# | Line 1 | Line 1 | |
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1 | < | #include <cstdlib> |
1 | > | #include <algorithm> |
2 | > | #include <stdlib.h> |
3 | #include <iostream> | |
4 | < | #include <cmath> |
5 | < | |
4 | > | #include <math.h> |
5 | > | #include <string> |
6 | > | #include <sprng.h> |
7 | #include "SimSetup.hpp" | |
8 | + | #include "ReadWrite.hpp" |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
12 | + | #include "ConjugateMinimizer.hpp" |
13 | ||
14 | #ifdef IS_MPI | |
15 | #include "mpiBASS.h" | |
# | Line 14 | Line 18 | |
18 | ||
19 | // some defines for ensemble and Forcefield cases | |
20 | ||
21 | < | #define NVE_ENS 0 |
22 | < | #define NVT_ENS 1 |
23 | < | #define NPT_ENS 2 |
21 | > | #define NVE_ENS 0 |
22 | > | #define NVT_ENS 1 |
23 | > | #define NPTi_ENS 2 |
24 | > | #define NPTf_ENS 3 |
25 | > | #define NPTxyz_ENS 4 |
26 | ||
21 | – | #define FF_DUFF 0 |
22 | – | #define FF_LJ 1 |
27 | ||
28 | + | #define FF_DUFF 0 |
29 | + | #define FF_LJ 1 |
30 | + | #define FF_EAM 2 |
31 | + | #define FF_H2O 3 |
32 | ||
33 | + | using namespace std; |
34 | + | |
35 | + | /** |
36 | + | * Check whether dividend is divisble by divisor or not |
37 | + | */ |
38 | + | bool isDivisible(double dividend, double divisor){ |
39 | + | double tolerance = 0.000001; |
40 | + | double quotient; |
41 | + | double diff; |
42 | + | int intQuotient; |
43 | + | |
44 | + | quotient = dividend / divisor; |
45 | + | |
46 | + | if (quotient < 0) |
47 | + | quotient = -quotient; |
48 | + | |
49 | + | intQuotient = int (quotient + tolerance); |
50 | + | |
51 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
52 | + | |
53 | + | if (diff <= tolerance) |
54 | + | return true; |
55 | + | else |
56 | + | return false; |
57 | + | } |
58 | + | |
59 | SimSetup::SimSetup(){ | |
60 | + | |
61 | + | initSuspend = false; |
62 | + | isInfoArray = 0; |
63 | + | nInfo = 1; |
64 | + | |
65 | stamps = new MakeStamps(); | |
66 | globals = new Globals(); | |
67 | < | |
67 | > | |
68 | > | |
69 | #ifdef IS_MPI | |
70 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
70 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
71 | MPIcheckPoint(); | |
72 | #endif // IS_MPI | |
73 | } | |
# | Line 37 | Line 77 | SimSetup::~SimSetup(){ | |
77 | delete globals; | |
78 | } | |
79 | ||
80 | < | void SimSetup::parseFile( char* fileName ){ |
80 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
81 | > | info = the_info; |
82 | > | nInfo = theNinfo; |
83 | > | isInfoArray = 1; |
84 | > | initSuspend = true; |
85 | > | } |
86 | ||
87 | + | |
88 | + | void SimSetup::parseFile(char* fileName){ |
89 | #ifdef IS_MPI | |
90 | < | if( worldRank == 0 ){ |
90 | > | if (worldRank == 0){ |
91 | #endif // is_mpi | |
92 | < | |
92 | > | |
93 | inFileName = fileName; | |
94 | < | set_interface_stamps( stamps, globals ); |
95 | < | |
94 | > | set_interface_stamps(stamps, globals); |
95 | > | |
96 | #ifdef IS_MPI | |
97 | mpiEventInit(); | |
98 | #endif | |
99 | ||
100 | < | yacc_BASS( fileName ); |
100 | > | yacc_BASS(fileName); |
101 | ||
102 | #ifdef IS_MPI | |
103 | throwMPIEvent(NULL); | |
104 | } | |
105 | < | else receiveParse(); |
105 | > | else{ |
106 | > | receiveParse(); |
107 | > | } |
108 | #endif | |
109 | ||
110 | } | |
111 | ||
112 | #ifdef IS_MPI | |
113 | void SimSetup::receiveParse(void){ | |
114 | < | |
115 | < | set_interface_stamps( stamps, globals ); |
116 | < | mpiEventInit(); |
117 | < | MPIcheckPoint(); |
69 | < | mpiEventLoop(); |
70 | < | |
114 | > | set_interface_stamps(stamps, globals); |
115 | > | mpiEventInit(); |
116 | > | MPIcheckPoint(); |
117 | > | mpiEventLoop(); |
118 | } | |
119 | ||
120 | #endif // is_mpi | |
121 | ||
122 | < | void SimSetup::createSim( void ){ |
122 | > | void SimSetup::createSim(void){ |
123 | ||
124 | < | MakeStamps *the_stamps; |
78 | < | Globals* the_globals; |
79 | < | int i, j, k, globalAtomIndex; |
80 | < | |
81 | < | int ensembleCase; |
82 | < | int ffCase; |
83 | < | |
84 | < | ensembleCase = -1; |
85 | < | ffCase = -1; |
124 | > | // gather all of the information from the Bass file |
125 | ||
126 | < | // get the stamps and globals; |
88 | < | the_stamps = stamps; |
89 | < | the_globals = globals; |
126 | > | gatherInfo(); |
127 | ||
128 | < | // set the easy ones first |
92 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
93 | < | simnfo->dt = the_globals->getDt(); |
94 | < | simnfo->run_time = the_globals->getRunTime(); |
128 | > | // creation of complex system objects |
129 | ||
130 | < | // get the ones we know are there, yet still may need some work. |
97 | < | n_components = the_globals->getNComponents(); |
98 | < | strcpy( force_field, the_globals->getForceField() ); |
130 | > | sysObjectsCreation(); |
131 | ||
132 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 | < | else{ |
103 | < | sprintf( painCave.errMsg, |
104 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
105 | < | force_field ); |
106 | < | painCave.isFatal = 1; |
107 | < | simError(); |
108 | < | } |
132 | > | // check on the post processing info |
133 | ||
134 | < | // get the ensemble: |
111 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
134 | > | finalInfoCheck(); |
135 | ||
136 | < | if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
137 | < | else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
138 | < | else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
139 | < | else{ |
140 | < | sprintf( painCave.errMsg, |
141 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
142 | < | "reverting to NVE for this simulation.\n", |
120 | < | ensemble ); |
121 | < | painCave.isFatal = 0; |
122 | < | simError(); |
123 | < | strcpy( ensemble, "NVE" ); |
124 | < | ensembleCase = NVE_ENS; |
136 | > | // initialize the system coordinates |
137 | > | |
138 | > | if ( !initSuspend ){ |
139 | > | initSystemCoords(); |
140 | > | |
141 | > | if( !(globals->getUseInitTime()) ) |
142 | > | info[0].currentTime = 0.0; |
143 | } | |
126 | – | strcpy( simnfo->ensemble, ensemble ); |
144 | ||
145 | + | // make the output filenames |
146 | ||
147 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
130 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
131 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 | < | // if (the_globals->haveTargetPressure()) |
133 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 | < | // else { |
135 | < | // sprintf( painCave.errMsg, |
136 | < | // "SimSetup error: If you use the constant pressure\n" |
137 | < | // " ensemble, you must set targetPressure.\n" |
138 | < | // " This was found in the BASS file.\n"); |
139 | < | // painCave.isFatal = 1; |
140 | < | // simError(); |
141 | < | // } |
147 | > | makeOutNames(); |
148 | ||
149 | < | // if (the_globals->haveTauThermostat()) |
150 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
151 | < | // else if (the_globals->haveQmass()) |
152 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
153 | < | // else { |
154 | < | // sprintf( painCave.errMsg, |
155 | < | // "SimSetup error: If you use one of the constant temperature\n" |
156 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
157 | < | // " Neither of these was found in the BASS file.\n"); |
158 | < | // painCave.isFatal = 1; |
153 | < | // simError(); |
154 | < | // } |
149 | > | if (globals->haveMinimizer()) |
150 | > | // make minimizer |
151 | > | makeMinimizer(); |
152 | > | else |
153 | > | // make the integrator |
154 | > | makeIntegrator(); |
155 | > | |
156 | > | #ifdef IS_MPI |
157 | > | mpiSim->mpiRefresh(); |
158 | > | #endif |
159 | ||
160 | < | // if (the_globals->haveTauBarostat()) |
157 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 | < | // else { |
159 | < | // sprintf( painCave.errMsg, |
160 | < | // "SimSetup error: If you use the constant pressure\n" |
161 | < | // " ensemble, you must set tauBarostat.\n" |
162 | < | // " This was found in the BASS file.\n"); |
163 | < | // painCave.isFatal = 1; |
164 | < | // simError(); |
165 | < | // } |
160 | > | // initialize the Fortran |
161 | ||
162 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
163 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
169 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
162 | > | initFortran(); |
163 | > | } |
164 | ||
171 | – | // if (the_globals->haveTauThermostat()) |
172 | – | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 | – | // else if (the_globals->haveQmass()) |
174 | – | // the_extendedsystem->setQmass(the_globals->getQmass()); |
175 | – | // else { |
176 | – | // sprintf( painCave.errMsg, |
177 | – | // "SimSetup error: If you use one of the constant temperature\n" |
178 | – | // " ensembles, you must set either tauThermostat or qMass.\n" |
179 | – | // " Neither of these was found in the BASS file.\n"); |
180 | – | // painCave.isFatal = 1; |
181 | – | // simError(); |
182 | – | // } |
165 | ||
166 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
167 | < | simnfo->usePBC = the_globals->getPBC(); |
168 | < | |
169 | < | int usesDipoles = 0; |
170 | < | switch( ffCase ){ |
166 | > | void SimSetup::makeMolecules(void){ |
167 | > | int k; |
168 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
169 | > | molInit molInfo; |
170 | > | DirectionalAtom* dAtom; |
171 | > | LinkedAssign* extras; |
172 | > | LinkedAssign* current_extra; |
173 | > | AtomStamp* currentAtom; |
174 | > | BondStamp* currentBond; |
175 | > | BendStamp* currentBend; |
176 | > | TorsionStamp* currentTorsion; |
177 | ||
178 | < | case FF_DUFF: |
179 | < | the_ff = new DUFF(); |
180 | < | usesDipoles = 1; |
193 | < | break; |
178 | > | bond_pair* theBonds; |
179 | > | bend_set* theBends; |
180 | > | torsion_set* theTorsions; |
181 | ||
182 | < | case FF_LJ: |
196 | < | the_ff = LJFF(); |
197 | < | break; |
182 | > | //init the forceField paramters |
183 | ||
184 | < | default: |
200 | < | sprintf( painCave.errMsg, |
201 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
202 | < | painCave.isFatal = 1; |
203 | < | simError(); |
204 | < | } |
184 | > | the_ff->readParams(); |
185 | ||
206 | – | #ifdef IS_MPI |
207 | – | strcpy( checkPointMsg, "ForceField creation successful" ); |
208 | – | MPIcheckPoint(); |
209 | – | #endif // is_mpi |
186 | ||
187 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
212 | < | the_components = the_globals->getComponents(); |
213 | < | components_nmol = new int[n_components]; |
214 | < | comp_stamps = new MoleculeStamp*[n_components]; |
187 | > | // init the atoms |
188 | ||
189 | < | if( !the_globals->haveNMol() ){ |
190 | < | // we don't have the total number of molecules, so we assume it is |
191 | < | // given in each component |
189 | > | double phi, theta, psi; |
190 | > | double sux, suy, suz; |
191 | > | double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
192 | > | double ux, uy, uz, u, uSqr; |
193 | ||
194 | < | tot_nmol = 0; |
195 | < | for( i=0; i<n_components; i++ ){ |
194 | > | for (k = 0; k < nInfo; k++){ |
195 | > | the_ff->setSimInfo(&(info[k])); |
196 | ||
197 | < | if( !the_components[i]->haveNMol() ){ |
198 | < | // we have a problem |
199 | < | sprintf( painCave.errMsg, |
200 | < | "SimSetup Error. No global NMol or component NMol" |
201 | < | " given. Cannot calculate the number of atoms.\n" ); |
202 | < | painCave.isFatal = 1; |
203 | < | simError(); |
204 | < | } |
197 | > | atomOffset = 0; |
198 | > | excludeOffset = 0; |
199 | > | for (i = 0; i < info[k].n_mol; i++){ |
200 | > | stampID = info[k].molecules[i].getStampID(); |
201 | > | |
202 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
203 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
204 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
205 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
206 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
207 | > | |
208 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
209 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
210 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
211 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
212 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
213 | > | |
214 | > | theBonds = new bond_pair[molInfo.nBonds]; |
215 | > | theBends = new bend_set[molInfo.nBends]; |
216 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
217 | ||
218 | < | tot_nmol += the_components[i]->getNMol(); |
233 | < | components_nmol[i] = the_components[i]->getNMol(); |
234 | < | } |
235 | < | } |
236 | < | else{ |
237 | < | sprintf( painCave.errMsg, |
238 | < | "SimSetup error.\n" |
239 | < | "\tSorry, the ability to specify total" |
240 | < | " nMols and then give molfractions in the components\n" |
241 | < | "\tis not currently supported." |
242 | < | " Please give nMol in the components.\n" ); |
243 | < | painCave.isFatal = 1; |
244 | < | simError(); |
245 | < | |
246 | < | |
247 | < | // tot_nmol = the_globals->getNMol(); |
248 | < | |
249 | < | // //we have the total number of molecules, now we check for molfractions |
250 | < | // for( i=0; i<n_components; i++ ){ |
251 | < | |
252 | < | // if( !the_components[i]->haveMolFraction() ){ |
253 | < | |
254 | < | // if( !the_components[i]->haveNMol() ){ |
255 | < | // //we have a problem |
256 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
257 | < | // << " nMol was given in component |
258 | < | |
259 | < | } |
218 | > | // make the Atoms |
219 | ||
220 | < | #ifdef IS_MPI |
221 | < | strcpy( checkPointMsg, "Have the number of components" ); |
222 | < | MPIcheckPoint(); |
223 | < | #endif // is_mpi |
220 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
221 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
222 | > | if (currentAtom->haveOrientation()){ |
223 | > | dAtom = new DirectionalAtom((j + atomOffset), |
224 | > | info[k].getConfiguration()); |
225 | > | info[k].n_oriented++; |
226 | > | molInfo.myAtoms[j] = dAtom; |
227 | ||
228 | < | // make an array of molecule stamps that match the components used. |
229 | < | // also extract the used stamps out into a separate linked list |
228 | > | // Directional Atoms have standard unit vectors which are oriented |
229 | > | // in space using the three Euler angles. We assume the standard |
230 | > | // unit vector was originally along the z axis below. |
231 | ||
232 | < | simnfo->nComponents = n_components; |
233 | < | simnfo->componentsNmol = components_nmol; |
234 | < | simnfo->compStamps = comp_stamps; |
235 | < | simnfo->headStamp = new LinkedMolStamp(); |
236 | < | |
237 | < | char* id; |
238 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
239 | < | LinkedMolStamp* currentStamp = NULL; |
240 | < | for( i=0; i<n_components; i++ ){ |
232 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
233 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
234 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
235 | > | |
236 | > | Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
237 | > | Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
238 | > | Axz = sin(theta) * sin(psi); |
239 | > | |
240 | > | Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
241 | > | Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
242 | > | Ayz = sin(theta) * cos(psi); |
243 | > | |
244 | > | Azx = sin(phi) * sin(theta); |
245 | > | Azy = -cos(phi) * sin(theta); |
246 | > | Azz = cos(theta); |
247 | ||
248 | < | id = the_components[i]->getType(); |
249 | < | comp_stamps[i] = NULL; |
250 | < | |
282 | < | // check to make sure the component isn't already in the list |
248 | > | sux = 0.0; |
249 | > | suy = 0.0; |
250 | > | suz = 1.0; |
251 | ||
252 | < | comp_stamps[i] = headStamp->match( id ); |
253 | < | if( comp_stamps[i] == NULL ){ |
254 | < | |
287 | < | // extract the component from the list; |
288 | < | |
289 | < | currentStamp = the_stamps->extractMolStamp( id ); |
290 | < | if( currentStamp == NULL ){ |
291 | < | sprintf( painCave.errMsg, |
292 | < | "SimSetup error: Component \"%s\" was not found in the " |
293 | < | "list of declared molecules\n", |
294 | < | id ); |
295 | < | painCave.isFatal = 1; |
296 | < | simError(); |
297 | < | } |
298 | < | |
299 | < | headStamp->add( currentStamp ); |
300 | < | comp_stamps[i] = headStamp->match( id ); |
301 | < | } |
302 | < | } |
252 | > | ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
253 | > | uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
254 | > | uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
255 | ||
256 | < | #ifdef IS_MPI |
305 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
306 | < | MPIcheckPoint(); |
307 | < | #endif // is_mpi |
308 | < | |
256 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
257 | ||
258 | + | u = sqrt(uSqr); |
259 | + | ux = ux / u; |
260 | + | uy = uy / u; |
261 | + | uz = uz / u; |
262 | ||
263 | + | dAtom->setSUx(ux); |
264 | + | dAtom->setSUy(uy); |
265 | + | dAtom->setSUz(uz); |
266 | + | } |
267 | + | else{ |
268 | + | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
269 | + | info[k].getConfiguration()); |
270 | + | } |
271 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
272 | ||
312 | – | // caclulate the number of atoms, bonds, bends and torsions |
313 | – | |
314 | – | tot_atoms = 0; |
315 | – | tot_bonds = 0; |
316 | – | tot_bends = 0; |
317 | – | tot_torsions = 0; |
318 | – | for( i=0; i<n_components; i++ ){ |
319 | – | |
320 | – | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
321 | – | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
322 | – | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
323 | – | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
324 | – | } |
325 | – | |
326 | – | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
327 | – | |
328 | – | simnfo->n_atoms = tot_atoms; |
329 | – | simnfo->n_bonds = tot_bonds; |
330 | – | simnfo->n_bends = tot_bends; |
331 | – | simnfo->n_torsions = tot_torsions; |
332 | – | simnfo->n_SRI = tot_SRI; |
333 | – | simnfo->n_mol = tot_nmol; |
334 | – | |
335 | – | simnfo->molMembershipArray = new int[tot_atoms]; |
336 | – | |
273 | #ifdef IS_MPI | |
274 | ||
275 | < | // divide the molecules among processors here. |
340 | < | |
341 | < | mpiSim = new mpiSimulation( simnfo ); |
342 | < | |
343 | < | globalIndex = mpiSim->divideLabor(); |
275 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
276 | ||
277 | < | // set up the local variables |
278 | < | |
347 | < | int localMol, allMol; |
348 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
277 | > | #endif // is_mpi |
278 | > | } |
279 | ||
280 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
281 | < | int* molCompType = mpiSim->getMolComponentType(); |
282 | < | |
283 | < | allMol = 0; |
284 | < | localMol = 0; |
355 | < | local_atoms = 0; |
356 | < | local_bonds = 0; |
357 | < | local_bends = 0; |
358 | < | local_torsions = 0; |
359 | < | globalAtomIndex = 0; |
280 | > | // make the bonds |
281 | > | for (j = 0; j < molInfo.nBonds; j++){ |
282 | > | currentBond = comp_stamps[stampID]->getBond(j); |
283 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
284 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
285 | ||
286 | + | exI = theBonds[j].a; |
287 | + | exJ = theBonds[j].b; |
288 | ||
289 | < | for( i=0; i<n_components; i++ ){ |
289 | > | // exclude_I must always be the smaller of the pair |
290 | > | if (exI > exJ){ |
291 | > | tempEx = exI; |
292 | > | exI = exJ; |
293 | > | exJ = tempEx; |
294 | > | } |
295 | > | #ifdef IS_MPI |
296 | > | tempEx = exI; |
297 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
298 | > | tempEx = exJ; |
299 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
300 | ||
301 | < | for( j=0; j<components_nmol[i]; j++ ){ |
302 | < | |
303 | < | if( mol2proc[allMol] == worldRank ){ |
304 | < | |
305 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
369 | < | local_bonds += comp_stamps[i]->getNBonds(); |
370 | < | local_bends += comp_stamps[i]->getNBends(); |
371 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
372 | < | localMol++; |
373 | < | } |
374 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 | < | globalAtomIndex++; |
301 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
302 | > | #else // isn't MPI |
303 | > | |
304 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
305 | > | #endif //is_mpi |
306 | } | |
307 | + | excludeOffset += molInfo.nBonds; |
308 | ||
309 | < | allMol++; |
310 | < | } |
311 | < | } |
312 | < | local_SRI = local_bonds + local_bends + local_torsions; |
313 | < | |
314 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 | < | |
386 | < | if( local_atoms != simnfo->n_atoms ){ |
387 | < | sprintf( painCave.errMsg, |
388 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 | < | " localAtom (%d) are not equal.\n", |
390 | < | simnfo->n_atoms, |
391 | < | local_atoms ); |
392 | < | painCave.isFatal = 1; |
393 | < | simError(); |
394 | < | } |
309 | > | //make the bends |
310 | > | for (j = 0; j < molInfo.nBends; j++){ |
311 | > | currentBend = comp_stamps[stampID]->getBend(j); |
312 | > | theBends[j].a = currentBend->getA() + atomOffset; |
313 | > | theBends[j].b = currentBend->getB() + atomOffset; |
314 | > | theBends[j].c = currentBend->getC() + atomOffset; |
315 | ||
316 | < | simnfo->n_bonds = local_bonds; |
317 | < | simnfo->n_bends = local_bends; |
318 | < | simnfo->n_torsions = local_torsions; |
399 | < | simnfo->n_SRI = local_SRI; |
400 | < | simnfo->n_mol = localMol; |
316 | > | if (currentBend->haveExtras()){ |
317 | > | extras = currentBend->getExtras(); |
318 | > | current_extra = extras; |
319 | ||
320 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
321 | < | MPIcheckPoint(); |
322 | < | |
323 | < | |
324 | < | #endif // is_mpi |
325 | < | |
320 | > | while (current_extra != NULL){ |
321 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
322 | > | switch (current_extra->getType()){ |
323 | > | case 0: |
324 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
325 | > | theBends[j].isGhost = 1; |
326 | > | break; |
327 | ||
328 | < | // create the atom and short range interaction arrays |
329 | < | |
330 | < | Atom::createArrays(simnfo->n_atoms); |
331 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
332 | < | the_molecules = new Molecule[simnfo->n_mol]; |
414 | < | int molIndex; |
415 | < | |
416 | < | // initialize the molecule's stampID's |
328 | > | case 1: |
329 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
330 | > | 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 | + | else{ |
345 | + | sprintf(painCave.errMsg, |
346 | + | "SimSetup Error: unhandled bend assignment:\n" |
347 | + | " -->%s in Bend[%d] in %s\n", |
348 | + | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
349 | + | painCave.isFatal = 1; |
350 | + | simError(); |
351 | + | } |
352 | + | |
353 | + | current_extra = current_extra->getNext(); |
354 | + | } |
355 | + | } |
356 | + | |
357 | + | if (!theBends[j].isGhost){ |
358 | + | exI = theBends[j].a; |
359 | + | exJ = theBends[j].c; |
360 | + | } |
361 | + | else{ |
362 | + | exI = theBends[j].a; |
363 | + | exJ = theBends[j].b; |
364 | + | } |
365 | + | |
366 | + | // exclude_I must always be the smaller of the pair |
367 | + | if (exI > exJ){ |
368 | + | tempEx = exI; |
369 | + | exI = exJ; |
370 | + | exJ = tempEx; |
371 | + | } |
372 | #ifdef IS_MPI | |
373 | < | |
373 | > | tempEx = exI; |
374 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 | > | tempEx = exJ; |
376 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
377 | ||
378 | < | molIndex = 0; |
379 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
380 | < | |
381 | < | if(mol2proc[i] == worldRank ){ |
382 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
383 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
427 | < | the_molecules[molIndex].setGlobalIndex( i ); |
428 | < | molIndex++; |
429 | < | } |
430 | < | } |
378 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
379 | > | #else // isn't MPI |
380 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
381 | > | #endif //is_mpi |
382 | > | } |
383 | > | excludeOffset += molInfo.nBends; |
384 | ||
385 | < | #else // is_mpi |
386 | < | |
387 | < | molIndex = 0; |
388 | < | globalAtomIndex = 0; |
389 | < | for(i=0; i<n_components; i++){ |
390 | < | for(j=0; j<components_nmol[i]; j++ ){ |
391 | < | the_molecules[molIndex].setStampID( i ); |
392 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
393 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
394 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
395 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
396 | < | globalAtomIndex++; |
385 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
386 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
387 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
388 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
389 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
390 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
391 | > | |
392 | > | exI = theTorsions[j].a; |
393 | > | exJ = theTorsions[j].d; |
394 | > | |
395 | > | // exclude_I must always be the smaller of the pair |
396 | > | if (exI > exJ){ |
397 | > | tempEx = exI; |
398 | > | exI = exJ; |
399 | > | exJ = tempEx; |
400 | > | } |
401 | > | #ifdef IS_MPI |
402 | > | tempEx = exI; |
403 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
404 | > | tempEx = exJ; |
405 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
406 | > | |
407 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
408 | > | #else // isn't MPI |
409 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
410 | > | #endif //is_mpi |
411 | } | |
412 | < | molIndex++; |
412 | > | excludeOffset += molInfo.nTorsions; |
413 | > | |
414 | > | |
415 | > | // send the arrays off to the forceField for init. |
416 | > | |
417 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
418 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
419 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
420 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
421 | > | theTorsions); |
422 | > | |
423 | > | |
424 | > | info[k].molecules[i].initialize(molInfo); |
425 | > | |
426 | > | |
427 | > | atomOffset += molInfo.nAtoms; |
428 | > | delete[] theBonds; |
429 | > | delete[] theBends; |
430 | > | delete[] theTorsions; |
431 | } | |
432 | } | |
448 | – | |
433 | ||
434 | + | #ifdef IS_MPI |
435 | + | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
436 | + | MPIcheckPoint(); |
437 | #endif // is_mpi | |
438 | ||
439 | + | // clean up the forcefield |
440 | ||
441 | < | if( simnfo->n_SRI ){ |
442 | < | |
443 | < | Exclude::createArray(simnfo->n_SRI); |
456 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
457 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 | < | simnfo->globalExcludes = new int; |
459 | < | simnfo->n_exclude = simnfo->n_SRI; |
460 | < | } |
461 | < | else{ |
462 | < | |
463 | < | Exclude::createArray( 1 ); |
464 | < | the_excludes = new Exclude*; |
465 | < | the_excludes[0] = new Exclude(0); |
466 | < | the_excludes[0]->setPair( 0,0 ); |
467 | < | simnfo->globalExcludes = new int; |
468 | < | simnfo->globalExcludes[0] = 0; |
469 | < | simnfo->n_exclude = 0; |
470 | < | } |
441 | > | the_ff->calcRcut(); |
442 | > | the_ff->cleanMe(); |
443 | > | } |
444 | ||
445 | < | // set the arrays into the SimInfo object |
445 | > | void SimSetup::initFromBass(void){ |
446 | > | int i, j, k; |
447 | > | int n_cells; |
448 | > | double cellx, celly, cellz; |
449 | > | double temp1, temp2, temp3; |
450 | > | int n_per_extra; |
451 | > | int n_extra; |
452 | > | int have_extra, done; |
453 | ||
454 | < | simnfo->atoms = the_atoms; |
455 | < | simnfo->molecules = the_molecules; |
456 | < | simnfo->nGlobalExcludes = 0; |
457 | < | simnfo->excludes = the_excludes; |
454 | > | double vel[3]; |
455 | > | vel[0] = 0.0; |
456 | > | vel[1] = 0.0; |
457 | > | vel[2] = 0.0; |
458 | ||
459 | + | temp1 = (double) tot_nmol / 4.0; |
460 | + | temp2 = pow(temp1, (1.0 / 3.0)); |
461 | + | temp3 = ceil(temp2); |
462 | ||
463 | < | // get some of the tricky things that may still be in the globals |
463 | > | have_extra = 0; |
464 | > | if (temp2 < temp3){ |
465 | > | // we have a non-complete lattice |
466 | > | have_extra = 1; |
467 | ||
468 | < | |
469 | < | if( the_globals->haveBox() ){ |
470 | < | simnfo->box_x = the_globals->getBox(); |
471 | < | simnfo->box_y = the_globals->getBox(); |
472 | < | simnfo->box_z = the_globals->getBox(); |
473 | < | } |
474 | < | else if( the_globals->haveDensity() ){ |
468 | > | n_cells = (int) temp3 - 1; |
469 | > | cellx = info[0].boxL[0] / temp3; |
470 | > | celly = info[0].boxL[1] / temp3; |
471 | > | cellz = info[0].boxL[2] / temp3; |
472 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
473 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
474 | > | n_per_extra = (int) ceil(temp1); |
475 | ||
476 | < | double vol; |
477 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
478 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
479 | < | simnfo->box_y = simnfo->box_x; |
494 | < | simnfo->box_z = simnfo->box_x; |
495 | < | } |
496 | < | else{ |
497 | < | if( !the_globals->haveBoxX() ){ |
498 | < | sprintf( painCave.errMsg, |
499 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
476 | > | if (n_per_extra > 4){ |
477 | > | sprintf(painCave.errMsg, |
478 | > | "SimSetup error. There has been an error in constructing" |
479 | > | " the non-complete lattice.\n"); |
480 | painCave.isFatal = 1; | |
481 | simError(); | |
482 | } | |
483 | < | simnfo->box_x = the_globals->getBoxX(); |
483 | > | } |
484 | > | else{ |
485 | > | n_cells = (int) temp3; |
486 | > | cellx = info[0].boxL[0] / temp3; |
487 | > | celly = info[0].boxL[1] / temp3; |
488 | > | cellz = info[0].boxL[2] / temp3; |
489 | > | } |
490 | ||
491 | < | if( !the_globals->haveBoxY() ){ |
492 | < | sprintf( painCave.errMsg, |
493 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
494 | < | painCave.isFatal = 1; |
509 | < | simError(); |
510 | < | } |
511 | < | simnfo->box_y = the_globals->getBoxY(); |
491 | > | current_mol = 0; |
492 | > | current_comp_mol = 0; |
493 | > | current_comp = 0; |
494 | > | current_atom_ndx = 0; |
495 | ||
496 | < | if( !the_globals->haveBoxZ() ){ |
497 | < | sprintf( painCave.errMsg, |
498 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
499 | < | painCave.isFatal = 1; |
500 | < | simError(); |
496 | > | for (i = 0; i < n_cells ; i++){ |
497 | > | for (j = 0; j < n_cells; j++){ |
498 | > | for (k = 0; k < n_cells; k++){ |
499 | > | makeElement(i * cellx, j * celly, k * cellz); |
500 | > | |
501 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
502 | > | |
503 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
504 | > | |
505 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
506 | > | } |
507 | } | |
519 | – | simnfo->box_z = the_globals->getBoxZ(); |
508 | } | |
509 | ||
510 | < | #ifdef IS_MPI |
511 | < | strcpy( checkPointMsg, "Box size set up" ); |
524 | < | MPIcheckPoint(); |
525 | < | #endif // is_mpi |
510 | > | if (have_extra){ |
511 | > | done = 0; |
512 | ||
513 | + | int start_ndx; |
514 | + | for (i = 0; i < (n_cells + 1) && !done; i++){ |
515 | + | for (j = 0; j < (n_cells + 1) && !done; j++){ |
516 | + | if (i < n_cells){ |
517 | + | if (j < n_cells){ |
518 | + | start_ndx = n_cells; |
519 | + | } |
520 | + | else |
521 | + | start_ndx = 0; |
522 | + | } |
523 | + | else |
524 | + | start_ndx = 0; |
525 | ||
526 | < | // initialize the arrays |
526 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
527 | > | makeElement(i * cellx, j * celly, k * cellz); |
528 | > | done = (current_mol >= tot_nmol); |
529 | ||
530 | < | the_ff->setSimInfo( simnfo ); |
530 | > | if (!done && n_per_extra > 1){ |
531 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
532 | > | k * cellz); |
533 | > | done = (current_mol >= tot_nmol); |
534 | > | } |
535 | ||
536 | < | makeMolecules(); |
537 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
538 | < | for(i=0; i<simnfo->n_atoms; i++){ |
539 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
540 | < | } |
537 | < | |
538 | < | if (the_globals->getUseRF() ) { |
539 | < | simnfo->useReactionField = 1; |
540 | < | |
541 | < | if( !the_globals->haveECR() ){ |
542 | < | sprintf( painCave.errMsg, |
543 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
544 | < | "box length for the electrostaticCutoffRadius.\n" |
545 | < | "I hope you have a very fast processor!\n"); |
546 | < | painCave.isFatal = 0; |
547 | < | simError(); |
548 | < | double smallest; |
549 | < | smallest = simnfo->box_x; |
550 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
551 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
552 | < | simnfo->ecr = 0.5 * smallest; |
553 | < | } else { |
554 | < | simnfo->ecr = the_globals->getECR(); |
555 | < | } |
536 | > | if (!done && n_per_extra > 2){ |
537 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
538 | > | k * cellz + 0.5 * cellz); |
539 | > | done = (current_mol >= tot_nmol); |
540 | > | } |
541 | ||
542 | < | if( !the_globals->haveEST() ){ |
543 | < | sprintf( painCave.errMsg, |
544 | < | "SimSetup Warning: using default value of 0.05 * the " |
545 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
546 | < | ); |
547 | < | painCave.isFatal = 0; |
548 | < | simError(); |
564 | < | simnfo->est = 0.05 * simnfo->ecr; |
565 | < | } else { |
566 | < | simnfo->est = the_globals->getEST(); |
542 | > | if (!done && n_per_extra > 3){ |
543 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
544 | > | k * cellz + 0.5 * cellz); |
545 | > | done = (current_mol >= tot_nmol); |
546 | > | } |
547 | > | } |
548 | > | } |
549 | } | |
550 | < | |
551 | < | if(!the_globals->haveDielectric() ){ |
552 | < | sprintf( painCave.errMsg, |
553 | < | "SimSetup Error: You are trying to use Reaction Field without" |
554 | < | "setting a dielectric constant!\n" |
555 | < | ); |
550 | > | } |
551 | > | |
552 | > | for (i = 0; i < info[0].n_atoms; i++){ |
553 | > | info[0].atoms[i]->setVel(vel); |
554 | > | } |
555 | > | } |
556 | > | |
557 | > | void SimSetup::makeElement(double x, double y, double z){ |
558 | > | int k; |
559 | > | AtomStamp* current_atom; |
560 | > | DirectionalAtom* dAtom; |
561 | > | double rotMat[3][3]; |
562 | > | double pos[3]; |
563 | > | |
564 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
565 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
566 | > | if (!current_atom->havePosition()){ |
567 | > | sprintf(painCave.errMsg, |
568 | > | "SimSetup:initFromBass error.\n" |
569 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
570 | > | "\tThe initialization routine is unable to give a start" |
571 | > | " position.\n", |
572 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
573 | painCave.isFatal = 1; | |
574 | simError(); | |
575 | } | |
576 | < | simnfo->dielectric = the_globals->getDielectric(); |
577 | < | } else { |
578 | < | if (usesDipoles) { |
579 | < | |
580 | < | if( !the_globals->haveECR() ){ |
581 | < | sprintf( painCave.errMsg, |
582 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
583 | < | "box length for the electrostaticCutoffRadius.\n" |
584 | < | "I hope you have a very fast processor!\n"); |
585 | < | painCave.isFatal = 0; |
586 | < | simError(); |
587 | < | double smallest; |
588 | < | smallest = simnfo->box_x; |
589 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
590 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
591 | < | simnfo->ecr = 0.5 * smallest; |
592 | < | } else { |
593 | < | simnfo->ecr = the_globals->getECR(); |
594 | < | } |
595 | < | |
596 | < | if( !the_globals->haveEST() ){ |
597 | < | sprintf( painCave.errMsg, |
598 | < | "SimSetup Warning: using default value of 5%% of the " |
600 | < | "electrostaticCutoffRadius for the " |
601 | < | "electrostaticSkinThickness\n" |
602 | < | ); |
603 | < | painCave.isFatal = 0; |
604 | < | simError(); |
605 | < | simnfo->est = 0.05 * simnfo->ecr; |
606 | < | } else { |
607 | < | simnfo->est = the_globals->getEST(); |
608 | < | } |
576 | > | |
577 | > | pos[0] = x + current_atom->getPosX(); |
578 | > | pos[1] = y + current_atom->getPosY(); |
579 | > | pos[2] = z + current_atom->getPosZ(); |
580 | > | |
581 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
582 | > | |
583 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
584 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
585 | > | |
586 | > | rotMat[0][0] = 1.0; |
587 | > | rotMat[0][1] = 0.0; |
588 | > | rotMat[0][2] = 0.0; |
589 | > | |
590 | > | rotMat[1][0] = 0.0; |
591 | > | rotMat[1][1] = 1.0; |
592 | > | rotMat[1][2] = 0.0; |
593 | > | |
594 | > | rotMat[2][0] = 0.0; |
595 | > | rotMat[2][1] = 0.0; |
596 | > | rotMat[2][2] = 1.0; |
597 | > | |
598 | > | dAtom->setA(rotMat); |
599 | } | |
610 | – | } |
600 | ||
601 | < | #ifdef IS_MPI |
602 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
614 | < | MPIcheckPoint(); |
615 | < | #endif // is_mpi |
601 | > | current_atom_ndx++; |
602 | > | } |
603 | ||
604 | < | if( the_globals->haveInitialConfig() ){ |
605 | < | |
619 | < | InitializeFromFile* fileInit; |
620 | < | #ifdef IS_MPI // is_mpi |
621 | < | if( worldRank == 0 ){ |
622 | < | #endif //is_mpi |
623 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
624 | < | #ifdef IS_MPI |
625 | < | }else fileInit = new InitializeFromFile( NULL ); |
626 | < | #endif |
627 | < | fileInit->read_xyz( simnfo ); // default velocities on |
604 | > | current_mol++; |
605 | > | current_comp_mol++; |
606 | ||
607 | < | delete fileInit; |
608 | < | } |
609 | < | else{ |
607 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
608 | > | current_comp_mol = 0; |
609 | > | current_comp++; |
610 | > | } |
611 | > | } |
612 | ||
633 | – | #ifdef IS_MPI |
613 | ||
614 | < | // no init from bass |
615 | < | |
637 | < | sprintf( painCave.errMsg, |
638 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
639 | < | painCave.isFatal; |
640 | < | simError(); |
641 | < | |
642 | < | #else |
614 | > | void SimSetup::gatherInfo(void){ |
615 | > | int i; |
616 | ||
617 | < | initFromBass(); |
617 | > | ensembleCase = -1; |
618 | > | ffCase = -1; |
619 | ||
620 | + | // set the easy ones first |
621 | ||
622 | < | #endif |
623 | < | } |
622 | > | for (i = 0; i < nInfo; i++){ |
623 | > | info[i].target_temp = globals->getTargetTemp(); |
624 | > | info[i].dt = globals->getDt(); |
625 | > | info[i].run_time = globals->getRunTime(); |
626 | > | } |
627 | > | n_components = globals->getNComponents(); |
628 | ||
650 | – | #ifdef IS_MPI |
651 | – | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
652 | – | MPIcheckPoint(); |
653 | – | #endif // is_mpi |
629 | ||
630 | + | // get the forceField |
631 | ||
632 | < | |
657 | < | |
658 | < | |
632 | > | strcpy(force_field, globals->getForceField()); |
633 | ||
634 | < | |
635 | < | #ifdef IS_MPI |
662 | < | if( worldRank == 0 ){ |
663 | < | #endif // is_mpi |
664 | < | |
665 | < | if( the_globals->haveFinalConfig() ){ |
666 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
667 | < | } |
668 | < | else{ |
669 | < | strcpy( simnfo->finalName, inFileName ); |
670 | < | char* endTest; |
671 | < | int nameLength = strlen( simnfo->finalName ); |
672 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
673 | < | if( !strcmp( endTest, ".bass" ) ){ |
674 | < | strcpy( endTest, ".eor" ); |
675 | < | } |
676 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
677 | < | strcpy( endTest, ".eor" ); |
678 | < | } |
679 | < | else{ |
680 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
681 | < | if( !strcmp( endTest, ".bss" ) ){ |
682 | < | strcpy( endTest, ".eor" ); |
683 | < | } |
684 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
685 | < | strcpy( endTest, ".eor" ); |
686 | < | } |
687 | < | else{ |
688 | < | strcat( simnfo->finalName, ".eor" ); |
689 | < | } |
690 | < | } |
691 | < | } |
692 | < | |
693 | < | // make the sample and status out names |
694 | < | |
695 | < | strcpy( simnfo->sampleName, inFileName ); |
696 | < | char* endTest; |
697 | < | int nameLength = strlen( simnfo->sampleName ); |
698 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
699 | < | if( !strcmp( endTest, ".bass" ) ){ |
700 | < | strcpy( endTest, ".dump" ); |
701 | < | } |
702 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
703 | < | strcpy( endTest, ".dump" ); |
704 | < | } |
705 | < | else{ |
706 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
707 | < | if( !strcmp( endTest, ".bss" ) ){ |
708 | < | strcpy( endTest, ".dump" ); |
709 | < | } |
710 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
711 | < | strcpy( endTest, ".dump" ); |
712 | < | } |
713 | < | else{ |
714 | < | strcat( simnfo->sampleName, ".dump" ); |
715 | < | } |
716 | < | } |
717 | < | |
718 | < | strcpy( simnfo->statusName, inFileName ); |
719 | < | nameLength = strlen( simnfo->statusName ); |
720 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
721 | < | if( !strcmp( endTest, ".bass" ) ){ |
722 | < | strcpy( endTest, ".stat" ); |
723 | < | } |
724 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
725 | < | strcpy( endTest, ".stat" ); |
726 | < | } |
727 | < | else{ |
728 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
729 | < | if( !strcmp( endTest, ".bss" ) ){ |
730 | < | strcpy( endTest, ".stat" ); |
731 | < | } |
732 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
733 | < | strcpy( endTest, ".stat" ); |
734 | < | } |
735 | < | else{ |
736 | < | strcat( simnfo->statusName, ".stat" ); |
737 | < | } |
738 | < | } |
739 | < | |
740 | < | #ifdef IS_MPI |
634 | > | if (!strcasecmp(force_field, "DUFF")){ |
635 | > | ffCase = FF_DUFF; |
636 | } | |
637 | < | #endif // is_mpi |
638 | < | |
744 | < | // set the status, sample, and themal kick times |
745 | < | |
746 | < | if( the_globals->haveSampleTime() ){ |
747 | < | simnfo->sampleTime = the_globals->getSampleTime(); |
748 | < | simnfo->statusTime = simnfo->sampleTime; |
749 | < | simnfo->thermalTime = simnfo->sampleTime; |
637 | > | else if (!strcasecmp(force_field, "LJ")){ |
638 | > | ffCase = FF_LJ; |
639 | } | |
640 | < | else{ |
641 | < | simnfo->sampleTime = the_globals->getRunTime(); |
753 | < | simnfo->statusTime = simnfo->sampleTime; |
754 | < | simnfo->thermalTime = simnfo->sampleTime; |
640 | > | else if (!strcasecmp(force_field, "EAM")){ |
641 | > | ffCase = FF_EAM; |
642 | } | |
643 | < | |
644 | < | if( the_globals->haveStatusTime() ){ |
758 | < | simnfo->statusTime = the_globals->getStatusTime(); |
643 | > | else if (!strcasecmp(force_field, "WATER")){ |
644 | > | ffCase = FF_H2O; |
645 | } | |
646 | < | |
647 | < | if( the_globals->haveThermalTime() ){ |
648 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
646 | > | else{ |
647 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
648 | > | force_field); |
649 | > | painCave.isFatal = 1; |
650 | > | simError(); |
651 | } | |
652 | ||
653 | < | // check for the temperature set flag |
653 | > | // get the ensemble |
654 | ||
655 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
655 | > | strcpy(ensemble, globals->getEnsemble()); |
656 | ||
657 | + | if (!strcasecmp(ensemble, "NVE")){ |
658 | + | ensembleCase = NVE_ENS; |
659 | + | } |
660 | + | else if (!strcasecmp(ensemble, "NVT")){ |
661 | + | ensembleCase = NVT_ENS; |
662 | + | } |
663 | + | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
664 | + | ensembleCase = NPTi_ENS; |
665 | + | } |
666 | + | else if (!strcasecmp(ensemble, "NPTf")){ |
667 | + | ensembleCase = NPTf_ENS; |
668 | + | } |
669 | + | else if (!strcasecmp(ensemble, "NPTxyz")){ |
670 | + | ensembleCase = NPTxyz_ENS; |
671 | + | } |
672 | + | else{ |
673 | + | sprintf(painCave.errMsg, |
674 | + | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
675 | + | "\treverting to NVE for this simulation.\n", |
676 | + | ensemble); |
677 | + | painCave.isFatal = 0; |
678 | + | simError(); |
679 | + | strcpy(ensemble, "NVE"); |
680 | + | ensembleCase = NVE_ENS; |
681 | + | } |
682 | ||
683 | < | // make the integrator |
683 | > | for (i = 0; i < nInfo; i++){ |
684 | > | strcpy(info[i].ensemble, ensemble); |
685 | ||
686 | + | // get the mixing rule |
687 | ||
688 | < | if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
689 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
688 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
689 | > | info[i].usePBC = globals->getPBC(); |
690 | } | |
776 | – | else if( !strcmp( force_field, "LJ" ) ){ |
777 | – | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
778 | – | } |
691 | ||
692 | < | #ifdef IS_MPI |
781 | < | mpiSim->mpiRefresh(); |
782 | < | #endif |
692 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
693 | ||
694 | < | // initialize the Fortran |
694 | > | the_components = globals->getComponents(); |
695 | > | components_nmol = new int[n_components]; |
696 | ||
697 | ||
698 | < | simnfo->refreshSim(); |
699 | < | |
700 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
701 | < | the_ff->initForceField( LB_MIXING_RULE ); |
698 | > | if (!globals->haveNMol()){ |
699 | > | // we don't have the total number of molecules, so we assume it is |
700 | > | // given in each component |
701 | > | |
702 | > | tot_nmol = 0; |
703 | > | for (i = 0; i < n_components; i++){ |
704 | > | if (!the_components[i]->haveNMol()){ |
705 | > | // we have a problem |
706 | > | sprintf(painCave.errMsg, |
707 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
708 | > | "\tCannot calculate the number of atoms.\n"); |
709 | > | painCave.isFatal = 1; |
710 | > | simError(); |
711 | > | } |
712 | > | |
713 | > | tot_nmol += the_components[i]->getNMol(); |
714 | > | components_nmol[i] = the_components[i]->getNMol(); |
715 | > | } |
716 | } | |
792 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
793 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
794 | – | } |
717 | else{ | |
718 | < | sprintf( painCave.errMsg, |
719 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
720 | < | simnfo->mixingRule ); |
718 | > | sprintf(painCave.errMsg, |
719 | > | "SimSetup error.\n" |
720 | > | "\tSorry, the ability to specify total" |
721 | > | " nMols and then give molfractions in the components\n" |
722 | > | "\tis not currently supported." |
723 | > | " Please give nMol in the components.\n"); |
724 | painCave.isFatal = 1; | |
725 | simError(); | |
726 | } | |
727 | ||
728 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
729 | + | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
730 | + | sprintf(painCave.errMsg, |
731 | + | "Sample time is not divisible by dt.\n" |
732 | + | "\tThis will result in samples that are not uniformly\n" |
733 | + | "\tdistributed in time. If this is a problem, change\n" |
734 | + | "\tyour sampleTime variable.\n"); |
735 | + | painCave.isFatal = 0; |
736 | + | simError(); |
737 | + | } |
738 | ||
739 | < | #ifdef IS_MPI |
740 | < | strcpy( checkPointMsg, |
741 | < | "Successfully intialized the mixingRule for Fortran." ); |
742 | < | MPIcheckPoint(); |
743 | < | #endif // is_mpi |
744 | < | } |
739 | > | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
740 | > | sprintf(painCave.errMsg, |
741 | > | "Status time is not divisible by dt.\n" |
742 | > | "\tThis will result in status reports that are not uniformly\n" |
743 | > | "\tdistributed in time. If this is a problem, change \n" |
744 | > | "\tyour statusTime variable.\n"); |
745 | > | painCave.isFatal = 0; |
746 | > | simError(); |
747 | > | } |
748 | ||
749 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
750 | + | sprintf(painCave.errMsg, |
751 | + | "Thermal time is not divisible by dt.\n" |
752 | + | "\tThis will result in thermalizations that are not uniformly\n" |
753 | + | "\tdistributed in time. If this is a problem, change \n" |
754 | + | "\tyour thermalTime variable.\n"); |
755 | + | painCave.isFatal = 0; |
756 | + | simError(); |
757 | + | } |
758 | ||
759 | < | void SimSetup::makeMolecules( void ){ |
759 | > | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
760 | > | sprintf(painCave.errMsg, |
761 | > | "Reset time is not divisible by dt.\n" |
762 | > | "\tThis will result in integrator resets that are not uniformly\n" |
763 | > | "\tdistributed in time. If this is a problem, change\n" |
764 | > | "\tyour resetTime variable.\n"); |
765 | > | painCave.isFatal = 0; |
766 | > | simError(); |
767 | > | } |
768 | ||
769 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
815 | < | molInit info; |
816 | < | DirectionalAtom* dAtom; |
817 | < | LinkedAssign* extras; |
818 | < | LinkedAssign* current_extra; |
819 | < | AtomStamp* currentAtom; |
820 | < | BondStamp* currentBond; |
821 | < | BendStamp* currentBend; |
822 | < | TorsionStamp* currentTorsion; |
769 | > | // set the status, sample, and thermal kick times |
770 | ||
771 | < | bond_pair* theBonds; |
772 | < | bend_set* theBends; |
773 | < | torsion_set* theTorsions; |
771 | > | for (i = 0; i < nInfo; i++){ |
772 | > | if (globals->haveSampleTime()){ |
773 | > | info[i].sampleTime = globals->getSampleTime(); |
774 | > | info[i].statusTime = info[i].sampleTime; |
775 | > | info[i].thermalTime = info[i].sampleTime; |
776 | > | } |
777 | > | else{ |
778 | > | info[i].sampleTime = globals->getRunTime(); |
779 | > | info[i].statusTime = info[i].sampleTime; |
780 | > | info[i].thermalTime = info[i].sampleTime; |
781 | > | } |
782 | ||
783 | < | |
784 | < | //init the forceField paramters |
783 | > | if (globals->haveStatusTime()){ |
784 | > | info[i].statusTime = globals->getStatusTime(); |
785 | > | } |
786 | ||
787 | < | the_ff->readParams(); |
787 | > | if (globals->haveThermalTime()){ |
788 | > | info[i].thermalTime = globals->getThermalTime(); |
789 | > | } |
790 | ||
791 | < | |
792 | < | // init the atoms |
791 | > | info[i].resetIntegrator = 0; |
792 | > | if( globals->haveResetTime() ){ |
793 | > | info[i].resetTime = globals->getResetTime(); |
794 | > | info[i].resetIntegrator = 1; |
795 | > | } |
796 | ||
797 | < | double ux, uy, uz, u, uSqr; |
837 | < | |
838 | < | atomOffset = 0; |
839 | < | excludeOffset = 0; |
840 | < | for(i=0; i<simnfo->n_mol; i++){ |
797 | > | // check for the temperature set flag |
798 | ||
799 | < | stampID = the_molecules[i].getStampID(); |
799 | > | if (globals->haveTempSet()) |
800 | > | info[i].setTemp = globals->getTempSet(); |
801 | ||
802 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
845 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
846 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
847 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
848 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
802 | > | // check for the extended State init |
803 | ||
804 | < | info.myAtoms = &the_atoms[atomOffset]; |
805 | < | info.myExcludes = &the_excludes[excludeOffset]; |
852 | < | info.myBonds = new Bond*[info.nBonds]; |
853 | < | info.myBends = new Bend*[info.nBends]; |
854 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
855 | < | |
856 | < | theBonds = new bond_pair[info.nBonds]; |
857 | < | theBends = new bend_set[info.nBends]; |
858 | < | theTorsions = new torsion_set[info.nTorsions]; |
804 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
805 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
806 | ||
807 | < | // make the Atoms |
808 | < | |
809 | < | for(j=0; j<info.nAtoms; j++){ |
810 | < | |
811 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
812 | < | if( currentAtom->haveOrientation() ){ |
813 | < | |
814 | < | dAtom = new DirectionalAtom(j + atomOffset); |
815 | < | simnfo->n_oriented++; |
816 | < | info.myAtoms[j] = dAtom; |
817 | < | |
818 | < | ux = currentAtom->getOrntX(); |
819 | < | uy = currentAtom->getOrntY(); |
820 | < | uz = currentAtom->getOrntZ(); |
821 | < | |
822 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
823 | < | |
824 | < | u = sqrt( uSqr ); |
825 | < | ux = ux / u; |
826 | < | uy = uy / u; |
827 | < | uz = uz / u; |
881 | < | |
882 | < | dAtom->setSUx( ux ); |
883 | < | dAtom->setSUy( uy ); |
884 | < | dAtom->setSUz( uz ); |
807 | > | } |
808 | > | |
809 | > | //setup seed for random number generator |
810 | > | int seedValue; |
811 | > | |
812 | > | if (globals->haveSeed()){ |
813 | > | seedValue = globals->getSeed(); |
814 | > | |
815 | > | if(seedValue / 1E9 == 0){ |
816 | > | sprintf(painCave.errMsg, |
817 | > | "Seed for sprng library should contain at least 9 digits\n" |
818 | > | "OOPSE will generate a seed for user\n"); |
819 | > | painCave.isFatal = 0; |
820 | > | simError(); |
821 | > | |
822 | > | //using seed generated by system instead of invalid seed set by user |
823 | > | #ifndef IS_MPI |
824 | > | seedValue = make_sprng_seed(); |
825 | > | #else |
826 | > | if (worldRank == 0){ |
827 | > | seedValue = make_sprng_seed(); |
828 | } | |
829 | < | else{ |
830 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
831 | < | } |
832 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
829 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
830 | > | #endif |
831 | > | } |
832 | > | }//end of if branch of globals->haveSeed() |
833 | > | else{ |
834 | ||
835 | + | #ifndef IS_MPI |
836 | + | seedValue = make_sprng_seed(); |
837 | + | #else |
838 | + | if (worldRank == 0){ |
839 | + | seedValue = make_sprng_seed(); |
840 | + | } |
841 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
842 | + | #endif |
843 | + | }//end of globals->haveSeed() |
844 | + | |
845 | + | for (int i = 0; i < nInfo; i++){ |
846 | + | info[i].setSeed(seedValue); |
847 | + | } |
848 | + | |
849 | #ifdef IS_MPI | |
850 | < | |
851 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
894 | < | |
850 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
851 | > | MPIcheckPoint(); |
852 | #endif // is_mpi | |
853 | < | } |
897 | < | |
898 | < | // make the bonds |
899 | < | for(j=0; j<info.nBonds; j++){ |
900 | < | |
901 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
902 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
903 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
853 | > | } |
854 | ||
905 | – | exI = theBonds[j].a; |
906 | – | exJ = theBonds[j].b; |
855 | ||
856 | < | // exclude_I must always be the smaller of the pair |
857 | < | if( exI > exJ ){ |
858 | < | tempEx = exI; |
859 | < | exI = exJ; |
912 | < | exJ = tempEx; |
913 | < | } |
914 | < | #ifdef IS_MPI |
915 | < | tempEx = exI; |
916 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
917 | < | tempEx = exJ; |
918 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
919 | < | |
920 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
921 | < | #else // isn't MPI |
856 | > | void SimSetup::finalInfoCheck(void){ |
857 | > | int index; |
858 | > | int usesDipoles; |
859 | > | int i; |
860 | ||
861 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
862 | < | #endif //is_mpi |
861 | > | for (i = 0; i < nInfo; i++){ |
862 | > | // check electrostatic parameters |
863 | > | |
864 | > | index = 0; |
865 | > | usesDipoles = 0; |
866 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
867 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
868 | > | index++; |
869 | } | |
926 | – | excludeOffset += info.nBonds; |
870 | ||
871 | < | //make the bends |
872 | < | for(j=0; j<info.nBends; j++){ |
873 | < | |
874 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
875 | < | theBends[j].a = currentBend->getA() + atomOffset; |
876 | < | theBends[j].b = currentBend->getB() + atomOffset; |
877 | < | theBends[j].c = currentBend->getC() + atomOffset; |
878 | < | |
879 | < | if( currentBend->haveExtras() ){ |
880 | < | |
881 | < | extras = currentBend->getExtras(); |
882 | < | current_extra = extras; |
883 | < | |
884 | < | while( current_extra != NULL ){ |
885 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
886 | < | |
887 | < | switch( current_extra->getType() ){ |
888 | < | |
946 | < | case 0: |
947 | < | theBends[j].ghost = |
948 | < | current_extra->getInt() + atomOffset; |
949 | < | theBends[j].isGhost = 1; |
950 | < | break; |
951 | < | |
952 | < | case 1: |
953 | < | theBends[j].ghost = |
954 | < | (int)current_extra->getDouble() + atomOffset; |
955 | < | theBends[j].isGhost = 1; |
956 | < | break; |
957 | < | |
958 | < | default: |
959 | < | sprintf( painCave.errMsg, |
960 | < | "SimSetup Error: ghostVectorSource was neither a " |
961 | < | "double nor an int.\n" |
962 | < | "-->Bend[%d] in %s\n", |
963 | < | j, comp_stamps[stampID]->getID() ); |
964 | < | painCave.isFatal = 1; |
965 | < | simError(); |
966 | < | } |
967 | < | } |
968 | < | |
969 | < | else{ |
970 | < | |
971 | < | sprintf( painCave.errMsg, |
972 | < | "SimSetup Error: unhandled bend assignment:\n" |
973 | < | " -->%s in Bend[%d] in %s\n", |
974 | < | current_extra->getlhs(), |
975 | < | j, comp_stamps[stampID]->getID() ); |
976 | < | painCave.isFatal = 1; |
977 | < | simError(); |
978 | < | } |
979 | < | |
980 | < | current_extra = current_extra->getNext(); |
981 | < | } |
871 | > | #ifdef IS_MPI |
872 | > | int myUse = usesDipoles; |
873 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
874 | > | #endif //is_mpi |
875 | > | |
876 | > | double theEcr, theEst; |
877 | > | |
878 | > | if (globals->getUseRF()){ |
879 | > | info[i].useReactionField = 1; |
880 | > | |
881 | > | if (!globals->haveECR()){ |
882 | > | sprintf(painCave.errMsg, |
883 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
884 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
885 | > | "\tfor the electrostaticCutoffRadius.\n"); |
886 | > | painCave.isFatal = 0; |
887 | > | simError(); |
888 | > | theEcr = 15.0; |
889 | } | |
890 | < | |
891 | < | if( !theBends[j].isGhost ){ |
985 | < | |
986 | < | exI = theBends[j].a; |
987 | < | exJ = theBends[j].c; |
890 | > | else{ |
891 | > | theEcr = globals->getECR(); |
892 | } | |
893 | + | |
894 | + | if (!globals->haveEST()){ |
895 | + | sprintf(painCave.errMsg, |
896 | + | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
897 | + | "\tOOPSE will use a default value of\n" |
898 | + | "\t0.05 * electrostaticCutoffRadius\n" |
899 | + | "\tfor the electrostaticSkinThickness\n"); |
900 | + | painCave.isFatal = 0; |
901 | + | simError(); |
902 | + | theEst = 0.05 * theEcr; |
903 | + | } |
904 | else{ | |
905 | < | |
991 | < | exI = theBends[j].a; |
992 | < | exJ = theBends[j].b; |
905 | > | theEst = globals->getEST(); |
906 | } | |
907 | < | |
908 | < | // exclude_I must always be the smaller of the pair |
909 | < | if( exI > exJ ){ |
910 | < | tempEx = exI; |
911 | < | exI = exJ; |
912 | < | exJ = tempEx; |
907 | > | |
908 | > | info[i].setDefaultEcr(theEcr, theEst); |
909 | > | |
910 | > | if (!globals->haveDielectric()){ |
911 | > | sprintf(painCave.errMsg, |
912 | > | "SimSetup Error: No Dielectric constant was set.\n" |
913 | > | "\tYou are trying to use Reaction Field without" |
914 | > | "\tsetting a dielectric constant!\n"); |
915 | > | painCave.isFatal = 1; |
916 | > | simError(); |
917 | } | |
918 | < | #ifdef IS_MPI |
1002 | < | tempEx = exI; |
1003 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1004 | < | tempEx = exJ; |
1005 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1006 | < | |
1007 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1008 | < | #else // isn't MPI |
1009 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1010 | < | #endif //is_mpi |
918 | > | info[i].dielectric = globals->getDielectric(); |
919 | } | |
920 | < | excludeOffset += info.nBends; |
920 | > | else{ |
921 | > | if (usesDipoles){ |
922 | > | if (!globals->haveECR()){ |
923 | > | sprintf(painCave.errMsg, |
924 | > | "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
925 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
926 | > | "\tfor the electrostaticCutoffRadius.\n"); |
927 | > | painCave.isFatal = 0; |
928 | > | simError(); |
929 | > | theEcr = 15.0; |
930 | > | } |
931 | > | else{ |
932 | > | theEcr = globals->getECR(); |
933 | > | } |
934 | > | |
935 | > | if (!globals->haveEST()){ |
936 | > | sprintf(painCave.errMsg, |
937 | > | "SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
938 | > | "\tOOPSE will use a default value of\n" |
939 | > | "\t0.05 * electrostaticCutoffRadius\n" |
940 | > | "\tfor the electrostaticSkinThickness\n"); |
941 | > | painCave.isFatal = 0; |
942 | > | simError(); |
943 | > | theEst = 0.05 * theEcr; |
944 | > | } |
945 | > | else{ |
946 | > | theEst = globals->getEST(); |
947 | > | } |
948 | > | |
949 | > | info[i].setDefaultEcr(theEcr, theEst); |
950 | > | } |
951 | > | } |
952 | > | } |
953 | > | #ifdef IS_MPI |
954 | > | strcpy(checkPointMsg, "post processing checks out"); |
955 | > | MPIcheckPoint(); |
956 | > | #endif // is_mpi |
957 | > | } |
958 | > | |
959 | > | void SimSetup::initSystemCoords(void){ |
960 | > | int i; |
961 | ||
962 | < | for(j=0; j<info.nTorsions; j++){ |
1015 | < | |
1016 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1017 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1018 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1019 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1020 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1021 | < | |
1022 | < | exI = theTorsions[j].a; |
1023 | < | exJ = theTorsions[j].d; |
962 | > | char* inName; |
963 | ||
964 | < | // exclude_I must always be the smaller of the pair |
965 | < | if( exI > exJ ){ |
966 | < | tempEx = exI; |
967 | < | exI = exJ; |
968 | < | exJ = tempEx; |
969 | < | } |
964 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
965 | > | |
966 | > | for (i = 0; i < info[0].n_atoms; i++) |
967 | > | info[0].atoms[i]->setCoords(); |
968 | > | |
969 | > | if (globals->haveInitialConfig()){ |
970 | > | InitializeFromFile* fileInit; |
971 | > | #ifdef IS_MPI // is_mpi |
972 | > | if (worldRank == 0){ |
973 | > | #endif //is_mpi |
974 | > | inName = globals->getInitialConfig(); |
975 | > | fileInit = new InitializeFromFile(inName); |
976 | #ifdef IS_MPI | |
1032 | – | tempEx = exI; |
1033 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1034 | – | tempEx = exJ; |
1035 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1036 | – | |
1037 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1038 | – | #else // isn't MPI |
1039 | – | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1040 | – | #endif //is_mpi |
977 | } | |
978 | < | excludeOffset += info.nTorsions; |
978 | > | else |
979 | > | fileInit = new InitializeFromFile(NULL); |
980 | > | #endif |
981 | > | fileInit->readInit(info); // default velocities on |
982 | ||
983 | + | delete fileInit; |
984 | + | } |
985 | + | else{ |
986 | ||
987 | < | // send the arrays off to the forceField for init. |
987 | > | // no init from bass |
988 | > | |
989 | > | sprintf(painCave.errMsg, |
990 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
991 | > | painCave.isFatal = 1;; |
992 | > | simError(); |
993 | > | |
994 | > | } |
995 | ||
996 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
997 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
998 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
999 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
996 | > | #ifdef IS_MPI |
997 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
998 | > | MPIcheckPoint(); |
999 | > | #endif // is_mpi |
1000 | > | } |
1001 | ||
1002 | ||
1003 | < | the_molecules[i].initialize( info ); |
1003 | > | void SimSetup::makeOutNames(void){ |
1004 | > | int k; |
1005 | ||
1006 | ||
1007 | < | atomOffset += info.nAtoms; |
1057 | < | delete[] theBonds; |
1058 | < | delete[] theBends; |
1059 | < | delete[] theTorsions; |
1060 | < | } |
1061 | < | |
1007 | > | for (k = 0; k < nInfo; k++){ |
1008 | #ifdef IS_MPI | |
1009 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1064 | < | MPIcheckPoint(); |
1009 | > | if (worldRank == 0){ |
1010 | #endif // is_mpi | |
1011 | ||
1012 | < | // clean up the forcefield |
1013 | < | the_ff->calcRcut(); |
1014 | < | the_ff->cleanMe(); |
1012 | > | if (globals->haveFinalConfig()){ |
1013 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1014 | > | } |
1015 | > | else{ |
1016 | > | strcpy(info[k].finalName, inFileName); |
1017 | > | char* endTest; |
1018 | > | int nameLength = strlen(info[k].finalName); |
1019 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1020 | > | if (!strcmp(endTest, ".bass")){ |
1021 | > | strcpy(endTest, ".eor"); |
1022 | > | } |
1023 | > | else if (!strcmp(endTest, ".BASS")){ |
1024 | > | strcpy(endTest, ".eor"); |
1025 | > | } |
1026 | > | else{ |
1027 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1028 | > | if (!strcmp(endTest, ".bss")){ |
1029 | > | strcpy(endTest, ".eor"); |
1030 | > | } |
1031 | > | else if (!strcmp(endTest, ".mdl")){ |
1032 | > | strcpy(endTest, ".eor"); |
1033 | > | } |
1034 | > | else{ |
1035 | > | strcat(info[k].finalName, ".eor"); |
1036 | > | } |
1037 | > | } |
1038 | > | } |
1039 | ||
1040 | + | // make the sample and status out names |
1041 | + | |
1042 | + | strcpy(info[k].sampleName, inFileName); |
1043 | + | char* endTest; |
1044 | + | int nameLength = strlen(info[k].sampleName); |
1045 | + | endTest = &(info[k].sampleName[nameLength - 5]); |
1046 | + | if (!strcmp(endTest, ".bass")){ |
1047 | + | strcpy(endTest, ".dump"); |
1048 | + | } |
1049 | + | else if (!strcmp(endTest, ".BASS")){ |
1050 | + | strcpy(endTest, ".dump"); |
1051 | + | } |
1052 | + | else{ |
1053 | + | endTest = &(info[k].sampleName[nameLength - 4]); |
1054 | + | if (!strcmp(endTest, ".bss")){ |
1055 | + | strcpy(endTest, ".dump"); |
1056 | + | } |
1057 | + | else if (!strcmp(endTest, ".mdl")){ |
1058 | + | strcpy(endTest, ".dump"); |
1059 | + | } |
1060 | + | else{ |
1061 | + | strcat(info[k].sampleName, ".dump"); |
1062 | + | } |
1063 | + | } |
1064 | + | |
1065 | + | strcpy(info[k].statusName, inFileName); |
1066 | + | nameLength = strlen(info[k].statusName); |
1067 | + | endTest = &(info[k].statusName[nameLength - 5]); |
1068 | + | if (!strcmp(endTest, ".bass")){ |
1069 | + | strcpy(endTest, ".stat"); |
1070 | + | } |
1071 | + | else if (!strcmp(endTest, ".BASS")){ |
1072 | + | strcpy(endTest, ".stat"); |
1073 | + | } |
1074 | + | else{ |
1075 | + | endTest = &(info[k].statusName[nameLength - 4]); |
1076 | + | if (!strcmp(endTest, ".bss")){ |
1077 | + | strcpy(endTest, ".stat"); |
1078 | + | } |
1079 | + | else if (!strcmp(endTest, ".mdl")){ |
1080 | + | strcpy(endTest, ".stat"); |
1081 | + | } |
1082 | + | else{ |
1083 | + | strcat(info[k].statusName, ".stat"); |
1084 | + | } |
1085 | + | } |
1086 | + | |
1087 | + | #ifdef IS_MPI |
1088 | + | |
1089 | + | } |
1090 | + | #endif // is_mpi |
1091 | + | } |
1092 | } | |
1093 | ||
1073 | – | void SimSetup::initFromBass( void ){ |
1094 | ||
1095 | < | int i, j, k; |
1096 | < | int n_cells; |
1077 | < | double cellx, celly, cellz; |
1078 | < | double temp1, temp2, temp3; |
1079 | < | int n_per_extra; |
1080 | < | int n_extra; |
1081 | < | int have_extra, done; |
1095 | > | void SimSetup::sysObjectsCreation(void){ |
1096 | > | int i, k; |
1097 | ||
1098 | < | temp1 = (double)tot_nmol / 4.0; |
1084 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1085 | < | temp3 = ceil( temp2 ); |
1098 | > | // create the forceField |
1099 | ||
1100 | < | have_extra =0; |
1088 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1089 | < | have_extra =1; |
1100 | > | createFF(); |
1101 | ||
1102 | < | n_cells = (int)temp3 - 1; |
1092 | < | cellx = simnfo->box_x / temp3; |
1093 | < | celly = simnfo->box_y / temp3; |
1094 | < | cellz = simnfo->box_z / temp3; |
1095 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1096 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1097 | < | n_per_extra = (int)ceil( temp1 ); |
1102 | > | // extract componentList |
1103 | ||
1104 | < | if( n_per_extra > 4){ |
1105 | < | sprintf( painCave.errMsg, |
1106 | < | "SimSetup error. There has been an error in constructing" |
1107 | < | " the non-complete lattice.\n" ); |
1104 | > | compList(); |
1105 | > | |
1106 | > | // calc the number of atoms, bond, bends, and torsions |
1107 | > | |
1108 | > | calcSysValues(); |
1109 | > | |
1110 | > | #ifdef IS_MPI |
1111 | > | // divide the molecules among the processors |
1112 | > | |
1113 | > | mpiMolDivide(); |
1114 | > | #endif //is_mpi |
1115 | > | |
1116 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1117 | > | |
1118 | > | makeSysArrays(); |
1119 | > | |
1120 | > | // make and initialize the molecules (all but atomic coordinates) |
1121 | > | |
1122 | > | makeMolecules(); |
1123 | > | |
1124 | > | for (k = 0; k < nInfo; k++){ |
1125 | > | info[k].identArray = new int[info[k].n_atoms]; |
1126 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1127 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1128 | > | } |
1129 | > | } |
1130 | > | } |
1131 | > | |
1132 | > | |
1133 | > | void SimSetup::createFF(void){ |
1134 | > | switch (ffCase){ |
1135 | > | case FF_DUFF: |
1136 | > | the_ff = new DUFF(); |
1137 | > | break; |
1138 | > | |
1139 | > | case FF_LJ: |
1140 | > | the_ff = new LJFF(); |
1141 | > | break; |
1142 | > | |
1143 | > | case FF_EAM: |
1144 | > | the_ff = new EAM_FF(); |
1145 | > | break; |
1146 | > | |
1147 | > | case FF_H2O: |
1148 | > | the_ff = new WATER(); |
1149 | > | break; |
1150 | > | |
1151 | > | default: |
1152 | > | sprintf(painCave.errMsg, |
1153 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1154 | painCave.isFatal = 1; | |
1155 | simError(); | |
1105 | – | } |
1156 | } | |
1107 | – | else{ |
1108 | – | n_cells = (int)temp3; |
1109 | – | cellx = simnfo->box_x / temp3; |
1110 | – | celly = simnfo->box_y / temp3; |
1111 | – | cellz = simnfo->box_z / temp3; |
1112 | – | } |
1157 | ||
1158 | < | current_mol = 0; |
1159 | < | current_comp_mol = 0; |
1160 | < | current_comp = 0; |
1161 | < | current_atom_ndx = 0; |
1158 | > | #ifdef IS_MPI |
1159 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1160 | > | MPIcheckPoint(); |
1161 | > | #endif // is_mpi |
1162 | > | } |
1163 | ||
1119 | – | for( i=0; i < n_cells ; i++ ){ |
1120 | – | for( j=0; j < n_cells; j++ ){ |
1121 | – | for( k=0; k < n_cells; k++ ){ |
1164 | ||
1165 | < | makeElement( i * cellx, |
1166 | < | j * celly, |
1167 | < | k * cellz ); |
1165 | > | void SimSetup::compList(void){ |
1166 | > | int i; |
1167 | > | char* id; |
1168 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1169 | > | LinkedMolStamp* currentStamp = NULL; |
1170 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1171 | ||
1172 | < | makeElement( i * cellx + 0.5 * cellx, |
1173 | < | j * celly + 0.5 * celly, |
1129 | < | k * cellz ); |
1172 | > | // make an array of molecule stamps that match the components used. |
1173 | > | // also extract the used stamps out into a separate linked list |
1174 | ||
1175 | < | makeElement( i * cellx, |
1176 | < | j * celly + 0.5 * celly, |
1177 | < | k * cellz + 0.5 * cellz ); |
1175 | > | for (i = 0; i < nInfo; i++){ |
1176 | > | info[i].nComponents = n_components; |
1177 | > | info[i].componentsNmol = components_nmol; |
1178 | > | info[i].compStamps = comp_stamps; |
1179 | > | info[i].headStamp = headStamp; |
1180 | > | } |
1181 | ||
1182 | < | makeElement( i * cellx + 0.5 * cellx, |
1183 | < | j * celly, |
1184 | < | k * cellz + 0.5 * cellz ); |
1182 | > | |
1183 | > | for (i = 0; i < n_components; i++){ |
1184 | > | id = the_components[i]->getType(); |
1185 | > | comp_stamps[i] = NULL; |
1186 | > | |
1187 | > | // check to make sure the component isn't already in the list |
1188 | > | |
1189 | > | comp_stamps[i] = headStamp->match(id); |
1190 | > | if (comp_stamps[i] == NULL){ |
1191 | > | // extract the component from the list; |
1192 | > | |
1193 | > | currentStamp = stamps->extractMolStamp(id); |
1194 | > | if (currentStamp == NULL){ |
1195 | > | sprintf(painCave.errMsg, |
1196 | > | "SimSetup error: Component \"%s\" was not found in the " |
1197 | > | "list of declared molecules\n", |
1198 | > | id); |
1199 | > | painCave.isFatal = 1; |
1200 | > | simError(); |
1201 | } | |
1202 | + | |
1203 | + | headStamp->add(currentStamp); |
1204 | + | comp_stamps[i] = headStamp->match(id); |
1205 | } | |
1206 | } | |
1207 | ||
1208 | < | if( have_extra ){ |
1209 | < | done = 0; |
1208 | > | #ifdef IS_MPI |
1209 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1210 | > | MPIcheckPoint(); |
1211 | > | #endif // is_mpi |
1212 | > | } |
1213 | ||
1214 | < | int start_ndx; |
1215 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1147 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1214 | > | void SimSetup::calcSysValues(void){ |
1215 | > | int i; |
1216 | ||
1217 | < | if( i < n_cells ){ |
1217 | > | int* molMembershipArray; |
1218 | ||
1219 | < | if( j < n_cells ){ |
1220 | < | start_ndx = n_cells; |
1221 | < | } |
1222 | < | else start_ndx = 0; |
1223 | < | } |
1224 | < | else start_ndx = 0; |
1219 | > | tot_atoms = 0; |
1220 | > | tot_bonds = 0; |
1221 | > | tot_bends = 0; |
1222 | > | tot_torsions = 0; |
1223 | > | for (i = 0; i < n_components; i++){ |
1224 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1225 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1226 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1227 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1228 | > | } |
1229 | ||
1230 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1230 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1231 | > | molMembershipArray = new int[tot_atoms]; |
1232 | ||
1233 | < | makeElement( i * cellx, |
1234 | < | j * celly, |
1235 | < | k * cellz ); |
1236 | < | done = ( current_mol >= tot_nmol ); |
1233 | > | for (i = 0; i < nInfo; i++){ |
1234 | > | info[i].n_atoms = tot_atoms; |
1235 | > | info[i].n_bonds = tot_bonds; |
1236 | > | info[i].n_bends = tot_bends; |
1237 | > | info[i].n_torsions = tot_torsions; |
1238 | > | info[i].n_SRI = tot_SRI; |
1239 | > | info[i].n_mol = tot_nmol; |
1240 | ||
1241 | < | if( !done && n_per_extra > 1 ){ |
1242 | < | makeElement( i * cellx + 0.5 * cellx, |
1243 | < | j * celly + 0.5 * celly, |
1168 | < | k * cellz ); |
1169 | < | done = ( current_mol >= tot_nmol ); |
1170 | < | } |
1241 | > | info[i].molMembershipArray = molMembershipArray; |
1242 | > | } |
1243 | > | } |
1244 | ||
1245 | < | if( !done && n_per_extra > 2){ |
1173 | < | makeElement( i * cellx, |
1174 | < | j * celly + 0.5 * celly, |
1175 | < | k * cellz + 0.5 * cellz ); |
1176 | < | done = ( current_mol >= tot_nmol ); |
1177 | < | } |
1245 | > | #ifdef IS_MPI |
1246 | ||
1247 | < | if( !done && n_per_extra > 3){ |
1248 | < | makeElement( i * cellx + 0.5 * cellx, |
1249 | < | j * celly, |
1250 | < | k * cellz + 0.5 * cellz ); |
1251 | < | done = ( current_mol >= tot_nmol ); |
1252 | < | } |
1253 | < | } |
1247 | > | void SimSetup::mpiMolDivide(void){ |
1248 | > | int i, j, k; |
1249 | > | int localMol, allMol; |
1250 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1251 | > | |
1252 | > | mpiSim = new mpiSimulation(info); |
1253 | > | |
1254 | > | globalIndex = mpiSim->divideLabor(); |
1255 | > | |
1256 | > | // set up the local variables |
1257 | > | |
1258 | > | mol2proc = mpiSim->getMolToProcMap(); |
1259 | > | molCompType = mpiSim->getMolComponentType(); |
1260 | > | |
1261 | > | allMol = 0; |
1262 | > | localMol = 0; |
1263 | > | local_atoms = 0; |
1264 | > | local_bonds = 0; |
1265 | > | local_bends = 0; |
1266 | > | local_torsions = 0; |
1267 | > | globalAtomIndex = 0; |
1268 | > | |
1269 | > | |
1270 | > | for (i = 0; i < n_components; i++){ |
1271 | > | for (j = 0; j < components_nmol[i]; j++){ |
1272 | > | if (mol2proc[allMol] == worldRank){ |
1273 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1274 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1275 | > | local_bends += comp_stamps[i]->getNBends(); |
1276 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1277 | > | localMol++; |
1278 | > | } |
1279 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1280 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1281 | > | globalAtomIndex++; |
1282 | } | |
1283 | + | |
1284 | + | allMol++; |
1285 | } | |
1286 | } | |
1287 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1288 | ||
1289 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1290 | ||
1291 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1292 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1293 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1294 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1291 | > | if (local_atoms != info[0].n_atoms){ |
1292 | > | sprintf(painCave.errMsg, |
1293 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1294 | > | "\tlocalAtom (%d) are not equal.\n", |
1295 | > | info[0].n_atoms, local_atoms); |
1296 | > | painCave.isFatal = 1; |
1297 | > | simError(); |
1298 | } | |
1299 | + | |
1300 | + | info[0].n_bonds = local_bonds; |
1301 | + | info[0].n_bends = local_bends; |
1302 | + | info[0].n_torsions = local_torsions; |
1303 | + | info[0].n_SRI = local_SRI; |
1304 | + | info[0].n_mol = localMol; |
1305 | + | |
1306 | + | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1307 | + | MPIcheckPoint(); |
1308 | } | |
1309 | ||
1310 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1310 | > | #endif // is_mpi |
1311 | ||
1200 | – | int k; |
1201 | – | AtomStamp* current_atom; |
1202 | – | DirectionalAtom* dAtom; |
1203 | – | double rotMat[3][3]; |
1312 | ||
1313 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1313 | > | void SimSetup::makeSysArrays(void){ |
1314 | > | |
1315 | > | #ifndef IS_MPI |
1316 | > | int k, j; |
1317 | > | #endif // is_mpi |
1318 | > | int i, l; |
1319 | ||
1320 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1321 | < | if( !current_atom->havePosition() ){ |
1322 | < | sprintf( painCave.errMsg, |
1210 | < | "SimSetup:initFromBass error.\n" |
1211 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1212 | < | "\tThe initialization routine is unable to give a start" |
1213 | < | " position.\n", |
1214 | < | comp_stamps[current_comp]->getID(), |
1215 | < | current_atom->getType() ); |
1216 | < | painCave.isFatal = 1; |
1217 | < | simError(); |
1218 | < | } |
1320 | > | Atom** the_atoms; |
1321 | > | Molecule* the_molecules; |
1322 | > | Exclude** the_excludes; |
1323 | ||
1220 | – | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1221 | – | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1222 | – | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1324 | ||
1325 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1325 | > | for (l = 0; l < nInfo; l++){ |
1326 | > | // create the atom and short range interaction arrays |
1327 | ||
1328 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1328 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1329 | > | the_molecules = new Molecule[info[l].n_mol]; |
1330 | > | int molIndex; |
1331 | ||
1332 | < | rotMat[0][0] = 1.0; |
1229 | < | rotMat[0][1] = 0.0; |
1230 | < | rotMat[0][2] = 0.0; |
1332 | > | // initialize the molecule's stampID's |
1333 | ||
1334 | < | rotMat[1][0] = 0.0; |
1233 | < | rotMat[1][1] = 1.0; |
1234 | < | rotMat[1][2] = 0.0; |
1334 | > | #ifdef IS_MPI |
1335 | ||
1236 | – | rotMat[2][0] = 0.0; |
1237 | – | rotMat[2][1] = 0.0; |
1238 | – | rotMat[2][2] = 1.0; |
1336 | ||
1337 | < | dAtom->setA( rotMat ); |
1337 | > | molIndex = 0; |
1338 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1339 | > | if (mol2proc[i] == worldRank){ |
1340 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1341 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1342 | > | the_molecules[molIndex].setGlobalIndex(i); |
1343 | > | molIndex++; |
1344 | > | } |
1345 | } | |
1346 | ||
1347 | < | current_atom_ndx++; |
1347 | > | #else // is_mpi |
1348 | > | |
1349 | > | molIndex = 0; |
1350 | > | globalAtomIndex = 0; |
1351 | > | for (i = 0; i < n_components; i++){ |
1352 | > | for (j = 0; j < components_nmol[i]; j++){ |
1353 | > | the_molecules[molIndex].setStampID(i); |
1354 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1355 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1356 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1357 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1358 | > | globalAtomIndex++; |
1359 | > | } |
1360 | > | molIndex++; |
1361 | > | } |
1362 | > | } |
1363 | > | |
1364 | > | |
1365 | > | #endif // is_mpi |
1366 | > | |
1367 | > | |
1368 | > | if (info[l].n_SRI){ |
1369 | > | Exclude::createArray(info[l].n_SRI); |
1370 | > | the_excludes = new Exclude * [info[l].n_SRI]; |
1371 | > | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1372 | > | the_excludes[ex] = new Exclude(ex); |
1373 | > | } |
1374 | > | info[l].globalExcludes = new int; |
1375 | > | info[l].n_exclude = info[l].n_SRI; |
1376 | > | } |
1377 | > | else{ |
1378 | > | Exclude::createArray(1); |
1379 | > | the_excludes = new Exclude * ; |
1380 | > | the_excludes[0] = new Exclude(0); |
1381 | > | the_excludes[0]->setPair(0, 0); |
1382 | > | info[l].globalExcludes = new int; |
1383 | > | info[l].globalExcludes[0] = 0; |
1384 | > | info[l].n_exclude = 0; |
1385 | > | } |
1386 | > | |
1387 | > | // set the arrays into the SimInfo object |
1388 | > | |
1389 | > | info[l].atoms = the_atoms; |
1390 | > | info[l].molecules = the_molecules; |
1391 | > | info[l].nGlobalExcludes = 0; |
1392 | > | info[l].excludes = the_excludes; |
1393 | > | |
1394 | > | the_ff->setSimInfo(info); |
1395 | } | |
1396 | + | } |
1397 | ||
1398 | < | current_mol++; |
1399 | < | current_comp_mol++; |
1398 | > | void SimSetup::makeIntegrator(void){ |
1399 | > | int k; |
1400 | ||
1401 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1401 | > | NVE<RealIntegrator>* myNVE = NULL; |
1402 | > | NVT<RealIntegrator>* myNVT = NULL; |
1403 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1404 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1405 | > | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1406 | > | |
1407 | > | for (k = 0; k < nInfo; k++){ |
1408 | > | switch (ensembleCase){ |
1409 | > | case NVE_ENS: |
1410 | > | if (globals->haveZconstraints()){ |
1411 | > | setupZConstraint(info[k]); |
1412 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1413 | > | } |
1414 | > | else{ |
1415 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1416 | > | } |
1417 | > | |
1418 | > | info->the_integrator = myNVE; |
1419 | > | break; |
1420 | ||
1421 | < | current_comp_mol = 0; |
1422 | < | current_comp++; |
1421 | > | case NVT_ENS: |
1422 | > | if (globals->haveZconstraints()){ |
1423 | > | setupZConstraint(info[k]); |
1424 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1425 | > | } |
1426 | > | else |
1427 | > | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1428 | > | |
1429 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1430 | > | |
1431 | > | if (globals->haveTauThermostat()) |
1432 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1433 | > | else{ |
1434 | > | sprintf(painCave.errMsg, |
1435 | > | "SimSetup error: If you use the NVT\n" |
1436 | > | "\tensemble, you must set tauThermostat.\n"); |
1437 | > | painCave.isFatal = 1; |
1438 | > | simError(); |
1439 | > | } |
1440 | > | |
1441 | > | info->the_integrator = myNVT; |
1442 | > | break; |
1443 | > | |
1444 | > | case NPTi_ENS: |
1445 | > | if (globals->haveZconstraints()){ |
1446 | > | setupZConstraint(info[k]); |
1447 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1448 | > | } |
1449 | > | else |
1450 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1451 | > | |
1452 | > | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1453 | > | |
1454 | > | if (globals->haveTargetPressure()) |
1455 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1456 | > | else{ |
1457 | > | sprintf(painCave.errMsg, |
1458 | > | "SimSetup error: If you use a constant pressure\n" |
1459 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1460 | > | painCave.isFatal = 1; |
1461 | > | simError(); |
1462 | > | } |
1463 | > | |
1464 | > | if (globals->haveTauThermostat()) |
1465 | > | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1466 | > | else{ |
1467 | > | sprintf(painCave.errMsg, |
1468 | > | "SimSetup error: If you use an NPT\n" |
1469 | > | "\tensemble, you must set tauThermostat.\n"); |
1470 | > | painCave.isFatal = 1; |
1471 | > | simError(); |
1472 | > | } |
1473 | > | |
1474 | > | if (globals->haveTauBarostat()) |
1475 | > | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1476 | > | else{ |
1477 | > | sprintf(painCave.errMsg, |
1478 | > | "SimSetup error: If you use an NPT\n" |
1479 | > | "\tensemble, you must set tauBarostat.\n"); |
1480 | > | painCave.isFatal = 1; |
1481 | > | simError(); |
1482 | > | } |
1483 | > | |
1484 | > | info->the_integrator = myNPTi; |
1485 | > | break; |
1486 | > | |
1487 | > | case NPTf_ENS: |
1488 | > | if (globals->haveZconstraints()){ |
1489 | > | setupZConstraint(info[k]); |
1490 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1491 | > | } |
1492 | > | else |
1493 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1494 | > | |
1495 | > | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1496 | > | |
1497 | > | if (globals->haveTargetPressure()) |
1498 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1499 | > | else{ |
1500 | > | sprintf(painCave.errMsg, |
1501 | > | "SimSetup error: If you use a constant pressure\n" |
1502 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1503 | > | painCave.isFatal = 1; |
1504 | > | simError(); |
1505 | > | } |
1506 | > | |
1507 | > | if (globals->haveTauThermostat()) |
1508 | > | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1509 | > | |
1510 | > | else{ |
1511 | > | sprintf(painCave.errMsg, |
1512 | > | "SimSetup error: If you use an NPT\n" |
1513 | > | "\tensemble, you must set tauThermostat.\n"); |
1514 | > | painCave.isFatal = 1; |
1515 | > | simError(); |
1516 | > | } |
1517 | > | |
1518 | > | if (globals->haveTauBarostat()) |
1519 | > | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1520 | > | |
1521 | > | else{ |
1522 | > | sprintf(painCave.errMsg, |
1523 | > | "SimSetup error: If you use an NPT\n" |
1524 | > | "\tensemble, you must set tauBarostat.\n"); |
1525 | > | painCave.isFatal = 1; |
1526 | > | simError(); |
1527 | > | } |
1528 | > | |
1529 | > | info->the_integrator = myNPTf; |
1530 | > | break; |
1531 | > | |
1532 | > | case NPTxyz_ENS: |
1533 | > | if (globals->haveZconstraints()){ |
1534 | > | setupZConstraint(info[k]); |
1535 | > | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1536 | > | } |
1537 | > | else |
1538 | > | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1539 | > | |
1540 | > | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1541 | > | |
1542 | > | if (globals->haveTargetPressure()) |
1543 | > | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1544 | > | else{ |
1545 | > | sprintf(painCave.errMsg, |
1546 | > | "SimSetup error: If you use a constant pressure\n" |
1547 | > | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1548 | > | painCave.isFatal = 1; |
1549 | > | simError(); |
1550 | > | } |
1551 | > | |
1552 | > | if (globals->haveTauThermostat()) |
1553 | > | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1554 | > | else{ |
1555 | > | sprintf(painCave.errMsg, |
1556 | > | "SimSetup error: If you use an NPT\n" |
1557 | > | "\tensemble, you must set tauThermostat.\n"); |
1558 | > | painCave.isFatal = 1; |
1559 | > | simError(); |
1560 | > | } |
1561 | > | |
1562 | > | if (globals->haveTauBarostat()) |
1563 | > | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1564 | > | else{ |
1565 | > | sprintf(painCave.errMsg, |
1566 | > | "SimSetup error: If you use an NPT\n" |
1567 | > | "\tensemble, you must set tauBarostat.\n"); |
1568 | > | painCave.isFatal = 1; |
1569 | > | simError(); |
1570 | > | } |
1571 | > | |
1572 | > | info->the_integrator = myNPTxyz; |
1573 | > | break; |
1574 | > | |
1575 | > | default: |
1576 | > | sprintf(painCave.errMsg, |
1577 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1578 | > | painCave.isFatal = 1; |
1579 | > | simError(); |
1580 | > | } |
1581 | } | |
1582 | } | |
1583 | + | |
1584 | + | void SimSetup::initFortran(void){ |
1585 | + | info[0].refreshSim(); |
1586 | + | |
1587 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1588 | + | the_ff->initForceField(LB_MIXING_RULE); |
1589 | + | } |
1590 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1591 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1592 | + | } |
1593 | + | else{ |
1594 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1595 | + | info[0].mixingRule); |
1596 | + | painCave.isFatal = 1; |
1597 | + | simError(); |
1598 | + | } |
1599 | + | |
1600 | + | |
1601 | + | #ifdef IS_MPI |
1602 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1603 | + | MPIcheckPoint(); |
1604 | + | #endif // is_mpi |
1605 | + | } |
1606 | + | |
1607 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1608 | + | int nZConstraints; |
1609 | + | ZconStamp** zconStamp; |
1610 | + | |
1611 | + | if (globals->haveZconstraintTime()){ |
1612 | + | //add sample time of z-constraint into SimInfo's property list |
1613 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1614 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1615 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1616 | + | theInfo.addProperty(zconsTimeProp); |
1617 | + | } |
1618 | + | else{ |
1619 | + | sprintf(painCave.errMsg, |
1620 | + | "ZConstraint error: If you use a ZConstraint,\n" |
1621 | + | "\tyou must set zconsTime.\n"); |
1622 | + | painCave.isFatal = 1; |
1623 | + | simError(); |
1624 | + | } |
1625 | + | |
1626 | + | //push zconsTol into siminfo, if user does not specify |
1627 | + | //value for zconsTol, a default value will be used |
1628 | + | DoubleData* zconsTol = new DoubleData(); |
1629 | + | zconsTol->setID(ZCONSTOL_ID); |
1630 | + | if (globals->haveZconsTol()){ |
1631 | + | zconsTol->setData(globals->getZconsTol()); |
1632 | + | } |
1633 | + | else{ |
1634 | + | double defaultZConsTol = 0.01; |
1635 | + | sprintf(painCave.errMsg, |
1636 | + | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1637 | + | "\tOOPSE will use a default value of %f.\n" |
1638 | + | "\tTo set the tolerance, use the zconsTol variable.\n", |
1639 | + | defaultZConsTol); |
1640 | + | painCave.isFatal = 0; |
1641 | + | simError(); |
1642 | + | |
1643 | + | zconsTol->setData(defaultZConsTol); |
1644 | + | } |
1645 | + | theInfo.addProperty(zconsTol); |
1646 | + | |
1647 | + | //set Force Subtraction Policy |
1648 | + | StringData* zconsForcePolicy = new StringData(); |
1649 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1650 | + | |
1651 | + | if (globals->haveZconsForcePolicy()){ |
1652 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1653 | + | } |
1654 | + | else{ |
1655 | + | sprintf(painCave.errMsg, |
1656 | + | "ZConstraint Warning: No force subtraction policy was set.\n" |
1657 | + | "\tOOPSE will use PolicyByMass.\n" |
1658 | + | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1659 | + | painCave.isFatal = 0; |
1660 | + | simError(); |
1661 | + | zconsForcePolicy->setData("BYMASS"); |
1662 | + | } |
1663 | + | |
1664 | + | theInfo.addProperty(zconsForcePolicy); |
1665 | + | |
1666 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1667 | + | //Be careful, do not use inFileName, since it is a pointer which |
1668 | + | //point to a string at master node, and slave nodes do not contain that string |
1669 | + | |
1670 | + | string zconsOutput(theInfo.finalName); |
1671 | + | |
1672 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1673 | + | |
1674 | + | StringData* zconsFilename = new StringData(); |
1675 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1676 | + | zconsFilename->setData(zconsOutput); |
1677 | + | |
1678 | + | theInfo.addProperty(zconsFilename); |
1679 | + | |
1680 | + | //setup index, pos and other parameters of z-constraint molecules |
1681 | + | nZConstraints = globals->getNzConstraints(); |
1682 | + | theInfo.nZconstraints = nZConstraints; |
1683 | + | |
1684 | + | zconStamp = globals->getZconStamp(); |
1685 | + | ZConsParaItem tempParaItem; |
1686 | + | |
1687 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1688 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1689 | + | |
1690 | + | for (int i = 0; i < nZConstraints; i++){ |
1691 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1692 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1693 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1694 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1695 | + | |
1696 | + | zconsParaData->addItem(tempParaItem); |
1697 | + | } |
1698 | + | |
1699 | + | //check the uniqueness of index |
1700 | + | if(!zconsParaData->isIndexUnique()){ |
1701 | + | sprintf(painCave.errMsg, |
1702 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1703 | + | painCave.isFatal = 1; |
1704 | + | simError(); |
1705 | + | } |
1706 | + | |
1707 | + | //sort the parameters by index of molecules |
1708 | + | zconsParaData->sortByIndex(); |
1709 | + | |
1710 | + | //push data into siminfo, therefore, we can retrieve later |
1711 | + | theInfo.addProperty(zconsParaData); |
1712 | + | } |
1713 | + | |
1714 | + | void SimSetup::makeMinimizer(){ |
1715 | + | |
1716 | + | OOPSEMinimizerBase* myOOPSEMinimizerBase; |
1717 | + | ObjFunctor1 * objFunc; |
1718 | + | OutputFunctor* outputFunc; |
1719 | + | ConcreteNLModel1* nlp; |
1720 | + | MinimizerParameterSet* param; |
1721 | + | ConjugateMinimizerBase* minimizer; |
1722 | + | int dim; |
1723 | + | |
1724 | + | for (int i = 0; i < nInfo; i++){ |
1725 | + | //creat |
1726 | + | myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff); |
1727 | + | |
1728 | + | info[i].the_integrator = myOOPSEMinimizerBase; |
1729 | + | //creat the object functor; |
1730 | + | objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase> |
1731 | + | (myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient); |
1732 | + | |
1733 | + | //creat output functor; |
1734 | + | outputFunc = new ClassMemOutputFunctor<OOPSEMinimizerBase> |
1735 | + | (myOOPSEMinimizerBase, &OOPSEMinimizerBase::output); |
1736 | + | |
1737 | + | //creat nonlinear model |
1738 | + | dim = myOOPSEMinimizerBase->getDim(); |
1739 | + | nlp = new ConcreteNLModel1(dim, objFunc); |
1740 | + | |
1741 | + | nlp->setX(myOOPSEMinimizerBase->getCoor()); |
1742 | + | |
1743 | + | //prepare parameter set for minimizer |
1744 | + | param = new MinimizerParameterSet(); |
1745 | + | param->setDefaultParameter(); |
1746 | + | |
1747 | + | if (globals->haveMinimizer()){ |
1748 | + | param->setFTol(globals->getMinFTol()); |
1749 | + | } |
1750 | + | |
1751 | + | if (globals->haveMinGTol()){ |
1752 | + | param->setGTol(globals->getMinGTol()); |
1753 | + | } |
1754 | + | |
1755 | + | if (globals->haveMinMaxIter()){ |
1756 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1757 | + | } |
1758 | + | |
1759 | + | if (globals->haveMinWriteFrq()){ |
1760 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1761 | + | } |
1762 | + | |
1763 | + | if (globals->haveMinWriteFrq()){ |
1764 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
1765 | + | } |
1766 | + | |
1767 | + | if (globals->haveMinResetFrq()){ |
1768 | + | param->setResetFrq(globals->getMinResetFrq()); |
1769 | + | } |
1770 | + | |
1771 | + | if (globals->haveMinLSMaxIter()){ |
1772 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1773 | + | } |
1774 | + | |
1775 | + | if (globals->haveMinLSTol()){ |
1776 | + | param->setLineSearchTol(globals->getMinLSTol()); |
1777 | + | } |
1778 | + | |
1779 | + | //creat the minimizer |
1780 | + | minimizer = new PRCGMinimizer(nlp, param); |
1781 | + | minimizer->setLineSearchStrategy(nlp, GoldenSection); |
1782 | + | minimizer->setOutputFunctor(outputFunc); |
1783 | + | |
1784 | + | //store the minimizer into simInfo |
1785 | + | info[i].the_minimizer = minimizer; |
1786 | + | info[i].has_minimizer = true; |
1787 | + | } |
1788 | + | |
1789 | + | } |
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