# | 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 "RigidBody.hpp" |
13 | + | //#include "ConjugateMinimizer.hpp" |
14 | + | #include "OOPSEMinimizer.hpp" |
15 | ||
16 | #ifdef IS_MPI | |
17 | #include "mpiBASS.h" | |
18 | #include "mpiSimulation.hpp" | |
19 | #endif | |
20 | ||
21 | + | // some defines for ensemble and Forcefield cases |
22 | + | |
23 | + | #define NVE_ENS 0 |
24 | + | #define NVT_ENS 1 |
25 | + | #define NPTi_ENS 2 |
26 | + | #define NPTf_ENS 3 |
27 | + | #define NPTxyz_ENS 4 |
28 | + | |
29 | + | |
30 | + | #define FF_DUFF 0 |
31 | + | #define FF_LJ 1 |
32 | + | #define FF_EAM 2 |
33 | + | #define FF_H2O 3 |
34 | + | |
35 | + | using namespace std; |
36 | + | |
37 | + | /** |
38 | + | * Check whether dividend is divisble by divisor or not |
39 | + | */ |
40 | + | bool isDivisible(double dividend, double divisor){ |
41 | + | double tolerance = 0.000001; |
42 | + | double quotient; |
43 | + | double diff; |
44 | + | int intQuotient; |
45 | + | |
46 | + | quotient = dividend / divisor; |
47 | + | |
48 | + | if (quotient < 0) |
49 | + | quotient = -quotient; |
50 | + | |
51 | + | intQuotient = int (quotient + tolerance); |
52 | + | |
53 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
54 | + | |
55 | + | if (diff <= tolerance) |
56 | + | return true; |
57 | + | else |
58 | + | return false; |
59 | + | } |
60 | + | |
61 | SimSetup::SimSetup(){ | |
62 | + | |
63 | + | initSuspend = false; |
64 | + | isInfoArray = 0; |
65 | + | nInfo = 1; |
66 | + | |
67 | stamps = new MakeStamps(); | |
68 | globals = new Globals(); | |
69 | < | |
69 | > | |
70 | > | |
71 | #ifdef IS_MPI | |
72 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
72 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
73 | MPIcheckPoint(); | |
74 | #endif // IS_MPI | |
75 | } | |
# | Line 27 | Line 79 | SimSetup::~SimSetup(){ | |
79 | delete globals; | |
80 | } | |
81 | ||
82 | < | void SimSetup::parseFile( char* fileName ){ |
82 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
83 | > | info = the_info; |
84 | > | nInfo = theNinfo; |
85 | > | isInfoArray = 1; |
86 | > | initSuspend = true; |
87 | > | } |
88 | ||
89 | + | |
90 | + | void SimSetup::parseFile(char* fileName){ |
91 | #ifdef IS_MPI | |
92 | < | if( worldRank == 0 ){ |
92 | > | if (worldRank == 0){ |
93 | #endif // is_mpi | |
94 | < | |
94 | > | |
95 | inFileName = fileName; | |
96 | < | set_interface_stamps( stamps, globals ); |
97 | < | |
96 | > | set_interface_stamps(stamps, globals); |
97 | > | |
98 | #ifdef IS_MPI | |
99 | mpiEventInit(); | |
100 | #endif | |
101 | ||
102 | < | yacc_BASS( fileName ); |
102 | > | yacc_BASS(fileName); |
103 | ||
104 | #ifdef IS_MPI | |
105 | throwMPIEvent(NULL); | |
106 | } | |
107 | < | else receiveParse(); |
107 | > | else{ |
108 | > | receiveParse(); |
109 | > | } |
110 | #endif | |
111 | ||
112 | } | |
113 | ||
114 | #ifdef IS_MPI | |
115 | void SimSetup::receiveParse(void){ | |
116 | < | |
117 | < | set_interface_stamps( stamps, globals ); |
118 | < | mpiEventInit(); |
119 | < | MPIcheckPoint(); |
59 | < | mpiEventLoop(); |
60 | < | |
116 | > | set_interface_stamps(stamps, globals); |
117 | > | mpiEventInit(); |
118 | > | MPIcheckPoint(); |
119 | > | mpiEventLoop(); |
120 | } | |
121 | ||
122 | #endif // is_mpi | |
123 | ||
124 | < | void SimSetup::createSim( void ){ |
124 | > | void SimSetup::createSim(void){ |
125 | ||
126 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | ExtendedSystem* the_extendedsystem; |
70 | < | int i, j, k, globalAtomIndex; |
126 | > | // gather all of the information from the Bass file |
127 | ||
128 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
128 | > | gatherInfo(); |
129 | ||
130 | < | // set the easy ones first |
77 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
78 | < | simnfo->dt = the_globals->getDt(); |
79 | < | simnfo->run_time = the_globals->getRunTime(); |
130 | > | // creation of complex system objects |
131 | ||
132 | < | // get the ones we know are there, yet still may need some work. |
82 | < | n_components = the_globals->getNComponents(); |
83 | < | strcpy( force_field, the_globals->getForceField() ); |
132 | > | sysObjectsCreation(); |
133 | ||
134 | < | // get the ensemble and set up an extended system if we need it: |
86 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
87 | < | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | < | if (the_globals->haveTargetPressure()) |
91 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | < | else { |
93 | < | sprintf( painCave.errMsg, |
94 | < | "SimSetup error: If you use the constant pressure\n" |
95 | < | " ensemble, you must set targetPressure.\n" |
96 | < | " This was found in the BASS file.\n"); |
97 | < | painCave.isFatal = 1; |
98 | < | simError(); |
99 | < | } |
134 | > | // check on the post processing info |
135 | ||
136 | < | if (the_globals->haveTauThermostat()) |
102 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | < | else if (the_globals->haveQmass()) |
104 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | < | else { |
106 | < | sprintf( painCave.errMsg, |
107 | < | "SimSetup error: If you use one of the constant temperature\n" |
108 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | < | " Neither of these was found in the BASS file.\n"); |
110 | < | painCave.isFatal = 1; |
111 | < | simError(); |
112 | < | } |
136 | > | finalInfoCheck(); |
137 | ||
138 | < | if (the_globals->haveTauBarostat()) |
115 | < | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 | < | else { |
117 | < | sprintf( painCave.errMsg, |
118 | < | "SimSetup error: If you use the constant pressure\n" |
119 | < | " ensemble, you must set tauBarostat.\n" |
120 | < | " This was found in the BASS file.\n"); |
121 | < | painCave.isFatal = 1; |
122 | < | simError(); |
123 | < | } |
138 | > | // initialize the system coordinates |
139 | ||
140 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
141 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
127 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 | > | if ( !initSuspend ){ |
141 | > | initSystemCoords(); |
142 | ||
143 | < | if (the_globals->haveTauThermostat()) |
144 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 | < | else if (the_globals->haveQmass()) |
132 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
133 | < | else { |
134 | < | sprintf( painCave.errMsg, |
135 | < | "SimSetup error: If you use one of the constant temperature\n" |
136 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
137 | < | " Neither of these was found in the BASS file.\n"); |
138 | < | painCave.isFatal = 1; |
139 | < | simError(); |
140 | < | } |
141 | < | |
142 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
143 | < | } else { |
144 | < | sprintf( painCave.errMsg, |
145 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | < | "reverting to NVE for this simulation.\n", |
147 | < | ensemble ); |
148 | < | painCave.isFatal = 0; |
149 | < | simError(); |
150 | < | strcpy( ensemble, "NVE" ); |
143 | > | if( !(globals->getUseInitTime()) ) |
144 | > | info[0].currentTime = 0.0; |
145 | } | |
152 | – | strcpy( simnfo->ensemble, ensemble ); |
146 | ||
147 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 | < | simnfo->usePBC = the_globals->getPBC(); |
156 | < | |
157 | < | int usesDipoles = 0; |
158 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 | < | the_ff = new TraPPE_ExFF(); |
160 | < | usesDipoles = 1; |
161 | < | } |
162 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 | < | else{ |
164 | < | sprintf( painCave.errMsg, |
165 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
166 | < | force_field ); |
167 | < | painCave.isFatal = 1; |
168 | < | simError(); |
169 | < | } |
147 | > | // make the output filenames |
148 | ||
149 | + | makeOutNames(); |
150 | + | |
151 | #ifdef IS_MPI | |
152 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
153 | < | MPIcheckPoint(); |
174 | < | #endif // is_mpi |
152 | > | mpiSim->mpiRefresh(); |
153 | > | #endif |
154 | ||
155 | < | |
155 | > | // initialize the Fortran |
156 | ||
157 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
179 | < | the_components = the_globals->getComponents(); |
180 | < | components_nmol = new int[n_components]; |
181 | < | comp_stamps = new MoleculeStamp*[n_components]; |
157 | > | initFortran(); |
158 | ||
159 | < | if( !the_globals->haveNMol() ){ |
160 | < | // we don't have the total number of molecules, so we assume it is |
161 | < | // given in each component |
159 | > | if (globals->haveMinimizer()) |
160 | > | // make minimizer |
161 | > | makeMinimizer(); |
162 | > | else |
163 | > | // make the integrator |
164 | > | makeIntegrator(); |
165 | ||
166 | < | tot_nmol = 0; |
188 | < | for( i=0; i<n_components; i++ ){ |
166 | > | } |
167 | ||
190 | – | if( !the_components[i]->haveNMol() ){ |
191 | – | // we have a problem |
192 | – | sprintf( painCave.errMsg, |
193 | – | "SimSetup Error. No global NMol or component NMol" |
194 | – | " given. Cannot calculate the number of atoms.\n" ); |
195 | – | painCave.isFatal = 1; |
196 | – | simError(); |
197 | – | } |
168 | ||
169 | < | tot_nmol += the_components[i]->getNMol(); |
170 | < | components_nmol[i] = the_components[i]->getNMol(); |
171 | < | } |
172 | < | } |
173 | < | else{ |
174 | < | sprintf( painCave.errMsg, |
175 | < | "SimSetup error.\n" |
176 | < | "\tSorry, the ability to specify total" |
177 | < | " nMols and then give molfractions in the components\n" |
178 | < | "\tis not currently supported." |
179 | < | " Please give nMol in the components.\n" ); |
180 | < | painCave.isFatal = 1; |
181 | < | simError(); |
182 | < | |
183 | < | |
184 | < | // tot_nmol = the_globals->getNMol(); |
185 | < | |
186 | < | // //we have the total number of molecules, now we check for molfractions |
187 | < | // for( i=0; i<n_components; i++ ){ |
188 | < | |
189 | < | // if( !the_components[i]->haveMolFraction() ){ |
190 | < | |
191 | < | // if( !the_components[i]->haveNMol() ){ |
192 | < | // //we have a problem |
193 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
194 | < | // << " nMol was given in component |
195 | < | |
196 | < | } |
197 | < | |
198 | < | #ifdef IS_MPI |
199 | < | strcpy( checkPointMsg, "Have the number of components" ); |
200 | < | MPIcheckPoint(); |
201 | < | #endif // is_mpi |
202 | < | |
203 | < | // make an array of molecule stamps that match the components used. |
204 | < | // also extract the used stamps out into a separate linked list |
205 | < | |
206 | < | simnfo->nComponents = n_components; |
207 | < | simnfo->componentsNmol = components_nmol; |
208 | < | simnfo->compStamps = comp_stamps; |
209 | < | simnfo->headStamp = new LinkedMolStamp(); |
210 | < | |
211 | < | char* id; |
212 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
213 | < | LinkedMolStamp* currentStamp = NULL; |
214 | < | for( i=0; i<n_components; i++ ){ |
215 | < | |
216 | < | id = the_components[i]->getType(); |
217 | < | comp_stamps[i] = NULL; |
218 | < | |
219 | < | // check to make sure the component isn't already in the list |
220 | < | |
221 | < | comp_stamps[i] = headStamp->match( id ); |
252 | < | if( comp_stamps[i] == NULL ){ |
253 | < | |
254 | < | // extract the component from the list; |
255 | < | |
256 | < | currentStamp = the_stamps->extractMolStamp( id ); |
257 | < | if( currentStamp == NULL ){ |
258 | < | sprintf( painCave.errMsg, |
259 | < | "SimSetup error: Component \"%s\" was not found in the " |
260 | < | "list of declared molecules\n", |
261 | < | id ); |
262 | < | painCave.isFatal = 1; |
263 | < | simError(); |
264 | < | } |
169 | > | void SimSetup::makeMolecules(void){ |
170 | > | int i, j, k; |
171 | > | int exI, exJ, exK, exL, slI, slJ; |
172 | > | int tempI, tempJ, tempK, tempL; |
173 | > | int molI; |
174 | > | int stampID, atomOffset, rbOffset; |
175 | > | molInit molInfo; |
176 | > | DirectionalAtom* dAtom; |
177 | > | RigidBody* myRB; |
178 | > | StuntDouble* mySD; |
179 | > | LinkedAssign* extras; |
180 | > | LinkedAssign* current_extra; |
181 | > | AtomStamp* currentAtom; |
182 | > | BondStamp* currentBond; |
183 | > | BendStamp* currentBend; |
184 | > | TorsionStamp* currentTorsion; |
185 | > | RigidBodyStamp* currentRigidBody; |
186 | > | CutoffGroupStamp* currentCutoffGroup; |
187 | > | CutoffGroup* myCutoffGroup; |
188 | > | |
189 | > | bond_pair* theBonds; |
190 | > | bend_set* theBends; |
191 | > | torsion_set* theTorsions; |
192 | > | |
193 | > | set<int> skipList; |
194 | > | |
195 | > | double phi, theta, psi; |
196 | > | char* molName; |
197 | > | char rbName[100]; |
198 | > | |
199 | > | //init the forceField paramters |
200 | > | |
201 | > | the_ff->readParams(); |
202 | > | |
203 | > | // init the atoms |
204 | > | |
205 | > | int nMembers, nNew, rb1, rb2; |
206 | > | |
207 | > | for (k = 0; k < nInfo; k++){ |
208 | > | the_ff->setSimInfo(&(info[k])); |
209 | > | |
210 | > | atomOffset = 0; |
211 | > | |
212 | > | for (i = 0; i < info[k].n_mol; i++){ |
213 | > | stampID = info[k].molecules[i].getStampID(); |
214 | > | molName = comp_stamps[stampID]->getID(); |
215 | > | |
216 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
217 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
218 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
219 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
220 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
221 | > | molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
222 | ||
223 | < | headStamp->add( currentStamp ); |
267 | < | comp_stamps[i] = headStamp->match( id ); |
268 | < | } |
269 | < | } |
223 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
224 | ||
225 | < | #ifdef IS_MPI |
226 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
227 | < | MPIcheckPoint(); |
228 | < | #endif // is_mpi |
275 | < | |
225 | > | if (molInfo.nBonds > 0) |
226 | > | molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
227 | > | else |
228 | > | molInfo.myBonds = NULL; |
229 | ||
230 | + | if (molInfo.nBends > 0) |
231 | + | molInfo.myBends = new (Bend *) [molInfo.nBends]; |
232 | + | else |
233 | + | molInfo.myBends = NULL; |
234 | ||
235 | + | if (molInfo.nTorsions > 0) |
236 | + | molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
237 | + | else |
238 | + | molInfo.myTorsions = NULL; |
239 | ||
240 | < | // caclulate the number of atoms, bonds, bends and torsions |
240 | > | theBonds = new bond_pair[molInfo.nBonds]; |
241 | > | theBends = new bend_set[molInfo.nBends]; |
242 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
243 | > | |
244 | > | // make the Atoms |
245 | ||
246 | < | tot_atoms = 0; |
247 | < | tot_bonds = 0; |
283 | < | tot_bends = 0; |
284 | < | tot_torsions = 0; |
285 | < | for( i=0; i<n_components; i++ ){ |
286 | < | |
287 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
288 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
289 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
290 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
291 | < | } |
246 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
247 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
248 | ||
249 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
249 | > | if (currentAtom->haveOrientation()){ |
250 | > | dAtom = new DirectionalAtom((j + atomOffset), |
251 | > | info[k].getConfiguration()); |
252 | > | info[k].n_oriented++; |
253 | > | molInfo.myAtoms[j] = dAtom; |
254 | ||
255 | < | simnfo->n_atoms = tot_atoms; |
256 | < | simnfo->n_bonds = tot_bonds; |
257 | < | simnfo->n_bends = tot_bends; |
298 | < | simnfo->n_torsions = tot_torsions; |
299 | < | simnfo->n_SRI = tot_SRI; |
300 | < | simnfo->n_mol = tot_nmol; |
301 | < | |
302 | < | simnfo->molMembershipArray = new int[tot_atoms]; |
255 | > | // Directional Atoms have standard unit vectors which are oriented |
256 | > | // in space using the three Euler angles. We assume the standard |
257 | > | // unit vector was originally along the z axis below. |
258 | ||
259 | + | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
260 | + | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
261 | + | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
262 | + | |
263 | + | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
264 | + | |
265 | + | } |
266 | + | else{ |
267 | + | |
268 | + | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
269 | + | |
270 | + | } |
271 | + | |
272 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
273 | #ifdef IS_MPI | |
274 | ||
275 | < | // divide the molecules among processors here. |
307 | < | |
308 | < | mpiSim = new mpiSimulation( simnfo ); |
309 | < | |
310 | < | globalIndex = mpiSim->divideLabor(); |
275 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
276 | ||
277 | < | // set up the local variables |
278 | < | |
314 | < | int localMol, allMol; |
315 | < | 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; |
322 | < | local_atoms = 0; |
323 | < | local_bonds = 0; |
324 | < | local_bends = 0; |
325 | < | local_torsions = 0; |
326 | < | 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 | + | tempI = theBonds[j].a; |
287 | + | tempJ = theBonds[j].b; |
288 | ||
289 | < | for( i=0; i<n_components; i++ ){ |
289 | > | #ifdef IS_MPI |
290 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
291 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
292 | > | #else |
293 | > | exI = tempI + 1; |
294 | > | exJ = tempJ + 1; |
295 | > | #endif |
296 | ||
297 | < | for( j=0; j<components_nmol[i]; j++ ){ |
332 | < | |
333 | < | if( mol2proc[allMol] == worldRank ){ |
334 | < | |
335 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
336 | < | local_bonds += comp_stamps[i]->getNBonds(); |
337 | < | local_bends += comp_stamps[i]->getNBends(); |
338 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
339 | < | localMol++; |
340 | < | } |
341 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 | < | globalAtomIndex++; |
297 | > | info[k].excludes->addPair(exI, exJ); |
298 | } | |
299 | ||
300 | < | allMol++; |
301 | < | } |
302 | < | } |
303 | < | local_SRI = local_bonds + local_bends + local_torsions; |
304 | < | |
305 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
352 | < | |
353 | < | if( local_atoms != simnfo->n_atoms ){ |
354 | < | sprintf( painCave.errMsg, |
355 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
356 | < | " localAtom (%d) are not equal.\n", |
357 | < | simnfo->n_atoms, |
358 | < | local_atoms ); |
359 | < | painCave.isFatal = 1; |
360 | < | simError(); |
361 | < | } |
300 | > | //make the bends |
301 | > | for (j = 0; j < molInfo.nBends; j++){ |
302 | > | currentBend = comp_stamps[stampID]->getBend(j); |
303 | > | theBends[j].a = currentBend->getA() + atomOffset; |
304 | > | theBends[j].b = currentBend->getB() + atomOffset; |
305 | > | theBends[j].c = currentBend->getC() + atomOffset; |
306 | ||
307 | < | simnfo->n_bonds = local_bonds; |
308 | < | simnfo->n_bends = local_bends; |
309 | < | simnfo->n_torsions = local_torsions; |
366 | < | simnfo->n_SRI = local_SRI; |
367 | < | simnfo->n_mol = localMol; |
307 | > | if (currentBend->haveExtras()){ |
308 | > | extras = currentBend->getExtras(); |
309 | > | current_extra = extras; |
310 | ||
311 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
312 | < | MPIcheckPoint(); |
313 | < | |
314 | < | |
315 | < | #endif // is_mpi |
316 | < | |
311 | > | while (current_extra != NULL){ |
312 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
313 | > | switch (current_extra->getType()){ |
314 | > | case 0: |
315 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
316 | > | theBends[j].isGhost = 1; |
317 | > | break; |
318 | ||
319 | < | // create the atom and short range interaction arrays |
319 | > | case 1: |
320 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
321 | > | atomOffset; |
322 | > | theBends[j].isGhost = 1; |
323 | > | break; |
324 | ||
325 | < | Atom::createArrays(simnfo->n_atoms); |
326 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
327 | < | the_molecules = new Molecule[simnfo->n_mol]; |
328 | < | int molIndex; |
325 | > | default: |
326 | > | sprintf(painCave.errMsg, |
327 | > | "SimSetup Error: ghostVectorSource was neither a " |
328 | > | "double nor an int.\n" |
329 | > | "-->Bend[%d] in %s\n", |
330 | > | j, comp_stamps[stampID]->getID()); |
331 | > | painCave.isFatal = 1; |
332 | > | simError(); |
333 | > | } |
334 | > | } |
335 | > | else{ |
336 | > | sprintf(painCave.errMsg, |
337 | > | "SimSetup Error: unhandled bend assignment:\n" |
338 | > | " -->%s in Bend[%d] in %s\n", |
339 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
340 | > | painCave.isFatal = 1; |
341 | > | simError(); |
342 | > | } |
343 | ||
344 | < | // initialize the molecule's stampID's |
344 | > | current_extra = current_extra->getNext(); |
345 | > | } |
346 | > | } |
347 | ||
348 | < | #ifdef IS_MPI |
349 | < | |
348 | > | if (theBends[j].isGhost) { |
349 | > | |
350 | > | tempI = theBends[j].a; |
351 | > | tempJ = theBends[j].b; |
352 | > | |
353 | > | #ifdef IS_MPI |
354 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
355 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
356 | > | #else |
357 | > | exI = tempI + 1; |
358 | > | exJ = tempJ + 1; |
359 | > | #endif |
360 | > | info[k].excludes->addPair(exI, exJ); |
361 | ||
362 | < | molIndex = 0; |
389 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
390 | < | |
391 | < | if(mol2proc[i] == worldRank ){ |
392 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
393 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
394 | < | the_molecules[molIndex].setGlobalIndex( i ); |
395 | < | molIndex++; |
396 | < | } |
397 | < | } |
362 | > | } else { |
363 | ||
364 | < | #else // is_mpi |
365 | < | |
366 | < | molIndex = 0; |
367 | < | globalAtomIndex = 0; |
368 | < | for(i=0; i<n_components; i++){ |
369 | < | for(j=0; j<components_nmol[i]; j++ ){ |
370 | < | the_molecules[molIndex].setStampID( i ); |
371 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
372 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
373 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
374 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
375 | < | globalAtomIndex++; |
364 | > | tempI = theBends[j].a; |
365 | > | tempJ = theBends[j].b; |
366 | > | tempK = theBends[j].c; |
367 | > | |
368 | > | #ifdef IS_MPI |
369 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
370 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
371 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
372 | > | #else |
373 | > | exI = tempI + 1; |
374 | > | exJ = tempJ + 1; |
375 | > | exK = tempK + 1; |
376 | > | #endif |
377 | > | |
378 | > | info[k].excludes->addPair(exI, exK); |
379 | > | info[k].excludes->addPair(exI, exJ); |
380 | > | info[k].excludes->addPair(exJ, exK); |
381 | > | } |
382 | } | |
412 | – | molIndex++; |
413 | – | } |
414 | – | } |
415 | – | |
383 | ||
384 | < | #endif // is_mpi |
384 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
385 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
386 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
387 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
388 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
389 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
390 | ||
391 | + | tempI = theTorsions[j].a; |
392 | + | tempJ = theTorsions[j].b; |
393 | + | tempK = theTorsions[j].c; |
394 | + | tempL = theTorsions[j].d; |
395 | ||
396 | < | if( simnfo->n_SRI ){ |
397 | < | |
398 | < | Exclude::createArray(simnfo->n_SRI); |
399 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
400 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
401 | < | simnfo->globalExcludes = new int; |
402 | < | simnfo->n_exclude = simnfo->n_SRI; |
403 | < | } |
404 | < | else{ |
405 | < | |
406 | < | Exclude::createArray( 1 ); |
431 | < | the_excludes = new Exclude*; |
432 | < | the_excludes[0] = new Exclude(0); |
433 | < | the_excludes[0]->setPair( 0,0 ); |
434 | < | simnfo->globalExcludes = new int; |
435 | < | simnfo->globalExcludes[0] = 0; |
436 | < | simnfo->n_exclude = 0; |
437 | < | } |
396 | > | #ifdef IS_MPI |
397 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
398 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
399 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
400 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
401 | > | #else |
402 | > | exI = tempI + 1; |
403 | > | exJ = tempJ + 1; |
404 | > | exK = tempK + 1; |
405 | > | exL = tempL + 1; |
406 | > | #endif |
407 | ||
408 | < | // set the arrays into the SimInfo object |
408 | > | info[k].excludes->addPair(exI, exJ); |
409 | > | info[k].excludes->addPair(exI, exK); |
410 | > | info[k].excludes->addPair(exI, exL); |
411 | > | info[k].excludes->addPair(exJ, exK); |
412 | > | info[k].excludes->addPair(exJ, exL); |
413 | > | info[k].excludes->addPair(exK, exL); |
414 | > | } |
415 | ||
416 | < | simnfo->atoms = the_atoms; |
417 | < | simnfo->molecules = the_molecules; |
418 | < | simnfo->nGlobalExcludes = 0; |
419 | < | simnfo->excludes = the_excludes; |
416 | > | |
417 | > | molInfo.myRigidBodies.clear(); |
418 | > | |
419 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
420 | ||
421 | + | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
422 | + | nMembers = currentRigidBody->getNMembers(); |
423 | ||
424 | < | // get some of the tricky things that may still be in the globals |
424 | > | // Create the Rigid Body: |
425 | ||
426 | < | |
450 | < | if( the_globals->haveBox() ){ |
451 | < | simnfo->box_x = the_globals->getBox(); |
452 | < | simnfo->box_y = the_globals->getBox(); |
453 | < | simnfo->box_z = the_globals->getBox(); |
454 | < | } |
455 | < | else if( the_globals->haveDensity() ){ |
426 | > | myRB = new RigidBody(); |
427 | ||
428 | < | double vol; |
429 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
430 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
431 | < | simnfo->box_y = simnfo->box_x; |
461 | < | simnfo->box_z = simnfo->box_x; |
462 | < | } |
463 | < | else{ |
464 | < | if( !the_globals->haveBoxX() ){ |
465 | < | sprintf( painCave.errMsg, |
466 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
467 | < | painCave.isFatal = 1; |
468 | < | simError(); |
469 | < | } |
470 | < | simnfo->box_x = the_globals->getBoxX(); |
428 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
429 | > | myRB->setType(rbName); |
430 | > | |
431 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
432 | ||
433 | < | if( !the_globals->haveBoxY() ){ |
434 | < | sprintf( painCave.errMsg, |
474 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
475 | < | painCave.isFatal = 1; |
476 | < | simError(); |
477 | < | } |
478 | < | simnfo->box_y = the_globals->getBoxY(); |
433 | > | // molI is atom numbering inside this molecule |
434 | > | molI = currentRigidBody->getMember(rb1); |
435 | ||
436 | < | if( !the_globals->haveBoxZ() ){ |
437 | < | sprintf( painCave.errMsg, |
482 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
483 | < | painCave.isFatal = 1; |
484 | < | simError(); |
485 | < | } |
486 | < | simnfo->box_z = the_globals->getBoxZ(); |
487 | < | } |
436 | > | // tempI is atom numbering on local processor |
437 | > | tempI = molI + atomOffset; |
438 | ||
439 | < | #ifdef IS_MPI |
440 | < | strcpy( checkPointMsg, "Box size set up" ); |
441 | < | MPIcheckPoint(); |
492 | < | #endif // is_mpi |
439 | > | // currentAtom is the AtomStamp (which we need for |
440 | > | // rigid body reference positions) |
441 | > | currentAtom = comp_stamps[stampID]->getAtom(molI); |
442 | ||
443 | + | // When we add to the rigid body, add the atom itself and |
444 | + | // the stamp info: |
445 | ||
446 | < | // initialize the arrays |
446 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
447 | > | |
448 | > | // Add this atom to the Skip List for the integrators |
449 | > | #ifdef IS_MPI |
450 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
451 | > | #else |
452 | > | slI = tempI; |
453 | > | #endif |
454 | > | skipList.insert(slI); |
455 | > | |
456 | > | } |
457 | > | |
458 | > | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
459 | > | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
460 | > | |
461 | > | tempI = currentRigidBody->getMember(rb1); |
462 | > | tempJ = currentRigidBody->getMember(rb2); |
463 | > | |
464 | > | // Some explanation is required here. |
465 | > | // Fortran indexing starts at 1, while c indexing starts at 0 |
466 | > | // Also, in parallel computations, the GlobalIndex is |
467 | > | // used for the exclude list: |
468 | > | |
469 | > | #ifdef IS_MPI |
470 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
471 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
472 | > | #else |
473 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
474 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
475 | > | #endif |
476 | > | |
477 | > | info[k].excludes->addPair(exI, exJ); |
478 | > | |
479 | > | } |
480 | > | } |
481 | ||
482 | < | the_ff->setSimInfo( simnfo ); |
482 | > | molInfo.myRigidBodies.push_back(myRB); |
483 | > | info[k].rigidBodies.push_back(myRB); |
484 | > | } |
485 | > | |
486 | ||
487 | < | makeMolecules(); |
488 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
489 | < | for(i=0; i<simnfo->n_atoms; i++){ |
502 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
503 | < | } |
504 | < | |
505 | < | if (the_globals->getUseRF() ) { |
506 | < | simnfo->useReactionField = 1; |
507 | < | |
508 | < | if( !the_globals->haveECR() ){ |
509 | < | sprintf( painCave.errMsg, |
510 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
511 | < | "box length for the electrostaticCutoffRadius.\n" |
512 | < | "I hope you have a very fast processor!\n"); |
513 | < | painCave.isFatal = 0; |
514 | < | simError(); |
515 | < | double smallest; |
516 | < | smallest = simnfo->box_x; |
517 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
518 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
519 | < | simnfo->ecr = 0.5 * smallest; |
520 | < | } else { |
521 | < | simnfo->ecr = the_globals->getECR(); |
522 | < | } |
487 | > | //creat cutoff group for molecule |
488 | > | molInfo.myCutoffGroups.clear(); |
489 | > | for (j = 0; j < molInfo.nCutoffGroups; j++){ |
490 | ||
491 | < | if( !the_globals->haveEST() ){ |
492 | < | sprintf( painCave.errMsg, |
493 | < | "SimSetup Warning: using default value of 0.05 * the " |
494 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
495 | < | ); |
496 | < | painCave.isFatal = 0; |
497 | < | simError(); |
498 | < | simnfo->est = 0.05 * simnfo->ecr; |
499 | < | } else { |
500 | < | simnfo->est = the_globals->getEST(); |
501 | < | } |
502 | < | |
503 | < | if(!the_globals->haveDielectric() ){ |
504 | < | sprintf( painCave.errMsg, |
505 | < | "SimSetup Error: You are trying to use Reaction Field without" |
506 | < | "setting a dielectric constant!\n" |
507 | < | ); |
508 | < | painCave.isFatal = 1; |
542 | < | simError(); |
543 | < | } |
544 | < | simnfo->dielectric = the_globals->getDielectric(); |
545 | < | } else { |
546 | < | if (usesDipoles) { |
491 | > | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
492 | > | nMembers = currentCutoffGroup->getNMembers(); |
493 | > | |
494 | > | myCutoffGroup = new CutoffGroup(); |
495 | > | |
496 | > | for (int cg = 0; cg < nMembers; cg++) { |
497 | > | |
498 | > | // molI is atom numbering inside this molecule |
499 | > | molI = currentCutoffGroup->getMember(cg); |
500 | > | |
501 | > | // tempI is atom numbering on local processor |
502 | > | tempI = molI + atomOffset; |
503 | > | |
504 | > | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
505 | > | } |
506 | > | |
507 | > | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
508 | > | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
509 | ||
510 | < | if( !the_globals->haveECR() ){ |
511 | < | sprintf( painCave.errMsg, |
512 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
513 | < | "box length for the electrostaticCutoffRadius.\n" |
514 | < | "I hope you have a very fast processor!\n"); |
515 | < | painCave.isFatal = 0; |
554 | < | simError(); |
555 | < | double smallest; |
556 | < | smallest = simnfo->box_x; |
557 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
558 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 | < | simnfo->ecr = 0.5 * smallest; |
560 | < | } else { |
561 | < | simnfo->ecr = the_globals->getECR(); |
562 | < | } |
510 | > | |
511 | > | |
512 | > | // After this is all set up, scan through the atoms to |
513 | > | // see if they can be added to the integrableObjects: |
514 | > | |
515 | > | molInfo.myIntegrableObjects.clear(); |
516 | ||
564 | – | if( !the_globals->haveEST() ){ |
565 | – | sprintf( painCave.errMsg, |
566 | – | "SimSetup Warning: using default value of 5%% of the " |
567 | – | "electrostaticCutoffRadius for the " |
568 | – | "electrostaticSkinThickness\n" |
569 | – | ); |
570 | – | painCave.isFatal = 0; |
571 | – | simError(); |
572 | – | simnfo->est = 0.05 * simnfo->ecr; |
573 | – | } else { |
574 | – | simnfo->est = the_globals->getEST(); |
575 | – | } |
576 | – | } |
577 | – | } |
517 | ||
518 | < | #ifdef IS_MPI |
580 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
581 | < | MPIcheckPoint(); |
582 | < | #endif // is_mpi |
518 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
519 | ||
584 | – | if( the_globals->haveInitialConfig() ){ |
585 | – | |
586 | – | InitializeFromFile* fileInit; |
587 | – | #ifdef IS_MPI // is_mpi |
588 | – | if( worldRank == 0 ){ |
589 | – | #endif //is_mpi |
590 | – | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
520 | #ifdef IS_MPI | |
521 | < | }else fileInit = new InitializeFromFile( NULL ); |
521 | > | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
522 | > | #else |
523 | > | slJ = j+atomOffset; |
524 | #endif | |
594 | – | fileInit->read_xyz( simnfo ); // default velocities on |
525 | ||
526 | < | delete fileInit; |
597 | < | } |
598 | < | else{ |
526 | > | // if they aren't on the skip list, then they can be integrated |
527 | ||
528 | < | #ifdef IS_MPI |
528 | > | if (skipList.find(slJ) == skipList.end()) { |
529 | > | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
530 | > | info[k].integrableObjects.push_back(mySD); |
531 | > | molInfo.myIntegrableObjects.push_back(mySD); |
532 | > | } |
533 | > | } |
534 | ||
535 | < | // no init from bass |
603 | < | |
604 | < | sprintf( painCave.errMsg, |
605 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
606 | < | painCave.isFatal; |
607 | < | simError(); |
608 | < | |
609 | < | #else |
535 | > | // all rigid bodies are integrated: |
536 | ||
537 | < | initFromBass(); |
537 | > | for (j = 0; j < molInfo.nRigidBodies; j++) { |
538 | > | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
539 | > | info[k].integrableObjects.push_back(mySD); |
540 | > | molInfo.myIntegrableObjects.push_back(mySD); |
541 | > | } |
542 | > | |
543 | > | |
544 | > | // send the arrays off to the forceField for init. |
545 | > | |
546 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
547 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
548 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
549 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
550 | > | theTorsions); |
551 | ||
552 | + | info[k].molecules[i].initialize(molInfo); |
553 | ||
614 | – | #endif |
615 | – | } |
554 | ||
555 | + | atomOffset += molInfo.nAtoms; |
556 | + | delete[] theBonds; |
557 | + | delete[] theBends; |
558 | + | delete[] theTorsions; |
559 | + | } |
560 | + | } |
561 | + | |
562 | #ifdef IS_MPI | |
563 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
563 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
564 | MPIcheckPoint(); | |
565 | #endif // is_mpi | |
566 | ||
567 | + | // clean up the forcefield |
568 | ||
569 | < | |
624 | < | |
625 | < | |
569 | > | if (!globals->haveRcut()){ |
570 | ||
571 | < | |
572 | < | #ifdef IS_MPI |
573 | < | if( worldRank == 0 ){ |
630 | < | #endif // is_mpi |
571 | > | the_ff->calcRcut(); |
572 | > | |
573 | > | } else { |
574 | ||
575 | < | if( the_globals->haveFinalConfig() ){ |
633 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
634 | < | } |
635 | < | else{ |
636 | < | strcpy( simnfo->finalName, inFileName ); |
637 | < | char* endTest; |
638 | < | int nameLength = strlen( simnfo->finalName ); |
639 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
640 | < | if( !strcmp( endTest, ".bass" ) ){ |
641 | < | strcpy( endTest, ".eor" ); |
642 | < | } |
643 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
644 | < | strcpy( endTest, ".eor" ); |
645 | < | } |
646 | < | else{ |
647 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
648 | < | if( !strcmp( endTest, ".bss" ) ){ |
649 | < | strcpy( endTest, ".eor" ); |
650 | < | } |
651 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
652 | < | strcpy( endTest, ".eor" ); |
653 | < | } |
654 | < | else{ |
655 | < | strcat( simnfo->finalName, ".eor" ); |
656 | < | } |
657 | < | } |
658 | < | } |
659 | < | |
660 | < | // make the sample and status out names |
661 | < | |
662 | < | strcpy( simnfo->sampleName, inFileName ); |
663 | < | char* endTest; |
664 | < | int nameLength = strlen( simnfo->sampleName ); |
665 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
666 | < | if( !strcmp( endTest, ".bass" ) ){ |
667 | < | strcpy( endTest, ".dump" ); |
668 | < | } |
669 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
670 | < | strcpy( endTest, ".dump" ); |
671 | < | } |
672 | < | else{ |
673 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
674 | < | if( !strcmp( endTest, ".bss" ) ){ |
675 | < | strcpy( endTest, ".dump" ); |
676 | < | } |
677 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
678 | < | strcpy( endTest, ".dump" ); |
679 | < | } |
680 | < | else{ |
681 | < | strcat( simnfo->sampleName, ".dump" ); |
682 | < | } |
683 | < | } |
684 | < | |
685 | < | strcpy( simnfo->statusName, inFileName ); |
686 | < | nameLength = strlen( simnfo->statusName ); |
687 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
688 | < | if( !strcmp( endTest, ".bass" ) ){ |
689 | < | strcpy( endTest, ".stat" ); |
690 | < | } |
691 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
692 | < | strcpy( endTest, ".stat" ); |
693 | < | } |
694 | < | else{ |
695 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
696 | < | if( !strcmp( endTest, ".bss" ) ){ |
697 | < | strcpy( endTest, ".stat" ); |
698 | < | } |
699 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
700 | < | strcpy( endTest, ".stat" ); |
701 | < | } |
702 | < | else{ |
703 | < | strcat( simnfo->statusName, ".stat" ); |
704 | < | } |
705 | < | } |
706 | < | |
707 | < | #ifdef IS_MPI |
575 | > | the_ff->setRcut( globals->getRcut() ); |
576 | } | |
709 | – | #endif // is_mpi |
710 | – | |
711 | – | // set the status, sample, and themal kick times |
712 | – | |
713 | – | if( the_globals->haveSampleTime() ){ |
714 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
715 | – | simnfo->statusTime = simnfo->sampleTime; |
716 | – | simnfo->thermalTime = simnfo->sampleTime; |
717 | – | } |
718 | – | else{ |
719 | – | simnfo->sampleTime = the_globals->getRunTime(); |
720 | – | simnfo->statusTime = simnfo->sampleTime; |
721 | – | simnfo->thermalTime = simnfo->sampleTime; |
722 | – | } |
577 | ||
578 | < | if( the_globals->haveStatusTime() ){ |
579 | < | simnfo->statusTime = the_globals->getStatusTime(); |
726 | < | } |
578 | > | the_ff->cleanMe(); |
579 | > | } |
580 | ||
581 | < | if( the_globals->haveThermalTime() ){ |
729 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
730 | < | } |
731 | < | |
732 | < | // check for the temperature set flag |
733 | < | |
734 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
735 | < | |
736 | < | |
737 | < | // // make the longe range forces and the integrator |
738 | < | |
739 | < | // new AllLong( simnfo ); |
740 | < | |
741 | < | |
742 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
743 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
744 | < | } |
745 | < | else if( !strcmp( force_field, "LJ" ) ){ |
746 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
747 | < | } |
748 | < | |
749 | < | #ifdef IS_MPI |
750 | < | mpiSim->mpiRefresh(); |
751 | < | #endif |
752 | < | |
753 | < | // initialize the Fortran |
754 | < | |
755 | < | |
756 | < | simnfo->refreshSim(); |
757 | < | |
758 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
759 | < | the_ff->initForceField( LB_MIXING_RULE ); |
760 | < | } |
761 | < | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
762 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
763 | < | } |
764 | < | else{ |
765 | < | sprintf( painCave.errMsg, |
766 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
767 | < | simnfo->mixingRule ); |
768 | < | painCave.isFatal = 1; |
769 | < | simError(); |
770 | < | } |
771 | < | |
772 | < | |
773 | < | #ifdef IS_MPI |
774 | < | strcpy( checkPointMsg, |
775 | < | "Successfully intialized the mixingRule for Fortran." ); |
776 | < | MPIcheckPoint(); |
777 | < | #endif // is_mpi |
778 | < | } |
779 | < | |
780 | < | |
781 | < | void SimSetup::makeMolecules( void ){ |
782 | < | |
783 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
784 | < | molInit info; |
785 | < | DirectionalAtom* dAtom; |
786 | < | LinkedAssign* extras; |
787 | < | LinkedAssign* current_extra; |
788 | < | AtomStamp* currentAtom; |
789 | < | BondStamp* currentBond; |
790 | < | BendStamp* currentBend; |
791 | < | TorsionStamp* currentTorsion; |
792 | < | |
793 | < | bond_pair* theBonds; |
794 | < | bend_set* theBends; |
795 | < | torsion_set* theTorsions; |
796 | < | |
797 | < | |
798 | < | //init the forceField paramters |
799 | < | |
800 | < | the_ff->readParams(); |
801 | < | |
802 | < | |
803 | < | // init the atoms |
804 | < | |
805 | < | double ux, uy, uz, u, uSqr; |
806 | < | |
807 | < | atomOffset = 0; |
808 | < | excludeOffset = 0; |
809 | < | for(i=0; i<simnfo->n_mol; i++){ |
810 | < | |
811 | < | stampID = the_molecules[i].getStampID(); |
812 | < | |
813 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
814 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
815 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
816 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
817 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
818 | < | |
819 | < | info.myAtoms = &the_atoms[atomOffset]; |
820 | < | info.myExcludes = &the_excludes[excludeOffset]; |
821 | < | info.myBonds = new Bond*[info.nBonds]; |
822 | < | info.myBends = new Bend*[info.nBends]; |
823 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
824 | < | |
825 | < | theBonds = new bond_pair[info.nBonds]; |
826 | < | theBends = new bend_set[info.nBends]; |
827 | < | theTorsions = new torsion_set[info.nTorsions]; |
828 | < | |
829 | < | // make the Atoms |
830 | < | |
831 | < | for(j=0; j<info.nAtoms; j++){ |
832 | < | |
833 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
834 | < | if( currentAtom->haveOrientation() ){ |
835 | < | |
836 | < | dAtom = new DirectionalAtom(j + atomOffset); |
837 | < | simnfo->n_oriented++; |
838 | < | info.myAtoms[j] = dAtom; |
839 | < | |
840 | < | ux = currentAtom->getOrntX(); |
841 | < | uy = currentAtom->getOrntY(); |
842 | < | uz = currentAtom->getOrntZ(); |
843 | < | |
844 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
845 | < | |
846 | < | u = sqrt( uSqr ); |
847 | < | ux = ux / u; |
848 | < | uy = uy / u; |
849 | < | uz = uz / u; |
850 | < | |
851 | < | dAtom->setSUx( ux ); |
852 | < | dAtom->setSUy( uy ); |
853 | < | dAtom->setSUz( uz ); |
854 | < | } |
855 | < | else{ |
856 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
857 | < | } |
858 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
859 | < | |
860 | < | #ifdef IS_MPI |
861 | < | |
862 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
863 | < | |
864 | < | #endif // is_mpi |
865 | < | } |
866 | < | |
867 | < | // make the bonds |
868 | < | for(j=0; j<info.nBonds; j++){ |
869 | < | |
870 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
871 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
872 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
873 | < | |
874 | < | exI = theBonds[j].a; |
875 | < | exJ = theBonds[j].b; |
876 | < | |
877 | < | // exclude_I must always be the smaller of the pair |
878 | < | if( exI > exJ ){ |
879 | < | tempEx = exI; |
880 | < | exI = exJ; |
881 | < | exJ = tempEx; |
882 | < | } |
883 | < | #ifdef IS_MPI |
884 | < | tempEx = exI; |
885 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
886 | < | tempEx = exJ; |
887 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
888 | < | |
889 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
890 | < | #else // isn't MPI |
891 | < | |
892 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
893 | < | #endif //is_mpi |
894 | < | } |
895 | < | excludeOffset += info.nBonds; |
896 | < | |
897 | < | //make the bends |
898 | < | for(j=0; j<info.nBends; j++){ |
899 | < | |
900 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
901 | < | theBends[j].a = currentBend->getA() + atomOffset; |
902 | < | theBends[j].b = currentBend->getB() + atomOffset; |
903 | < | theBends[j].c = currentBend->getC() + atomOffset; |
904 | < | |
905 | < | if( currentBend->haveExtras() ){ |
906 | < | |
907 | < | extras = currentBend->getExtras(); |
908 | < | current_extra = extras; |
909 | < | |
910 | < | while( current_extra != NULL ){ |
911 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
912 | < | |
913 | < | switch( current_extra->getType() ){ |
914 | < | |
915 | < | case 0: |
916 | < | theBends[j].ghost = |
917 | < | current_extra->getInt() + atomOffset; |
918 | < | theBends[j].isGhost = 1; |
919 | < | break; |
920 | < | |
921 | < | case 1: |
922 | < | theBends[j].ghost = |
923 | < | (int)current_extra->getDouble() + atomOffset; |
924 | < | theBends[j].isGhost = 1; |
925 | < | break; |
926 | < | |
927 | < | default: |
928 | < | sprintf( painCave.errMsg, |
929 | < | "SimSetup Error: ghostVectorSource was neither a " |
930 | < | "double nor an int.\n" |
931 | < | "-->Bend[%d] in %s\n", |
932 | < | j, comp_stamps[stampID]->getID() ); |
933 | < | painCave.isFatal = 1; |
934 | < | simError(); |
935 | < | } |
936 | < | } |
937 | < | |
938 | < | else{ |
939 | < | |
940 | < | sprintf( painCave.errMsg, |
941 | < | "SimSetup Error: unhandled bend assignment:\n" |
942 | < | " -->%s in Bend[%d] in %s\n", |
943 | < | current_extra->getlhs(), |
944 | < | j, comp_stamps[stampID]->getID() ); |
945 | < | painCave.isFatal = 1; |
946 | < | simError(); |
947 | < | } |
948 | < | |
949 | < | current_extra = current_extra->getNext(); |
950 | < | } |
951 | < | } |
952 | < | |
953 | < | if( !theBends[j].isGhost ){ |
954 | < | |
955 | < | exI = theBends[j].a; |
956 | < | exJ = theBends[j].c; |
957 | < | } |
958 | < | else{ |
959 | < | |
960 | < | exI = theBends[j].a; |
961 | < | exJ = theBends[j].b; |
962 | < | } |
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 | < | } |
970 | < | #ifdef IS_MPI |
971 | < | tempEx = exI; |
972 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
973 | < | tempEx = exJ; |
974 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
975 | < | |
976 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
977 | < | #else // isn't MPI |
978 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
979 | < | #endif //is_mpi |
980 | < | } |
981 | < | excludeOffset += info.nBends; |
982 | < | |
983 | < | for(j=0; j<info.nTorsions; j++){ |
984 | < | |
985 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
986 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
987 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
988 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
989 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
990 | < | |
991 | < | exI = theTorsions[j].a; |
992 | < | exJ = theTorsions[j].d; |
993 | < | |
994 | < | // exclude_I must always be the smaller of the pair |
995 | < | if( exI > exJ ){ |
996 | < | tempEx = exI; |
997 | < | exI = exJ; |
998 | < | exJ = tempEx; |
999 | < | } |
1000 | < | #ifdef IS_MPI |
1001 | < | tempEx = exI; |
1002 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1003 | < | tempEx = exJ; |
1004 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1005 | < | |
1006 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1007 | < | #else // isn't MPI |
1008 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1009 | < | #endif //is_mpi |
1010 | < | } |
1011 | < | excludeOffset += info.nTorsions; |
1012 | < | |
1013 | < | |
1014 | < | // send the arrays off to the forceField for init. |
1015 | < | |
1016 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1017 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1018 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1019 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1020 | < | |
1021 | < | |
1022 | < | the_molecules[i].initialize( info ); |
1023 | < | |
1024 | < | |
1025 | < | atomOffset += info.nAtoms; |
1026 | < | delete[] theBonds; |
1027 | < | delete[] theBends; |
1028 | < | delete[] theTorsions; |
1029 | < | } |
1030 | < | |
1031 | < | #ifdef IS_MPI |
1032 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1033 | < | MPIcheckPoint(); |
1034 | < | #endif // is_mpi |
1035 | < | |
1036 | < | // clean up the forcefield |
1037 | < | the_ff->calcRcut(); |
1038 | < | the_ff->cleanMe(); |
1039 | < | |
1040 | < | } |
1041 | < | |
1042 | < | void SimSetup::initFromBass( void ){ |
1043 | < | |
581 | > | void SimSetup::initFromBass(void){ |
582 | int i, j, k; | |
583 | int n_cells; | |
584 | double cellx, celly, cellz; | |
# | Line 1049 | Line 587 | void SimSetup::initFromBass( void ){ | |
587 | int n_extra; | |
588 | int have_extra, done; | |
589 | ||
590 | < | temp1 = (double)tot_nmol / 4.0; |
591 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
592 | < | temp3 = ceil( temp2 ); |
590 | > | double vel[3]; |
591 | > | vel[0] = 0.0; |
592 | > | vel[1] = 0.0; |
593 | > | vel[2] = 0.0; |
594 | ||
595 | < | have_extra =0; |
596 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
597 | < | have_extra =1; |
595 | > | temp1 = (double) tot_nmol / 4.0; |
596 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
597 | > | temp3 = ceil(temp2); |
598 | ||
599 | < | n_cells = (int)temp3 - 1; |
600 | < | cellx = simnfo->box_x / temp3; |
601 | < | celly = simnfo->box_y / temp3; |
602 | < | cellz = simnfo->box_z / temp3; |
1064 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1065 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1066 | < | n_per_extra = (int)ceil( temp1 ); |
599 | > | have_extra = 0; |
600 | > | if (temp2 < temp3){ |
601 | > | // we have a non-complete lattice |
602 | > | have_extra = 1; |
603 | ||
604 | < | if( n_per_extra > 4){ |
605 | < | sprintf( painCave.errMsg, |
606 | < | "SimSetup error. There has been an error in constructing" |
607 | < | " the non-complete lattice.\n" ); |
604 | > | n_cells = (int) temp3 - 1; |
605 | > | cellx = info[0].boxL[0] / temp3; |
606 | > | celly = info[0].boxL[1] / temp3; |
607 | > | cellz = info[0].boxL[2] / temp3; |
608 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
609 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
610 | > | n_per_extra = (int) ceil(temp1); |
611 | > | |
612 | > | if (n_per_extra > 4){ |
613 | > | sprintf(painCave.errMsg, |
614 | > | "SimSetup error. There has been an error in constructing" |
615 | > | " the non-complete lattice.\n"); |
616 | painCave.isFatal = 1; | |
617 | simError(); | |
618 | } | |
619 | } | |
620 | else{ | |
621 | < | n_cells = (int)temp3; |
622 | < | cellx = simnfo->box_x / temp3; |
623 | < | celly = simnfo->box_y / temp3; |
624 | < | cellz = simnfo->box_z / temp3; |
621 | > | n_cells = (int) temp3; |
622 | > | cellx = info[0].boxL[0] / temp3; |
623 | > | celly = info[0].boxL[1] / temp3; |
624 | > | cellz = info[0].boxL[2] / temp3; |
625 | } | |
626 | ||
627 | current_mol = 0; | |
# | Line 1085 | Line 629 | void SimSetup::initFromBass( void ){ | |
629 | current_comp = 0; | |
630 | current_atom_ndx = 0; | |
631 | ||
632 | < | for( i=0; i < n_cells ; i++ ){ |
633 | < | for( j=0; j < n_cells; j++ ){ |
634 | < | for( k=0; k < n_cells; k++ ){ |
632 | > | for (i = 0; i < n_cells ; i++){ |
633 | > | for (j = 0; j < n_cells; j++){ |
634 | > | for (k = 0; k < n_cells; k++){ |
635 | > | makeElement(i * cellx, j * celly, k * cellz); |
636 | ||
637 | < | makeElement( i * cellx, |
1093 | < | j * celly, |
1094 | < | k * cellz ); |
637 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
638 | ||
639 | < | makeElement( i * cellx + 0.5 * cellx, |
1097 | < | j * celly + 0.5 * celly, |
1098 | < | k * cellz ); |
639 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
640 | ||
641 | < | makeElement( i * cellx, |
1101 | < | j * celly + 0.5 * celly, |
1102 | < | k * cellz + 0.5 * cellz ); |
1103 | < | |
1104 | < | makeElement( i * cellx + 0.5 * cellx, |
1105 | < | j * celly, |
1106 | < | k * cellz + 0.5 * cellz ); |
641 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
642 | } | |
643 | } | |
644 | } | |
645 | ||
646 | < | if( have_extra ){ |
646 | > | if (have_extra){ |
647 | done = 0; | |
648 | ||
649 | int start_ndx; | |
650 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
651 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
650 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
651 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
652 | > | if (i < n_cells){ |
653 | > | if (j < n_cells){ |
654 | > | start_ndx = n_cells; |
655 | > | } |
656 | > | else |
657 | > | start_ndx = 0; |
658 | > | } |
659 | > | else |
660 | > | start_ndx = 0; |
661 | ||
662 | < | if( i < n_cells ){ |
662 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
663 | > | makeElement(i * cellx, j * celly, k * cellz); |
664 | > | done = (current_mol >= tot_nmol); |
665 | ||
666 | < | if( j < n_cells ){ |
667 | < | start_ndx = n_cells; |
668 | < | } |
669 | < | else start_ndx = 0; |
670 | < | } |
1125 | < | else start_ndx = 0; |
666 | > | if (!done && n_per_extra > 1){ |
667 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
668 | > | k * cellz); |
669 | > | done = (current_mol >= tot_nmol); |
670 | > | } |
671 | ||
672 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
673 | < | |
674 | < | makeElement( i * cellx, |
675 | < | j * celly, |
676 | < | k * cellz ); |
1132 | < | done = ( current_mol >= tot_nmol ); |
1133 | < | |
1134 | < | if( !done && n_per_extra > 1 ){ |
1135 | < | makeElement( i * cellx + 0.5 * cellx, |
1136 | < | j * celly + 0.5 * celly, |
1137 | < | k * cellz ); |
1138 | < | done = ( current_mol >= tot_nmol ); |
1139 | < | } |
672 | > | if (!done && n_per_extra > 2){ |
673 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
674 | > | k * cellz + 0.5 * cellz); |
675 | > | done = (current_mol >= tot_nmol); |
676 | > | } |
677 | ||
678 | < | if( !done && n_per_extra > 2){ |
679 | < | makeElement( i * cellx, |
680 | < | j * celly + 0.5 * celly, |
681 | < | k * cellz + 0.5 * cellz ); |
682 | < | done = ( current_mol >= tot_nmol ); |
683 | < | } |
1147 | < | |
1148 | < | if( !done && n_per_extra > 3){ |
1149 | < | makeElement( i * cellx + 0.5 * cellx, |
1150 | < | j * celly, |
1151 | < | k * cellz + 0.5 * cellz ); |
1152 | < | done = ( current_mol >= tot_nmol ); |
1153 | < | } |
1154 | < | } |
678 | > | if (!done && n_per_extra > 3){ |
679 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
680 | > | k * cellz + 0.5 * cellz); |
681 | > | done = (current_mol >= tot_nmol); |
682 | > | } |
683 | > | } |
684 | } | |
685 | } | |
686 | } | |
687 | ||
688 | < | |
689 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1161 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1162 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1163 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
688 | > | for (i = 0; i < info[0].n_atoms; i++){ |
689 | > | info[0].atoms[i]->setVel(vel); |
690 | } | |
691 | } | |
692 | ||
693 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1168 | < | |
693 | > | void SimSetup::makeElement(double x, double y, double z){ |
694 | int k; | |
695 | AtomStamp* current_atom; | |
696 | DirectionalAtom* dAtom; | |
697 | double rotMat[3][3]; | |
698 | + | double pos[3]; |
699 | ||
700 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
701 | < | |
702 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
703 | < | if( !current_atom->havePosition() ){ |
704 | < | sprintf( painCave.errMsg, |
705 | < | "SimSetup:initFromBass error.\n" |
706 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
707 | < | "\tThe initialization routine is unable to give a start" |
708 | < | " position.\n", |
1183 | < | comp_stamps[current_comp]->getID(), |
1184 | < | current_atom->getType() ); |
700 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
701 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
702 | > | if (!current_atom->havePosition()){ |
703 | > | sprintf(painCave.errMsg, |
704 | > | "SimSetup:initFromBass error.\n" |
705 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
706 | > | "\tThe initialization routine is unable to give a start" |
707 | > | " position.\n", |
708 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
709 | painCave.isFatal = 1; | |
710 | simError(); | |
711 | } | |
712 | ||
713 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
714 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
715 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
713 | > | pos[0] = x + current_atom->getPosX(); |
714 | > | pos[1] = y + current_atom->getPosY(); |
715 | > | pos[2] = z + current_atom->getPosZ(); |
716 | ||
717 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
717 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
718 | ||
719 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
719 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
720 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
721 | ||
722 | rotMat[0][0] = 1.0; | |
723 | rotMat[0][1] = 0.0; | |
# | Line 1206 | Line 731 | void SimSetup::makeElement( double x, double y, double | |
731 | rotMat[2][1] = 0.0; | |
732 | rotMat[2][2] = 1.0; | |
733 | ||
734 | < | dAtom->setA( rotMat ); |
734 | > | dAtom->setA(rotMat); |
735 | } | |
736 | ||
737 | current_atom_ndx++; | |
# | Line 1215 | Line 740 | void SimSetup::makeElement( double x, double y, double | |
740 | current_mol++; | |
741 | current_comp_mol++; | |
742 | ||
743 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1219 | < | |
743 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
744 | current_comp_mol = 0; | |
745 | < | current_comp++; |
745 | > | current_comp++; |
746 | > | } |
747 | > | } |
748 | > | |
749 | > | |
750 | > | void SimSetup::gatherInfo(void){ |
751 | > | int i; |
752 | > | |
753 | > | ensembleCase = -1; |
754 | > | ffCase = -1; |
755 | > | |
756 | > | // set the easy ones first |
757 | > | |
758 | > | for (i = 0; i < nInfo; i++){ |
759 | > | info[i].target_temp = globals->getTargetTemp(); |
760 | > | info[i].dt = globals->getDt(); |
761 | > | info[i].run_time = globals->getRunTime(); |
762 | > | } |
763 | > | n_components = globals->getNComponents(); |
764 | > | |
765 | > | |
766 | > | // get the forceField |
767 | > | |
768 | > | strcpy(force_field, globals->getForceField()); |
769 | > | |
770 | > | if (!strcasecmp(force_field, "DUFF")){ |
771 | > | ffCase = FF_DUFF; |
772 | > | } |
773 | > | else if (!strcasecmp(force_field, "LJ")){ |
774 | > | ffCase = FF_LJ; |
775 | > | } |
776 | > | else if (!strcasecmp(force_field, "EAM")){ |
777 | > | ffCase = FF_EAM; |
778 | > | } |
779 | > | else if (!strcasecmp(force_field, "WATER")){ |
780 | > | ffCase = FF_H2O; |
781 | > | } |
782 | > | else{ |
783 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
784 | > | force_field); |
785 | > | painCave.isFatal = 1; |
786 | > | simError(); |
787 | > | } |
788 | > | |
789 | > | // get the ensemble |
790 | > | |
791 | > | strcpy(ensemble, globals->getEnsemble()); |
792 | > | |
793 | > | if (!strcasecmp(ensemble, "NVE")){ |
794 | > | ensembleCase = NVE_ENS; |
795 | > | } |
796 | > | else if (!strcasecmp(ensemble, "NVT")){ |
797 | > | ensembleCase = NVT_ENS; |
798 | > | } |
799 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
800 | > | ensembleCase = NPTi_ENS; |
801 | > | } |
802 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
803 | > | ensembleCase = NPTf_ENS; |
804 | > | } |
805 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
806 | > | ensembleCase = NPTxyz_ENS; |
807 | > | } |
808 | > | else{ |
809 | > | sprintf(painCave.errMsg, |
810 | > | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
811 | > | "\treverting to NVE for this simulation.\n", |
812 | > | ensemble); |
813 | > | painCave.isFatal = 0; |
814 | > | simError(); |
815 | > | strcpy(ensemble, "NVE"); |
816 | > | ensembleCase = NVE_ENS; |
817 | > | } |
818 | > | |
819 | > | for (i = 0; i < nInfo; i++){ |
820 | > | strcpy(info[i].ensemble, ensemble); |
821 | > | |
822 | > | // get the mixing rule |
823 | > | |
824 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
825 | > | info[i].usePBC = globals->getPBC(); |
826 | > | } |
827 | > | |
828 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
829 | > | |
830 | > | the_components = globals->getComponents(); |
831 | > | components_nmol = new int[n_components]; |
832 | > | |
833 | > | |
834 | > | if (!globals->haveNMol()){ |
835 | > | // we don't have the total number of molecules, so we assume it is |
836 | > | // given in each component |
837 | > | |
838 | > | tot_nmol = 0; |
839 | > | for (i = 0; i < n_components; i++){ |
840 | > | if (!the_components[i]->haveNMol()){ |
841 | > | // we have a problem |
842 | > | sprintf(painCave.errMsg, |
843 | > | "SimSetup Error. No global NMol or component NMol given.\n" |
844 | > | "\tCannot calculate the number of atoms.\n"); |
845 | > | painCave.isFatal = 1; |
846 | > | simError(); |
847 | > | } |
848 | > | |
849 | > | tot_nmol += the_components[i]->getNMol(); |
850 | > | components_nmol[i] = the_components[i]->getNMol(); |
851 | > | } |
852 | > | } |
853 | > | else{ |
854 | > | sprintf(painCave.errMsg, |
855 | > | "SimSetup error.\n" |
856 | > | "\tSorry, the ability to specify total" |
857 | > | " nMols and then give molfractions in the components\n" |
858 | > | "\tis not currently supported." |
859 | > | " Please give nMol in the components.\n"); |
860 | > | painCave.isFatal = 1; |
861 | > | simError(); |
862 | > | } |
863 | > | |
864 | > | //check whether sample time, status time, thermal time and reset time are divisble by dt |
865 | > | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
866 | > | sprintf(painCave.errMsg, |
867 | > | "Sample time is not divisible by dt.\n" |
868 | > | "\tThis will result in samples that are not uniformly\n" |
869 | > | "\tdistributed in time. If this is a problem, change\n" |
870 | > | "\tyour sampleTime variable.\n"); |
871 | > | painCave.isFatal = 0; |
872 | > | simError(); |
873 | > | } |
874 | > | |
875 | > | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
876 | > | sprintf(painCave.errMsg, |
877 | > | "Status time is not divisible by dt.\n" |
878 | > | "\tThis will result in status reports that are not uniformly\n" |
879 | > | "\tdistributed in time. If this is a problem, change \n" |
880 | > | "\tyour statusTime variable.\n"); |
881 | > | painCave.isFatal = 0; |
882 | > | simError(); |
883 | > | } |
884 | > | |
885 | > | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
886 | > | sprintf(painCave.errMsg, |
887 | > | "Thermal time is not divisible by dt.\n" |
888 | > | "\tThis will result in thermalizations that are not uniformly\n" |
889 | > | "\tdistributed in time. If this is a problem, change \n" |
890 | > | "\tyour thermalTime variable.\n"); |
891 | > | painCave.isFatal = 0; |
892 | > | simError(); |
893 | > | } |
894 | > | |
895 | > | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
896 | > | sprintf(painCave.errMsg, |
897 | > | "Reset time is not divisible by dt.\n" |
898 | > | "\tThis will result in integrator resets that are not uniformly\n" |
899 | > | "\tdistributed in time. If this is a problem, change\n" |
900 | > | "\tyour resetTime variable.\n"); |
901 | > | painCave.isFatal = 0; |
902 | > | simError(); |
903 | > | } |
904 | > | |
905 | > | // set the status, sample, and thermal kick times |
906 | > | |
907 | > | for (i = 0; i < nInfo; i++){ |
908 | > | if (globals->haveSampleTime()){ |
909 | > | info[i].sampleTime = globals->getSampleTime(); |
910 | > | info[i].statusTime = info[i].sampleTime; |
911 | > | } |
912 | > | else{ |
913 | > | info[i].sampleTime = globals->getRunTime(); |
914 | > | info[i].statusTime = info[i].sampleTime; |
915 | > | } |
916 | > | |
917 | > | if (globals->haveStatusTime()){ |
918 | > | info[i].statusTime = globals->getStatusTime(); |
919 | > | } |
920 | > | |
921 | > | if (globals->haveThermalTime()){ |
922 | > | info[i].thermalTime = globals->getThermalTime(); |
923 | > | } else { |
924 | > | info[i].thermalTime = globals->getRunTime(); |
925 | > | } |
926 | > | |
927 | > | info[i].resetIntegrator = 0; |
928 | > | if( globals->haveResetTime() ){ |
929 | > | info[i].resetTime = globals->getResetTime(); |
930 | > | info[i].resetIntegrator = 1; |
931 | > | } |
932 | > | |
933 | > | // check for the temperature set flag |
934 | > | |
935 | > | if (globals->haveTempSet()) |
936 | > | info[i].setTemp = globals->getTempSet(); |
937 | > | |
938 | > | // check for the extended State init |
939 | > | |
940 | > | info[i].useInitXSstate = globals->getUseInitXSstate(); |
941 | > | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
942 | > | |
943 | > | } |
944 | > | |
945 | > | //setup seed for random number generator |
946 | > | int seedValue; |
947 | > | |
948 | > | if (globals->haveSeed()){ |
949 | > | seedValue = globals->getSeed(); |
950 | > | |
951 | > | if(seedValue / 1E9 == 0){ |
952 | > | sprintf(painCave.errMsg, |
953 | > | "Seed for sprng library should contain at least 9 digits\n" |
954 | > | "OOPSE will generate a seed for user\n"); |
955 | > | painCave.isFatal = 0; |
956 | > | simError(); |
957 | > | |
958 | > | //using seed generated by system instead of invalid seed set by user |
959 | > | #ifndef IS_MPI |
960 | > | seedValue = make_sprng_seed(); |
961 | > | #else |
962 | > | if (worldRank == 0){ |
963 | > | seedValue = make_sprng_seed(); |
964 | > | } |
965 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
966 | > | #endif |
967 | > | } |
968 | > | }//end of if branch of globals->haveSeed() |
969 | > | else{ |
970 | > | |
971 | > | #ifndef IS_MPI |
972 | > | seedValue = make_sprng_seed(); |
973 | > | #else |
974 | > | if (worldRank == 0){ |
975 | > | seedValue = make_sprng_seed(); |
976 | > | } |
977 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
978 | > | #endif |
979 | > | }//end of globals->haveSeed() |
980 | > | |
981 | > | for (int i = 0; i < nInfo; i++){ |
982 | > | info[i].setSeed(seedValue); |
983 | > | } |
984 | > | |
985 | > | #ifdef IS_MPI |
986 | > | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
987 | > | MPIcheckPoint(); |
988 | > | #endif // is_mpi |
989 | > | } |
990 | > | |
991 | > | |
992 | > | void SimSetup::finalInfoCheck(void){ |
993 | > | int index; |
994 | > | int usesDipoles; |
995 | > | int usesCharges; |
996 | > | int i; |
997 | > | |
998 | > | for (i = 0; i < nInfo; i++){ |
999 | > | // check electrostatic parameters |
1000 | > | |
1001 | > | index = 0; |
1002 | > | usesDipoles = 0; |
1003 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
1004 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
1005 | > | index++; |
1006 | > | } |
1007 | > | index = 0; |
1008 | > | usesCharges = 0; |
1009 | > | while ((index < info[i].n_atoms) && !usesCharges){ |
1010 | > | usesCharges= (info[i].atoms[index])->hasCharge(); |
1011 | > | index++; |
1012 | > | } |
1013 | > | #ifdef IS_MPI |
1014 | > | int myUse = usesDipoles; |
1015 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
1016 | > | #endif //is_mpi |
1017 | > | |
1018 | > | double theRcut, theRsw; |
1019 | > | |
1020 | > | if (globals->getUseRF()){ |
1021 | > | info[i].useReactionField = 1; |
1022 | > | |
1023 | > | if (!globals->haveRcut()){ |
1024 | > | sprintf(painCave.errMsg, |
1025 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1026 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1027 | > | "\tfor the cutoffRadius.\n"); |
1028 | > | painCave.isFatal = 0; |
1029 | > | simError(); |
1030 | > | theRcut = 15.0; |
1031 | > | } |
1032 | > | else{ |
1033 | > | theRcut = globals->getRcut(); |
1034 | > | } |
1035 | > | |
1036 | > | if (!globals->haveRsw()){ |
1037 | > | sprintf(painCave.errMsg, |
1038 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1039 | > | "\tOOPSE will use a default value of\n" |
1040 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1041 | > | painCave.isFatal = 0; |
1042 | > | simError(); |
1043 | > | theRsw = 0.95 * theRcut; |
1044 | > | } |
1045 | > | else{ |
1046 | > | theRsw = globals->getRsw(); |
1047 | > | } |
1048 | > | |
1049 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1050 | > | |
1051 | > | if (!globals->haveDielectric()){ |
1052 | > | sprintf(painCave.errMsg, |
1053 | > | "SimSetup Error: No Dielectric constant was set.\n" |
1054 | > | "\tYou are trying to use Reaction Field without" |
1055 | > | "\tsetting a dielectric constant!\n"); |
1056 | > | painCave.isFatal = 1; |
1057 | > | simError(); |
1058 | > | } |
1059 | > | info[i].dielectric = globals->getDielectric(); |
1060 | > | } |
1061 | > | else{ |
1062 | > | if (usesDipoles || usesCharges){ |
1063 | > | |
1064 | > | if (!globals->haveRcut()){ |
1065 | > | sprintf(painCave.errMsg, |
1066 | > | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1067 | > | "\tOOPSE will use a default value of 15.0 angstroms" |
1068 | > | "\tfor the cutoffRadius.\n"); |
1069 | > | painCave.isFatal = 0; |
1070 | > | simError(); |
1071 | > | theRcut = 15.0; |
1072 | > | } |
1073 | > | else{ |
1074 | > | theRcut = globals->getRcut(); |
1075 | > | } |
1076 | > | |
1077 | > | if (!globals->haveRsw()){ |
1078 | > | sprintf(painCave.errMsg, |
1079 | > | "SimSetup Warning: No value was set for switchingRadius.\n" |
1080 | > | "\tOOPSE will use a default value of\n" |
1081 | > | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1082 | > | painCave.isFatal = 0; |
1083 | > | simError(); |
1084 | > | theRsw = 0.95 * theRcut; |
1085 | > | } |
1086 | > | else{ |
1087 | > | theRsw = globals->getRsw(); |
1088 | > | } |
1089 | > | |
1090 | > | info[i].setDefaultRcut(theRcut, theRsw); |
1091 | > | |
1092 | > | } |
1093 | > | } |
1094 | > | } |
1095 | > | #ifdef IS_MPI |
1096 | > | strcpy(checkPointMsg, "post processing checks out"); |
1097 | > | MPIcheckPoint(); |
1098 | > | #endif // is_mpi |
1099 | > | } |
1100 | > | |
1101 | > | void SimSetup::initSystemCoords(void){ |
1102 | > | int i; |
1103 | > | |
1104 | > | char* inName; |
1105 | > | |
1106 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1107 | > | |
1108 | > | for (i = 0; i < info[0].n_atoms; i++) |
1109 | > | info[0].atoms[i]->setCoords(); |
1110 | > | |
1111 | > | if (globals->haveInitialConfig()){ |
1112 | > | InitializeFromFile* fileInit; |
1113 | > | #ifdef IS_MPI // is_mpi |
1114 | > | if (worldRank == 0){ |
1115 | > | #endif //is_mpi |
1116 | > | inName = globals->getInitialConfig(); |
1117 | > | fileInit = new InitializeFromFile(inName); |
1118 | > | #ifdef IS_MPI |
1119 | > | } |
1120 | > | else |
1121 | > | fileInit = new InitializeFromFile(NULL); |
1122 | > | #endif |
1123 | > | fileInit->readInit(info); // default velocities on |
1124 | > | |
1125 | > | delete fileInit; |
1126 | > | } |
1127 | > | else{ |
1128 | > | |
1129 | > | // no init from bass |
1130 | > | |
1131 | > | sprintf(painCave.errMsg, |
1132 | > | "Cannot intialize a simulation without an initial configuration file.\n"); |
1133 | > | painCave.isFatal = 1;; |
1134 | > | simError(); |
1135 | > | |
1136 | > | } |
1137 | > | |
1138 | > | #ifdef IS_MPI |
1139 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1140 | > | MPIcheckPoint(); |
1141 | > | #endif // is_mpi |
1142 | > | } |
1143 | > | |
1144 | > | |
1145 | > | void SimSetup::makeOutNames(void){ |
1146 | > | int k; |
1147 | > | |
1148 | > | |
1149 | > | for (k = 0; k < nInfo; k++){ |
1150 | > | #ifdef IS_MPI |
1151 | > | if (worldRank == 0){ |
1152 | > | #endif // is_mpi |
1153 | > | |
1154 | > | if (globals->haveFinalConfig()){ |
1155 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
1156 | > | } |
1157 | > | else{ |
1158 | > | strcpy(info[k].finalName, inFileName); |
1159 | > | char* endTest; |
1160 | > | int nameLength = strlen(info[k].finalName); |
1161 | > | endTest = &(info[k].finalName[nameLength - 5]); |
1162 | > | if (!strcmp(endTest, ".bass")){ |
1163 | > | strcpy(endTest, ".eor"); |
1164 | > | } |
1165 | > | else if (!strcmp(endTest, ".BASS")){ |
1166 | > | strcpy(endTest, ".eor"); |
1167 | > | } |
1168 | > | else{ |
1169 | > | endTest = &(info[k].finalName[nameLength - 4]); |
1170 | > | if (!strcmp(endTest, ".bss")){ |
1171 | > | strcpy(endTest, ".eor"); |
1172 | > | } |
1173 | > | else if (!strcmp(endTest, ".mdl")){ |
1174 | > | strcpy(endTest, ".eor"); |
1175 | > | } |
1176 | > | else{ |
1177 | > | strcat(info[k].finalName, ".eor"); |
1178 | > | } |
1179 | > | } |
1180 | > | } |
1181 | > | |
1182 | > | // make the sample and status out names |
1183 | > | |
1184 | > | strcpy(info[k].sampleName, inFileName); |
1185 | > | char* endTest; |
1186 | > | int nameLength = strlen(info[k].sampleName); |
1187 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
1188 | > | if (!strcmp(endTest, ".bass")){ |
1189 | > | strcpy(endTest, ".dump"); |
1190 | > | } |
1191 | > | else if (!strcmp(endTest, ".BASS")){ |
1192 | > | strcpy(endTest, ".dump"); |
1193 | > | } |
1194 | > | else{ |
1195 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1196 | > | if (!strcmp(endTest, ".bss")){ |
1197 | > | strcpy(endTest, ".dump"); |
1198 | > | } |
1199 | > | else if (!strcmp(endTest, ".mdl")){ |
1200 | > | strcpy(endTest, ".dump"); |
1201 | > | } |
1202 | > | else{ |
1203 | > | strcat(info[k].sampleName, ".dump"); |
1204 | > | } |
1205 | > | } |
1206 | > | |
1207 | > | strcpy(info[k].statusName, inFileName); |
1208 | > | nameLength = strlen(info[k].statusName); |
1209 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1210 | > | if (!strcmp(endTest, ".bass")){ |
1211 | > | strcpy(endTest, ".stat"); |
1212 | > | } |
1213 | > | else if (!strcmp(endTest, ".BASS")){ |
1214 | > | strcpy(endTest, ".stat"); |
1215 | > | } |
1216 | > | else{ |
1217 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1218 | > | if (!strcmp(endTest, ".bss")){ |
1219 | > | strcpy(endTest, ".stat"); |
1220 | > | } |
1221 | > | else if (!strcmp(endTest, ".mdl")){ |
1222 | > | strcpy(endTest, ".stat"); |
1223 | > | } |
1224 | > | else{ |
1225 | > | strcat(info[k].statusName, ".stat"); |
1226 | > | } |
1227 | > | } |
1228 | > | |
1229 | > | #ifdef IS_MPI |
1230 | > | |
1231 | > | } |
1232 | > | #endif // is_mpi |
1233 | > | } |
1234 | > | } |
1235 | > | |
1236 | > | |
1237 | > | void SimSetup::sysObjectsCreation(void){ |
1238 | > | int i, k; |
1239 | > | |
1240 | > | // create the forceField |
1241 | > | |
1242 | > | createFF(); |
1243 | > | |
1244 | > | // extract componentList |
1245 | > | |
1246 | > | compList(); |
1247 | > | |
1248 | > | // calc the number of atoms, bond, bends, and torsions |
1249 | > | |
1250 | > | calcSysValues(); |
1251 | > | |
1252 | > | #ifdef IS_MPI |
1253 | > | // divide the molecules among the processors |
1254 | > | |
1255 | > | mpiMolDivide(); |
1256 | > | #endif //is_mpi |
1257 | > | |
1258 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1259 | > | |
1260 | > | makeSysArrays(); |
1261 | > | |
1262 | > | // make and initialize the molecules (all but atomic coordinates) |
1263 | > | |
1264 | > | makeMolecules(); |
1265 | > | |
1266 | > | for (k = 0; k < nInfo; k++){ |
1267 | > | info[k].identArray = new int[info[k].n_atoms]; |
1268 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1269 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1270 | > | } |
1271 | > | } |
1272 | > | } |
1273 | > | |
1274 | > | |
1275 | > | void SimSetup::createFF(void){ |
1276 | > | switch (ffCase){ |
1277 | > | case FF_DUFF: |
1278 | > | the_ff = new DUFF(); |
1279 | > | break; |
1280 | > | |
1281 | > | case FF_LJ: |
1282 | > | the_ff = new LJFF(); |
1283 | > | break; |
1284 | > | |
1285 | > | case FF_EAM: |
1286 | > | the_ff = new EAM_FF(); |
1287 | > | break; |
1288 | > | |
1289 | > | case FF_H2O: |
1290 | > | the_ff = new WATER(); |
1291 | > | break; |
1292 | > | |
1293 | > | default: |
1294 | > | sprintf(painCave.errMsg, |
1295 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1296 | > | painCave.isFatal = 1; |
1297 | > | simError(); |
1298 | > | } |
1299 | > | |
1300 | > | #ifdef IS_MPI |
1301 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1302 | > | MPIcheckPoint(); |
1303 | > | #endif // is_mpi |
1304 | > | } |
1305 | > | |
1306 | > | |
1307 | > | void SimSetup::compList(void){ |
1308 | > | int i; |
1309 | > | char* id; |
1310 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1311 | > | LinkedMolStamp* currentStamp = NULL; |
1312 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1313 | > | bool haveCutoffGroups; |
1314 | > | |
1315 | > | haveCutoffGroups = false; |
1316 | > | |
1317 | > | // make an array of molecule stamps that match the components used. |
1318 | > | // also extract the used stamps out into a separate linked list |
1319 | > | |
1320 | > | for (i = 0; i < nInfo; i++){ |
1321 | > | info[i].nComponents = n_components; |
1322 | > | info[i].componentsNmol = components_nmol; |
1323 | > | info[i].compStamps = comp_stamps; |
1324 | > | info[i].headStamp = headStamp; |
1325 | > | } |
1326 | > | |
1327 | > | |
1328 | > | for (i = 0; i < n_components; i++){ |
1329 | > | id = the_components[i]->getType(); |
1330 | > | comp_stamps[i] = NULL; |
1331 | > | |
1332 | > | // check to make sure the component isn't already in the list |
1333 | > | |
1334 | > | comp_stamps[i] = headStamp->match(id); |
1335 | > | if (comp_stamps[i] == NULL){ |
1336 | > | // extract the component from the list; |
1337 | > | |
1338 | > | currentStamp = stamps->extractMolStamp(id); |
1339 | > | if (currentStamp == NULL){ |
1340 | > | sprintf(painCave.errMsg, |
1341 | > | "SimSetup error: Component \"%s\" was not found in the " |
1342 | > | "list of declared molecules\n", |
1343 | > | id); |
1344 | > | painCave.isFatal = 1; |
1345 | > | simError(); |
1346 | > | } |
1347 | > | |
1348 | > | headStamp->add(currentStamp); |
1349 | > | comp_stamps[i] = headStamp->match(id); |
1350 | > | } |
1351 | > | |
1352 | > | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1353 | > | haveCutoffGroups = true; |
1354 | > | } |
1355 | > | |
1356 | > | for (i = 0; i < nInfo; i++) |
1357 | > | info[i].haveCutoffGroups = haveCutoffGroups; |
1358 | > | |
1359 | > | #ifdef IS_MPI |
1360 | > | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1361 | > | MPIcheckPoint(); |
1362 | > | #endif // is_mpi |
1363 | > | } |
1364 | > | |
1365 | > | void SimSetup::calcSysValues(void){ |
1366 | > | int i; |
1367 | > | |
1368 | > | int* molMembershipArray; |
1369 | > | |
1370 | > | tot_atoms = 0; |
1371 | > | tot_bonds = 0; |
1372 | > | tot_bends = 0; |
1373 | > | tot_torsions = 0; |
1374 | > | tot_rigid = 0; |
1375 | > | for (i = 0; i < n_components; i++){ |
1376 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1377 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1378 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1379 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1380 | > | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1381 | > | } |
1382 | > | |
1383 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1384 | > | molMembershipArray = new int[tot_atoms]; |
1385 | > | |
1386 | > | for (i = 0; i < nInfo; i++){ |
1387 | > | info[i].n_atoms = tot_atoms; |
1388 | > | info[i].n_bonds = tot_bonds; |
1389 | > | info[i].n_bends = tot_bends; |
1390 | > | info[i].n_torsions = tot_torsions; |
1391 | > | info[i].n_SRI = tot_SRI; |
1392 | > | info[i].n_mol = tot_nmol; |
1393 | > | |
1394 | > | info[i].molMembershipArray = molMembershipArray; |
1395 | > | } |
1396 | > | } |
1397 | > | |
1398 | > | #ifdef IS_MPI |
1399 | > | |
1400 | > | void SimSetup::mpiMolDivide(void){ |
1401 | > | int i, j, k; |
1402 | > | int localMol, allMol; |
1403 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1404 | > | int local_rigid; |
1405 | > | vector<int> globalMolIndex; |
1406 | > | |
1407 | > | mpiSim = new mpiSimulation(info); |
1408 | > | |
1409 | > | mpiSim->divideLabor(); |
1410 | > | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1411 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1412 | > | |
1413 | > | // set up the local variables |
1414 | > | |
1415 | > | mol2proc = mpiSim->getMolToProcMap(); |
1416 | > | molCompType = mpiSim->getMolComponentType(); |
1417 | > | |
1418 | > | allMol = 0; |
1419 | > | localMol = 0; |
1420 | > | local_atoms = 0; |
1421 | > | local_bonds = 0; |
1422 | > | local_bends = 0; |
1423 | > | local_torsions = 0; |
1424 | > | local_rigid = 0; |
1425 | > | globalAtomCounter = 0; |
1426 | > | |
1427 | > | for (i = 0; i < n_components; i++){ |
1428 | > | for (j = 0; j < components_nmol[i]; j++){ |
1429 | > | if (mol2proc[allMol] == worldRank){ |
1430 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1431 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1432 | > | local_bends += comp_stamps[i]->getNBends(); |
1433 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1434 | > | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1435 | > | localMol++; |
1436 | > | } |
1437 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1438 | > | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1439 | > | globalAtomCounter++; |
1440 | > | } |
1441 | > | |
1442 | > | allMol++; |
1443 | > | } |
1444 | > | } |
1445 | > | local_SRI = local_bonds + local_bends + local_torsions; |
1446 | > | |
1447 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1448 | > | |
1449 | > | |
1450 | > | if (local_atoms != info[0].n_atoms){ |
1451 | > | sprintf(painCave.errMsg, |
1452 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1453 | > | "\tlocalAtom (%d) are not equal.\n", |
1454 | > | info[0].n_atoms, local_atoms); |
1455 | > | painCave.isFatal = 1; |
1456 | > | simError(); |
1457 | > | } |
1458 | > | |
1459 | > | info[0].n_bonds = local_bonds; |
1460 | > | info[0].n_bends = local_bends; |
1461 | > | info[0].n_torsions = local_torsions; |
1462 | > | info[0].n_SRI = local_SRI; |
1463 | > | info[0].n_mol = localMol; |
1464 | > | |
1465 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1466 | > | MPIcheckPoint(); |
1467 | > | } |
1468 | > | |
1469 | > | #endif // is_mpi |
1470 | > | |
1471 | > | |
1472 | > | void SimSetup::makeSysArrays(void){ |
1473 | > | |
1474 | > | #ifndef IS_MPI |
1475 | > | int k, j; |
1476 | > | #endif // is_mpi |
1477 | > | int i, l; |
1478 | > | |
1479 | > | Atom** the_atoms; |
1480 | > | Molecule* the_molecules; |
1481 | > | |
1482 | > | for (l = 0; l < nInfo; l++){ |
1483 | > | // create the atom and short range interaction arrays |
1484 | > | |
1485 | > | the_atoms = new Atom * [info[l].n_atoms]; |
1486 | > | the_molecules = new Molecule[info[l].n_mol]; |
1487 | > | int molIndex; |
1488 | > | |
1489 | > | // initialize the molecule's stampID's |
1490 | > | |
1491 | > | #ifdef IS_MPI |
1492 | > | |
1493 | > | |
1494 | > | molIndex = 0; |
1495 | > | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1496 | > | if (mol2proc[i] == worldRank){ |
1497 | > | the_molecules[molIndex].setStampID(molCompType[i]); |
1498 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1499 | > | the_molecules[molIndex].setGlobalIndex(i); |
1500 | > | molIndex++; |
1501 | > | } |
1502 | > | } |
1503 | > | |
1504 | > | #else // is_mpi |
1505 | > | |
1506 | > | molIndex = 0; |
1507 | > | globalAtomCounter = 0; |
1508 | > | for (i = 0; i < n_components; i++){ |
1509 | > | for (j = 0; j < components_nmol[i]; j++){ |
1510 | > | the_molecules[molIndex].setStampID(i); |
1511 | > | the_molecules[molIndex].setMyIndex(molIndex); |
1512 | > | the_molecules[molIndex].setGlobalIndex(molIndex); |
1513 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1514 | > | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1515 | > | globalAtomCounter++; |
1516 | > | } |
1517 | > | molIndex++; |
1518 | > | } |
1519 | > | } |
1520 | > | |
1521 | > | |
1522 | > | #endif // is_mpi |
1523 | > | |
1524 | > | info[l].globalExcludes = new int; |
1525 | > | info[l].globalExcludes[0] = 0; |
1526 | > | |
1527 | > | // set the arrays into the SimInfo object |
1528 | > | |
1529 | > | info[l].atoms = the_atoms; |
1530 | > | info[l].molecules = the_molecules; |
1531 | > | info[l].nGlobalExcludes = 0; |
1532 | > | |
1533 | > | the_ff->setSimInfo(info); |
1534 | } | |
1535 | } | |
1536 | + | |
1537 | + | void SimSetup::makeIntegrator(void){ |
1538 | + | int k; |
1539 | + | |
1540 | + | NVE<RealIntegrator>* myNVE = NULL; |
1541 | + | NVT<RealIntegrator>* myNVT = NULL; |
1542 | + | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1543 | + | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1544 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1545 | + | |
1546 | + | for (k = 0; k < nInfo; k++){ |
1547 | + | switch (ensembleCase){ |
1548 | + | case NVE_ENS: |
1549 | + | if (globals->haveZconstraints()){ |
1550 | + | setupZConstraint(info[k]); |
1551 | + | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1552 | + | } |
1553 | + | else{ |
1554 | + | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1555 | + | } |
1556 | + | |
1557 | + | info->the_integrator = myNVE; |
1558 | + | break; |
1559 | + | |
1560 | + | case NVT_ENS: |
1561 | + | if (globals->haveZconstraints()){ |
1562 | + | setupZConstraint(info[k]); |
1563 | + | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1564 | + | } |
1565 | + | else |
1566 | + | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1567 | + | |
1568 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1569 | + | |
1570 | + | if (globals->haveTauThermostat()) |
1571 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1572 | + | else{ |
1573 | + | sprintf(painCave.errMsg, |
1574 | + | "SimSetup error: If you use the NVT\n" |
1575 | + | "\tensemble, you must set tauThermostat.\n"); |
1576 | + | painCave.isFatal = 1; |
1577 | + | simError(); |
1578 | + | } |
1579 | + | |
1580 | + | info->the_integrator = myNVT; |
1581 | + | break; |
1582 | + | |
1583 | + | case NPTi_ENS: |
1584 | + | if (globals->haveZconstraints()){ |
1585 | + | setupZConstraint(info[k]); |
1586 | + | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1587 | + | } |
1588 | + | else |
1589 | + | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1590 | + | |
1591 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1592 | + | |
1593 | + | if (globals->haveTargetPressure()) |
1594 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1595 | + | else{ |
1596 | + | sprintf(painCave.errMsg, |
1597 | + | "SimSetup error: If you use a constant pressure\n" |
1598 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1599 | + | painCave.isFatal = 1; |
1600 | + | simError(); |
1601 | + | } |
1602 | + | |
1603 | + | if (globals->haveTauThermostat()) |
1604 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1605 | + | else{ |
1606 | + | sprintf(painCave.errMsg, |
1607 | + | "SimSetup error: If you use an NPT\n" |
1608 | + | "\tensemble, you must set tauThermostat.\n"); |
1609 | + | painCave.isFatal = 1; |
1610 | + | simError(); |
1611 | + | } |
1612 | + | |
1613 | + | if (globals->haveTauBarostat()) |
1614 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1615 | + | else{ |
1616 | + | sprintf(painCave.errMsg, |
1617 | + | "SimSetup error: If you use an NPT\n" |
1618 | + | "\tensemble, you must set tauBarostat.\n"); |
1619 | + | painCave.isFatal = 1; |
1620 | + | simError(); |
1621 | + | } |
1622 | + | |
1623 | + | info->the_integrator = myNPTi; |
1624 | + | break; |
1625 | + | |
1626 | + | case NPTf_ENS: |
1627 | + | if (globals->haveZconstraints()){ |
1628 | + | setupZConstraint(info[k]); |
1629 | + | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1630 | + | } |
1631 | + | else |
1632 | + | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1633 | + | |
1634 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1635 | + | |
1636 | + | if (globals->haveTargetPressure()) |
1637 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1638 | + | else{ |
1639 | + | sprintf(painCave.errMsg, |
1640 | + | "SimSetup error: If you use a constant pressure\n" |
1641 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1642 | + | painCave.isFatal = 1; |
1643 | + | simError(); |
1644 | + | } |
1645 | + | |
1646 | + | if (globals->haveTauThermostat()) |
1647 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1648 | + | |
1649 | + | else{ |
1650 | + | sprintf(painCave.errMsg, |
1651 | + | "SimSetup error: If you use an NPT\n" |
1652 | + | "\tensemble, you must set tauThermostat.\n"); |
1653 | + | painCave.isFatal = 1; |
1654 | + | simError(); |
1655 | + | } |
1656 | + | |
1657 | + | if (globals->haveTauBarostat()) |
1658 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1659 | + | |
1660 | + | else{ |
1661 | + | sprintf(painCave.errMsg, |
1662 | + | "SimSetup error: If you use an NPT\n" |
1663 | + | "\tensemble, you must set tauBarostat.\n"); |
1664 | + | painCave.isFatal = 1; |
1665 | + | simError(); |
1666 | + | } |
1667 | + | |
1668 | + | info->the_integrator = myNPTf; |
1669 | + | break; |
1670 | + | |
1671 | + | case NPTxyz_ENS: |
1672 | + | if (globals->haveZconstraints()){ |
1673 | + | setupZConstraint(info[k]); |
1674 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1675 | + | } |
1676 | + | else |
1677 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1678 | + | |
1679 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1680 | + | |
1681 | + | if (globals->haveTargetPressure()) |
1682 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1683 | + | else{ |
1684 | + | sprintf(painCave.errMsg, |
1685 | + | "SimSetup error: If you use a constant pressure\n" |
1686 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1687 | + | painCave.isFatal = 1; |
1688 | + | simError(); |
1689 | + | } |
1690 | + | |
1691 | + | if (globals->haveTauThermostat()) |
1692 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1693 | + | else{ |
1694 | + | sprintf(painCave.errMsg, |
1695 | + | "SimSetup error: If you use an NPT\n" |
1696 | + | "\tensemble, you must set tauThermostat.\n"); |
1697 | + | painCave.isFatal = 1; |
1698 | + | simError(); |
1699 | + | } |
1700 | + | |
1701 | + | if (globals->haveTauBarostat()) |
1702 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1703 | + | else{ |
1704 | + | sprintf(painCave.errMsg, |
1705 | + | "SimSetup error: If you use an NPT\n" |
1706 | + | "\tensemble, you must set tauBarostat.\n"); |
1707 | + | painCave.isFatal = 1; |
1708 | + | simError(); |
1709 | + | } |
1710 | + | |
1711 | + | info->the_integrator = myNPTxyz; |
1712 | + | break; |
1713 | + | |
1714 | + | default: |
1715 | + | sprintf(painCave.errMsg, |
1716 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1717 | + | painCave.isFatal = 1; |
1718 | + | simError(); |
1719 | + | } |
1720 | + | } |
1721 | + | } |
1722 | + | |
1723 | + | void SimSetup::initFortran(void){ |
1724 | + | info[0].refreshSim(); |
1725 | + | |
1726 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1727 | + | the_ff->initForceField(LB_MIXING_RULE); |
1728 | + | } |
1729 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1730 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1731 | + | } |
1732 | + | else{ |
1733 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1734 | + | info[0].mixingRule); |
1735 | + | painCave.isFatal = 1; |
1736 | + | simError(); |
1737 | + | } |
1738 | + | |
1739 | + | |
1740 | + | #ifdef IS_MPI |
1741 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1742 | + | MPIcheckPoint(); |
1743 | + | #endif // is_mpi |
1744 | + | } |
1745 | + | |
1746 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1747 | + | int nZConstraints; |
1748 | + | ZconStamp** zconStamp; |
1749 | + | |
1750 | + | if (globals->haveZconstraintTime()){ |
1751 | + | //add sample time of z-constraint into SimInfo's property list |
1752 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1753 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1754 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1755 | + | theInfo.addProperty(zconsTimeProp); |
1756 | + | } |
1757 | + | else{ |
1758 | + | sprintf(painCave.errMsg, |
1759 | + | "ZConstraint error: If you use a ZConstraint,\n" |
1760 | + | "\tyou must set zconsTime.\n"); |
1761 | + | painCave.isFatal = 1; |
1762 | + | simError(); |
1763 | + | } |
1764 | + | |
1765 | + | //push zconsTol into siminfo, if user does not specify |
1766 | + | //value for zconsTol, a default value will be used |
1767 | + | DoubleData* zconsTol = new DoubleData(); |
1768 | + | zconsTol->setID(ZCONSTOL_ID); |
1769 | + | if (globals->haveZconsTol()){ |
1770 | + | zconsTol->setData(globals->getZconsTol()); |
1771 | + | } |
1772 | + | else{ |
1773 | + | double defaultZConsTol = 0.01; |
1774 | + | sprintf(painCave.errMsg, |
1775 | + | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1776 | + | "\tOOPSE will use a default value of %f.\n" |
1777 | + | "\tTo set the tolerance, use the zconsTol variable.\n", |
1778 | + | defaultZConsTol); |
1779 | + | painCave.isFatal = 0; |
1780 | + | simError(); |
1781 | + | |
1782 | + | zconsTol->setData(defaultZConsTol); |
1783 | + | } |
1784 | + | theInfo.addProperty(zconsTol); |
1785 | + | |
1786 | + | //set Force Subtraction Policy |
1787 | + | StringData* zconsForcePolicy = new StringData(); |
1788 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1789 | + | |
1790 | + | if (globals->haveZconsForcePolicy()){ |
1791 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1792 | + | } |
1793 | + | else{ |
1794 | + | sprintf(painCave.errMsg, |
1795 | + | "ZConstraint Warning: No force subtraction policy was set.\n" |
1796 | + | "\tOOPSE will use PolicyByMass.\n" |
1797 | + | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1798 | + | painCave.isFatal = 0; |
1799 | + | simError(); |
1800 | + | zconsForcePolicy->setData("BYMASS"); |
1801 | + | } |
1802 | + | |
1803 | + | theInfo.addProperty(zconsForcePolicy); |
1804 | + | |
1805 | + | //set zcons gap |
1806 | + | DoubleData* zconsGap = new DoubleData(); |
1807 | + | zconsGap->setID(ZCONSGAP_ID); |
1808 | + | |
1809 | + | if (globals->haveZConsGap()){ |
1810 | + | zconsGap->setData(globals->getZconsGap()); |
1811 | + | theInfo.addProperty(zconsGap); |
1812 | + | } |
1813 | + | |
1814 | + | //set zcons fixtime |
1815 | + | DoubleData* zconsFixtime = new DoubleData(); |
1816 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
1817 | + | |
1818 | + | if (globals->haveZConsFixTime()){ |
1819 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
1820 | + | theInfo.addProperty(zconsFixtime); |
1821 | + | } |
1822 | + | |
1823 | + | //set zconsUsingSMD |
1824 | + | IntData* zconsUsingSMD = new IntData(); |
1825 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
1826 | + | |
1827 | + | if (globals->haveZConsUsingSMD()){ |
1828 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
1829 | + | theInfo.addProperty(zconsUsingSMD); |
1830 | + | } |
1831 | + | |
1832 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1833 | + | //Be careful, do not use inFileName, since it is a pointer which |
1834 | + | //point to a string at master node, and slave nodes do not contain that string |
1835 | + | |
1836 | + | string zconsOutput(theInfo.finalName); |
1837 | + | |
1838 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1839 | + | |
1840 | + | StringData* zconsFilename = new StringData(); |
1841 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1842 | + | zconsFilename->setData(zconsOutput); |
1843 | + | |
1844 | + | theInfo.addProperty(zconsFilename); |
1845 | + | |
1846 | + | //setup index, pos and other parameters of z-constraint molecules |
1847 | + | nZConstraints = globals->getNzConstraints(); |
1848 | + | theInfo.nZconstraints = nZConstraints; |
1849 | + | |
1850 | + | zconStamp = globals->getZconStamp(); |
1851 | + | ZConsParaItem tempParaItem; |
1852 | + | |
1853 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1854 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1855 | + | |
1856 | + | for (int i = 0; i < nZConstraints; i++){ |
1857 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1858 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1859 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1860 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1861 | + | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
1862 | + | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
1863 | + | zconsParaData->addItem(tempParaItem); |
1864 | + | } |
1865 | + | |
1866 | + | //check the uniqueness of index |
1867 | + | if(!zconsParaData->isIndexUnique()){ |
1868 | + | sprintf(painCave.errMsg, |
1869 | + | "ZConstraint Error: molIndex is not unique!\n"); |
1870 | + | painCave.isFatal = 1; |
1871 | + | simError(); |
1872 | + | } |
1873 | + | |
1874 | + | //sort the parameters by index of molecules |
1875 | + | zconsParaData->sortByIndex(); |
1876 | + | |
1877 | + | //push data into siminfo, therefore, we can retrieve later |
1878 | + | theInfo.addProperty(zconsParaData); |
1879 | + | } |
1880 | + | |
1881 | + | void SimSetup::makeMinimizer(){ |
1882 | + | |
1883 | + | OOPSEMinimizer* myOOPSEMinimizer; |
1884 | + | MinimizerParameterSet* param; |
1885 | + | char minimizerName[100]; |
1886 | + | |
1887 | + | for (int i = 0; i < nInfo; i++){ |
1888 | + | |
1889 | + | //prepare parameter set for minimizer |
1890 | + | param = new MinimizerParameterSet(); |
1891 | + | param->setDefaultParameter(); |
1892 | + | |
1893 | + | if (globals->haveMinimizer()){ |
1894 | + | param->setFTol(globals->getMinFTol()); |
1895 | + | } |
1896 | + | |
1897 | + | if (globals->haveMinGTol()){ |
1898 | + | param->setGTol(globals->getMinGTol()); |
1899 | + | } |
1900 | + | |
1901 | + | if (globals->haveMinMaxIter()){ |
1902 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1903 | + | } |
1904 | + | |
1905 | + | if (globals->haveMinWriteFrq()){ |
1906 | + | param->setMaxIteration(globals->getMinMaxIter()); |
1907 | + | } |
1908 | + | |
1909 | + | if (globals->haveMinWriteFrq()){ |
1910 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
1911 | + | } |
1912 | + | |
1913 | + | if (globals->haveMinStepSize()){ |
1914 | + | param->setStepSize(globals->getMinStepSize()); |
1915 | + | } |
1916 | + | |
1917 | + | if (globals->haveMinLSMaxIter()){ |
1918 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
1919 | + | } |
1920 | + | |
1921 | + | if (globals->haveMinLSTol()){ |
1922 | + | param->setLineSearchTol(globals->getMinLSTol()); |
1923 | + | } |
1924 | + | |
1925 | + | strcpy(minimizerName, globals->getMinimizer()); |
1926 | + | |
1927 | + | if (!strcasecmp(minimizerName, "CG")){ |
1928 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1929 | + | } |
1930 | + | else if (!strcasecmp(minimizerName, "SD")){ |
1931 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
1932 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
1933 | + | } |
1934 | + | else{ |
1935 | + | sprintf(painCave.errMsg, |
1936 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
1937 | + | painCave.isFatal = 0; |
1938 | + | simError(); |
1939 | + | |
1940 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
1941 | + | } |
1942 | + | info[i].the_integrator = myOOPSEMinimizer; |
1943 | + | |
1944 | + | //store the minimizer into simInfo |
1945 | + | info[i].the_minimizer = myOOPSEMinimizer; |
1946 | + | info[i].has_minimizer = true; |
1947 | + | } |
1948 | + | |
1949 | + | } |
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