# | Line 3 | Line 3 | |
---|---|---|
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | #include <string> | |
6 | + | #include <sprng.h> |
7 | ||
8 | #include "SimSetup.hpp" | |
9 | + | #include "ReadWrite.hpp" |
10 | #include "parse_me.h" | |
11 | #include "Integrator.hpp" | |
12 | #include "simError.h" | |
# | Line 22 | Line 24 | |
24 | #define NPTf_ENS 3 | |
25 | #define NPTim_ENS 4 | |
26 | #define NPTfm_ENS 5 | |
25 | – | #define NVEZCONS_ENS 6 |
26 | – | #define NVTZCONS_ENS 7 |
27 | – | #define NPTiZCONS_ENS 8 |
28 | – | #define NPTfZCONS_ENS 9 |
29 | – | #define NPTimZCONS_ENS 10 |
30 | – | #define NPTfmZCONS_ENS 11 |
27 | ||
28 | #define FF_DUFF 0 | |
29 | #define FF_LJ 1 | |
# | Line 36 | Line 32 | SimSetup::SimSetup(){ | |
32 | using namespace std; | |
33 | ||
34 | SimSetup::SimSetup(){ | |
39 | – | |
35 | isInfoArray = 0; | |
36 | nInfo = 1; | |
37 | < | |
37 | > | |
38 | stamps = new MakeStamps(); | |
39 | globals = new Globals(); | |
40 | < | |
41 | < | |
40 | > | |
41 | > | |
42 | #ifdef IS_MPI | |
43 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
43 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
44 | MPIcheckPoint(); | |
45 | #endif // IS_MPI | |
46 | } | |
# | Line 55 | Line 50 | SimSetup::~SimSetup(){ | |
50 | delete globals; | |
51 | } | |
52 | ||
53 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
54 | < | info = the_info; |
55 | < | nInfo = theNinfo; |
56 | < | isInfoArray = 1; |
53 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
54 | > | info = the_info; |
55 | > | nInfo = theNinfo; |
56 | > | isInfoArray = 1; |
57 | } | |
58 | ||
59 | ||
60 | < | void SimSetup::parseFile( char* fileName ){ |
66 | < | |
60 | > | void SimSetup::parseFile(char* fileName){ |
61 | #ifdef IS_MPI | |
62 | < | if( worldRank == 0 ){ |
62 | > | if (worldRank == 0){ |
63 | #endif // is_mpi | |
64 | < | |
64 | > | |
65 | inFileName = fileName; | |
66 | < | set_interface_stamps( stamps, globals ); |
67 | < | |
66 | > | set_interface_stamps(stamps, globals); |
67 | > | |
68 | #ifdef IS_MPI | |
69 | mpiEventInit(); | |
70 | #endif | |
71 | ||
72 | < | yacc_BASS( fileName ); |
72 | > | yacc_BASS(fileName); |
73 | ||
74 | #ifdef IS_MPI | |
75 | throwMPIEvent(NULL); | |
76 | } | |
77 | < | else receiveParse(); |
77 | > | else{ |
78 | > | receiveParse(); |
79 | > | } |
80 | #endif | |
81 | ||
82 | } | |
83 | ||
84 | #ifdef IS_MPI | |
85 | void SimSetup::receiveParse(void){ | |
86 | < | |
87 | < | set_interface_stamps( stamps, globals ); |
88 | < | mpiEventInit(); |
89 | < | MPIcheckPoint(); |
94 | < | mpiEventLoop(); |
95 | < | |
86 | > | set_interface_stamps(stamps, globals); |
87 | > | mpiEventInit(); |
88 | > | MPIcheckPoint(); |
89 | > | mpiEventLoop(); |
90 | } | |
91 | ||
92 | #endif // is_mpi | |
93 | ||
94 | void SimSetup::createSim(void){ | |
101 | – | |
95 | int i, j, k, globalAtomIndex; | |
96 | < | |
96 | > | |
97 | // gather all of the information from the Bass file | |
98 | < | |
98 | > | |
99 | gatherInfo(); | |
100 | ||
101 | // creation of complex system objects | |
# | Line 110 | Line 103 | void SimSetup::createSim(void){ | |
103 | sysObjectsCreation(); | |
104 | ||
105 | // check on the post processing info | |
106 | < | |
106 | > | |
107 | finalInfoCheck(); | |
108 | ||
109 | // initialize the system coordinates | |
110 | ||
111 | < | if( !isInfoArray ) initSystemCoords(); |
111 | > | if (!isInfoArray){ |
112 | > | initSystemCoords(); |
113 | > | } |
114 | ||
115 | // make the output filenames | |
116 | ||
117 | makeOutNames(); | |
118 | < | |
118 | > | |
119 | // make the integrator | |
120 | < | |
120 | > | |
121 | makeIntegrator(); | |
122 | < | |
122 | > | |
123 | #ifdef IS_MPI | |
124 | mpiSim->mpiRefresh(); | |
125 | #endif | |
# | Line 132 | Line 127 | void SimSetup::createSim(void){ | |
127 | // initialize the Fortran | |
128 | ||
129 | initFortran(); | |
135 | – | |
136 | – | |
137 | – | |
130 | } | |
131 | ||
132 | ||
133 | < | void SimSetup::makeMolecules( void ){ |
134 | < | |
143 | < | int k,l; |
133 | > | void SimSetup::makeMolecules(void){ |
134 | > | int k, l; |
135 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
136 | molInit molInfo; | |
137 | DirectionalAtom* dAtom; | |
# | Line 155 | Line 146 | void SimSetup::makeMolecules( void ){ | |
146 | bend_set* theBends; | |
147 | torsion_set* theTorsions; | |
148 | ||
149 | < | |
149 | > | |
150 | //init the forceField paramters | |
151 | ||
152 | the_ff->readParams(); | |
153 | ||
154 | < | |
154 | > | |
155 | // init the atoms | |
156 | ||
157 | double ux, uy, uz, u, uSqr; | |
167 | – | |
168 | – | for(k=0; k<nInfo; k++){ |
169 | – | |
170 | – | the_ff->setSimInfo( &(info[k]) ); |
158 | ||
159 | + | for (k = 0; k < nInfo; k++){ |
160 | + | the_ff->setSimInfo(&(info[k])); |
161 | + | |
162 | atomOffset = 0; | |
163 | excludeOffset = 0; | |
164 | < | for(i=0; i<info[k].n_mol; i++){ |
175 | < | |
164 | > | for (i = 0; i < info[k].n_mol; i++){ |
165 | stampID = info[k].molecules[i].getStampID(); | |
166 | ||
167 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
169 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
167 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
169 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
170 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
171 | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; | |
172 | < | |
172 | > | |
173 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
174 | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); | |
175 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
176 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
177 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
175 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
176 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
177 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
178 | ||
179 | theBonds = new bond_pair[molInfo.nBonds]; | |
180 | theBends = new bend_set[molInfo.nBends]; | |
181 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
182 | < | |
182 | > | |
183 | // make the Atoms | |
184 | < | |
185 | < | for(j=0; j<molInfo.nAtoms; j++){ |
186 | < | |
187 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
188 | < | if( currentAtom->haveOrientation() ){ |
189 | < | |
190 | < | dAtom = new DirectionalAtom( (j + atomOffset), |
191 | < | info[k].getConfiguration() ); |
192 | < | info[k].n_oriented++; |
193 | < | molInfo.myAtoms[j] = dAtom; |
194 | < | |
195 | < | ux = currentAtom->getOrntX(); |
196 | < | uy = currentAtom->getOrntY(); |
197 | < | uz = currentAtom->getOrntZ(); |
198 | < | |
199 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
200 | < | |
201 | < | u = sqrt( uSqr ); |
202 | < | ux = ux / u; |
203 | < | uy = uy / u; |
204 | < | uz = uz / u; |
205 | < | |
206 | < | dAtom->setSUx( ux ); |
207 | < | dAtom->setSUy( uy ); |
208 | < | dAtom->setSUz( uz ); |
209 | < | } |
210 | < | else{ |
211 | < | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
212 | < | info[k].getConfiguration() ); |
213 | < | } |
225 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
226 | < | |
184 | > | |
185 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
186 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
187 | > | if (currentAtom->haveOrientation()){ |
188 | > | dAtom = new DirectionalAtom((j + atomOffset), |
189 | > | info[k].getConfiguration()); |
190 | > | info[k].n_oriented++; |
191 | > | molInfo.myAtoms[j] = dAtom; |
192 | > | |
193 | > | ux = currentAtom->getOrntX(); |
194 | > | uy = currentAtom->getOrntY(); |
195 | > | uz = currentAtom->getOrntZ(); |
196 | > | |
197 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
198 | > | |
199 | > | u = sqrt(uSqr); |
200 | > | ux = ux / u; |
201 | > | uy = uy / u; |
202 | > | uz = uz / u; |
203 | > | |
204 | > | dAtom->setSUx(ux); |
205 | > | dAtom->setSUy(uy); |
206 | > | dAtom->setSUz(uz); |
207 | > | } |
208 | > | else{ |
209 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
210 | > | info[k].getConfiguration()); |
211 | > | } |
212 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
213 | > | |
214 | #ifdef IS_MPI | |
215 | < | |
216 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
217 | < | |
215 | > | |
216 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
217 | > | |
218 | #endif // is_mpi | |
219 | } | |
220 | < | |
221 | < | // make the bonds |
222 | < | for(j=0; j<molInfo.nBonds; j++){ |
223 | < | |
224 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
225 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
226 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
227 | < | |
228 | < | exI = theBonds[j].a; |
229 | < | exJ = theBonds[j].b; |
230 | < | |
231 | < | // exclude_I must always be the smaller of the pair |
232 | < | if( exI > exJ ){ |
233 | < | tempEx = exI; |
234 | < | exI = exJ; |
235 | < | exJ = tempEx; |
249 | < | } |
220 | > | |
221 | > | // make the bonds |
222 | > | for (j = 0; j < molInfo.nBonds; j++){ |
223 | > | currentBond = comp_stamps[stampID]->getBond(j); |
224 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
225 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
226 | > | |
227 | > | exI = theBonds[j].a; |
228 | > | exJ = theBonds[j].b; |
229 | > | |
230 | > | // exclude_I must always be the smaller of the pair |
231 | > | if (exI > exJ){ |
232 | > | tempEx = exI; |
233 | > | exI = exJ; |
234 | > | exJ = tempEx; |
235 | > | } |
236 | #ifdef IS_MPI | |
237 | < | tempEx = exI; |
238 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
239 | < | tempEx = exJ; |
240 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
241 | < | |
242 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
237 | > | tempEx = exI; |
238 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
239 | > | tempEx = exJ; |
240 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
241 | > | |
242 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
243 | #else // isn't MPI | |
244 | < | |
245 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
244 | > | |
245 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
246 | #endif //is_mpi | |
247 | } | |
248 | excludeOffset += molInfo.nBonds; | |
249 | < | |
249 | > | |
250 | //make the bends | |
251 | < | for(j=0; j<molInfo.nBends; j++){ |
252 | < | |
253 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
254 | < | theBends[j].a = currentBend->getA() + atomOffset; |
255 | < | theBends[j].b = currentBend->getB() + atomOffset; |
256 | < | theBends[j].c = currentBend->getC() + atomOffset; |
257 | < | |
258 | < | if( currentBend->haveExtras() ){ |
259 | < | |
260 | < | extras = currentBend->getExtras(); |
261 | < | current_extra = extras; |
262 | < | |
263 | < | while( current_extra != NULL ){ |
264 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
265 | < | |
266 | < | switch( current_extra->getType() ){ |
267 | < | |
268 | < | case 0: |
269 | < | theBends[j].ghost = |
270 | < | current_extra->getInt() + atomOffset; |
271 | < | theBends[j].isGhost = 1; |
272 | < | break; |
273 | < | |
274 | < | case 1: |
275 | < | theBends[j].ghost = |
276 | < | (int)current_extra->getDouble() + atomOffset; |
277 | < | theBends[j].isGhost = 1; |
278 | < | break; |
279 | < | |
280 | < | default: |
281 | < | sprintf( painCave.errMsg, |
282 | < | "SimSetup Error: ghostVectorSource was neither a " |
283 | < | "double nor an int.\n" |
284 | < | "-->Bend[%d] in %s\n", |
285 | < | j, comp_stamps[stampID]->getID() ); |
286 | < | painCave.isFatal = 1; |
287 | < | simError(); |
288 | < | } |
289 | < | } |
290 | < | |
291 | < | else{ |
292 | < | |
293 | < | sprintf( painCave.errMsg, |
294 | < | "SimSetup Error: unhandled bend assignment:\n" |
295 | < | " -->%s in Bend[%d] in %s\n", |
296 | < | current_extra->getlhs(), |
297 | < | j, comp_stamps[stampID]->getID() ); |
298 | < | painCave.isFatal = 1; |
299 | < | simError(); |
300 | < | } |
301 | < | |
302 | < | current_extra = current_extra->getNext(); |
303 | < | } |
304 | < | } |
305 | < | |
306 | < | if( !theBends[j].isGhost ){ |
307 | < | |
308 | < | exI = theBends[j].a; |
309 | < | exJ = theBends[j].c; |
310 | < | } |
311 | < | else{ |
312 | < | |
327 | < | exI = theBends[j].a; |
328 | < | exJ = theBends[j].b; |
329 | < | } |
330 | < | |
331 | < | // exclude_I must always be the smaller of the pair |
332 | < | if( exI > exJ ){ |
333 | < | tempEx = exI; |
334 | < | exI = exJ; |
335 | < | exJ = tempEx; |
336 | < | } |
251 | > | for (j = 0; j < molInfo.nBends; j++){ |
252 | > | currentBend = comp_stamps[stampID]->getBend(j); |
253 | > | theBends[j].a = currentBend->getA() + atomOffset; |
254 | > | theBends[j].b = currentBend->getB() + atomOffset; |
255 | > | theBends[j].c = currentBend->getC() + atomOffset; |
256 | > | |
257 | > | if (currentBend->haveExtras()){ |
258 | > | extras = currentBend->getExtras(); |
259 | > | current_extra = extras; |
260 | > | |
261 | > | while (current_extra != NULL){ |
262 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
263 | > | switch (current_extra->getType()){ |
264 | > | case 0: |
265 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
266 | > | theBends[j].isGhost = 1; |
267 | > | break; |
268 | > | |
269 | > | case 1: |
270 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
271 | > | atomOffset; |
272 | > | theBends[j].isGhost = 1; |
273 | > | break; |
274 | > | |
275 | > | default: |
276 | > | sprintf(painCave.errMsg, |
277 | > | "SimSetup Error: ghostVectorSource was neither a " |
278 | > | "double nor an int.\n" |
279 | > | "-->Bend[%d] in %s\n", |
280 | > | j, comp_stamps[stampID]->getID()); |
281 | > | painCave.isFatal = 1; |
282 | > | simError(); |
283 | > | } |
284 | > | } |
285 | > | else{ |
286 | > | sprintf(painCave.errMsg, |
287 | > | "SimSetup Error: unhandled bend assignment:\n" |
288 | > | " -->%s in Bend[%d] in %s\n", |
289 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
290 | > | painCave.isFatal = 1; |
291 | > | simError(); |
292 | > | } |
293 | > | |
294 | > | current_extra = current_extra->getNext(); |
295 | > | } |
296 | > | } |
297 | > | |
298 | > | if (!theBends[j].isGhost){ |
299 | > | exI = theBends[j].a; |
300 | > | exJ = theBends[j].c; |
301 | > | } |
302 | > | else{ |
303 | > | exI = theBends[j].a; |
304 | > | exJ = theBends[j].b; |
305 | > | } |
306 | > | |
307 | > | // exclude_I must always be the smaller of the pair |
308 | > | if (exI > exJ){ |
309 | > | tempEx = exI; |
310 | > | exI = exJ; |
311 | > | exJ = tempEx; |
312 | > | } |
313 | #ifdef IS_MPI | |
314 | < | tempEx = exI; |
315 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
316 | < | tempEx = exJ; |
317 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
318 | < | |
319 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
314 | > | tempEx = exI; |
315 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
316 | > | tempEx = exJ; |
317 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
318 | > | |
319 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
320 | #else // isn't MPI | |
321 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
321 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
322 | #endif //is_mpi | |
323 | } | |
324 | excludeOffset += molInfo.nBends; | |
325 | < | |
326 | < | for(j=0; j<molInfo.nTorsions; j++){ |
327 | < | |
328 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
329 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
330 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
331 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
332 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
333 | < | |
334 | < | exI = theTorsions[j].a; |
335 | < | exJ = theTorsions[j].d; |
336 | < | |
337 | < | // exclude_I must always be the smaller of the pair |
338 | < | if( exI > exJ ){ |
339 | < | tempEx = exI; |
340 | < | exI = exJ; |
341 | < | exJ = tempEx; |
366 | < | } |
325 | > | |
326 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
327 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
328 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
329 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
330 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
331 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
332 | > | |
333 | > | exI = theTorsions[j].a; |
334 | > | exJ = theTorsions[j].d; |
335 | > | |
336 | > | // exclude_I must always be the smaller of the pair |
337 | > | if (exI > exJ){ |
338 | > | tempEx = exI; |
339 | > | exI = exJ; |
340 | > | exJ = tempEx; |
341 | > | } |
342 | #ifdef IS_MPI | |
343 | < | tempEx = exI; |
344 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 | < | tempEx = exJ; |
346 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
347 | < | |
348 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
343 | > | tempEx = exI; |
344 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 | > | tempEx = exJ; |
346 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
347 | > | |
348 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
349 | #else // isn't MPI | |
350 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
350 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
351 | #endif //is_mpi | |
352 | } | |
353 | excludeOffset += molInfo.nTorsions; | |
354 | < | |
355 | < | |
354 | > | |
355 | > | |
356 | // send the arrays off to the forceField for init. | |
382 | – | |
383 | – | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
384 | – | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
385 | – | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
386 | – | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
387 | – | |
388 | – | |
389 | – | info[k].molecules[i].initialize( molInfo ); |
357 | ||
358 | < | |
358 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
359 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
360 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
361 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
362 | > | theTorsions); |
363 | > | |
364 | > | |
365 | > | info[k].molecules[i].initialize(molInfo); |
366 | > | |
367 | > | |
368 | atomOffset += molInfo.nAtoms; | |
369 | delete[] theBonds; | |
370 | delete[] theBends; | |
371 | delete[] theTorsions; | |
372 | } | |
373 | } | |
374 | < | |
374 | > | |
375 | #ifdef IS_MPI | |
376 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
376 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
377 | MPIcheckPoint(); | |
378 | #endif // is_mpi | |
379 | < | |
379 | > | |
380 | // clean up the forcefield | |
381 | ||
382 | the_ff->calcRcut(); | |
383 | the_ff->cleanMe(); | |
408 | – | |
384 | } | |
385 | ||
386 | < | void SimSetup::initFromBass( void ){ |
412 | < | |
386 | > | void SimSetup::initFromBass(void){ |
387 | int i, j, k; | |
388 | int n_cells; | |
389 | double cellx, celly, cellz; | |
# | Line 423 | Line 397 | void SimSetup::initFromBass( void ){ | |
397 | vel[1] = 0.0; | |
398 | vel[2] = 0.0; | |
399 | ||
400 | < | temp1 = (double)tot_nmol / 4.0; |
401 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
402 | < | temp3 = ceil( temp2 ); |
400 | > | temp1 = (double) tot_nmol / 4.0; |
401 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
402 | > | temp3 = ceil(temp2); |
403 | ||
404 | < | have_extra =0; |
405 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
406 | < | have_extra =1; |
404 | > | have_extra = 0; |
405 | > | if (temp2 < temp3){ |
406 | > | // we have a non-complete lattice |
407 | > | have_extra = 1; |
408 | ||
409 | < | n_cells = (int)temp3 - 1; |
409 | > | n_cells = (int) temp3 - 1; |
410 | cellx = info[0].boxL[0] / temp3; | |
411 | celly = info[0].boxL[1] / temp3; | |
412 | cellz = info[0].boxL[2] / temp3; | |
413 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
414 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
415 | < | n_per_extra = (int)ceil( temp1 ); |
413 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
414 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
415 | > | n_per_extra = (int) ceil(temp1); |
416 | ||
417 | < | if( n_per_extra > 4){ |
418 | < | sprintf( painCave.errMsg, |
419 | < | "SimSetup error. There has been an error in constructing" |
420 | < | " the non-complete lattice.\n" ); |
417 | > | if (n_per_extra > 4){ |
418 | > | sprintf(painCave.errMsg, |
419 | > | "SimSetup error. There has been an error in constructing" |
420 | > | " the non-complete lattice.\n"); |
421 | painCave.isFatal = 1; | |
422 | simError(); | |
423 | } | |
424 | } | |
425 | else{ | |
426 | < | n_cells = (int)temp3; |
426 | > | n_cells = (int) temp3; |
427 | cellx = info[0].boxL[0] / temp3; | |
428 | celly = info[0].boxL[1] / temp3; | |
429 | cellz = info[0].boxL[2] / temp3; | |
# | Line 459 | Line 434 | void SimSetup::initFromBass( void ){ | |
434 | current_comp = 0; | |
435 | current_atom_ndx = 0; | |
436 | ||
437 | < | for( i=0; i < n_cells ; i++ ){ |
438 | < | for( j=0; j < n_cells; j++ ){ |
439 | < | for( k=0; k < n_cells; k++ ){ |
437 | > | for (i = 0; i < n_cells ; i++){ |
438 | > | for (j = 0; j < n_cells; j++){ |
439 | > | for (k = 0; k < n_cells; k++){ |
440 | > | makeElement(i * cellx, j * celly, k * cellz); |
441 | ||
442 | < | makeElement( i * cellx, |
467 | < | j * celly, |
468 | < | k * cellz ); |
442 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
443 | ||
444 | < | makeElement( i * cellx + 0.5 * cellx, |
471 | < | j * celly + 0.5 * celly, |
472 | < | k * cellz ); |
444 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
445 | ||
446 | < | makeElement( i * cellx, |
475 | < | j * celly + 0.5 * celly, |
476 | < | k * cellz + 0.5 * cellz ); |
477 | < | |
478 | < | makeElement( i * cellx + 0.5 * cellx, |
479 | < | j * celly, |
480 | < | k * cellz + 0.5 * cellz ); |
446 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
447 | } | |
448 | } | |
449 | } | |
450 | ||
451 | < | if( have_extra ){ |
451 | > | if (have_extra){ |
452 | done = 0; | |
453 | ||
454 | int start_ndx; | |
455 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
456 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
455 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
456 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
457 | > | if (i < n_cells){ |
458 | > | if (j < n_cells){ |
459 | > | start_ndx = n_cells; |
460 | > | } |
461 | > | else |
462 | > | start_ndx = 0; |
463 | > | } |
464 | > | else |
465 | > | start_ndx = 0; |
466 | ||
467 | < | if( i < n_cells ){ |
467 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
468 | > | makeElement(i * cellx, j * celly, k * cellz); |
469 | > | done = (current_mol >= tot_nmol); |
470 | ||
471 | < | if( j < n_cells ){ |
472 | < | start_ndx = n_cells; |
473 | < | } |
474 | < | else start_ndx = 0; |
475 | < | } |
499 | < | else start_ndx = 0; |
471 | > | if (!done && n_per_extra > 1){ |
472 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
473 | > | k * cellz); |
474 | > | done = (current_mol >= tot_nmol); |
475 | > | } |
476 | ||
477 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
477 | > | if (!done && n_per_extra > 2){ |
478 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
479 | > | k * cellz + 0.5 * cellz); |
480 | > | done = (current_mol >= tot_nmol); |
481 | > | } |
482 | ||
483 | < | makeElement( i * cellx, |
484 | < | j * celly, |
485 | < | k * cellz ); |
486 | < | done = ( current_mol >= tot_nmol ); |
487 | < | |
488 | < | if( !done && n_per_extra > 1 ){ |
509 | < | makeElement( i * cellx + 0.5 * cellx, |
510 | < | j * celly + 0.5 * celly, |
511 | < | k * cellz ); |
512 | < | done = ( current_mol >= tot_nmol ); |
513 | < | } |
514 | < | |
515 | < | if( !done && n_per_extra > 2){ |
516 | < | makeElement( i * cellx, |
517 | < | j * celly + 0.5 * celly, |
518 | < | k * cellz + 0.5 * cellz ); |
519 | < | done = ( current_mol >= tot_nmol ); |
520 | < | } |
521 | < | |
522 | < | if( !done && n_per_extra > 3){ |
523 | < | makeElement( i * cellx + 0.5 * cellx, |
524 | < | j * celly, |
525 | < | k * cellz + 0.5 * cellz ); |
526 | < | done = ( current_mol >= tot_nmol ); |
527 | < | } |
528 | < | } |
483 | > | if (!done && n_per_extra > 3){ |
484 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
485 | > | k * cellz + 0.5 * cellz); |
486 | > | done = (current_mol >= tot_nmol); |
487 | > | } |
488 | > | } |
489 | } | |
490 | } | |
491 | } | |
492 | ||
493 | < | for( i=0; i<info[0].n_atoms; i++ ){ |
494 | < | info[0].atoms[i]->setVel( vel ); |
493 | > | for (i = 0; i < info[0].n_atoms; i++){ |
494 | > | info[0].atoms[i]->setVel(vel); |
495 | } | |
496 | } | |
497 | ||
498 | < | void SimSetup::makeElement( double x, double y, double z ){ |
539 | < | |
498 | > | void SimSetup::makeElement(double x, double y, double z){ |
499 | int k; | |
500 | AtomStamp* current_atom; | |
501 | DirectionalAtom* dAtom; | |
502 | double rotMat[3][3]; | |
503 | double pos[3]; | |
504 | ||
505 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
506 | < | |
507 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
508 | < | if( !current_atom->havePosition() ){ |
509 | < | sprintf( painCave.errMsg, |
510 | < | "SimSetup:initFromBass error.\n" |
511 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
512 | < | "\tThe initialization routine is unable to give a start" |
513 | < | " position.\n", |
555 | < | comp_stamps[current_comp]->getID(), |
556 | < | current_atom->getType() ); |
505 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
506 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
507 | > | if (!current_atom->havePosition()){ |
508 | > | sprintf(painCave.errMsg, |
509 | > | "SimSetup:initFromBass error.\n" |
510 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
511 | > | "\tThe initialization routine is unable to give a start" |
512 | > | " position.\n", |
513 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
514 | painCave.isFatal = 1; | |
515 | simError(); | |
516 | } | |
517 | < | |
517 | > | |
518 | pos[0] = x + current_atom->getPosX(); | |
519 | pos[1] = y + current_atom->getPosY(); | |
520 | pos[2] = z + current_atom->getPosZ(); | |
564 | – | |
565 | – | info[0].atoms[current_atom_ndx]->setPos( pos ); |
521 | ||
522 | < | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
522 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
523 | ||
524 | < | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
524 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
525 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
526 | ||
527 | rotMat[0][0] = 1.0; | |
528 | rotMat[0][1] = 0.0; | |
# | Line 580 | Line 536 | void SimSetup::makeElement( double x, double y, double | |
536 | rotMat[2][1] = 0.0; | |
537 | rotMat[2][2] = 1.0; | |
538 | ||
539 | < | dAtom->setA( rotMat ); |
539 | > | dAtom->setA(rotMat); |
540 | } | |
541 | ||
542 | current_atom_ndx++; | |
# | Line 589 | Line 545 | void SimSetup::makeElement( double x, double y, double | |
545 | current_mol++; | |
546 | current_comp_mol++; | |
547 | ||
548 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
593 | < | |
548 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
549 | current_comp_mol = 0; | |
550 | current_comp++; | |
551 | } | |
552 | } | |
553 | ||
554 | ||
555 | < | void SimSetup::gatherInfo( void ){ |
556 | < | int i,j,k; |
555 | > | void SimSetup::gatherInfo(void){ |
556 | > | int i, j, k; |
557 | ||
558 | ensembleCase = -1; | |
559 | ffCase = -1; | |
560 | ||
561 | // set the easy ones first | |
562 | ||
563 | < | for( i=0; i<nInfo; i++){ |
563 | > | for (i = 0; i < nInfo; i++){ |
564 | info[i].target_temp = globals->getTargetTemp(); | |
565 | info[i].dt = globals->getDt(); | |
566 | info[i].run_time = globals->getRunTime(); | |
# | Line 615 | Line 570 | void SimSetup::gatherInfo( void ){ | |
570 | ||
571 | // get the forceField | |
572 | ||
573 | < | strcpy( force_field, globals->getForceField() ); |
573 | > | strcpy(force_field, globals->getForceField()); |
574 | ||
575 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
576 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
577 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
575 | > | if (!strcasecmp(force_field, "DUFF")){ |
576 | > | ffCase = FF_DUFF; |
577 | > | } |
578 | > | else if (!strcasecmp(force_field, "LJ")){ |
579 | > | ffCase = FF_LJ; |
580 | > | } |
581 | > | else if (!strcasecmp(force_field, "EAM")){ |
582 | > | ffCase = FF_EAM; |
583 | > | } |
584 | else{ | |
585 | < | sprintf( painCave.errMsg, |
586 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
587 | < | force_field ); |
588 | < | painCave.isFatal = 1; |
628 | < | simError(); |
585 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
586 | > | force_field); |
587 | > | painCave.isFatal = 1; |
588 | > | simError(); |
589 | } | |
590 | ||
591 | < | // get the ensemble |
591 | > | // get the ensemble |
592 | ||
593 | < | strcpy( ensemble, globals->getEnsemble() ); |
593 | > | strcpy(ensemble, globals->getEnsemble()); |
594 | ||
595 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
596 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
597 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
595 | > | if (!strcasecmp(ensemble, "NVE")){ |
596 | > | ensembleCase = NVE_ENS; |
597 | > | } |
598 | > | else if (!strcasecmp(ensemble, "NVT")){ |
599 | > | ensembleCase = NVT_ENS; |
600 | > | } |
601 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
602 | ensembleCase = NPTi_ENS; | |
603 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
604 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
605 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
606 | < | |
607 | < | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
608 | < | else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
609 | < | else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS")) |
610 | < | ensembleCase = NPTiZCONS_ENS; |
611 | < | else if( !strcasecmp( ensemble, "NPTfZCONS")) ensembleCase = NPTfZCONS_ENS; |
612 | < | else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
649 | < | else if( !strcasecmp( ensemble, "NPTfmZCONS")) ensembleCase = NPTfmZCONS_ENS; |
650 | < | |
603 | > | } |
604 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
605 | > | ensembleCase = NPTf_ENS; |
606 | > | } |
607 | > | else if (!strcasecmp(ensemble, "NPTim")){ |
608 | > | ensembleCase = NPTim_ENS; |
609 | > | } |
610 | > | else if (!strcasecmp(ensemble, "NPTfm")){ |
611 | > | ensembleCase = NPTfm_ENS; |
612 | > | } |
613 | else{ | |
614 | < | sprintf( painCave.errMsg, |
615 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
616 | < | "reverting to NVE for this simulation.\n", |
617 | < | ensemble ); |
618 | < | painCave.isFatal = 0; |
619 | < | simError(); |
620 | < | strcpy( ensemble, "NVE" ); |
621 | < | ensembleCase = NVE_ENS; |
614 | > | sprintf(painCave.errMsg, |
615 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
616 | > | "reverting to NVE for this simulation.\n", |
617 | > | ensemble); |
618 | > | painCave.isFatal = 0; |
619 | > | simError(); |
620 | > | strcpy(ensemble, "NVE"); |
621 | > | ensembleCase = NVE_ENS; |
622 | } | |
661 | – | |
662 | – | for(i=0; i<nInfo; i++){ |
663 | – | |
664 | – | strcpy( info[i].ensemble, ensemble ); |
623 | ||
624 | + | for (i = 0; i < nInfo; i++){ |
625 | + | strcpy(info[i].ensemble, ensemble); |
626 | + | |
627 | // get the mixing rule | |
628 | ||
629 | < | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
629 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
630 | info[i].usePBC = globals->getPBC(); | |
631 | } | |
632 | < | |
632 | > | |
633 | // get the components and calculate the tot_nMol and indvidual n_mol | |
634 | < | |
634 | > | |
635 | the_components = globals->getComponents(); | |
636 | components_nmol = new int[n_components]; | |
637 | ||
638 | ||
639 | < | if( !globals->haveNMol() ){ |
639 | > | if (!globals->haveNMol()){ |
640 | // we don't have the total number of molecules, so we assume it is | |
641 | // given in each component | |
642 | ||
643 | tot_nmol = 0; | |
644 | < | for( i=0; i<n_components; i++ ){ |
645 | < | |
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; |
691 | < | simError(); |
644 | > | for (i = 0; i < n_components; i++){ |
645 | > | if (!the_components[i]->haveNMol()){ |
646 | > | // we have a problem |
647 | > | sprintf(painCave.errMsg, |
648 | > | "SimSetup Error. No global NMol or component NMol" |
649 | > | " given. Cannot calculate the number of atoms.\n"); |
650 | > | painCave.isFatal = 1; |
651 | > | simError(); |
652 | } | |
653 | ||
654 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 696 | Line 656 | void SimSetup::gatherInfo( void ){ | |
656 | } | |
657 | } | |
658 | else{ | |
659 | < | sprintf( painCave.errMsg, |
660 | < | "SimSetup error.\n" |
661 | < | "\tSorry, the ability to specify total" |
662 | < | " nMols and then give molfractions in the components\n" |
663 | < | "\tis not currently supported." |
664 | < | " Please give nMol in the components.\n" ); |
659 | > | sprintf(painCave.errMsg, |
660 | > | "SimSetup error.\n" |
661 | > | "\tSorry, the ability to specify total" |
662 | > | " nMols and then give molfractions in the components\n" |
663 | > | "\tis not currently supported." |
664 | > | " Please give nMol in the components.\n"); |
665 | painCave.isFatal = 1; | |
666 | simError(); | |
667 | } | |
668 | ||
669 | // set the status, sample, and thermal kick times | |
710 | – | |
711 | – | for(i=0; i<nInfo; i++){ |
670 | ||
671 | < | if( globals->haveSampleTime() ){ |
671 | > | for (i = 0; i < nInfo; i++){ |
672 | > | if (globals->haveSampleTime()){ |
673 | info[i].sampleTime = globals->getSampleTime(); | |
674 | info[i].statusTime = info[i].sampleTime; | |
675 | info[i].thermalTime = info[i].sampleTime; | |
# | Line 720 | Line 679 | void SimSetup::gatherInfo( void ){ | |
679 | info[i].statusTime = info[i].sampleTime; | |
680 | info[i].thermalTime = info[i].sampleTime; | |
681 | } | |
682 | < | |
683 | < | if( globals->haveStatusTime() ){ |
682 | > | |
683 | > | if (globals->haveStatusTime()){ |
684 | info[i].statusTime = globals->getStatusTime(); | |
685 | } | |
686 | < | |
687 | < | if( globals->haveThermalTime() ){ |
686 | > | |
687 | > | if (globals->haveThermalTime()){ |
688 | info[i].thermalTime = globals->getThermalTime(); | |
689 | } | |
690 | ||
691 | // check for the temperature set flag | |
692 | ||
693 | < | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
694 | < | |
693 | > | if (globals->haveTempSet()) |
694 | > | info[i].setTemp = globals->getTempSet(); |
695 | > | |
696 | // get some of the tricky things that may still be in the globals | |
697 | < | |
697 | > | |
698 | double boxVector[3]; | |
699 | < | if( globals->haveBox() ){ |
699 | > | if (globals->haveBox()){ |
700 | boxVector[0] = globals->getBox(); | |
701 | boxVector[1] = globals->getBox(); | |
702 | boxVector[2] = globals->getBox(); | |
703 | < | |
704 | < | info[i].setBox( boxVector ); |
703 | > | |
704 | > | info[i].setBox(boxVector); |
705 | } | |
706 | < | else if( globals->haveDensity() ){ |
747 | < | |
706 | > | else if (globals->haveDensity()){ |
707 | double vol; | |
708 | < | vol = (double)tot_nmol / globals->getDensity(); |
709 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
708 | > | vol = (double) tot_nmol / globals->getDensity(); |
709 | > | boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 | boxVector[1] = boxVector[0]; | |
711 | boxVector[2] = boxVector[0]; | |
712 | < | |
713 | < | info[i].setBox( boxVector ); |
714 | < | } |
712 | > | |
713 | > | info[i].setBox(boxVector); |
714 | > | } |
715 | else{ | |
716 | < | if( !globals->haveBoxX() ){ |
717 | < | sprintf( painCave.errMsg, |
718 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
719 | < | painCave.isFatal = 1; |
720 | < | simError(); |
716 | > | if (!globals->haveBoxX()){ |
717 | > | sprintf(painCave.errMsg, |
718 | > | "SimSetup error, no periodic BoxX size given.\n"); |
719 | > | painCave.isFatal = 1; |
720 | > | simError(); |
721 | } | |
722 | boxVector[0] = globals->getBoxX(); | |
723 | < | |
724 | < | if( !globals->haveBoxY() ){ |
725 | < | sprintf( painCave.errMsg, |
726 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
727 | < | painCave.isFatal = 1; |
728 | < | simError(); |
723 | > | |
724 | > | if (!globals->haveBoxY()){ |
725 | > | sprintf(painCave.errMsg, |
726 | > | "SimSetup error, no periodic BoxY size given.\n"); |
727 | > | painCave.isFatal = 1; |
728 | > | simError(); |
729 | } | |
730 | boxVector[1] = globals->getBoxY(); | |
731 | < | |
732 | < | if( !globals->haveBoxZ() ){ |
733 | < | sprintf( painCave.errMsg, |
734 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
735 | < | painCave.isFatal = 1; |
736 | < | simError(); |
731 | > | |
732 | > | if (!globals->haveBoxZ()){ |
733 | > | sprintf(painCave.errMsg, |
734 | > | "SimSetup error, no periodic BoxZ size given.\n"); |
735 | > | painCave.isFatal = 1; |
736 | > | simError(); |
737 | } | |
738 | boxVector[2] = globals->getBoxZ(); | |
780 | – | |
781 | – | info[i].setBox( boxVector ); |
782 | – | } |
739 | ||
740 | + | info[i].setBox(boxVector); |
741 | + | } |
742 | } | |
743 | + | |
744 | + | //setup seed for random number generator |
745 | + | int seedValue; |
746 | + | |
747 | + | if (globals->haveSeed()){ |
748 | + | seedValue = globals->getSeed(); |
749 | + | |
750 | + | if(seedValue / 1E9 == 0){ |
751 | + | sprintf(painCave.errMsg, |
752 | + | "Seed for sprng library should contain at least 9 digits\n" |
753 | + | "OOPSE will generate a seed for user\n"); |
754 | + | painCave.isFatal = 0; |
755 | + | simError(); |
756 | + | |
757 | + | //using seed generated by system instead of invalid seed set by user |
758 | + | #ifndef IS_MPI |
759 | + | seedValue = make_sprng_seed(); |
760 | + | #else |
761 | + | if (worldRank == 0){ |
762 | + | seedValue = make_sprng_seed(); |
763 | + | } |
764 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
765 | + | #endif |
766 | + | } |
767 | + | }//end of if branch of globals->haveSeed() |
768 | + | else{ |
769 | ||
770 | + | #ifndef IS_MPI |
771 | + | seedValue = make_sprng_seed(); |
772 | + | #else |
773 | + | if (worldRank == 0){ |
774 | + | seedValue = make_sprng_seed(); |
775 | + | } |
776 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
777 | + | #endif |
778 | + | }//end of globals->haveSeed() |
779 | + | |
780 | + | for (int i = 0; i < nInfo; i++){ |
781 | + | info[i].setSeed(seedValue); |
782 | + | } |
783 | + | |
784 | #ifdef IS_MPI | |
785 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
785 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
786 | MPIcheckPoint(); | |
787 | #endif // is_mpi | |
790 | – | |
788 | } | |
789 | ||
790 | ||
791 | < | void SimSetup::finalInfoCheck( void ){ |
791 | > | void SimSetup::finalInfoCheck(void){ |
792 | int index; | |
793 | int usesDipoles; | |
794 | int i; | |
795 | ||
796 | < | for(i=0; i<nInfo; i++){ |
796 | > | for (i = 0; i < nInfo; i++){ |
797 | // check electrostatic parameters | |
798 | < | |
798 | > | |
799 | index = 0; | |
800 | usesDipoles = 0; | |
801 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
801 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
802 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
803 | index++; | |
804 | } | |
805 | < | |
805 | > | |
806 | #ifdef IS_MPI | |
807 | int myUse = usesDipoles; | |
808 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
808 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
809 | #endif //is_mpi | |
810 | < | |
810 | > | |
811 | double theEcr, theEst; | |
812 | < | |
813 | < | if (globals->getUseRF() ) { |
812 | > | |
813 | > | if (globals->getUseRF()){ |
814 | info[i].useReactionField = 1; | |
815 | < | |
816 | < | if( !globals->haveECR() ){ |
817 | < | sprintf( painCave.errMsg, |
818 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
819 | < | "box length for the electrostaticCutoffRadius.\n" |
820 | < | "I hope you have a very fast processor!\n"); |
821 | < | painCave.isFatal = 0; |
822 | < | simError(); |
823 | < | double smallest; |
824 | < | smallest = info[i].boxL[0]; |
825 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
826 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
827 | < | theEcr = 0.5 * smallest; |
828 | < | } else { |
829 | < | theEcr = globals->getECR(); |
815 | > | |
816 | > | if (!globals->haveECR()){ |
817 | > | sprintf(painCave.errMsg, |
818 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
819 | > | "box length for the electrostaticCutoffRadius.\n" |
820 | > | "I hope you have a very fast processor!\n"); |
821 | > | painCave.isFatal = 0; |
822 | > | simError(); |
823 | > | double smallest; |
824 | > | smallest = info[i].boxL[0]; |
825 | > | if (info[i].boxL[1] <= smallest) |
826 | > | smallest = info[i].boxL[1]; |
827 | > | if (info[i].boxL[2] <= smallest) |
828 | > | smallest = info[i].boxL[2]; |
829 | > | theEcr = 0.5 * smallest; |
830 | } | |
831 | < | |
832 | < | if( !globals->haveEST() ){ |
836 | < | sprintf( painCave.errMsg, |
837 | < | "SimSetup Warning: using default value of 0.05 * the " |
838 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
839 | < | ); |
840 | < | painCave.isFatal = 0; |
841 | < | simError(); |
842 | < | theEst = 0.05 * theEcr; |
843 | < | } else { |
844 | < | theEst= globals->getEST(); |
831 | > | else{ |
832 | > | theEcr = globals->getECR(); |
833 | } | |
834 | < | |
835 | < | info[i].setEcr( theEcr, theEst ); |
836 | < | |
837 | < | if(!globals->haveDielectric() ){ |
838 | < | sprintf( painCave.errMsg, |
839 | < | "SimSetup Error: You are trying to use Reaction Field without" |
840 | < | "setting a dielectric constant!\n" |
841 | < | ); |
854 | < | painCave.isFatal = 1; |
855 | < | simError(); |
834 | > | |
835 | > | if (!globals->haveEST()){ |
836 | > | sprintf(painCave.errMsg, |
837 | > | "SimSetup Warning: using default value of 0.05 * the " |
838 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
839 | > | painCave.isFatal = 0; |
840 | > | simError(); |
841 | > | theEst = 0.05 * theEcr; |
842 | } | |
843 | < | info[i].dielectric = globals->getDielectric(); |
844 | < | } |
859 | < | else { |
860 | < | if (usesDipoles) { |
861 | < | |
862 | < | if( !globals->haveECR() ){ |
863 | < | sprintf( painCave.errMsg, |
864 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
865 | < | "box length for the electrostaticCutoffRadius.\n" |
866 | < | "I hope you have a very fast processor!\n"); |
867 | < | painCave.isFatal = 0; |
868 | < | simError(); |
869 | < | double smallest; |
870 | < | smallest = info[i].boxL[0]; |
871 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
872 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
873 | < | theEcr = 0.5 * smallest; |
874 | < | } else { |
875 | < | theEcr = globals->getECR(); |
876 | < | } |
877 | < | |
878 | < | if( !globals->haveEST() ){ |
879 | < | sprintf( painCave.errMsg, |
880 | < | "SimSetup Warning: using default value of 0.05 * the " |
881 | < | "electrostaticCutoffRadius for the " |
882 | < | "electrostaticSkinThickness\n" |
883 | < | ); |
884 | < | painCave.isFatal = 0; |
885 | < | simError(); |
886 | < | theEst = 0.05 * theEcr; |
887 | < | } else { |
888 | < | theEst= globals->getEST(); |
889 | < | } |
890 | < | |
891 | < | info[i].setEcr( theEcr, theEst ); |
843 | > | else{ |
844 | > | theEst = globals->getEST(); |
845 | } | |
893 | – | } |
894 | – | } |
846 | ||
847 | < | #ifdef IS_MPI |
897 | < | strcpy( checkPointMsg, "post processing checks out" ); |
898 | < | MPIcheckPoint(); |
899 | < | #endif // is_mpi |
847 | > | info[i].setEcr(theEcr, theEst); |
848 | ||
849 | < | } |
849 | > | if (!globals->haveDielectric()){ |
850 | > | sprintf(painCave.errMsg, |
851 | > | "SimSetup Error: You are trying to use Reaction Field without" |
852 | > | "setting a dielectric constant!\n"); |
853 | > | painCave.isFatal = 1; |
854 | > | simError(); |
855 | > | } |
856 | > | info[i].dielectric = globals->getDielectric(); |
857 | > | } |
858 | > | else{ |
859 | > | if (usesDipoles){ |
860 | > | if (!globals->haveECR()){ |
861 | > | sprintf(painCave.errMsg, |
862 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
863 | > | "box length for the electrostaticCutoffRadius.\n" |
864 | > | "I hope you have a very fast processor!\n"); |
865 | > | painCave.isFatal = 0; |
866 | > | simError(); |
867 | > | double smallest; |
868 | > | smallest = info[i].boxL[0]; |
869 | > | if (info[i].boxL[1] <= smallest) |
870 | > | smallest = info[i].boxL[1]; |
871 | > | if (info[i].boxL[2] <= smallest) |
872 | > | smallest = info[i].boxL[2]; |
873 | > | theEcr = 0.5 * smallest; |
874 | > | } |
875 | > | else{ |
876 | > | theEcr = globals->getECR(); |
877 | > | } |
878 | ||
879 | < | void SimSetup::initSystemCoords( void ){ |
880 | < | int i; |
881 | < | |
882 | < | std::cerr << "Setting atom Coords\n"; |
883 | < | |
884 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
885 | < | |
886 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
887 | < | |
888 | < | if( globals->haveInitialConfig() ){ |
889 | < | |
879 | > | if (!globals->haveEST()){ |
880 | > | sprintf(painCave.errMsg, |
881 | > | "SimSetup Warning: using default value of 0.05 * the " |
882 | > | "electrostaticCutoffRadius for the " |
883 | > | "electrostaticSkinThickness\n"); |
884 | > | painCave.isFatal = 0; |
885 | > | simError(); |
886 | > | theEst = 0.05 * theEcr; |
887 | > | } |
888 | > | else{ |
889 | > | theEst = globals->getEST(); |
890 | > | } |
891 | > | |
892 | > | info[i].setEcr(theEcr, theEst); |
893 | > | } |
894 | > | } |
895 | > | } |
896 | > | |
897 | > | #ifdef IS_MPI |
898 | > | strcpy(checkPointMsg, "post processing checks out"); |
899 | > | MPIcheckPoint(); |
900 | > | #endif // is_mpi |
901 | > | } |
902 | > | |
903 | > | void SimSetup::initSystemCoords(void){ |
904 | > | int i; |
905 | > | |
906 | > | char* inName; |
907 | > | |
908 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
909 | > | |
910 | > | for (i = 0; i < info[0].n_atoms; i++) |
911 | > | info[0].atoms[i]->setCoords(); |
912 | > | |
913 | > | if (globals->haveInitialConfig()){ |
914 | InitializeFromFile* fileInit; | |
915 | #ifdef IS_MPI // is_mpi | |
916 | < | if( worldRank == 0 ){ |
916 | > | if (worldRank == 0){ |
917 | #endif //is_mpi | |
918 | < | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
918 | > | inName = globals->getInitialConfig(); |
919 | > | double* tempDouble = new double[1000000]; |
920 | > | fileInit = new InitializeFromFile(inName); |
921 | #ifdef IS_MPI | |
922 | < | }else fileInit = new InitializeFromFile( NULL ); |
922 | > | } |
923 | > | else |
924 | > | fileInit = new InitializeFromFile(NULL); |
925 | #endif | |
926 | < | fileInit->readInit( info ); // default velocities on |
927 | < | |
926 | > | fileInit->readInit(info); // default velocities on |
927 | > | |
928 | delete fileInit; | |
929 | } | |
930 | else{ | |
927 | – | |
931 | #ifdef IS_MPI | |
932 | < | |
932 | > | |
933 | // no init from bass | |
934 | < | |
935 | < | sprintf( painCave.errMsg, |
936 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
934 | > | |
935 | > | sprintf(painCave.errMsg, |
936 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
937 | painCave.isFatal; | |
938 | simError(); | |
939 | < | |
939 | > | |
940 | #else | |
941 | < | |
941 | > | |
942 | initFromBass(); | |
943 | < | |
944 | < | |
943 | > | |
944 | > | |
945 | #endif | |
946 | } | |
947 | < | |
947 | > | |
948 | #ifdef IS_MPI | |
949 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
949 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
950 | MPIcheckPoint(); | |
951 | #endif // is_mpi | |
949 | – | |
952 | } | |
953 | ||
954 | ||
955 | < | void SimSetup::makeOutNames( void ){ |
954 | < | |
955 | > | void SimSetup::makeOutNames(void){ |
956 | int k; | |
957 | ||
957 | – | |
958 | – | for(k=0; k<nInfo; k++){ |
958 | ||
959 | + | for (k = 0; k < nInfo; k++){ |
960 | #ifdef IS_MPI | |
961 | < | if( worldRank == 0 ){ |
961 | > | if (worldRank == 0){ |
962 | #endif // is_mpi | |
963 | < | |
964 | < | if( globals->haveFinalConfig() ){ |
965 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
963 | > | |
964 | > | if (globals->haveFinalConfig()){ |
965 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
966 | } | |
967 | else{ | |
968 | < | strcpy( info[k].finalName, inFileName ); |
969 | < | char* endTest; |
970 | < | int nameLength = strlen( info[k].finalName ); |
971 | < | endTest = &(info[k].finalName[nameLength - 5]); |
972 | < | if( !strcmp( endTest, ".bass" ) ){ |
973 | < | strcpy( endTest, ".eor" ); |
974 | < | } |
975 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
976 | < | strcpy( endTest, ".eor" ); |
977 | < | } |
978 | < | else{ |
979 | < | endTest = &(info[k].finalName[nameLength - 4]); |
980 | < | if( !strcmp( endTest, ".bss" ) ){ |
981 | < | strcpy( endTest, ".eor" ); |
982 | < | } |
983 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
984 | < | strcpy( endTest, ".eor" ); |
985 | < | } |
986 | < | else{ |
987 | < | strcat( info[k].finalName, ".eor" ); |
988 | < | } |
989 | < | } |
968 | > | strcpy(info[k].finalName, inFileName); |
969 | > | char* endTest; |
970 | > | int nameLength = strlen(info[k].finalName); |
971 | > | endTest = &(info[k].finalName[nameLength - 5]); |
972 | > | if (!strcmp(endTest, ".bass")){ |
973 | > | strcpy(endTest, ".eor"); |
974 | > | } |
975 | > | else if (!strcmp(endTest, ".BASS")){ |
976 | > | strcpy(endTest, ".eor"); |
977 | > | } |
978 | > | else{ |
979 | > | endTest = &(info[k].finalName[nameLength - 4]); |
980 | > | if (!strcmp(endTest, ".bss")){ |
981 | > | strcpy(endTest, ".eor"); |
982 | > | } |
983 | > | else if (!strcmp(endTest, ".mdl")){ |
984 | > | strcpy(endTest, ".eor"); |
985 | > | } |
986 | > | else{ |
987 | > | strcat(info[k].finalName, ".eor"); |
988 | > | } |
989 | > | } |
990 | } | |
991 | < | |
991 | > | |
992 | // make the sample and status out names | |
993 | < | |
994 | < | strcpy( info[k].sampleName, inFileName ); |
993 | > | |
994 | > | strcpy(info[k].sampleName, inFileName); |
995 | char* endTest; | |
996 | < | int nameLength = strlen( info[k].sampleName ); |
996 | > | int nameLength = strlen(info[k].sampleName); |
997 | endTest = &(info[k].sampleName[nameLength - 5]); | |
998 | < | if( !strcmp( endTest, ".bass" ) ){ |
999 | < | strcpy( endTest, ".dump" ); |
998 | > | if (!strcmp(endTest, ".bass")){ |
999 | > | strcpy(endTest, ".dump"); |
1000 | } | |
1001 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1002 | < | strcpy( endTest, ".dump" ); |
1001 | > | else if (!strcmp(endTest, ".BASS")){ |
1002 | > | strcpy(endTest, ".dump"); |
1003 | } | |
1004 | else{ | |
1005 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1006 | < | if( !strcmp( endTest, ".bss" ) ){ |
1007 | < | strcpy( endTest, ".dump" ); |
1008 | < | } |
1009 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1010 | < | strcpy( endTest, ".dump" ); |
1011 | < | } |
1012 | < | else{ |
1013 | < | strcat( info[k].sampleName, ".dump" ); |
1014 | < | } |
1015 | < | } |
1016 | < | |
1017 | < | strcpy( info[k].statusName, inFileName ); |
1018 | < | nameLength = strlen( info[k].statusName ); |
1019 | < | endTest = &(info[k].statusName[nameLength - 5]); |
1020 | < | if( !strcmp( endTest, ".bass" ) ){ |
1021 | < | strcpy( endTest, ".stat" ); |
1022 | < | } |
1023 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1024 | < | strcpy( endTest, ".stat" ); |
1005 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1006 | > | if (!strcmp(endTest, ".bss")){ |
1007 | > | strcpy(endTest, ".dump"); |
1008 | > | } |
1009 | > | else if (!strcmp(endTest, ".mdl")){ |
1010 | > | strcpy(endTest, ".dump"); |
1011 | > | } |
1012 | > | else{ |
1013 | > | strcat(info[k].sampleName, ".dump"); |
1014 | > | } |
1015 | } | |
1016 | + | |
1017 | + | strcpy(info[k].statusName, inFileName); |
1018 | + | nameLength = strlen(info[k].statusName); |
1019 | + | endTest = &(info[k].statusName[nameLength - 5]); |
1020 | + | if (!strcmp(endTest, ".bass")){ |
1021 | + | strcpy(endTest, ".stat"); |
1022 | + | } |
1023 | + | else if (!strcmp(endTest, ".BASS")){ |
1024 | + | strcpy(endTest, ".stat"); |
1025 | + | } |
1026 | else{ | |
1027 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1028 | < | if( !strcmp( endTest, ".bss" ) ){ |
1029 | < | strcpy( endTest, ".stat" ); |
1030 | < | } |
1031 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1032 | < | strcpy( endTest, ".stat" ); |
1033 | < | } |
1034 | < | else{ |
1035 | < | strcat( info[k].statusName, ".stat" ); |
1036 | < | } |
1027 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1028 | > | if (!strcmp(endTest, ".bss")){ |
1029 | > | strcpy(endTest, ".stat"); |
1030 | > | } |
1031 | > | else if (!strcmp(endTest, ".mdl")){ |
1032 | > | strcpy(endTest, ".stat"); |
1033 | > | } |
1034 | > | else{ |
1035 | > | strcat(info[k].statusName, ".stat"); |
1036 | > | } |
1037 | } | |
1038 | < | |
1038 | > | |
1039 | #ifdef IS_MPI | |
1040 | + | |
1041 | } | |
1042 | #endif // is_mpi | |
1043 | } | |
1044 | } | |
1045 | ||
1046 | ||
1047 | < | void SimSetup::sysObjectsCreation( void ){ |
1048 | < | |
1049 | < | int i,k; |
1049 | < | |
1047 | > | void SimSetup::sysObjectsCreation(void){ |
1048 | > | int i, k; |
1049 | > | |
1050 | // create the forceField | |
1051 | < | |
1051 | > | |
1052 | createFF(); | |
1053 | ||
1054 | // extract componentList | |
# | Line 1061 | Line 1061 | void SimSetup::sysObjectsCreation( void ){ | |
1061 | ||
1062 | #ifdef IS_MPI | |
1063 | // divide the molecules among the processors | |
1064 | < | |
1064 | > | |
1065 | mpiMolDivide(); | |
1066 | #endif //is_mpi | |
1067 | < | |
1067 | > | |
1068 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1069 | < | |
1069 | > | |
1070 | makeSysArrays(); | |
1071 | ||
1072 | // make and initialize the molecules (all but atomic coordinates) | |
1073 | < | |
1073 | > | |
1074 | makeMolecules(); | |
1075 | < | |
1076 | < | for(k=0; k<nInfo; k++){ |
1075 | > | |
1076 | > | for (k = 0; k < nInfo; k++){ |
1077 | info[k].identArray = new int[info[k].n_atoms]; | |
1078 | < | for(i=0; i<info[k].n_atoms; i++){ |
1078 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1079 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1080 | } | |
1081 | } | |
1082 | } | |
1083 | ||
1084 | ||
1085 | < | void SimSetup::createFF( void ){ |
1085 | > | void SimSetup::createFF(void){ |
1086 | > | switch (ffCase){ |
1087 | > | case FF_DUFF: |
1088 | > | the_ff = new DUFF(); |
1089 | > | break; |
1090 | ||
1091 | < | switch( ffCase ){ |
1091 | > | case FF_LJ: |
1092 | > | the_ff = new LJFF(); |
1093 | > | break; |
1094 | ||
1095 | < | case FF_DUFF: |
1096 | < | the_ff = new DUFF(); |
1097 | < | break; |
1095 | > | case FF_EAM: |
1096 | > | the_ff = new EAM_FF(); |
1097 | > | break; |
1098 | ||
1099 | < | case FF_LJ: |
1100 | < | the_ff = new LJFF(); |
1101 | < | break; |
1102 | < | |
1103 | < | case FF_EAM: |
1098 | < | the_ff = new EAM_FF(); |
1099 | < | break; |
1100 | < | |
1101 | < | default: |
1102 | < | sprintf( painCave.errMsg, |
1103 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1104 | < | painCave.isFatal = 1; |
1105 | < | simError(); |
1099 | > | default: |
1100 | > | sprintf(painCave.errMsg, |
1101 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1102 | > | painCave.isFatal = 1; |
1103 | > | simError(); |
1104 | } | |
1105 | ||
1106 | #ifdef IS_MPI | |
1107 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1107 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1108 | MPIcheckPoint(); | |
1109 | #endif // is_mpi | |
1112 | – | |
1110 | } | |
1111 | ||
1112 | ||
1113 | < | void SimSetup::compList( void ){ |
1117 | < | |
1113 | > | void SimSetup::compList(void){ |
1114 | int i; | |
1115 | char* id; | |
1116 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1117 | LinkedMolStamp* currentStamp = NULL; | |
1118 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1119 | < | |
1118 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1119 | > | |
1120 | // make an array of molecule stamps that match the components used. | |
1121 | // also extract the used stamps out into a separate linked list | |
1122 | < | |
1123 | < | for(i=0; i<nInfo; i++){ |
1122 | > | |
1123 | > | for (i = 0; i < nInfo; i++){ |
1124 | info[i].nComponents = n_components; | |
1125 | info[i].componentsNmol = components_nmol; | |
1126 | info[i].compStamps = comp_stamps; | |
1127 | info[i].headStamp = headStamp; | |
1128 | } | |
1133 | – | |
1129 | ||
1135 | – | for( i=0; i<n_components; i++ ){ |
1130 | ||
1131 | + | for (i = 0; i < n_components; i++){ |
1132 | id = the_components[i]->getType(); | |
1133 | comp_stamps[i] = NULL; | |
1134 | < | |
1134 | > | |
1135 | // check to make sure the component isn't already in the list | |
1136 | ||
1137 | < | comp_stamps[i] = headStamp->match( id ); |
1138 | < | if( comp_stamps[i] == NULL ){ |
1144 | < | |
1137 | > | comp_stamps[i] = headStamp->match(id); |
1138 | > | if (comp_stamps[i] == NULL){ |
1139 | // extract the component from the list; | |
1140 | < | |
1141 | < | currentStamp = stamps->extractMolStamp( id ); |
1142 | < | if( currentStamp == NULL ){ |
1143 | < | sprintf( painCave.errMsg, |
1144 | < | "SimSetup error: Component \"%s\" was not found in the " |
1145 | < | "list of declared molecules\n", |
1146 | < | id ); |
1147 | < | painCave.isFatal = 1; |
1148 | < | simError(); |
1140 | > | |
1141 | > | currentStamp = stamps->extractMolStamp(id); |
1142 | > | if (currentStamp == NULL){ |
1143 | > | sprintf(painCave.errMsg, |
1144 | > | "SimSetup error: Component \"%s\" was not found in the " |
1145 | > | "list of declared molecules\n", |
1146 | > | id); |
1147 | > | painCave.isFatal = 1; |
1148 | > | simError(); |
1149 | } | |
1150 | < | |
1151 | < | headStamp->add( currentStamp ); |
1152 | < | comp_stamps[i] = headStamp->match( id ); |
1150 | > | |
1151 | > | headStamp->add(currentStamp); |
1152 | > | comp_stamps[i] = headStamp->match(id); |
1153 | } | |
1154 | } | |
1155 | ||
1156 | #ifdef IS_MPI | |
1157 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1157 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1158 | MPIcheckPoint(); | |
1159 | #endif // is_mpi | |
1166 | – | |
1167 | – | |
1160 | } | |
1161 | ||
1162 | < | void SimSetup::calcSysValues( void ){ |
1162 | > | void SimSetup::calcSysValues(void){ |
1163 | int i, j, k; | |
1164 | < | |
1165 | < | int *molMembershipArray; |
1166 | < | |
1164 | > | |
1165 | > | int* molMembershipArray; |
1166 | > | |
1167 | tot_atoms = 0; | |
1168 | tot_bonds = 0; | |
1169 | tot_bends = 0; | |
1170 | tot_torsions = 0; | |
1171 | < | for( i=0; i<n_components; i++ ){ |
1172 | < | |
1173 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1174 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1183 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1171 | > | for (i = 0; i < n_components; i++){ |
1172 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1173 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1174 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1175 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1176 | } | |
1177 | < | |
1177 | > | |
1178 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1179 | molMembershipArray = new int[tot_atoms]; | |
1180 | < | |
1181 | < | for(i=0; i<nInfo; i++){ |
1180 | > | |
1181 | > | for (i = 0; i < nInfo; i++){ |
1182 | info[i].n_atoms = tot_atoms; | |
1183 | info[i].n_bonds = tot_bonds; | |
1184 | info[i].n_bends = tot_bends; | |
1185 | info[i].n_torsions = tot_torsions; | |
1186 | info[i].n_SRI = tot_SRI; | |
1187 | info[i].n_mol = tot_nmol; | |
1188 | < | |
1188 | > | |
1189 | info[i].molMembershipArray = molMembershipArray; | |
1190 | < | } |
1190 | > | } |
1191 | } | |
1192 | ||
1193 | #ifdef IS_MPI | |
1194 | ||
1195 | < | void SimSetup::mpiMolDivide( void ){ |
1205 | < | |
1195 | > | void SimSetup::mpiMolDivide(void){ |
1196 | int i, j, k; | |
1197 | int localMol, allMol; | |
1198 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1199 | ||
1200 | < | mpiSim = new mpiSimulation( info ); |
1201 | < | |
1200 | > | mpiSim = new mpiSimulation(info); |
1201 | > | |
1202 | globalIndex = mpiSim->divideLabor(); | |
1203 | ||
1204 | // set up the local variables | |
1205 | < | |
1205 | > | |
1206 | mol2proc = mpiSim->getMolToProcMap(); | |
1207 | molCompType = mpiSim->getMolComponentType(); | |
1208 | < | |
1208 | > | |
1209 | allMol = 0; | |
1210 | localMol = 0; | |
1211 | local_atoms = 0; | |
# | Line 1225 | Line 1215 | void SimSetup::mpiMolDivide( void ){ | |
1215 | globalAtomIndex = 0; | |
1216 | ||
1217 | ||
1218 | < | for( i=0; i<n_components; i++ ){ |
1219 | < | |
1220 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1221 | < | |
1222 | < | if( mol2proc[allMol] == worldRank ){ |
1223 | < | |
1224 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1225 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1236 | < | local_bends += comp_stamps[i]->getNBends(); |
1237 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1238 | < | localMol++; |
1218 | > | for (i = 0; i < n_components; i++){ |
1219 | > | for (j = 0; j < components_nmol[i]; j++){ |
1220 | > | if (mol2proc[allMol] == worldRank){ |
1221 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1222 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1223 | > | local_bends += comp_stamps[i]->getNBends(); |
1224 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1225 | > | localMol++; |
1226 | } | |
1227 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1227 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1228 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
1229 | globalAtomIndex++; | |
1230 | } | |
1231 | ||
1232 | < | allMol++; |
1232 | > | allMol++; |
1233 | } | |
1234 | } | |
1235 | local_SRI = local_bonds + local_bends + local_torsions; | |
1236 | < | |
1236 | > | |
1237 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1238 | < | |
1239 | < | if( local_atoms != info[0].n_atoms ){ |
1240 | < | sprintf( painCave.errMsg, |
1241 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1242 | < | " localAtom (%d) are not equal.\n", |
1243 | < | info[0].n_atoms, |
1257 | < | local_atoms ); |
1238 | > | |
1239 | > | if (local_atoms != info[0].n_atoms){ |
1240 | > | sprintf(painCave.errMsg, |
1241 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1242 | > | " localAtom (%d) are not equal.\n", |
1243 | > | info[0].n_atoms, local_atoms); |
1244 | painCave.isFatal = 1; | |
1245 | simError(); | |
1246 | } | |
# | Line 1265 | Line 1251 | void SimSetup::mpiMolDivide( void ){ | |
1251 | info[0].n_SRI = local_SRI; | |
1252 | info[0].n_mol = localMol; | |
1253 | ||
1254 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1254 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1255 | MPIcheckPoint(); | |
1256 | } | |
1257 | < | |
1257 | > | |
1258 | #endif // is_mpi | |
1259 | ||
1260 | ||
1261 | < | void SimSetup::makeSysArrays( void ){ |
1261 | > | void SimSetup::makeSysArrays(void){ |
1262 | int i, j, k, l; | |
1263 | ||
1264 | Atom** the_atoms; | |
1265 | Molecule* the_molecules; | |
1266 | Exclude** the_excludes; | |
1267 | ||
1268 | < | |
1269 | < | for(l=0; l<nInfo; l++){ |
1284 | < | |
1268 | > | |
1269 | > | for (l = 0; l < nInfo; l++){ |
1270 | // create the atom and short range interaction arrays | |
1271 | < | |
1272 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1271 | > | |
1272 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1273 | the_molecules = new Molecule[info[l].n_mol]; | |
1274 | int molIndex; | |
1275 | ||
1276 | // initialize the molecule's stampID's | |
1277 | < | |
1277 | > | |
1278 | #ifdef IS_MPI | |
1279 | < | |
1280 | < | |
1279 | > | |
1280 | > | |
1281 | molIndex = 0; | |
1282 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1283 | < | |
1284 | < | if(mol2proc[i] == worldRank ){ |
1285 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1286 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1287 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1303 | < | molIndex++; |
1282 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1283 | > | if (mol2proc[i] == worldRank){ |
1284 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1285 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1286 | > | the_molecules[molIndex].setGlobalIndex(i); |
1287 | > | molIndex++; |
1288 | } | |
1289 | } | |
1290 | < | |
1290 | > | |
1291 | #else // is_mpi | |
1292 | < | |
1292 | > | |
1293 | molIndex = 0; | |
1294 | globalAtomIndex = 0; | |
1295 | < | for(i=0; i<n_components; i++){ |
1296 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1297 | < | the_molecules[molIndex].setStampID( i ); |
1298 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1299 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1300 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1301 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1302 | < | globalAtomIndex++; |
1303 | < | } |
1304 | < | molIndex++; |
1295 | > | for (i = 0; i < n_components; i++){ |
1296 | > | for (j = 0; j < components_nmol[i]; j++){ |
1297 | > | the_molecules[molIndex].setStampID(i); |
1298 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1299 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1300 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1301 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1302 | > | globalAtomIndex++; |
1303 | > | } |
1304 | > | molIndex++; |
1305 | } | |
1306 | } | |
1307 | < | |
1308 | < | |
1307 | > | |
1308 | > | |
1309 | #endif // is_mpi | |
1310 | ||
1311 | ||
1312 | < | if( info[l].n_SRI ){ |
1329 | < | |
1312 | > | if (info[l].n_SRI){ |
1313 | Exclude::createArray(info[l].n_SRI); | |
1314 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1315 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1316 | < | the_excludes[ex] = new Exclude(ex); |
1314 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1315 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1316 | > | the_excludes[ex] = new Exclude(ex); |
1317 | } | |
1318 | info[l].globalExcludes = new int; | |
1319 | info[l].n_exclude = info[l].n_SRI; | |
1320 | } | |
1321 | else{ | |
1322 | < | |
1323 | < | Exclude::createArray( 1 ); |
1341 | < | the_excludes = new Exclude*; |
1322 | > | Exclude::createArray(1); |
1323 | > | the_excludes = new Exclude * ; |
1324 | the_excludes[0] = new Exclude(0); | |
1325 | < | the_excludes[0]->setPair( 0,0 ); |
1325 | > | the_excludes[0]->setPair(0, 0); |
1326 | info[l].globalExcludes = new int; | |
1327 | info[l].globalExcludes[0] = 0; | |
1328 | info[l].n_exclude = 0; | |
# | Line 1353 | Line 1335 | void SimSetup::makeSysArrays( void ){ | |
1335 | info[l].nGlobalExcludes = 0; | |
1336 | info[l].excludes = the_excludes; | |
1337 | ||
1338 | < | the_ff->setSimInfo( info ); |
1357 | < | |
1338 | > | the_ff->setSimInfo(info); |
1339 | } | |
1340 | } | |
1341 | ||
1342 | < | void SimSetup::makeIntegrator( void ){ |
1362 | < | |
1342 | > | void SimSetup::makeIntegrator(void){ |
1343 | int k; | |
1344 | ||
1345 | < | NVT<RealIntegrator>* myNVT = NULL; |
1345 | > | NVT<RealIntegrator>* myNVT = NULL; |
1346 | NPTi<RealIntegrator>* myNPTi = NULL; | |
1347 | NPTf<RealIntegrator>* myNPTf = NULL; | |
1348 | NPTim<RealIntegrator>* myNPTim = NULL; | |
1349 | NPTfm<RealIntegrator>* myNPTfm = NULL; | |
1350 | < | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1351 | < | ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1352 | < | ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1353 | < | ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1354 | < | ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1355 | < | ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1356 | < | |
1357 | < | for(k=0; k<nInfo; k++){ |
1358 | < | |
1359 | < | switch( ensembleCase ){ |
1360 | < | |
1361 | < | case NVE_ENS: |
1362 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1363 | < | break; |
1364 | < | |
1365 | < | case NVT_ENS: |
1366 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1367 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1368 | < | |
1369 | < | if (globals->haveTauThermostat()) |
1370 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1371 | < | |
1372 | < | else { |
1373 | < | sprintf( painCave.errMsg, |
1374 | < | "SimSetup error: If you use the NVT\n" |
1375 | < | " ensemble, you must set tauThermostat.\n"); |
1376 | < | painCave.isFatal = 1; |
1377 | < | simError(); |
1378 | < | } |
1379 | < | break; |
1380 | < | |
1381 | < | case NPTi_ENS: |
1382 | < | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1383 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1384 | < | |
1385 | < | if (globals->haveTargetPressure()) |
1386 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1387 | < | else { |
1388 | < | sprintf( painCave.errMsg, |
1389 | < | "SimSetup error: If you use a constant pressure\n" |
1390 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1391 | < | painCave.isFatal = 1; |
1392 | < | simError(); |
1393 | < | } |
1394 | < | |
1395 | < | if( globals->haveTauThermostat() ) |
1396 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1397 | < | else{ |
1398 | < | sprintf( painCave.errMsg, |
1399 | < | "SimSetup error: If you use an NPT\n" |
1400 | < | " ensemble, you must set tauThermostat.\n"); |
1401 | < | painCave.isFatal = 1; |
1402 | < | simError(); |
1403 | < | } |
1404 | < | |
1405 | < | if( globals->haveTauBarostat() ) |
1406 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1407 | < | else{ |
1408 | < | sprintf( painCave.errMsg, |
1409 | < | "SimSetup error: If you use an NPT\n" |
1410 | < | " ensemble, you must set tauBarostat.\n"); |
1411 | < | painCave.isFatal = 1; |
1412 | < | simError(); |
1413 | < | } |
1414 | < | break; |
1415 | < | |
1416 | < | case NPTf_ENS: |
1417 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1418 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1419 | < | |
1420 | < | if (globals->haveTargetPressure()) |
1421 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1422 | < | else { |
1423 | < | sprintf( painCave.errMsg, |
1424 | < | "SimSetup error: If you use a constant pressure\n" |
1425 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1426 | < | painCave.isFatal = 1; |
1427 | < | simError(); |
1428 | < | } |
1429 | < | |
1430 | < | if( globals->haveTauThermostat() ) |
1431 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1432 | < | else{ |
1433 | < | sprintf( painCave.errMsg, |
1434 | < | "SimSetup error: If you use an NPT\n" |
1435 | < | " ensemble, you must set tauThermostat.\n"); |
1436 | < | painCave.isFatal = 1; |
1437 | < | simError(); |
1438 | < | } |
1439 | < | |
1440 | < | if( globals->haveTauBarostat() ) |
1441 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1442 | < | else{ |
1443 | < | sprintf( painCave.errMsg, |
1444 | < | "SimSetup error: If you use an NPT\n" |
1445 | < | " ensemble, you must set tauBarostat.\n"); |
1446 | < | painCave.isFatal = 1; |
1447 | < | simError(); |
1448 | < | } |
1449 | < | break; |
1450 | < | |
1451 | < | case NPTim_ENS: |
1452 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1453 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1454 | < | |
1455 | < | if (globals->haveTargetPressure()) |
1456 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1457 | < | else { |
1458 | < | sprintf( painCave.errMsg, |
1459 | < | "SimSetup error: If you use a constant pressure\n" |
1460 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1461 | < | painCave.isFatal = 1; |
1462 | < | simError(); |
1463 | < | } |
1464 | < | |
1465 | < | if( globals->haveTauThermostat() ) |
1466 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1467 | < | else{ |
1468 | < | sprintf( painCave.errMsg, |
1469 | < | "SimSetup error: If you use an NPT\n" |
1470 | < | " ensemble, you must set tauThermostat.\n"); |
1471 | < | painCave.isFatal = 1; |
1472 | < | simError(); |
1473 | < | } |
1474 | < | |
1475 | < | if( globals->haveTauBarostat() ) |
1476 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1477 | < | else{ |
1478 | < | sprintf( painCave.errMsg, |
1479 | < | "SimSetup error: If you use an NPT\n" |
1480 | < | " ensemble, you must set tauBarostat.\n"); |
1481 | < | painCave.isFatal = 1; |
1482 | < | simError(); |
1483 | < | } |
1484 | < | break; |
1485 | < | |
1486 | < | case NPTfm_ENS: |
1487 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1488 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1489 | < | |
1490 | < | if (globals->haveTargetPressure()) |
1491 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1492 | < | else { |
1493 | < | sprintf( painCave.errMsg, |
1494 | < | "SimSetup error: If you use a constant pressure\n" |
1495 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1496 | < | painCave.isFatal = 1; |
1497 | < | simError(); |
1498 | < | } |
1499 | < | |
1500 | < | if( globals->haveTauThermostat() ) |
1501 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1502 | < | else{ |
1503 | < | sprintf( painCave.errMsg, |
1504 | < | "SimSetup error: If you use an NPT\n" |
1505 | < | " ensemble, you must set tauThermostat.\n"); |
1506 | < | painCave.isFatal = 1; |
1507 | < | simError(); |
1508 | < | } |
1509 | < | |
1510 | < | if( globals->haveTauBarostat() ) |
1511 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1512 | < | else{ |
1513 | < | sprintf( painCave.errMsg, |
1514 | < | "SimSetup error: If you use an NPT\n" |
1515 | < | " ensemble, you must set tauBarostat.\n"); |
1516 | < | painCave.isFatal = 1; |
1517 | < | simError(); |
1518 | < | } |
1519 | < | break; |
1520 | < | |
1521 | < | case NVEZCONS_ENS: |
1522 | < | |
1523 | < | |
1524 | < | //setup index of z-constraint molecules, z-constraint sampel time |
1525 | < | //and z-constraint force output name. These parameter should be known |
1526 | < | //before constructing the z-constraint integrator |
1527 | < | setupZConstraint(); |
1528 | < | |
1529 | < | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1530 | < | |
1531 | < | break; |
1532 | < | |
1533 | < | |
1534 | < | case NVTZCONS_ENS: |
1535 | < | |
1536 | < | setupZConstraint(); |
1537 | < | |
1538 | < | myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1539 | < | myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1540 | < | |
1541 | < | if (globals->haveTauThermostat()) |
1542 | < | myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1543 | < | |
1544 | < | else { |
1545 | < | sprintf( painCave.errMsg, |
1546 | < | "SimSetup error: If you use the NVT\n" |
1547 | < | " ensemble, you must set tauThermostat.\n"); |
1548 | < | painCave.isFatal = 1; |
1549 | < | simError(); |
1550 | < | } |
1551 | < | break; |
1572 | < | |
1573 | < | case NPTiZCONS_ENS: |
1574 | < | |
1575 | < | setupZConstraint(); |
1576 | < | |
1577 | < | myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1578 | < | myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1579 | < | |
1580 | < | if (globals->haveTargetPressure()) |
1581 | < | myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1582 | < | else { |
1583 | < | sprintf( painCave.errMsg, |
1584 | < | "SimSetup error: If you use a constant pressure\n" |
1585 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1586 | < | painCave.isFatal = 1; |
1587 | < | simError(); |
1588 | < | } |
1589 | < | |
1590 | < | if( globals->haveTauThermostat() ) |
1591 | < | myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1592 | < | else{ |
1593 | < | sprintf( painCave.errMsg, |
1594 | < | "SimSetup error: If you use an NPT\n" |
1595 | < | " ensemble, you must set tauThermostat.\n"); |
1596 | < | painCave.isFatal = 1; |
1597 | < | simError(); |
1598 | < | } |
1599 | < | |
1600 | < | if( globals->haveTauBarostat() ) |
1601 | < | myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1602 | < | else{ |
1603 | < | sprintf( painCave.errMsg, |
1604 | < | "SimSetup error: If you use an NPT\n" |
1605 | < | " ensemble, you must set tauBarostat.\n"); |
1606 | < | painCave.isFatal = 1; |
1607 | < | simError(); |
1608 | < | } |
1609 | < | |
1610 | < | break; |
1611 | < | |
1612 | < | case NPTfZCONS_ENS: |
1613 | < | |
1614 | < | setupZConstraint(); |
1615 | < | |
1616 | < | myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1617 | < | myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1618 | < | |
1619 | < | if (globals->haveTargetPressure()) |
1620 | < | myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1621 | < | else { |
1622 | < | sprintf( painCave.errMsg, |
1623 | < | "SimSetup error: If you use a constant pressure\n" |
1624 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1625 | < | painCave.isFatal = 1; |
1626 | < | simError(); |
1627 | < | } |
1628 | < | |
1629 | < | if( globals->haveTauThermostat() ) |
1630 | < | myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1631 | < | else{ |
1632 | < | sprintf( painCave.errMsg, |
1633 | < | "SimSetup error: If you use an NPT\n" |
1634 | < | " ensemble, you must set tauThermostat.\n"); |
1635 | < | painCave.isFatal = 1; |
1636 | < | simError(); |
1637 | < | } |
1638 | < | |
1639 | < | if( globals->haveTauBarostat() ) |
1640 | < | myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1641 | < | else{ |
1642 | < | sprintf( painCave.errMsg, |
1643 | < | "SimSetup error: If you use an NPT\n" |
1644 | < | " ensemble, you must set tauBarostat.\n"); |
1645 | < | painCave.isFatal = 1; |
1646 | < | simError(); |
1647 | < | } |
1648 | < | |
1649 | < | break; |
1650 | < | |
1651 | < | case NPTimZCONS_ENS: |
1652 | < | |
1653 | < | setupZConstraint(); |
1654 | < | |
1655 | < | myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1656 | < | myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1657 | < | |
1658 | < | if (globals->haveTargetPressure()) |
1659 | < | myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1660 | < | else { |
1661 | < | sprintf( painCave.errMsg, |
1662 | < | "SimSetup error: If you use a constant pressure\n" |
1663 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1664 | < | painCave.isFatal = 1; |
1665 | < | simError(); |
1666 | < | } |
1667 | < | |
1668 | < | if( globals->haveTauThermostat() ) |
1669 | < | myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1670 | < | else{ |
1671 | < | sprintf( painCave.errMsg, |
1672 | < | "SimSetup error: If you use an NPT\n" |
1673 | < | " ensemble, you must set tauThermostat.\n"); |
1674 | < | painCave.isFatal = 1; |
1675 | < | simError(); |
1676 | < | } |
1677 | < | |
1678 | < | if( globals->haveTauBarostat() ) |
1679 | < | myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1680 | < | else{ |
1681 | < | sprintf( painCave.errMsg, |
1682 | < | "SimSetup error: If you use an NPT\n" |
1683 | < | " ensemble, you must set tauBarostat.\n"); |
1684 | < | painCave.isFatal = 1; |
1685 | < | simError(); |
1686 | < | } |
1687 | < | |
1688 | < | break; |
1689 | < | |
1690 | < | case NPTfmZCONS_ENS: |
1691 | < | |
1692 | < | setupZConstraint(); |
1693 | < | |
1694 | < | myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1695 | < | myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1696 | < | |
1697 | < | if (globals->haveTargetPressure()) |
1698 | < | myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1699 | < | else { |
1700 | < | sprintf( painCave.errMsg, |
1701 | < | "SimSetup error: If you use a constant pressure\n" |
1702 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1703 | < | painCave.isFatal = 1; |
1704 | < | simError(); |
1705 | < | } |
1706 | < | |
1707 | < | if( globals->haveTauThermostat() ) |
1708 | < | myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1709 | < | else{ |
1710 | < | sprintf( painCave.errMsg, |
1711 | < | "SimSetup error: If you use an NPT\n" |
1712 | < | " ensemble, you must set tauThermostat.\n"); |
1713 | < | painCave.isFatal = 1; |
1714 | < | simError(); |
1715 | < | } |
1716 | < | |
1717 | < | if( globals->haveTauBarostat() ) |
1718 | < | myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1719 | < | else{ |
1720 | < | sprintf( painCave.errMsg, |
1721 | < | "SimSetup error: If you use an NPT\n" |
1722 | < | " ensemble, you must set tauBarostat.\n"); |
1723 | < | painCave.isFatal = 1; |
1724 | < | simError(); |
1725 | < | } |
1726 | < | break; |
1727 | < | |
1728 | < | |
1729 | < | |
1730 | < | default: |
1731 | < | sprintf( painCave.errMsg, |
1732 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1733 | < | painCave.isFatal = 1; |
1734 | < | simError(); |
1350 | > | |
1351 | > | for (k = 0; k < nInfo; k++){ |
1352 | > | switch (ensembleCase){ |
1353 | > | case NVE_ENS: |
1354 | > | if (globals->haveZconstraints()){ |
1355 | > | setupZConstraint(info[k]); |
1356 | > | new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1357 | > | } |
1358 | > | else |
1359 | > | new NVE<RealIntegrator>(&(info[k]), the_ff); |
1360 | > | break; |
1361 | > | |
1362 | > | case NVT_ENS: |
1363 | > | if (globals->haveZconstraints()){ |
1364 | > | setupZConstraint(info[k]); |
1365 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1366 | > | } |
1367 | > | else |
1368 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1369 | > | |
1370 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1371 | > | |
1372 | > | if (globals->haveTauThermostat()) |
1373 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1374 | > | else{ |
1375 | > | sprintf(painCave.errMsg, |
1376 | > | "SimSetup error: If you use the NVT\n" |
1377 | > | " ensemble, you must set tauThermostat.\n"); |
1378 | > | painCave.isFatal = 1; |
1379 | > | simError(); |
1380 | > | } |
1381 | > | break; |
1382 | > | |
1383 | > | case NPTi_ENS: |
1384 | > | if (globals->haveZconstraints()){ |
1385 | > | setupZConstraint(info[k]); |
1386 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1387 | > | } |
1388 | > | else |
1389 | > | myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1390 | > | |
1391 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1392 | > | |
1393 | > | if (globals->haveTargetPressure()) |
1394 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1395 | > | else{ |
1396 | > | sprintf(painCave.errMsg, |
1397 | > | "SimSetup error: If you use a constant pressure\n" |
1398 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1399 | > | painCave.isFatal = 1; |
1400 | > | simError(); |
1401 | > | } |
1402 | > | |
1403 | > | if (globals->haveTauThermostat()) |
1404 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1405 | > | else{ |
1406 | > | sprintf(painCave.errMsg, |
1407 | > | "SimSetup error: If you use an NPT\n" |
1408 | > | " ensemble, you must set tauThermostat.\n"); |
1409 | > | painCave.isFatal = 1; |
1410 | > | simError(); |
1411 | > | } |
1412 | > | |
1413 | > | if (globals->haveTauBarostat()) |
1414 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1415 | > | else{ |
1416 | > | sprintf(painCave.errMsg, |
1417 | > | "SimSetup error: If you use an NPT\n" |
1418 | > | " ensemble, you must set tauBarostat.\n"); |
1419 | > | painCave.isFatal = 1; |
1420 | > | simError(); |
1421 | > | } |
1422 | > | break; |
1423 | > | |
1424 | > | case NPTf_ENS: |
1425 | > | if (globals->haveZconstraints()){ |
1426 | > | setupZConstraint(info[k]); |
1427 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1428 | > | } |
1429 | > | else |
1430 | > | myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1431 | > | |
1432 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1433 | > | |
1434 | > | if (globals->haveTargetPressure()) |
1435 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1436 | > | else{ |
1437 | > | sprintf(painCave.errMsg, |
1438 | > | "SimSetup error: If you use a constant pressure\n" |
1439 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1440 | > | painCave.isFatal = 1; |
1441 | > | simError(); |
1442 | > | } |
1443 | > | |
1444 | > | if (globals->haveTauThermostat()) |
1445 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1446 | > | else{ |
1447 | > | sprintf(painCave.errMsg, |
1448 | > | "SimSetup error: If you use an NPT\n" |
1449 | > | " ensemble, you must set tauThermostat.\n"); |
1450 | > | painCave.isFatal = 1; |
1451 | > | simError(); |
1452 | > | } |
1453 | > | |
1454 | > | if (globals->haveTauBarostat()) |
1455 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1456 | > | else{ |
1457 | > | sprintf(painCave.errMsg, |
1458 | > | "SimSetup error: If you use an NPT\n" |
1459 | > | " ensemble, you must set tauBarostat.\n"); |
1460 | > | painCave.isFatal = 1; |
1461 | > | simError(); |
1462 | > | } |
1463 | > | break; |
1464 | > | |
1465 | > | case NPTim_ENS: |
1466 | > | if (globals->haveZconstraints()){ |
1467 | > | setupZConstraint(info[k]); |
1468 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1469 | > | } |
1470 | > | else |
1471 | > | myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1472 | > | |
1473 | > | myNPTim->setTargetTemp(globals->getTargetTemp()); |
1474 | > | |
1475 | > | if (globals->haveTargetPressure()) |
1476 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 | > | else{ |
1478 | > | sprintf(painCave.errMsg, |
1479 | > | "SimSetup error: If you use a constant pressure\n" |
1480 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1481 | > | painCave.isFatal = 1; |
1482 | > | simError(); |
1483 | > | } |
1484 | > | |
1485 | > | if (globals->haveTauThermostat()) |
1486 | > | myNPTim->setTauThermostat(globals->getTauThermostat()); |
1487 | > | else{ |
1488 | > | sprintf(painCave.errMsg, |
1489 | > | "SimSetup error: If you use an NPT\n" |
1490 | > | " ensemble, you must set tauThermostat.\n"); |
1491 | > | painCave.isFatal = 1; |
1492 | > | simError(); |
1493 | > | } |
1494 | > | |
1495 | > | if (globals->haveTauBarostat()) |
1496 | > | myNPTim->setTauBarostat(globals->getTauBarostat()); |
1497 | > | else{ |
1498 | > | sprintf(painCave.errMsg, |
1499 | > | "SimSetup error: If you use an NPT\n" |
1500 | > | " ensemble, you must set tauBarostat.\n"); |
1501 | > | painCave.isFatal = 1; |
1502 | > | simError(); |
1503 | > | } |
1504 | > | break; |
1505 | > | |
1506 | > | case NPTfm_ENS: |
1507 | > | if (globals->haveZconstraints()){ |
1508 | > | setupZConstraint(info[k]); |
1509 | > | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1510 | > | } |
1511 | > | else |
1512 | > | myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1513 | > | |
1514 | > | myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1515 | > | |
1516 | > | if (globals->haveTargetPressure()) |
1517 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1518 | > | else{ |
1519 | > | sprintf(painCave.errMsg, |
1520 | > | "SimSetup error: If you use a constant pressure\n" |
1521 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1522 | > | painCave.isFatal = 1; |
1523 | > | simError(); |
1524 | > | } |
1525 | > | |
1526 | > | if (globals->haveTauThermostat()) |
1527 | > | myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1528 | > | else{ |
1529 | > | sprintf(painCave.errMsg, |
1530 | > | "SimSetup error: If you use an NPT\n" |
1531 | > | " ensemble, you must set tauThermostat.\n"); |
1532 | > | painCave.isFatal = 1; |
1533 | > | simError(); |
1534 | > | } |
1535 | > | |
1536 | > | if (globals->haveTauBarostat()) |
1537 | > | myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1538 | > | else{ |
1539 | > | sprintf(painCave.errMsg, |
1540 | > | "SimSetup error: If you use an NPT\n" |
1541 | > | " ensemble, you must set tauBarostat.\n"); |
1542 | > | painCave.isFatal = 1; |
1543 | > | simError(); |
1544 | > | } |
1545 | > | break; |
1546 | > | |
1547 | > | default: |
1548 | > | sprintf(painCave.errMsg, |
1549 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1550 | > | painCave.isFatal = 1; |
1551 | > | simError(); |
1552 | } | |
1553 | } | |
1554 | } | |
1555 | ||
1556 | < | void SimSetup::initFortran( void ){ |
1740 | < | |
1556 | > | void SimSetup::initFortran(void){ |
1557 | info[0].refreshSim(); | |
1558 | < | |
1559 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1560 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1558 | > | |
1559 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1560 | > | the_ff->initForceField(LB_MIXING_RULE); |
1561 | } | |
1562 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1563 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1562 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1563 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1564 | } | |
1565 | else{ | |
1566 | < | sprintf( painCave.errMsg, |
1567 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1752 | < | info[0].mixingRule ); |
1566 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1567 | > | info[0].mixingRule); |
1568 | painCave.isFatal = 1; | |
1569 | simError(); | |
1570 | } | |
1571 | ||
1572 | ||
1573 | #ifdef IS_MPI | |
1574 | < | strcpy( checkPointMsg, |
1760 | < | "Successfully intialized the mixingRule for Fortran." ); |
1574 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1575 | MPIcheckPoint(); | |
1576 | #endif // is_mpi | |
1763 | – | |
1577 | } | |
1578 | ||
1579 | < | void SimSetup::setupZConstraint() |
1580 | < | { |
1581 | < | int k; |
1579 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1580 | > | int nZConstraints; |
1581 | > | ZconStamp** zconStamp; |
1582 | ||
1583 | < | for(k=0; k<nInfo; k++){ |
1584 | < | |
1585 | < | if(globals->haveZConsTime()){ |
1586 | < | |
1587 | < | //add sample time of z-constraint into SimInfo's property list |
1588 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1776 | < | zconsTimeProp->setID("zconstime"); |
1777 | < | zconsTimeProp->setData(globals->getZConsTime()); |
1778 | < | info[k].addProperty(zconsTimeProp); |
1779 | < | } |
1780 | < | else{ |
1781 | < | sprintf( painCave.errMsg, |
1782 | < | "ZConstraint error: If you use an ZConstraint\n" |
1783 | < | " , you must set sample time.\n"); |
1784 | < | painCave.isFatal = 1; |
1785 | < | simError(); |
1786 | < | } |
1787 | < | |
1788 | < | if(globals->haveIndexOfAllZConsMols()){ |
1789 | < | |
1790 | < | //add index of z-constraint molecules into SimInfo's property list |
1791 | < | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1792 | < | |
1793 | < | //sort the index |
1794 | < | sort(tempIndex.begin(), tempIndex.end()); |
1795 | < | |
1796 | < | IndexData* zconsIndex = new IndexData(); |
1797 | < | zconsIndex->setID("zconsindex"); |
1798 | < | zconsIndex->setIndexData(tempIndex); |
1799 | < | info[k].addProperty(zconsIndex); |
1800 | < | } |
1801 | < | else{ |
1802 | < | sprintf( painCave.errMsg, |
1803 | < | "SimSetup error: If you use an ZConstraint\n" |
1804 | < | " , you must set index of z-constraint molecules.\n"); |
1805 | < | painCave.isFatal = 1; |
1806 | < | simError(); |
1807 | < | |
1808 | < | } |
1809 | < | |
1810 | < | //Determine the name of ouput file and add it into SimInfo's property list |
1811 | < | //Be careful, do not use inFileName, since it is a pointer which |
1812 | < | //point to a string at master node, and slave nodes do not contain that string |
1813 | < | |
1814 | < | string zconsOutput(info[k].finalName); |
1815 | < | |
1816 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1817 | < | |
1818 | < | StringData* zconsFilename = new StringData(); |
1819 | < | zconsFilename->setID("zconsfilename"); |
1820 | < | zconsFilename->setData(zconsOutput); |
1821 | < | |
1822 | < | info[k].addProperty(zconsFilename); |
1583 | > | if (globals->haveZconstraintTime()){ |
1584 | > | //add sample time of z-constraint into SimInfo's property list |
1585 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1586 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1587 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1588 | > | theInfo.addProperty(zconsTimeProp); |
1589 | } | |
1590 | + | else{ |
1591 | + | sprintf(painCave.errMsg, |
1592 | + | "ZConstraint error: If you use an ZConstraint\n" |
1593 | + | " , you must set sample time.\n"); |
1594 | + | painCave.isFatal = 1; |
1595 | + | simError(); |
1596 | + | } |
1597 | + | |
1598 | + | //push zconsTol into siminfo, if user does not specify |
1599 | + | //value for zconsTol, a default value will be used |
1600 | + | DoubleData* zconsTol = new DoubleData(); |
1601 | + | zconsTol->setID(ZCONSTOL_ID); |
1602 | + | if (globals->haveZconsTol()){ |
1603 | + | zconsTol->setData(globals->getZconsTol()); |
1604 | + | } |
1605 | + | else{ |
1606 | + | double defaultZConsTol = 0.01; |
1607 | + | sprintf(painCave.errMsg, |
1608 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1609 | + | " , default value %f is used.\n", |
1610 | + | defaultZConsTol); |
1611 | + | painCave.isFatal = 0; |
1612 | + | simError(); |
1613 | + | |
1614 | + | zconsTol->setData(defaultZConsTol); |
1615 | + | } |
1616 | + | theInfo.addProperty(zconsTol); |
1617 | + | |
1618 | + | //set Force Substraction Policy |
1619 | + | StringData* zconsForcePolicy = new StringData(); |
1620 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1621 | + | |
1622 | + | if (globals->haveZconsForcePolicy()){ |
1623 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1624 | + | } |
1625 | + | else{ |
1626 | + | sprintf(painCave.errMsg, |
1627 | + | "ZConstraint Warning: User does not set force substraction policy, " |
1628 | + | "PolicyByMass is used\n"); |
1629 | + | painCave.isFatal = 0; |
1630 | + | simError(); |
1631 | + | zconsForcePolicy->setData("BYMASS"); |
1632 | + | } |
1633 | + | |
1634 | + | theInfo.addProperty(zconsForcePolicy); |
1635 | + | |
1636 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1637 | + | //Be careful, do not use inFileName, since it is a pointer which |
1638 | + | //point to a string at master node, and slave nodes do not contain that string |
1639 | + | |
1640 | + | string zconsOutput(theInfo.finalName); |
1641 | + | |
1642 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1643 | + | |
1644 | + | StringData* zconsFilename = new StringData(); |
1645 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1646 | + | zconsFilename->setData(zconsOutput); |
1647 | + | |
1648 | + | theInfo.addProperty(zconsFilename); |
1649 | + | |
1650 | + | //setup index, pos and other parameters of z-constraint molecules |
1651 | + | nZConstraints = globals->getNzConstraints(); |
1652 | + | theInfo.nZconstraints = nZConstraints; |
1653 | + | |
1654 | + | zconStamp = globals->getZconStamp(); |
1655 | + | ZConsParaItem tempParaItem; |
1656 | + | |
1657 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1658 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1659 | + | |
1660 | + | for (int i = 0; i < nZConstraints; i++){ |
1661 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1662 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1663 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1664 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1665 | + | |
1666 | + | zconsParaData->addItem(tempParaItem); |
1667 | + | } |
1668 | + | |
1669 | + | //check the uniqueness of index |
1670 | + | if(!zconsParaData->isIndexUnique()){ |
1671 | + | sprintf(painCave.errMsg, |
1672 | + | "ZConstraint Error: molIndex is not unique\n"); |
1673 | + | painCave.isFatal = 1; |
1674 | + | simError(); |
1675 | + | } |
1676 | + | |
1677 | + | //sort the parameters by index of molecules |
1678 | + | zconsParaData->sortByIndex(); |
1679 | + | |
1680 | + | //push data into siminfo, therefore, we can retrieve later |
1681 | + | theInfo.addProperty(zconsParaData); |
1682 | } |
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