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" |
21 |
|
#define NVT_ENS 1 |
22 |
|
#define NPTi_ENS 2 |
23 |
|
#define NPTf_ENS 3 |
24 |
< |
#define NPTim_ENS 4 |
25 |
< |
#define NPTfm_ENS 5 |
24 |
> |
#define NPTxyz_ENS 4 |
25 |
|
|
26 |
+ |
|
27 |
|
#define FF_DUFF 0 |
28 |
|
#define FF_LJ 1 |
29 |
|
#define FF_EAM 2 |
30 |
|
|
31 |
|
using namespace std; |
32 |
|
|
33 |
+ |
/** |
34 |
+ |
* Check whether dividend is divisble by divisor or not |
35 |
+ |
*/ |
36 |
+ |
bool isDivisible(double dividend, double divisor){ |
37 |
+ |
double tolerance = 0.000001; |
38 |
+ |
double quotient; |
39 |
+ |
double diff; |
40 |
+ |
int intQuotient; |
41 |
+ |
|
42 |
+ |
quotient = dividend / divisor; |
43 |
+ |
|
44 |
+ |
if (quotient < 0) |
45 |
+ |
quotient = -quotient; |
46 |
+ |
|
47 |
+ |
intQuotient = int (quotient + tolerance); |
48 |
+ |
|
49 |
+ |
diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
50 |
+ |
|
51 |
+ |
if (diff <= tolerance) |
52 |
+ |
return true; |
53 |
+ |
else |
54 |
+ |
return false; |
55 |
+ |
} |
56 |
+ |
|
57 |
|
SimSetup::SimSetup(){ |
58 |
|
|
59 |
+ |
initSuspend = false; |
60 |
|
isInfoArray = 0; |
61 |
|
nInfo = 1; |
62 |
< |
|
62 |
> |
|
63 |
|
stamps = new MakeStamps(); |
64 |
|
globals = new Globals(); |
65 |
< |
|
66 |
< |
|
65 |
> |
|
66 |
> |
|
67 |
|
#ifdef IS_MPI |
68 |
< |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
68 |
> |
strcpy(checkPointMsg, "SimSetup creation successful"); |
69 |
|
MPIcheckPoint(); |
70 |
|
#endif // IS_MPI |
71 |
|
} |
75 |
|
delete globals; |
76 |
|
} |
77 |
|
|
78 |
< |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
79 |
< |
info = the_info; |
80 |
< |
nInfo = theNinfo; |
81 |
< |
isInfoArray = 1; |
78 |
> |
void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
79 |
> |
info = the_info; |
80 |
> |
nInfo = theNinfo; |
81 |
> |
isInfoArray = 1; |
82 |
> |
initSuspend = true; |
83 |
|
} |
84 |
|
|
85 |
|
|
86 |
< |
void SimSetup::parseFile( char* fileName ){ |
61 |
< |
|
86 |
> |
void SimSetup::parseFile(char* fileName){ |
87 |
|
#ifdef IS_MPI |
88 |
< |
if( worldRank == 0 ){ |
88 |
> |
if (worldRank == 0){ |
89 |
|
#endif // is_mpi |
90 |
< |
|
90 |
> |
|
91 |
|
inFileName = fileName; |
92 |
< |
set_interface_stamps( stamps, globals ); |
93 |
< |
|
92 |
> |
set_interface_stamps(stamps, globals); |
93 |
> |
|
94 |
|
#ifdef IS_MPI |
95 |
|
mpiEventInit(); |
96 |
|
#endif |
97 |
|
|
98 |
< |
yacc_BASS( fileName ); |
98 |
> |
yacc_BASS(fileName); |
99 |
|
|
100 |
|
#ifdef IS_MPI |
101 |
|
throwMPIEvent(NULL); |
102 |
|
} |
103 |
< |
else receiveParse(); |
103 |
> |
else{ |
104 |
> |
receiveParse(); |
105 |
> |
} |
106 |
|
#endif |
107 |
|
|
108 |
|
} |
109 |
|
|
110 |
|
#ifdef IS_MPI |
111 |
|
void SimSetup::receiveParse(void){ |
112 |
< |
|
113 |
< |
set_interface_stamps( stamps, globals ); |
114 |
< |
mpiEventInit(); |
115 |
< |
MPIcheckPoint(); |
89 |
< |
mpiEventLoop(); |
90 |
< |
|
112 |
> |
set_interface_stamps(stamps, globals); |
113 |
> |
mpiEventInit(); |
114 |
> |
MPIcheckPoint(); |
115 |
> |
mpiEventLoop(); |
116 |
|
} |
117 |
|
|
118 |
|
#endif // is_mpi |
119 |
|
|
120 |
|
void SimSetup::createSim(void){ |
121 |
|
|
97 |
– |
int i, j, k, globalAtomIndex; |
98 |
– |
|
122 |
|
// gather all of the information from the Bass file |
123 |
|
|
124 |
|
gatherInfo(); |
133 |
|
|
134 |
|
// initialize the system coordinates |
135 |
|
|
136 |
< |
if( !isInfoArray ) initSystemCoords(); |
136 |
> |
if ( !initSuspend ){ |
137 |
> |
initSystemCoords(); |
138 |
|
|
139 |
+ |
if( !(globals->getUseInitTime()) ) |
140 |
+ |
info[0].currentTime = 0.0; |
141 |
+ |
} |
142 |
+ |
|
143 |
|
// make the output filenames |
144 |
|
|
145 |
|
makeOutNames(); |
146 |
< |
|
146 |
> |
|
147 |
|
// make the integrator |
148 |
< |
|
148 |
> |
|
149 |
|
makeIntegrator(); |
150 |
< |
|
150 |
> |
|
151 |
|
#ifdef IS_MPI |
152 |
|
mpiSim->mpiRefresh(); |
153 |
|
#endif |
155 |
|
// initialize the Fortran |
156 |
|
|
157 |
|
initFortran(); |
130 |
– |
|
131 |
– |
|
132 |
– |
|
158 |
|
} |
159 |
|
|
160 |
|
|
161 |
< |
void SimSetup::makeMolecules( void ){ |
162 |
< |
|
138 |
< |
int k,l; |
161 |
> |
void SimSetup::makeMolecules(void){ |
162 |
> |
int k; |
163 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
164 |
|
molInit molInfo; |
165 |
|
DirectionalAtom* dAtom; |
174 |
|
bend_set* theBends; |
175 |
|
torsion_set* theTorsions; |
176 |
|
|
153 |
– |
|
177 |
|
//init the forceField paramters |
178 |
|
|
179 |
|
the_ff->readParams(); |
180 |
|
|
181 |
< |
|
181 |
> |
|
182 |
|
// init the atoms |
183 |
|
|
184 |
+ |
double phi, theta, psi; |
185 |
+ |
double sux, suy, suz; |
186 |
+ |
double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
187 |
|
double ux, uy, uz, u, uSqr; |
162 |
– |
|
163 |
– |
for(k=0; k<nInfo; k++){ |
164 |
– |
|
165 |
– |
the_ff->setSimInfo( &(info[k]) ); |
188 |
|
|
189 |
+ |
for (k = 0; k < nInfo; k++){ |
190 |
+ |
the_ff->setSimInfo(&(info[k])); |
191 |
+ |
|
192 |
|
atomOffset = 0; |
193 |
|
excludeOffset = 0; |
194 |
< |
for(i=0; i<info[k].n_mol; i++){ |
170 |
< |
|
194 |
> |
for (i = 0; i < info[k].n_mol; i++){ |
195 |
|
stampID = info[k].molecules[i].getStampID(); |
196 |
|
|
197 |
< |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
198 |
< |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
199 |
< |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
197 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
198 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
199 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
200 |
|
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
201 |
|
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
202 |
< |
|
202 |
> |
|
203 |
|
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
204 |
|
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
205 |
< |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
206 |
< |
molInfo.myBends = new Bend*[molInfo.nBends]; |
207 |
< |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
205 |
> |
molInfo.myBonds = new Bond * [molInfo.nBonds]; |
206 |
> |
molInfo.myBends = new Bend * [molInfo.nBends]; |
207 |
> |
molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
208 |
|
|
209 |
|
theBonds = new bond_pair[molInfo.nBonds]; |
210 |
|
theBends = new bend_set[molInfo.nBends]; |
211 |
|
theTorsions = new torsion_set[molInfo.nTorsions]; |
212 |
< |
|
212 |
> |
|
213 |
|
// make the Atoms |
214 |
< |
|
215 |
< |
for(j=0; j<molInfo.nAtoms; j++){ |
216 |
< |
|
217 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
218 |
< |
if( currentAtom->haveOrientation() ){ |
219 |
< |
|
220 |
< |
dAtom = new DirectionalAtom( (j + atomOffset), |
221 |
< |
info[k].getConfiguration() ); |
222 |
< |
info[k].n_oriented++; |
223 |
< |
molInfo.myAtoms[j] = dAtom; |
224 |
< |
|
225 |
< |
ux = currentAtom->getOrntX(); |
226 |
< |
uy = currentAtom->getOrntY(); |
227 |
< |
uz = currentAtom->getOrntZ(); |
228 |
< |
|
229 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
230 |
< |
|
231 |
< |
u = sqrt( uSqr ); |
232 |
< |
ux = ux / u; |
233 |
< |
uy = uy / u; |
234 |
< |
uz = uz / u; |
235 |
< |
|
236 |
< |
dAtom->setSUx( ux ); |
237 |
< |
dAtom->setSUy( uy ); |
238 |
< |
dAtom->setSUz( uz ); |
239 |
< |
} |
240 |
< |
else{ |
241 |
< |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
242 |
< |
info[k].getConfiguration() ); |
243 |
< |
} |
244 |
< |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
245 |
< |
|
214 |
> |
|
215 |
> |
for (j = 0; j < molInfo.nAtoms; j++){ |
216 |
> |
currentAtom = comp_stamps[stampID]->getAtom(j); |
217 |
> |
if (currentAtom->haveOrientation()){ |
218 |
> |
dAtom = new DirectionalAtom((j + atomOffset), |
219 |
> |
info[k].getConfiguration()); |
220 |
> |
info[k].n_oriented++; |
221 |
> |
molInfo.myAtoms[j] = dAtom; |
222 |
> |
|
223 |
> |
// Directional Atoms have standard unit vectors which are oriented |
224 |
> |
// in space using the three Euler angles. We assume the standard |
225 |
> |
// unit vector was originally along the z axis below. |
226 |
> |
|
227 |
> |
phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
228 |
> |
theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
229 |
> |
psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
230 |
> |
|
231 |
> |
Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
232 |
> |
Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
233 |
> |
Axz = sin(theta) * sin(psi); |
234 |
> |
|
235 |
> |
Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
236 |
> |
Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
237 |
> |
Ayz = sin(theta) * cos(psi); |
238 |
> |
|
239 |
> |
Azx = sin(phi) * sin(theta); |
240 |
> |
Azy = -cos(phi) * sin(theta); |
241 |
> |
Azz = cos(theta); |
242 |
> |
|
243 |
> |
sux = 0.0; |
244 |
> |
suy = 0.0; |
245 |
> |
suz = 1.0; |
246 |
> |
|
247 |
> |
ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
248 |
> |
uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
249 |
> |
uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
250 |
> |
|
251 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
252 |
> |
|
253 |
> |
u = sqrt(uSqr); |
254 |
> |
ux = ux / u; |
255 |
> |
uy = uy / u; |
256 |
> |
uz = uz / u; |
257 |
> |
|
258 |
> |
dAtom->setSUx(ux); |
259 |
> |
dAtom->setSUy(uy); |
260 |
> |
dAtom->setSUz(uz); |
261 |
> |
} |
262 |
> |
else{ |
263 |
> |
molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
264 |
> |
info[k].getConfiguration()); |
265 |
> |
} |
266 |
> |
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
267 |
> |
|
268 |
|
#ifdef IS_MPI |
269 |
< |
|
270 |
< |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
271 |
< |
|
269 |
> |
|
270 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
271 |
> |
|
272 |
|
#endif // is_mpi |
273 |
|
} |
274 |
< |
|
275 |
< |
// make the bonds |
276 |
< |
for(j=0; j<molInfo.nBonds; j++){ |
277 |
< |
|
278 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
279 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
280 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
281 |
< |
|
282 |
< |
exI = theBonds[j].a; |
283 |
< |
exJ = theBonds[j].b; |
284 |
< |
|
285 |
< |
// exclude_I must always be the smaller of the pair |
286 |
< |
if( exI > exJ ){ |
287 |
< |
tempEx = exI; |
288 |
< |
exI = exJ; |
289 |
< |
exJ = tempEx; |
244 |
< |
} |
274 |
> |
|
275 |
> |
// make the bonds |
276 |
> |
for (j = 0; j < molInfo.nBonds; j++){ |
277 |
> |
currentBond = comp_stamps[stampID]->getBond(j); |
278 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
279 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
280 |
> |
|
281 |
> |
exI = theBonds[j].a; |
282 |
> |
exJ = theBonds[j].b; |
283 |
> |
|
284 |
> |
// exclude_I must always be the smaller of the pair |
285 |
> |
if (exI > exJ){ |
286 |
> |
tempEx = exI; |
287 |
> |
exI = exJ; |
288 |
> |
exJ = tempEx; |
289 |
> |
} |
290 |
|
#ifdef IS_MPI |
291 |
< |
tempEx = exI; |
292 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
293 |
< |
tempEx = exJ; |
294 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
295 |
< |
|
296 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
291 |
> |
tempEx = exI; |
292 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
293 |
> |
tempEx = exJ; |
294 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
295 |
> |
|
296 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
297 |
|
#else // isn't MPI |
298 |
< |
|
299 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
298 |
> |
|
299 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
300 |
|
#endif //is_mpi |
301 |
|
} |
302 |
|
excludeOffset += molInfo.nBonds; |
303 |
< |
|
303 |
> |
|
304 |
|
//make the bends |
305 |
< |
for(j=0; j<molInfo.nBends; j++){ |
306 |
< |
|
307 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
308 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
309 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
310 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
311 |
< |
|
312 |
< |
if( currentBend->haveExtras() ){ |
313 |
< |
|
314 |
< |
extras = currentBend->getExtras(); |
315 |
< |
current_extra = extras; |
316 |
< |
|
317 |
< |
while( current_extra != NULL ){ |
318 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
319 |
< |
|
320 |
< |
switch( current_extra->getType() ){ |
321 |
< |
|
322 |
< |
case 0: |
323 |
< |
theBends[j].ghost = |
324 |
< |
current_extra->getInt() + atomOffset; |
325 |
< |
theBends[j].isGhost = 1; |
326 |
< |
break; |
327 |
< |
|
328 |
< |
case 1: |
329 |
< |
theBends[j].ghost = |
330 |
< |
(int)current_extra->getDouble() + atomOffset; |
331 |
< |
theBends[j].isGhost = 1; |
332 |
< |
break; |
333 |
< |
|
334 |
< |
default: |
335 |
< |
sprintf( painCave.errMsg, |
336 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
337 |
< |
"double nor an int.\n" |
338 |
< |
"-->Bend[%d] in %s\n", |
339 |
< |
j, comp_stamps[stampID]->getID() ); |
340 |
< |
painCave.isFatal = 1; |
341 |
< |
simError(); |
342 |
< |
} |
343 |
< |
} |
344 |
< |
|
345 |
< |
else{ |
346 |
< |
|
347 |
< |
sprintf( painCave.errMsg, |
348 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
349 |
< |
" -->%s in Bend[%d] in %s\n", |
350 |
< |
current_extra->getlhs(), |
351 |
< |
j, comp_stamps[stampID]->getID() ); |
352 |
< |
painCave.isFatal = 1; |
353 |
< |
simError(); |
354 |
< |
} |
355 |
< |
|
356 |
< |
current_extra = current_extra->getNext(); |
357 |
< |
} |
358 |
< |
} |
359 |
< |
|
360 |
< |
if( !theBends[j].isGhost ){ |
361 |
< |
|
362 |
< |
exI = theBends[j].a; |
363 |
< |
exJ = theBends[j].c; |
364 |
< |
} |
365 |
< |
else{ |
366 |
< |
|
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 |
< |
} |
305 |
> |
for (j = 0; j < molInfo.nBends; j++){ |
306 |
> |
currentBend = comp_stamps[stampID]->getBend(j); |
307 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
308 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
309 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
310 |
> |
|
311 |
> |
if (currentBend->haveExtras()){ |
312 |
> |
extras = currentBend->getExtras(); |
313 |
> |
current_extra = extras; |
314 |
> |
|
315 |
> |
while (current_extra != NULL){ |
316 |
> |
if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
317 |
> |
switch (current_extra->getType()){ |
318 |
> |
case 0: |
319 |
> |
theBends[j].ghost = current_extra->getInt() + atomOffset; |
320 |
> |
theBends[j].isGhost = 1; |
321 |
> |
break; |
322 |
> |
|
323 |
> |
case 1: |
324 |
> |
theBends[j].ghost = (int) current_extra->getDouble() + |
325 |
> |
atomOffset; |
326 |
> |
theBends[j].isGhost = 1; |
327 |
> |
break; |
328 |
> |
|
329 |
> |
default: |
330 |
> |
sprintf(painCave.errMsg, |
331 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
332 |
> |
"double nor an int.\n" |
333 |
> |
"-->Bend[%d] in %s\n", |
334 |
> |
j, comp_stamps[stampID]->getID()); |
335 |
> |
painCave.isFatal = 1; |
336 |
> |
simError(); |
337 |
> |
} |
338 |
> |
} |
339 |
> |
else{ |
340 |
> |
sprintf(painCave.errMsg, |
341 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
342 |
> |
" -->%s in Bend[%d] in %s\n", |
343 |
> |
current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
344 |
> |
painCave.isFatal = 1; |
345 |
> |
simError(); |
346 |
> |
} |
347 |
> |
|
348 |
> |
current_extra = current_extra->getNext(); |
349 |
> |
} |
350 |
> |
} |
351 |
> |
|
352 |
> |
if (!theBends[j].isGhost){ |
353 |
> |
exI = theBends[j].a; |
354 |
> |
exJ = theBends[j].c; |
355 |
> |
} |
356 |
> |
else{ |
357 |
> |
exI = theBends[j].a; |
358 |
> |
exJ = theBends[j].b; |
359 |
> |
} |
360 |
> |
|
361 |
> |
// exclude_I must always be the smaller of the pair |
362 |
> |
if (exI > exJ){ |
363 |
> |
tempEx = exI; |
364 |
> |
exI = exJ; |
365 |
> |
exJ = tempEx; |
366 |
> |
} |
367 |
|
#ifdef IS_MPI |
368 |
< |
tempEx = exI; |
369 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
370 |
< |
tempEx = exJ; |
371 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
372 |
< |
|
373 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
368 |
> |
tempEx = exI; |
369 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
370 |
> |
tempEx = exJ; |
371 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
372 |
> |
|
373 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
374 |
|
#else // isn't MPI |
375 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
375 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
376 |
|
#endif //is_mpi |
377 |
|
} |
378 |
|
excludeOffset += molInfo.nBends; |
379 |
< |
|
380 |
< |
for(j=0; j<molInfo.nTorsions; j++){ |
381 |
< |
|
382 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
383 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
384 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
385 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
386 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
387 |
< |
|
388 |
< |
exI = theTorsions[j].a; |
389 |
< |
exJ = theTorsions[j].d; |
390 |
< |
|
391 |
< |
// exclude_I must always be the smaller of the pair |
392 |
< |
if( exI > exJ ){ |
393 |
< |
tempEx = exI; |
394 |
< |
exI = exJ; |
395 |
< |
exJ = tempEx; |
361 |
< |
} |
379 |
> |
|
380 |
> |
for (j = 0; j < molInfo.nTorsions; j++){ |
381 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
382 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
383 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
384 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
385 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
386 |
> |
|
387 |
> |
exI = theTorsions[j].a; |
388 |
> |
exJ = theTorsions[j].d; |
389 |
> |
|
390 |
> |
// exclude_I must always be the smaller of the pair |
391 |
> |
if (exI > exJ){ |
392 |
> |
tempEx = exI; |
393 |
> |
exI = exJ; |
394 |
> |
exJ = tempEx; |
395 |
> |
} |
396 |
|
#ifdef IS_MPI |
397 |
< |
tempEx = exI; |
398 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
399 |
< |
tempEx = exJ; |
400 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
401 |
< |
|
402 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
397 |
> |
tempEx = exI; |
398 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
399 |
> |
tempEx = exJ; |
400 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
401 |
> |
|
402 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
403 |
|
#else // isn't MPI |
404 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
404 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
405 |
|
#endif //is_mpi |
406 |
|
} |
407 |
|
excludeOffset += molInfo.nTorsions; |
408 |
< |
|
409 |
< |
|
408 |
> |
|
409 |
> |
|
410 |
|
// 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 ); |
411 |
|
|
412 |
< |
|
412 |
> |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
413 |
> |
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
414 |
> |
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
415 |
> |
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
416 |
> |
theTorsions); |
417 |
> |
|
418 |
> |
|
419 |
> |
info[k].molecules[i].initialize(molInfo); |
420 |
> |
|
421 |
> |
|
422 |
|
atomOffset += molInfo.nAtoms; |
423 |
|
delete[] theBonds; |
424 |
|
delete[] theBends; |
425 |
|
delete[] theTorsions; |
426 |
|
} |
427 |
|
} |
428 |
< |
|
428 |
> |
|
429 |
|
#ifdef IS_MPI |
430 |
< |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
430 |
> |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
431 |
|
MPIcheckPoint(); |
432 |
|
#endif // is_mpi |
433 |
< |
|
433 |
> |
|
434 |
|
// clean up the forcefield |
435 |
|
|
436 |
|
the_ff->calcRcut(); |
437 |
|
the_ff->cleanMe(); |
403 |
– |
|
438 |
|
} |
439 |
|
|
440 |
< |
void SimSetup::initFromBass( void ){ |
407 |
< |
|
440 |
> |
void SimSetup::initFromBass(void){ |
441 |
|
int i, j, k; |
442 |
|
int n_cells; |
443 |
|
double cellx, celly, cellz; |
451 |
|
vel[1] = 0.0; |
452 |
|
vel[2] = 0.0; |
453 |
|
|
454 |
< |
temp1 = (double)tot_nmol / 4.0; |
455 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
456 |
< |
temp3 = ceil( temp2 ); |
454 |
> |
temp1 = (double) tot_nmol / 4.0; |
455 |
> |
temp2 = pow(temp1, (1.0 / 3.0)); |
456 |
> |
temp3 = ceil(temp2); |
457 |
|
|
458 |
< |
have_extra =0; |
459 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
460 |
< |
have_extra =1; |
458 |
> |
have_extra = 0; |
459 |
> |
if (temp2 < temp3){ |
460 |
> |
// we have a non-complete lattice |
461 |
> |
have_extra = 1; |
462 |
|
|
463 |
< |
n_cells = (int)temp3 - 1; |
463 |
> |
n_cells = (int) temp3 - 1; |
464 |
|
cellx = info[0].boxL[0] / temp3; |
465 |
|
celly = info[0].boxL[1] / temp3; |
466 |
|
cellz = info[0].boxL[2] / temp3; |
467 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
468 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
469 |
< |
n_per_extra = (int)ceil( temp1 ); |
467 |
> |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
468 |
> |
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
469 |
> |
n_per_extra = (int) ceil(temp1); |
470 |
|
|
471 |
< |
if( n_per_extra > 4){ |
472 |
< |
sprintf( painCave.errMsg, |
473 |
< |
"SimSetup error. There has been an error in constructing" |
474 |
< |
" the non-complete lattice.\n" ); |
471 |
> |
if (n_per_extra > 4){ |
472 |
> |
sprintf(painCave.errMsg, |
473 |
> |
"SimSetup error. There has been an error in constructing" |
474 |
> |
" the non-complete lattice.\n"); |
475 |
|
painCave.isFatal = 1; |
476 |
|
simError(); |
477 |
|
} |
478 |
|
} |
479 |
|
else{ |
480 |
< |
n_cells = (int)temp3; |
480 |
> |
n_cells = (int) temp3; |
481 |
|
cellx = info[0].boxL[0] / temp3; |
482 |
|
celly = info[0].boxL[1] / temp3; |
483 |
|
cellz = info[0].boxL[2] / temp3; |
488 |
|
current_comp = 0; |
489 |
|
current_atom_ndx = 0; |
490 |
|
|
491 |
< |
for( i=0; i < n_cells ; i++ ){ |
492 |
< |
for( j=0; j < n_cells; j++ ){ |
493 |
< |
for( k=0; k < n_cells; k++ ){ |
494 |
< |
|
461 |
< |
makeElement( i * cellx, |
462 |
< |
j * celly, |
463 |
< |
k * cellz ); |
491 |
> |
for (i = 0; i < n_cells ; i++){ |
492 |
> |
for (j = 0; j < n_cells; j++){ |
493 |
> |
for (k = 0; k < n_cells; k++){ |
494 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
495 |
|
|
496 |
< |
makeElement( i * cellx + 0.5 * cellx, |
466 |
< |
j * celly + 0.5 * celly, |
467 |
< |
k * cellz ); |
496 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
497 |
|
|
498 |
< |
makeElement( i * cellx, |
470 |
< |
j * celly + 0.5 * celly, |
471 |
< |
k * cellz + 0.5 * cellz ); |
498 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
499 |
|
|
500 |
< |
makeElement( i * cellx + 0.5 * cellx, |
474 |
< |
j * celly, |
475 |
< |
k * cellz + 0.5 * cellz ); |
500 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
501 |
|
} |
502 |
|
} |
503 |
|
} |
504 |
|
|
505 |
< |
if( have_extra ){ |
505 |
> |
if (have_extra){ |
506 |
|
done = 0; |
507 |
|
|
508 |
|
int start_ndx; |
509 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
510 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
509 |
> |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
510 |
> |
for (j = 0; j < (n_cells + 1) && !done; j++){ |
511 |
> |
if (i < n_cells){ |
512 |
> |
if (j < n_cells){ |
513 |
> |
start_ndx = n_cells; |
514 |
> |
} |
515 |
> |
else |
516 |
> |
start_ndx = 0; |
517 |
> |
} |
518 |
> |
else |
519 |
> |
start_ndx = 0; |
520 |
|
|
521 |
< |
if( i < n_cells ){ |
521 |
> |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
522 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
523 |
> |
done = (current_mol >= tot_nmol); |
524 |
|
|
525 |
< |
if( j < n_cells ){ |
526 |
< |
start_ndx = n_cells; |
527 |
< |
} |
528 |
< |
else start_ndx = 0; |
529 |
< |
} |
494 |
< |
else start_ndx = 0; |
525 |
> |
if (!done && n_per_extra > 1){ |
526 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
527 |
> |
k * cellz); |
528 |
> |
done = (current_mol >= tot_nmol); |
529 |
> |
} |
530 |
|
|
531 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
531 |
> |
if (!done && n_per_extra > 2){ |
532 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, |
533 |
> |
k * cellz + 0.5 * cellz); |
534 |
> |
done = (current_mol >= tot_nmol); |
535 |
> |
} |
536 |
|
|
537 |
< |
makeElement( i * cellx, |
538 |
< |
j * celly, |
539 |
< |
k * cellz ); |
540 |
< |
done = ( current_mol >= tot_nmol ); |
541 |
< |
|
542 |
< |
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 |
< |
} |
537 |
> |
if (!done && n_per_extra > 3){ |
538 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, |
539 |
> |
k * cellz + 0.5 * cellz); |
540 |
> |
done = (current_mol >= tot_nmol); |
541 |
> |
} |
542 |
> |
} |
543 |
|
} |
544 |
|
} |
545 |
|
} |
546 |
|
|
547 |
< |
for( i=0; i<info[0].n_atoms; i++ ){ |
548 |
< |
info[0].atoms[i]->setVel( vel ); |
547 |
> |
for (i = 0; i < info[0].n_atoms; i++){ |
548 |
> |
info[0].atoms[i]->setVel(vel); |
549 |
|
} |
550 |
|
} |
551 |
|
|
552 |
< |
void SimSetup::makeElement( double x, double y, double z ){ |
534 |
< |
|
552 |
> |
void SimSetup::makeElement(double x, double y, double z){ |
553 |
|
int k; |
554 |
|
AtomStamp* current_atom; |
555 |
|
DirectionalAtom* dAtom; |
556 |
|
double rotMat[3][3]; |
557 |
|
double pos[3]; |
558 |
|
|
559 |
< |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
560 |
< |
|
561 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
562 |
< |
if( !current_atom->havePosition() ){ |
563 |
< |
sprintf( painCave.errMsg, |
564 |
< |
"SimSetup:initFromBass error.\n" |
565 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
566 |
< |
"\tThe initialization routine is unable to give a start" |
567 |
< |
" position.\n", |
550 |
< |
comp_stamps[current_comp]->getID(), |
551 |
< |
current_atom->getType() ); |
559 |
> |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
560 |
> |
current_atom = comp_stamps[current_comp]->getAtom(k); |
561 |
> |
if (!current_atom->havePosition()){ |
562 |
> |
sprintf(painCave.errMsg, |
563 |
> |
"SimSetup:initFromBass error.\n" |
564 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
565 |
> |
"\tThe initialization routine is unable to give a start" |
566 |
> |
" position.\n", |
567 |
> |
comp_stamps[current_comp]->getID(), current_atom->getType()); |
568 |
|
painCave.isFatal = 1; |
569 |
|
simError(); |
570 |
|
} |
571 |
< |
|
571 |
> |
|
572 |
|
pos[0] = x + current_atom->getPosX(); |
573 |
|
pos[1] = y + current_atom->getPosY(); |
574 |
|
pos[2] = z + current_atom->getPosZ(); |
559 |
– |
|
560 |
– |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
575 |
|
|
576 |
< |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
576 |
> |
info[0].atoms[current_atom_ndx]->setPos(pos); |
577 |
|
|
578 |
< |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
578 |
> |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
579 |
> |
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
580 |
|
|
581 |
|
rotMat[0][0] = 1.0; |
582 |
|
rotMat[0][1] = 0.0; |
590 |
|
rotMat[2][1] = 0.0; |
591 |
|
rotMat[2][2] = 1.0; |
592 |
|
|
593 |
< |
dAtom->setA( rotMat ); |
593 |
> |
dAtom->setA(rotMat); |
594 |
|
} |
595 |
|
|
596 |
|
current_atom_ndx++; |
599 |
|
current_mol++; |
600 |
|
current_comp_mol++; |
601 |
|
|
602 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
588 |
< |
|
602 |
> |
if (current_comp_mol >= components_nmol[current_comp]){ |
603 |
|
current_comp_mol = 0; |
604 |
|
current_comp++; |
605 |
|
} |
606 |
|
} |
607 |
|
|
608 |
|
|
609 |
< |
void SimSetup::gatherInfo( void ){ |
610 |
< |
int i,j,k; |
609 |
> |
void SimSetup::gatherInfo(void){ |
610 |
> |
int i; |
611 |
|
|
612 |
|
ensembleCase = -1; |
613 |
|
ffCase = -1; |
614 |
|
|
615 |
|
// set the easy ones first |
616 |
|
|
617 |
< |
for( i=0; i<nInfo; i++){ |
617 |
> |
for (i = 0; i < nInfo; i++){ |
618 |
|
info[i].target_temp = globals->getTargetTemp(); |
619 |
|
info[i].dt = globals->getDt(); |
620 |
|
info[i].run_time = globals->getRunTime(); |
624 |
|
|
625 |
|
// get the forceField |
626 |
|
|
627 |
< |
strcpy( force_field, globals->getForceField() ); |
627 |
> |
strcpy(force_field, globals->getForceField()); |
628 |
|
|
629 |
< |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
630 |
< |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
631 |
< |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
629 |
> |
if (!strcasecmp(force_field, "DUFF")){ |
630 |
> |
ffCase = FF_DUFF; |
631 |
> |
} |
632 |
> |
else if (!strcasecmp(force_field, "LJ")){ |
633 |
> |
ffCase = FF_LJ; |
634 |
> |
} |
635 |
> |
else if (!strcasecmp(force_field, "EAM")){ |
636 |
> |
ffCase = FF_EAM; |
637 |
> |
} |
638 |
|
else{ |
639 |
< |
sprintf( painCave.errMsg, |
640 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
641 |
< |
force_field ); |
642 |
< |
painCave.isFatal = 1; |
623 |
< |
simError(); |
639 |
> |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
640 |
> |
force_field); |
641 |
> |
painCave.isFatal = 1; |
642 |
> |
simError(); |
643 |
|
} |
644 |
|
|
645 |
< |
// get the ensemble |
645 |
> |
// get the ensemble |
646 |
|
|
647 |
< |
strcpy( ensemble, globals->getEnsemble() ); |
647 |
> |
strcpy(ensemble, globals->getEnsemble()); |
648 |
|
|
649 |
< |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
650 |
< |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
651 |
< |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
649 |
> |
if (!strcasecmp(ensemble, "NVE")){ |
650 |
> |
ensembleCase = NVE_ENS; |
651 |
> |
} |
652 |
> |
else if (!strcasecmp(ensemble, "NVT")){ |
653 |
> |
ensembleCase = NVT_ENS; |
654 |
> |
} |
655 |
> |
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
656 |
|
ensembleCase = NPTi_ENS; |
657 |
< |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
658 |
< |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
659 |
< |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
657 |
> |
} |
658 |
> |
else if (!strcasecmp(ensemble, "NPTf")){ |
659 |
> |
ensembleCase = NPTf_ENS; |
660 |
> |
} |
661 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
662 |
> |
ensembleCase = NPTxyz_ENS; |
663 |
> |
} |
664 |
|
else{ |
665 |
< |
sprintf( painCave.errMsg, |
666 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
667 |
< |
"reverting to NVE for this simulation.\n", |
668 |
< |
ensemble ); |
669 |
< |
painCave.isFatal = 0; |
670 |
< |
simError(); |
671 |
< |
strcpy( ensemble, "NVE" ); |
672 |
< |
ensembleCase = NVE_ENS; |
665 |
> |
sprintf(painCave.errMsg, |
666 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s \n" |
667 |
> |
"\treverting to NVE for this simulation.\n", |
668 |
> |
ensemble); |
669 |
> |
painCave.isFatal = 0; |
670 |
> |
simError(); |
671 |
> |
strcpy(ensemble, "NVE"); |
672 |
> |
ensembleCase = NVE_ENS; |
673 |
|
} |
647 |
– |
|
648 |
– |
for(i=0; i<nInfo; i++){ |
649 |
– |
|
650 |
– |
strcpy( info[i].ensemble, ensemble ); |
674 |
|
|
675 |
+ |
for (i = 0; i < nInfo; i++){ |
676 |
+ |
strcpy(info[i].ensemble, ensemble); |
677 |
+ |
|
678 |
|
// get the mixing rule |
679 |
|
|
680 |
< |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
680 |
> |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
681 |
|
info[i].usePBC = globals->getPBC(); |
682 |
|
} |
683 |
< |
|
683 |
> |
|
684 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
685 |
< |
|
685 |
> |
|
686 |
|
the_components = globals->getComponents(); |
687 |
|
components_nmol = new int[n_components]; |
688 |
|
|
689 |
|
|
690 |
< |
if( !globals->haveNMol() ){ |
690 |
> |
if (!globals->haveNMol()){ |
691 |
|
// we don't have the total number of molecules, so we assume it is |
692 |
|
// given in each component |
693 |
|
|
694 |
|
tot_nmol = 0; |
695 |
< |
for( i=0; i<n_components; i++ ){ |
696 |
< |
|
697 |
< |
if( !the_components[i]->haveNMol() ){ |
698 |
< |
// we have a problem |
699 |
< |
sprintf( painCave.errMsg, |
700 |
< |
"SimSetup Error. No global NMol or component NMol" |
701 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
702 |
< |
painCave.isFatal = 1; |
677 |
< |
simError(); |
695 |
> |
for (i = 0; i < n_components; i++){ |
696 |
> |
if (!the_components[i]->haveNMol()){ |
697 |
> |
// we have a problem |
698 |
> |
sprintf(painCave.errMsg, |
699 |
> |
"SimSetup Error. No global NMol or component NMol given.\n" |
700 |
> |
"\tCannot calculate the number of atoms.\n"); |
701 |
> |
painCave.isFatal = 1; |
702 |
> |
simError(); |
703 |
|
} |
704 |
|
|
705 |
|
tot_nmol += the_components[i]->getNMol(); |
707 |
|
} |
708 |
|
} |
709 |
|
else{ |
710 |
< |
sprintf( painCave.errMsg, |
711 |
< |
"SimSetup error.\n" |
712 |
< |
"\tSorry, the ability to specify total" |
713 |
< |
" nMols and then give molfractions in the components\n" |
714 |
< |
"\tis not currently supported." |
715 |
< |
" Please give nMol in the components.\n" ); |
710 |
> |
sprintf(painCave.errMsg, |
711 |
> |
"SimSetup error.\n" |
712 |
> |
"\tSorry, the ability to specify total" |
713 |
> |
" nMols and then give molfractions in the components\n" |
714 |
> |
"\tis not currently supported." |
715 |
> |
" Please give nMol in the components.\n"); |
716 |
|
painCave.isFatal = 1; |
717 |
|
simError(); |
718 |
|
} |
719 |
|
|
720 |
< |
// set the status, sample, and thermal kick times |
721 |
< |
|
722 |
< |
for(i=0; i<nInfo; i++){ |
720 |
> |
//check whether sample time, status time, thermal time and reset time are divisble by dt |
721 |
> |
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
722 |
> |
sprintf(painCave.errMsg, |
723 |
> |
"Sample time is not divisible by dt.\n" |
724 |
> |
"\tThis will result in samples that are not uniformly\n" |
725 |
> |
"\tdistributed in time. If this is a problem, change\n" |
726 |
> |
"\tyour sampleTime variable.\n"); |
727 |
> |
painCave.isFatal = 0; |
728 |
> |
simError(); |
729 |
> |
} |
730 |
|
|
731 |
< |
if( globals->haveSampleTime() ){ |
731 |
> |
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
732 |
> |
sprintf(painCave.errMsg, |
733 |
> |
"Status time is not divisible by dt.\n" |
734 |
> |
"\tThis will result in status reports that are not uniformly\n" |
735 |
> |
"\tdistributed in time. If this is a problem, change \n" |
736 |
> |
"\tyour statusTime variable.\n"); |
737 |
> |
painCave.isFatal = 0; |
738 |
> |
simError(); |
739 |
> |
} |
740 |
> |
|
741 |
> |
if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
742 |
> |
sprintf(painCave.errMsg, |
743 |
> |
"Thermal time is not divisible by dt.\n" |
744 |
> |
"\tThis will result in thermalizations that are not uniformly\n" |
745 |
> |
"\tdistributed in time. If this is a problem, change \n" |
746 |
> |
"\tyour thermalTime variable.\n"); |
747 |
> |
painCave.isFatal = 0; |
748 |
> |
simError(); |
749 |
> |
} |
750 |
> |
|
751 |
> |
if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
752 |
> |
sprintf(painCave.errMsg, |
753 |
> |
"Reset time is not divisible by dt.\n" |
754 |
> |
"\tThis will result in integrator resets that are not uniformly\n" |
755 |
> |
"\tdistributed in time. If this is a problem, change\n" |
756 |
> |
"\tyour resetTime variable.\n"); |
757 |
> |
painCave.isFatal = 0; |
758 |
> |
simError(); |
759 |
> |
} |
760 |
> |
|
761 |
> |
// set the status, sample, and thermal kick times |
762 |
> |
|
763 |
> |
for (i = 0; i < nInfo; i++){ |
764 |
> |
if (globals->haveSampleTime()){ |
765 |
|
info[i].sampleTime = globals->getSampleTime(); |
766 |
|
info[i].statusTime = info[i].sampleTime; |
767 |
|
info[i].thermalTime = info[i].sampleTime; |
771 |
|
info[i].statusTime = info[i].sampleTime; |
772 |
|
info[i].thermalTime = info[i].sampleTime; |
773 |
|
} |
774 |
< |
|
775 |
< |
if( globals->haveStatusTime() ){ |
774 |
> |
|
775 |
> |
if (globals->haveStatusTime()){ |
776 |
|
info[i].statusTime = globals->getStatusTime(); |
777 |
|
} |
778 |
< |
|
779 |
< |
if( globals->haveThermalTime() ){ |
778 |
> |
|
779 |
> |
if (globals->haveThermalTime()){ |
780 |
|
info[i].thermalTime = globals->getThermalTime(); |
781 |
|
} |
782 |
|
|
783 |
+ |
info[i].resetIntegrator = 0; |
784 |
+ |
if( globals->haveResetTime() ){ |
785 |
+ |
info[i].resetTime = globals->getResetTime(); |
786 |
+ |
info[i].resetIntegrator = 1; |
787 |
+ |
} |
788 |
+ |
|
789 |
|
// check for the temperature set flag |
790 |
+ |
|
791 |
+ |
if (globals->haveTempSet()) |
792 |
+ |
info[i].setTemp = globals->getTempSet(); |
793 |
|
|
794 |
< |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
794 |
> |
// check for the extended State init |
795 |
> |
|
796 |
> |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
797 |
> |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
798 |
|
|
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 ); |
799 |
|
} |
800 |
< |
else{ |
801 |
< |
if( !globals->haveBoxX() ){ |
802 |
< |
sprintf( painCave.errMsg, |
803 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
804 |
< |
painCave.isFatal = 1; |
805 |
< |
simError(); |
800 |
> |
|
801 |
> |
//setup seed for random number generator |
802 |
> |
int seedValue; |
803 |
> |
|
804 |
> |
if (globals->haveSeed()){ |
805 |
> |
seedValue = globals->getSeed(); |
806 |
> |
|
807 |
> |
if(seedValue / 1E9 == 0){ |
808 |
> |
sprintf(painCave.errMsg, |
809 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
810 |
> |
"OOPSE will generate a seed for user\n"); |
811 |
> |
painCave.isFatal = 0; |
812 |
> |
simError(); |
813 |
> |
|
814 |
> |
//using seed generated by system instead of invalid seed set by user |
815 |
> |
#ifndef IS_MPI |
816 |
> |
seedValue = make_sprng_seed(); |
817 |
> |
#else |
818 |
> |
if (worldRank == 0){ |
819 |
> |
seedValue = make_sprng_seed(); |
820 |
|
} |
821 |
< |
boxVector[0] = globals->getBoxX(); |
822 |
< |
|
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 ); |
821 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
822 |
> |
#endif |
823 |
|
} |
824 |
+ |
}//end of if branch of globals->haveSeed() |
825 |
+ |
else{ |
826 |
+ |
|
827 |
+ |
#ifndef IS_MPI |
828 |
+ |
seedValue = make_sprng_seed(); |
829 |
+ |
#else |
830 |
+ |
if (worldRank == 0){ |
831 |
+ |
seedValue = make_sprng_seed(); |
832 |
+ |
} |
833 |
+ |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
834 |
+ |
#endif |
835 |
+ |
}//end of globals->haveSeed() |
836 |
|
|
837 |
+ |
for (int i = 0; i < nInfo; i++){ |
838 |
+ |
info[i].setSeed(seedValue); |
839 |
|
} |
840 |
< |
|
840 |
> |
|
841 |
|
#ifdef IS_MPI |
842 |
< |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
842 |
> |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
843 |
|
MPIcheckPoint(); |
844 |
|
#endif // is_mpi |
776 |
– |
|
845 |
|
} |
846 |
|
|
847 |
|
|
848 |
< |
void SimSetup::finalInfoCheck( void ){ |
848 |
> |
void SimSetup::finalInfoCheck(void){ |
849 |
|
int index; |
850 |
|
int usesDipoles; |
851 |
|
int i; |
852 |
|
|
853 |
< |
for(i=0; i<nInfo; i++){ |
853 |
> |
for (i = 0; i < nInfo; i++){ |
854 |
|
// check electrostatic parameters |
855 |
< |
|
855 |
> |
|
856 |
|
index = 0; |
857 |
|
usesDipoles = 0; |
858 |
< |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
858 |
> |
while ((index < info[i].n_atoms) && !usesDipoles){ |
859 |
|
usesDipoles = (info[i].atoms[index])->hasDipole(); |
860 |
|
index++; |
861 |
|
} |
862 |
< |
|
862 |
> |
|
863 |
|
#ifdef IS_MPI |
864 |
|
int myUse = usesDipoles; |
865 |
< |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
865 |
> |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
866 |
|
#endif //is_mpi |
867 |
< |
|
867 |
> |
|
868 |
|
double theEcr, theEst; |
869 |
< |
|
870 |
< |
if (globals->getUseRF() ) { |
869 |
> |
|
870 |
> |
if (globals->getUseRF()){ |
871 |
|
info[i].useReactionField = 1; |
872 |
< |
|
873 |
< |
if( !globals->haveECR() ){ |
874 |
< |
sprintf( painCave.errMsg, |
875 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
876 |
< |
"box length for the electrostaticCutoffRadius.\n" |
877 |
< |
"I hope you have a very fast processor!\n"); |
878 |
< |
painCave.isFatal = 0; |
879 |
< |
simError(); |
880 |
< |
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(); |
872 |
> |
|
873 |
> |
if (!globals->haveECR()){ |
874 |
> |
sprintf(painCave.errMsg, |
875 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
876 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
877 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
878 |
> |
painCave.isFatal = 0; |
879 |
> |
simError(); |
880 |
> |
theEcr = 15.0; |
881 |
|
} |
882 |
< |
|
883 |
< |
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(); |
882 |
> |
else{ |
883 |
> |
theEcr = globals->getECR(); |
884 |
|
} |
885 |
< |
|
886 |
< |
info[i].setEcr( theEcr, theEst ); |
887 |
< |
|
888 |
< |
if(!globals->haveDielectric() ){ |
889 |
< |
sprintf( painCave.errMsg, |
890 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
891 |
< |
"setting a dielectric constant!\n" |
892 |
< |
); |
893 |
< |
painCave.isFatal = 1; |
894 |
< |
simError(); |
885 |
> |
|
886 |
> |
if (!globals->haveEST()){ |
887 |
> |
sprintf(painCave.errMsg, |
888 |
> |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
889 |
> |
"\tOOPSE will use a default value of\n" |
890 |
> |
"\t0.05 * electrostaticCutoffRadius\n" |
891 |
> |
"\tfor the electrostaticSkinThickness\n"); |
892 |
> |
painCave.isFatal = 0; |
893 |
> |
simError(); |
894 |
> |
theEst = 0.05 * theEcr; |
895 |
|
} |
896 |
< |
info[i].dielectric = globals->getDielectric(); |
897 |
< |
} |
898 |
< |
else { |
899 |
< |
if (usesDipoles) { |
900 |
< |
|
901 |
< |
if( !globals->haveECR() ){ |
902 |
< |
sprintf( painCave.errMsg, |
903 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
904 |
< |
"box length for the electrostaticCutoffRadius.\n" |
905 |
< |
"I hope you have a very fast processor!\n"); |
906 |
< |
painCave.isFatal = 0; |
907 |
< |
simError(); |
908 |
< |
double smallest; |
909 |
< |
smallest = info[i].boxL[0]; |
910 |
< |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
911 |
< |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
912 |
< |
theEcr = 0.5 * smallest; |
913 |
< |
} else { |
914 |
< |
theEcr = globals->getECR(); |
915 |
< |
} |
916 |
< |
|
917 |
< |
if( !globals->haveEST() ){ |
918 |
< |
sprintf( painCave.errMsg, |
866 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
< |
"electrostaticCutoffRadius for the " |
868 |
< |
"electrostaticSkinThickness\n" |
869 |
< |
); |
896 |
> |
else{ |
897 |
> |
theEst = globals->getEST(); |
898 |
> |
} |
899 |
> |
|
900 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
901 |
> |
|
902 |
> |
if (!globals->haveDielectric()){ |
903 |
> |
sprintf(painCave.errMsg, |
904 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
905 |
> |
"\tYou are trying to use Reaction Field without" |
906 |
> |
"\tsetting a dielectric constant!\n"); |
907 |
> |
painCave.isFatal = 1; |
908 |
> |
simError(); |
909 |
> |
} |
910 |
> |
info[i].dielectric = globals->getDielectric(); |
911 |
> |
} |
912 |
> |
else{ |
913 |
> |
if (usesDipoles){ |
914 |
> |
if (!globals->haveECR()){ |
915 |
> |
sprintf(painCave.errMsg, |
916 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
917 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
918 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
919 |
|
painCave.isFatal = 0; |
920 |
|
simError(); |
921 |
< |
theEst = 0.05 * theEcr; |
922 |
< |
} else { |
923 |
< |
theEst= globals->getEST(); |
924 |
< |
} |
921 |
> |
theEcr = 15.0; |
922 |
> |
} |
923 |
> |
else{ |
924 |
> |
theEcr = globals->getECR(); |
925 |
> |
} |
926 |
|
|
927 |
< |
info[i].setEcr( theEcr, theEst ); |
927 |
> |
if (!globals->haveEST()){ |
928 |
> |
sprintf(painCave.errMsg, |
929 |
> |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
930 |
> |
"\tOOPSE will use a default value of\n" |
931 |
> |
"\t0.05 * electrostaticCutoffRadius\n" |
932 |
> |
"\tfor the electrostaticSkinThickness\n"); |
933 |
> |
painCave.isFatal = 0; |
934 |
> |
simError(); |
935 |
> |
theEst = 0.05 * theEcr; |
936 |
> |
} |
937 |
> |
else{ |
938 |
> |
theEst = globals->getEST(); |
939 |
> |
} |
940 |
> |
|
941 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
942 |
|
} |
943 |
< |
} |
943 |
> |
} |
944 |
|
} |
881 |
– |
|
945 |
|
#ifdef IS_MPI |
946 |
< |
strcpy( checkPointMsg, "post processing checks out" ); |
946 |
> |
strcpy(checkPointMsg, "post processing checks out"); |
947 |
|
MPIcheckPoint(); |
948 |
|
#endif // is_mpi |
886 |
– |
|
949 |
|
} |
888 |
– |
|
889 |
– |
void SimSetup::initSystemCoords( void ){ |
890 |
– |
int i; |
950 |
|
|
951 |
+ |
void SimSetup::initSystemCoords(void){ |
952 |
+ |
int i; |
953 |
+ |
|
954 |
|
char* inName; |
955 |
|
|
956 |
+ |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
957 |
|
|
958 |
< |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
959 |
< |
|
960 |
< |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
961 |
< |
|
899 |
< |
if( globals->haveInitialConfig() ){ |
900 |
< |
|
958 |
> |
for (i = 0; i < info[0].n_atoms; i++) |
959 |
> |
info[0].atoms[i]->setCoords(); |
960 |
> |
|
961 |
> |
if (globals->haveInitialConfig()){ |
962 |
|
InitializeFromFile* fileInit; |
963 |
|
#ifdef IS_MPI // is_mpi |
964 |
< |
if( worldRank == 0 ){ |
964 |
> |
if (worldRank == 0){ |
965 |
|
#endif //is_mpi |
966 |
|
inName = globals->getInitialConfig(); |
967 |
< |
double* tempDouble = new double[1000000]; |
907 |
< |
fileInit = new InitializeFromFile( inName ); |
967 |
> |
fileInit = new InitializeFromFile(inName); |
968 |
|
#ifdef IS_MPI |
969 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
969 |
> |
} |
970 |
> |
else |
971 |
> |
fileInit = new InitializeFromFile(NULL); |
972 |
|
#endif |
973 |
< |
fileInit->readInit( info ); // default velocities on |
974 |
< |
|
973 |
> |
fileInit->readInit(info); // default velocities on |
974 |
> |
|
975 |
|
delete fileInit; |
976 |
|
} |
977 |
|
else{ |
978 |
|
|
917 |
– |
#ifdef IS_MPI |
918 |
– |
|
979 |
|
// no init from bass |
980 |
|
|
981 |
< |
sprintf( painCave.errMsg, |
982 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
983 |
< |
painCave.isFatal; |
981 |
> |
sprintf(painCave.errMsg, |
982 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
983 |
> |
painCave.isFatal = 1;; |
984 |
|
simError(); |
985 |
|
|
926 |
– |
#else |
927 |
– |
|
928 |
– |
initFromBass(); |
929 |
– |
|
930 |
– |
|
931 |
– |
#endif |
986 |
|
} |
987 |
< |
|
987 |
> |
|
988 |
|
#ifdef IS_MPI |
989 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
989 |
> |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
990 |
|
MPIcheckPoint(); |
991 |
|
#endif // is_mpi |
938 |
– |
|
992 |
|
} |
993 |
|
|
994 |
|
|
995 |
< |
void SimSetup::makeOutNames( void ){ |
943 |
< |
|
995 |
> |
void SimSetup::makeOutNames(void){ |
996 |
|
int k; |
997 |
|
|
946 |
– |
|
947 |
– |
for(k=0; k<nInfo; k++){ |
998 |
|
|
999 |
+ |
for (k = 0; k < nInfo; k++){ |
1000 |
|
#ifdef IS_MPI |
1001 |
< |
if( worldRank == 0 ){ |
1001 |
> |
if (worldRank == 0){ |
1002 |
|
#endif // is_mpi |
1003 |
< |
|
1004 |
< |
if( globals->haveFinalConfig() ){ |
1005 |
< |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
1003 |
> |
|
1004 |
> |
if (globals->haveFinalConfig()){ |
1005 |
> |
strcpy(info[k].finalName, globals->getFinalConfig()); |
1006 |
|
} |
1007 |
|
else{ |
1008 |
< |
strcpy( info[k].finalName, inFileName ); |
1009 |
< |
char* endTest; |
1010 |
< |
int nameLength = strlen( info[k].finalName ); |
1011 |
< |
endTest = &(info[k].finalName[nameLength - 5]); |
1012 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
1013 |
< |
strcpy( endTest, ".eor" ); |
1014 |
< |
} |
1015 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
1016 |
< |
strcpy( endTest, ".eor" ); |
1017 |
< |
} |
1018 |
< |
else{ |
1019 |
< |
endTest = &(info[k].finalName[nameLength - 4]); |
1020 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1021 |
< |
strcpy( endTest, ".eor" ); |
1022 |
< |
} |
1023 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1024 |
< |
strcpy( endTest, ".eor" ); |
1025 |
< |
} |
1026 |
< |
else{ |
1027 |
< |
strcat( info[k].finalName, ".eor" ); |
1028 |
< |
} |
1029 |
< |
} |
1008 |
> |
strcpy(info[k].finalName, inFileName); |
1009 |
> |
char* endTest; |
1010 |
> |
int nameLength = strlen(info[k].finalName); |
1011 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
1012 |
> |
if (!strcmp(endTest, ".bass")){ |
1013 |
> |
strcpy(endTest, ".eor"); |
1014 |
> |
} |
1015 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1016 |
> |
strcpy(endTest, ".eor"); |
1017 |
> |
} |
1018 |
> |
else{ |
1019 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
1020 |
> |
if (!strcmp(endTest, ".bss")){ |
1021 |
> |
strcpy(endTest, ".eor"); |
1022 |
> |
} |
1023 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1024 |
> |
strcpy(endTest, ".eor"); |
1025 |
> |
} |
1026 |
> |
else{ |
1027 |
> |
strcat(info[k].finalName, ".eor"); |
1028 |
> |
} |
1029 |
> |
} |
1030 |
|
} |
1031 |
< |
|
1031 |
> |
|
1032 |
|
// make the sample and status out names |
1033 |
< |
|
1034 |
< |
strcpy( info[k].sampleName, inFileName ); |
1033 |
> |
|
1034 |
> |
strcpy(info[k].sampleName, inFileName); |
1035 |
|
char* endTest; |
1036 |
< |
int nameLength = strlen( info[k].sampleName ); |
1036 |
> |
int nameLength = strlen(info[k].sampleName); |
1037 |
|
endTest = &(info[k].sampleName[nameLength - 5]); |
1038 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
1039 |
< |
strcpy( endTest, ".dump" ); |
1038 |
> |
if (!strcmp(endTest, ".bass")){ |
1039 |
> |
strcpy(endTest, ".dump"); |
1040 |
|
} |
1041 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
1042 |
< |
strcpy( endTest, ".dump" ); |
1041 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1042 |
> |
strcpy(endTest, ".dump"); |
1043 |
|
} |
1044 |
|
else{ |
1045 |
< |
endTest = &(info[k].sampleName[nameLength - 4]); |
1046 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1047 |
< |
strcpy( endTest, ".dump" ); |
1048 |
< |
} |
1049 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1050 |
< |
strcpy( endTest, ".dump" ); |
1051 |
< |
} |
1052 |
< |
else{ |
1053 |
< |
strcat( info[k].sampleName, ".dump" ); |
1054 |
< |
} |
1045 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
1046 |
> |
if (!strcmp(endTest, ".bss")){ |
1047 |
> |
strcpy(endTest, ".dump"); |
1048 |
> |
} |
1049 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1050 |
> |
strcpy(endTest, ".dump"); |
1051 |
> |
} |
1052 |
> |
else{ |
1053 |
> |
strcat(info[k].sampleName, ".dump"); |
1054 |
> |
} |
1055 |
|
} |
1056 |
< |
|
1057 |
< |
strcpy( info[k].statusName, inFileName ); |
1058 |
< |
nameLength = strlen( info[k].statusName ); |
1056 |
> |
|
1057 |
> |
strcpy(info[k].statusName, inFileName); |
1058 |
> |
nameLength = strlen(info[k].statusName); |
1059 |
|
endTest = &(info[k].statusName[nameLength - 5]); |
1060 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
1061 |
< |
strcpy( endTest, ".stat" ); |
1060 |
> |
if (!strcmp(endTest, ".bass")){ |
1061 |
> |
strcpy(endTest, ".stat"); |
1062 |
|
} |
1063 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
1064 |
< |
strcpy( endTest, ".stat" ); |
1063 |
> |
else if (!strcmp(endTest, ".BASS")){ |
1064 |
> |
strcpy(endTest, ".stat"); |
1065 |
|
} |
1066 |
|
else{ |
1067 |
< |
endTest = &(info[k].statusName[nameLength - 4]); |
1068 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1069 |
< |
strcpy( endTest, ".stat" ); |
1070 |
< |
} |
1071 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1072 |
< |
strcpy( endTest, ".stat" ); |
1073 |
< |
} |
1074 |
< |
else{ |
1075 |
< |
strcat( info[k].statusName, ".stat" ); |
1076 |
< |
} |
1067 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1068 |
> |
if (!strcmp(endTest, ".bss")){ |
1069 |
> |
strcpy(endTest, ".stat"); |
1070 |
> |
} |
1071 |
> |
else if (!strcmp(endTest, ".mdl")){ |
1072 |
> |
strcpy(endTest, ".stat"); |
1073 |
> |
} |
1074 |
> |
else{ |
1075 |
> |
strcat(info[k].statusName, ".stat"); |
1076 |
> |
} |
1077 |
|
} |
1078 |
< |
|
1078 |
> |
|
1079 |
|
#ifdef IS_MPI |
1080 |
+ |
|
1081 |
|
} |
1082 |
|
#endif // is_mpi |
1083 |
|
} |
1084 |
|
} |
1085 |
|
|
1086 |
|
|
1087 |
< |
void SimSetup::sysObjectsCreation( void ){ |
1088 |
< |
|
1089 |
< |
int i,k; |
1038 |
< |
|
1087 |
> |
void SimSetup::sysObjectsCreation(void){ |
1088 |
> |
int i, k; |
1089 |
> |
|
1090 |
|
// create the forceField |
1091 |
|
|
1092 |
|
createFF(); |
1101 |
|
|
1102 |
|
#ifdef IS_MPI |
1103 |
|
// divide the molecules among the processors |
1104 |
< |
|
1104 |
> |
|
1105 |
|
mpiMolDivide(); |
1106 |
|
#endif //is_mpi |
1107 |
< |
|
1107 |
> |
|
1108 |
|
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1109 |
< |
|
1109 |
> |
|
1110 |
|
makeSysArrays(); |
1111 |
|
|
1112 |
|
// make and initialize the molecules (all but atomic coordinates) |
1113 |
< |
|
1113 |
> |
|
1114 |
|
makeMolecules(); |
1115 |
< |
|
1116 |
< |
for(k=0; k<nInfo; k++){ |
1115 |
> |
|
1116 |
> |
for (k = 0; k < nInfo; k++){ |
1117 |
|
info[k].identArray = new int[info[k].n_atoms]; |
1118 |
< |
for(i=0; i<info[k].n_atoms; i++){ |
1118 |
> |
for (i = 0; i < info[k].n_atoms; i++){ |
1119 |
|
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1120 |
|
} |
1121 |
|
} |
1122 |
|
} |
1123 |
|
|
1124 |
|
|
1125 |
< |
void SimSetup::createFF( void ){ |
1125 |
> |
void SimSetup::createFF(void){ |
1126 |
> |
switch (ffCase){ |
1127 |
> |
case FF_DUFF: |
1128 |
> |
the_ff = new DUFF(); |
1129 |
> |
break; |
1130 |
|
|
1131 |
< |
switch( ffCase ){ |
1131 |
> |
case FF_LJ: |
1132 |
> |
the_ff = new LJFF(); |
1133 |
> |
break; |
1134 |
|
|
1135 |
< |
case FF_DUFF: |
1136 |
< |
the_ff = new DUFF(); |
1137 |
< |
break; |
1081 |
< |
|
1082 |
< |
case FF_LJ: |
1083 |
< |
the_ff = new LJFF(); |
1084 |
< |
break; |
1085 |
< |
|
1086 |
< |
case FF_EAM: |
1087 |
< |
the_ff = new EAM_FF(); |
1088 |
< |
break; |
1135 |
> |
case FF_EAM: |
1136 |
> |
the_ff = new EAM_FF(); |
1137 |
> |
break; |
1138 |
|
|
1139 |
< |
default: |
1140 |
< |
sprintf( painCave.errMsg, |
1141 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1142 |
< |
painCave.isFatal = 1; |
1143 |
< |
simError(); |
1139 |
> |
default: |
1140 |
> |
sprintf(painCave.errMsg, |
1141 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1142 |
> |
painCave.isFatal = 1; |
1143 |
> |
simError(); |
1144 |
|
} |
1145 |
|
|
1146 |
|
#ifdef IS_MPI |
1147 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1147 |
> |
strcpy(checkPointMsg, "ForceField creation successful"); |
1148 |
|
MPIcheckPoint(); |
1149 |
|
#endif // is_mpi |
1101 |
– |
|
1150 |
|
} |
1151 |
|
|
1152 |
|
|
1153 |
< |
void SimSetup::compList( void ){ |
1106 |
< |
|
1153 |
> |
void SimSetup::compList(void){ |
1154 |
|
int i; |
1155 |
|
char* id; |
1156 |
|
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1157 |
|
LinkedMolStamp* currentStamp = NULL; |
1158 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
1159 |
< |
|
1158 |
> |
comp_stamps = new MoleculeStamp * [n_components]; |
1159 |
> |
|
1160 |
|
// make an array of molecule stamps that match the components used. |
1161 |
|
// also extract the used stamps out into a separate linked list |
1162 |
< |
|
1163 |
< |
for(i=0; i<nInfo; i++){ |
1162 |
> |
|
1163 |
> |
for (i = 0; i < nInfo; i++){ |
1164 |
|
info[i].nComponents = n_components; |
1165 |
|
info[i].componentsNmol = components_nmol; |
1166 |
|
info[i].compStamps = comp_stamps; |
1167 |
|
info[i].headStamp = headStamp; |
1168 |
|
} |
1122 |
– |
|
1169 |
|
|
1124 |
– |
for( i=0; i<n_components; i++ ){ |
1170 |
|
|
1171 |
+ |
for (i = 0; i < n_components; i++){ |
1172 |
|
id = the_components[i]->getType(); |
1173 |
|
comp_stamps[i] = NULL; |
1174 |
< |
|
1174 |
> |
|
1175 |
|
// check to make sure the component isn't already in the list |
1176 |
|
|
1177 |
< |
comp_stamps[i] = headStamp->match( id ); |
1178 |
< |
if( comp_stamps[i] == NULL ){ |
1133 |
< |
|
1177 |
> |
comp_stamps[i] = headStamp->match(id); |
1178 |
> |
if (comp_stamps[i] == NULL){ |
1179 |
|
// extract the component from the list; |
1180 |
< |
|
1181 |
< |
currentStamp = stamps->extractMolStamp( id ); |
1182 |
< |
if( currentStamp == NULL ){ |
1183 |
< |
sprintf( painCave.errMsg, |
1184 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
1185 |
< |
"list of declared molecules\n", |
1186 |
< |
id ); |
1187 |
< |
painCave.isFatal = 1; |
1188 |
< |
simError(); |
1180 |
> |
|
1181 |
> |
currentStamp = stamps->extractMolStamp(id); |
1182 |
> |
if (currentStamp == NULL){ |
1183 |
> |
sprintf(painCave.errMsg, |
1184 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1185 |
> |
"list of declared molecules\n", |
1186 |
> |
id); |
1187 |
> |
painCave.isFatal = 1; |
1188 |
> |
simError(); |
1189 |
|
} |
1190 |
< |
|
1191 |
< |
headStamp->add( currentStamp ); |
1192 |
< |
comp_stamps[i] = headStamp->match( id ); |
1190 |
> |
|
1191 |
> |
headStamp->add(currentStamp); |
1192 |
> |
comp_stamps[i] = headStamp->match(id); |
1193 |
|
} |
1194 |
|
} |
1195 |
|
|
1196 |
|
#ifdef IS_MPI |
1197 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1197 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1198 |
|
MPIcheckPoint(); |
1199 |
|
#endif // is_mpi |
1200 |
+ |
} |
1201 |
|
|
1202 |
+ |
void SimSetup::calcSysValues(void){ |
1203 |
+ |
int i; |
1204 |
|
|
1205 |
< |
} |
1205 |
> |
int* molMembershipArray; |
1206 |
|
|
1159 |
– |
void SimSetup::calcSysValues( void ){ |
1160 |
– |
int i, j, k; |
1161 |
– |
|
1162 |
– |
int *molMembershipArray; |
1163 |
– |
|
1207 |
|
tot_atoms = 0; |
1208 |
|
tot_bonds = 0; |
1209 |
|
tot_bends = 0; |
1210 |
|
tot_torsions = 0; |
1211 |
< |
for( i=0; i<n_components; i++ ){ |
1212 |
< |
|
1213 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1214 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1172 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1211 |
> |
for (i = 0; i < n_components; i++){ |
1212 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1213 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1214 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1215 |
|
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1216 |
|
} |
1217 |
< |
|
1217 |
> |
|
1218 |
|
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1219 |
|
molMembershipArray = new int[tot_atoms]; |
1220 |
< |
|
1221 |
< |
for(i=0; i<nInfo; i++){ |
1220 |
> |
|
1221 |
> |
for (i = 0; i < nInfo; i++){ |
1222 |
|
info[i].n_atoms = tot_atoms; |
1223 |
|
info[i].n_bonds = tot_bonds; |
1224 |
|
info[i].n_bends = tot_bends; |
1225 |
|
info[i].n_torsions = tot_torsions; |
1226 |
|
info[i].n_SRI = tot_SRI; |
1227 |
|
info[i].n_mol = tot_nmol; |
1228 |
< |
|
1228 |
> |
|
1229 |
|
info[i].molMembershipArray = molMembershipArray; |
1230 |
< |
} |
1230 |
> |
} |
1231 |
|
} |
1232 |
|
|
1233 |
|
#ifdef IS_MPI |
1234 |
|
|
1235 |
< |
void SimSetup::mpiMolDivide( void ){ |
1194 |
< |
|
1235 |
> |
void SimSetup::mpiMolDivide(void){ |
1236 |
|
int i, j, k; |
1237 |
|
int localMol, allMol; |
1238 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1239 |
|
|
1240 |
< |
mpiSim = new mpiSimulation( info ); |
1241 |
< |
|
1240 |
> |
mpiSim = new mpiSimulation(info); |
1241 |
> |
|
1242 |
|
globalIndex = mpiSim->divideLabor(); |
1243 |
|
|
1244 |
|
// set up the local variables |
1245 |
< |
|
1245 |
> |
|
1246 |
|
mol2proc = mpiSim->getMolToProcMap(); |
1247 |
|
molCompType = mpiSim->getMolComponentType(); |
1248 |
< |
|
1248 |
> |
|
1249 |
|
allMol = 0; |
1250 |
|
localMol = 0; |
1251 |
|
local_atoms = 0; |
1255 |
|
globalAtomIndex = 0; |
1256 |
|
|
1257 |
|
|
1258 |
< |
for( i=0; i<n_components; i++ ){ |
1259 |
< |
|
1260 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1261 |
< |
|
1262 |
< |
if( mol2proc[allMol] == worldRank ){ |
1263 |
< |
|
1264 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
1265 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
1225 |
< |
local_bends += comp_stamps[i]->getNBends(); |
1226 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
1227 |
< |
localMol++; |
1258 |
> |
for (i = 0; i < n_components; i++){ |
1259 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1260 |
> |
if (mol2proc[allMol] == worldRank){ |
1261 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1262 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1263 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1264 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1265 |
> |
localMol++; |
1266 |
|
} |
1267 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1267 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1268 |
|
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1269 |
|
globalAtomIndex++; |
1270 |
|
} |
1271 |
|
|
1272 |
< |
allMol++; |
1272 |
> |
allMol++; |
1273 |
|
} |
1274 |
|
} |
1275 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
1276 |
< |
|
1276 |
> |
|
1277 |
|
info[0].n_atoms = mpiSim->getMyNlocal(); |
1278 |
< |
|
1279 |
< |
if( local_atoms != info[0].n_atoms ){ |
1280 |
< |
sprintf( painCave.errMsg, |
1281 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1282 |
< |
" localAtom (%d) are not equal.\n", |
1283 |
< |
info[0].n_atoms, |
1246 |
< |
local_atoms ); |
1278 |
> |
|
1279 |
> |
if (local_atoms != info[0].n_atoms){ |
1280 |
> |
sprintf(painCave.errMsg, |
1281 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1282 |
> |
"\tlocalAtom (%d) are not equal.\n", |
1283 |
> |
info[0].n_atoms, local_atoms); |
1284 |
|
painCave.isFatal = 1; |
1285 |
|
simError(); |
1286 |
|
} |
1291 |
|
info[0].n_SRI = local_SRI; |
1292 |
|
info[0].n_mol = localMol; |
1293 |
|
|
1294 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1294 |
> |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1295 |
|
MPIcheckPoint(); |
1296 |
|
} |
1297 |
< |
|
1297 |
> |
|
1298 |
|
#endif // is_mpi |
1299 |
|
|
1300 |
|
|
1301 |
< |
void SimSetup::makeSysArrays( void ){ |
1302 |
< |
int i, j, k, l; |
1301 |
> |
void SimSetup::makeSysArrays(void){ |
1302 |
> |
|
1303 |
> |
#ifndef IS_MPI |
1304 |
> |
int k, j; |
1305 |
> |
#endif // is_mpi |
1306 |
> |
int i, l; |
1307 |
|
|
1308 |
|
Atom** the_atoms; |
1309 |
|
Molecule* the_molecules; |
1310 |
|
Exclude** the_excludes; |
1311 |
|
|
1312 |
< |
|
1313 |
< |
for(l=0; l<nInfo; l++){ |
1273 |
< |
|
1312 |
> |
|
1313 |
> |
for (l = 0; l < nInfo; l++){ |
1314 |
|
// create the atom and short range interaction arrays |
1315 |
< |
|
1316 |
< |
the_atoms = new Atom*[info[l].n_atoms]; |
1315 |
> |
|
1316 |
> |
the_atoms = new Atom * [info[l].n_atoms]; |
1317 |
|
the_molecules = new Molecule[info[l].n_mol]; |
1318 |
|
int molIndex; |
1319 |
|
|
1320 |
|
// initialize the molecule's stampID's |
1321 |
< |
|
1321 |
> |
|
1322 |
|
#ifdef IS_MPI |
1323 |
< |
|
1324 |
< |
|
1323 |
> |
|
1324 |
> |
|
1325 |
|
molIndex = 0; |
1326 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1327 |
< |
|
1328 |
< |
if(mol2proc[i] == worldRank ){ |
1329 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1330 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1331 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
1292 |
< |
molIndex++; |
1326 |
> |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1327 |
> |
if (mol2proc[i] == worldRank){ |
1328 |
> |
the_molecules[molIndex].setStampID(molCompType[i]); |
1329 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1330 |
> |
the_molecules[molIndex].setGlobalIndex(i); |
1331 |
> |
molIndex++; |
1332 |
|
} |
1333 |
|
} |
1334 |
< |
|
1334 |
> |
|
1335 |
|
#else // is_mpi |
1336 |
< |
|
1336 |
> |
|
1337 |
|
molIndex = 0; |
1338 |
|
globalAtomIndex = 0; |
1339 |
< |
for(i=0; i<n_components; i++){ |
1340 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
1341 |
< |
the_molecules[molIndex].setStampID( i ); |
1342 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1343 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1344 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1345 |
< |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1346 |
< |
globalAtomIndex++; |
1347 |
< |
} |
1348 |
< |
molIndex++; |
1339 |
> |
for (i = 0; i < n_components; i++){ |
1340 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1341 |
> |
the_molecules[molIndex].setStampID(i); |
1342 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1343 |
> |
the_molecules[molIndex].setGlobalIndex(molIndex); |
1344 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1345 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1346 |
> |
globalAtomIndex++; |
1347 |
> |
} |
1348 |
> |
molIndex++; |
1349 |
|
} |
1350 |
|
} |
1351 |
< |
|
1352 |
< |
|
1351 |
> |
|
1352 |
> |
|
1353 |
|
#endif // is_mpi |
1354 |
|
|
1355 |
|
|
1356 |
< |
if( info[l].n_SRI ){ |
1318 |
< |
|
1356 |
> |
if (info[l].n_SRI){ |
1357 |
|
Exclude::createArray(info[l].n_SRI); |
1358 |
< |
the_excludes = new Exclude*[info[l].n_SRI]; |
1359 |
< |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1360 |
< |
the_excludes[ex] = new Exclude(ex); |
1358 |
> |
the_excludes = new Exclude * [info[l].n_SRI]; |
1359 |
> |
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1360 |
> |
the_excludes[ex] = new Exclude(ex); |
1361 |
|
} |
1362 |
|
info[l].globalExcludes = new int; |
1363 |
|
info[l].n_exclude = info[l].n_SRI; |
1364 |
|
} |
1365 |
|
else{ |
1366 |
< |
|
1367 |
< |
Exclude::createArray( 1 ); |
1330 |
< |
the_excludes = new Exclude*; |
1366 |
> |
Exclude::createArray(1); |
1367 |
> |
the_excludes = new Exclude * ; |
1368 |
|
the_excludes[0] = new Exclude(0); |
1369 |
< |
the_excludes[0]->setPair( 0,0 ); |
1369 |
> |
the_excludes[0]->setPair(0, 0); |
1370 |
|
info[l].globalExcludes = new int; |
1371 |
|
info[l].globalExcludes[0] = 0; |
1372 |
|
info[l].n_exclude = 0; |
1379 |
|
info[l].nGlobalExcludes = 0; |
1380 |
|
info[l].excludes = the_excludes; |
1381 |
|
|
1382 |
< |
the_ff->setSimInfo( info ); |
1346 |
< |
|
1382 |
> |
the_ff->setSimInfo(info); |
1383 |
|
} |
1384 |
|
} |
1385 |
|
|
1386 |
< |
void SimSetup::makeIntegrator( void ){ |
1351 |
< |
|
1386 |
> |
void SimSetup::makeIntegrator(void){ |
1387 |
|
int k; |
1388 |
|
|
1389 |
< |
NVT<RealIntegrator>* myNVT = NULL; |
1390 |
< |
NPTi<RealIntegrator>* myNPTi = NULL; |
1391 |
< |
NPTf<RealIntegrator>* myNPTf = NULL; |
1392 |
< |
NPTim<RealIntegrator>* myNPTim = NULL; |
1393 |
< |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1394 |
< |
|
1395 |
< |
for(k=0; k<nInfo; k++){ |
1396 |
< |
|
1397 |
< |
switch( ensembleCase ){ |
1398 |
< |
|
1399 |
< |
case NVE_ENS: |
1400 |
< |
if (globals->haveZconstraints()){ |
1401 |
< |
setupZConstraint(info[k]); |
1402 |
< |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1389 |
> |
NVE<RealIntegrator>* myNVE = NULL; |
1390 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1391 |
> |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1392 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1393 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1394 |
> |
|
1395 |
> |
for (k = 0; k < nInfo; k++){ |
1396 |
> |
switch (ensembleCase){ |
1397 |
> |
case NVE_ENS: |
1398 |
> |
if (globals->haveZconstraints()){ |
1399 |
> |
setupZConstraint(info[k]); |
1400 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1401 |
> |
} |
1402 |
> |
else{ |
1403 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1404 |
|
} |
1405 |
+ |
|
1406 |
+ |
info->the_integrator = myNVE; |
1407 |
+ |
break; |
1408 |
|
|
1409 |
< |
else |
1410 |
< |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1411 |
< |
break; |
1412 |
< |
|
1413 |
< |
case NVT_ENS: |
1414 |
< |
if (globals->haveZconstraints()){ |
1415 |
< |
setupZConstraint(info[k]); |
1377 |
< |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1378 |
< |
} |
1379 |
< |
else |
1380 |
< |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1409 |
> |
case NVT_ENS: |
1410 |
> |
if (globals->haveZconstraints()){ |
1411 |
> |
setupZConstraint(info[k]); |
1412 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1413 |
> |
} |
1414 |
> |
else |
1415 |
> |
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1416 |
|
|
1417 |
< |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1383 |
< |
|
1384 |
< |
if (globals->haveTauThermostat()) |
1385 |
< |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1386 |
< |
|
1387 |
< |
else { |
1388 |
< |
sprintf( painCave.errMsg, |
1389 |
< |
"SimSetup error: If you use the NVT\n" |
1390 |
< |
" ensemble, you must set tauThermostat.\n"); |
1391 |
< |
painCave.isFatal = 1; |
1392 |
< |
simError(); |
1393 |
< |
} |
1394 |
< |
break; |
1395 |
< |
|
1396 |
< |
case NPTi_ENS: |
1397 |
< |
if (globals->haveZconstraints()){ |
1398 |
< |
setupZConstraint(info[k]); |
1399 |
< |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1400 |
< |
} |
1401 |
< |
else |
1402 |
< |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1417 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1418 |
|
|
1419 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1420 |
< |
|
1421 |
< |
if (globals->haveTargetPressure()) |
1422 |
< |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1423 |
< |
else { |
1424 |
< |
sprintf( painCave.errMsg, |
1425 |
< |
"SimSetup error: If you use a constant pressure\n" |
1426 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1427 |
< |
painCave.isFatal = 1; |
1413 |
< |
simError(); |
1414 |
< |
} |
1415 |
< |
|
1416 |
< |
if( globals->haveTauThermostat() ) |
1417 |
< |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1418 |
< |
else{ |
1419 |
< |
sprintf( painCave.errMsg, |
1420 |
< |
"SimSetup error: If you use an NPT\n" |
1421 |
< |
" ensemble, you must set tauThermostat.\n"); |
1422 |
< |
painCave.isFatal = 1; |
1423 |
< |
simError(); |
1424 |
< |
} |
1425 |
< |
|
1426 |
< |
if( globals->haveTauBarostat() ) |
1427 |
< |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1428 |
< |
else{ |
1429 |
< |
sprintf( painCave.errMsg, |
1430 |
< |
"SimSetup error: If you use an NPT\n" |
1431 |
< |
" ensemble, you must set tauBarostat.\n"); |
1432 |
< |
painCave.isFatal = 1; |
1433 |
< |
simError(); |
1434 |
< |
} |
1435 |
< |
break; |
1436 |
< |
|
1437 |
< |
case NPTf_ENS: |
1438 |
< |
if (globals->haveZconstraints()){ |
1439 |
< |
setupZConstraint(info[k]); |
1440 |
< |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1441 |
< |
} |
1442 |
< |
else |
1443 |
< |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1419 |
> |
if (globals->haveTauThermostat()) |
1420 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1421 |
> |
else{ |
1422 |
> |
sprintf(painCave.errMsg, |
1423 |
> |
"SimSetup error: If you use the NVT\n" |
1424 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1425 |
> |
painCave.isFatal = 1; |
1426 |
> |
simError(); |
1427 |
> |
} |
1428 |
|
|
1429 |
< |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1430 |
< |
|
1447 |
< |
if (globals->haveTargetPressure()) |
1448 |
< |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1449 |
< |
else { |
1450 |
< |
sprintf( painCave.errMsg, |
1451 |
< |
"SimSetup error: If you use a constant pressure\n" |
1452 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1453 |
< |
painCave.isFatal = 1; |
1454 |
< |
simError(); |
1455 |
< |
} |
1456 |
< |
|
1457 |
< |
if( globals->haveTauThermostat() ) |
1458 |
< |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1459 |
< |
else{ |
1460 |
< |
sprintf( painCave.errMsg, |
1461 |
< |
"SimSetup error: If you use an NPT\n" |
1462 |
< |
" ensemble, you must set tauThermostat.\n"); |
1463 |
< |
painCave.isFatal = 1; |
1464 |
< |
simError(); |
1465 |
< |
} |
1466 |
< |
|
1467 |
< |
if( globals->haveTauBarostat() ) |
1468 |
< |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1469 |
< |
else{ |
1470 |
< |
sprintf( painCave.errMsg, |
1471 |
< |
"SimSetup error: If you use an NPT\n" |
1472 |
< |
" ensemble, you must set tauBarostat.\n"); |
1473 |
< |
painCave.isFatal = 1; |
1474 |
< |
simError(); |
1475 |
< |
} |
1476 |
< |
break; |
1477 |
< |
|
1478 |
< |
case NPTim_ENS: |
1479 |
< |
if (globals->haveZconstraints()){ |
1480 |
< |
setupZConstraint(info[k]); |
1481 |
< |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1482 |
< |
} |
1483 |
< |
else |
1484 |
< |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1429 |
> |
info->the_integrator = myNVT; |
1430 |
> |
break; |
1431 |
|
|
1432 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1433 |
< |
|
1434 |
< |
if (globals->haveTargetPressure()) |
1435 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1436 |
< |
else { |
1437 |
< |
sprintf( painCave.errMsg, |
1438 |
< |
"SimSetup error: If you use a constant pressure\n" |
1493 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1494 |
< |
painCave.isFatal = 1; |
1495 |
< |
simError(); |
1496 |
< |
} |
1497 |
< |
|
1498 |
< |
if( globals->haveTauThermostat() ) |
1499 |
< |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1500 |
< |
else{ |
1501 |
< |
sprintf( painCave.errMsg, |
1502 |
< |
"SimSetup error: If you use an NPT\n" |
1503 |
< |
" ensemble, you must set tauThermostat.\n"); |
1504 |
< |
painCave.isFatal = 1; |
1505 |
< |
simError(); |
1506 |
< |
} |
1507 |
< |
|
1508 |
< |
if( globals->haveTauBarostat() ) |
1509 |
< |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1510 |
< |
else{ |
1511 |
< |
sprintf( painCave.errMsg, |
1512 |
< |
"SimSetup error: If you use an NPT\n" |
1513 |
< |
" ensemble, you must set tauBarostat.\n"); |
1514 |
< |
painCave.isFatal = 1; |
1515 |
< |
simError(); |
1516 |
< |
} |
1517 |
< |
break; |
1518 |
< |
|
1519 |
< |
case NPTfm_ENS: |
1520 |
< |
if (globals->haveZconstraints()){ |
1521 |
< |
setupZConstraint(info[k]); |
1522 |
< |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1523 |
< |
} |
1524 |
< |
else |
1525 |
< |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1432 |
> |
case NPTi_ENS: |
1433 |
> |
if (globals->haveZconstraints()){ |
1434 |
> |
setupZConstraint(info[k]); |
1435 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1436 |
> |
} |
1437 |
> |
else |
1438 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1439 |
|
|
1440 |
< |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1441 |
< |
|
1442 |
< |
if (globals->haveTargetPressure()) |
1443 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1444 |
< |
else { |
1445 |
< |
sprintf( painCave.errMsg, |
1446 |
< |
"SimSetup error: If you use a constant pressure\n" |
1447 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1448 |
< |
painCave.isFatal = 1; |
1449 |
< |
simError(); |
1450 |
< |
} |
1451 |
< |
|
1452 |
< |
if( globals->haveTauThermostat() ) |
1453 |
< |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1454 |
< |
else{ |
1455 |
< |
sprintf( painCave.errMsg, |
1456 |
< |
"SimSetup error: If you use an NPT\n" |
1457 |
< |
" ensemble, you must set tauThermostat.\n"); |
1458 |
< |
painCave.isFatal = 1; |
1459 |
< |
simError(); |
1460 |
< |
} |
1461 |
< |
|
1462 |
< |
if( globals->haveTauBarostat() ) |
1463 |
< |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1464 |
< |
else{ |
1465 |
< |
sprintf( painCave.errMsg, |
1466 |
< |
"SimSetup error: If you use an NPT\n" |
1467 |
< |
" ensemble, you must set tauBarostat.\n"); |
1468 |
< |
painCave.isFatal = 1; |
1469 |
< |
simError(); |
1470 |
< |
} |
1471 |
< |
break; |
1472 |
< |
|
1473 |
< |
default: |
1474 |
< |
sprintf( painCave.errMsg, |
1475 |
< |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1476 |
< |
painCave.isFatal = 1; |
1477 |
< |
simError(); |
1440 |
> |
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1441 |
> |
|
1442 |
> |
if (globals->haveTargetPressure()) |
1443 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1444 |
> |
else{ |
1445 |
> |
sprintf(painCave.errMsg, |
1446 |
> |
"SimSetup error: If you use a constant pressure\n" |
1447 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1448 |
> |
painCave.isFatal = 1; |
1449 |
> |
simError(); |
1450 |
> |
} |
1451 |
> |
|
1452 |
> |
if (globals->haveTauThermostat()) |
1453 |
> |
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1454 |
> |
else{ |
1455 |
> |
sprintf(painCave.errMsg, |
1456 |
> |
"SimSetup error: If you use an NPT\n" |
1457 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1458 |
> |
painCave.isFatal = 1; |
1459 |
> |
simError(); |
1460 |
> |
} |
1461 |
> |
|
1462 |
> |
if (globals->haveTauBarostat()) |
1463 |
> |
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1464 |
> |
else{ |
1465 |
> |
sprintf(painCave.errMsg, |
1466 |
> |
"SimSetup error: If you use an NPT\n" |
1467 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1468 |
> |
painCave.isFatal = 1; |
1469 |
> |
simError(); |
1470 |
> |
} |
1471 |
> |
|
1472 |
> |
info->the_integrator = myNPTi; |
1473 |
> |
break; |
1474 |
> |
|
1475 |
> |
case NPTf_ENS: |
1476 |
> |
if (globals->haveZconstraints()){ |
1477 |
> |
setupZConstraint(info[k]); |
1478 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1479 |
> |
} |
1480 |
> |
else |
1481 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1482 |
> |
|
1483 |
> |
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1484 |
> |
|
1485 |
> |
if (globals->haveTargetPressure()) |
1486 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1487 |
> |
else{ |
1488 |
> |
sprintf(painCave.errMsg, |
1489 |
> |
"SimSetup error: If you use a constant pressure\n" |
1490 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1491 |
> |
painCave.isFatal = 1; |
1492 |
> |
simError(); |
1493 |
> |
} |
1494 |
> |
|
1495 |
> |
if (globals->haveTauThermostat()) |
1496 |
> |
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1497 |
> |
|
1498 |
> |
else{ |
1499 |
> |
sprintf(painCave.errMsg, |
1500 |
> |
"SimSetup error: If you use an NPT\n" |
1501 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1502 |
> |
painCave.isFatal = 1; |
1503 |
> |
simError(); |
1504 |
> |
} |
1505 |
> |
|
1506 |
> |
if (globals->haveTauBarostat()) |
1507 |
> |
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1508 |
> |
|
1509 |
> |
else{ |
1510 |
> |
sprintf(painCave.errMsg, |
1511 |
> |
"SimSetup error: If you use an NPT\n" |
1512 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1513 |
> |
painCave.isFatal = 1; |
1514 |
> |
simError(); |
1515 |
> |
} |
1516 |
> |
|
1517 |
> |
info->the_integrator = myNPTf; |
1518 |
> |
break; |
1519 |
> |
|
1520 |
> |
case NPTxyz_ENS: |
1521 |
> |
if (globals->haveZconstraints()){ |
1522 |
> |
setupZConstraint(info[k]); |
1523 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1524 |
> |
} |
1525 |
> |
else |
1526 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1527 |
> |
|
1528 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1529 |
> |
|
1530 |
> |
if (globals->haveTargetPressure()) |
1531 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1532 |
> |
else{ |
1533 |
> |
sprintf(painCave.errMsg, |
1534 |
> |
"SimSetup error: If you use a constant pressure\n" |
1535 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1536 |
> |
painCave.isFatal = 1; |
1537 |
> |
simError(); |
1538 |
> |
} |
1539 |
> |
|
1540 |
> |
if (globals->haveTauThermostat()) |
1541 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1542 |
> |
else{ |
1543 |
> |
sprintf(painCave.errMsg, |
1544 |
> |
"SimSetup error: If you use an NPT\n" |
1545 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1546 |
> |
painCave.isFatal = 1; |
1547 |
> |
simError(); |
1548 |
> |
} |
1549 |
> |
|
1550 |
> |
if (globals->haveTauBarostat()) |
1551 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1552 |
> |
else{ |
1553 |
> |
sprintf(painCave.errMsg, |
1554 |
> |
"SimSetup error: If you use an NPT\n" |
1555 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1556 |
> |
painCave.isFatal = 1; |
1557 |
> |
simError(); |
1558 |
> |
} |
1559 |
> |
|
1560 |
> |
info->the_integrator = myNPTxyz; |
1561 |
> |
break; |
1562 |
> |
|
1563 |
> |
default: |
1564 |
> |
sprintf(painCave.errMsg, |
1565 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1566 |
> |
painCave.isFatal = 1; |
1567 |
> |
simError(); |
1568 |
|
} |
1569 |
|
} |
1570 |
|
} |
1571 |
|
|
1572 |
< |
void SimSetup::initFortran( void ){ |
1570 |
< |
|
1572 |
> |
void SimSetup::initFortran(void){ |
1573 |
|
info[0].refreshSim(); |
1574 |
< |
|
1575 |
< |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1576 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
1574 |
> |
|
1575 |
> |
if (!strcmp(info[0].mixingRule, "standard")){ |
1576 |
> |
the_ff->initForceField(LB_MIXING_RULE); |
1577 |
|
} |
1578 |
< |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1579 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1578 |
> |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1579 |
> |
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1580 |
|
} |
1581 |
|
else{ |
1582 |
< |
sprintf( painCave.errMsg, |
1583 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1582 |
< |
info[0].mixingRule ); |
1582 |
> |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1583 |
> |
info[0].mixingRule); |
1584 |
|
painCave.isFatal = 1; |
1585 |
|
simError(); |
1586 |
|
} |
1587 |
|
|
1588 |
|
|
1589 |
|
#ifdef IS_MPI |
1590 |
< |
strcpy( checkPointMsg, |
1590 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
1590 |
> |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1591 |
|
MPIcheckPoint(); |
1592 |
|
#endif // is_mpi |
1593 |
– |
|
1593 |
|
} |
1594 |
|
|
1595 |
< |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 |
< |
{ |
1597 |
< |
int nZConstraints; |
1599 |
< |
ZconStamp** zconStamp; |
1600 |
< |
|
1601 |
< |
if(globals->haveZconstraintTime()){ |
1602 |
< |
|
1603 |
< |
//add sample time of z-constraint into SimInfo's property list |
1604 |
< |
DoubleData* zconsTimeProp = new DoubleData(); |
1605 |
< |
zconsTimeProp->setID(ZCONSTIME_ID); |
1606 |
< |
zconsTimeProp->setData(globals->getZconsTime()); |
1607 |
< |
theInfo.addProperty(zconsTimeProp); |
1608 |
< |
} |
1609 |
< |
else{ |
1610 |
< |
sprintf( painCave.errMsg, |
1611 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
1612 |
< |
" , you must set sample time.\n"); |
1613 |
< |
painCave.isFatal = 1; |
1614 |
< |
simError(); |
1615 |
< |
} |
1595 |
> |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1596 |
> |
int nZConstraints; |
1597 |
> |
ZconStamp** zconStamp; |
1598 |
|
|
1599 |
< |
// |
1600 |
< |
nZConstraints = globals->getNzConstraints(); |
1601 |
< |
theInfo.nZconstraints = nZConstraints; |
1602 |
< |
|
1603 |
< |
zconStamp = globals->getZconStamp(); |
1604 |
< |
ZConsParaItem tempParaItem; |
1599 |
> |
if (globals->haveZconstraintTime()){ |
1600 |
> |
//add sample time of z-constraint into SimInfo's property list |
1601 |
> |
DoubleData* zconsTimeProp = new DoubleData(); |
1602 |
> |
zconsTimeProp->setID(ZCONSTIME_ID); |
1603 |
> |
zconsTimeProp->setData(globals->getZconsTime()); |
1604 |
> |
theInfo.addProperty(zconsTimeProp); |
1605 |
> |
} |
1606 |
> |
else{ |
1607 |
> |
sprintf(painCave.errMsg, |
1608 |
> |
"ZConstraint error: If you use a ZConstraint,\n" |
1609 |
> |
"\tyou must set zconsTime.\n"); |
1610 |
> |
painCave.isFatal = 1; |
1611 |
> |
simError(); |
1612 |
> |
} |
1613 |
|
|
1614 |
< |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1615 |
< |
zconsParaData->setID(ZCONSPARADATA_ID); |
1616 |
< |
|
1617 |
< |
for(int i = 0; i < nZConstraints; i++){ |
1614 |
> |
//push zconsTol into siminfo, if user does not specify |
1615 |
> |
//value for zconsTol, a default value will be used |
1616 |
> |
DoubleData* zconsTol = new DoubleData(); |
1617 |
> |
zconsTol->setID(ZCONSTOL_ID); |
1618 |
> |
if (globals->haveZconsTol()){ |
1619 |
> |
zconsTol->setData(globals->getZconsTol()); |
1620 |
> |
} |
1621 |
> |
else{ |
1622 |
> |
double defaultZConsTol = 0.01; |
1623 |
> |
sprintf(painCave.errMsg, |
1624 |
> |
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1625 |
> |
"\tOOPSE will use a default value of %f.\n" |
1626 |
> |
"\tTo set the tolerance, use the zconsTol variable.\n", |
1627 |
> |
defaultZConsTol); |
1628 |
> |
painCave.isFatal = 0; |
1629 |
> |
simError(); |
1630 |
> |
|
1631 |
> |
zconsTol->setData(defaultZConsTol); |
1632 |
> |
} |
1633 |
> |
theInfo.addProperty(zconsTol); |
1634 |
> |
|
1635 |
> |
//set Force Subtraction Policy |
1636 |
> |
StringData* zconsForcePolicy = new StringData(); |
1637 |
> |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1638 |
> |
|
1639 |
> |
if (globals->haveZconsForcePolicy()){ |
1640 |
> |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1641 |
> |
} |
1642 |
> |
else{ |
1643 |
> |
sprintf(painCave.errMsg, |
1644 |
> |
"ZConstraint Warning: No force subtraction policy was set.\n" |
1645 |
> |
"\tOOPSE will use PolicyByMass.\n" |
1646 |
> |
"\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1647 |
> |
painCave.isFatal = 0; |
1648 |
> |
simError(); |
1649 |
> |
zconsForcePolicy->setData("BYMASS"); |
1650 |
> |
} |
1651 |
> |
|
1652 |
> |
theInfo.addProperty(zconsForcePolicy); |
1653 |
> |
|
1654 |
> |
//Determine the name of ouput file and add it into SimInfo's property list |
1655 |
> |
//Be careful, do not use inFileName, since it is a pointer which |
1656 |
> |
//point to a string at master node, and slave nodes do not contain that string |
1657 |
> |
|
1658 |
> |
string zconsOutput(theInfo.finalName); |
1659 |
> |
|
1660 |
> |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1661 |
> |
|
1662 |
> |
StringData* zconsFilename = new StringData(); |
1663 |
> |
zconsFilename->setID(ZCONSFILENAME_ID); |
1664 |
> |
zconsFilename->setData(zconsOutput); |
1665 |
> |
|
1666 |
> |
theInfo.addProperty(zconsFilename); |
1667 |
> |
|
1668 |
> |
//setup index, pos and other parameters of z-constraint molecules |
1669 |
> |
nZConstraints = globals->getNzConstraints(); |
1670 |
> |
theInfo.nZconstraints = nZConstraints; |
1671 |
> |
|
1672 |
> |
zconStamp = globals->getZconStamp(); |
1673 |
> |
ZConsParaItem tempParaItem; |
1674 |
> |
|
1675 |
> |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1676 |
> |
zconsParaData->setID(ZCONSPARADATA_ID); |
1677 |
> |
|
1678 |
> |
for (int i = 0; i < nZConstraints; i++){ |
1679 |
|
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1680 |
|
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1681 |
|
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1682 |
|
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1683 |
|
|
1684 |
|
zconsParaData->addItem(tempParaItem); |
1685 |
< |
} |
1685 |
> |
} |
1686 |
|
|
1687 |
< |
//sort the parameters by index of molecules |
1688 |
< |
zconsParaData->sortByIndex(); |
1689 |
< |
|
1690 |
< |
//push data into siminfo, therefore, we can retrieve later |
1691 |
< |
theInfo.addProperty(zconsParaData); |
1687 |
> |
//check the uniqueness of index |
1688 |
> |
if(!zconsParaData->isIndexUnique()){ |
1689 |
> |
sprintf(painCave.errMsg, |
1690 |
> |
"ZConstraint Error: molIndex is not unique!\n"); |
1691 |
> |
painCave.isFatal = 1; |
1692 |
> |
simError(); |
1693 |
> |
} |
1694 |
|
|
1695 |
< |
//push zconsTol into siminfo, if user does not specify |
1696 |
< |
//value for zconsTol, a default value will be used |
1697 |
< |
DoubleData* zconsTol = new DoubleData(); |
1698 |
< |
zconsTol->setID(ZCONSTOL_ID); |
1699 |
< |
if(globals->haveZconsTol()){ |
1647 |
< |
zconsTol->setData(globals->getZconsTol()); |
1648 |
< |
} |
1649 |
< |
else{ |
1650 |
< |
double defaultZConsTol = 1E-6; |
1651 |
< |
sprintf( painCave.errMsg, |
1652 |
< |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1653 |
< |
" , default value %f is used.\n", defaultZConsTol); |
1654 |
< |
painCave.isFatal = 0; |
1655 |
< |
simError(); |
1656 |
< |
|
1657 |
< |
zconsTol->setData(defaultZConsTol); |
1658 |
< |
} |
1659 |
< |
theInfo.addProperty(zconsTol); |
1660 |
< |
|
1661 |
< |
//Determine the name of ouput file and add it into SimInfo's property list |
1662 |
< |
//Be careful, do not use inFileName, since it is a pointer which |
1663 |
< |
//point to a string at master node, and slave nodes do not contain that string |
1664 |
< |
|
1665 |
< |
string zconsOutput(theInfo.finalName); |
1666 |
< |
|
1667 |
< |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1668 |
< |
|
1669 |
< |
StringData* zconsFilename = new StringData(); |
1670 |
< |
zconsFilename->setID(ZCONSFILENAME_ID); |
1671 |
< |
zconsFilename->setData(zconsOutput); |
1672 |
< |
|
1673 |
< |
theInfo.addProperty(zconsFilename); |
1695 |
> |
//sort the parameters by index of molecules |
1696 |
> |
zconsParaData->sortByIndex(); |
1697 |
> |
|
1698 |
> |
//push data into siminfo, therefore, we can retrieve later |
1699 |
> |
theInfo.addProperty(zconsParaData); |
1700 |
|
} |