | local_atoms = 0; | |
# | Line 1210 | Line 1221 | void SimSetup::mpiMolDivide( void ){ | |
1221 | globalAtomIndex = 0; | |
1222 | ||
1223 | ||
1224 | < | for( i=0; i<n_components; i++ ){ |
1225 | < | |
1226 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1227 | < | |
1228 | < | if( mol2proc[allMol] == worldRank ){ |
1229 | < | |
1230 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1231 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1221 | < | local_bends += comp_stamps[i]->getNBends(); |
1222 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1223 | < | localMol++; |
1224 | > | for (i = 0; i < n_components; i++){ |
1225 | > | for (j = 0; j < components_nmol[i]; j++){ |
1226 | > | if (mol2proc[allMol] == worldRank){ |
1227 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1228 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1229 | > | local_bends += comp_stamps[i]->getNBends(); |
1230 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1231 | > | localMol++; |
1232 | } | |
1233 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1233 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1234 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
1235 | globalAtomIndex++; | |
1236 | } | |
1237 | ||
1238 | < | allMol++; |
1238 | > | allMol++; |
1239 | } | |
1240 | } | |
1241 | local_SRI = local_bonds + local_bends + local_torsions; | |
1242 | < | |
1242 | > | |
1243 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1244 | < | |
1245 | < | if( local_atoms != info[0].n_atoms ){ |
1246 | < | sprintf( painCave.errMsg, |
1247 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1248 | < | " localAtom (%d) are not equal.\n", |
1249 | < | info[0].n_atoms, |
1242 | < | local_atoms ); |
1244 | > | |
1245 | > | if (local_atoms != info[0].n_atoms){ |
1246 | > | sprintf(painCave.errMsg, |
1247 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1248 | > | " localAtom (%d) are not equal.\n", |
1249 | > | info[0].n_atoms, local_atoms); |
1250 | painCave.isFatal = 1; | |
1251 | simError(); | |
1252 | } | |
# | Line 1250 | Line 1257 | void SimSetup::mpiMolDivide( void ){ | |
1257 | info[0].n_SRI = local_SRI; | |
1258 | info[0].n_mol = localMol; | |
1259 | ||
1260 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1260 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1261 | MPIcheckPoint(); | |
1262 | } | |
1263 | < | |
1263 | > | |
1264 | #endif // is_mpi | |
1265 | ||
1266 | ||
1267 | < | void SimSetup::makeSysArrays( void ){ |
1268 | < | int i, j, k, l; |
1267 | > | void SimSetup::makeSysArrays(void){ |
1268 | > | |
1269 | > | #ifndef IS_MPI |
1270 | > | int k, j; |
1271 | > | #endif // is_mpi |
1272 | > | int i, l; |
1273 | ||
1274 | Atom** the_atoms; | |
1275 | Molecule* the_molecules; | |
1276 | Exclude** the_excludes; | |
1277 | ||
1278 | < | |
1279 | < | for(l=0; l<nInfo; l++){ |
1269 | < | |
1278 | > | |
1279 | > | for (l = 0; l < nInfo; l++){ |
1280 | // create the atom and short range interaction arrays | |
1281 | < | |
1282 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1281 | > | |
1282 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1283 | the_molecules = new Molecule[info[l].n_mol]; | |
1284 | int molIndex; | |
1285 | ||
1286 | // initialize the molecule's stampID's | |
1287 | < | |
1287 | > | |
1288 | #ifdef IS_MPI | |
1289 | < | |
1290 | < | |
1289 | > | |
1290 | > | |
1291 | molIndex = 0; | |
1292 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1293 | < | |
1294 | < | if(mol2proc[i] == worldRank ){ |
1295 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1296 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1297 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1288 | < | molIndex++; |
1292 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1293 | > | if (mol2proc[i] == worldRank){ |
1294 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1295 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1296 | > | the_molecules[molIndex].setGlobalIndex(i); |
1297 | > | molIndex++; |
1298 | } | |
1299 | } | |
1300 | < | |
1300 | > | |
1301 | #else // is_mpi | |
1302 | < | |
1302 | > | |
1303 | molIndex = 0; | |
1304 | globalAtomIndex = 0; | |
1305 | < | for(i=0; i<n_components; i++){ |
1306 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1307 | < | the_molecules[molIndex].setStampID( i ); |
1308 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1309 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1310 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1311 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1312 | < | globalAtomIndex++; |
1313 | < | } |
1314 | < | molIndex++; |
1305 | > | for (i = 0; i < n_components; i++){ |
1306 | > | for (j = 0; j < components_nmol[i]; j++){ |
1307 | > | the_molecules[molIndex].setStampID(i); |
1308 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1309 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1310 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1311 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1312 | > | globalAtomIndex++; |
1313 | > | } |
1314 | > | molIndex++; |
1315 | } | |
1316 | } | |
1317 | < | |
1318 | < | |
1317 | > | |
1318 | > | |
1319 | #endif // is_mpi | |
1320 | ||
1321 | ||
1322 | < | if( info[l].n_SRI ){ |
1314 | < | |
1322 | > | if (info[l].n_SRI){ |
1323 | Exclude::createArray(info[l].n_SRI); | |
1324 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1325 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1326 | < | the_excludes[ex] = new Exclude(ex); |
1324 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1325 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1326 | > | the_excludes[ex] = new Exclude(ex); |
1327 | } | |
1328 | info[l].globalExcludes = new int; | |
1329 | info[l].n_exclude = info[l].n_SRI; | |
1330 | } | |
1331 | else{ | |
1332 | < | |
1333 | < | Exclude::createArray( 1 ); |
1326 | < | the_excludes = new Exclude*; |
1332 | > | Exclude::createArray(1); |
1333 | > | the_excludes = new Exclude * ; |
1334 | the_excludes[0] = new Exclude(0); | |
1335 | < | the_excludes[0]->setPair( 0,0 ); |
1335 | > | the_excludes[0]->setPair(0, 0); |
1336 | info[l].globalExcludes = new int; | |
1337 | info[l].globalExcludes[0] = 0; | |
1338 | info[l].n_exclude = 0; | |
# | Line 1338 | Line 1345 | void SimSetup::makeSysArrays( void ){ | |
1345 | info[l].nGlobalExcludes = 0; | |
1346 | info[l].excludes = the_excludes; | |
1347 | ||
1348 | < | the_ff->setSimInfo( info ); |
1342 | < | |
1348 | > | the_ff->setSimInfo(info); |
1349 | } | |
1350 | } | |
1351 | ||
1352 | < | void SimSetup::makeIntegrator( void ){ |
1347 | < | |
1352 | > | void SimSetup::makeIntegrator(void){ |
1353 | int k; | |
1354 | ||
1355 | < | NVT<RealIntegrator>* myNVT = NULL; |
1356 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1357 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1358 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1359 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1360 | < | |
1361 | < | for(k=0; k<nInfo; k++){ |
1362 | < | |
1363 | < | switch( ensembleCase ){ |
1364 | < | |
1365 | < | case NVE_ENS: |
1366 | < | if (globals->haveZconstraints()){ |
1367 | < | setupZConstraint(info[k]); |
1368 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1355 | > | NVE<RealIntegrator>* myNVE = NULL; |
1356 | > | NVT<RealIntegrator>* myNVT = NULL; |
1357 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1358 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1359 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1360 | > | |
1361 | > | for (k = 0; k < nInfo; k++){ |
1362 | > | switch (ensembleCase){ |
1363 | > | case NVE_ENS: |
1364 | > | if (globals->haveZconstraints()){ |
1365 | > | setupZConstraint(info[k]); |
1366 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1367 | > | } |
1368 | > | else{ |
1369 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1370 | } | |
1371 | + | |
1372 | + | info->the_integrator = myNVE; |
1373 | + | break; |
1374 | ||
1375 | < | else |
1376 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1377 | < | break; |
1378 | < | |
1379 | < | case NVT_ENS: |
1380 | < | if (globals->haveZconstraints()){ |
1381 | < | setupZConstraint(info[k]); |
1373 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1374 | < | } |
1375 | < | else |
1376 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1375 | > | case NVT_ENS: |
1376 | > | if (globals->haveZconstraints()){ |
1377 | > | setupZConstraint(info[k]); |
1378 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1379 | > | } |
1380 | > | else |
1381 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1382 | ||
1383 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1379 | < | |
1380 | < | if (globals->haveTauThermostat()) |
1381 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1382 | < | |
1383 | < | else { |
1384 | < | sprintf( painCave.errMsg, |
1385 | < | "SimSetup error: If you use the NVT\n" |
1386 | < | " ensemble, you must set tauThermostat.\n"); |
1387 | < | painCave.isFatal = 1; |
1388 | < | simError(); |
1389 | < | } |
1390 | < | break; |
1391 | < | |
1392 | < | case NPTi_ENS: |
1393 | < | if (globals->haveZconstraints()){ |
1394 | < | setupZConstraint(info[k]); |
1395 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1396 | < | } |
1397 | < | else |
1398 | < | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1383 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1384 | ||
1385 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1386 | < | |
1387 | < | if (globals->haveTargetPressure()) |
1388 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1389 | < | else { |
1390 | < | sprintf( painCave.errMsg, |
1391 | < | "SimSetup error: If you use a constant pressure\n" |
1392 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1393 | < | painCave.isFatal = 1; |
1409 | < | simError(); |
1410 | < | } |
1411 | < | |
1412 | < | if( globals->haveTauThermostat() ) |
1413 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1414 | < | else{ |
1415 | < | sprintf( painCave.errMsg, |
1416 | < | "SimSetup error: If you use an NPT\n" |
1417 | < | " ensemble, you must set tauThermostat.\n"); |
1418 | < | painCave.isFatal = 1; |
1419 | < | simError(); |
1420 | < | } |
1421 | < | |
1422 | < | if( globals->haveTauBarostat() ) |
1423 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1424 | < | else{ |
1425 | < | sprintf( painCave.errMsg, |
1426 | < | "SimSetup error: If you use an NPT\n" |
1427 | < | " ensemble, you must set tauBarostat.\n"); |
1428 | < | painCave.isFatal = 1; |
1429 | < | simError(); |
1430 | < | } |
1431 | < | break; |
1432 | < | |
1433 | < | case NPTf_ENS: |
1434 | < | if (globals->haveZconstraints()){ |
1435 | < | setupZConstraint(info[k]); |
1436 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1437 | < | } |
1438 | < | else |
1439 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1385 | > | if (globals->haveTauThermostat()) |
1386 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1387 | > | else{ |
1388 | > | sprintf(painCave.errMsg, |
1389 | > | "SimSetup error: If you use the NVT\n" |
1390 | > | " ensemble, you must set tauThermostat.\n"); |
1391 | > | painCave.isFatal = 1; |
1392 | > | simError(); |
1393 | > | } |
1394 | ||
1395 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1396 | < | |
1443 | < | if (globals->haveTargetPressure()) |
1444 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1445 | < | else { |
1446 | < | sprintf( painCave.errMsg, |
1447 | < | "SimSetup error: If you use a constant pressure\n" |
1448 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1449 | < | painCave.isFatal = 1; |
1450 | < | simError(); |
1451 | < | } |
1452 | < | |
1453 | < | if( globals->haveTauThermostat() ) |
1454 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1455 | < | else{ |
1456 | < | sprintf( painCave.errMsg, |
1457 | < | "SimSetup error: If you use an NPT\n" |
1458 | < | " ensemble, you must set tauThermostat.\n"); |
1459 | < | painCave.isFatal = 1; |
1460 | < | simError(); |
1461 | < | } |
1462 | < | |
1463 | < | if( globals->haveTauBarostat() ) |
1464 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1465 | < | else{ |
1466 | < | sprintf( painCave.errMsg, |
1467 | < | "SimSetup error: If you use an NPT\n" |
1468 | < | " ensemble, you must set tauBarostat.\n"); |
1469 | < | painCave.isFatal = 1; |
1470 | < | simError(); |
1471 | < | } |
1472 | < | break; |
1473 | < | |
1474 | < | case NPTim_ENS: |
1475 | < | if (globals->haveZconstraints()){ |
1476 | < | setupZConstraint(info[k]); |
1477 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1478 | < | } |
1479 | < | else |
1480 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1395 | > | info->the_integrator = myNVT; |
1396 | > | break; |
1397 | ||
1398 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1399 | < | |
1400 | < | if (globals->haveTargetPressure()) |
1401 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1402 | < | else { |
1403 | < | sprintf( painCave.errMsg, |
1404 | < | "SimSetup error: If you use a constant pressure\n" |
1489 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1490 | < | painCave.isFatal = 1; |
1491 | < | simError(); |
1492 | < | } |
1493 | < | |
1494 | < | if( globals->haveTauThermostat() ) |
1495 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1496 | < | else{ |
1497 | < | sprintf( painCave.errMsg, |
1498 | < | "SimSetup error: If you use an NPT\n" |
1499 | < | " ensemble, you must set tauThermostat.\n"); |
1500 | < | painCave.isFatal = 1; |
1501 | < | simError(); |
1502 | < | } |
1503 | < | |
1504 | < | if( globals->haveTauBarostat() ) |
1505 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1506 | < | else{ |
1507 | < | sprintf( painCave.errMsg, |
1508 | < | "SimSetup error: If you use an NPT\n" |
1509 | < | " ensemble, you must set tauBarostat.\n"); |
1510 | < | painCave.isFatal = 1; |
1511 | < | simError(); |
1512 | < | } |
1513 | < | break; |
1514 | < | |
1515 | < | case NPTfm_ENS: |
1516 | < | if (globals->haveZconstraints()){ |
1517 | < | setupZConstraint(info[k]); |
1518 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1519 | < | } |
1520 | < | else |
1521 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1398 | > | case NPTi_ENS: |
1399 | > | if (globals->haveZconstraints()){ |
1400 | > | setupZConstraint(info[k]); |
1401 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1402 | > | } |
1403 | > | else |
1404 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1405 | ||
1406 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1407 | < | |
1408 | < | if (globals->haveTargetPressure()) |
1409 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1410 | < | else { |
1411 | < | sprintf( painCave.errMsg, |
1412 | < | "SimSetup error: If you use a constant pressure\n" |
1413 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1414 | < | painCave.isFatal = 1; |
1415 | < | simError(); |
1416 | < | } |
1417 | < | |
1418 | < | if( globals->haveTauThermostat() ) |
1419 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1420 | < | else{ |
1421 | < | sprintf( painCave.errMsg, |
1422 | < | "SimSetup error: If you use an NPT\n" |
1423 | < | " ensemble, you must set tauThermostat.\n"); |
1424 | < | painCave.isFatal = 1; |
1425 | < | simError(); |
1426 | < | } |
1427 | < | |
1428 | < | if( globals->haveTauBarostat() ) |
1429 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1430 | < | else{ |
1431 | < | sprintf( painCave.errMsg, |
1432 | < | "SimSetup error: If you use an NPT\n" |
1433 | < | " ensemble, you must set tauBarostat.\n"); |
1434 | < | painCave.isFatal = 1; |
1435 | < | simError(); |
1436 | < | } |
1437 | < | break; |
1438 | < | |
1439 | < | default: |
1440 | < | sprintf( painCave.errMsg, |
1441 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1442 | < | painCave.isFatal = 1; |
1443 | < | simError(); |
1406 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1407 | > | |
1408 | > | if (globals->haveTargetPressure()) |
1409 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1410 | > | else{ |
1411 | > | sprintf(painCave.errMsg, |
1412 | > | "SimSetup error: If you use a constant pressure\n" |
1413 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1414 | > | painCave.isFatal = 1; |
1415 | > | simError(); |
1416 | > | } |
1417 | > | |
1418 | > | if (globals->haveTauThermostat()) |
1419 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1420 | > | else{ |
1421 | > | sprintf(painCave.errMsg, |
1422 | > | "SimSetup error: If you use an NPT\n" |
1423 | > | " ensemble, you must set tauThermostat.\n"); |
1424 | > | painCave.isFatal = 1; |
1425 | > | simError(); |
1426 | > | } |
1427 | > | |
1428 | > | if (globals->haveTauBarostat()) |
1429 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1430 | > | else{ |
1431 | > | sprintf(painCave.errMsg, |
1432 | > | "SimSetup error: If you use an NPT\n" |
1433 | > | " ensemble, you must set tauBarostat.\n"); |
1434 | > | painCave.isFatal = 1; |
1435 | > | simError(); |
1436 | > | } |
1437 | > | |
1438 | > | info->the_integrator = myNPTi; |
1439 | > | break; |
1440 | > | |
1441 | > | case NPTf_ENS: |
1442 | > | if (globals->haveZconstraints()){ |
1443 | > | setupZConstraint(info[k]); |
1444 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1445 | > | } |
1446 | > | else |
1447 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1448 | > | |
1449 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1450 | > | |
1451 | > | if (globals->haveTargetPressure()) |
1452 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1453 | > | else{ |
1454 | > | sprintf(painCave.errMsg, |
1455 | > | "SimSetup error: If you use a constant pressure\n" |
1456 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1457 | > | painCave.isFatal = 1; |
1458 | > | simError(); |
1459 | > | } |
1460 | > | |
1461 | > | if (globals->haveTauThermostat()) |
1462 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1463 | > | else{ |
1464 | > | sprintf(painCave.errMsg, |
1465 | > | "SimSetup error: If you use an NPT\n" |
1466 | > | " ensemble, you must set tauThermostat.\n"); |
1467 | > | painCave.isFatal = 1; |
1468 | > | simError(); |
1469 | > | } |
1470 | > | |
1471 | > | if (globals->haveTauBarostat()) |
1472 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1473 | > | else{ |
1474 | > | sprintf(painCave.errMsg, |
1475 | > | "SimSetup error: If you use an NPT\n" |
1476 | > | " ensemble, you must set tauBarostat.\n"); |
1477 | > | painCave.isFatal = 1; |
1478 | > | simError(); |
1479 | > | } |
1480 | > | |
1481 | > | info->the_integrator = myNPTf; |
1482 | > | break; |
1483 | > | |
1484 | > | case NPTxyz_ENS: |
1485 | > | if (globals->haveZconstraints()){ |
1486 | > | setupZConstraint(info[k]); |
1487 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1488 | > | } |
1489 | > | else |
1490 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1491 | > | |
1492 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1493 | > | |
1494 | > | if (globals->haveTargetPressure()) |
1495 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1496 | > | else{ |
1497 | > | sprintf(painCave.errMsg, |
1498 | > | "SimSetup error: If you use a constant pressure\n" |
1499 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1500 | > | painCave.isFatal = 1; |
1501 | > | simError(); |
1502 | > | } |
1503 | > | |
1504 | > | if (globals->haveTauThermostat()) |
1505 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1506 | > | else{ |
1507 | > | sprintf(painCave.errMsg, |
1508 | > | "SimSetup error: If you use an NPT\n" |
1509 | > | " ensemble, you must set tauThermostat.\n"); |
1510 | > | painCave.isFatal = 1; |
1511 | > | simError(); |
1512 | > | } |
1513 | > | |
1514 | > | if (globals->haveTauBarostat()) |
1515 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1516 | > | else{ |
1517 | > | sprintf(painCave.errMsg, |
1518 | > | "SimSetup error: If you use an NPT\n" |
1519 | > | " ensemble, you must set tauBarostat.\n"); |
1520 | > | painCave.isFatal = 1; |
1521 | > | simError(); |
1522 | > | } |
1523 | > | |
1524 | > | info->the_integrator = myNPTxyz; |
1525 | > | break; |
1526 | > | |
1527 | > | default: |
1528 | > | sprintf(painCave.errMsg, |
1529 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1530 | > | painCave.isFatal = 1; |
1531 | > | simError(); |
1532 | } | |
1533 | } | |
1534 | } | |
1535 | ||
1536 | < | void SimSetup::initFortran( void ){ |
1566 | < | |
1536 | > | void SimSetup::initFortran(void){ |
1537 | info[0].refreshSim(); | |
1538 | < | |
1539 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1540 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1538 | > | |
1539 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1540 | > | the_ff->initForceField(LB_MIXING_RULE); |
1541 | } | |
1542 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1543 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1542 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1543 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1544 | } | |
1545 | else{ | |
1546 | < | sprintf( painCave.errMsg, |
1547 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1578 | < | info[0].mixingRule ); |
1546 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1547 | > | info[0].mixingRule); |
1548 | painCave.isFatal = 1; | |
1549 | simError(); | |
1550 | } | |
1551 | ||
1552 | ||
1553 | #ifdef IS_MPI | |
1554 | < | strcpy( checkPointMsg, |
1586 | < | "Successfully intialized the mixingRule for Fortran." ); |
1554 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1555 | MPIcheckPoint(); | |
1556 | #endif // is_mpi | |
1589 | – | |
1557 | } | |
1558 | ||
1559 | < | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1560 | < | { |
1561 | < | int nZConstraints; |
1595 | < | ZconStamp** zconStamp; |
1596 | < | |
1597 | < | if(globals->haveZconstraintTime()){ |
1598 | < | |
1599 | < | //add sample time of z-constraint into SimInfo's property list |
1600 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1601 | < | zconsTimeProp->setID(ZCONSTIME_ID); |
1602 | < | zconsTimeProp->setData(globals->getZconsTime()); |
1603 | < | theInfo.addProperty(zconsTimeProp); |
1604 | < | } |
1605 | < | else{ |
1606 | < | sprintf( painCave.errMsg, |
1607 | < | "ZConstraint error: If you use an ZConstraint\n" |
1608 | < | " , you must set sample time.\n"); |
1609 | < | painCave.isFatal = 1; |
1610 | < | simError(); |
1611 | < | } |
1559 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1560 | > | int nZConstraints; |
1561 | > | ZconStamp** zconStamp; |
1562 | ||
1563 | < | // |
1564 | < | nZConstraints = globals->getNzConstraints(); |
1565 | < | zconStamp = globals->getZconStamp(); |
1566 | < | ZConsParaItem tempParaItem; |
1563 | > | if (globals->haveZconstraintTime()){ |
1564 | > | //add sample time of z-constraint into SimInfo's property list |
1565 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1566 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1567 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1568 | > | theInfo.addProperty(zconsTimeProp); |
1569 | > | } |
1570 | > | else{ |
1571 | > | sprintf(painCave.errMsg, |
1572 | > | "ZConstraint error: If you use an ZConstraint\n" |
1573 | > | " , you must set sample time.\n"); |
1574 | > | painCave.isFatal = 1; |
1575 | > | simError(); |
1576 | > | } |
1577 | ||
1578 | < | ZConsParaData* zconsParaData = new ZConsParaData(); |
1579 | < | zconsParaData->setID(ZCONSPARADATA_ID); |
1580 | < | |
1581 | < | for(int i = 0; i < nZConstraints; i++){ |
1578 | > | //push zconsTol into siminfo, if user does not specify |
1579 | > | //value for zconsTol, a default value will be used |
1580 | > | DoubleData* zconsTol = new DoubleData(); |
1581 | > | zconsTol->setID(ZCONSTOL_ID); |
1582 | > | if (globals->haveZconsTol()){ |
1583 | > | zconsTol->setData(globals->getZconsTol()); |
1584 | > | } |
1585 | > | else{ |
1586 | > | double defaultZConsTol = 0.01; |
1587 | > | sprintf(painCave.errMsg, |
1588 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1589 | > | " , default value %f is used.\n", |
1590 | > | defaultZConsTol); |
1591 | > | painCave.isFatal = 0; |
1592 | > | simError(); |
1593 | > | |
1594 | > | zconsTol->setData(defaultZConsTol); |
1595 | > | } |
1596 | > | theInfo.addProperty(zconsTol); |
1597 | > | |
1598 | > | //set Force Subtraction Policy |
1599 | > | StringData* zconsForcePolicy = new StringData(); |
1600 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1601 | > | |
1602 | > | if (globals->haveZconsForcePolicy()){ |
1603 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1604 | > | } |
1605 | > | else{ |
1606 | > | sprintf(painCave.errMsg, |
1607 | > | "ZConstraint Warning: User does not set force Subtraction policy, " |
1608 | > | "PolicyByMass is used\n"); |
1609 | > | painCave.isFatal = 0; |
1610 | > | simError(); |
1611 | > | zconsForcePolicy->setData("BYMASS"); |
1612 | > | } |
1613 | > | |
1614 | > | theInfo.addProperty(zconsForcePolicy); |
1615 | > | |
1616 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1617 | > | //Be careful, do not use inFileName, since it is a pointer which |
1618 | > | //point to a string at master node, and slave nodes do not contain that string |
1619 | > | |
1620 | > | string zconsOutput(theInfo.finalName); |
1621 | > | |
1622 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1623 | > | |
1624 | > | StringData* zconsFilename = new StringData(); |
1625 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1626 | > | zconsFilename->setData(zconsOutput); |
1627 | > | |
1628 | > | theInfo.addProperty(zconsFilename); |
1629 | > | |
1630 | > | //setup index, pos and other parameters of z-constraint molecules |
1631 | > | nZConstraints = globals->getNzConstraints(); |
1632 | > | theInfo.nZconstraints = nZConstraints; |
1633 | > | |
1634 | > | zconStamp = globals->getZconStamp(); |
1635 | > | ZConsParaItem tempParaItem; |
1636 | > | |
1637 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1638 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1639 | > | |
1640 | > | for (int i = 0; i < nZConstraints; i++){ |
1641 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
1642 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1643 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1644 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1645 | ||
1646 | zconsParaData->addItem(tempParaItem); | |
1647 | < | } |
1647 | > | } |
1648 | ||
1649 | < | //sort the parameters by index of molecules |
1650 | < | zconsParaData->sortByIndex(); |
1651 | < | |
1652 | < | //push data into siminfo, therefore, we can retrieve later |
1653 | < | theInfo.addProperty(zconsParaData); |
1649 | > | //check the uniqueness of index |
1650 | > | if(!zconsParaData->isIndexUnique()){ |
1651 | > | sprintf(painCave.errMsg, |
1652 | > | "ZConstraint Error: molIndex is not unique\n"); |
1653 | > | painCave.isFatal = 1; |
1654 | > | simError(); |
1655 | > | } |
1656 | ||
1657 | < | //push zconsTol into siminfo, if user does not specify |
1658 | < | //value for zconsTol, a default value will be used |
1659 | < | DoubleData* zconsTol = new DoubleData(); |
1660 | < | zconsTol->setID(ZCONSTOL_ID); |
1661 | < | if(globals->haveZconsTol()){ |
1641 | < | zconsTol->setData(globals->getZconsTol()); |
1642 | < | } |
1643 | < | else{ |
1644 | < | double defaultZConsTol = 1E-6; |
1645 | < | sprintf( painCave.errMsg, |
1646 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1647 | < | " , default value %f is used.\n", defaultZConsTol); |
1648 | < | painCave.isFatal = 0; |
1649 | < | simError(); |
1650 | < | |
1651 | < | zconsTol->setData(defaultZConsTol); |
1652 | < | } |
1653 | < | theInfo.addProperty(zconsTol); |
1654 | < | |
1655 | < | //Determine the name of ouput file and add it into SimInfo's property list |
1656 | < | //Be careful, do not use inFileName, since it is a pointer which |
1657 | < | //point to a string at master node, and slave nodes do not contain that string |
1658 | < | |
1659 | < | string zconsOutput(theInfo.finalName); |
1660 | < | |
1661 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1662 | < | |
1663 | < | StringData* zconsFilename = new StringData(); |
1664 | < | zconsFilename->setID(ZCONSFILENAME_ID); |
1665 | < | zconsFilename->setData(zconsOutput); |
1666 | < | |
1667 | < | theInfo.addProperty(zconsFilename); |
1657 | > | //sort the parameters by index of molecules |
1658 | > | zconsParaData->sortByIndex(); |
1659 | > | |
1660 | > | //push data into siminfo, therefore, we can retrieve later |
1661 | > | theInfo.addProperty(zconsParaData); |
1662 | } |
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