# | Line 1 | Line 1 | |
---|---|---|
1 | #include <algorithm> | |
2 | < | #include <cstdlib> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
4 | > | #include <math.h> |
5 | #include <string> | |
6 | < | |
6 | > | #include <sprng.h> |
7 | #include "SimSetup.hpp" | |
8 | #include "ReadWrite.hpp" | |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
12 | + | //#include "ConjugateMinimizer.hpp" |
13 | + | #include "OOPSEMinimizer.hpp" |
14 | ||
15 | #ifdef IS_MPI | |
16 | #include "mpiBASS.h" | |
# | Line 21 | Line 23 | |
23 | #define NVT_ENS 1 | |
24 | #define NPTi_ENS 2 | |
25 | #define NPTf_ENS 3 | |
26 | < | #define NPTim_ENS 4 |
25 | < | #define NPTfm_ENS 5 |
26 | > | #define NPTxyz_ENS 4 |
27 | ||
27 | – | #define FF_DUFF 0 |
28 | – | #define FF_LJ 1 |
29 | – | #define FF_EAM 2 |
28 | ||
29 | + | #define FF_DUFF 0 |
30 | + | #define FF_LJ 1 |
31 | + | #define FF_EAM 2 |
32 | + | #define FF_H2O 3 |
33 | + | |
34 | using namespace std; | |
35 | ||
36 | + | /** |
37 | + | * Check whether dividend is divisble by divisor or not |
38 | + | */ |
39 | + | bool isDivisible(double dividend, double divisor){ |
40 | + | double tolerance = 0.000001; |
41 | + | double quotient; |
42 | + | double diff; |
43 | + | int intQuotient; |
44 | + | |
45 | + | quotient = dividend / divisor; |
46 | + | |
47 | + | if (quotient < 0) |
48 | + | quotient = -quotient; |
49 | + | |
50 | + | intQuotient = int (quotient + tolerance); |
51 | + | |
52 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
53 | + | |
54 | + | if (diff <= tolerance) |
55 | + | return true; |
56 | + | else |
57 | + | return false; |
58 | + | } |
59 | + | |
60 | SimSetup::SimSetup(){ | |
61 | ||
62 | + | initSuspend = false; |
63 | isInfoArray = 0; | |
64 | nInfo = 1; | |
65 | < | |
65 | > | |
66 | stamps = new MakeStamps(); | |
67 | globals = new Globals(); | |
68 | < | |
69 | < | |
68 | > | |
69 | > | |
70 | #ifdef IS_MPI | |
71 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
71 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
72 | MPIcheckPoint(); | |
73 | #endif // IS_MPI | |
74 | } | |
# | Line 50 | Line 78 | SimSetup::~SimSetup(){ | |
78 | delete globals; | |
79 | } | |
80 | ||
81 | < | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
82 | < | info = the_info; |
83 | < | nInfo = theNinfo; |
84 | < | isInfoArray = 1; |
81 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
82 | > | info = the_info; |
83 | > | nInfo = theNinfo; |
84 | > | isInfoArray = 1; |
85 | > | initSuspend = true; |
86 | } | |
87 | ||
88 | ||
89 | < | void SimSetup::parseFile( char* fileName ){ |
61 | < | |
89 | > | void SimSetup::parseFile(char* fileName){ |
90 | #ifdef IS_MPI | |
91 | < | if( worldRank == 0 ){ |
91 | > | if (worldRank == 0){ |
92 | #endif // is_mpi | |
93 | < | |
93 | > | |
94 | inFileName = fileName; | |
95 | < | set_interface_stamps( stamps, globals ); |
96 | < | |
95 | > | set_interface_stamps(stamps, globals); |
96 | > | |
97 | #ifdef IS_MPI | |
98 | mpiEventInit(); | |
99 | #endif | |
100 | ||
101 | < | yacc_BASS( fileName ); |
101 | > | yacc_BASS(fileName); |
102 | ||
103 | #ifdef IS_MPI | |
104 | throwMPIEvent(NULL); | |
105 | } | |
106 | < | else receiveParse(); |
106 | > | else{ |
107 | > | receiveParse(); |
108 | > | } |
109 | #endif | |
110 | ||
111 | } | |
112 | ||
113 | #ifdef IS_MPI | |
114 | void SimSetup::receiveParse(void){ | |
115 | < | |
116 | < | set_interface_stamps( stamps, globals ); |
117 | < | mpiEventInit(); |
118 | < | MPIcheckPoint(); |
89 | < | mpiEventLoop(); |
90 | < | |
115 | > | set_interface_stamps(stamps, globals); |
116 | > | mpiEventInit(); |
117 | > | MPIcheckPoint(); |
118 | > | mpiEventLoop(); |
119 | } | |
120 | ||
121 | #endif // is_mpi | |
122 | ||
123 | void SimSetup::createSim(void){ | |
124 | ||
97 | – | int i, j, k, globalAtomIndex; |
98 | – | |
125 | // gather all of the information from the Bass file | |
126 | ||
127 | gatherInfo(); | |
# | Line 110 | Line 136 | void SimSetup::createSim(void){ | |
136 | ||
137 | // initialize the system coordinates | |
138 | ||
139 | < | if( !isInfoArray ) initSystemCoords(); |
139 | > | if ( !initSuspend ){ |
140 | > | initSystemCoords(); |
141 | ||
142 | + | if( !(globals->getUseInitTime()) ) |
143 | + | info[0].currentTime = 0.0; |
144 | + | } |
145 | + | |
146 | // make the output filenames | |
147 | ||
148 | makeOutNames(); | |
149 | < | |
150 | < | // make the integrator |
149 | > | |
150 | > | if (globals->haveMinimizer()) |
151 | > | // make minimizer |
152 | > | makeMinimizer(); |
153 | > | else |
154 | > | // make the integrator |
155 | > | makeIntegrator(); |
156 | ||
121 | – | makeIntegrator(); |
122 | – | |
157 | #ifdef IS_MPI | |
158 | mpiSim->mpiRefresh(); | |
159 | #endif | |
# | Line 127 | Line 161 | void SimSetup::createSim(void){ | |
161 | // initialize the Fortran | |
162 | ||
163 | initFortran(); | |
130 | – | |
131 | – | |
132 | – | |
164 | } | |
165 | ||
166 | ||
167 | < | void SimSetup::makeMolecules( void ){ |
168 | < | |
138 | < | int k,l; |
167 | > | void SimSetup::makeMolecules(void){ |
168 | > | int k; |
169 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
170 | molInit molInfo; | |
171 | DirectionalAtom* dAtom; | |
# | Line 150 | Line 180 | void SimSetup::makeMolecules( void ){ | |
180 | bend_set* theBends; | |
181 | torsion_set* theTorsions; | |
182 | ||
153 | – | |
183 | //init the forceField paramters | |
184 | ||
185 | the_ff->readParams(); | |
186 | ||
187 | < | |
187 | > | |
188 | // init the atoms | |
189 | ||
190 | + | double phi, theta, psi; |
191 | + | double sux, suy, suz; |
192 | + | double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
193 | double ux, uy, uz, u, uSqr; | |
162 | – | |
163 | – | for(k=0; k<nInfo; k++){ |
164 | – | |
165 | – | the_ff->setSimInfo( &(info[k]) ); |
194 | ||
195 | + | for (k = 0; k < nInfo; k++){ |
196 | + | the_ff->setSimInfo(&(info[k])); |
197 | + | |
198 | atomOffset = 0; | |
199 | excludeOffset = 0; | |
200 | < | for(i=0; i<info[k].n_mol; i++){ |
170 | < | |
200 | > | for (i = 0; i < info[k].n_mol; i++){ |
201 | stampID = info[k].molecules[i].getStampID(); | |
202 | ||
203 | < | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
204 | < | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
205 | < | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
203 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
204 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
205 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
206 | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); | |
207 | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; | |
208 | < | |
208 | > | |
209 | molInfo.myAtoms = &(info[k].atoms[atomOffset]); | |
210 | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); | |
211 | < | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
212 | < | molInfo.myBends = new Bend*[molInfo.nBends]; |
213 | < | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
211 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
212 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
213 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
214 | ||
215 | theBonds = new bond_pair[molInfo.nBonds]; | |
216 | theBends = new bend_set[molInfo.nBends]; | |
217 | theTorsions = new torsion_set[molInfo.nTorsions]; | |
218 | < | |
218 | > | |
219 | // make the Atoms | |
220 | < | |
221 | < | for(j=0; j<molInfo.nAtoms; j++){ |
222 | < | |
223 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
224 | < | if( currentAtom->haveOrientation() ){ |
225 | < | |
226 | < | dAtom = new DirectionalAtom( (j + atomOffset), |
227 | < | info[k].getConfiguration() ); |
228 | < | info[k].n_oriented++; |
229 | < | molInfo.myAtoms[j] = dAtom; |
230 | < | |
231 | < | ux = currentAtom->getOrntX(); |
232 | < | uy = currentAtom->getOrntY(); |
233 | < | uz = currentAtom->getOrntZ(); |
234 | < | |
235 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
236 | < | |
237 | < | u = sqrt( uSqr ); |
238 | < | ux = ux / u; |
239 | < | uy = uy / u; |
240 | < | uz = uz / u; |
241 | < | |
242 | < | dAtom->setSUx( ux ); |
243 | < | dAtom->setSUy( uy ); |
244 | < | dAtom->setSUz( uz ); |
245 | < | } |
246 | < | else{ |
247 | < | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
248 | < | info[k].getConfiguration() ); |
249 | < | } |
250 | < | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
251 | < | |
220 | > | |
221 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
222 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
223 | > | if (currentAtom->haveOrientation()){ |
224 | > | dAtom = new DirectionalAtom((j + atomOffset), |
225 | > | info[k].getConfiguration()); |
226 | > | info[k].n_oriented++; |
227 | > | molInfo.myAtoms[j] = dAtom; |
228 | > | |
229 | > | // Directional Atoms have standard unit vectors which are oriented |
230 | > | // in space using the three Euler angles. We assume the standard |
231 | > | // unit vector was originally along the z axis below. |
232 | > | |
233 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
234 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
235 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
236 | > | |
237 | > | Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
238 | > | Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
239 | > | Axz = sin(theta) * sin(psi); |
240 | > | |
241 | > | Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
242 | > | Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
243 | > | Ayz = sin(theta) * cos(psi); |
244 | > | |
245 | > | Azx = sin(phi) * sin(theta); |
246 | > | Azy = -cos(phi) * sin(theta); |
247 | > | Azz = cos(theta); |
248 | > | |
249 | > | sux = 0.0; |
250 | > | suy = 0.0; |
251 | > | suz = 1.0; |
252 | > | |
253 | > | ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
254 | > | uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
255 | > | uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
256 | > | |
257 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
258 | > | |
259 | > | u = sqrt(uSqr); |
260 | > | ux = ux / u; |
261 | > | uy = uy / u; |
262 | > | uz = uz / u; |
263 | > | |
264 | > | dAtom->setSUx(ux); |
265 | > | dAtom->setSUy(uy); |
266 | > | dAtom->setSUz(uz); |
267 | > | } |
268 | > | else{ |
269 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
270 | > | info[k].getConfiguration()); |
271 | > | } |
272 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
273 | > | |
274 | #ifdef IS_MPI | |
275 | < | |
276 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
277 | < | |
275 | > | |
276 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
277 | > | |
278 | #endif // is_mpi | |
279 | } | |
280 | < | |
281 | < | // make the bonds |
282 | < | for(j=0; j<molInfo.nBonds; j++){ |
283 | < | |
284 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
285 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
286 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
287 | < | |
288 | < | exI = theBonds[j].a; |
289 | < | exJ = theBonds[j].b; |
290 | < | |
291 | < | // exclude_I must always be the smaller of the pair |
292 | < | if( exI > exJ ){ |
293 | < | tempEx = exI; |
294 | < | exI = exJ; |
295 | < | exJ = tempEx; |
244 | < | } |
280 | > | |
281 | > | // make the bonds |
282 | > | for (j = 0; j < molInfo.nBonds; j++){ |
283 | > | currentBond = comp_stamps[stampID]->getBond(j); |
284 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
285 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
286 | > | |
287 | > | exI = theBonds[j].a; |
288 | > | exJ = theBonds[j].b; |
289 | > | |
290 | > | // exclude_I must always be the smaller of the pair |
291 | > | if (exI > exJ){ |
292 | > | tempEx = exI; |
293 | > | exI = exJ; |
294 | > | exJ = tempEx; |
295 | > | } |
296 | #ifdef IS_MPI | |
297 | < | tempEx = exI; |
298 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
299 | < | tempEx = exJ; |
300 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
301 | < | |
302 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
297 | > | tempEx = exI; |
298 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
299 | > | tempEx = exJ; |
300 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
301 | > | |
302 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
303 | #else // isn't MPI | |
304 | < | |
305 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
304 | > | |
305 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
306 | #endif //is_mpi | |
307 | } | |
308 | excludeOffset += molInfo.nBonds; | |
309 | < | |
309 | > | |
310 | //make the bends | |
311 | < | for(j=0; j<molInfo.nBends; j++){ |
312 | < | |
313 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
314 | < | theBends[j].a = currentBend->getA() + atomOffset; |
315 | < | theBends[j].b = currentBend->getB() + atomOffset; |
316 | < | theBends[j].c = currentBend->getC() + atomOffset; |
317 | < | |
318 | < | if( currentBend->haveExtras() ){ |
319 | < | |
320 | < | extras = currentBend->getExtras(); |
321 | < | current_extra = extras; |
322 | < | |
323 | < | while( current_extra != NULL ){ |
324 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
325 | < | |
326 | < | switch( current_extra->getType() ){ |
327 | < | |
328 | < | case 0: |
329 | < | theBends[j].ghost = |
330 | < | current_extra->getInt() + atomOffset; |
331 | < | theBends[j].isGhost = 1; |
332 | < | break; |
333 | < | |
334 | < | case 1: |
335 | < | theBends[j].ghost = |
336 | < | (int)current_extra->getDouble() + atomOffset; |
337 | < | theBends[j].isGhost = 1; |
338 | < | break; |
339 | < | |
340 | < | default: |
341 | < | sprintf( painCave.errMsg, |
342 | < | "SimSetup Error: ghostVectorSource was neither a " |
343 | < | "double nor an int.\n" |
344 | < | "-->Bend[%d] in %s\n", |
345 | < | j, comp_stamps[stampID]->getID() ); |
346 | < | painCave.isFatal = 1; |
347 | < | simError(); |
348 | < | } |
349 | < | } |
350 | < | |
351 | < | else{ |
352 | < | |
353 | < | sprintf( painCave.errMsg, |
354 | < | "SimSetup Error: unhandled bend assignment:\n" |
355 | < | " -->%s in Bend[%d] in %s\n", |
356 | < | current_extra->getlhs(), |
357 | < | j, comp_stamps[stampID]->getID() ); |
358 | < | painCave.isFatal = 1; |
359 | < | simError(); |
360 | < | } |
361 | < | |
362 | < | current_extra = current_extra->getNext(); |
363 | < | } |
364 | < | } |
365 | < | |
366 | < | if( !theBends[j].isGhost ){ |
367 | < | |
368 | < | exI = theBends[j].a; |
369 | < | exJ = theBends[j].c; |
370 | < | } |
371 | < | else{ |
372 | < | |
322 | < | exI = theBends[j].a; |
323 | < | exJ = theBends[j].b; |
324 | < | } |
325 | < | |
326 | < | // exclude_I must always be the smaller of the pair |
327 | < | if( exI > exJ ){ |
328 | < | tempEx = exI; |
329 | < | exI = exJ; |
330 | < | exJ = tempEx; |
331 | < | } |
311 | > | for (j = 0; j < molInfo.nBends; j++){ |
312 | > | currentBend = comp_stamps[stampID]->getBend(j); |
313 | > | theBends[j].a = currentBend->getA() + atomOffset; |
314 | > | theBends[j].b = currentBend->getB() + atomOffset; |
315 | > | theBends[j].c = currentBend->getC() + atomOffset; |
316 | > | |
317 | > | if (currentBend->haveExtras()){ |
318 | > | extras = currentBend->getExtras(); |
319 | > | current_extra = extras; |
320 | > | |
321 | > | while (current_extra != NULL){ |
322 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
323 | > | switch (current_extra->getType()){ |
324 | > | case 0: |
325 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
326 | > | theBends[j].isGhost = 1; |
327 | > | break; |
328 | > | |
329 | > | case 1: |
330 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
331 | > | atomOffset; |
332 | > | theBends[j].isGhost = 1; |
333 | > | break; |
334 | > | |
335 | > | default: |
336 | > | sprintf(painCave.errMsg, |
337 | > | "SimSetup Error: ghostVectorSource was neither a " |
338 | > | "double nor an int.\n" |
339 | > | "-->Bend[%d] in %s\n", |
340 | > | j, comp_stamps[stampID]->getID()); |
341 | > | painCave.isFatal = 1; |
342 | > | simError(); |
343 | > | } |
344 | > | } |
345 | > | else{ |
346 | > | sprintf(painCave.errMsg, |
347 | > | "SimSetup Error: unhandled bend assignment:\n" |
348 | > | " -->%s in Bend[%d] in %s\n", |
349 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
350 | > | painCave.isFatal = 1; |
351 | > | simError(); |
352 | > | } |
353 | > | |
354 | > | current_extra = current_extra->getNext(); |
355 | > | } |
356 | > | } |
357 | > | |
358 | > | if (!theBends[j].isGhost){ |
359 | > | exI = theBends[j].a; |
360 | > | exJ = theBends[j].c; |
361 | > | } |
362 | > | else{ |
363 | > | exI = theBends[j].a; |
364 | > | exJ = theBends[j].b; |
365 | > | } |
366 | > | |
367 | > | // exclude_I must always be the smaller of the pair |
368 | > | if (exI > exJ){ |
369 | > | tempEx = exI; |
370 | > | exI = exJ; |
371 | > | exJ = tempEx; |
372 | > | } |
373 | #ifdef IS_MPI | |
374 | < | tempEx = exI; |
375 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
376 | < | tempEx = exJ; |
377 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
378 | < | |
379 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
374 | > | tempEx = exI; |
375 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
376 | > | tempEx = exJ; |
377 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
378 | > | |
379 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
380 | #else // isn't MPI | |
381 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
381 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
382 | #endif //is_mpi | |
383 | } | |
384 | excludeOffset += molInfo.nBends; | |
385 | < | |
386 | < | for(j=0; j<molInfo.nTorsions; j++){ |
387 | < | |
388 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
389 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
390 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
391 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
392 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
393 | < | |
394 | < | exI = theTorsions[j].a; |
395 | < | exJ = theTorsions[j].d; |
396 | < | |
397 | < | // exclude_I must always be the smaller of the pair |
398 | < | if( exI > exJ ){ |
399 | < | tempEx = exI; |
400 | < | exI = exJ; |
401 | < | exJ = tempEx; |
361 | < | } |
385 | > | |
386 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
387 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
388 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
389 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
390 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
391 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
392 | > | |
393 | > | exI = theTorsions[j].a; |
394 | > | exJ = theTorsions[j].d; |
395 | > | |
396 | > | // exclude_I must always be the smaller of the pair |
397 | > | if (exI > exJ){ |
398 | > | tempEx = exI; |
399 | > | exI = exJ; |
400 | > | exJ = tempEx; |
401 | > | } |
402 | #ifdef IS_MPI | |
403 | < | tempEx = exI; |
404 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
405 | < | tempEx = exJ; |
406 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
407 | < | |
408 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
403 | > | tempEx = exI; |
404 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
405 | > | tempEx = exJ; |
406 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
407 | > | |
408 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
409 | #else // isn't MPI | |
410 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
410 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
411 | #endif //is_mpi | |
412 | } | |
413 | excludeOffset += molInfo.nTorsions; | |
414 | < | |
415 | < | |
414 | > | |
415 | > | |
416 | // send the arrays off to the forceField for init. | |
377 | – | |
378 | – | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 | – | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 | – | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 | – | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 | – | |
383 | – | |
384 | – | info[k].molecules[i].initialize( molInfo ); |
417 | ||
418 | < | |
418 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
419 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
420 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
421 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
422 | > | theTorsions); |
423 | > | |
424 | > | |
425 | > | info[k].molecules[i].initialize(molInfo); |
426 | > | |
427 | > | |
428 | atomOffset += molInfo.nAtoms; | |
429 | delete[] theBonds; | |
430 | delete[] theBends; | |
431 | delete[] theTorsions; | |
432 | } | |
433 | } | |
434 | < | |
434 | > | |
435 | #ifdef IS_MPI | |
436 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
436 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
437 | MPIcheckPoint(); | |
438 | #endif // is_mpi | |
439 | < | |
439 | > | |
440 | // clean up the forcefield | |
441 | ||
442 | the_ff->calcRcut(); | |
443 | the_ff->cleanMe(); | |
403 | – | |
444 | } | |
445 | ||
446 | < | void SimSetup::initFromBass( void ){ |
407 | < | |
446 | > | void SimSetup::initFromBass(void){ |
447 | int i, j, k; | |
448 | int n_cells; | |
449 | double cellx, celly, cellz; | |
# | Line 418 | Line 457 | void SimSetup::initFromBass( void ){ | |
457 | vel[1] = 0.0; | |
458 | vel[2] = 0.0; | |
459 | ||
460 | < | temp1 = (double)tot_nmol / 4.0; |
461 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
462 | < | temp3 = ceil( temp2 ); |
460 | > | temp1 = (double) tot_nmol / 4.0; |
461 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
462 | > | temp3 = ceil(temp2); |
463 | ||
464 | < | have_extra =0; |
465 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
466 | < | have_extra =1; |
464 | > | have_extra = 0; |
465 | > | if (temp2 < temp3){ |
466 | > | // we have a non-complete lattice |
467 | > | have_extra = 1; |
468 | ||
469 | < | n_cells = (int)temp3 - 1; |
469 | > | n_cells = (int) temp3 - 1; |
470 | cellx = info[0].boxL[0] / temp3; | |
471 | celly = info[0].boxL[1] / temp3; | |
472 | cellz = info[0].boxL[2] / temp3; | |
473 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
474 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
475 | < | n_per_extra = (int)ceil( temp1 ); |
473 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
474 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
475 | > | n_per_extra = (int) ceil(temp1); |
476 | ||
477 | < | if( n_per_extra > 4){ |
478 | < | sprintf( painCave.errMsg, |
479 | < | "SimSetup error. There has been an error in constructing" |
480 | < | " the non-complete lattice.\n" ); |
477 | > | if (n_per_extra > 4){ |
478 | > | sprintf(painCave.errMsg, |
479 | > | "SimSetup error. There has been an error in constructing" |
480 | > | " the non-complete lattice.\n"); |
481 | painCave.isFatal = 1; | |
482 | simError(); | |
483 | } | |
484 | } | |
485 | else{ | |
486 | < | n_cells = (int)temp3; |
486 | > | n_cells = (int) temp3; |
487 | cellx = info[0].boxL[0] / temp3; | |
488 | celly = info[0].boxL[1] / temp3; | |
489 | cellz = info[0].boxL[2] / temp3; | |
# | Line 454 | Line 494 | void SimSetup::initFromBass( void ){ | |
494 | current_comp = 0; | |
495 | current_atom_ndx = 0; | |
496 | ||
497 | < | for( i=0; i < n_cells ; i++ ){ |
498 | < | for( j=0; j < n_cells; j++ ){ |
499 | < | for( k=0; k < n_cells; k++ ){ |
497 | > | for (i = 0; i < n_cells ; i++){ |
498 | > | for (j = 0; j < n_cells; j++){ |
499 | > | for (k = 0; k < n_cells; k++){ |
500 | > | makeElement(i * cellx, j * celly, k * cellz); |
501 | ||
502 | < | makeElement( i * cellx, |
462 | < | j * celly, |
463 | < | k * cellz ); |
502 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
503 | ||
504 | < | makeElement( i * cellx + 0.5 * cellx, |
466 | < | j * celly + 0.5 * celly, |
467 | < | k * cellz ); |
504 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
505 | ||
506 | < | makeElement( i * cellx, |
470 | < | j * celly + 0.5 * celly, |
471 | < | k * cellz + 0.5 * cellz ); |
472 | < | |
473 | < | makeElement( i * cellx + 0.5 * cellx, |
474 | < | j * celly, |
475 | < | k * cellz + 0.5 * cellz ); |
506 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
507 | } | |
508 | } | |
509 | } | |
510 | ||
511 | < | if( have_extra ){ |
511 | > | if (have_extra){ |
512 | done = 0; | |
513 | ||
514 | int start_ndx; | |
515 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
516 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
515 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
516 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
517 | > | if (i < n_cells){ |
518 | > | if (j < n_cells){ |
519 | > | start_ndx = n_cells; |
520 | > | } |
521 | > | else |
522 | > | start_ndx = 0; |
523 | > | } |
524 | > | else |
525 | > | start_ndx = 0; |
526 | ||
527 | < | if( i < n_cells ){ |
527 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
528 | > | makeElement(i * cellx, j * celly, k * cellz); |
529 | > | done = (current_mol >= tot_nmol); |
530 | ||
531 | < | if( j < n_cells ){ |
532 | < | start_ndx = n_cells; |
533 | < | } |
534 | < | else start_ndx = 0; |
535 | < | } |
494 | < | else start_ndx = 0; |
531 | > | if (!done && n_per_extra > 1){ |
532 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
533 | > | k * cellz); |
534 | > | done = (current_mol >= tot_nmol); |
535 | > | } |
536 | ||
537 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
537 | > | if (!done && n_per_extra > 2){ |
538 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
539 | > | k * cellz + 0.5 * cellz); |
540 | > | done = (current_mol >= tot_nmol); |
541 | > | } |
542 | ||
543 | < | makeElement( i * cellx, |
544 | < | j * celly, |
545 | < | k * cellz ); |
546 | < | done = ( current_mol >= tot_nmol ); |
547 | < | |
548 | < | if( !done && n_per_extra > 1 ){ |
504 | < | makeElement( i * cellx + 0.5 * cellx, |
505 | < | j * celly + 0.5 * celly, |
506 | < | k * cellz ); |
507 | < | done = ( current_mol >= tot_nmol ); |
508 | < | } |
509 | < | |
510 | < | if( !done && n_per_extra > 2){ |
511 | < | makeElement( i * cellx, |
512 | < | j * celly + 0.5 * celly, |
513 | < | k * cellz + 0.5 * cellz ); |
514 | < | done = ( current_mol >= tot_nmol ); |
515 | < | } |
516 | < | |
517 | < | if( !done && n_per_extra > 3){ |
518 | < | makeElement( i * cellx + 0.5 * cellx, |
519 | < | j * celly, |
520 | < | k * cellz + 0.5 * cellz ); |
521 | < | done = ( current_mol >= tot_nmol ); |
522 | < | } |
523 | < | } |
543 | > | if (!done && n_per_extra > 3){ |
544 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
545 | > | k * cellz + 0.5 * cellz); |
546 | > | done = (current_mol >= tot_nmol); |
547 | > | } |
548 | > | } |
549 | } | |
550 | } | |
551 | } | |
552 | ||
553 | < | for( i=0; i<info[0].n_atoms; i++ ){ |
554 | < | info[0].atoms[i]->setVel( vel ); |
553 | > | for (i = 0; i < info[0].n_atoms; i++){ |
554 | > | info[0].atoms[i]->setVel(vel); |
555 | } | |
556 | } | |
557 | ||
558 | < | void SimSetup::makeElement( double x, double y, double z ){ |
534 | < | |
558 | > | void SimSetup::makeElement(double x, double y, double z){ |
559 | int k; | |
560 | AtomStamp* current_atom; | |
561 | DirectionalAtom* dAtom; | |
562 | double rotMat[3][3]; | |
563 | double pos[3]; | |
564 | ||
565 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
566 | < | |
567 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
568 | < | if( !current_atom->havePosition() ){ |
569 | < | sprintf( painCave.errMsg, |
570 | < | "SimSetup:initFromBass error.\n" |
571 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
572 | < | "\tThe initialization routine is unable to give a start" |
573 | < | " position.\n", |
550 | < | comp_stamps[current_comp]->getID(), |
551 | < | current_atom->getType() ); |
565 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
566 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
567 | > | if (!current_atom->havePosition()){ |
568 | > | sprintf(painCave.errMsg, |
569 | > | "SimSetup:initFromBass error.\n" |
570 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
571 | > | "\tThe initialization routine is unable to give a start" |
572 | > | " position.\n", |
573 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
574 | painCave.isFatal = 1; | |
575 | simError(); | |
576 | } | |
577 | < | |
577 | > | |
578 | pos[0] = x + current_atom->getPosX(); | |
579 | pos[1] = y + current_atom->getPosY(); | |
580 | pos[2] = z + current_atom->getPosZ(); | |
559 | – | |
560 | – | info[0].atoms[current_atom_ndx]->setPos( pos ); |
581 | ||
582 | < | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
582 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
583 | ||
584 | < | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
584 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
585 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
586 | ||
587 | rotMat[0][0] = 1.0; | |
588 | rotMat[0][1] = 0.0; | |
# | Line 575 | Line 596 | void SimSetup::makeElement( double x, double y, double | |
596 | rotMat[2][1] = 0.0; | |
597 | rotMat[2][2] = 1.0; | |
598 | ||
599 | < | dAtom->setA( rotMat ); |
599 | > | dAtom->setA(rotMat); |
600 | } | |
601 | ||
602 | current_atom_ndx++; | |
# | Line 584 | Line 605 | void SimSetup::makeElement( double x, double y, double | |
605 | current_mol++; | |
606 | current_comp_mol++; | |
607 | ||
608 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
588 | < | |
608 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
609 | current_comp_mol = 0; | |
610 | current_comp++; | |
611 | } | |
612 | } | |
613 | ||
614 | ||
615 | < | void SimSetup::gatherInfo( void ){ |
616 | < | int i,j,k; |
615 | > | void SimSetup::gatherInfo(void){ |
616 | > | int i; |
617 | ||
618 | ensembleCase = -1; | |
619 | ffCase = -1; | |
620 | ||
621 | // set the easy ones first | |
622 | ||
623 | < | for( i=0; i<nInfo; i++){ |
623 | > | for (i = 0; i < nInfo; i++){ |
624 | info[i].target_temp = globals->getTargetTemp(); | |
625 | info[i].dt = globals->getDt(); | |
626 | info[i].run_time = globals->getRunTime(); | |
# | Line 610 | Line 630 | void SimSetup::gatherInfo( void ){ | |
630 | ||
631 | // get the forceField | |
632 | ||
633 | < | strcpy( force_field, globals->getForceField() ); |
633 | > | strcpy(force_field, globals->getForceField()); |
634 | ||
635 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
636 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
637 | < | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
635 | > | if (!strcasecmp(force_field, "DUFF")){ |
636 | > | ffCase = FF_DUFF; |
637 | > | } |
638 | > | else if (!strcasecmp(force_field, "LJ")){ |
639 | > | ffCase = FF_LJ; |
640 | > | } |
641 | > | else if (!strcasecmp(force_field, "EAM")){ |
642 | > | ffCase = FF_EAM; |
643 | > | } |
644 | > | else if (!strcasecmp(force_field, "WATER")){ |
645 | > | ffCase = FF_H2O; |
646 | > | } |
647 | else{ | |
648 | < | sprintf( painCave.errMsg, |
649 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
650 | < | force_field ); |
651 | < | painCave.isFatal = 1; |
623 | < | simError(); |
648 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
649 | > | force_field); |
650 | > | painCave.isFatal = 1; |
651 | > | simError(); |
652 | } | |
653 | ||
654 | < | // get the ensemble |
654 | > | // get the ensemble |
655 | ||
656 | < | strcpy( ensemble, globals->getEnsemble() ); |
656 | > | strcpy(ensemble, globals->getEnsemble()); |
657 | ||
658 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
659 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
660 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
658 | > | if (!strcasecmp(ensemble, "NVE")){ |
659 | > | ensembleCase = NVE_ENS; |
660 | > | } |
661 | > | else if (!strcasecmp(ensemble, "NVT")){ |
662 | > | ensembleCase = NVT_ENS; |
663 | > | } |
664 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
665 | ensembleCase = NPTi_ENS; | |
666 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
667 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
668 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
666 | > | } |
667 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
668 | > | ensembleCase = NPTf_ENS; |
669 | > | } |
670 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
671 | > | ensembleCase = NPTxyz_ENS; |
672 | > | } |
673 | else{ | |
674 | < | sprintf( painCave.errMsg, |
675 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
676 | < | "reverting to NVE for this simulation.\n", |
677 | < | ensemble ); |
678 | < | painCave.isFatal = 0; |
679 | < | simError(); |
680 | < | strcpy( ensemble, "NVE" ); |
681 | < | ensembleCase = NVE_ENS; |
674 | > | sprintf(painCave.errMsg, |
675 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
676 | > | "\treverting to NVE for this simulation.\n", |
677 | > | ensemble); |
678 | > | painCave.isFatal = 0; |
679 | > | simError(); |
680 | > | strcpy(ensemble, "NVE"); |
681 | > | ensembleCase = NVE_ENS; |
682 | } | |
647 | – | |
648 | – | for(i=0; i<nInfo; i++){ |
649 | – | |
650 | – | strcpy( info[i].ensemble, ensemble ); |
683 | ||
684 | + | for (i = 0; i < nInfo; i++){ |
685 | + | strcpy(info[i].ensemble, ensemble); |
686 | + | |
687 | // get the mixing rule | |
688 | ||
689 | < | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
689 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
690 | info[i].usePBC = globals->getPBC(); | |
691 | } | |
692 | < | |
692 | > | |
693 | // get the components and calculate the tot_nMol and indvidual n_mol | |
694 | < | |
694 | > | |
695 | the_components = globals->getComponents(); | |
696 | components_nmol = new int[n_components]; | |
697 | ||
698 | ||
699 | < | if( !globals->haveNMol() ){ |
699 | > | if (!globals->haveNMol()){ |
700 | // we don't have the total number of molecules, so we assume it is | |
701 | // given in each component | |
702 | ||
703 | tot_nmol = 0; | |
704 | < | for( i=0; i<n_components; i++ ){ |
705 | < | |
706 | < | if( !the_components[i]->haveNMol() ){ |
707 | < | // we have a problem |
708 | < | sprintf( painCave.errMsg, |
709 | < | "SimSetup Error. No global NMol or component NMol" |
710 | < | " given. Cannot calculate the number of atoms.\n" ); |
711 | < | painCave.isFatal = 1; |
677 | < | simError(); |
704 | > | for (i = 0; i < n_components; i++){ |
705 | > | if (!the_components[i]->haveNMol()){ |
706 | > | // we have a problem |
707 | > | sprintf(painCave.errMsg, |
708 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
709 | > | "\tCannot calculate the number of atoms.\n"); |
710 | > | painCave.isFatal = 1; |
711 | > | simError(); |
712 | } | |
713 | ||
714 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 682 | Line 716 | void SimSetup::gatherInfo( void ){ | |
716 | } | |
717 | } | |
718 | else{ | |
719 | < | sprintf( painCave.errMsg, |
720 | < | "SimSetup error.\n" |
721 | < | "\tSorry, the ability to specify total" |
722 | < | " nMols and then give molfractions in the components\n" |
723 | < | "\tis not currently supported." |
724 | < | " Please give nMol in the components.\n" ); |
719 | > | sprintf(painCave.errMsg, |
720 | > | "SimSetup error.\n" |
721 | > | "\tSorry, the ability to specify total" |
722 | > | " nMols and then give molfractions in the components\n" |
723 | > | "\tis not currently supported." |
724 | > | " Please give nMol in the components.\n"); |
725 | painCave.isFatal = 1; | |
726 | simError(); | |
727 | } | |
728 | ||
729 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
730 | + | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
731 | + | sprintf(painCave.errMsg, |
732 | + | "Sample time is not divisible by dt.\n" |
733 | + | "\tThis will result in samples that are not uniformly\n" |
734 | + | "\tdistributed in time. If this is a problem, change\n" |
735 | + | "\tyour sampleTime variable.\n"); |
736 | + | painCave.isFatal = 0; |
737 | + | simError(); |
738 | + | } |
739 | + | |
740 | + | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
741 | + | sprintf(painCave.errMsg, |
742 | + | "Status time is not divisible by dt.\n" |
743 | + | "\tThis will result in status reports that are not uniformly\n" |
744 | + | "\tdistributed in time. If this is a problem, change \n" |
745 | + | "\tyour statusTime variable.\n"); |
746 | + | painCave.isFatal = 0; |
747 | + | simError(); |
748 | + | } |
749 | + | |
750 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
751 | + | sprintf(painCave.errMsg, |
752 | + | "Thermal time is not divisible by dt.\n" |
753 | + | "\tThis will result in thermalizations that are not uniformly\n" |
754 | + | "\tdistributed in time. If this is a problem, change \n" |
755 | + | "\tyour thermalTime variable.\n"); |
756 | + | painCave.isFatal = 0; |
757 | + | simError(); |
758 | + | } |
759 | + | |
760 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
761 | + | sprintf(painCave.errMsg, |
762 | + | "Reset time is not divisible by dt.\n" |
763 | + | "\tThis will result in integrator resets that are not uniformly\n" |
764 | + | "\tdistributed in time. If this is a problem, change\n" |
765 | + | "\tyour resetTime variable.\n"); |
766 | + | painCave.isFatal = 0; |
767 | + | simError(); |
768 | + | } |
769 | + | |
770 | // set the status, sample, and thermal kick times | |
696 | – | |
697 | – | for(i=0; i<nInfo; i++){ |
771 | ||
772 | < | if( globals->haveSampleTime() ){ |
772 | > | for (i = 0; i < nInfo; i++){ |
773 | > | if (globals->haveSampleTime()){ |
774 | info[i].sampleTime = globals->getSampleTime(); | |
775 | info[i].statusTime = info[i].sampleTime; | |
776 | info[i].thermalTime = info[i].sampleTime; | |
# | Line 706 | Line 780 | void SimSetup::gatherInfo( void ){ | |
780 | info[i].statusTime = info[i].sampleTime; | |
781 | info[i].thermalTime = info[i].sampleTime; | |
782 | } | |
783 | < | |
784 | < | if( globals->haveStatusTime() ){ |
783 | > | |
784 | > | if (globals->haveStatusTime()){ |
785 | info[i].statusTime = globals->getStatusTime(); | |
786 | } | |
787 | < | |
788 | < | if( globals->haveThermalTime() ){ |
787 | > | |
788 | > | if (globals->haveThermalTime()){ |
789 | info[i].thermalTime = globals->getThermalTime(); | |
790 | } | |
791 | ||
792 | + | info[i].resetIntegrator = 0; |
793 | + | if( globals->haveResetTime() ){ |
794 | + | info[i].resetTime = globals->getResetTime(); |
795 | + | info[i].resetIntegrator = 1; |
796 | + | } |
797 | + | |
798 | // check for the temperature set flag | |
799 | + | |
800 | + | if (globals->haveTempSet()) |
801 | + | info[i].setTemp = globals->getTempSet(); |
802 | ||
803 | < | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
803 | > | // check for the extended State init |
804 | > | |
805 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
806 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
807 | ||
722 | – | // get some of the tricky things that may still be in the globals |
723 | – | |
724 | – | double boxVector[3]; |
725 | – | if( globals->haveBox() ){ |
726 | – | boxVector[0] = globals->getBox(); |
727 | – | boxVector[1] = globals->getBox(); |
728 | – | boxVector[2] = globals->getBox(); |
729 | – | |
730 | – | info[i].setBox( boxVector ); |
731 | – | } |
732 | – | else if( globals->haveDensity() ){ |
733 | – | |
734 | – | double vol; |
735 | – | vol = (double)tot_nmol / globals->getDensity(); |
736 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 | – | boxVector[1] = boxVector[0]; |
738 | – | boxVector[2] = boxVector[0]; |
739 | – | |
740 | – | info[i].setBox( boxVector ); |
808 | } | |
809 | < | else{ |
810 | < | if( !globals->haveBoxX() ){ |
811 | < | sprintf( painCave.errMsg, |
812 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
813 | < | painCave.isFatal = 1; |
814 | < | simError(); |
809 | > | |
810 | > | //setup seed for random number generator |
811 | > | int seedValue; |
812 | > | |
813 | > | if (globals->haveSeed()){ |
814 | > | seedValue = globals->getSeed(); |
815 | > | |
816 | > | if(seedValue / 1E9 == 0){ |
817 | > | sprintf(painCave.errMsg, |
818 | > | "Seed for sprng library should contain at least 9 digits\n" |
819 | > | "OOPSE will generate a seed for user\n"); |
820 | > | painCave.isFatal = 0; |
821 | > | simError(); |
822 | > | |
823 | > | //using seed generated by system instead of invalid seed set by user |
824 | > | #ifndef IS_MPI |
825 | > | seedValue = make_sprng_seed(); |
826 | > | #else |
827 | > | if (worldRank == 0){ |
828 | > | seedValue = make_sprng_seed(); |
829 | } | |
830 | < | boxVector[0] = globals->getBoxX(); |
831 | < | |
751 | < | if( !globals->haveBoxY() ){ |
752 | < | sprintf( painCave.errMsg, |
753 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
754 | < | painCave.isFatal = 1; |
755 | < | simError(); |
756 | < | } |
757 | < | boxVector[1] = globals->getBoxY(); |
758 | < | |
759 | < | if( !globals->haveBoxZ() ){ |
760 | < | sprintf( painCave.errMsg, |
761 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
762 | < | painCave.isFatal = 1; |
763 | < | simError(); |
764 | < | } |
765 | < | boxVector[2] = globals->getBoxZ(); |
766 | < | |
767 | < | info[i].setBox( boxVector ); |
830 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
831 | > | #endif |
832 | } | |
833 | + | }//end of if branch of globals->haveSeed() |
834 | + | else{ |
835 | + | |
836 | + | #ifndef IS_MPI |
837 | + | seedValue = make_sprng_seed(); |
838 | + | #else |
839 | + | if (worldRank == 0){ |
840 | + | seedValue = make_sprng_seed(); |
841 | + | } |
842 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
843 | + | #endif |
844 | + | }//end of globals->haveSeed() |
845 | ||
846 | + | for (int i = 0; i < nInfo; i++){ |
847 | + | info[i].setSeed(seedValue); |
848 | } | |
849 | < | |
849 | > | |
850 | #ifdef IS_MPI | |
851 | < | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
851 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
852 | MPIcheckPoint(); | |
853 | #endif // is_mpi | |
776 | – | |
854 | } | |
855 | ||
856 | ||
857 | < | void SimSetup::finalInfoCheck( void ){ |
857 | > | void SimSetup::finalInfoCheck(void){ |
858 | int index; | |
859 | int usesDipoles; | |
860 | int i; | |
861 | ||
862 | < | for(i=0; i<nInfo; i++){ |
862 | > | for (i = 0; i < nInfo; i++){ |
863 | // check electrostatic parameters | |
864 | < | |
864 | > | |
865 | index = 0; | |
866 | usesDipoles = 0; | |
867 | < | while( (index < info[i].n_atoms) && !usesDipoles ){ |
867 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
868 | usesDipoles = (info[i].atoms[index])->hasDipole(); | |
869 | index++; | |
870 | } | |
871 | < | |
871 | > | |
872 | #ifdef IS_MPI | |
873 | int myUse = usesDipoles; | |
874 | < | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
874 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
875 | #endif //is_mpi | |
876 | < | |
876 | > | |
877 | double theEcr, theEst; | |
878 | < | |
879 | < | if (globals->getUseRF() ) { |
878 | > | |
879 | > | if (globals->getUseRF()){ |
880 | info[i].useReactionField = 1; | |
881 | < | |
882 | < | if( !globals->haveECR() ){ |
883 | < | sprintf( painCave.errMsg, |
884 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
885 | < | "box length for the electrostaticCutoffRadius.\n" |
886 | < | "I hope you have a very fast processor!\n"); |
887 | < | painCave.isFatal = 0; |
888 | < | simError(); |
889 | < | double smallest; |
813 | < | smallest = info[i].boxL[0]; |
814 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 | < | theEcr = 0.5 * smallest; |
817 | < | } else { |
818 | < | theEcr = globals->getECR(); |
881 | > | |
882 | > | if (!globals->haveECR()){ |
883 | > | sprintf(painCave.errMsg, |
884 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
885 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
886 | > | "\tfor the electrostaticCutoffRadius.\n"); |
887 | > | painCave.isFatal = 0; |
888 | > | simError(); |
889 | > | theEcr = 15.0; |
890 | } | |
891 | < | |
892 | < | if( !globals->haveEST() ){ |
822 | < | sprintf( painCave.errMsg, |
823 | < | "SimSetup Warning: using default value of 0.05 * the " |
824 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 | < | ); |
826 | < | painCave.isFatal = 0; |
827 | < | simError(); |
828 | < | theEst = 0.05 * theEcr; |
829 | < | } else { |
830 | < | theEst= globals->getEST(); |
891 | > | else{ |
892 | > | theEcr = globals->getECR(); |
893 | } | |
894 | < | |
895 | < | info[i].setEcr( theEcr, theEst ); |
896 | < | |
897 | < | if(!globals->haveDielectric() ){ |
898 | < | sprintf( painCave.errMsg, |
899 | < | "SimSetup Error: You are trying to use Reaction Field without" |
900 | < | "setting a dielectric constant!\n" |
901 | < | ); |
902 | < | painCave.isFatal = 1; |
903 | < | simError(); |
904 | < | } |
905 | < | info[i].dielectric = globals->getDielectric(); |
906 | < | } |
907 | < | else { |
908 | < | if (usesDipoles) { |
909 | < | |
910 | < | if( !globals->haveECR() ){ |
911 | < | sprintf( painCave.errMsg, |
912 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
913 | < | "box length for the electrostaticCutoffRadius.\n" |
914 | < | "I hope you have a very fast processor!\n"); |
894 | > | |
895 | > | if (!globals->haveEST()){ |
896 | > | sprintf(painCave.errMsg, |
897 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
898 | > | "\tOOPSE will use a default value of\n" |
899 | > | "\t0.05 * electrostaticCutoffRadius\n" |
900 | > | "\tfor the electrostaticSkinThickness\n"); |
901 | > | painCave.isFatal = 0; |
902 | > | simError(); |
903 | > | theEst = 0.05 * theEcr; |
904 | > | } |
905 | > | else{ |
906 | > | theEst = globals->getEST(); |
907 | > | } |
908 | > | |
909 | > | info[i].setDefaultEcr(theEcr, theEst); |
910 | > | |
911 | > | if (!globals->haveDielectric()){ |
912 | > | sprintf(painCave.errMsg, |
913 | > | "SimSetup Error: No Dielectric constant was set.\n" |
914 | > | "\tYou are trying to use Reaction Field without" |
915 | > | "\tsetting a dielectric constant!\n"); |
916 | > | painCave.isFatal = 1; |
917 | > | simError(); |
918 | > | } |
919 | > | info[i].dielectric = globals->getDielectric(); |
920 | > | } |
921 | > | else{ |
922 | > | if (usesDipoles){ |
923 | > | if (!globals->haveECR()){ |
924 | > | sprintf(painCave.errMsg, |
925 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
926 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
927 | > | "\tfor the electrostaticCutoffRadius.\n"); |
928 | painCave.isFatal = 0; | |
929 | simError(); | |
930 | < | double smallest; |
931 | < | smallest = info[i].boxL[0]; |
932 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
933 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
934 | < | theEcr = 0.5 * smallest; |
860 | < | } else { |
861 | < | theEcr = globals->getECR(); |
862 | < | } |
930 | > | theEcr = 15.0; |
931 | > | } |
932 | > | else{ |
933 | > | theEcr = globals->getECR(); |
934 | > | } |
935 | ||
936 | < | if( !globals->haveEST() ){ |
937 | < | sprintf( painCave.errMsg, |
938 | < | "SimSetup Warning: using default value of 0.05 * the " |
939 | < | "electrostaticCutoffRadius for the " |
940 | < | "electrostaticSkinThickness\n" |
941 | < | ); |
942 | < | painCave.isFatal = 0; |
943 | < | simError(); |
944 | < | theEst = 0.05 * theEcr; |
945 | < | } else { |
946 | < | theEst= globals->getEST(); |
947 | < | } |
936 | > | if (!globals->haveEST()){ |
937 | > | sprintf(painCave.errMsg, |
938 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
939 | > | "\tOOPSE will use a default value of\n" |
940 | > | "\t0.05 * electrostaticCutoffRadius\n" |
941 | > | "\tfor the electrostaticSkinThickness\n"); |
942 | > | painCave.isFatal = 0; |
943 | > | simError(); |
944 | > | theEst = 0.05 * theEcr; |
945 | > | } |
946 | > | else{ |
947 | > | theEst = globals->getEST(); |
948 | > | } |
949 | ||
950 | < | info[i].setEcr( theEcr, theEst ); |
950 | > | info[i].setDefaultEcr(theEcr, theEst); |
951 | } | |
952 | < | } |
952 | > | } |
953 | } | |
881 | – | |
954 | #ifdef IS_MPI | |
955 | < | strcpy( checkPointMsg, "post processing checks out" ); |
955 | > | strcpy(checkPointMsg, "post processing checks out"); |
956 | MPIcheckPoint(); | |
957 | #endif // is_mpi | |
886 | – | |
958 | } | |
888 | – | |
889 | – | void SimSetup::initSystemCoords( void ){ |
890 | – | int i; |
959 | ||
960 | + | void SimSetup::initSystemCoords(void){ |
961 | + | int i; |
962 | + | |
963 | char* inName; | |
964 | ||
965 | + | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
966 | ||
967 | < | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
968 | < | |
969 | < | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
970 | < | |
899 | < | if( globals->haveInitialConfig() ){ |
900 | < | |
967 | > | for (i = 0; i < info[0].n_atoms; i++) |
968 | > | info[0].atoms[i]->setCoords(); |
969 | > | |
970 | > | if (globals->haveInitialConfig()){ |
971 | InitializeFromFile* fileInit; | |
972 | #ifdef IS_MPI // is_mpi | |
973 | < | if( worldRank == 0 ){ |
973 | > | if (worldRank == 0){ |
974 | #endif //is_mpi | |
975 | inName = globals->getInitialConfig(); | |
976 | < | fileInit = new InitializeFromFile( inName ); |
976 | > | fileInit = new InitializeFromFile(inName); |
977 | #ifdef IS_MPI | |
978 | < | }else fileInit = new InitializeFromFile( NULL ); |
978 | > | } |
979 | > | else |
980 | > | fileInit = new InitializeFromFile(NULL); |
981 | #endif | |
982 | < | fileInit->readInit( info ); // default velocities on |
983 | < | |
982 | > | fileInit->readInit(info); // default velocities on |
983 | > | |
984 | delete fileInit; | |
985 | } | |
986 | else{ | |
987 | ||
916 | – | #ifdef IS_MPI |
917 | – | |
988 | // no init from bass | |
989 | ||
990 | < | sprintf( painCave.errMsg, |
991 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
992 | < | painCave.isFatal; |
990 | > | sprintf(painCave.errMsg, |
991 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
992 | > | painCave.isFatal = 1;; |
993 | simError(); | |
994 | ||
925 | – | #else |
926 | – | |
927 | – | initFromBass(); |
928 | – | |
929 | – | |
930 | – | #endif |
995 | } | |
996 | < | |
996 | > | |
997 | #ifdef IS_MPI | |
998 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
998 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
999 | MPIcheckPoint(); | |
1000 | #endif // is_mpi | |
937 | – | |
1001 | } | |
1002 | ||
1003 | ||
1004 | < | void SimSetup::makeOutNames( void ){ |
942 | < | |
1004 | > | void SimSetup::makeOutNames(void){ |
1005 | int k; | |
1006 | ||
945 | – | |
946 | – | for(k=0; k<nInfo; k++){ |
1007 | ||
1008 | + | for (k = 0; k < nInfo; k++){ |
1009 | #ifdef IS_MPI | |
1010 | < | if( worldRank == 0 ){ |
1010 | > | if (worldRank == 0){ |
1011 | #endif // is_mpi | |
1012 | < | |
1013 | < | if( globals->haveFinalConfig() ){ |
1014 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
1012 | > | |
1013 | > | if (globals->haveFinalConfig()){ |
1014 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1015 | } | |
1016 | else{ | |
1017 | < | strcpy( info[k].finalName, inFileName ); |
1018 | < | char* endTest; |
1019 | < | int nameLength = strlen( info[k].finalName ); |
1020 | < | endTest = &(info[k].finalName[nameLength - 5]); |
1021 | < | if( !strcmp( endTest, ".bass" ) ){ |
1022 | < | strcpy( endTest, ".eor" ); |
1023 | < | } |
1024 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1025 | < | strcpy( endTest, ".eor" ); |
1026 | < | } |
1027 | < | else{ |
1028 | < | endTest = &(info[k].finalName[nameLength - 4]); |
1029 | < | if( !strcmp( endTest, ".bss" ) ){ |
1030 | < | strcpy( endTest, ".eor" ); |
1031 | < | } |
1032 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1033 | < | strcpy( endTest, ".eor" ); |
1034 | < | } |
1035 | < | else{ |
1036 | < | strcat( info[k].finalName, ".eor" ); |
1037 | < | } |
1038 | < | } |
1017 | > | strcpy(info[k].finalName, inFileName); |
1018 | > | char* endTest; |
1019 | > | int nameLength = strlen(info[k].finalName); |
1020 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1021 | > | if (!strcmp(endTest, ".bass")){ |
1022 | > | strcpy(endTest, ".eor"); |
1023 | > | } |
1024 | > | else if (!strcmp(endTest, ".BASS")){ |
1025 | > | strcpy(endTest, ".eor"); |
1026 | > | } |
1027 | > | else{ |
1028 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1029 | > | if (!strcmp(endTest, ".bss")){ |
1030 | > | strcpy(endTest, ".eor"); |
1031 | > | } |
1032 | > | else if (!strcmp(endTest, ".mdl")){ |
1033 | > | strcpy(endTest, ".eor"); |
1034 | > | } |
1035 | > | else{ |
1036 | > | strcat(info[k].finalName, ".eor"); |
1037 | > | } |
1038 | > | } |
1039 | } | |
1040 | < | |
1040 | > | |
1041 | // make the sample and status out names | |
1042 | < | |
1043 | < | strcpy( info[k].sampleName, inFileName ); |
1042 | > | |
1043 | > | strcpy(info[k].sampleName, inFileName); |
1044 | char* endTest; | |
1045 | < | int nameLength = strlen( info[k].sampleName ); |
1045 | > | int nameLength = strlen(info[k].sampleName); |
1046 | endTest = &(info[k].sampleName[nameLength - 5]); | |
1047 | < | if( !strcmp( endTest, ".bass" ) ){ |
1048 | < | strcpy( endTest, ".dump" ); |
1047 | > | if (!strcmp(endTest, ".bass")){ |
1048 | > | strcpy(endTest, ".dump"); |
1049 | } | |
1050 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1051 | < | strcpy( endTest, ".dump" ); |
1050 | > | else if (!strcmp(endTest, ".BASS")){ |
1051 | > | strcpy(endTest, ".dump"); |
1052 | } | |
1053 | else{ | |
1054 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1055 | < | if( !strcmp( endTest, ".bss" ) ){ |
1056 | < | strcpy( endTest, ".dump" ); |
1057 | < | } |
1058 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1059 | < | strcpy( endTest, ".dump" ); |
1060 | < | } |
1061 | < | else{ |
1062 | < | strcat( info[k].sampleName, ".dump" ); |
1063 | < | } |
1054 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1055 | > | if (!strcmp(endTest, ".bss")){ |
1056 | > | strcpy(endTest, ".dump"); |
1057 | > | } |
1058 | > | else if (!strcmp(endTest, ".mdl")){ |
1059 | > | strcpy(endTest, ".dump"); |
1060 | > | } |
1061 | > | else{ |
1062 | > | strcat(info[k].sampleName, ".dump"); |
1063 | > | } |
1064 | } | |
1065 | < | |
1066 | < | strcpy( info[k].statusName, inFileName ); |
1067 | < | nameLength = strlen( info[k].statusName ); |
1065 | > | |
1066 | > | strcpy(info[k].statusName, inFileName); |
1067 | > | nameLength = strlen(info[k].statusName); |
1068 | endTest = &(info[k].statusName[nameLength - 5]); | |
1069 | < | if( !strcmp( endTest, ".bass" ) ){ |
1070 | < | strcpy( endTest, ".stat" ); |
1069 | > | if (!strcmp(endTest, ".bass")){ |
1070 | > | strcpy(endTest, ".stat"); |
1071 | } | |
1072 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1073 | < | strcpy( endTest, ".stat" ); |
1072 | > | else if (!strcmp(endTest, ".BASS")){ |
1073 | > | strcpy(endTest, ".stat"); |
1074 | } | |
1075 | else{ | |
1076 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1077 | < | if( !strcmp( endTest, ".bss" ) ){ |
1078 | < | strcpy( endTest, ".stat" ); |
1079 | < | } |
1080 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1081 | < | strcpy( endTest, ".stat" ); |
1082 | < | } |
1083 | < | else{ |
1084 | < | strcat( info[k].statusName, ".stat" ); |
1085 | < | } |
1076 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1077 | > | if (!strcmp(endTest, ".bss")){ |
1078 | > | strcpy(endTest, ".stat"); |
1079 | > | } |
1080 | > | else if (!strcmp(endTest, ".mdl")){ |
1081 | > | strcpy(endTest, ".stat"); |
1082 | > | } |
1083 | > | else{ |
1084 | > | strcat(info[k].statusName, ".stat"); |
1085 | > | } |
1086 | } | |
1087 | < | |
1087 | > | |
1088 | #ifdef IS_MPI | |
1089 | + | |
1090 | } | |
1091 | #endif // is_mpi | |
1092 | } | |
1093 | } | |
1094 | ||
1095 | ||
1096 | < | void SimSetup::sysObjectsCreation( void ){ |
1097 | < | |
1098 | < | int i,k; |
1037 | < | |
1096 | > | void SimSetup::sysObjectsCreation(void){ |
1097 | > | int i, k; |
1098 | > | |
1099 | // create the forceField | |
1100 | ||
1101 | createFF(); | |
# | Line 1049 | Line 1110 | void SimSetup::sysObjectsCreation( void ){ | |
1110 | ||
1111 | #ifdef IS_MPI | |
1112 | // divide the molecules among the processors | |
1113 | < | |
1113 | > | |
1114 | mpiMolDivide(); | |
1115 | #endif //is_mpi | |
1116 | < | |
1116 | > | |
1117 | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's | |
1118 | < | |
1118 | > | |
1119 | makeSysArrays(); | |
1120 | ||
1121 | // make and initialize the molecules (all but atomic coordinates) | |
1122 | < | |
1122 | > | |
1123 | makeMolecules(); | |
1124 | < | |
1125 | < | for(k=0; k<nInfo; k++){ |
1124 | > | |
1125 | > | for (k = 0; k < nInfo; k++){ |
1126 | info[k].identArray = new int[info[k].n_atoms]; | |
1127 | < | for(i=0; i<info[k].n_atoms; i++){ |
1127 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1128 | info[k].identArray[i] = info[k].atoms[i]->getIdent(); | |
1129 | } | |
1130 | } | |
1131 | } | |
1132 | ||
1133 | ||
1134 | < | void SimSetup::createFF( void ){ |
1134 | > | void SimSetup::createFF(void){ |
1135 | > | switch (ffCase){ |
1136 | > | case FF_DUFF: |
1137 | > | the_ff = new DUFF(); |
1138 | > | break; |
1139 | ||
1140 | < | switch( ffCase ){ |
1140 | > | case FF_LJ: |
1141 | > | the_ff = new LJFF(); |
1142 | > | break; |
1143 | ||
1144 | < | case FF_DUFF: |
1145 | < | the_ff = new DUFF(); |
1146 | < | break; |
1144 | > | case FF_EAM: |
1145 | > | the_ff = new EAM_FF(); |
1146 | > | break; |
1147 | ||
1148 | < | case FF_LJ: |
1149 | < | the_ff = new LJFF(); |
1150 | < | break; |
1148 | > | case FF_H2O: |
1149 | > | the_ff = new WATER(); |
1150 | > | break; |
1151 | ||
1152 | < | case FF_EAM: |
1153 | < | the_ff = new EAM_FF(); |
1154 | < | break; |
1155 | < | |
1156 | < | default: |
1090 | < | sprintf( painCave.errMsg, |
1091 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 | < | painCave.isFatal = 1; |
1093 | < | simError(); |
1152 | > | default: |
1153 | > | sprintf(painCave.errMsg, |
1154 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1155 | > | painCave.isFatal = 1; |
1156 | > | simError(); |
1157 | } | |
1158 | ||
1159 | #ifdef IS_MPI | |
1160 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
1160 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1161 | MPIcheckPoint(); | |
1162 | #endif // is_mpi | |
1100 | – | |
1163 | } | |
1164 | ||
1165 | ||
1166 | < | void SimSetup::compList( void ){ |
1105 | < | |
1166 | > | void SimSetup::compList(void){ |
1167 | int i; | |
1168 | char* id; | |
1169 | LinkedMolStamp* headStamp = new LinkedMolStamp(); | |
1170 | LinkedMolStamp* currentStamp = NULL; | |
1171 | < | comp_stamps = new MoleculeStamp*[n_components]; |
1172 | < | |
1171 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1172 | > | |
1173 | // make an array of molecule stamps that match the components used. | |
1174 | // also extract the used stamps out into a separate linked list | |
1175 | < | |
1176 | < | for(i=0; i<nInfo; i++){ |
1175 | > | |
1176 | > | for (i = 0; i < nInfo; i++){ |
1177 | info[i].nComponents = n_components; | |
1178 | info[i].componentsNmol = components_nmol; | |
1179 | info[i].compStamps = comp_stamps; | |
1180 | info[i].headStamp = headStamp; | |
1181 | } | |
1121 | – | |
1182 | ||
1123 | – | for( i=0; i<n_components; i++ ){ |
1183 | ||
1184 | + | for (i = 0; i < n_components; i++){ |
1185 | id = the_components[i]->getType(); | |
1186 | comp_stamps[i] = NULL; | |
1187 | < | |
1187 | > | |
1188 | // check to make sure the component isn't already in the list | |
1189 | ||
1190 | < | comp_stamps[i] = headStamp->match( id ); |
1191 | < | if( comp_stamps[i] == NULL ){ |
1132 | < | |
1190 | > | comp_stamps[i] = headStamp->match(id); |
1191 | > | if (comp_stamps[i] == NULL){ |
1192 | // extract the component from the list; | |
1193 | < | |
1194 | < | currentStamp = stamps->extractMolStamp( id ); |
1195 | < | if( currentStamp == NULL ){ |
1196 | < | sprintf( painCave.errMsg, |
1197 | < | "SimSetup error: Component \"%s\" was not found in the " |
1198 | < | "list of declared molecules\n", |
1199 | < | id ); |
1200 | < | painCave.isFatal = 1; |
1201 | < | simError(); |
1193 | > | |
1194 | > | currentStamp = stamps->extractMolStamp(id); |
1195 | > | if (currentStamp == NULL){ |
1196 | > | sprintf(painCave.errMsg, |
1197 | > | "SimSetup error: Component \"%s\" was not found in the " |
1198 | > | "list of declared molecules\n", |
1199 | > | id); |
1200 | > | painCave.isFatal = 1; |
1201 | > | simError(); |
1202 | } | |
1203 | < | |
1204 | < | headStamp->add( currentStamp ); |
1205 | < | comp_stamps[i] = headStamp->match( id ); |
1203 | > | |
1204 | > | headStamp->add(currentStamp); |
1205 | > | comp_stamps[i] = headStamp->match(id); |
1206 | } | |
1207 | } | |
1208 | ||
1209 | #ifdef IS_MPI | |
1210 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1210 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1211 | MPIcheckPoint(); | |
1212 | #endif // is_mpi | |
1213 | + | } |
1214 | ||
1215 | + | void SimSetup::calcSysValues(void){ |
1216 | + | int i; |
1217 | ||
1218 | < | } |
1218 | > | int* molMembershipArray; |
1219 | ||
1158 | – | void SimSetup::calcSysValues( void ){ |
1159 | – | int i, j, k; |
1160 | – | |
1161 | – | int *molMembershipArray; |
1162 | – | |
1220 | tot_atoms = 0; | |
1221 | tot_bonds = 0; | |
1222 | tot_bends = 0; | |
1223 | tot_torsions = 0; | |
1224 | < | for( i=0; i<n_components; i++ ){ |
1225 | < | |
1226 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1227 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1171 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1224 | > | for (i = 0; i < n_components; i++){ |
1225 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1226 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1227 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1228 | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); | |
1229 | } | |
1230 | < | |
1230 | > | |
1231 | tot_SRI = tot_bonds + tot_bends + tot_torsions; | |
1232 | molMembershipArray = new int[tot_atoms]; | |
1233 | < | |
1234 | < | for(i=0; i<nInfo; i++){ |
1233 | > | |
1234 | > | for (i = 0; i < nInfo; i++){ |
1235 | info[i].n_atoms = tot_atoms; | |
1236 | info[i].n_bonds = tot_bonds; | |
1237 | info[i].n_bends = tot_bends; | |
1238 | info[i].n_torsions = tot_torsions; | |
1239 | info[i].n_SRI = tot_SRI; | |
1240 | info[i].n_mol = tot_nmol; | |
1241 | < | |
1241 | > | |
1242 | info[i].molMembershipArray = molMembershipArray; | |
1243 | < | } |
1243 | > | } |
1244 | } | |
1245 | ||
1246 | #ifdef IS_MPI | |
1247 | ||
1248 | < | void SimSetup::mpiMolDivide( void ){ |
1193 | < | |
1248 | > | void SimSetup::mpiMolDivide(void){ |
1249 | int i, j, k; | |
1250 | int localMol, allMol; | |
1251 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1252 | ||
1253 | < | mpiSim = new mpiSimulation( info ); |
1254 | < | |
1253 | > | mpiSim = new mpiSimulation(info); |
1254 | > | |
1255 | globalIndex = mpiSim->divideLabor(); | |
1256 | ||
1257 | // set up the local variables | |
1258 | < | |
1258 | > | |
1259 | mol2proc = mpiSim->getMolToProcMap(); | |
1260 | molCompType = mpiSim->getMolComponentType(); | |
1261 | < | |
1261 | > | |
1262 | allMol = 0; | |
1263 | localMol = 0; | |
1264 | local_atoms = 0; | |
# | Line 1213 | Line 1268 | void SimSetup::mpiMolDivide( void ){ | |
1268 | globalAtomIndex = 0; | |
1269 | ||
1270 | ||
1271 | < | for( i=0; i<n_components; i++ ){ |
1272 | < | |
1273 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1274 | < | |
1275 | < | if( mol2proc[allMol] == worldRank ){ |
1276 | < | |
1277 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1278 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1224 | < | local_bends += comp_stamps[i]->getNBends(); |
1225 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1226 | < | localMol++; |
1271 | > | for (i = 0; i < n_components; i++){ |
1272 | > | for (j = 0; j < components_nmol[i]; j++){ |
1273 | > | if (mol2proc[allMol] == worldRank){ |
1274 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1275 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1276 | > | local_bends += comp_stamps[i]->getNBends(); |
1277 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1278 | > | localMol++; |
1279 | } | |
1280 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1280 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1281 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
1282 | globalAtomIndex++; | |
1283 | } | |
1284 | ||
1285 | < | allMol++; |
1285 | > | allMol++; |
1286 | } | |
1287 | } | |
1288 | local_SRI = local_bonds + local_bends + local_torsions; | |
1289 | < | |
1289 | > | |
1290 | info[0].n_atoms = mpiSim->getMyNlocal(); | |
1291 | < | |
1292 | < | if( local_atoms != info[0].n_atoms ){ |
1293 | < | sprintf( painCave.errMsg, |
1294 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1295 | < | " localAtom (%d) are not equal.\n", |
1296 | < | info[0].n_atoms, |
1245 | < | local_atoms ); |
1291 | > | |
1292 | > | if (local_atoms != info[0].n_atoms){ |
1293 | > | sprintf(painCave.errMsg, |
1294 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1295 | > | "\tlocalAtom (%d) are not equal.\n", |
1296 | > | info[0].n_atoms, local_atoms); |
1297 | painCave.isFatal = 1; | |
1298 | simError(); | |
1299 | } | |
# | Line 1253 | Line 1304 | void SimSetup::mpiMolDivide( void ){ | |
1304 | info[0].n_SRI = local_SRI; | |
1305 | info[0].n_mol = localMol; | |
1306 | ||
1307 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1307 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1308 | MPIcheckPoint(); | |
1309 | } | |
1310 | < | |
1310 | > | |
1311 | #endif // is_mpi | |
1312 | ||
1313 | ||
1314 | < | void SimSetup::makeSysArrays( void ){ |
1315 | < | int i, j, k, l; |
1314 | > | void SimSetup::makeSysArrays(void){ |
1315 | > | |
1316 | > | #ifndef IS_MPI |
1317 | > | int k, j; |
1318 | > | #endif // is_mpi |
1319 | > | int i, l; |
1320 | ||
1321 | Atom** the_atoms; | |
1322 | Molecule* the_molecules; | |
1323 | Exclude** the_excludes; | |
1324 | ||
1325 | < | |
1326 | < | for(l=0; l<nInfo; l++){ |
1272 | < | |
1325 | > | |
1326 | > | for (l = 0; l < nInfo; l++){ |
1327 | // create the atom and short range interaction arrays | |
1328 | < | |
1329 | < | the_atoms = new Atom*[info[l].n_atoms]; |
1328 | > | |
1329 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1330 | the_molecules = new Molecule[info[l].n_mol]; | |
1331 | int molIndex; | |
1332 | ||
1333 | // initialize the molecule's stampID's | |
1334 | < | |
1334 | > | |
1335 | #ifdef IS_MPI | |
1336 | < | |
1337 | < | |
1336 | > | |
1337 | > | |
1338 | molIndex = 0; | |
1339 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1340 | < | |
1341 | < | if(mol2proc[i] == worldRank ){ |
1342 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1343 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1344 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1291 | < | molIndex++; |
1339 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1340 | > | if (mol2proc[i] == worldRank){ |
1341 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1342 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1343 | > | the_molecules[molIndex].setGlobalIndex(i); |
1344 | > | molIndex++; |
1345 | } | |
1346 | } | |
1347 | < | |
1347 | > | |
1348 | #else // is_mpi | |
1349 | < | |
1349 | > | |
1350 | molIndex = 0; | |
1351 | globalAtomIndex = 0; | |
1352 | < | for(i=0; i<n_components; i++){ |
1353 | < | for(j=0; j<components_nmol[i]; j++ ){ |
1354 | < | the_molecules[molIndex].setStampID( i ); |
1355 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1356 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1357 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1358 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1359 | < | globalAtomIndex++; |
1360 | < | } |
1361 | < | molIndex++; |
1352 | > | for (i = 0; i < n_components; i++){ |
1353 | > | for (j = 0; j < components_nmol[i]; j++){ |
1354 | > | the_molecules[molIndex].setStampID(i); |
1355 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1356 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1357 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1358 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1359 | > | globalAtomIndex++; |
1360 | > | } |
1361 | > | molIndex++; |
1362 | } | |
1363 | } | |
1364 | < | |
1365 | < | |
1364 | > | |
1365 | > | |
1366 | #endif // is_mpi | |
1367 | ||
1368 | ||
1369 | < | if( info[l].n_SRI ){ |
1317 | < | |
1369 | > | if (info[l].n_SRI){ |
1370 | Exclude::createArray(info[l].n_SRI); | |
1371 | < | the_excludes = new Exclude*[info[l].n_SRI]; |
1372 | < | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1373 | < | the_excludes[ex] = new Exclude(ex); |
1371 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1372 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1373 | > | the_excludes[ex] = new Exclude(ex); |
1374 | } | |
1375 | info[l].globalExcludes = new int; | |
1376 | info[l].n_exclude = info[l].n_SRI; | |
1377 | } | |
1378 | else{ | |
1379 | < | |
1380 | < | Exclude::createArray( 1 ); |
1329 | < | the_excludes = new Exclude*; |
1379 | > | Exclude::createArray(1); |
1380 | > | the_excludes = new Exclude * ; |
1381 | the_excludes[0] = new Exclude(0); | |
1382 | < | the_excludes[0]->setPair( 0,0 ); |
1382 | > | the_excludes[0]->setPair(0, 0); |
1383 | info[l].globalExcludes = new int; | |
1384 | info[l].globalExcludes[0] = 0; | |
1385 | info[l].n_exclude = 0; | |
# | Line 1341 | Line 1392 | void SimSetup::makeSysArrays( void ){ | |
1392 | info[l].nGlobalExcludes = 0; | |
1393 | info[l].excludes = the_excludes; | |
1394 | ||
1395 | < | the_ff->setSimInfo( info ); |
1345 | < | |
1395 | > | the_ff->setSimInfo(info); |
1396 | } | |
1397 | } | |
1398 | ||
1399 | < | void SimSetup::makeIntegrator( void ){ |
1350 | < | |
1399 | > | void SimSetup::makeIntegrator(void){ |
1400 | int k; | |
1401 | ||
1402 | < | NVT<RealIntegrator>* myNVT = NULL; |
1403 | < | NPTi<RealIntegrator>* myNPTi = NULL; |
1404 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1405 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1406 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1407 | < | |
1408 | < | for(k=0; k<nInfo; k++){ |
1409 | < | |
1410 | < | switch( ensembleCase ){ |
1411 | < | |
1412 | < | case NVE_ENS: |
1413 | < | if (globals->haveZconstraints()){ |
1414 | < | setupZConstraint(info[k]); |
1415 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1402 | > | NVE<RealIntegrator>* myNVE = NULL; |
1403 | > | NVT<RealIntegrator>* myNVT = NULL; |
1404 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1405 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1406 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1407 | > | |
1408 | > | for (k = 0; k < nInfo; k++){ |
1409 | > | switch (ensembleCase){ |
1410 | > | case NVE_ENS: |
1411 | > | if (globals->haveZconstraints()){ |
1412 | > | setupZConstraint(info[k]); |
1413 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1414 | > | } |
1415 | > | else{ |
1416 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1417 | } | |
1418 | + | |
1419 | + | info->the_integrator = myNVE; |
1420 | + | break; |
1421 | ||
1422 | < | else |
1423 | < | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1424 | < | break; |
1425 | < | |
1426 | < | case NVT_ENS: |
1427 | < | if (globals->haveZconstraints()){ |
1428 | < | setupZConstraint(info[k]); |
1376 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 | < | } |
1378 | < | else |
1379 | < | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1422 | > | case NVT_ENS: |
1423 | > | if (globals->haveZconstraints()){ |
1424 | > | setupZConstraint(info[k]); |
1425 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1426 | > | } |
1427 | > | else |
1428 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1429 | ||
1430 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 | < | |
1383 | < | if (globals->haveTauThermostat()) |
1384 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1385 | < | |
1386 | < | else { |
1387 | < | sprintf( painCave.errMsg, |
1388 | < | "SimSetup error: If you use the NVT\n" |
1389 | < | " ensemble, you must set tauThermostat.\n"); |
1390 | < | painCave.isFatal = 1; |
1391 | < | simError(); |
1392 | < | } |
1393 | < | break; |
1394 | < | |
1395 | < | case NPTi_ENS: |
1396 | < | if (globals->haveZconstraints()){ |
1397 | < | setupZConstraint(info[k]); |
1398 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 | < | } |
1400 | < | else |
1401 | < | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1430 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1431 | ||
1432 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1433 | < | |
1434 | < | if (globals->haveTargetPressure()) |
1435 | < | myNPTi->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; |
1412 | < | simError(); |
1413 | < | } |
1414 | < | |
1415 | < | if( globals->haveTauThermostat() ) |
1416 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 | < | else{ |
1418 | < | sprintf( painCave.errMsg, |
1419 | < | "SimSetup error: If you use an NPT\n" |
1420 | < | " ensemble, you must set tauThermostat.\n"); |
1421 | < | painCave.isFatal = 1; |
1422 | < | simError(); |
1423 | < | } |
1424 | < | |
1425 | < | if( globals->haveTauBarostat() ) |
1426 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 | < | else{ |
1428 | < | sprintf( painCave.errMsg, |
1429 | < | "SimSetup error: If you use an NPT\n" |
1430 | < | " ensemble, you must set tauBarostat.\n"); |
1431 | < | painCave.isFatal = 1; |
1432 | < | simError(); |
1433 | < | } |
1434 | < | break; |
1435 | < | |
1436 | < | case NPTf_ENS: |
1437 | < | if (globals->haveZconstraints()){ |
1438 | < | setupZConstraint(info[k]); |
1439 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 | < | } |
1441 | < | else |
1442 | < | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1432 | > | if (globals->haveTauThermostat()) |
1433 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1434 | > | else{ |
1435 | > | sprintf(painCave.errMsg, |
1436 | > | "SimSetup error: If you use the NVT\n" |
1437 | > | "\tensemble, you must set tauThermostat.\n"); |
1438 | > | painCave.isFatal = 1; |
1439 | > | simError(); |
1440 | > | } |
1441 | ||
1442 | < | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1443 | < | |
1446 | < | if (globals->haveTargetPressure()) |
1447 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 | < | else { |
1449 | < | sprintf( painCave.errMsg, |
1450 | < | "SimSetup error: If you use a constant pressure\n" |
1451 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1452 | < | painCave.isFatal = 1; |
1453 | < | simError(); |
1454 | < | } |
1455 | < | |
1456 | < | if( globals->haveTauThermostat() ) |
1457 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 | < | else{ |
1459 | < | sprintf( painCave.errMsg, |
1460 | < | "SimSetup error: If you use an NPT\n" |
1461 | < | " ensemble, you must set tauThermostat.\n"); |
1462 | < | painCave.isFatal = 1; |
1463 | < | simError(); |
1464 | < | } |
1465 | < | |
1466 | < | if( globals->haveTauBarostat() ) |
1467 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 | < | else{ |
1469 | < | sprintf( painCave.errMsg, |
1470 | < | "SimSetup error: If you use an NPT\n" |
1471 | < | " ensemble, you must set tauBarostat.\n"); |
1472 | < | painCave.isFatal = 1; |
1473 | < | simError(); |
1474 | < | } |
1475 | < | break; |
1476 | < | |
1477 | < | case NPTim_ENS: |
1478 | < | if (globals->haveZconstraints()){ |
1479 | < | setupZConstraint(info[k]); |
1480 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 | < | } |
1482 | < | else |
1483 | < | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1442 | > | info->the_integrator = myNVT; |
1443 | > | break; |
1444 | ||
1445 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1446 | < | |
1447 | < | if (globals->haveTargetPressure()) |
1448 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1449 | < | else { |
1450 | < | sprintf( painCave.errMsg, |
1451 | < | "SimSetup error: If you use a constant pressure\n" |
1492 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1493 | < | painCave.isFatal = 1; |
1494 | < | simError(); |
1495 | < | } |
1496 | < | |
1497 | < | if( globals->haveTauThermostat() ) |
1498 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1499 | < | else{ |
1500 | < | sprintf( painCave.errMsg, |
1501 | < | "SimSetup error: If you use an NPT\n" |
1502 | < | " ensemble, you must set tauThermostat.\n"); |
1503 | < | painCave.isFatal = 1; |
1504 | < | simError(); |
1505 | < | } |
1506 | < | |
1507 | < | if( globals->haveTauBarostat() ) |
1508 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 | < | else{ |
1510 | < | sprintf( painCave.errMsg, |
1511 | < | "SimSetup error: If you use an NPT\n" |
1512 | < | " ensemble, you must set tauBarostat.\n"); |
1513 | < | painCave.isFatal = 1; |
1514 | < | simError(); |
1515 | < | } |
1516 | < | break; |
1517 | < | |
1518 | < | case NPTfm_ENS: |
1519 | < | if (globals->haveZconstraints()){ |
1520 | < | setupZConstraint(info[k]); |
1521 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 | < | } |
1523 | < | else |
1524 | < | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1445 | > | case NPTi_ENS: |
1446 | > | if (globals->haveZconstraints()){ |
1447 | > | setupZConstraint(info[k]); |
1448 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1449 | > | } |
1450 | > | else |
1451 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1452 | ||
1453 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1454 | < | |
1455 | < | if (globals->haveTargetPressure()) |
1456 | < | myNPTfm->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 | < | myNPTfm->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 | < | myNPTfm->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 | < | default: |
1487 | < | sprintf( painCave.errMsg, |
1488 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1489 | < | painCave.isFatal = 1; |
1490 | < | simError(); |
1453 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1454 | > | |
1455 | > | if (globals->haveTargetPressure()) |
1456 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1457 | > | else{ |
1458 | > | sprintf(painCave.errMsg, |
1459 | > | "SimSetup error: If you use a constant pressure\n" |
1460 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1461 | > | painCave.isFatal = 1; |
1462 | > | simError(); |
1463 | > | } |
1464 | > | |
1465 | > | if (globals->haveTauThermostat()) |
1466 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1467 | > | else{ |
1468 | > | sprintf(painCave.errMsg, |
1469 | > | "SimSetup error: If you use an NPT\n" |
1470 | > | "\tensemble, you must set tauThermostat.\n"); |
1471 | > | painCave.isFatal = 1; |
1472 | > | simError(); |
1473 | > | } |
1474 | > | |
1475 | > | if (globals->haveTauBarostat()) |
1476 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1477 | > | else{ |
1478 | > | sprintf(painCave.errMsg, |
1479 | > | "SimSetup error: If you use an NPT\n" |
1480 | > | "\tensemble, you must set tauBarostat.\n"); |
1481 | > | painCave.isFatal = 1; |
1482 | > | simError(); |
1483 | > | } |
1484 | > | |
1485 | > | info->the_integrator = myNPTi; |
1486 | > | break; |
1487 | > | |
1488 | > | case NPTf_ENS: |
1489 | > | if (globals->haveZconstraints()){ |
1490 | > | setupZConstraint(info[k]); |
1491 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1492 | > | } |
1493 | > | else |
1494 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1495 | > | |
1496 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1497 | > | |
1498 | > | if (globals->haveTargetPressure()) |
1499 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1500 | > | else{ |
1501 | > | sprintf(painCave.errMsg, |
1502 | > | "SimSetup error: If you use a constant pressure\n" |
1503 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1504 | > | painCave.isFatal = 1; |
1505 | > | simError(); |
1506 | > | } |
1507 | > | |
1508 | > | if (globals->haveTauThermostat()) |
1509 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1510 | > | |
1511 | > | else{ |
1512 | > | sprintf(painCave.errMsg, |
1513 | > | "SimSetup error: If you use an NPT\n" |
1514 | > | "\tensemble, you must set tauThermostat.\n"); |
1515 | > | painCave.isFatal = 1; |
1516 | > | simError(); |
1517 | > | } |
1518 | > | |
1519 | > | if (globals->haveTauBarostat()) |
1520 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1521 | > | |
1522 | > | else{ |
1523 | > | sprintf(painCave.errMsg, |
1524 | > | "SimSetup error: If you use an NPT\n" |
1525 | > | "\tensemble, you must set tauBarostat.\n"); |
1526 | > | painCave.isFatal = 1; |
1527 | > | simError(); |
1528 | > | } |
1529 | > | |
1530 | > | info->the_integrator = myNPTf; |
1531 | > | break; |
1532 | > | |
1533 | > | case NPTxyz_ENS: |
1534 | > | if (globals->haveZconstraints()){ |
1535 | > | setupZConstraint(info[k]); |
1536 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1537 | > | } |
1538 | > | else |
1539 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1540 | > | |
1541 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1542 | > | |
1543 | > | if (globals->haveTargetPressure()) |
1544 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1545 | > | else{ |
1546 | > | sprintf(painCave.errMsg, |
1547 | > | "SimSetup error: If you use a constant pressure\n" |
1548 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1549 | > | painCave.isFatal = 1; |
1550 | > | simError(); |
1551 | > | } |
1552 | > | |
1553 | > | if (globals->haveTauThermostat()) |
1554 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1555 | > | else{ |
1556 | > | sprintf(painCave.errMsg, |
1557 | > | "SimSetup error: If you use an NPT\n" |
1558 | > | "\tensemble, you must set tauThermostat.\n"); |
1559 | > | painCave.isFatal = 1; |
1560 | > | simError(); |
1561 | > | } |
1562 | > | |
1563 | > | if (globals->haveTauBarostat()) |
1564 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1565 | > | else{ |
1566 | > | sprintf(painCave.errMsg, |
1567 | > | "SimSetup error: If you use an NPT\n" |
1568 | > | "\tensemble, you must set tauBarostat.\n"); |
1569 | > | painCave.isFatal = 1; |
1570 | > | simError(); |
1571 | > | } |
1572 | > | |
1573 | > | info->the_integrator = myNPTxyz; |
1574 | > | break; |
1575 | > | |
1576 | > | default: |
1577 | > | sprintf(painCave.errMsg, |
1578 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1579 | > | painCave.isFatal = 1; |
1580 | > | simError(); |
1581 | } | |
1582 | } | |
1583 | } | |
1584 | ||
1585 | < | void SimSetup::initFortran( void ){ |
1569 | < | |
1585 | > | void SimSetup::initFortran(void){ |
1586 | info[0].refreshSim(); | |
1587 | < | |
1588 | < | if( !strcmp( info[0].mixingRule, "standard") ){ |
1589 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1587 | > | |
1588 | > | if (!strcmp(info[0].mixingRule, "standard")){ |
1589 | > | the_ff->initForceField(LB_MIXING_RULE); |
1590 | } | |
1591 | < | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1592 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1591 | > | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1592 | > | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1593 | } | |
1594 | else{ | |
1595 | < | sprintf( painCave.errMsg, |
1596 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 | < | info[0].mixingRule ); |
1595 | > | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1596 | > | info[0].mixingRule); |
1597 | painCave.isFatal = 1; | |
1598 | simError(); | |
1599 | } | |
1600 | ||
1601 | ||
1602 | #ifdef IS_MPI | |
1603 | < | strcpy( checkPointMsg, |
1589 | < | "Successfully intialized the mixingRule for Fortran." ); |
1603 | > | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1604 | MPIcheckPoint(); | |
1605 | #endif // is_mpi | |
1592 | – | |
1606 | } | |
1607 | ||
1608 | < | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1609 | < | { |
1610 | < | int nZConstraints; |
1598 | < | ZconStamp** zconStamp; |
1599 | < | |
1600 | < | if(globals->haveZconstraintTime()){ |
1601 | < | |
1602 | < | //add sample time of z-constraint into SimInfo's property list |
1603 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1604 | < | zconsTimeProp->setID(ZCONSTIME_ID); |
1605 | < | zconsTimeProp->setData(globals->getZconsTime()); |
1606 | < | theInfo.addProperty(zconsTimeProp); |
1607 | < | } |
1608 | < | else{ |
1609 | < | sprintf( painCave.errMsg, |
1610 | < | "ZConstraint error: If you use an ZConstraint\n" |
1611 | < | " , you must set sample time.\n"); |
1612 | < | painCave.isFatal = 1; |
1613 | < | simError(); |
1614 | < | } |
1608 | > | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1609 | > | int nZConstraints; |
1610 | > | ZconStamp** zconStamp; |
1611 | ||
1612 | < | // |
1613 | < | nZConstraints = globals->getNzConstraints(); |
1614 | < | zconStamp = globals->getZconStamp(); |
1615 | < | ZConsParaItem tempParaItem; |
1612 | > | if (globals->haveZconstraintTime()){ |
1613 | > | //add sample time of z-constraint into SimInfo's property list |
1614 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1615 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1616 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1617 | > | theInfo.addProperty(zconsTimeProp); |
1618 | > | } |
1619 | > | else{ |
1620 | > | sprintf(painCave.errMsg, |
1621 | > | "ZConstraint error: If you use a ZConstraint,\n" |
1622 | > | "\tyou must set zconsTime.\n"); |
1623 | > | painCave.isFatal = 1; |
1624 | > | simError(); |
1625 | > | } |
1626 | ||
1627 | < | ZConsParaData* zconsParaData = new ZConsParaData(); |
1628 | < | zconsParaData->setID(ZCONSPARADATA_ID); |
1629 | < | |
1630 | < | for(int i = 0; i < nZConstraints; i++){ |
1627 | > | //push zconsTol into siminfo, if user does not specify |
1628 | > | //value for zconsTol, a default value will be used |
1629 | > | DoubleData* zconsTol = new DoubleData(); |
1630 | > | zconsTol->setID(ZCONSTOL_ID); |
1631 | > | if (globals->haveZconsTol()){ |
1632 | > | zconsTol->setData(globals->getZconsTol()); |
1633 | > | } |
1634 | > | else{ |
1635 | > | double defaultZConsTol = 0.01; |
1636 | > | sprintf(painCave.errMsg, |
1637 | > | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1638 | > | "\tOOPSE will use a default value of %f.\n" |
1639 | > | "\tTo set the tolerance, use the zconsTol variable.\n", |
1640 | > | defaultZConsTol); |
1641 | > | painCave.isFatal = 0; |
1642 | > | simError(); |
1643 | > | |
1644 | > | zconsTol->setData(defaultZConsTol); |
1645 | > | } |
1646 | > | theInfo.addProperty(zconsTol); |
1647 | > | |
1648 | > | //set Force Subtraction Policy |
1649 | > | StringData* zconsForcePolicy = new StringData(); |
1650 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1651 | > | |
1652 | > | if (globals->haveZconsForcePolicy()){ |
1653 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1654 | > | } |
1655 | > | else{ |
1656 | > | sprintf(painCave.errMsg, |
1657 | > | "ZConstraint Warning: No force subtraction policy was set.\n" |
1658 | > | "\tOOPSE will use PolicyByMass.\n" |
1659 | > | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1660 | > | painCave.isFatal = 0; |
1661 | > | simError(); |
1662 | > | zconsForcePolicy->setData("BYMASS"); |
1663 | > | } |
1664 | > | |
1665 | > | theInfo.addProperty(zconsForcePolicy); |
1666 | > | |
1667 | > | //set zcons gap |
1668 | > | DoubleData* zconsGap = new DoubleData(); |
1669 | > | zconsGap->setID(ZCONSGAP_ID); |
1670 | > | |
1671 | > | if (globals->haveZConsGap()){ |
1672 | > | zconsGap->setData(globals->getZconsGap()); |
1673 | > | theInfo.addProperty(zconsGap); |
1674 | > | } |
1675 | > | |
1676 | > | //set zcons fixtime |
1677 | > | DoubleData* zconsFixtime = new DoubleData(); |
1678 | > | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1679 | > | |
1680 | > | if (globals->haveZConsFixTime()){ |
1681 | > | zconsFixtime->setData(globals->getZconsFixtime()); |
1682 | > | theInfo.addProperty(zconsFixtime); |
1683 | > | } |
1684 | > | |
1685 | > | |
1686 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1687 | > | //Be careful, do not use inFileName, since it is a pointer which |
1688 | > | //point to a string at master node, and slave nodes do not contain that string |
1689 | > | |
1690 | > | string zconsOutput(theInfo.finalName); |
1691 | > | |
1692 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1693 | > | |
1694 | > | StringData* zconsFilename = new StringData(); |
1695 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1696 | > | zconsFilename->setData(zconsOutput); |
1697 | > | |
1698 | > | theInfo.addProperty(zconsFilename); |
1699 | > | |
1700 | > | //setup index, pos and other parameters of z-constraint molecules |
1701 | > | nZConstraints = globals->getNzConstraints(); |
1702 | > | theInfo.nZconstraints = nZConstraints; |
1703 | > | |
1704 | > | zconStamp = globals->getZconStamp(); |
1705 | > | ZConsParaItem tempParaItem; |
1706 | > | |
1707 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1708 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1709 | > | |
1710 | > | for (int i = 0; i < nZConstraints; i++){ |
1711 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
1712 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1713 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1714 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1715 | ||
1716 | zconsParaData->addItem(tempParaItem); | |
1717 | + | } |
1718 | + | |
1719 | + | //check the uniqueness of index |
1720 | + | if(!zconsParaData->isIndexUnique()){ |
1721 | + | sprintf(painCave.errMsg, |
1722 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1723 | + | painCave.isFatal = 1; |
1724 | + | simError(); |
1725 | + | } |
1726 | + | |
1727 | + | //sort the parameters by index of molecules |
1728 | + | zconsParaData->sortByIndex(); |
1729 | + | |
1730 | + | //push data into siminfo, therefore, we can retrieve later |
1731 | + | theInfo.addProperty(zconsParaData); |
1732 | + | } |
1733 | + | |
1734 | + | void SimSetup::makeMinimizer(){ |
1735 | + | |
1736 | + | OOPSEMinimizer* myOOPSEMinimizer; |
1737 | + | MinimizerParameterSet* param; |
1738 | + | char minimizerName[100]; |
1739 | + | |
1740 | + | for (int i = 0; i < nInfo; i++){ |
1741 | + | |
1742 | + | //prepare parameter set for minimizer |
1743 | + | param = new MinimizerParameterSet(); |
1744 | + | param->setDefaultParameter(); |
1745 | + | |
1746 | + | if (globals->haveMinimizer()){ |
1747 | + | param->setFTol(globals->getMinFTol()); |
1748 | } | |
1749 | ||
1750 | < | //sort the parameters by index of molecules |
1751 | < | zconsParaData->sortByIndex(); |
1752 | < | |
1636 | < | //push data into siminfo, therefore, we can retrieve later |
1637 | < | theInfo.addProperty(zconsParaData); |
1750 | > | if (globals->haveMinGTol()){ |
1751 | > | param->setGTol(globals->getMinGTol()); |
1752 | > | } |
1753 | ||
1754 | < | //push zconsTol into siminfo, if user does not specify |
1755 | < | //value for zconsTol, a default value will be used |
1641 | < | DoubleData* zconsTol = new DoubleData(); |
1642 | < | zconsTol->setID(ZCONSTOL_ID); |
1643 | < | if(globals->haveZconsTol()){ |
1644 | < | zconsTol->setData(globals->getZconsTol()); |
1754 | > | if (globals->haveMinMaxIter()){ |
1755 | > | param->setMaxIteration(globals->getMinMaxIter()); |
1756 | } | |
1646 | – | else{ |
1647 | – | double defaultZConsTol = 1E-6; |
1648 | – | sprintf( painCave.errMsg, |
1649 | – | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1650 | – | " , default value %f is used.\n", defaultZConsTol); |
1651 | – | painCave.isFatal = 0; |
1652 | – | simError(); |
1757 | ||
1758 | < | zconsTol->setData(defaultZConsTol); |
1759 | < | } |
1760 | < | theInfo.addProperty(zconsTol); |
1761 | < | |
1762 | < | //Determine the name of ouput file and add it into SimInfo's property list |
1763 | < | //Be careful, do not use inFileName, since it is a pointer which |
1764 | < | //point to a string at master node, and slave nodes do not contain that string |
1758 | > | if (globals->haveMinWriteFrq()){ |
1759 | > | param->setMaxIteration(globals->getMinMaxIter()); |
1760 | > | } |
1761 | > | |
1762 | > | if (globals->haveMinWriteFrq()){ |
1763 | > | param->setWriteFrq(globals->getMinWriteFrq()); |
1764 | > | } |
1765 | ||
1766 | < | string zconsOutput(theInfo.finalName); |
1767 | < | |
1768 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1769 | < | |
1770 | < | StringData* zconsFilename = new StringData(); |
1771 | < | zconsFilename->setID(ZCONSFILENAME_ID); |
1772 | < | zconsFilename->setData(zconsOutput); |
1773 | < | |
1774 | < | theInfo.addProperty(zconsFilename); |
1766 | > | if (globals->haveMinStepSize()){ |
1767 | > | param->setStepSize(globals->getMinStepSize()); |
1768 | > | } |
1769 | > | |
1770 | > | if (globals->haveMinLSMaxIter()){ |
1771 | > | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1772 | > | } |
1773 | > | |
1774 | > | if (globals->haveMinLSTol()){ |
1775 | > | param->setLineSearchTol(globals->getMinLSTol()); |
1776 | > | } |
1777 | > | |
1778 | > | strcpy(minimizerName, globals->getMinimizer()); |
1779 | > | |
1780 | > | if (!strcasecmp(minimizerName, "CG")){ |
1781 | > | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1782 | > | } |
1783 | > | else if (!strcasecmp(minimizerName, "SD")){ |
1784 | > | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1785 | > | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1786 | > | } |
1787 | > | else{ |
1788 | > | sprintf(painCave.errMsg, |
1789 | > | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1790 | > | painCave.isFatal = 0; |
1791 | > | simError(); |
1792 | > | |
1793 | > | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1794 | > | } |
1795 | > | info[i].the_integrator = myOOPSEMinimizer; |
1796 | > | |
1797 | > | //store the minimizer into simInfo |
1798 | > | info[i].the_minimizer = myOOPSEMinimizer; |
1799 | > | info[i].has_minimizer = true; |
1800 | > | } |
1801 | > | |
1802 | } |
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