# | 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 | < | #include <sys/time.h> |
7 | < | |
6 | > | #include <sprng.h> |
7 | #include "SimSetup.hpp" | |
8 | #include "ReadWrite.hpp" | |
9 | #include "parse_me.h" | |
# | Line 22 | Line 21 | |
21 | #define NVT_ENS 1 | |
22 | #define NPTi_ENS 2 | |
23 | #define NPTf_ENS 3 | |
24 | < | #define NPTim_ENS 4 |
26 | < | #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 | |
30 | ||
31 | using namespace std; | |
32 | ||
33 | + | /** |
34 | + | * Check whether dividend is divisble by divisor or not |
35 | + | */ |
36 | + | bool isDivisible(double dividend, double divisor){ |
37 | + | double tolerance = 0.000001; |
38 | + | double quotient; |
39 | + | double diff; |
40 | + | int intQuotient; |
41 | + | |
42 | + | quotient = dividend / divisor; |
43 | + | |
44 | + | if (quotient < 0) |
45 | + | quotient = -quotient; |
46 | + | |
47 | + | intQuotient = int (quotient + tolerance); |
48 | + | |
49 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
50 | + | |
51 | + | if (diff <= tolerance) |
52 | + | return true; |
53 | + | else |
54 | + | return false; |
55 | + | } |
56 | + | |
57 | SimSetup::SimSetup(){ | |
58 | ||
59 | + | initSuspend = false; |
60 | isInfoArray = 0; | |
61 | nInfo = 1; | |
62 | < | |
62 | > | |
63 | stamps = new MakeStamps(); | |
64 | globals = new Globals(); | |
65 | < | |
66 | < | |
65 | > | |
66 | > | |
67 | #ifdef IS_MPI | |
68 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
68 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
69 | MPIcheckPoint(); | |
70 | #endif // IS_MPI | |
71 | } | |
# | Line 51 | Line 75 | SimSetup::~SimSetup(){ | |
75 | delete globals; | |
76 | } | |
77 | ||
78 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
79 | < | info = the_info; |
80 | < | nInfo = theNinfo; |
81 | < | isInfoArray = 1; |
78 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
79 | > | info = the_info; |
80 | > | nInfo = theNinfo; |
81 | > | isInfoArray = 1; |
82 | > | initSuspend = true; |
83 | } | |
84 | ||
85 | ||
86 | < | void SimSetup::parseFile( char* fileName ){ |
62 | < | |
86 | > | void SimSetup::parseFile(char* fileName){ |
87 | #ifdef IS_MPI | |
88 | < | if( worldRank == 0 ){ |
88 | > | if (worldRank == 0){ |
89 | #endif // is_mpi | |
90 | < | |
90 | > | |
91 | inFileName = fileName; | |
92 | < | set_interface_stamps( stamps, globals ); |
93 | < | |
92 | > | set_interface_stamps(stamps, globals); |
93 | > | |
94 | #ifdef IS_MPI | |
95 | mpiEventInit(); | |
96 | #endif | |
97 | ||
98 | < | yacc_BASS( fileName ); |
98 | > | yacc_BASS(fileName); |
99 | ||
100 | #ifdef IS_MPI | |
101 | throwMPIEvent(NULL); | |
102 | } | |
103 | < | else receiveParse(); |
103 | > | else{ |
104 | > | receiveParse(); |
105 | > | } |
106 | #endif | |
107 | ||
108 | } | |
109 | ||
110 | #ifdef IS_MPI | |
111 | void SimSetup::receiveParse(void){ | |
112 | < | |
113 | < | set_interface_stamps( stamps, globals ); |
114 | < | mpiEventInit(); |
115 | < | MPIcheckPoint(); |
90 | < | mpiEventLoop(); |
91 | < | |
112 | > | set_interface_stamps(stamps, globals); |
113 | > | mpiEventInit(); |
114 | > | MPIcheckPoint(); |
115 | > | mpiEventLoop(); |
116 | } | |
117 | ||
118 | #endif // is_mpi | |
119 | ||
120 | void SimSetup::createSim(void){ | |
121 | ||
98 | – | int i, j, k, globalAtomIndex; |
99 | – | |
122 | // gather all of the information from the Bass file | |
123 | ||
124 | gatherInfo(); | |
# | Line 111 | Line 133 | void SimSetup::createSim(void){ | |
133 | ||
134 | // initialize the system coordinates | |
135 | ||
136 | < | if( !isInfoArray ) initSystemCoords(); |
136 | > | if ( !initSuspend ){ |
137 | > | initSystemCoords(); |
138 | ||
139 | + | if( !(globals->getUseInitTime()) ) |
140 | + | info[0].currentTime = 0.0; |
141 | + | } |
142 | + | |
143 | // make the output filenames | |
144 | ||
145 | makeOutNames(); | |
146 | < | |
146 | > | |
147 | // make the integrator | |
148 | < | |
148 | > | |
149 | makeIntegrator(); | |
150 | < | |
150 | > | |
151 | #ifdef IS_MPI | |
152 | mpiSim->mpiRefresh(); | |
153 | #endif | |
# | Line 128 | Line 155 | void SimSetup::createSim(void){ | |
155 | // initialize the Fortran | |
156 | ||
157 | initFortran(); | |
131 | – | |
132 | – | |
133 | – | |
158 | } | |
159 | ||
160 | ||
161 | < | void SimSetup::makeMolecules( void ){ |
162 | < | |
139 | < | int k,l; |
161 | > | void SimSetup::makeMolecules(void){ |
162 | > | int k; |
163 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
164 | molInit molInfo; | |
165 | DirectionalAtom* dAtom; | |
# | Line 151 | Line 174 | void SimSetup::makeMolecules( void ){ | |
174 | bend_set* theBends; | |
175 | torsion_set* theTorsions; | |
176 | ||
177 | < | |
177 | > | |
178 | //init the forceField paramters | |
179 | ||
180 | the_ff->readParams(); | |
181 | ||
182 | < | |
182 | > | |
183 | // init the atoms | |
184 | ||
185 | double ux, uy, uz, u, uSqr; | |
163 | – | |
164 | – | for(k=0; k<nInfo; k++){ |
165 | – | |
166 | – | the_ff->setSimInfo( &(info[k]) ); |
186 | ||
187 | + | for (k = 0; k < nInfo; k++){ |
188 | + | the_ff->setSimInfo(&(info[k])); |
189 | + | |
190 | atomOffset = 0; | |
191 | excludeOffset = 0; | |
192 | < | for(i=0; i<info[k].n_mol; i++){ |
171 | < | |
192 | > | for (i = 0; i < info[k].n_mol; i++){ |
193 | stampID = info[k].molecules[i].getStampID(); | |
194 | ||
195 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
196 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
197 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
195 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
196 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
197 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
198 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
199 | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; | |
200 | < | |
200 | > | |
201 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
202 | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); | |
203 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
204 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
205 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
203 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
204 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
205 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
206 | ||
207 | theBonds = new bond_pair[molInfo.nBonds]; | |
208 | theBends = new bend_set[molInfo.nBends]; | |
209 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
210 | < | |
210 | > | |
211 | // make the Atoms | |
212 | < | |
213 | < | for(j=0; j<molInfo.nAtoms; j++){ |
214 | < | |
215 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
216 | < | if( currentAtom->haveOrientation() ){ |
217 | < | |
218 | < | dAtom = new DirectionalAtom( (j + atomOffset), |
219 | < | info[k].getConfiguration() ); |
220 | < | info[k].n_oriented++; |
221 | < | molInfo.myAtoms[j] = dAtom; |
222 | < | |
223 | < | ux = currentAtom->getOrntX(); |
224 | < | uy = currentAtom->getOrntY(); |
225 | < | uz = currentAtom->getOrntZ(); |
226 | < | |
227 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
228 | < | |
229 | < | u = sqrt( uSqr ); |
230 | < | ux = ux / u; |
231 | < | uy = uy / u; |
232 | < | uz = uz / u; |
233 | < | |
234 | < | dAtom->setSUx( ux ); |
235 | < | dAtom->setSUy( uy ); |
236 | < | dAtom->setSUz( uz ); |
237 | < | } |
238 | < | else{ |
239 | < | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
240 | < | info[k].getConfiguration() ); |
241 | < | } |
221 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
222 | < | |
212 | > | |
213 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
214 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
215 | > | if (currentAtom->haveOrientation()){ |
216 | > | dAtom = new DirectionalAtom((j + atomOffset), |
217 | > | info[k].getConfiguration()); |
218 | > | info[k].n_oriented++; |
219 | > | molInfo.myAtoms[j] = dAtom; |
220 | > | |
221 | > | ux = currentAtom->getOrntX(); |
222 | > | uy = currentAtom->getOrntY(); |
223 | > | uz = currentAtom->getOrntZ(); |
224 | > | |
225 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
226 | > | |
227 | > | u = sqrt(uSqr); |
228 | > | ux = ux / u; |
229 | > | uy = uy / u; |
230 | > | uz = uz / u; |
231 | > | |
232 | > | dAtom->setSUx(ux); |
233 | > | dAtom->setSUy(uy); |
234 | > | dAtom->setSUz(uz); |
235 | > | } |
236 | > | else{ |
237 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
238 | > | info[k].getConfiguration()); |
239 | > | } |
240 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
241 | > | |
242 | #ifdef IS_MPI | |
243 | < | |
244 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
245 | < | |
243 | > | |
244 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
245 | > | |
246 | #endif // is_mpi | |
247 | } | |
248 | < | |
249 | < | // make the bonds |
250 | < | for(j=0; j<molInfo.nBonds; j++){ |
251 | < | |
252 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
253 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
254 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
255 | < | |
256 | < | exI = theBonds[j].a; |
257 | < | exJ = theBonds[j].b; |
258 | < | |
259 | < | // exclude_I must always be the smaller of the pair |
260 | < | if( exI > exJ ){ |
261 | < | tempEx = exI; |
262 | < | exI = exJ; |
263 | < | exJ = tempEx; |
245 | < | } |
248 | > | |
249 | > | // make the bonds |
250 | > | for (j = 0; j < molInfo.nBonds; j++){ |
251 | > | currentBond = comp_stamps[stampID]->getBond(j); |
252 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
253 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
254 | > | |
255 | > | exI = theBonds[j].a; |
256 | > | exJ = theBonds[j].b; |
257 | > | |
258 | > | // exclude_I must always be the smaller of the pair |
259 | > | if (exI > exJ){ |
260 | > | tempEx = exI; |
261 | > | exI = exJ; |
262 | > | exJ = tempEx; |
263 | > | } |
264 | #ifdef IS_MPI | |
265 | < | tempEx = exI; |
266 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
267 | < | tempEx = exJ; |
268 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
269 | < | |
270 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
265 | > | tempEx = exI; |
266 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
267 | > | tempEx = exJ; |
268 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
269 | > | |
270 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
271 | #else // isn't MPI | |
272 | < | |
273 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
272 | > | |
273 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
274 | #endif //is_mpi | |
275 | } | |
276 | excludeOffset += molInfo.nBonds; | |
277 | < | |
277 | > | |
278 | //make the bends | |
279 | < | for(j=0; j<molInfo.nBends; j++){ |
280 | < | |
281 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
282 | < | theBends[j].a = currentBend->getA() + atomOffset; |
283 | < | theBends[j].b = currentBend->getB() + atomOffset; |
284 | < | theBends[j].c = currentBend->getC() + atomOffset; |
285 | < | |
286 | < | if( currentBend->haveExtras() ){ |
287 | < | |
288 | < | extras = currentBend->getExtras(); |
289 | < | current_extra = extras; |
290 | < | |
291 | < | while( current_extra != NULL ){ |
292 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
293 | < | |
294 | < | switch( current_extra->getType() ){ |
295 | < | |
296 | < | case 0: |
297 | < | theBends[j].ghost = |
298 | < | current_extra->getInt() + atomOffset; |
299 | < | theBends[j].isGhost = 1; |
300 | < | break; |
301 | < | |
302 | < | case 1: |
303 | < | theBends[j].ghost = |
304 | < | (int)current_extra->getDouble() + atomOffset; |
305 | < | theBends[j].isGhost = 1; |
306 | < | break; |
307 | < | |
308 | < | default: |
309 | < | sprintf( painCave.errMsg, |
310 | < | "SimSetup Error: ghostVectorSource was neither a " |
311 | < | "double nor an int.\n" |
312 | < | "-->Bend[%d] in %s\n", |
313 | < | j, comp_stamps[stampID]->getID() ); |
314 | < | painCave.isFatal = 1; |
315 | < | simError(); |
279 | > | for (j = 0; j < molInfo.nBends; j++){ |
280 | > | currentBend = comp_stamps[stampID]->getBend(j); |
281 | > | theBends[j].a = currentBend->getA() + atomOffset; |
282 | > | theBends[j].b = currentBend->getB() + atomOffset; |
283 | > | theBends[j].c = currentBend->getC() + atomOffset; |
284 | > | |
285 | > | if (currentBend->haveExtras()){ |
286 | > | extras = currentBend->getExtras(); |
287 | > | current_extra = extras; |
288 | > | |
289 | > | while (current_extra != NULL){ |
290 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
291 | > | switch (current_extra->getType()){ |
292 | > | case 0: |
293 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
294 | > | theBends[j].isGhost = 1; |
295 | > | break; |
296 | > | |
297 | > | case 1: |
298 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
299 | > | atomOffset; |
300 | > | theBends[j].isGhost = 1; |
301 | > | break; |
302 | > | |
303 | > | default: |
304 | > | sprintf(painCave.errMsg, |
305 | > | "SimSetup Error: ghostVectorSource was neither a " |
306 | > | "double nor an int.\n" |
307 | > | "-->Bend[%d] in %s\n", |
308 | > | j, comp_stamps[stampID]->getID()); |
309 | > | painCave.isFatal = 1; |
310 | > | simError(); |
311 | > | } |
312 | > | } |
313 | > | else{ |
314 | > | sprintf(painCave.errMsg, |
315 | > | "SimSetup Error: unhandled bend assignment:\n" |
316 | > | " -->%s in Bend[%d] in %s\n", |
317 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
318 | > | painCave.isFatal = 1; |
319 | > | simError(); |
320 | > | } |
321 | > | |
322 | > | current_extra = current_extra->getNext(); |
323 | > | } |
324 | } | |
325 | < | } |
326 | < | |
327 | < | else{ |
328 | < | |
329 | < | sprintf( painCave.errMsg, |
330 | < | "SimSetup Error: unhandled bend assignment:\n" |
331 | < | " -->%s in Bend[%d] in %s\n", |
332 | < | current_extra->getlhs(), |
333 | < | j, comp_stamps[stampID]->getID() ); |
334 | < | painCave.isFatal = 1; |
335 | < | simError(); |
336 | < | } |
337 | < | |
338 | < | current_extra = current_extra->getNext(); |
339 | < | } |
340 | < | } |
315 | < | |
316 | < | if( !theBends[j].isGhost ){ |
317 | < | |
318 | < | exI = theBends[j].a; |
319 | < | exJ = theBends[j].c; |
320 | < | } |
321 | < | else{ |
322 | < | |
323 | < | exI = theBends[j].a; |
324 | < | exJ = theBends[j].b; |
325 | < | } |
326 | < | |
327 | < | // exclude_I must always be the smaller of the pair |
328 | < | if( exI > exJ ){ |
329 | < | tempEx = exI; |
330 | < | exI = exJ; |
331 | < | exJ = tempEx; |
332 | < | } |
325 | > | |
326 | > | if (!theBends[j].isGhost){ |
327 | > | exI = theBends[j].a; |
328 | > | exJ = theBends[j].c; |
329 | > | } |
330 | > | else{ |
331 | > | exI = theBends[j].a; |
332 | > | exJ = theBends[j].b; |
333 | > | } |
334 | > | |
335 | > | // exclude_I must always be the smaller of the pair |
336 | > | if (exI > exJ){ |
337 | > | tempEx = exI; |
338 | > | exI = exJ; |
339 | > | exJ = tempEx; |
340 | > | } |
341 | #ifdef IS_MPI | |
342 | < | tempEx = exI; |
343 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
344 | < | tempEx = exJ; |
345 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
346 | < | |
347 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
342 | > | tempEx = exI; |
343 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
344 | > | tempEx = exJ; |
345 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
346 | > | |
347 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
348 | #else // isn't MPI | |
349 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
350 | #endif //is_mpi | |
351 | } | |
352 | excludeOffset += molInfo.nBends; | |
353 | < | |
354 | < | for(j=0; j<molInfo.nTorsions; j++){ |
355 | < | |
356 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
357 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
358 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
359 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
360 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
361 | < | |
362 | < | exI = theTorsions[j].a; |
363 | < | exJ = theTorsions[j].d; |
364 | < | |
365 | < | // exclude_I must always be the smaller of the pair |
366 | < | if( exI > exJ ){ |
367 | < | tempEx = exI; |
368 | < | exI = exJ; |
369 | < | exJ = tempEx; |
362 | < | } |
353 | > | |
354 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
355 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
356 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
357 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
358 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
359 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
360 | > | |
361 | > | exI = theTorsions[j].a; |
362 | > | exJ = theTorsions[j].d; |
363 | > | |
364 | > | // exclude_I must always be the smaller of the pair |
365 | > | if (exI > exJ){ |
366 | > | tempEx = exI; |
367 | > | exI = exJ; |
368 | > | exJ = tempEx; |
369 | > | } |
370 | #ifdef IS_MPI | |
371 | < | tempEx = exI; |
372 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
373 | < | tempEx = exJ; |
374 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 | < | |
376 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
371 | > | tempEx = exI; |
372 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
373 | > | tempEx = exJ; |
374 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 | > | |
376 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
377 | #else // isn't MPI | |
378 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
378 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
379 | #endif //is_mpi | |
380 | } | |
381 | excludeOffset += molInfo.nTorsions; | |
382 | < | |
383 | < | |
382 | > | |
383 | > | |
384 | // send the arrays off to the forceField for init. | |
378 | – | |
379 | – | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
380 | – | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
381 | – | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
382 | – | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
383 | – | |
384 | – | |
385 | – | info[k].molecules[i].initialize( molInfo ); |
385 | ||
386 | < | |
386 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
387 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
388 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
389 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
390 | > | theTorsions); |
391 | > | |
392 | > | |
393 | > | info[k].molecules[i].initialize(molInfo); |
394 | > | |
395 | > | |
396 | atomOffset += molInfo.nAtoms; | |
397 | delete[] theBonds; | |
398 | delete[] theBends; | |
399 | delete[] theTorsions; | |
400 | } | |
401 | } | |
402 | < | |
402 | > | |
403 | #ifdef IS_MPI | |
404 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
404 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
405 | MPIcheckPoint(); | |
406 | #endif // is_mpi | |
407 | < | |
407 | > | |
408 | // clean up the forcefield | |
409 | ||
410 | the_ff->calcRcut(); | |
411 | the_ff->cleanMe(); | |
404 | – | |
412 | } | |
413 | ||
414 | < | void SimSetup::initFromBass( void ){ |
408 | < | |
414 | > | void SimSetup::initFromBass(void){ |
415 | int i, j, k; | |
416 | int n_cells; | |
417 | double cellx, celly, cellz; | |
# | Line 419 | Line 425 | void SimSetup::initFromBass( void ){ | |
425 | vel[1] = 0.0; | |
426 | vel[2] = 0.0; | |
427 | ||
428 | < | temp1 = (double)tot_nmol / 4.0; |
429 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
430 | < | temp3 = ceil( temp2 ); |
428 | > | temp1 = (double) tot_nmol / 4.0; |
429 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
430 | > | temp3 = ceil(temp2); |
431 | ||
432 | < | have_extra =0; |
433 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
434 | < | have_extra =1; |
432 | > | have_extra = 0; |
433 | > | if (temp2 < temp3){ |
434 | > | // we have a non-complete lattice |
435 | > | have_extra = 1; |
436 | ||
437 | < | n_cells = (int)temp3 - 1; |
437 | > | n_cells = (int) temp3 - 1; |
438 | cellx = info[0].boxL[0] / temp3; | |
439 | celly = info[0].boxL[1] / temp3; | |
440 | cellz = info[0].boxL[2] / temp3; | |
441 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
442 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
443 | < | n_per_extra = (int)ceil( temp1 ); |
441 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
442 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
443 | > | n_per_extra = (int) ceil(temp1); |
444 | ||
445 | < | if( n_per_extra > 4){ |
446 | < | sprintf( painCave.errMsg, |
447 | < | "SimSetup error. There has been an error in constructing" |
448 | < | " the non-complete lattice.\n" ); |
445 | > | if (n_per_extra > 4){ |
446 | > | sprintf(painCave.errMsg, |
447 | > | "SimSetup error. There has been an error in constructing" |
448 | > | " the non-complete lattice.\n"); |
449 | painCave.isFatal = 1; | |
450 | simError(); | |
451 | } | |
452 | } | |
453 | else{ | |
454 | < | n_cells = (int)temp3; |
454 | > | n_cells = (int) temp3; |
455 | cellx = info[0].boxL[0] / temp3; | |
456 | celly = info[0].boxL[1] / temp3; | |
457 | cellz = info[0].boxL[2] / temp3; | |
# | Line 455 | Line 462 | void SimSetup::initFromBass( void ){ | |
462 | current_comp = 0; | |
463 | current_atom_ndx = 0; | |
464 | ||
465 | < | for( i=0; i < n_cells ; i++ ){ |
466 | < | for( j=0; j < n_cells; j++ ){ |
467 | < | for( k=0; k < n_cells; k++ ){ |
465 | > | for (i = 0; i < n_cells ; i++){ |
466 | > | for (j = 0; j < n_cells; j++){ |
467 | > | for (k = 0; k < n_cells; k++){ |
468 | > | makeElement(i * cellx, j * celly, k * cellz); |
469 | ||
470 | < | makeElement( i * cellx, |
463 | < | j * celly, |
464 | < | k * cellz ); |
470 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
471 | ||
472 | < | makeElement( i * cellx + 0.5 * cellx, |
467 | < | j * celly + 0.5 * celly, |
468 | < | k * cellz ); |
472 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
473 | ||
474 | < | makeElement( i * cellx, |
471 | < | j * celly + 0.5 * celly, |
472 | < | k * cellz + 0.5 * cellz ); |
473 | < | |
474 | < | makeElement( i * cellx + 0.5 * cellx, |
475 | < | j * celly, |
476 | < | k * cellz + 0.5 * cellz ); |
474 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
475 | } | |
476 | } | |
477 | } | |
478 | ||
479 | < | if( have_extra ){ |
479 | > | if (have_extra){ |
480 | done = 0; | |
481 | ||
482 | int start_ndx; | |
483 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
484 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
485 | < | |
486 | < | if( i < n_cells ){ |
487 | < | |
488 | < | if( j < n_cells ){ |
489 | < | start_ndx = n_cells; |
490 | < | } |
491 | < | else start_ndx = 0; |
492 | < | } |
493 | < | else start_ndx = 0; |
483 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
484 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
485 | > | if (i < n_cells){ |
486 | > | if (j < n_cells){ |
487 | > | start_ndx = n_cells; |
488 | > | } |
489 | > | else |
490 | > | start_ndx = 0; |
491 | > | } |
492 | > | else |
493 | > | start_ndx = 0; |
494 | ||
495 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
495 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
496 | > | makeElement(i * cellx, j * celly, k * cellz); |
497 | > | done = (current_mol >= tot_nmol); |
498 | ||
499 | < | makeElement( i * cellx, |
500 | < | j * celly, |
501 | < | k * cellz ); |
502 | < | done = ( current_mol >= tot_nmol ); |
499 | > | if (!done && n_per_extra > 1){ |
500 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
501 | > | k * cellz); |
502 | > | done = (current_mol >= tot_nmol); |
503 | > | } |
504 | ||
505 | < | if( !done && n_per_extra > 1 ){ |
506 | < | makeElement( i * cellx + 0.5 * cellx, |
507 | < | j * celly + 0.5 * celly, |
508 | < | k * cellz ); |
509 | < | done = ( current_mol >= tot_nmol ); |
509 | < | } |
505 | > | if (!done && n_per_extra > 2){ |
506 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
507 | > | k * cellz + 0.5 * cellz); |
508 | > | done = (current_mol >= tot_nmol); |
509 | > | } |
510 | ||
511 | < | if( !done && n_per_extra > 2){ |
512 | < | makeElement( i * cellx, |
513 | < | j * celly + 0.5 * celly, |
514 | < | k * cellz + 0.5 * cellz ); |
515 | < | done = ( current_mol >= tot_nmol ); |
516 | < | } |
517 | < | |
518 | < | if( !done && n_per_extra > 3){ |
519 | < | makeElement( i * cellx + 0.5 * cellx, |
520 | < | j * celly, |
521 | < | k * cellz + 0.5 * cellz ); |
522 | < | done = ( current_mol >= tot_nmol ); |
523 | < | } |
524 | < | } |
511 | > | if (!done && n_per_extra > 3){ |
512 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
513 | > | k * cellz + 0.5 * cellz); |
514 | > | done = (current_mol >= tot_nmol); |
515 | > | } |
516 | > | } |
517 | } | |
518 | } | |
519 | } | |
520 | ||
521 | < | for( i=0; i<info[0].n_atoms; i++ ){ |
522 | < | info[0].atoms[i]->setVel( vel ); |
521 | > | for (i = 0; i < info[0].n_atoms; i++){ |
522 | > | info[0].atoms[i]->setVel(vel); |
523 | } | |
524 | } | |
525 | ||
526 | < | void SimSetup::makeElement( double x, double y, double z ){ |
535 | < | |
526 | > | void SimSetup::makeElement(double x, double y, double z){ |
527 | int k; | |
528 | AtomStamp* current_atom; | |
529 | DirectionalAtom* dAtom; | |
530 | double rotMat[3][3]; | |
531 | double pos[3]; | |
532 | ||
533 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
534 | < | |
535 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
536 | < | if( !current_atom->havePosition() ){ |
537 | < | sprintf( painCave.errMsg, |
538 | < | "SimSetup:initFromBass error.\n" |
539 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
540 | < | "\tThe initialization routine is unable to give a start" |
541 | < | " position.\n", |
551 | < | comp_stamps[current_comp]->getID(), |
552 | < | current_atom->getType() ); |
533 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
534 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
535 | > | if (!current_atom->havePosition()){ |
536 | > | sprintf(painCave.errMsg, |
537 | > | "SimSetup:initFromBass error.\n" |
538 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
539 | > | "\tThe initialization routine is unable to give a start" |
540 | > | " position.\n", |
541 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
542 | painCave.isFatal = 1; | |
543 | simError(); | |
544 | } | |
545 | < | |
545 | > | |
546 | pos[0] = x + current_atom->getPosX(); | |
547 | pos[1] = y + current_atom->getPosY(); | |
548 | pos[2] = z + current_atom->getPosZ(); | |
560 | – | |
561 | – | info[0].atoms[current_atom_ndx]->setPos( pos ); |
549 | ||
550 | < | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
550 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
551 | ||
552 | < | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
552 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
553 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
554 | ||
555 | rotMat[0][0] = 1.0; | |
556 | rotMat[0][1] = 0.0; | |
# | Line 576 | Line 564 | void SimSetup::makeElement( double x, double y, double | |
564 | rotMat[2][1] = 0.0; | |
565 | rotMat[2][2] = 1.0; | |
566 | ||
567 | < | dAtom->setA( rotMat ); |
567 | > | dAtom->setA(rotMat); |
568 | } | |
569 | ||
570 | current_atom_ndx++; | |
# | Line 585 | Line 573 | void SimSetup::makeElement( double x, double y, double | |
573 | current_mol++; | |
574 | current_comp_mol++; | |
575 | ||
576 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
589 | < | |
576 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
577 | current_comp_mol = 0; | |
578 | current_comp++; | |
579 | } | |
580 | } | |
581 | ||
582 | ||
583 | < | void SimSetup::gatherInfo( void ){ |
584 | < | int i,j,k; |
583 | > | void SimSetup::gatherInfo(void){ |
584 | > | int i; |
585 | ||
586 | ensembleCase = -1; | |
587 | ffCase = -1; | |
588 | ||
589 | // set the easy ones first | |
590 | ||
591 | < | for( i=0; i<nInfo; i++){ |
591 | > | for (i = 0; i < nInfo; i++){ |
592 | info[i].target_temp = globals->getTargetTemp(); | |
593 | info[i].dt = globals->getDt(); | |
594 | info[i].run_time = globals->getRunTime(); | |
# | Line 611 | Line 598 | void SimSetup::gatherInfo( void ){ | |
598 | ||
599 | // get the forceField | |
600 | ||
601 | < | strcpy( force_field, globals->getForceField() ); |
601 | > | strcpy(force_field, globals->getForceField()); |
602 | ||
603 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
604 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
605 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
603 | > | if (!strcasecmp(force_field, "DUFF")){ |
604 | > | ffCase = FF_DUFF; |
605 | > | } |
606 | > | else if (!strcasecmp(force_field, "LJ")){ |
607 | > | ffCase = FF_LJ; |
608 | > | } |
609 | > | else if (!strcasecmp(force_field, "EAM")){ |
610 | > | ffCase = FF_EAM; |
611 | > | } |
612 | else{ | |
613 | < | sprintf( painCave.errMsg, |
614 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
615 | < | force_field ); |
616 | < | painCave.isFatal = 1; |
624 | < | simError(); |
613 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
614 | > | force_field); |
615 | > | painCave.isFatal = 1; |
616 | > | simError(); |
617 | } | |
618 | ||
619 | < | // get the ensemble |
619 | > | // get the ensemble |
620 | ||
621 | < | strcpy( ensemble, globals->getEnsemble() ); |
621 | > | strcpy(ensemble, globals->getEnsemble()); |
622 | ||
623 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
624 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
625 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
623 | > | if (!strcasecmp(ensemble, "NVE")){ |
624 | > | ensembleCase = NVE_ENS; |
625 | > | } |
626 | > | else if (!strcasecmp(ensemble, "NVT")){ |
627 | > | ensembleCase = NVT_ENS; |
628 | > | } |
629 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
630 | ensembleCase = NPTi_ENS; | |
631 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
632 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
633 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
631 | > | } |
632 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
633 | > | ensembleCase = NPTf_ENS; |
634 | > | } |
635 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
636 | > | ensembleCase = NPTxyz_ENS; |
637 | > | } |
638 | else{ | |
639 | < | sprintf( painCave.errMsg, |
640 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
641 | < | "reverting to NVE for this simulation.\n", |
642 | < | ensemble ); |
643 | < | painCave.isFatal = 0; |
644 | < | simError(); |
645 | < | strcpy( ensemble, "NVE" ); |
646 | < | ensembleCase = NVE_ENS; |
639 | > | sprintf(painCave.errMsg, |
640 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
641 | > | "\treverting to NVE for this simulation.\n", |
642 | > | ensemble); |
643 | > | painCave.isFatal = 0; |
644 | > | simError(); |
645 | > | strcpy(ensemble, "NVE"); |
646 | > | ensembleCase = NVE_ENS; |
647 | } | |
648 | – | |
649 | – | for(i=0; i<nInfo; i++){ |
650 | – | |
651 | – | strcpy( info[i].ensemble, ensemble ); |
648 | ||
649 | + | for (i = 0; i < nInfo; i++){ |
650 | + | strcpy(info[i].ensemble, ensemble); |
651 | + | |
652 | // get the mixing rule | |
653 | ||
654 | < | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
654 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
655 | info[i].usePBC = globals->getPBC(); | |
656 | } | |
657 | < | |
657 | > | |
658 | // get the components and calculate the tot_nMol and indvidual n_mol | |
659 | < | |
659 | > | |
660 | the_components = globals->getComponents(); | |
661 | components_nmol = new int[n_components]; | |
662 | ||
663 | ||
664 | < | if( !globals->haveNMol() ){ |
664 | > | if (!globals->haveNMol()){ |
665 | // we don't have the total number of molecules, so we assume it is | |
666 | // given in each component | |
667 | ||
668 | tot_nmol = 0; | |
669 | < | for( i=0; i<n_components; i++ ){ |
670 | < | |
671 | < | if( !the_components[i]->haveNMol() ){ |
672 | < | // we have a problem |
673 | < | sprintf( painCave.errMsg, |
674 | < | "SimSetup Error. No global NMol or component NMol" |
675 | < | " given. Cannot calculate the number of atoms.\n" ); |
676 | < | painCave.isFatal = 1; |
678 | < | simError(); |
669 | > | for (i = 0; i < n_components; i++){ |
670 | > | if (!the_components[i]->haveNMol()){ |
671 | > | // we have a problem |
672 | > | sprintf(painCave.errMsg, |
673 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
674 | > | "\tCannot calculate the number of atoms.\n"); |
675 | > | painCave.isFatal = 1; |
676 | > | simError(); |
677 | } | |
678 | ||
679 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 683 | Line 681 | void SimSetup::gatherInfo( void ){ | |
681 | } | |
682 | } | |
683 | else{ | |
684 | < | sprintf( painCave.errMsg, |
685 | < | "SimSetup error.\n" |
686 | < | "\tSorry, the ability to specify total" |
687 | < | " nMols and then give molfractions in the components\n" |
688 | < | "\tis not currently supported." |
689 | < | " Please give nMol in the components.\n" ); |
684 | > | sprintf(painCave.errMsg, |
685 | > | "SimSetup error.\n" |
686 | > | "\tSorry, the ability to specify total" |
687 | > | " nMols and then give molfractions in the components\n" |
688 | > | "\tis not currently supported." |
689 | > | " Please give nMol in the components.\n"); |
690 | painCave.isFatal = 1; | |
691 | simError(); | |
692 | } | |
693 | ||
694 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
695 | + | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
696 | + | sprintf(painCave.errMsg, |
697 | + | "Sample time is not divisible by dt.\n" |
698 | + | "\tThis will result in samples that are not uniformly\n" |
699 | + | "\tdistributed in time. If this is a problem, change\n" |
700 | + | "\tyour sampleTime variable.\n"); |
701 | + | painCave.isFatal = 0; |
702 | + | simError(); |
703 | + | } |
704 | + | |
705 | + | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
706 | + | sprintf(painCave.errMsg, |
707 | + | "Status time is not divisible by dt.\n" |
708 | + | "\tThis will result in status reports that are not uniformly\n" |
709 | + | "\tdistributed in time. If this is a problem, change \n" |
710 | + | "\tyour statusTime variable.\n"); |
711 | + | painCave.isFatal = 0; |
712 | + | simError(); |
713 | + | } |
714 | + | |
715 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
716 | + | sprintf(painCave.errMsg, |
717 | + | "Thermal time is not divisible by dt.\n" |
718 | + | "\tThis will result in thermalizations that are not uniformly\n" |
719 | + | "\tdistributed in time. If this is a problem, change \n" |
720 | + | "\tyour thermalTime variable.\n"); |
721 | + | painCave.isFatal = 0; |
722 | + | simError(); |
723 | + | } |
724 | + | |
725 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
726 | + | sprintf(painCave.errMsg, |
727 | + | "Reset time is not divisible by dt.\n" |
728 | + | "\tThis will result in integrator resets that are not uniformly\n" |
729 | + | "\tdistributed in time. If this is a problem, change\n" |
730 | + | "\tyour resetTime variable.\n"); |
731 | + | painCave.isFatal = 0; |
732 | + | simError(); |
733 | + | } |
734 | + | |
735 | // set the status, sample, and thermal kick times | |
697 | – | |
698 | – | for(i=0; i<nInfo; i++){ |
736 | ||
737 | < | if( globals->haveSampleTime() ){ |
737 | > | for (i = 0; i < nInfo; i++){ |
738 | > | if (globals->haveSampleTime()){ |
739 | info[i].sampleTime = globals->getSampleTime(); | |
740 | info[i].statusTime = info[i].sampleTime; | |
741 | info[i].thermalTime = info[i].sampleTime; | |
# | Line 707 | Line 745 | void SimSetup::gatherInfo( void ){ | |
745 | info[i].statusTime = info[i].sampleTime; | |
746 | info[i].thermalTime = info[i].sampleTime; | |
747 | } | |
748 | < | |
749 | < | if( globals->haveStatusTime() ){ |
748 | > | |
749 | > | if (globals->haveStatusTime()){ |
750 | info[i].statusTime = globals->getStatusTime(); | |
751 | } | |
752 | < | |
753 | < | if( globals->haveThermalTime() ){ |
752 | > | |
753 | > | if (globals->haveThermalTime()){ |
754 | info[i].thermalTime = globals->getThermalTime(); | |
755 | } | |
756 | ||
757 | + | info[i].resetIntegrator = 0; |
758 | + | if( globals->haveResetTime() ){ |
759 | + | info[i].resetTime = globals->getResetTime(); |
760 | + | info[i].resetIntegrator = 1; |
761 | + | } |
762 | + | |
763 | // check for the temperature set flag | |
764 | + | |
765 | + | if (globals->haveTempSet()) |
766 | + | info[i].setTemp = globals->getTempSet(); |
767 | ||
768 | < | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
768 | > | // check for the extended State init |
769 | > | |
770 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
771 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
772 | ||
723 | – | // get some of the tricky things that may still be in the globals |
724 | – | |
725 | – | double boxVector[3]; |
726 | – | if( globals->haveBox() ){ |
727 | – | boxVector[0] = globals->getBox(); |
728 | – | boxVector[1] = globals->getBox(); |
729 | – | boxVector[2] = globals->getBox(); |
730 | – | |
731 | – | info[i].setBox( boxVector ); |
732 | – | } |
733 | – | else if( globals->haveDensity() ){ |
734 | – | |
735 | – | double vol; |
736 | – | vol = (double)tot_nmol / globals->getDensity(); |
737 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
738 | – | boxVector[1] = boxVector[0]; |
739 | – | boxVector[2] = boxVector[0]; |
740 | – | |
741 | – | info[i].setBox( boxVector ); |
773 | } | |
774 | < | else{ |
775 | < | if( !globals->haveBoxX() ){ |
745 | < | sprintf( painCave.errMsg, |
746 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
747 | < | painCave.isFatal = 1; |
748 | < | simError(); |
749 | < | } |
750 | < | boxVector[0] = globals->getBoxX(); |
751 | < | |
752 | < | if( !globals->haveBoxY() ){ |
753 | < | sprintf( painCave.errMsg, |
754 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
755 | < | painCave.isFatal = 1; |
756 | < | simError(); |
757 | < | } |
758 | < | boxVector[1] = globals->getBoxY(); |
759 | < | |
760 | < | if( !globals->haveBoxZ() ){ |
761 | < | sprintf( painCave.errMsg, |
762 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
763 | < | painCave.isFatal = 1; |
764 | < | simError(); |
765 | < | } |
766 | < | boxVector[2] = globals->getBoxZ(); |
767 | < | |
768 | < | info[i].setBox( boxVector ); |
769 | < | } |
770 | < | } |
771 | < | |
774 | > | |
775 | > | //setup seed for random number generator |
776 | int seedValue; | |
773 | – | struct timeval now_time_val; |
774 | – | struct timezone time_zone; |
777 | ||
778 | < | if(globals->haveSeed()){ |
778 | > | if (globals->haveSeed()){ |
779 | seedValue = globals->getSeed(); | |
780 | < | } |
780 | > | |
781 | > | if(seedValue / 1E9 == 0){ |
782 | > | sprintf(painCave.errMsg, |
783 | > | "Seed for sprng library should contain at least 9 digits\n" |
784 | > | "OOPSE will generate a seed for user\n"); |
785 | > | painCave.isFatal = 0; |
786 | > | simError(); |
787 | > | |
788 | > | //using seed generated by system instead of invalid seed set by user |
789 | > | #ifndef IS_MPI |
790 | > | seedValue = make_sprng_seed(); |
791 | > | #else |
792 | > | if (worldRank == 0){ |
793 | > | seedValue = make_sprng_seed(); |
794 | > | } |
795 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
796 | > | #endif |
797 | > | } |
798 | > | }//end of if branch of globals->haveSeed() |
799 | else{ | |
800 | + | |
801 | #ifndef IS_MPI | |
802 | < | gettimeofday(&now_time_val, &time_zone); // get the time now |
782 | < | seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
802 | > | seedValue = make_sprng_seed(); |
803 | #else | |
804 | < | if(worldRank == 0){ |
805 | < | gettimeofday(&now_time_val, &time_zone); // get the time now |
786 | < | seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
804 | > | if (worldRank == 0){ |
805 | > | seedValue = make_sprng_seed(); |
806 | } | |
807 | < | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
807 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
808 | #endif | |
809 | < | } |
809 | > | }//end of globals->haveSeed() |
810 | ||
811 | < | for(int i = 0; i < nInfo; i++){ |
811 | > | for (int i = 0; i < nInfo; i++){ |
812 | info[i].setSeed(seedValue); | |
813 | } | |
814 | ||
815 | #ifdef IS_MPI | |
816 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
816 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
817 | MPIcheckPoint(); | |
818 | #endif // is_mpi | |
800 | – | |
819 | } | |
820 | ||
821 | ||
822 | < | void SimSetup::finalInfoCheck( void ){ |
822 | > | void SimSetup::finalInfoCheck(void){ |
823 | int index; | |
824 | int usesDipoles; | |
825 | int i; | |
826 | ||
827 | < | for(i=0; i<nInfo; i++){ |
827 | > | for (i = 0; i < nInfo; i++){ |
828 | // check electrostatic parameters | |
829 | < | |
829 | > | |
830 | index = 0; | |
831 | usesDipoles = 0; | |
832 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
832 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
833 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
834 | index++; | |
835 | } | |
836 | < | |
836 | > | |
837 | #ifdef IS_MPI | |
838 | int myUse = usesDipoles; | |
839 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
839 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
840 | #endif //is_mpi | |
841 | < | |
841 | > | |
842 | double theEcr, theEst; | |
843 | < | |
844 | < | if (globals->getUseRF() ) { |
843 | > | |
844 | > | if (globals->getUseRF()){ |
845 | info[i].useReactionField = 1; | |
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; |
837 | < | smallest = info[i].boxL[0]; |
838 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
839 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
840 | < | theEcr = 0.5 * smallest; |
841 | < | } else { |
842 | < | theEcr = globals->getECR(); |
846 | > | |
847 | > | if (!globals->haveECR()){ |
848 | > | sprintf(painCave.errMsg, |
849 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
850 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
851 | > | "\tfor the electrostaticCutoffRadius.\n"); |
852 | > | painCave.isFatal = 0; |
853 | > | simError(); |
854 | > | theEcr = 15.0; |
855 | } | |
856 | < | |
857 | < | if( !globals->haveEST() ){ |
846 | < | sprintf( painCave.errMsg, |
847 | < | "SimSetup Warning: using default value of 0.05 * the " |
848 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
849 | < | ); |
850 | < | painCave.isFatal = 0; |
851 | < | simError(); |
852 | < | theEst = 0.05 * theEcr; |
853 | < | } else { |
854 | < | theEst= globals->getEST(); |
856 | > | else{ |
857 | > | theEcr = globals->getECR(); |
858 | } | |
856 | – | |
857 | – | info[i].setEcr( theEcr, theEst ); |
858 | – | |
859 | – | if(!globals->haveDielectric() ){ |
860 | – | sprintf( painCave.errMsg, |
861 | – | "SimSetup Error: You are trying to use Reaction Field without" |
862 | – | "setting a dielectric constant!\n" |
863 | – | ); |
864 | – | painCave.isFatal = 1; |
865 | – | simError(); |
866 | – | } |
867 | – | info[i].dielectric = globals->getDielectric(); |
868 | – | } |
869 | – | else { |
870 | – | if (usesDipoles) { |
871 | – | |
872 | – | if( !globals->haveECR() ){ |
873 | – | sprintf( painCave.errMsg, |
874 | – | "SimSetup Warning: using default value of 1/2 the smallest " |
875 | – | "box length for the electrostaticCutoffRadius.\n" |
876 | – | "I hope you have a very fast processor!\n"); |
877 | – | painCave.isFatal = 0; |
878 | – | simError(); |
879 | – | double smallest; |
880 | – | smallest = info[i].boxL[0]; |
881 | – | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
882 | – | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
883 | – | theEcr = 0.5 * smallest; |
884 | – | } else { |
885 | – | theEcr = globals->getECR(); |
886 | – | } |
887 | – | |
888 | – | if( !globals->haveEST() ){ |
889 | – | sprintf( painCave.errMsg, |
890 | – | "SimSetup Warning: using default value of 0.05 * the " |
891 | – | "electrostaticCutoffRadius for the " |
892 | – | "electrostaticSkinThickness\n" |
893 | – | ); |
894 | – | painCave.isFatal = 0; |
895 | – | simError(); |
896 | – | theEst = 0.05 * theEcr; |
897 | – | } else { |
898 | – | theEst= globals->getEST(); |
899 | – | } |
900 | – | |
901 | – | info[i].setEcr( theEcr, theEst ); |
902 | – | } |
903 | – | } |
904 | – | } |
859 | ||
860 | < | #ifdef IS_MPI |
861 | < | strcpy( checkPointMsg, "post processing checks out" ); |
862 | < | MPIcheckPoint(); |
863 | < | #endif // is_mpi |
864 | < | |
865 | < | } |
860 | > | if (!globals->haveEST()){ |
861 | > | sprintf(painCave.errMsg, |
862 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
863 | > | "\tOOPSE will use a default value of\n" |
864 | > | "\t0.05 * electrostaticCutoffRadius\n" |
865 | > | "\tfor the electrostaticSkinThickness\n"); |
866 | > | painCave.isFatal = 0; |
867 | > | simError(); |
868 | > | theEst = 0.05 * theEcr; |
869 | > | } |
870 | > | else{ |
871 | > | theEst = globals->getEST(); |
872 | > | } |
873 | ||
874 | < | void SimSetup::initSystemCoords( void ){ |
875 | < | int i; |
874 | > | info[i].setDefaultEcr(theEcr, theEst); |
875 | > | |
876 | > | if (!globals->haveDielectric()){ |
877 | > | sprintf(painCave.errMsg, |
878 | > | "SimSetup Error: No Dielectric constant was set.\n" |
879 | > | "\tYou are trying to use Reaction Field without" |
880 | > | "\tsetting a dielectric constant!\n"); |
881 | > | painCave.isFatal = 1; |
882 | > | simError(); |
883 | > | } |
884 | > | info[i].dielectric = globals->getDielectric(); |
885 | > | } |
886 | > | else{ |
887 | > | if (usesDipoles){ |
888 | > | if (!globals->haveECR()){ |
889 | > | sprintf(painCave.errMsg, |
890 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
891 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
892 | > | "\tfor the electrostaticCutoffRadius.\n"); |
893 | > | painCave.isFatal = 0; |
894 | > | simError(); |
895 | > | theEcr = 15.0; |
896 | > | } |
897 | > | else{ |
898 | > | theEcr = globals->getECR(); |
899 | > | } |
900 | > | |
901 | > | if (!globals->haveEST()){ |
902 | > | sprintf(painCave.errMsg, |
903 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
904 | > | "\tOOPSE will use a default value of\n" |
905 | > | "\t0.05 * electrostaticCutoffRadius\n" |
906 | > | "\tfor the electrostaticSkinThickness\n"); |
907 | > | painCave.isFatal = 0; |
908 | > | simError(); |
909 | > | theEst = 0.05 * theEcr; |
910 | > | } |
911 | > | else{ |
912 | > | theEst = globals->getEST(); |
913 | > | } |
914 | > | |
915 | > | info[i].setDefaultEcr(theEcr, theEst); |
916 | > | } |
917 | > | } |
918 | > | } |
919 | > | #ifdef IS_MPI |
920 | > | strcpy(checkPointMsg, "post processing checks out"); |
921 | > | MPIcheckPoint(); |
922 | > | #endif // is_mpi |
923 | > | } |
924 | ||
925 | + | void SimSetup::initSystemCoords(void){ |
926 | + | int i; |
927 | + | |
928 | char* inName; | |
929 | ||
930 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
930 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
931 | ||
932 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
933 | < | |
934 | < | if( globals->haveInitialConfig() ){ |
935 | < | |
932 | > | for (i = 0; i < info[0].n_atoms; i++) |
933 | > | info[0].atoms[i]->setCoords(); |
934 | > | |
935 | > | if (globals->haveInitialConfig()){ |
936 | InitializeFromFile* fileInit; | |
937 | #ifdef IS_MPI // is_mpi | |
938 | < | if( worldRank == 0 ){ |
938 | > | if (worldRank == 0){ |
939 | #endif //is_mpi | |
940 | inName = globals->getInitialConfig(); | |
941 | < | double* tempDouble = new double[1000000]; |
930 | < | fileInit = new InitializeFromFile( inName ); |
941 | > | fileInit = new InitializeFromFile(inName); |
942 | #ifdef IS_MPI | |
943 | < | }else fileInit = new InitializeFromFile( NULL ); |
943 | > | } |
944 | > | else |
945 | > | fileInit = new InitializeFromFile(NULL); |
946 | #endif | |
947 | < | fileInit->readInit( info ); // default velocities on |
948 | < | |
947 | > | fileInit->readInit(info); // default velocities on |
948 | > | |
949 | delete fileInit; | |
950 | } | |
951 | else{ | |
952 | ||
940 | – | #ifdef IS_MPI |
941 | – | |
953 | // no init from bass | |
954 | ||
955 | < | sprintf( painCave.errMsg, |
956 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
957 | < | painCave.isFatal; |
955 | > | sprintf(painCave.errMsg, |
956 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
957 | > | painCave.isFatal = 1;; |
958 | simError(); | |
959 | ||
949 | – | #else |
950 | – | |
951 | – | initFromBass(); |
952 | – | |
953 | – | |
954 | – | #endif |
960 | } | |
961 | < | |
961 | > | |
962 | #ifdef IS_MPI | |
963 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
963 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
964 | MPIcheckPoint(); | |
965 | #endif // is_mpi | |
961 | – | |
966 | } | |
967 | ||
968 | ||
969 | < | void SimSetup::makeOutNames( void ){ |
966 | < | |
969 | > | void SimSetup::makeOutNames(void){ |
970 | int k; | |
971 | ||
969 | – | |
970 | – | for(k=0; k<nInfo; k++){ |
972 | ||
973 | + | for (k = 0; k < nInfo; k++){ |
974 | #ifdef IS_MPI | |
975 | < | if( worldRank == 0 ){ |
975 | > | if (worldRank == 0){ |
976 | #endif // is_mpi | |
977 | < | |
978 | < | if( globals->haveFinalConfig() ){ |
979 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
977 | > | |
978 | > | if (globals->haveFinalConfig()){ |
979 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
980 | } | |
981 | else{ | |
982 | < | strcpy( info[k].finalName, inFileName ); |
983 | < | char* endTest; |
984 | < | int nameLength = strlen( info[k].finalName ); |
985 | < | endTest = &(info[k].finalName[nameLength - 5]); |
986 | < | if( !strcmp( endTest, ".bass" ) ){ |
987 | < | strcpy( endTest, ".eor" ); |
988 | < | } |
989 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
990 | < | strcpy( endTest, ".eor" ); |
991 | < | } |
992 | < | else{ |
993 | < | endTest = &(info[k].finalName[nameLength - 4]); |
994 | < | if( !strcmp( endTest, ".bss" ) ){ |
995 | < | strcpy( endTest, ".eor" ); |
996 | < | } |
997 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
998 | < | strcpy( endTest, ".eor" ); |
999 | < | } |
1000 | < | else{ |
1001 | < | strcat( info[k].finalName, ".eor" ); |
1002 | < | } |
1003 | < | } |
982 | > | strcpy(info[k].finalName, inFileName); |
983 | > | char* endTest; |
984 | > | int nameLength = strlen(info[k].finalName); |
985 | > | endTest = &(info[k].finalName[nameLength - 5]); |
986 | > | if (!strcmp(endTest, ".bass")){ |
987 | > | strcpy(endTest, ".eor"); |
988 | > | } |
989 | > | else if (!strcmp(endTest, ".BASS")){ |
990 | > | strcpy(endTest, ".eor"); |
991 | > | } |
992 | > | else{ |
993 | > | endTest = &(info[k].finalName[nameLength - 4]); |
994 | > | if (!strcmp(endTest, ".bss")){ |
995 | > | strcpy(endTest, ".eor"); |
996 | > | } |
997 | > | else if (!strcmp(endTest, ".mdl")){ |
998 | > | strcpy(endTest, ".eor"); |
999 | > | } |
1000 | > | else{ |
1001 | > | strcat(info[k].finalName, ".eor"); |
1002 | > | } |
1003 | > | } |
1004 | } | |
1005 | < | |
1005 | > | |
1006 | // make the sample and status out names | |
1007 | < | |
1008 | < | strcpy( info[k].sampleName, inFileName ); |
1007 | > | |
1008 | > | strcpy(info[k].sampleName, inFileName); |
1009 | char* endTest; | |
1010 | < | int nameLength = strlen( info[k].sampleName ); |
1010 | > | int nameLength = strlen(info[k].sampleName); |
1011 | endTest = &(info[k].sampleName[nameLength - 5]); | |
1012 | < | if( !strcmp( endTest, ".bass" ) ){ |
1013 | < | strcpy( endTest, ".dump" ); |
1012 | > | if (!strcmp(endTest, ".bass")){ |
1013 | > | strcpy(endTest, ".dump"); |
1014 | } | |
1015 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1016 | < | strcpy( endTest, ".dump" ); |
1015 | > | else if (!strcmp(endTest, ".BASS")){ |
1016 | > | strcpy(endTest, ".dump"); |
1017 | } | |
1018 | else{ | |
1019 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1020 | < | if( !strcmp( endTest, ".bss" ) ){ |
1021 | < | strcpy( endTest, ".dump" ); |
1022 | < | } |
1023 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1024 | < | strcpy( endTest, ".dump" ); |
1025 | < | } |
1026 | < | else{ |
1027 | < | strcat( info[k].sampleName, ".dump" ); |
1028 | < | } |
1019 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1020 | > | if (!strcmp(endTest, ".bss")){ |
1021 | > | strcpy(endTest, ".dump"); |
1022 | > | } |
1023 | > | else if (!strcmp(endTest, ".mdl")){ |
1024 | > | strcpy(endTest, ".dump"); |
1025 | > | } |
1026 | > | else{ |
1027 | > | strcat(info[k].sampleName, ".dump"); |
1028 | > | } |
1029 | } | |
1030 | < | |
1031 | < | strcpy( info[k].statusName, inFileName ); |
1032 | < | nameLength = strlen( info[k].statusName ); |
1030 | > | |
1031 | > | strcpy(info[k].statusName, inFileName); |
1032 | > | nameLength = strlen(info[k].statusName); |
1033 | endTest = &(info[k].statusName[nameLength - 5]); | |
1034 | < | if( !strcmp( endTest, ".bass" ) ){ |
1035 | < | strcpy( endTest, ".stat" ); |
1034 | > | if (!strcmp(endTest, ".bass")){ |
1035 | > | strcpy(endTest, ".stat"); |
1036 | } | |
1037 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1038 | < | strcpy( endTest, ".stat" ); |
1037 | > | else if (!strcmp(endTest, ".BASS")){ |
1038 | > | strcpy(endTest, ".stat"); |
1039 | } | |
1040 | else{ | |
1041 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1042 | < | if( !strcmp( endTest, ".bss" ) ){ |
1043 | < | strcpy( endTest, ".stat" ); |
1044 | < | } |
1045 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1046 | < | strcpy( endTest, ".stat" ); |
1047 | < | } |
1048 | < | else{ |
1049 | < | strcat( info[k].statusName, ".stat" ); |
1050 | < | } |
1041 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1042 | > | if (!strcmp(endTest, ".bss")){ |
1043 | > | strcpy(endTest, ".stat"); |
1044 | > | } |
1045 | > | else if (!strcmp(endTest, ".mdl")){ |
1046 | > | strcpy(endTest, ".stat"); |
1047 | > | } |
1048 | > | else{ |
1049 | > | strcat(info[k].statusName, ".stat"); |
1050 | > | } |
1051 | } | |
1052 | < | |
1052 | > | |
1053 | #ifdef IS_MPI | |
1054 | + | |
1055 | } | |
1056 | #endif // is_mpi | |
1057 | } | |
1058 | } | |
1059 | ||
1060 | ||
1061 | < | void SimSetup::sysObjectsCreation( void ){ |
1062 | < | |
1063 | < | int i,k; |
1061 | < | |
1061 | > | void SimSetup::sysObjectsCreation(void){ |
1062 | > | int i, k; |
1063 | > | |
1064 | // create the forceField | |
1065 | ||
1066 | createFF(); | |
# | Line 1073 | Line 1075 | void SimSetup::sysObjectsCreation( void ){ | |
1075 | ||
1076 | #ifdef IS_MPI | |
1077 | // divide the molecules among the processors | |
1078 | < | |
1078 | > | |
1079 | mpiMolDivide(); | |
1080 | #endif //is_mpi | |
1081 | < | |
1081 | > | |
1082 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1083 | < | |
1083 | > | |
1084 | makeSysArrays(); | |
1085 | ||
1086 | // make and initialize the molecules (all but atomic coordinates) | |
1087 | < | |
1087 | > | |
1088 | makeMolecules(); | |
1089 | < | |
1090 | < | for(k=0; k<nInfo; k++){ |
1089 | > | |
1090 | > | for (k = 0; k < nInfo; k++){ |
1091 | info[k].identArray = new int[info[k].n_atoms]; | |
1092 | < | for(i=0; i<info[k].n_atoms; i++){ |
1092 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1093 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1094 | } | |
1095 | } | |
1096 | } | |
1097 | ||
1098 | ||
1099 | < | void SimSetup::createFF( void ){ |
1099 | > | void SimSetup::createFF(void){ |
1100 | > | switch (ffCase){ |
1101 | > | case FF_DUFF: |
1102 | > | the_ff = new DUFF(); |
1103 | > | break; |
1104 | ||
1105 | < | switch( ffCase ){ |
1105 | > | case FF_LJ: |
1106 | > | the_ff = new LJFF(); |
1107 | > | break; |
1108 | ||
1109 | < | case FF_DUFF: |
1110 | < | the_ff = new DUFF(); |
1111 | < | break; |
1109 | > | case FF_EAM: |
1110 | > | the_ff = new EAM_FF(); |
1111 | > | break; |
1112 | ||
1113 | < | case FF_LJ: |
1114 | < | the_ff = new LJFF(); |
1115 | < | break; |
1116 | < | |
1117 | < | case FF_EAM: |
1110 | < | the_ff = new EAM_FF(); |
1111 | < | break; |
1112 | < | |
1113 | < | default: |
1114 | < | sprintf( painCave.errMsg, |
1115 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1116 | < | painCave.isFatal = 1; |
1117 | < | simError(); |
1113 | > | default: |
1114 | > | sprintf(painCave.errMsg, |
1115 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1116 | > | painCave.isFatal = 1; |
1117 | > | simError(); |
1118 | } | |
1119 | ||
1120 | #ifdef IS_MPI | |
1121 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1121 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1122 | MPIcheckPoint(); | |
1123 | #endif // is_mpi | |
1124 | – | |
1124 | } | |
1125 | ||
1126 | ||
1127 | < | void SimSetup::compList( void ){ |
1129 | < | |
1127 | > | void SimSetup::compList(void){ |
1128 | int i; | |
1129 | char* id; | |
1130 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1131 | LinkedMolStamp* currentStamp = NULL; | |
1132 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1133 | < | |
1132 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1133 | > | |
1134 | // make an array of molecule stamps that match the components used. | |
1135 | // also extract the used stamps out into a separate linked list | |
1136 | < | |
1137 | < | for(i=0; i<nInfo; i++){ |
1136 | > | |
1137 | > | for (i = 0; i < nInfo; i++){ |
1138 | info[i].nComponents = n_components; | |
1139 | info[i].componentsNmol = components_nmol; | |
1140 | info[i].compStamps = comp_stamps; | |
1141 | info[i].headStamp = headStamp; | |
1142 | } | |
1145 | – | |
1143 | ||
1147 | – | for( i=0; i<n_components; i++ ){ |
1144 | ||
1145 | + | for (i = 0; i < n_components; i++){ |
1146 | id = the_components[i]->getType(); | |
1147 | comp_stamps[i] = NULL; | |
1148 | < | |
1148 | > | |
1149 | // check to make sure the component isn't already in the list | |
1150 | ||
1151 | < | comp_stamps[i] = headStamp->match( id ); |
1152 | < | if( comp_stamps[i] == NULL ){ |
1156 | < | |
1151 | > | comp_stamps[i] = headStamp->match(id); |
1152 | > | if (comp_stamps[i] == NULL){ |
1153 | // extract the component from the list; | |
1154 | < | |
1155 | < | currentStamp = stamps->extractMolStamp( id ); |
1156 | < | if( currentStamp == NULL ){ |
1157 | < | sprintf( painCave.errMsg, |
1158 | < | "SimSetup error: Component \"%s\" was not found in the " |
1159 | < | "list of declared molecules\n", |
1160 | < | id ); |
1161 | < | painCave.isFatal = 1; |
1162 | < | simError(); |
1154 | > | |
1155 | > | currentStamp = stamps->extractMolStamp(id); |
1156 | > | if (currentStamp == NULL){ |
1157 | > | sprintf(painCave.errMsg, |
1158 | > | "SimSetup error: Component \"%s\" was not found in the " |
1159 | > | "list of declared molecules\n", |
1160 | > | id); |
1161 | > | painCave.isFatal = 1; |
1162 | > | simError(); |
1163 | } | |
1164 | < | |
1165 | < | headStamp->add( currentStamp ); |
1166 | < | comp_stamps[i] = headStamp->match( id ); |
1164 | > | |
1165 | > | headStamp->add(currentStamp); |
1166 | > | comp_stamps[i] = headStamp->match(id); |
1167 | } | |
1168 | } | |
1169 | ||
1170 | #ifdef IS_MPI | |
1171 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1171 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1172 | MPIcheckPoint(); | |
1173 | #endif // is_mpi | |
1174 | + | } |
1175 | ||
1176 | + | void SimSetup::calcSysValues(void){ |
1177 | + | int i; |
1178 | ||
1179 | < | } |
1179 | > | int* molMembershipArray; |
1180 | ||
1182 | – | void SimSetup::calcSysValues( void ){ |
1183 | – | int i, j, k; |
1184 | – | |
1185 | – | int *molMembershipArray; |
1186 | – | |
1181 | tot_atoms = 0; | |
1182 | tot_bonds = 0; | |
1183 | tot_bends = 0; | |
1184 | tot_torsions = 0; | |
1185 | < | for( i=0; i<n_components; i++ ){ |
1186 | < | |
1187 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1188 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1195 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1185 | > | for (i = 0; i < n_components; i++){ |
1186 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1187 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1188 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1189 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1190 | } | |
1191 | < | |
1191 | > | |
1192 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1193 | molMembershipArray = new int[tot_atoms]; | |
1194 | < | |
1195 | < | for(i=0; i<nInfo; i++){ |
1194 | > | |
1195 | > | for (i = 0; i < nInfo; i++){ |
1196 | info[i].n_atoms = tot_atoms; | |
1197 | info[i].n_bonds = tot_bonds; | |
1198 | info[i].n_bends = tot_bends; | |
1199 | info[i].n_torsions = tot_torsions; | |
1200 | info[i].n_SRI = tot_SRI; | |
1201 | info[i].n_mol = tot_nmol; | |
1202 | < | |
1202 | > | |
1203 | info[i].molMembershipArray = molMembershipArray; | |
1204 | < | } |
1204 | > | } |
1205 | } | |
1206 | ||
1207 | #ifdef IS_MPI | |
1208 | ||
1209 | < | void SimSetup::mpiMolDivide( void ){ |
1217 | < | |
1209 | > | void SimSetup::mpiMolDivide(void){ |
1210 | int i, j, k; | |
1211 | int localMol, allMol; | |
1212 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1213 | ||
1214 | < | mpiSim = new mpiSimulation( info ); |
1215 | < | |
1214 | > | mpiSim = new mpiSimulation(info); |
1215 | > | |
1216 | globalIndex = mpiSim->divideLabor(); | |
1217 | ||
1218 | // set up the local variables | |
1219 | < | |
1219 | > | |
1220 | mol2proc = mpiSim->getMolToProcMap(); | |
1221 | molCompType = mpiSim->getMolComponentType(); | |
1222 | < | |
1222 | > | |
1223 | allMol = 0; | |
1224 | localMol = 0; | |
1225 | local_atoms = 0; | |
# | Line 1237 | Line 1229 | void SimSetup::mpiMolDivide( void ){ | |
1229 | globalAtomIndex = 0; | |
1230 | ||
1231 | ||
1232 | < | for( i=0; i<n_components; i++ ){ |
1233 | < | |
1234 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1235 | < | |
1236 | < | if( mol2proc[allMol] == worldRank ){ |
1237 | < | |
1238 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1239 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1248 | < | local_bends += comp_stamps[i]->getNBends(); |
1249 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1250 | < | localMol++; |
1232 | > | for (i = 0; i < n_components; i++){ |
1233 | > | for (j = 0; j < components_nmol[i]; j++){ |
1234 | > | if (mol2proc[allMol] == worldRank){ |
1235 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1236 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1237 | > | local_bends += comp_stamps[i]->getNBends(); |
1238 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1239 | > | localMol++; |
1240 | } | |
1241 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1242 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
1243 | globalAtomIndex++; | |
1244 | } | |
1245 | ||
1246 | < | allMol++; |
1246 | > | allMol++; |
1247 | } | |
1248 | } | |
1249 | local_SRI = local_bonds + local_bends + local_torsions; | |
1250 | < | |
1250 | > | |
1251 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1252 | < | |
1253 | < | if( local_atoms != info[0].n_atoms ){ |
1254 | < | sprintf( painCave.errMsg, |
1255 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1256 | < | " localAtom (%d) are not equal.\n", |
1257 | < | info[0].n_atoms, |
1269 | < | local_atoms ); |
1252 | > | |
1253 | > | if (local_atoms != info[0].n_atoms){ |
1254 | > | sprintf(painCave.errMsg, |
1255 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1256 | > | "\tlocalAtom (%d) are not equal.\n", |
1257 | > | info[0].n_atoms, local_atoms); |
1258 | painCave.isFatal = 1; | |
1259 | simError(); | |
1260 | } | |
# | Line 1277 | Line 1265 | void SimSetup::mpiMolDivide( void ){ | |
1265 | info[0].n_SRI = local_SRI; | |
1266 | info[0].n_mol = localMol; | |
1267 | ||
1268 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1268 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1269 | MPIcheckPoint(); | |
1270 | } | |
1271 | < | |
1271 | > | |
1272 | #endif // is_mpi | |
1273 | ||
1274 | ||
1275 | < | void SimSetup::makeSysArrays( void ){ |
1276 | < | int i, j, k, l; |
1275 | > | void SimSetup::makeSysArrays(void){ |
1276 | > | |
1277 | > | #ifndef IS_MPI |
1278 | > | int k, j; |
1279 | > | #endif // is_mpi |
1280 | > | int i, l; |
1281 | ||
1282 | Atom** the_atoms; | |
1283 | Molecule* the_molecules; | |
1284 | Exclude** the_excludes; | |
1285 | ||
1286 | < | |
1287 | < | for(l=0; l<nInfo; l++){ |
1296 | < | |
1286 | > | |
1287 | > | for (l = 0; l < nInfo; l++){ |
1288 | // create the atom and short range interaction arrays | |
1289 | < | |
1290 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1289 | > | |
1290 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1291 | the_molecules = new Molecule[info[l].n_mol]; | |
1292 | int molIndex; | |
1293 | ||
1294 | // initialize the molecule's stampID's | |
1295 | < | |
1295 | > | |
1296 | #ifdef IS_MPI | |
1297 | < | |
1298 | < | |
1297 | > | |
1298 | > | |
1299 | molIndex = 0; | |
1300 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1301 | < | |
1302 | < | if(mol2proc[i] == worldRank ){ |
1303 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1304 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1305 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1315 | < | molIndex++; |
1300 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1301 | > | if (mol2proc[i] == worldRank){ |
1302 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1303 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1304 | > | the_molecules[molIndex].setGlobalIndex(i); |
1305 | > | molIndex++; |
1306 | } | |
1307 | } | |
1308 | < | |
1308 | > | |
1309 | #else // is_mpi | |
1310 | < | |
1310 | > | |
1311 | molIndex = 0; | |
1312 | globalAtomIndex = 0; | |
1313 | < | for(i=0; i<n_components; i++){ |
1314 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1315 | < | the_molecules[molIndex].setStampID( i ); |
1316 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1317 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1318 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1319 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1320 | < | globalAtomIndex++; |
1321 | < | } |
1322 | < | molIndex++; |
1313 | > | for (i = 0; i < n_components; i++){ |
1314 | > | for (j = 0; j < components_nmol[i]; j++){ |
1315 | > | the_molecules[molIndex].setStampID(i); |
1316 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1317 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1318 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1319 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1320 | > | globalAtomIndex++; |
1321 | > | } |
1322 | > | molIndex++; |
1323 | } | |
1324 | } | |
1325 | < | |
1326 | < | |
1325 | > | |
1326 | > | |
1327 | #endif // is_mpi | |
1328 | ||
1329 | ||
1330 | < | if( info[l].n_SRI ){ |
1341 | < | |
1330 | > | if (info[l].n_SRI){ |
1331 | Exclude::createArray(info[l].n_SRI); | |
1332 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1333 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1334 | < | the_excludes[ex] = new Exclude(ex); |
1332 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1333 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1334 | > | the_excludes[ex] = new Exclude(ex); |
1335 | } | |
1336 | info[l].globalExcludes = new int; | |
1337 | info[l].n_exclude = info[l].n_SRI; | |
1338 | } | |
1339 | else{ | |
1340 | < | |
1341 | < | Exclude::createArray( 1 ); |
1353 | < | the_excludes = new Exclude*; |
1340 | > | Exclude::createArray(1); |
1341 | > | the_excludes = new Exclude * ; |
1342 | the_excludes[0] = new Exclude(0); | |
1343 | < | the_excludes[0]->setPair( 0,0 ); |
1343 | > | the_excludes[0]->setPair(0, 0); |
1344 | info[l].globalExcludes = new int; | |
1345 | info[l].globalExcludes[0] = 0; | |
1346 | info[l].n_exclude = 0; | |
# | Line 1365 | Line 1353 | void SimSetup::makeSysArrays( void ){ | |
1353 | info[l].nGlobalExcludes = 0; | |
1354 | info[l].excludes = the_excludes; | |
1355 | ||
1356 | < | the_ff->setSimInfo( info ); |
1369 | < | |
1356 | > | the_ff->setSimInfo(info); |
1357 | } | |
1358 | } | |
1359 | ||
1360 | < | void SimSetup::makeIntegrator( void ){ |
1374 | < | |
1360 | > | void SimSetup::makeIntegrator(void){ |
1361 | int k; | |
1362 | ||
1363 | < | NVT<RealIntegrator>* myNVT = NULL; |
1364 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1365 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1366 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1367 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1368 | < | |
1369 | < | for(k=0; k<nInfo; k++){ |
1370 | < | |
1371 | < | switch( ensembleCase ){ |
1372 | < | |
1373 | < | case NVE_ENS: |
1374 | < | if (globals->haveZconstraints()){ |
1375 | < | setupZConstraint(info[k]); |
1376 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1377 | < | } |
1363 | > | NVE<RealIntegrator>* myNVE = NULL; |
1364 | > | NVT<RealIntegrator>* myNVT = NULL; |
1365 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1366 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1367 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1368 | > | |
1369 | > | for (k = 0; k < nInfo; k++){ |
1370 | > | switch (ensembleCase){ |
1371 | > | case NVE_ENS: |
1372 | > | if (globals->haveZconstraints()){ |
1373 | > | setupZConstraint(info[k]); |
1374 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1375 | > | } |
1376 | > | else{ |
1377 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1378 | > | } |
1379 | > | |
1380 | > | info->the_integrator = myNVE; |
1381 | > | break; |
1382 | ||
1383 | < | else |
1384 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1385 | < | break; |
1386 | < | |
1387 | < | case NVT_ENS: |
1388 | < | if (globals->haveZconstraints()){ |
1389 | < | setupZConstraint(info[k]); |
1400 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1401 | < | } |
1402 | < | else |
1403 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1383 | > | case NVT_ENS: |
1384 | > | if (globals->haveZconstraints()){ |
1385 | > | setupZConstraint(info[k]); |
1386 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1387 | > | } |
1388 | > | else |
1389 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1390 | ||
1391 | myNVT->setTargetTemp(globals->getTargetTemp()); | |
1392 | < | |
1393 | < | if (globals->haveTauThermostat()) |
1392 | > | |
1393 | > | if (globals->haveTauThermostat()) |
1394 | myNVT->setTauThermostat(globals->getTauThermostat()); | |
1395 | < | |
1396 | < | else { |
1397 | < | sprintf( painCave.errMsg, |
1398 | < | "SimSetup error: If you use the NVT\n" |
1413 | < | " ensemble, you must set tauThermostat.\n"); |
1395 | > | else{ |
1396 | > | sprintf(painCave.errMsg, |
1397 | > | "SimSetup error: If you use the NVT\n" |
1398 | > | "\tensemble, you must set tauThermostat.\n"); |
1399 | painCave.isFatal = 1; | |
1400 | simError(); | |
1401 | } | |
1402 | + | |
1403 | + | info->the_integrator = myNVT; |
1404 | break; | |
1418 | – | |
1419 | – | case NPTi_ENS: |
1420 | – | if (globals->haveZconstraints()){ |
1421 | – | setupZConstraint(info[k]); |
1422 | – | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1423 | – | } |
1424 | – | else |
1425 | – | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1405 | ||
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" |
1434 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1435 | < | painCave.isFatal = 1; |
1436 | < | simError(); |
1437 | < | } |
1438 | < | |
1439 | < | if( globals->haveTauThermostat() ) |
1440 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1441 | < | else{ |
1442 | < | sprintf( painCave.errMsg, |
1443 | < | "SimSetup error: If you use an NPT\n" |
1444 | < | " ensemble, you must set tauThermostat.\n"); |
1445 | < | painCave.isFatal = 1; |
1446 | < | simError(); |
1447 | < | } |
1448 | < | |
1449 | < | if( globals->haveTauBarostat() ) |
1450 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1451 | < | else{ |
1452 | < | sprintf( painCave.errMsg, |
1453 | < | "SimSetup error: If you use an NPT\n" |
1454 | < | " ensemble, you must set tauBarostat.\n"); |
1455 | < | painCave.isFatal = 1; |
1456 | < | simError(); |
1457 | < | } |
1458 | < | break; |
1459 | < | |
1460 | < | case NPTf_ENS: |
1461 | < | if (globals->haveZconstraints()){ |
1462 | < | setupZConstraint(info[k]); |
1463 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1464 | < | } |
1465 | < | else |
1466 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1406 | > | case NPTi_ENS: |
1407 | > | if (globals->haveZconstraints()){ |
1408 | > | setupZConstraint(info[k]); |
1409 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1410 | > | } |
1411 | > | else |
1412 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1413 | ||
1414 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1415 | < | |
1416 | < | if (globals->haveTargetPressure()) |
1417 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1418 | < | else { |
1419 | < | sprintf( painCave.errMsg, |
1414 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1415 | > | |
1416 | > | if (globals->haveTargetPressure()) |
1417 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1418 | > | else{ |
1419 | > | sprintf(painCave.errMsg, |
1420 | "SimSetup error: If you use a constant pressure\n" | |
1421 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1422 | < | painCave.isFatal = 1; |
1423 | < | simError(); |
1424 | < | } |
1425 | < | |
1426 | < | if( globals->haveTauThermostat() ) |
1427 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1428 | < | else{ |
1429 | < | sprintf( painCave.errMsg, |
1484 | < | "SimSetup error: If you use an NPT\n" |
1485 | < | " ensemble, you must set tauThermostat.\n"); |
1486 | < | painCave.isFatal = 1; |
1487 | < | simError(); |
1488 | < | } |
1489 | < | |
1490 | < | if( globals->haveTauBarostat() ) |
1491 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1492 | < | else{ |
1493 | < | sprintf( painCave.errMsg, |
1421 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1422 | > | painCave.isFatal = 1; |
1423 | > | simError(); |
1424 | > | } |
1425 | > | |
1426 | > | if (globals->haveTauThermostat()) |
1427 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1428 | > | else{ |
1429 | > | sprintf(painCave.errMsg, |
1430 | "SimSetup error: If you use an NPT\n" | |
1431 | < | " ensemble, you must set tauBarostat.\n"); |
1432 | < | painCave.isFatal = 1; |
1433 | < | simError(); |
1434 | < | } |
1499 | < | break; |
1500 | < | |
1501 | < | case NPTim_ENS: |
1502 | < | if (globals->haveZconstraints()){ |
1503 | < | setupZConstraint(info[k]); |
1504 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1505 | < | } |
1506 | < | else |
1507 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1431 | > | "\tensemble, you must set tauThermostat.\n"); |
1432 | > | painCave.isFatal = 1; |
1433 | > | simError(); |
1434 | > | } |
1435 | ||
1436 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1437 | < | |
1438 | < | if (globals->haveTargetPressure()) |
1439 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1513 | < | else { |
1514 | < | sprintf( painCave.errMsg, |
1515 | < | "SimSetup error: If you use a constant pressure\n" |
1516 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1517 | < | painCave.isFatal = 1; |
1518 | < | simError(); |
1519 | < | } |
1520 | < | |
1521 | < | if( globals->haveTauThermostat() ) |
1522 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1523 | < | else{ |
1524 | < | sprintf( painCave.errMsg, |
1436 | > | if (globals->haveTauBarostat()) |
1437 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1438 | > | else{ |
1439 | > | sprintf(painCave.errMsg, |
1440 | "SimSetup error: If you use an NPT\n" | |
1441 | < | " ensemble, you must set tauThermostat.\n"); |
1442 | < | painCave.isFatal = 1; |
1443 | < | simError(); |
1444 | < | } |
1530 | < | |
1531 | < | if( globals->haveTauBarostat() ) |
1532 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1533 | < | else{ |
1534 | < | sprintf( painCave.errMsg, |
1535 | < | "SimSetup error: If you use an NPT\n" |
1536 | < | " ensemble, you must set tauBarostat.\n"); |
1537 | < | painCave.isFatal = 1; |
1538 | < | simError(); |
1539 | < | } |
1540 | < | break; |
1541 | < | |
1542 | < | case NPTfm_ENS: |
1543 | < | if (globals->haveZconstraints()){ |
1544 | < | setupZConstraint(info[k]); |
1545 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1546 | < | } |
1547 | < | else |
1548 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1441 | > | "\tensemble, you must set tauBarostat.\n"); |
1442 | > | painCave.isFatal = 1; |
1443 | > | simError(); |
1444 | > | } |
1445 | ||
1446 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 | > | info->the_integrator = myNPTi; |
1447 | > | break; |
1448 | ||
1449 | < | if (globals->haveTargetPressure()) |
1450 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1451 | < | else { |
1452 | < | sprintf( painCave.errMsg, |
1449 | > | case NPTf_ENS: |
1450 | > | if (globals->haveZconstraints()){ |
1451 | > | setupZConstraint(info[k]); |
1452 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1453 | > | } |
1454 | > | else |
1455 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1456 | > | |
1457 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1458 | > | |
1459 | > | if (globals->haveTargetPressure()) |
1460 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1461 | > | else{ |
1462 | > | sprintf(painCave.errMsg, |
1463 | "SimSetup error: If you use a constant pressure\n" | |
1464 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1465 | < | painCave.isFatal = 1; |
1466 | < | simError(); |
1467 | < | } |
1464 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1465 | > | painCave.isFatal = 1; |
1466 | > | simError(); |
1467 | > | } |
1468 | ||
1469 | < | if( globals->haveTauThermostat() ) |
1470 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1471 | < | else{ |
1472 | < | sprintf( painCave.errMsg, |
1469 | > | if (globals->haveTauThermostat()) |
1470 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1471 | > | |
1472 | > | else{ |
1473 | > | sprintf(painCave.errMsg, |
1474 | "SimSetup error: If you use an NPT\n" | |
1475 | < | " ensemble, you must set tauThermostat.\n"); |
1476 | < | painCave.isFatal = 1; |
1477 | < | simError(); |
1478 | < | } |
1475 | > | "\tensemble, you must set tauThermostat.\n"); |
1476 | > | painCave.isFatal = 1; |
1477 | > | simError(); |
1478 | > | } |
1479 | ||
1480 | < | if( globals->haveTauBarostat() ) |
1481 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1482 | < | else{ |
1483 | < | sprintf( painCave.errMsg, |
1480 | > | if (globals->haveTauBarostat()) |
1481 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1482 | > | |
1483 | > | else{ |
1484 | > | sprintf(painCave.errMsg, |
1485 | "SimSetup error: If you use an NPT\n" | |
1486 | < | " ensemble, you must set tauBarostat.\n"); |
1486 | > | "\tensemble, you must set tauBarostat.\n"); |
1487 | > | painCave.isFatal = 1; |
1488 | > | simError(); |
1489 | > | } |
1490 | > | |
1491 | > | info->the_integrator = myNPTf; |
1492 | > | break; |
1493 | > | |
1494 | > | case NPTxyz_ENS: |
1495 | > | if (globals->haveZconstraints()){ |
1496 | > | setupZConstraint(info[k]); |
1497 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1498 | > | } |
1499 | > | else |
1500 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1501 | > | |
1502 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1503 | > | |
1504 | > | if (globals->haveTargetPressure()) |
1505 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1506 | > | else{ |
1507 | > | sprintf(painCave.errMsg, |
1508 | > | "SimSetup error: If you use a constant pressure\n" |
1509 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1510 | > | painCave.isFatal = 1; |
1511 | > | simError(); |
1512 | > | } |
1513 | > | |
1514 | > | if (globals->haveTauThermostat()) |
1515 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1516 | > | else{ |
1517 | > | sprintf(painCave.errMsg, |
1518 | > | "SimSetup error: If you use an NPT\n" |
1519 | > | "\tensemble, you must set tauThermostat.\n"); |
1520 | > | painCave.isFatal = 1; |
1521 | > | simError(); |
1522 | > | } |
1523 | > | |
1524 | > | if (globals->haveTauBarostat()) |
1525 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1526 | > | else{ |
1527 | > | sprintf(painCave.errMsg, |
1528 | > | "SimSetup error: If you use an NPT\n" |
1529 | > | "\tensemble, you must set tauBarostat.\n"); |
1530 | > | painCave.isFatal = 1; |
1531 | > | simError(); |
1532 | > | } |
1533 | > | |
1534 | > | info->the_integrator = myNPTxyz; |
1535 | > | break; |
1536 | > | |
1537 | > | default: |
1538 | > | sprintf(painCave.errMsg, |
1539 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1540 | painCave.isFatal = 1; | |
1541 | simError(); | |
1580 | – | } |
1581 | – | break; |
1582 | – | |
1583 | – | default: |
1584 | – | sprintf( painCave.errMsg, |
1585 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1586 | – | painCave.isFatal = 1; |
1587 | – | simError(); |
1542 | } | |
1543 | } | |
1544 | } | |
1545 | ||
1546 | < | void SimSetup::initFortran( void ){ |
1593 | < | |
1546 | > | void SimSetup::initFortran(void){ |
1547 | info[0].refreshSim(); | |
1548 | < | |
1549 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1550 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1548 | > | |
1549 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1550 | > | the_ff->initForceField(LB_MIXING_RULE); |
1551 | } | |
1552 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1553 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1552 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1553 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1554 | } | |
1555 | else{ | |
1556 | < | sprintf( painCave.errMsg, |
1557 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 | < | info[0].mixingRule ); |
1556 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1557 | > | info[0].mixingRule); |
1558 | painCave.isFatal = 1; | |
1559 | simError(); | |
1560 | } | |
1561 | ||
1562 | ||
1563 | #ifdef IS_MPI | |
1564 | < | strcpy( checkPointMsg, |
1613 | < | "Successfully intialized the mixingRule for Fortran." ); |
1564 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1565 | MPIcheckPoint(); | |
1566 | #endif // is_mpi | |
1616 | – | |
1567 | } | |
1568 | ||
1569 | < | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1620 | < | { |
1569 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1570 | int nZConstraints; | |
1571 | ZconStamp** zconStamp; | |
1572 | ||
1573 | < | if(globals->haveZconstraintTime()){ |
1625 | < | |
1573 | > | if (globals->haveZconstraintTime()){ |
1574 | //add sample time of z-constraint into SimInfo's property list | |
1575 | DoubleData* zconsTimeProp = new DoubleData(); | |
1576 | zconsTimeProp->setID(ZCONSTIME_ID); | |
# | Line 1630 | Line 1578 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1578 | theInfo.addProperty(zconsTimeProp); | |
1579 | } | |
1580 | else{ | |
1581 | < | sprintf( painCave.errMsg, |
1582 | < | "ZConstraint error: If you use an ZConstraint\n" |
1583 | < | " , you must set sample time.\n"); |
1581 | > | sprintf(painCave.errMsg, |
1582 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1583 | > | "\tyou must set zconsTime.\n"); |
1584 | painCave.isFatal = 1; | |
1585 | < | simError(); |
1585 | > | simError(); |
1586 | } | |
1587 | ||
1588 | //push zconsTol into siminfo, if user does not specify | |
1589 | //value for zconsTol, a default value will be used | |
1590 | DoubleData* zconsTol = new DoubleData(); | |
1591 | zconsTol->setID(ZCONSTOL_ID); | |
1592 | < | if(globals->haveZconsTol()){ |
1592 | > | if (globals->haveZconsTol()){ |
1593 | zconsTol->setData(globals->getZconsTol()); | |
1594 | } | |
1595 | else{ | |
1596 | < | double defaultZConsTol = 0.01; |
1597 | < | sprintf( painCave.errMsg, |
1598 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1599 | < | " , default value %f is used.\n", defaultZConsTol); |
1596 | > | double defaultZConsTol = 0.01; |
1597 | > | sprintf(painCave.errMsg, |
1598 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1599 | > | "\tOOPSE will use a default value of %f.\n" |
1600 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
1601 | > | defaultZConsTol); |
1602 | painCave.isFatal = 0; | |
1603 | simError(); | |
1604 | ||
# | Line 1656 | Line 1606 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1606 | } | |
1607 | theInfo.addProperty(zconsTol); | |
1608 | ||
1609 | < | //set Force Substraction Policy |
1610 | < | StringData* zconsForcePolicy = new StringData(); |
1609 | > | //set Force Subtraction Policy |
1610 | > | StringData* zconsForcePolicy = new StringData(); |
1611 | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); | |
1612 | < | |
1613 | < | if(globals->haveZconsForcePolicy()){ |
1612 | > | |
1613 | > | if (globals->haveZconsForcePolicy()){ |
1614 | zconsForcePolicy->setData(globals->getZconsForcePolicy()); | |
1615 | < | } |
1615 | > | } |
1616 | else{ | |
1617 | < | sprintf( painCave.errMsg, |
1618 | < | "ZConstraint Warning: User does not set force substraction policy, " |
1619 | < | "average force substraction policy is used\n"); |
1620 | < | painCave.isFatal = 0; |
1621 | < | simError(); |
1622 | < | zconsForcePolicy->setData("BYNUMBER"); |
1617 | > | sprintf(painCave.errMsg, |
1618 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1619 | > | "\tOOPSE will use PolicyByMass.\n" |
1620 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1621 | > | painCave.isFatal = 0; |
1622 | > | simError(); |
1623 | > | zconsForcePolicy->setData("BYMASS"); |
1624 | } | |
1625 | < | |
1626 | < | theInfo.addProperty(zconsForcePolicy); |
1627 | < | |
1625 | > | |
1626 | > | theInfo.addProperty(zconsForcePolicy); |
1627 | > | |
1628 | //Determine the name of ouput file and add it into SimInfo's property list | |
1629 | //Be careful, do not use inFileName, since it is a pointer which | |
1630 | //point to a string at master node, and slave nodes do not contain that string | |
1631 | < | |
1631 | > | |
1632 | string zconsOutput(theInfo.finalName); | |
1633 | < | |
1633 | > | |
1634 | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; | |
1635 | < | |
1635 | > | |
1636 | StringData* zconsFilename = new StringData(); | |
1637 | zconsFilename->setID(ZCONSFILENAME_ID); | |
1638 | zconsFilename->setData(zconsOutput); | |
1639 | < | |
1639 | > | |
1640 | theInfo.addProperty(zconsFilename); | |
1641 | < | |
1641 | > | |
1642 | //setup index, pos and other parameters of z-constraint molecules | |
1643 | nZConstraints = globals->getNzConstraints(); | |
1644 | theInfo.nZconstraints = nZConstraints; | |
# | Line 1697 | Line 1648 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1648 | ||
1649 | ZConsParaData* zconsParaData = new ZConsParaData(); | |
1650 | zconsParaData->setID(ZCONSPARADATA_ID); | |
1651 | < | |
1652 | < | for(int i = 0; i < nZConstraints; i++){ |
1651 | > | |
1652 | > | for (int i = 0; i < nZConstraints; i++){ |
1653 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
1654 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1655 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
# | Line 1707 | Line 1658 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1658 | zconsParaData->addItem(tempParaItem); | |
1659 | } | |
1660 | ||
1661 | + | //check the uniqueness of index |
1662 | + | if(!zconsParaData->isIndexUnique()){ |
1663 | + | sprintf(painCave.errMsg, |
1664 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1665 | + | painCave.isFatal = 1; |
1666 | + | simError(); |
1667 | + | } |
1668 | + | |
1669 | //sort the parameters by index of molecules | |
1670 | zconsParaData->sortByIndex(); | |
1671 | ||
1672 | //push data into siminfo, therefore, we can retrieve later | |
1673 | theInfo.addProperty(zconsParaData); | |
1715 | – | |
1674 | } |
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