# | Line 1 | Line 1 | |
---|---|---|
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 "OOPSEMinimizer.hpp" |
14 | + | #include "ConstraintElement.hpp" |
15 | + | #include "ConstraintPair.hpp" |
16 | + | #include "ConstraintManager.hpp" |
17 | ||
18 | #ifdef IS_MPI | |
19 | #include "mpiBASS.h" | |
20 | #include "mpiSimulation.hpp" | |
21 | #endif | |
22 | ||
23 | + | // some defines for ensemble and Forcefield cases |
24 | + | |
25 | + | #define NVE_ENS 0 |
26 | + | #define NVT_ENS 1 |
27 | + | #define NPTi_ENS 2 |
28 | + | #define NPTf_ENS 3 |
29 | + | #define NPTxyz_ENS 4 |
30 | + | |
31 | + | |
32 | + | #define FF_DUFF 0 |
33 | + | #define FF_LJ 1 |
34 | + | #define FF_EAM 2 |
35 | + | #define FF_H2O 3 |
36 | + | |
37 | + | using namespace std; |
38 | + | |
39 | + | /** |
40 | + | * Check whether dividend is divisble by divisor or not |
41 | + | */ |
42 | + | bool isDivisible(double dividend, double divisor){ |
43 | + | double tolerance = 0.000001; |
44 | + | double quotient; |
45 | + | double diff; |
46 | + | int intQuotient; |
47 | + | |
48 | + | quotient = dividend / divisor; |
49 | + | |
50 | + | if (quotient < 0) |
51 | + | quotient = -quotient; |
52 | + | |
53 | + | intQuotient = int (quotient + tolerance); |
54 | + | |
55 | + | diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
56 | + | |
57 | + | if (diff <= tolerance) |
58 | + | return true; |
59 | + | else |
60 | + | return false; |
61 | + | } |
62 | + | |
63 | SimSetup::SimSetup(){ | |
64 | + | |
65 | + | initSuspend = false; |
66 | + | isInfoArray = 0; |
67 | + | nInfo = 1; |
68 | + | |
69 | stamps = new MakeStamps(); | |
70 | globals = new Globals(); | |
71 | < | |
71 | > | |
72 | > | |
73 | #ifdef IS_MPI | |
74 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
74 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
75 | MPIcheckPoint(); | |
76 | #endif // IS_MPI | |
77 | } | |
# | Line 27 | Line 81 | SimSetup::~SimSetup(){ | |
81 | delete globals; | |
82 | } | |
83 | ||
84 | < | void SimSetup::parseFile( char* fileName ){ |
84 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
85 | > | info = the_info; |
86 | > | nInfo = theNinfo; |
87 | > | isInfoArray = 1; |
88 | > | initSuspend = true; |
89 | > | } |
90 | ||
91 | + | |
92 | + | void SimSetup::parseFile(char* fileName){ |
93 | #ifdef IS_MPI | |
94 | < | if( worldRank == 0 ){ |
94 | > | if (worldRank == 0){ |
95 | #endif // is_mpi | |
96 | < | |
96 | > | |
97 | inFileName = fileName; | |
98 | < | set_interface_stamps( stamps, globals ); |
99 | < | |
98 | > | set_interface_stamps(stamps, globals); |
99 | > | |
100 | #ifdef IS_MPI | |
101 | mpiEventInit(); | |
102 | #endif | |
103 | ||
104 | < | yacc_BASS( fileName ); |
104 | > | yacc_BASS(fileName); |
105 | ||
106 | #ifdef IS_MPI | |
107 | throwMPIEvent(NULL); | |
108 | } | |
109 | < | else receiveParse(); |
109 | > | else{ |
110 | > | receiveParse(); |
111 | > | } |
112 | #endif | |
113 | ||
114 | } | |
115 | ||
116 | #ifdef IS_MPI | |
117 | void SimSetup::receiveParse(void){ | |
118 | < | |
119 | < | set_interface_stamps( stamps, globals ); |
120 | < | mpiEventInit(); |
121 | < | MPIcheckPoint(); |
59 | < | mpiEventLoop(); |
60 | < | |
118 | > | set_interface_stamps(stamps, globals); |
119 | > | mpiEventInit(); |
120 | > | MPIcheckPoint(); |
121 | > | mpiEventLoop(); |
122 | } | |
123 | ||
124 | #endif // is_mpi | |
125 | ||
126 | < | void SimSetup::createSim( void ){ |
126 | > | void SimSetup::createSim(void){ |
127 | ||
128 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | ExtendedSystem* the_extendedsystem; |
70 | < | int i, j; |
128 | > | // gather all of the information from the Bass file |
129 | ||
130 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
130 | > | gatherInfo(); |
131 | ||
132 | < | // 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(); |
132 | > | // creation of complex system objects |
133 | ||
134 | < | // 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() ); |
134 | > | sysObjectsCreation(); |
135 | ||
136 | < | // 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 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
92 | < | the_extendedsystem->setTauRelax(the_globals->getTauRelax()); |
93 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
94 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
95 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
96 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
97 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
98 | < | } else { |
99 | < | sprintf( painCave.errMsg, |
100 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
101 | < | "reverting to NVE for this simulation.\n", |
102 | < | ensemble ); |
103 | < | painCave.isFatal = 0; |
104 | < | simError(); |
105 | < | strcpy( ensemble, "NVE" ); |
106 | < | } |
107 | < | strcpy( simnfo->ensemble, ensemble ); |
136 | > | // check on the post processing info |
137 | ||
138 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
110 | < | simnfo->usePBC = the_globals->getPBC(); |
111 | < | |
112 | < | int usesDipoles = 0; |
113 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
114 | < | the_ff = new TraPPE_ExFF(); |
115 | < | usesDipoles = 1; |
116 | < | } |
117 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
118 | < | else{ |
119 | < | sprintf( painCave.errMsg, |
120 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
121 | < | force_field ); |
122 | < | painCave.isFatal = 1; |
123 | < | simError(); |
124 | < | } |
138 | > | finalInfoCheck(); |
139 | ||
140 | < | #ifdef IS_MPI |
127 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
128 | < | MPIcheckPoint(); |
129 | < | #endif // is_mpi |
140 | > | // initialize the system coordinates |
141 | ||
142 | < | |
142 | > | if ( !initSuspend ){ |
143 | > | initSystemCoords(); |
144 | ||
145 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
146 | < | the_components = the_globals->getComponents(); |
147 | < | components_nmol = new int[n_components]; |
136 | < | comp_stamps = new MoleculeStamp*[n_components]; |
145 | > | if( !(globals->getUseInitTime()) ) |
146 | > | info[0].currentTime = 0.0; |
147 | > | } |
148 | ||
149 | < | if( !the_globals->haveNMol() ){ |
139 | < | // we don't have the total number of molecules, so we assume it is |
140 | < | // given in each component |
149 | > | // make the output filenames |
150 | ||
151 | < | tot_nmol = 0; |
152 | < | for( i=0; i<n_components; i++ ){ |
151 | > | makeOutNames(); |
152 | > | |
153 | > | #ifdef IS_MPI |
154 | > | mpiSim->mpiRefresh(); |
155 | > | #endif |
156 | ||
157 | < | if( !the_components[i]->haveNMol() ){ |
146 | < | // we have a problem |
147 | < | sprintf( painCave.errMsg, |
148 | < | "SimSetup Error. No global NMol or component NMol" |
149 | < | " given. Cannot calculate the number of atoms.\n" ); |
150 | < | painCave.isFatal = 1; |
151 | < | simError(); |
152 | < | } |
157 | > | // initialize the Fortran |
158 | ||
159 | < | tot_nmol += the_components[i]->getNMol(); |
155 | < | components_nmol[i] = the_components[i]->getNMol(); |
156 | < | } |
157 | < | } |
158 | < | else{ |
159 | < | sprintf( painCave.errMsg, |
160 | < | "SimSetup error.\n" |
161 | < | "\tSorry, the ability to specify total" |
162 | < | " nMols and then give molfractions in the components\n" |
163 | < | "\tis not currently supported." |
164 | < | " Please give nMol in the components.\n" ); |
165 | < | painCave.isFatal = 1; |
166 | < | simError(); |
167 | < | |
168 | < | |
169 | < | // tot_nmol = the_globals->getNMol(); |
170 | < | |
171 | < | // //we have the total number of molecules, now we check for molfractions |
172 | < | // for( i=0; i<n_components; i++ ){ |
173 | < | |
174 | < | // if( !the_components[i]->haveMolFraction() ){ |
175 | < | |
176 | < | // if( !the_components[i]->haveNMol() ){ |
177 | < | // //we have a problem |
178 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
179 | < | // << " nMol was given in component |
180 | < | |
181 | < | } |
159 | > | initFortran(); |
160 | ||
161 | < | #ifdef IS_MPI |
162 | < | strcpy( checkPointMsg, "Have the number of components" ); |
163 | < | MPIcheckPoint(); |
186 | < | #endif // is_mpi |
161 | > | //creat constraint manager |
162 | > | for(int i = 0; i < nInfo; i++) |
163 | > | info[i].consMan = new ConstraintManager(&info[i]); |
164 | ||
165 | < | // make an array of molecule stamps that match the components used. |
166 | < | // also extract the used stamps out into a separate linked list |
165 | > | if (globals->haveMinimizer()) |
166 | > | // make minimizer |
167 | > | makeMinimizer(); |
168 | > | else |
169 | > | // make the integrator |
170 | > | makeIntegrator(); |
171 | ||
172 | < | simnfo->nComponents = n_components; |
192 | < | simnfo->componentsNmol = components_nmol; |
193 | < | simnfo->compStamps = comp_stamps; |
194 | < | simnfo->headStamp = new LinkedMolStamp(); |
195 | < | |
196 | < | char* id; |
197 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
198 | < | LinkedMolStamp* currentStamp = NULL; |
199 | < | for( i=0; i<n_components; i++ ){ |
172 | > | } |
173 | ||
201 | – | id = the_components[i]->getType(); |
202 | – | comp_stamps[i] = NULL; |
203 | – | |
204 | – | // check to make sure the component isn't already in the list |
174 | ||
175 | < | comp_stamps[i] = headStamp->match( id ); |
176 | < | if( comp_stamps[i] == NULL ){ |
177 | < | |
178 | < | // extract the component from the list; |
179 | < | |
180 | < | currentStamp = the_stamps->extractMolStamp( id ); |
181 | < | if( currentStamp == NULL ){ |
182 | < | sprintf( painCave.errMsg, |
183 | < | "SimSetup error: Component \"%s\" was not found in the " |
184 | < | "list of declared molecules\n", |
185 | < | id ); |
186 | < | painCave.isFatal = 1; |
187 | < | simError(); |
188 | < | } |
189 | < | |
190 | < | headStamp->add( currentStamp ); |
191 | < | comp_stamps[i] = headStamp->match( id ); |
192 | < | } |
193 | < | } |
194 | < | |
195 | < | #ifdef IS_MPI |
227 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
228 | < | MPIcheckPoint(); |
229 | < | #endif // is_mpi |
230 | < | |
175 | > | void SimSetup::makeMolecules(void){ |
176 | > | int i, j, k; |
177 | > | int exI, exJ, exK, exL, slI, slJ; |
178 | > | int tempI, tempJ, tempK, tempL; |
179 | > | int molI, globalID; |
180 | > | int stampID, atomOffset, rbOffset, groupOffset; |
181 | > | molInit molInfo; |
182 | > | DirectionalAtom* dAtom; |
183 | > | RigidBody* myRB; |
184 | > | StuntDouble* mySD; |
185 | > | LinkedAssign* extras; |
186 | > | LinkedAssign* current_extra; |
187 | > | AtomStamp* currentAtom; |
188 | > | BondStamp* currentBond; |
189 | > | BendStamp* currentBend; |
190 | > | TorsionStamp* currentTorsion; |
191 | > | RigidBodyStamp* currentRigidBody; |
192 | > | CutoffGroupStamp* currentCutoffGroup; |
193 | > | CutoffGroup* myCutoffGroup; |
194 | > | int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file |
195 | > | set<int> cutoffAtomSet; //atoms belong to cutoffgroup defined at mdl file |
196 | ||
197 | + | bond_pair* theBonds; |
198 | + | bend_set* theBends; |
199 | + | torsion_set* theTorsions; |
200 | ||
201 | + | set<int> skipList; |
202 | ||
203 | < | // caclulate the number of atoms, bonds, bends and torsions |
203 | > | double phi, theta, psi; |
204 | > | char* molName; |
205 | > | char rbName[100]; |
206 | ||
207 | < | tot_atoms = 0; |
208 | < | tot_bonds = 0; |
209 | < | tot_bends = 0; |
210 | < | tot_torsions = 0; |
211 | < | for( i=0; i<n_components; i++ ){ |
212 | < | |
213 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
214 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
244 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
245 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
246 | < | } |
207 | > | ConstraintPair* consPair; //constraint pair |
208 | > | ConstraintElement* consElement1; //first element of constraint pair |
209 | > | ConstraintElement* consElement2; //second element of constraint pair |
210 | > | int whichRigidBody; |
211 | > | int consAtomIndex; //index of constraint atom in rigid body's atom array |
212 | > | vector<pair<int, int> > jointAtoms; |
213 | > | double bondLength2; |
214 | > | //init the forceField paramters |
215 | ||
216 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
216 | > | the_ff->readParams(); |
217 | ||
218 | < | simnfo->n_atoms = tot_atoms; |
251 | < | simnfo->n_bonds = tot_bonds; |
252 | < | simnfo->n_bends = tot_bends; |
253 | < | simnfo->n_torsions = tot_torsions; |
254 | < | simnfo->n_SRI = tot_SRI; |
255 | < | simnfo->n_mol = tot_nmol; |
218 | > | // init the atoms |
219 | ||
220 | < | |
220 | > | int nMembers, nNew, rb1, rb2; |
221 | > | |
222 | > | for (k = 0; k < nInfo; k++){ |
223 | > | the_ff->setSimInfo(&(info[k])); |
224 | > | |
225 | #ifdef IS_MPI | |
226 | + | info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()]; |
227 | + | for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
228 | + | info[k].globalGroupMembership[i] = 0; |
229 | + | #else |
230 | + | info[k].globalGroupMembership = new int[info[k].n_atoms]; |
231 | + | for (i = 0; i < info[k].n_atoms; i++) |
232 | + | info[k].globalGroupMembership[i] = 0; |
233 | + | #endif |
234 | ||
235 | < | // divide the molecules among processors here. |
236 | < | |
262 | < | mpiSim = new mpiSimulation( simnfo ); |
263 | < | |
264 | < | |
235 | > | atomOffset = 0; |
236 | > | groupOffset = 0; |
237 | ||
238 | < | globalIndex = mpiSim->divideLabor(); |
238 | > | for (i = 0; i < info[k].n_mol; i++){ |
239 | > | stampID = info[k].molecules[i].getStampID(); |
240 | > | molName = comp_stamps[stampID]->getID(); |
241 | ||
242 | < | // set up the local variables |
243 | < | |
244 | < | int localMol, allMol; |
245 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
242 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
243 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
244 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
245 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
246 | > | molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies(); |
247 | ||
248 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
249 | < | int* molCompType = mpiSim->getMolComponentType(); |
250 | < | |
276 | < | allMol = 0; |
277 | < | localMol = 0; |
278 | < | local_atoms = 0; |
279 | < | local_bonds = 0; |
280 | < | local_bends = 0; |
281 | < | local_torsions = 0; |
282 | < | for( i=0; i<n_components; i++ ){ |
248 | > | nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups(); |
249 | > | |
250 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
251 | ||
252 | < | for( j=0; j<components_nmol[i]; j++ ){ |
252 | > | if (molInfo.nBonds > 0) |
253 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
254 | > | else |
255 | > | molInfo.myBonds = NULL; |
256 | > | |
257 | > | if (molInfo.nBends > 0) |
258 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
259 | > | else |
260 | > | molInfo.myBends = NULL; |
261 | > | |
262 | > | if (molInfo.nTorsions > 0) |
263 | > | molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
264 | > | else |
265 | > | molInfo.myTorsions = NULL; |
266 | > | |
267 | > | theBonds = new bond_pair[molInfo.nBonds]; |
268 | > | theBends = new bend_set[molInfo.nBends]; |
269 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
270 | ||
271 | < | if( mol2proc[j] == worldRank ){ |
287 | < | |
288 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
289 | < | local_bonds += comp_stamps[i]->getNBonds(); |
290 | < | local_bends += comp_stamps[i]->getNBends(); |
291 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
292 | < | localMol++; |
293 | < | } |
294 | < | allMol++; |
295 | < | } |
296 | < | } |
297 | < | local_SRI = local_bonds + local_bends + local_torsions; |
298 | < | |
271 | > | // make the Atoms |
272 | ||
273 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
274 | < | |
302 | < | if( local_atoms != simnfo->n_atoms ){ |
303 | < | sprintf( painCave.errMsg, |
304 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
305 | < | " localAtom (%d) are not equal.\n", |
306 | < | simnfo->n_atoms, |
307 | < | local_atoms ); |
308 | < | painCave.isFatal = 1; |
309 | < | simError(); |
310 | < | } |
273 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
274 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
275 | ||
276 | < | simnfo->n_bonds = local_bonds; |
277 | < | simnfo->n_bends = local_bends; |
278 | < | simnfo->n_torsions = local_torsions; |
279 | < | simnfo->n_SRI = local_SRI; |
280 | < | simnfo->n_mol = localMol; |
276 | > | if (currentAtom->haveOrientation()){ |
277 | > | dAtom = new DirectionalAtom((j + atomOffset), |
278 | > | info[k].getConfiguration()); |
279 | > | info[k].n_oriented++; |
280 | > | molInfo.myAtoms[j] = dAtom; |
281 | ||
282 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
283 | < | MPIcheckPoint(); |
284 | < | |
321 | < | |
322 | < | #endif // is_mpi |
323 | < | |
282 | > | // Directional Atoms have standard unit vectors which are oriented |
283 | > | // in space using the three Euler angles. We assume the standard |
284 | > | // unit vector was originally along the z axis below. |
285 | ||
286 | < | // create the atom and short range interaction arrays |
286 | > | phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
287 | > | theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
288 | > | psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
289 | ||
290 | < | Atom::createArrays(simnfo->n_atoms); |
291 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
292 | < | the_molecules = new Molecule[simnfo->n_mol]; |
293 | < | int molIndex; |
290 | > | dAtom->setUnitFrameFromEuler(phi, theta, psi); |
291 | > | |
292 | > | } |
293 | > | else{ |
294 | ||
295 | < | // initialize the molecule's stampID's |
295 | > | molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration()); |
296 | ||
297 | + | } |
298 | + | |
299 | + | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
300 | #ifdef IS_MPI | |
301 | < | |
301 | > | molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]); |
302 | > | #endif // is_mpi |
303 | > | } |
304 | ||
305 | < | molIndex = 0; |
306 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
307 | < | |
308 | < | if(mol2proc[i] == worldRank ){ |
309 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
342 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
343 | < | molIndex++; |
344 | < | } |
345 | < | } |
305 | > | // make the bonds |
306 | > | for (j = 0; j < molInfo.nBonds; j++){ |
307 | > | currentBond = comp_stamps[stampID]->getBond(j); |
308 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
309 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
310 | ||
311 | < | #else // is_mpi |
312 | < | |
349 | < | molIndex = 0; |
350 | < | for(i=0; i<n_components; i++){ |
351 | < | for(j=0; j<components_nmol[i]; j++ ){ |
352 | < | the_molecules[molIndex].setStampID( i ); |
353 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
354 | < | molIndex++; |
355 | < | } |
356 | < | } |
357 | < | |
311 | > | tempI = theBonds[j].a; |
312 | > | tempJ = theBonds[j].b; |
313 | ||
314 | < | #endif // is_mpi |
314 | > | #ifdef IS_MPI |
315 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
316 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
317 | > | #else |
318 | > | exI = tempI + 1; |
319 | > | exJ = tempJ + 1; |
320 | > | #endif |
321 | ||
322 | + | info[k].excludes->addPair(exI, exJ); |
323 | + | } |
324 | ||
325 | < | if( simnfo->n_SRI ){ |
326 | < | |
327 | < | Exclude::createArray(simnfo->n_SRI); |
328 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
329 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
330 | < | simnfo->globalExcludes = new int; |
368 | < | simnfo->n_exclude = simnfo->n_SRI; |
369 | < | } |
370 | < | else{ |
371 | < | |
372 | < | Exclude::createArray( 1 ); |
373 | < | the_excludes = new Exclude*; |
374 | < | the_excludes[0] = new Exclude(0); |
375 | < | the_excludes[0]->setPair( 0,0 ); |
376 | < | simnfo->globalExcludes = new int; |
377 | < | simnfo->globalExcludes[0] = 0; |
378 | < | simnfo->n_exclude = 0; |
379 | < | } |
325 | > | //make the bends |
326 | > | for (j = 0; j < molInfo.nBends; j++){ |
327 | > | currentBend = comp_stamps[stampID]->getBend(j); |
328 | > | theBends[j].a = currentBend->getA() + atomOffset; |
329 | > | theBends[j].b = currentBend->getB() + atomOffset; |
330 | > | theBends[j].c = currentBend->getC() + atomOffset; |
331 | ||
332 | < | // set the arrays into the SimInfo object |
332 | > | if (currentBend->haveExtras()){ |
333 | > | extras = currentBend->getExtras(); |
334 | > | current_extra = extras; |
335 | ||
336 | < | simnfo->atoms = the_atoms; |
337 | < | simnfo->molecules = the_molecules; |
338 | < | simnfo->nGlobalExcludes = 0; |
339 | < | simnfo->excludes = the_excludes; |
336 | > | while (current_extra != NULL){ |
337 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
338 | > | switch (current_extra->getType()){ |
339 | > | case 0: |
340 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
341 | > | theBends[j].isGhost = 1; |
342 | > | break; |
343 | ||
344 | + | case 1: |
345 | + | theBends[j].ghost = (int) current_extra->getDouble() + |
346 | + | atomOffset; |
347 | + | theBends[j].isGhost = 1; |
348 | + | break; |
349 | ||
350 | < | // get some of the tricky things that may still be in the globals |
350 | > | default: |
351 | > | sprintf(painCave.errMsg, |
352 | > | "SimSetup Error: ghostVectorSource was neither a " |
353 | > | "double nor an int.\n" |
354 | > | "-->Bend[%d] in %s\n", |
355 | > | j, comp_stamps[stampID]->getID()); |
356 | > | painCave.isFatal = 1; |
357 | > | simError(); |
358 | > | } |
359 | > | } |
360 | > | else{ |
361 | > | sprintf(painCave.errMsg, |
362 | > | "SimSetup Error: unhandled bend assignment:\n" |
363 | > | " -->%s in Bend[%d] in %s\n", |
364 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
365 | > | painCave.isFatal = 1; |
366 | > | simError(); |
367 | > | } |
368 | ||
369 | < | |
370 | < | if( the_globals->haveBox() ){ |
371 | < | simnfo->box_x = the_globals->getBox(); |
394 | < | simnfo->box_y = the_globals->getBox(); |
395 | < | simnfo->box_z = the_globals->getBox(); |
396 | < | } |
397 | < | else if( the_globals->haveDensity() ){ |
369 | > | current_extra = current_extra->getNext(); |
370 | > | } |
371 | > | } |
372 | ||
373 | < | double vol; |
374 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
375 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
376 | < | simnfo->box_y = simnfo->box_x; |
377 | < | simnfo->box_z = simnfo->box_x; |
378 | < | } |
379 | < | else{ |
380 | < | if( !the_globals->haveBoxX() ){ |
381 | < | sprintf( painCave.errMsg, |
382 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
383 | < | painCave.isFatal = 1; |
384 | < | simError(); |
385 | < | } |
412 | < | simnfo->box_x = the_globals->getBoxX(); |
373 | > | if (theBends[j].isGhost) { |
374 | > | |
375 | > | tempI = theBends[j].a; |
376 | > | tempJ = theBends[j].b; |
377 | > | |
378 | > | #ifdef IS_MPI |
379 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
380 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
381 | > | #else |
382 | > | exI = tempI + 1; |
383 | > | exJ = tempJ + 1; |
384 | > | #endif |
385 | > | info[k].excludes->addPair(exI, exJ); |
386 | ||
387 | < | if( !the_globals->haveBoxY() ){ |
415 | < | sprintf( painCave.errMsg, |
416 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
417 | < | painCave.isFatal = 1; |
418 | < | simError(); |
419 | < | } |
420 | < | simnfo->box_y = the_globals->getBoxY(); |
387 | > | } else { |
388 | ||
389 | < | if( !the_globals->haveBoxZ() ){ |
390 | < | sprintf( painCave.errMsg, |
391 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
392 | < | painCave.isFatal = 1; |
426 | < | simError(); |
427 | < | } |
428 | < | simnfo->box_z = the_globals->getBoxZ(); |
429 | < | } |
430 | < | |
389 | > | tempI = theBends[j].a; |
390 | > | tempJ = theBends[j].b; |
391 | > | tempK = theBends[j].c; |
392 | > | |
393 | #ifdef IS_MPI | |
394 | < | strcpy( checkPointMsg, "Box size set up" ); |
395 | < | MPIcheckPoint(); |
396 | < | #endif // is_mpi |
394 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
395 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
396 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
397 | > | #else |
398 | > | exI = tempI + 1; |
399 | > | exJ = tempJ + 1; |
400 | > | exK = tempK + 1; |
401 | > | #endif |
402 | > | |
403 | > | info[k].excludes->addPair(exI, exK); |
404 | > | info[k].excludes->addPair(exI, exJ); |
405 | > | info[k].excludes->addPair(exJ, exK); |
406 | > | } |
407 | > | } |
408 | ||
409 | + | for (j = 0; j < molInfo.nTorsions; j++){ |
410 | + | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
411 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
412 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
413 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
414 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
415 | ||
416 | < | // initialize the arrays |
416 | > | tempI = theTorsions[j].a; |
417 | > | tempJ = theTorsions[j].b; |
418 | > | tempK = theTorsions[j].c; |
419 | > | tempL = theTorsions[j].d; |
420 | ||
421 | < | the_ff->setSimInfo( simnfo ); |
421 | > | #ifdef IS_MPI |
422 | > | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
423 | > | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
424 | > | exK = info[k].atoms[tempK]->getGlobalIndex() + 1; |
425 | > | exL = info[k].atoms[tempL]->getGlobalIndex() + 1; |
426 | > | #else |
427 | > | exI = tempI + 1; |
428 | > | exJ = tempJ + 1; |
429 | > | exK = tempK + 1; |
430 | > | exL = tempL + 1; |
431 | > | #endif |
432 | ||
433 | < | makeMolecules(); |
434 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
435 | < | for(i=0; i<simnfo->n_atoms; i++){ |
436 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
437 | < | } |
438 | < | |
439 | < | if (the_globals->getUseRF() ) { |
448 | < | simnfo->useReactionField = 1; |
449 | < | |
450 | < | if( !the_globals->haveECR() ){ |
451 | < | sprintf( painCave.errMsg, |
452 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
453 | < | "box length for the electrostaticCutoffRadius.\n" |
454 | < | "I hope you have a very fast processor!\n"); |
455 | < | painCave.isFatal = 0; |
456 | < | simError(); |
457 | < | double smallest; |
458 | < | smallest = simnfo->box_x; |
459 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
460 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
461 | < | simnfo->ecr = 0.5 * smallest; |
462 | < | } else { |
463 | < | simnfo->ecr = the_globals->getECR(); |
464 | < | } |
433 | > | info[k].excludes->addPair(exI, exJ); |
434 | > | info[k].excludes->addPair(exI, exK); |
435 | > | info[k].excludes->addPair(exI, exL); |
436 | > | info[k].excludes->addPair(exJ, exK); |
437 | > | info[k].excludes->addPair(exJ, exL); |
438 | > | info[k].excludes->addPair(exK, exL); |
439 | > | } |
440 | ||
466 | – | if( !the_globals->haveEST() ){ |
467 | – | sprintf( painCave.errMsg, |
468 | – | "SimSetup Warning: using default value of 0.05 * the " |
469 | – | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
470 | – | ); |
471 | – | painCave.isFatal = 0; |
472 | – | simError(); |
473 | – | simnfo->est = 0.05 * simnfo->ecr; |
474 | – | } else { |
475 | – | simnfo->est = the_globals->getEST(); |
476 | – | } |
477 | – | |
478 | – | if(!the_globals->haveDielectric() ){ |
479 | – | sprintf( painCave.errMsg, |
480 | – | "SimSetup Error: You are trying to use Reaction Field without" |
481 | – | "setting a dielectric constant!\n" |
482 | – | ); |
483 | – | painCave.isFatal = 1; |
484 | – | simError(); |
485 | – | } |
486 | – | simnfo->dielectric = the_globals->getDielectric(); |
487 | – | } else { |
488 | – | if (usesDipoles) { |
441 | ||
442 | < | if( !the_globals->haveECR() ){ |
491 | < | sprintf( painCave.errMsg, |
492 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
493 | < | "box length for the electrostaticCutoffRadius.\n" |
494 | < | "I hope you have a very fast processor!\n"); |
495 | < | painCave.isFatal = 0; |
496 | < | simError(); |
497 | < | double smallest; |
498 | < | smallest = simnfo->box_x; |
499 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
500 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
501 | < | simnfo->ecr = 0.5 * smallest; |
502 | < | } else { |
503 | < | simnfo->ecr = the_globals->getECR(); |
504 | < | } |
442 | > | molInfo.myRigidBodies.clear(); |
443 | ||
444 | < | if( !the_globals->haveEST() ){ |
507 | < | sprintf( painCave.errMsg, |
508 | < | "SimSetup Warning: using default value of 5%% of the " |
509 | < | "electrostaticCutoffRadius for the " |
510 | < | "electrostaticSkinThickness\n" |
511 | < | ); |
512 | < | painCave.isFatal = 0; |
513 | < | simError(); |
514 | < | simnfo->est = 0.05 * simnfo->ecr; |
515 | < | } else { |
516 | < | simnfo->est = the_globals->getEST(); |
517 | < | } |
518 | < | } |
519 | < | } |
444 | > | for (j = 0; j < molInfo.nRigidBodies; j++){ |
445 | ||
446 | < | #ifdef IS_MPI |
447 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
523 | < | MPIcheckPoint(); |
524 | < | #endif // is_mpi |
446 | > | currentRigidBody = comp_stamps[stampID]->getRigidBody(j); |
447 | > | nMembers = currentRigidBody->getNMembers(); |
448 | ||
449 | < | if( the_globals->haveInitialConfig() ){ |
527 | < | |
528 | < | InitializeFromFile* fileInit; |
529 | < | #ifdef IS_MPI // is_mpi |
530 | < | if( worldRank == 0 ){ |
531 | < | #endif //is_mpi |
532 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
533 | < | #ifdef IS_MPI |
534 | < | }else fileInit = new InitializeFromFile( NULL ); |
535 | < | #endif |
536 | < | fileInit->read_xyz( simnfo ); // default velocities on |
449 | > | // Create the Rigid Body: |
450 | ||
451 | < | delete fileInit; |
539 | < | } |
540 | < | else{ |
451 | > | myRB = new RigidBody(); |
452 | ||
453 | < | #ifdef IS_MPI |
453 | > | sprintf(rbName,"%s_RB_%d", molName, j); |
454 | > | myRB->setType(rbName); |
455 | > | |
456 | > | for (rb1 = 0; rb1 < nMembers; rb1++) { |
457 | ||
458 | < | // no init from bass |
459 | < | |
546 | < | sprintf( painCave.errMsg, |
547 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
548 | < | painCave.isFatal; |
549 | < | simError(); |
550 | < | |
551 | < | #else |
458 | > | // molI is atom numbering inside this molecule |
459 | > | molI = currentRigidBody->getMember(rb1); |
460 | ||
461 | < | initFromBass(); |
461 | > | // tempI is atom numbering on local processor |
462 | > | tempI = molI + atomOffset; |
463 | ||
464 | + | // currentAtom is the AtomStamp (which we need for |
465 | + | // rigid body reference positions) |
466 | + | currentAtom = comp_stamps[stampID]->getAtom(molI); |
467 | ||
468 | < | #endif |
469 | < | } |
468 | > | // When we add to the rigid body, add the atom itself and |
469 | > | // the stamp info: |
470 | ||
471 | < | #ifdef IS_MPI |
472 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
473 | < | MPIcheckPoint(); |
562 | < | #endif // is_mpi |
563 | < | |
564 | < | |
565 | < | |
566 | < | |
567 | < | |
568 | < | |
569 | < | |
471 | > | myRB->addAtom(info[k].atoms[tempI], currentAtom); |
472 | > | |
473 | > | // Add this atom to the Skip List for the integrators |
474 | #ifdef IS_MPI | |
475 | < | if( worldRank == 0 ){ |
476 | < | #endif // is_mpi |
477 | < | |
478 | < | if( the_globals->haveFinalConfig() ){ |
479 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
480 | < | } |
481 | < | else{ |
482 | < | strcpy( simnfo->finalName, inFileName ); |
483 | < | char* endTest; |
484 | < | int nameLength = strlen( simnfo->finalName ); |
485 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
486 | < | if( !strcmp( endTest, ".bass" ) ){ |
487 | < | strcpy( endTest, ".eor" ); |
488 | < | } |
489 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
490 | < | strcpy( endTest, ".eor" ); |
491 | < | } |
492 | < | else{ |
493 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
590 | < | if( !strcmp( endTest, ".bss" ) ){ |
591 | < | strcpy( endTest, ".eor" ); |
592 | < | } |
593 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
594 | < | strcpy( endTest, ".eor" ); |
595 | < | } |
596 | < | else{ |
597 | < | strcat( simnfo->finalName, ".eor" ); |
598 | < | } |
599 | < | } |
600 | < | } |
601 | < | |
602 | < | // make the sample and status out names |
603 | < | |
604 | < | strcpy( simnfo->sampleName, inFileName ); |
605 | < | char* endTest; |
606 | < | int nameLength = strlen( simnfo->sampleName ); |
607 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
608 | < | if( !strcmp( endTest, ".bass" ) ){ |
609 | < | strcpy( endTest, ".dump" ); |
610 | < | } |
611 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
612 | < | strcpy( endTest, ".dump" ); |
613 | < | } |
614 | < | else{ |
615 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
616 | < | if( !strcmp( endTest, ".bss" ) ){ |
617 | < | strcpy( endTest, ".dump" ); |
618 | < | } |
619 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
620 | < | strcpy( endTest, ".dump" ); |
621 | < | } |
622 | < | else{ |
623 | < | strcat( simnfo->sampleName, ".dump" ); |
624 | < | } |
625 | < | } |
626 | < | |
627 | < | strcpy( simnfo->statusName, inFileName ); |
628 | < | nameLength = strlen( simnfo->statusName ); |
629 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
630 | < | if( !strcmp( endTest, ".bass" ) ){ |
631 | < | strcpy( endTest, ".stat" ); |
632 | < | } |
633 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
634 | < | strcpy( endTest, ".stat" ); |
635 | < | } |
636 | < | else{ |
637 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
638 | < | if( !strcmp( endTest, ".bss" ) ){ |
639 | < | strcpy( endTest, ".stat" ); |
640 | < | } |
641 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
642 | < | strcpy( endTest, ".stat" ); |
643 | < | } |
644 | < | else{ |
645 | < | strcat( simnfo->statusName, ".stat" ); |
646 | < | } |
647 | < | } |
648 | < | |
475 | > | slI = info[k].atoms[tempI]->getGlobalIndex(); |
476 | > | #else |
477 | > | slI = tempI; |
478 | > | #endif |
479 | > | skipList.insert(slI); |
480 | > | |
481 | > | } |
482 | > | |
483 | > | for(rb1 = 0; rb1 < nMembers - 1; rb1++) { |
484 | > | for(rb2 = rb1+1; rb2 < nMembers; rb2++) { |
485 | > | |
486 | > | tempI = currentRigidBody->getMember(rb1); |
487 | > | tempJ = currentRigidBody->getMember(rb2); |
488 | > | |
489 | > | // Some explanation is required here. |
490 | > | // Fortran indexing starts at 1, while c indexing starts at 0 |
491 | > | // Also, in parallel computations, the GlobalIndex is |
492 | > | // used for the exclude list: |
493 | > | |
494 | #ifdef IS_MPI | |
495 | < | } |
496 | < | #endif // is_mpi |
497 | < | |
498 | < | // set the status, sample, and themal kick times |
499 | < | |
500 | < | if( the_globals->haveSampleTime() ){ |
501 | < | simnfo->sampleTime = the_globals->getSampleTime(); |
502 | < | simnfo->statusTime = simnfo->sampleTime; |
503 | < | simnfo->thermalTime = simnfo->sampleTime; |
504 | < | } |
505 | < | else{ |
661 | < | simnfo->sampleTime = the_globals->getRunTime(); |
662 | < | simnfo->statusTime = simnfo->sampleTime; |
663 | < | simnfo->thermalTime = simnfo->sampleTime; |
664 | < | } |
495 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
496 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
497 | > | #else |
498 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
499 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
500 | > | #endif |
501 | > | |
502 | > | info[k].excludes->addPair(exI, exJ); |
503 | > | |
504 | > | } |
505 | > | } |
506 | ||
507 | < | if( the_globals->haveStatusTime() ){ |
508 | < | simnfo->statusTime = the_globals->getStatusTime(); |
509 | < | } |
507 | > | molInfo.myRigidBodies.push_back(myRB); |
508 | > | info[k].rigidBodies.push_back(myRB); |
509 | > | } |
510 | > | |
511 | ||
512 | < | if( the_globals->haveThermalTime() ){ |
671 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
672 | < | } |
512 | > | //create cutoff group for molecule |
513 | ||
514 | < | // check for the temperature set flag |
514 | > | cutoffAtomSet.clear(); |
515 | > | molInfo.myCutoffGroups.clear(); |
516 | > | |
517 | > | for (j = 0; j < nCutoffGroups; j++){ |
518 | ||
519 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
519 | > | currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j); |
520 | > | nMembers = currentCutoffGroup->getNMembers(); |
521 | ||
522 | < | |
523 | < | // // make the longe range forces and the integrator |
680 | < | |
681 | < | // new AllLong( simnfo ); |
682 | < | |
683 | < | |
684 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
685 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
686 | < | std::cerr << "called new Symplecic\n"; |
687 | < | fprintf( stderr, "called new Symplectic. stderr\n" ); |
688 | < | } |
689 | < | else if( !strcmp( force_field, "LJ" ) ){ |
690 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
691 | < | std::cerr << "called new Verlet\n"; |
692 | < | fprintf( stderr, "called new Verlet. stderr\n" ); |
693 | < | } |
694 | < | else { |
695 | < | std::cerr << "I'm a bug.\n"; |
696 | < | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
697 | < | } |
522 | > | myCutoffGroup = new CutoffGroup(); |
523 | > | |
524 | #ifdef IS_MPI | |
525 | < | mpiSim->mpiRefresh(); |
525 | > | myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
526 | > | #else |
527 | > | myCutoffGroup->setGlobalIndex(groupOffset); |
528 | #endif | |
529 | + | |
530 | + | for (int cg = 0; cg < nMembers; cg++) { |
531 | ||
532 | < | // initialize the Fortran |
532 | > | // molI is atom numbering inside this molecule |
533 | > | molI = currentCutoffGroup->getMember(cg); |
534 | ||
535 | + | // tempI is atom numbering on local processor |
536 | + | tempI = molI + atomOffset; |
537 | ||
705 | – | simnfo->refreshSim(); |
706 | – | |
707 | – | if( !strcmp( simnfo->mixingRule, "standard") ){ |
708 | – | the_ff->initForceField( LB_MIXING_RULE ); |
709 | – | } |
710 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
711 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
712 | – | } |
713 | – | else{ |
714 | – | sprintf( painCave.errMsg, |
715 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
716 | – | simnfo->mixingRule ); |
717 | – | painCave.isFatal = 1; |
718 | – | simError(); |
719 | – | } |
720 | – | |
721 | – | |
538 | #ifdef IS_MPI | |
539 | < | strcpy( checkPointMsg, |
540 | < | "Successfully intialized the mixingRule for Fortran." ); |
541 | < | MPIcheckPoint(); |
542 | < | #endif // is_mpi |
543 | < | } |
539 | > | globalID = info[k].atoms[tempI]->getGlobalIndex(); |
540 | > | info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
541 | > | #else |
542 | > | globalID = info[k].atoms[tempI]->getIndex(); |
543 | > | info[k].globalGroupMembership[globalID] = groupOffset; |
544 | > | #endif |
545 | > | myCutoffGroup->addAtom(info[k].atoms[tempI]); |
546 | > | cutoffAtomSet.insert(tempI); |
547 | > | } |
548 | > | |
549 | > | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
550 | > | groupOffset++; |
551 | ||
552 | < | |
553 | < | void SimSetup::makeMolecules( void ){ |
554 | < | |
555 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
556 | < | molInit info; |
557 | < | DirectionalAtom* dAtom; |
558 | < | LinkedAssign* extras; |
559 | < | LinkedAssign* current_extra; |
560 | < | AtomStamp* currentAtom; |
561 | < | BondStamp* currentBond; |
562 | < | BendStamp* currentBend; |
563 | < | TorsionStamp* currentTorsion; |
564 | < | |
565 | < | bond_pair* theBonds; |
566 | < | bend_set* theBends; |
567 | < | torsion_set* theTorsions; |
552 | > | }//end for (j = 0; j < molInfo.nCutoffGroups; j++) |
553 | > | |
554 | > | |
555 | > | // create a cutoff group for every atom in current molecule which |
556 | > | // does not belong to cutoffgroup defined at mdl file |
557 | > | |
558 | > | for(j = 0; j < molInfo.nAtoms; j++){ |
559 | > | |
560 | > | if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){ |
561 | > | myCutoffGroup = new CutoffGroup(); |
562 | > | myCutoffGroup->addAtom(molInfo.myAtoms[j]); |
563 | > | |
564 | > | #ifdef IS_MPI |
565 | > | myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]); |
566 | > | globalID = info[k].atoms[atomOffset + j]->getGlobalIndex(); |
567 | > | info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset]; |
568 | > | #else |
569 | > | myCutoffGroup->setGlobalIndex(groupOffset); |
570 | > | globalID = info[k].atoms[atomOffset + j]->getIndex(); |
571 | > | info[k].globalGroupMembership[globalID] = groupOffset; |
572 | > | #endif |
573 | > | molInfo.myCutoffGroups.push_back(myCutoffGroup); |
574 | > | groupOffset++; |
575 | > | } |
576 | > | } |
577 | ||
578 | < | |
579 | < | //init the forceField paramters |
578 | > | // After this is all set up, scan through the atoms to |
579 | > | // see if they can be added to the integrableObjects: |
580 | ||
581 | < | the_ff->readParams(); |
581 | > | molInfo.myIntegrableObjects.clear(); |
582 | > | |
583 | ||
584 | < | |
752 | < | // init the atoms |
584 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
585 | ||
586 | < | double ux, uy, uz, u, uSqr; |
587 | < | |
588 | < | atomOffset = 0; |
589 | < | excludeOffset = 0; |
590 | < | for(i=0; i<simnfo->n_mol; i++){ |
759 | < | |
760 | < | stampID = the_molecules[i].getStampID(); |
586 | > | #ifdef IS_MPI |
587 | > | slJ = molInfo.myAtoms[j]->getGlobalIndex(); |
588 | > | #else |
589 | > | slJ = j+atomOffset; |
590 | > | #endif |
591 | ||
592 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
763 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
764 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
765 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
766 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
592 | > | // if they aren't on the skip list, then they can be integrated |
593 | ||
594 | < | info.myAtoms = &the_atoms[atomOffset]; |
595 | < | info.myExcludes = &the_excludes[excludeOffset]; |
596 | < | info.myBonds = new Bond*[info.nBonds]; |
597 | < | info.myBends = new Bend*[info.nBends]; |
598 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
594 | > | if (skipList.find(slJ) == skipList.end()) { |
595 | > | mySD = (StuntDouble *) molInfo.myAtoms[j]; |
596 | > | info[k].integrableObjects.push_back(mySD); |
597 | > | molInfo.myIntegrableObjects.push_back(mySD); |
598 | > | } |
599 | > | } |
600 | ||
601 | < | theBonds = new bond_pair[info.nBonds]; |
602 | < | theBends = new bend_set[info.nBends]; |
603 | < | theTorsions = new torsion_set[info.nTorsions]; |
604 | < | |
605 | < | // make the Atoms |
606 | < | |
780 | < | for(j=0; j<info.nAtoms; j++){ |
781 | < | |
782 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
783 | < | if( currentAtom->haveOrientation() ){ |
784 | < | |
785 | < | dAtom = new DirectionalAtom(j + atomOffset); |
786 | < | simnfo->n_oriented++; |
787 | < | info.myAtoms[j] = dAtom; |
788 | < | |
789 | < | ux = currentAtom->getOrntX(); |
790 | < | uy = currentAtom->getOrntY(); |
791 | < | uz = currentAtom->getOrntZ(); |
792 | < | |
793 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
794 | < | |
795 | < | u = sqrt( uSqr ); |
796 | < | ux = ux / u; |
797 | < | uy = uy / u; |
798 | < | uz = uz / u; |
799 | < | |
800 | < | dAtom->setSUx( ux ); |
801 | < | dAtom->setSUy( uy ); |
802 | < | dAtom->setSUz( uz ); |
601 | > | // all rigid bodies are integrated: |
602 | > | |
603 | > | for (j = 0; j < molInfo.nRigidBodies; j++) { |
604 | > | mySD = (StuntDouble *) molInfo.myRigidBodies[j]; |
605 | > | info[k].integrableObjects.push_back(mySD); |
606 | > | molInfo.myIntegrableObjects.push_back(mySD); |
607 | } | |
608 | < | else{ |
609 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
806 | < | } |
807 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
808 | < | |
809 | < | #ifdef IS_MPI |
608 | > | |
609 | > | // send the arrays off to the forceField for init. |
610 | ||
611 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
611 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
612 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
613 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
614 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
615 | > | theTorsions); |
616 | > | |
617 | > | |
618 | > | //creat ConstraintPair. |
619 | > | molInfo.myConstraintPairs.clear(); |
620 | ||
621 | < | #endif // is_mpi |
622 | < | } |
623 | < | |
624 | < | // make the bonds |
625 | < | for(j=0; j<info.nBonds; j++){ |
621 | > | for (j = 0; j < molInfo.nBonds; j++){ |
622 | > | |
623 | > | //if bond is constrained bond, add it into constraint pair |
624 | > | if(molInfo.myBonds[j]->is_constrained()){ |
625 | > | |
626 | > | //if both atoms are in the same rigid body, just skip it |
627 | > | currentBond = comp_stamps[stampID]->getBond(j); |
628 | > | |
629 | > | if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){ |
630 | > | |
631 | > | tempI = currentBond->getA() + atomOffset; |
632 | > | if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex)) |
633 | > | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
634 | > | else |
635 | > | consElement1 = new ConstraintAtom(info[k].atoms[tempI]); |
636 | > | |
637 | > | tempJ = currentBond->getB() + atomOffset; |
638 | > | if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex)) |
639 | > | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex); |
640 | > | else |
641 | > | consElement2 = new ConstraintAtom(info[k].atoms[tempJ]); |
642 | > | |
643 | > | bondLength2 = molInfo.myBonds[j]->get_constraint()->get_dsqr(); |
644 | > | consPair = new DistanceConstraintPair(consElement1, consElement2, bondLength2); |
645 | > | |
646 | > | molInfo.myConstraintPairs.push_back(consPair); |
647 | > | } |
648 | > | }//end if(molInfo.myBonds[j]->is_constrained()) |
649 | > | } |
650 | ||
651 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
652 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
653 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
651 | > | //loop over rigid bodies, if two rigid bodies share same joint, creat a JointConstraintPair |
652 | > | for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){ |
653 | > | for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){ |
654 | > | |
655 | > | jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2); |
656 | ||
657 | < | exI = theBonds[j].a; |
658 | < | exJ = theBonds[j].b; |
657 | > | for(size_t m = 0; m < jointAtoms.size(); m++){ |
658 | > | consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first); |
659 | > | consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second); |
660 | ||
661 | < | // exclude_I must always be the smaller of the pair |
662 | < | if( exI > exJ ){ |
663 | < | tempEx = exI; |
664 | < | exI = exJ; |
665 | < | exJ = tempEx; |
661 | > | consPair = new JointConstraintPair(consElement1, consElement2); |
662 | > | molInfo.myConstraintPairs.push_back(consPair); |
663 | > | } |
664 | > | |
665 | > | } |
666 | } | |
832 | – | #ifdef IS_MPI |
833 | – | tempEx = exI; |
834 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
835 | – | tempEx = exJ; |
836 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
667 | ||
838 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
839 | – | #else // isn't MPI |
668 | ||
669 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
670 | < | #endif //is_mpi |
669 | > | info[k].molecules[i].initialize(molInfo); |
670 | > | |
671 | > | |
672 | > | atomOffset += molInfo.nAtoms; |
673 | > | delete[] theBonds; |
674 | > | delete[] theBends; |
675 | > | delete[] theTorsions; |
676 | } | |
844 | – | excludeOffset += info.nBonds; |
677 | ||
678 | < | //make the bends |
847 | < | for(j=0; j<info.nBends; j++){ |
848 | < | |
849 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
850 | < | theBends[j].a = currentBend->getA() + atomOffset; |
851 | < | theBends[j].b = currentBend->getB() + atomOffset; |
852 | < | theBends[j].c = currentBend->getC() + atomOffset; |
853 | < | |
854 | < | if( currentBend->haveExtras() ){ |
855 | < | |
856 | < | extras = currentBend->getExtras(); |
857 | < | current_extra = extras; |
858 | < | |
859 | < | while( current_extra != NULL ){ |
860 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
861 | < | |
862 | < | switch( current_extra->getType() ){ |
863 | < | |
864 | < | case 0: |
865 | < | theBends[j].ghost = |
866 | < | current_extra->getInt() + atomOffset; |
867 | < | theBends[j].isGhost = 1; |
868 | < | break; |
869 | < | |
870 | < | case 1: |
871 | < | theBends[j].ghost = |
872 | < | (int)current_extra->getDouble() + atomOffset; |
873 | < | theBends[j].isGhost = 1; |
874 | < | break; |
875 | < | |
876 | < | default: |
877 | < | sprintf( painCave.errMsg, |
878 | < | "SimSetup Error: ghostVectorSource was neither a " |
879 | < | "double nor an int.\n" |
880 | < | "-->Bend[%d] in %s\n", |
881 | < | j, comp_stamps[stampID]->getID() ); |
882 | < | painCave.isFatal = 1; |
883 | < | simError(); |
884 | < | } |
885 | < | } |
886 | < | |
887 | < | else{ |
888 | < | |
889 | < | sprintf( painCave.errMsg, |
890 | < | "SimSetup Error: unhandled bend assignment:\n" |
891 | < | " -->%s in Bend[%d] in %s\n", |
892 | < | current_extra->getlhs(), |
893 | < | j, comp_stamps[stampID]->getID() ); |
894 | < | painCave.isFatal = 1; |
895 | < | simError(); |
896 | < | } |
897 | < | |
898 | < | current_extra = current_extra->getNext(); |
899 | < | } |
900 | < | } |
901 | < | |
902 | < | if( !theBends[j].isGhost ){ |
903 | < | |
904 | < | exI = theBends[j].a; |
905 | < | exJ = theBends[j].c; |
906 | < | } |
907 | < | else{ |
908 | < | |
909 | < | exI = theBends[j].a; |
910 | < | exJ = theBends[j].b; |
911 | < | } |
912 | < | |
913 | < | // exclude_I must always be the smaller of the pair |
914 | < | if( exI > exJ ){ |
915 | < | tempEx = exI; |
916 | < | exI = exJ; |
917 | < | exJ = tempEx; |
918 | < | } |
919 | < | #ifdef IS_MPI |
920 | < | tempEx = exI; |
921 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
922 | < | tempEx = exJ; |
923 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
924 | < | |
925 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
926 | < | #else // isn't MPI |
927 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
928 | < | #endif //is_mpi |
929 | < | } |
930 | < | excludeOffset += info.nBends; |
678 | > | |
679 | ||
680 | < | for(j=0; j<info.nTorsions; j++){ |
681 | < | |
682 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
683 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
684 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
685 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
938 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
939 | < | |
940 | < | exI = theTorsions[j].a; |
941 | < | exJ = theTorsions[j].d; |
680 | > | #ifdef IS_MPI |
681 | > | // Since the globalGroupMembership has been zero filled and we've only |
682 | > | // poked values into the atoms we know, we can do an Allreduce |
683 | > | // to get the full globalGroupMembership array (We think). |
684 | > | // This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
685 | > | // docs said we could. |
686 | ||
687 | < | // exclude_I must always be the smaller of the pair |
944 | < | if( exI > exJ ){ |
945 | < | tempEx = exI; |
946 | < | exI = exJ; |
947 | < | exJ = tempEx; |
948 | < | } |
949 | < | #ifdef IS_MPI |
950 | < | tempEx = exI; |
951 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
952 | < | tempEx = exJ; |
953 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
954 | < | |
955 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
956 | < | #else // isn't MPI |
957 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
958 | < | #endif //is_mpi |
959 | < | } |
960 | < | excludeOffset += info.nTorsions; |
687 | > | int* ggMjunk = new int[mpiSim->getNAtomsGlobal()]; |
688 | ||
689 | < | |
690 | < | // send the arrays off to the forceField for init. |
689 | > | MPI_Allreduce(info[k].globalGroupMembership, |
690 | > | ggMjunk, |
691 | > | mpiSim->getNAtomsGlobal(), |
692 | > | MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
693 | ||
694 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
695 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
967 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
968 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
694 | > | for (i = 0; i < mpiSim->getNAtomsGlobal(); i++) |
695 | > | info[k].globalGroupMembership[i] = ggMjunk[i]; |
696 | ||
697 | + | delete[] ggMjunk; |
698 | + | |
699 | + | #endif |
700 | ||
971 | – | the_molecules[i].initialize( info ); |
701 | ||
702 | ||
974 | – | atomOffset += info.nAtoms; |
975 | – | delete[] theBonds; |
976 | – | delete[] theBends; |
977 | – | delete[] theTorsions; |
703 | } | |
704 | ||
705 | #ifdef IS_MPI | |
706 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
706 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
707 | MPIcheckPoint(); | |
708 | #endif // is_mpi | |
709 | ||
985 | – | // clean up the forcefield |
986 | – | the_ff->calcRcut(); |
987 | – | the_ff->cleanMe(); |
988 | – | |
710 | } | |
711 | ||
712 | < | void SimSetup::initFromBass( void ){ |
992 | < | |
712 | > | void SimSetup::initFromBass(void){ |
713 | int i, j, k; | |
714 | int n_cells; | |
715 | double cellx, celly, cellz; | |
# | Line 998 | Line 718 | void SimSetup::initFromBass( void ){ | |
718 | int n_extra; | |
719 | int have_extra, done; | |
720 | ||
721 | < | temp1 = (double)tot_nmol / 4.0; |
722 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
723 | < | temp3 = ceil( temp2 ); |
721 | > | double vel[3]; |
722 | > | vel[0] = 0.0; |
723 | > | vel[1] = 0.0; |
724 | > | vel[2] = 0.0; |
725 | ||
726 | < | have_extra =0; |
727 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
728 | < | have_extra =1; |
726 | > | temp1 = (double) tot_nmol / 4.0; |
727 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
728 | > | temp3 = ceil(temp2); |
729 | ||
730 | < | n_cells = (int)temp3 - 1; |
731 | < | cellx = simnfo->box_x / temp3; |
732 | < | celly = simnfo->box_y / temp3; |
733 | < | cellz = simnfo->box_z / temp3; |
1013 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1014 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1015 | < | n_per_extra = (int)ceil( temp1 ); |
730 | > | have_extra = 0; |
731 | > | if (temp2 < temp3){ |
732 | > | // we have a non-complete lattice |
733 | > | have_extra = 1; |
734 | ||
735 | < | if( n_per_extra > 4){ |
736 | < | sprintf( painCave.errMsg, |
737 | < | "SimSetup error. There has been an error in constructing" |
738 | < | " the non-complete lattice.\n" ); |
735 | > | n_cells = (int) temp3 - 1; |
736 | > | cellx = info[0].boxL[0] / temp3; |
737 | > | celly = info[0].boxL[1] / temp3; |
738 | > | cellz = info[0].boxL[2] / temp3; |
739 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
740 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
741 | > | n_per_extra = (int) ceil(temp1); |
742 | > | |
743 | > | if (n_per_extra > 4){ |
744 | > | sprintf(painCave.errMsg, |
745 | > | "SimSetup error. There has been an error in constructing" |
746 | > | " the non-complete lattice.\n"); |
747 | painCave.isFatal = 1; | |
748 | simError(); | |
749 | } | |
750 | } | |
751 | else{ | |
752 | < | n_cells = (int)temp3; |
753 | < | cellx = simnfo->box_x / temp3; |
754 | < | celly = simnfo->box_y / temp3; |
755 | < | cellz = simnfo->box_z / temp3; |
752 | > | n_cells = (int) temp3; |
753 | > | cellx = info[0].boxL[0] / temp3; |
754 | > | celly = info[0].boxL[1] / temp3; |
755 | > | cellz = info[0].boxL[2] / temp3; |
756 | } | |
757 | ||
758 | current_mol = 0; | |
# | Line 1034 | Line 760 | void SimSetup::initFromBass( void ){ | |
760 | current_comp = 0; | |
761 | current_atom_ndx = 0; | |
762 | ||
763 | < | for( i=0; i < n_cells ; i++ ){ |
764 | < | for( j=0; j < n_cells; j++ ){ |
765 | < | for( k=0; k < n_cells; k++ ){ |
763 | > | for (i = 0; i < n_cells ; i++){ |
764 | > | for (j = 0; j < n_cells; j++){ |
765 | > | for (k = 0; k < n_cells; k++){ |
766 | > | makeElement(i * cellx, j * celly, k * cellz); |
767 | ||
768 | < | makeElement( i * cellx, |
1042 | < | j * celly, |
1043 | < | k * cellz ); |
768 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
769 | ||
770 | < | makeElement( i * cellx + 0.5 * cellx, |
1046 | < | j * celly + 0.5 * celly, |
1047 | < | k * cellz ); |
770 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
771 | ||
772 | < | makeElement( i * cellx, |
1050 | < | j * celly + 0.5 * celly, |
1051 | < | k * cellz + 0.5 * cellz ); |
1052 | < | |
1053 | < | makeElement( i * cellx + 0.5 * cellx, |
1054 | < | j * celly, |
1055 | < | k * cellz + 0.5 * cellz ); |
772 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
773 | } | |
774 | } | |
775 | } | |
776 | ||
777 | < | if( have_extra ){ |
777 | > | if (have_extra){ |
778 | done = 0; | |
779 | ||
780 | int start_ndx; | |
781 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
782 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
781 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
782 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
783 | > | if (i < n_cells){ |
784 | > | if (j < n_cells){ |
785 | > | start_ndx = n_cells; |
786 | > | } |
787 | > | else |
788 | > | start_ndx = 0; |
789 | > | } |
790 | > | else |
791 | > | start_ndx = 0; |
792 | ||
793 | < | if( i < n_cells ){ |
793 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
794 | > | makeElement(i * cellx, j * celly, k * cellz); |
795 | > | done = (current_mol >= tot_nmol); |
796 | ||
797 | < | if( j < n_cells ){ |
798 | < | start_ndx = n_cells; |
799 | < | } |
800 | < | else start_ndx = 0; |
801 | < | } |
1074 | < | else start_ndx = 0; |
797 | > | if (!done && n_per_extra > 1){ |
798 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
799 | > | k * cellz); |
800 | > | done = (current_mol >= tot_nmol); |
801 | > | } |
802 | ||
803 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
803 | > | if (!done && n_per_extra > 2){ |
804 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
805 | > | k * cellz + 0.5 * cellz); |
806 | > | done = (current_mol >= tot_nmol); |
807 | > | } |
808 | ||
809 | < | makeElement( i * cellx, |
810 | < | j * celly, |
811 | < | k * cellz ); |
812 | < | done = ( current_mol >= tot_nmol ); |
813 | < | |
814 | < | if( !done && n_per_extra > 1 ){ |
1084 | < | makeElement( i * cellx + 0.5 * cellx, |
1085 | < | j * celly + 0.5 * celly, |
1086 | < | k * cellz ); |
1087 | < | done = ( current_mol >= tot_nmol ); |
1088 | < | } |
1089 | < | |
1090 | < | if( !done && n_per_extra > 2){ |
1091 | < | makeElement( i * cellx, |
1092 | < | j * celly + 0.5 * celly, |
1093 | < | k * cellz + 0.5 * cellz ); |
1094 | < | done = ( current_mol >= tot_nmol ); |
1095 | < | } |
1096 | < | |
1097 | < | if( !done && n_per_extra > 3){ |
1098 | < | makeElement( i * cellx + 0.5 * cellx, |
1099 | < | j * celly, |
1100 | < | k * cellz + 0.5 * cellz ); |
1101 | < | done = ( current_mol >= tot_nmol ); |
1102 | < | } |
1103 | < | } |
809 | > | if (!done && n_per_extra > 3){ |
810 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
811 | > | k * cellz + 0.5 * cellz); |
812 | > | done = (current_mol >= tot_nmol); |
813 | > | } |
814 | > | } |
815 | } | |
816 | } | |
817 | } | |
818 | ||
819 | < | |
820 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1110 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1111 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1112 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
819 | > | for (i = 0; i < info[0].n_atoms; i++){ |
820 | > | info[0].atoms[i]->setVel(vel); |
821 | } | |
822 | } | |
823 | ||
824 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1117 | < | |
824 | > | void SimSetup::makeElement(double x, double y, double z){ |
825 | int k; | |
826 | AtomStamp* current_atom; | |
827 | DirectionalAtom* dAtom; | |
828 | double rotMat[3][3]; | |
829 | + | double pos[3]; |
830 | ||
831 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
832 | < | |
833 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
834 | < | if( !current_atom->havePosition() ){ |
835 | < | sprintf( painCave.errMsg, |
836 | < | "SimSetup:initFromBass error.\n" |
837 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
838 | < | "\tThe initialization routine is unable to give a start" |
839 | < | " position.\n", |
1132 | < | comp_stamps[current_comp]->getID(), |
1133 | < | current_atom->getType() ); |
831 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
832 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
833 | > | if (!current_atom->havePosition()){ |
834 | > | sprintf(painCave.errMsg, |
835 | > | "SimSetup:initFromBass error.\n" |
836 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
837 | > | "\tThe initialization routine is unable to give a start" |
838 | > | " position.\n", |
839 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
840 | painCave.isFatal = 1; | |
841 | simError(); | |
842 | } | |
843 | ||
844 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
845 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
846 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
844 | > | pos[0] = x + current_atom->getPosX(); |
845 | > | pos[1] = y + current_atom->getPosY(); |
846 | > | pos[2] = z + current_atom->getPosZ(); |
847 | ||
848 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
848 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
849 | ||
850 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
850 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
851 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
852 | ||
853 | rotMat[0][0] = 1.0; | |
854 | rotMat[0][1] = 0.0; | |
# | Line 1155 | Line 862 | void SimSetup::makeElement( double x, double y, double | |
862 | rotMat[2][1] = 0.0; | |
863 | rotMat[2][2] = 1.0; | |
864 | ||
865 | < | dAtom->setA( rotMat ); |
865 | > | dAtom->setA(rotMat); |
866 | } | |
867 | ||
868 | current_atom_ndx++; | |
# | Line 1164 | Line 871 | void SimSetup::makeElement( double x, double y, double | |
871 | current_mol++; | |
872 | current_comp_mol++; | |
873 | ||
874 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1168 | < | |
874 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
875 | current_comp_mol = 0; | |
876 | current_comp++; | |
877 | } | |
878 | } | |
879 | + | |
880 | + | |
881 | + | void SimSetup::gatherInfo(void){ |
882 | + | int i; |
883 | + | |
884 | + | ensembleCase = -1; |
885 | + | ffCase = -1; |
886 | + | |
887 | + | // set the easy ones first |
888 | + | |
889 | + | for (i = 0; i < nInfo; i++){ |
890 | + | info[i].target_temp = globals->getTargetTemp(); |
891 | + | info[i].dt = globals->getDt(); |
892 | + | info[i].run_time = globals->getRunTime(); |
893 | + | } |
894 | + | n_components = globals->getNComponents(); |
895 | + | |
896 | + | |
897 | + | // get the forceField |
898 | + | |
899 | + | strcpy(force_field, globals->getForceField()); |
900 | + | |
901 | + | if (!strcasecmp(force_field, "DUFF")){ |
902 | + | ffCase = FF_DUFF; |
903 | + | } |
904 | + | else if (!strcasecmp(force_field, "LJ")){ |
905 | + | ffCase = FF_LJ; |
906 | + | } |
907 | + | else if (!strcasecmp(force_field, "EAM")){ |
908 | + | ffCase = FF_EAM; |
909 | + | } |
910 | + | else if (!strcasecmp(force_field, "WATER")){ |
911 | + | ffCase = FF_H2O; |
912 | + | } |
913 | + | else{ |
914 | + | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
915 | + | force_field); |
916 | + | painCave.isFatal = 1; |
917 | + | simError(); |
918 | + | } |
919 | + | if (globals->haveForceFieldVariant()) { |
920 | + | strcpy(forcefield_variant, globals->getForceFieldVariant()); |
921 | + | has_forcefield_variant = 1; |
922 | + | } |
923 | + | |
924 | + | // get the ensemble |
925 | + | |
926 | + | strcpy(ensemble, globals->getEnsemble()); |
927 | + | |
928 | + | if (!strcasecmp(ensemble, "NVE")){ |
929 | + | ensembleCase = NVE_ENS; |
930 | + | } |
931 | + | else if (!strcasecmp(ensemble, "NVT")){ |
932 | + | ensembleCase = NVT_ENS; |
933 | + | } |
934 | + | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
935 | + | ensembleCase = NPTi_ENS; |
936 | + | } |
937 | + | else if (!strcasecmp(ensemble, "NPTf")){ |
938 | + | ensembleCase = NPTf_ENS; |
939 | + | } |
940 | + | else if (!strcasecmp(ensemble, "NPTxyz")){ |
941 | + | ensembleCase = NPTxyz_ENS; |
942 | + | } |
943 | + | else{ |
944 | + | sprintf(painCave.errMsg, |
945 | + | "SimSetup Warning. Unrecognized Ensemble -> %s \n" |
946 | + | "\treverting to NVE for this simulation.\n", |
947 | + | ensemble); |
948 | + | painCave.isFatal = 0; |
949 | + | simError(); |
950 | + | strcpy(ensemble, "NVE"); |
951 | + | ensembleCase = NVE_ENS; |
952 | + | } |
953 | + | |
954 | + | for (i = 0; i < nInfo; i++){ |
955 | + | strcpy(info[i].ensemble, ensemble); |
956 | + | |
957 | + | // get the mixing rule |
958 | + | |
959 | + | strcpy(info[i].mixingRule, globals->getMixingRule()); |
960 | + | info[i].usePBC = globals->getPBC(); |
961 | + | } |
962 | + | |
963 | + | // get the components and calculate the tot_nMol and indvidual n_mol |
964 | + | |
965 | + | the_components = globals->getComponents(); |
966 | + | components_nmol = new int[n_components]; |
967 | + | |
968 | + | |
969 | + | if (!globals->haveNMol()){ |
970 | + | // we don't have the total number of molecules, so we assume it is |
971 | + | // given in each component |
972 | + | |
973 | + | tot_nmol = 0; |
974 | + | for (i = 0; i < n_components; i++){ |
975 | + | if (!the_components[i]->haveNMol()){ |
976 | + | // we have a problem |
977 | + | sprintf(painCave.errMsg, |
978 | + | "SimSetup Error. No global NMol or component NMol given.\n" |
979 | + | "\tCannot calculate the number of atoms.\n"); |
980 | + | painCave.isFatal = 1; |
981 | + | simError(); |
982 | + | } |
983 | + | |
984 | + | tot_nmol += the_components[i]->getNMol(); |
985 | + | components_nmol[i] = the_components[i]->getNMol(); |
986 | + | } |
987 | + | } |
988 | + | else{ |
989 | + | sprintf(painCave.errMsg, |
990 | + | "SimSetup error.\n" |
991 | + | "\tSorry, the ability to specify total" |
992 | + | " nMols and then give molfractions in the components\n" |
993 | + | "\tis not currently supported." |
994 | + | " Please give nMol in the components.\n"); |
995 | + | painCave.isFatal = 1; |
996 | + | simError(); |
997 | + | } |
998 | + | |
999 | + | //check whether sample time, status time, thermal time and reset time are divisble by dt |
1000 | + | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
1001 | + | sprintf(painCave.errMsg, |
1002 | + | "Sample time is not divisible by dt.\n" |
1003 | + | "\tThis will result in samples that are not uniformly\n" |
1004 | + | "\tdistributed in time. If this is a problem, change\n" |
1005 | + | "\tyour sampleTime variable.\n"); |
1006 | + | painCave.isFatal = 0; |
1007 | + | simError(); |
1008 | + | } |
1009 | + | |
1010 | + | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
1011 | + | sprintf(painCave.errMsg, |
1012 | + | "Status time is not divisible by dt.\n" |
1013 | + | "\tThis will result in status reports that are not uniformly\n" |
1014 | + | "\tdistributed in time. If this is a problem, change \n" |
1015 | + | "\tyour statusTime variable.\n"); |
1016 | + | painCave.isFatal = 0; |
1017 | + | simError(); |
1018 | + | } |
1019 | + | |
1020 | + | if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
1021 | + | sprintf(painCave.errMsg, |
1022 | + | "Thermal time is not divisible by dt.\n" |
1023 | + | "\tThis will result in thermalizations that are not uniformly\n" |
1024 | + | "\tdistributed in time. If this is a problem, change \n" |
1025 | + | "\tyour thermalTime variable.\n"); |
1026 | + | painCave.isFatal = 0; |
1027 | + | simError(); |
1028 | + | } |
1029 | + | |
1030 | + | if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
1031 | + | sprintf(painCave.errMsg, |
1032 | + | "Reset time is not divisible by dt.\n" |
1033 | + | "\tThis will result in integrator resets that are not uniformly\n" |
1034 | + | "\tdistributed in time. If this is a problem, change\n" |
1035 | + | "\tyour resetTime variable.\n"); |
1036 | + | painCave.isFatal = 0; |
1037 | + | simError(); |
1038 | + | } |
1039 | + | |
1040 | + | // set the status, sample, and thermal kick times |
1041 | + | |
1042 | + | for (i = 0; i < nInfo; i++){ |
1043 | + | if (globals->haveSampleTime()){ |
1044 | + | info[i].sampleTime = globals->getSampleTime(); |
1045 | + | info[i].statusTime = info[i].sampleTime; |
1046 | + | } |
1047 | + | else{ |
1048 | + | info[i].sampleTime = globals->getRunTime(); |
1049 | + | info[i].statusTime = info[i].sampleTime; |
1050 | + | } |
1051 | + | |
1052 | + | if (globals->haveStatusTime()){ |
1053 | + | info[i].statusTime = globals->getStatusTime(); |
1054 | + | } |
1055 | + | |
1056 | + | if (globals->haveThermalTime()){ |
1057 | + | info[i].thermalTime = globals->getThermalTime(); |
1058 | + | } else { |
1059 | + | info[i].thermalTime = globals->getRunTime(); |
1060 | + | } |
1061 | + | |
1062 | + | info[i].resetIntegrator = 0; |
1063 | + | if( globals->haveResetTime() ){ |
1064 | + | info[i].resetTime = globals->getResetTime(); |
1065 | + | info[i].resetIntegrator = 1; |
1066 | + | } |
1067 | + | |
1068 | + | // check for the temperature set flag |
1069 | + | |
1070 | + | if (globals->haveTempSet()) |
1071 | + | info[i].setTemp = globals->getTempSet(); |
1072 | + | |
1073 | + | // check for the extended State init |
1074 | + | |
1075 | + | info[i].useInitXSstate = globals->getUseInitXSstate(); |
1076 | + | info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
1077 | + | |
1078 | + | // check for thermodynamic integration |
1079 | + | if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) { |
1080 | + | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1081 | + | info[i].useSolidThermInt = globals->getUseSolidThermInt(); |
1082 | + | info[i].thermIntLambda = globals->getThermIntLambda(); |
1083 | + | info[i].thermIntK = globals->getThermIntK(); |
1084 | + | |
1085 | + | Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
1086 | + | info[i].restraint = myRestraint; |
1087 | + | } |
1088 | + | else { |
1089 | + | sprintf(painCave.errMsg, |
1090 | + | "SimSetup Error:\n" |
1091 | + | "\tKeyword useSolidThermInt was set to 'true' but\n" |
1092 | + | "\tthermodynamicIntegrationLambda (and/or\n" |
1093 | + | "\tthermodynamicIntegrationK) was not specified.\n" |
1094 | + | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1095 | + | painCave.isFatal = 1; |
1096 | + | simError(); |
1097 | + | } |
1098 | + | } |
1099 | + | else if(globals->getUseLiquidThermInt()) { |
1100 | + | if (globals->getUseSolidThermInt()) { |
1101 | + | sprintf( painCave.errMsg, |
1102 | + | "SimSetup Warning: It appears that you have both solid and\n" |
1103 | + | "\tliquid thermodynamic integration activated in your .bass\n" |
1104 | + | "\tfile. To avoid confusion, specify only one technique in\n" |
1105 | + | "\tyour .bass file. Liquid-state thermodynamic integration\n" |
1106 | + | "\twill be assumed for the current simulation. If this is not\n" |
1107 | + | "\twhat you desire, set useSolidThermInt to 'true' and\n" |
1108 | + | "\tuseLiquidThermInt to 'false' in your .bass file.\n"); |
1109 | + | painCave.isFatal = 0; |
1110 | + | simError(); |
1111 | + | } |
1112 | + | if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
1113 | + | info[i].useLiquidThermInt = globals->getUseLiquidThermInt(); |
1114 | + | info[i].thermIntLambda = globals->getThermIntLambda(); |
1115 | + | info[i].thermIntK = globals->getThermIntK(); |
1116 | + | } |
1117 | + | else { |
1118 | + | sprintf(painCave.errMsg, |
1119 | + | "SimSetup Error:\n" |
1120 | + | "\tKeyword useLiquidThermInt was set to 'true' but\n" |
1121 | + | "\tthermodynamicIntegrationLambda (and/or\n" |
1122 | + | "\tthermodynamicIntegrationK) was not specified.\n" |
1123 | + | "\tPlease provide a lambda value and k value in your .bass file.\n"); |
1124 | + | painCave.isFatal = 1; |
1125 | + | simError(); |
1126 | + | } |
1127 | + | } |
1128 | + | else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
1129 | + | sprintf(painCave.errMsg, |
1130 | + | "SimSetup Warning: If you want to use Thermodynamic\n" |
1131 | + | "\tIntegration, set useSolidThermInt or useLiquidThermInt to\n" |
1132 | + | "\t'true' in your .bass file. These keywords are set to\n" |
1133 | + | "\t'false' by default, so your lambda and/or k values are\n" |
1134 | + | "\tbeing ignored.\n"); |
1135 | + | painCave.isFatal = 0; |
1136 | + | simError(); |
1137 | + | } |
1138 | + | } |
1139 | + | |
1140 | + | //setup seed for random number generator |
1141 | + | int seedValue; |
1142 | + | |
1143 | + | if (globals->haveSeed()){ |
1144 | + | seedValue = globals->getSeed(); |
1145 | + | |
1146 | + | if(seedValue / 1E9 == 0){ |
1147 | + | sprintf(painCave.errMsg, |
1148 | + | "Seed for sprng library should contain at least 9 digits\n" |
1149 | + | "OOPSE will generate a seed for user\n"); |
1150 | + | painCave.isFatal = 0; |
1151 | + | simError(); |
1152 | + | |
1153 | + | //using seed generated by system instead of invalid seed set by user |
1154 | + | #ifndef IS_MPI |
1155 | + | seedValue = make_sprng_seed(); |
1156 | + | #else |
1157 | + | if (worldRank == 0){ |
1158 | + | seedValue = make_sprng_seed(); |
1159 | + | } |
1160 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1161 | + | #endif |
1162 | + | } |
1163 | + | }//end of if branch of globals->haveSeed() |
1164 | + | else{ |
1165 | + | |
1166 | + | #ifndef IS_MPI |
1167 | + | seedValue = make_sprng_seed(); |
1168 | + | #else |
1169 | + | if (worldRank == 0){ |
1170 | + | seedValue = make_sprng_seed(); |
1171 | + | } |
1172 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
1173 | + | #endif |
1174 | + | }//end of globals->haveSeed() |
1175 | + | |
1176 | + | for (int i = 0; i < nInfo; i++){ |
1177 | + | info[i].setSeed(seedValue); |
1178 | + | } |
1179 | + | |
1180 | + | #ifdef IS_MPI |
1181 | + | strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
1182 | + | MPIcheckPoint(); |
1183 | + | #endif // is_mpi |
1184 | + | } |
1185 | + | |
1186 | + | |
1187 | + | void SimSetup::finalInfoCheck(void){ |
1188 | + | int index; |
1189 | + | int usesDipoles; |
1190 | + | int usesCharges; |
1191 | + | int i; |
1192 | + | |
1193 | + | for (i = 0; i < nInfo; i++){ |
1194 | + | // check electrostatic parameters |
1195 | + | |
1196 | + | index = 0; |
1197 | + | usesDipoles = 0; |
1198 | + | while ((index < info[i].n_atoms) && !usesDipoles){ |
1199 | + | usesDipoles = (info[i].atoms[index])->hasDipole(); |
1200 | + | index++; |
1201 | + | } |
1202 | + | index = 0; |
1203 | + | usesCharges = 0; |
1204 | + | while ((index < info[i].n_atoms) && !usesCharges){ |
1205 | + | usesCharges= (info[i].atoms[index])->hasCharge(); |
1206 | + | index++; |
1207 | + | } |
1208 | + | #ifdef IS_MPI |
1209 | + | int myUse = usesDipoles; |
1210 | + | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
1211 | + | #endif //is_mpi |
1212 | + | |
1213 | + | double theRcut, theRsw; |
1214 | + | |
1215 | + | if (globals->haveRcut()) { |
1216 | + | theRcut = globals->getRcut(); |
1217 | + | |
1218 | + | if (globals->haveRsw()) |
1219 | + | theRsw = globals->getRsw(); |
1220 | + | else |
1221 | + | theRsw = theRcut; |
1222 | + | |
1223 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1224 | + | |
1225 | + | } else { |
1226 | + | |
1227 | + | the_ff->calcRcut(); |
1228 | + | theRcut = info[i].getRcut(); |
1229 | + | |
1230 | + | if (globals->haveRsw()) |
1231 | + | theRsw = globals->getRsw(); |
1232 | + | else |
1233 | + | theRsw = theRcut; |
1234 | + | |
1235 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1236 | + | } |
1237 | + | |
1238 | + | if (globals->getUseRF()){ |
1239 | + | info[i].useReactionField = 1; |
1240 | + | |
1241 | + | if (!globals->haveRcut()){ |
1242 | + | sprintf(painCave.errMsg, |
1243 | + | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1244 | + | "\tOOPSE will use a default value of 15.0 angstroms" |
1245 | + | "\tfor the cutoffRadius.\n"); |
1246 | + | painCave.isFatal = 0; |
1247 | + | simError(); |
1248 | + | theRcut = 15.0; |
1249 | + | } |
1250 | + | else{ |
1251 | + | theRcut = globals->getRcut(); |
1252 | + | } |
1253 | + | |
1254 | + | if (!globals->haveRsw()){ |
1255 | + | sprintf(painCave.errMsg, |
1256 | + | "SimSetup Warning: No value was set for switchingRadius.\n" |
1257 | + | "\tOOPSE will use a default value of\n" |
1258 | + | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1259 | + | painCave.isFatal = 0; |
1260 | + | simError(); |
1261 | + | theRsw = 0.95 * theRcut; |
1262 | + | } |
1263 | + | else{ |
1264 | + | theRsw = globals->getRsw(); |
1265 | + | } |
1266 | + | |
1267 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1268 | + | |
1269 | + | if (!globals->haveDielectric()){ |
1270 | + | sprintf(painCave.errMsg, |
1271 | + | "SimSetup Error: No Dielectric constant was set.\n" |
1272 | + | "\tYou are trying to use Reaction Field without" |
1273 | + | "\tsetting a dielectric constant!\n"); |
1274 | + | painCave.isFatal = 1; |
1275 | + | simError(); |
1276 | + | } |
1277 | + | info[i].dielectric = globals->getDielectric(); |
1278 | + | } |
1279 | + | else{ |
1280 | + | if (usesDipoles || usesCharges){ |
1281 | + | |
1282 | + | if (!globals->haveRcut()){ |
1283 | + | sprintf(painCave.errMsg, |
1284 | + | "SimSetup Warning: No value was set for the cutoffRadius.\n" |
1285 | + | "\tOOPSE will use a default value of 15.0 angstroms" |
1286 | + | "\tfor the cutoffRadius.\n"); |
1287 | + | painCave.isFatal = 0; |
1288 | + | simError(); |
1289 | + | theRcut = 15.0; |
1290 | + | } |
1291 | + | else{ |
1292 | + | theRcut = globals->getRcut(); |
1293 | + | } |
1294 | + | |
1295 | + | if (!globals->haveRsw()){ |
1296 | + | sprintf(painCave.errMsg, |
1297 | + | "SimSetup Warning: No value was set for switchingRadius.\n" |
1298 | + | "\tOOPSE will use a default value of\n" |
1299 | + | "\t0.95 * cutoffRadius for the switchingRadius\n"); |
1300 | + | painCave.isFatal = 0; |
1301 | + | simError(); |
1302 | + | theRsw = 0.95 * theRcut; |
1303 | + | } |
1304 | + | else{ |
1305 | + | theRsw = globals->getRsw(); |
1306 | + | } |
1307 | + | |
1308 | + | info[i].setDefaultRcut(theRcut, theRsw); |
1309 | + | |
1310 | + | } |
1311 | + | } |
1312 | + | } |
1313 | + | #ifdef IS_MPI |
1314 | + | strcpy(checkPointMsg, "post processing checks out"); |
1315 | + | MPIcheckPoint(); |
1316 | + | #endif // is_mpi |
1317 | + | |
1318 | + | // clean up the forcefield |
1319 | + | the_ff->cleanMe(); |
1320 | + | } |
1321 | + | |
1322 | + | void SimSetup::initSystemCoords(void){ |
1323 | + | int i; |
1324 | + | |
1325 | + | char* inName; |
1326 | + | |
1327 | + | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
1328 | + | |
1329 | + | for (i = 0; i < info[0].n_atoms; i++) |
1330 | + | info[0].atoms[i]->setCoords(); |
1331 | + | |
1332 | + | if (globals->haveInitialConfig()){ |
1333 | + | InitializeFromFile* fileInit; |
1334 | + | #ifdef IS_MPI // is_mpi |
1335 | + | if (worldRank == 0){ |
1336 | + | #endif //is_mpi |
1337 | + | inName = globals->getInitialConfig(); |
1338 | + | fileInit = new InitializeFromFile(inName); |
1339 | + | #ifdef IS_MPI |
1340 | + | } |
1341 | + | else |
1342 | + | fileInit = new InitializeFromFile(NULL); |
1343 | + | #endif |
1344 | + | fileInit->readInit(info); // default velocities on |
1345 | + | |
1346 | + | delete fileInit; |
1347 | + | } |
1348 | + | else{ |
1349 | + | |
1350 | + | // no init from bass |
1351 | + | |
1352 | + | sprintf(painCave.errMsg, |
1353 | + | "Cannot intialize a simulation without an initial configuration file.\n"); |
1354 | + | painCave.isFatal = 1;; |
1355 | + | simError(); |
1356 | + | |
1357 | + | } |
1358 | + | |
1359 | + | #ifdef IS_MPI |
1360 | + | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
1361 | + | MPIcheckPoint(); |
1362 | + | #endif // is_mpi |
1363 | + | } |
1364 | + | |
1365 | + | |
1366 | + | void SimSetup::makeOutNames(void){ |
1367 | + | int k; |
1368 | + | |
1369 | + | |
1370 | + | for (k = 0; k < nInfo; k++){ |
1371 | + | #ifdef IS_MPI |
1372 | + | if (worldRank == 0){ |
1373 | + | #endif // is_mpi |
1374 | + | |
1375 | + | if (globals->haveFinalConfig()){ |
1376 | + | strcpy(info[k].finalName, globals->getFinalConfig()); |
1377 | + | } |
1378 | + | else{ |
1379 | + | strcpy(info[k].finalName, inFileName); |
1380 | + | char* endTest; |
1381 | + | int nameLength = strlen(info[k].finalName); |
1382 | + | endTest = &(info[k].finalName[nameLength - 5]); |
1383 | + | if (!strcmp(endTest, ".bass")){ |
1384 | + | strcpy(endTest, ".eor"); |
1385 | + | } |
1386 | + | else if (!strcmp(endTest, ".BASS")){ |
1387 | + | strcpy(endTest, ".eor"); |
1388 | + | } |
1389 | + | else{ |
1390 | + | endTest = &(info[k].finalName[nameLength - 4]); |
1391 | + | if (!strcmp(endTest, ".bss")){ |
1392 | + | strcpy(endTest, ".eor"); |
1393 | + | } |
1394 | + | else if (!strcmp(endTest, ".mdl")){ |
1395 | + | strcpy(endTest, ".eor"); |
1396 | + | } |
1397 | + | else{ |
1398 | + | strcat(info[k].finalName, ".eor"); |
1399 | + | } |
1400 | + | } |
1401 | + | } |
1402 | + | |
1403 | + | // make the sample and status out names |
1404 | + | |
1405 | + | strcpy(info[k].sampleName, inFileName); |
1406 | + | char* endTest; |
1407 | + | int nameLength = strlen(info[k].sampleName); |
1408 | + | endTest = &(info[k].sampleName[nameLength - 5]); |
1409 | + | if (!strcmp(endTest, ".bass")){ |
1410 | + | strcpy(endTest, ".dump"); |
1411 | + | } |
1412 | + | else if (!strcmp(endTest, ".BASS")){ |
1413 | + | strcpy(endTest, ".dump"); |
1414 | + | } |
1415 | + | else{ |
1416 | + | endTest = &(info[k].sampleName[nameLength - 4]); |
1417 | + | if (!strcmp(endTest, ".bss")){ |
1418 | + | strcpy(endTest, ".dump"); |
1419 | + | } |
1420 | + | else if (!strcmp(endTest, ".mdl")){ |
1421 | + | strcpy(endTest, ".dump"); |
1422 | + | } |
1423 | + | else{ |
1424 | + | strcat(info[k].sampleName, ".dump"); |
1425 | + | } |
1426 | + | } |
1427 | + | |
1428 | + | strcpy(info[k].statusName, inFileName); |
1429 | + | nameLength = strlen(info[k].statusName); |
1430 | + | endTest = &(info[k].statusName[nameLength - 5]); |
1431 | + | if (!strcmp(endTest, ".bass")){ |
1432 | + | strcpy(endTest, ".stat"); |
1433 | + | } |
1434 | + | else if (!strcmp(endTest, ".BASS")){ |
1435 | + | strcpy(endTest, ".stat"); |
1436 | + | } |
1437 | + | else{ |
1438 | + | endTest = &(info[k].statusName[nameLength - 4]); |
1439 | + | if (!strcmp(endTest, ".bss")){ |
1440 | + | strcpy(endTest, ".stat"); |
1441 | + | } |
1442 | + | else if (!strcmp(endTest, ".mdl")){ |
1443 | + | strcpy(endTest, ".stat"); |
1444 | + | } |
1445 | + | else{ |
1446 | + | strcat(info[k].statusName, ".stat"); |
1447 | + | } |
1448 | + | } |
1449 | + | |
1450 | + | strcpy(info[k].rawPotName, inFileName); |
1451 | + | nameLength = strlen(info[k].rawPotName); |
1452 | + | endTest = &(info[k].rawPotName[nameLength - 5]); |
1453 | + | if (!strcmp(endTest, ".bass")){ |
1454 | + | strcpy(endTest, ".raw"); |
1455 | + | } |
1456 | + | else if (!strcmp(endTest, ".BASS")){ |
1457 | + | strcpy(endTest, ".raw"); |
1458 | + | } |
1459 | + | else{ |
1460 | + | endTest = &(info[k].rawPotName[nameLength - 4]); |
1461 | + | if (!strcmp(endTest, ".bss")){ |
1462 | + | strcpy(endTest, ".raw"); |
1463 | + | } |
1464 | + | else if (!strcmp(endTest, ".mdl")){ |
1465 | + | strcpy(endTest, ".raw"); |
1466 | + | } |
1467 | + | else{ |
1468 | + | strcat(info[k].rawPotName, ".raw"); |
1469 | + | } |
1470 | + | } |
1471 | + | |
1472 | + | #ifdef IS_MPI |
1473 | + | |
1474 | + | } |
1475 | + | #endif // is_mpi |
1476 | + | } |
1477 | + | } |
1478 | + | |
1479 | + | |
1480 | + | void SimSetup::sysObjectsCreation(void){ |
1481 | + | int i, k; |
1482 | + | |
1483 | + | // create the forceField |
1484 | + | |
1485 | + | createFF(); |
1486 | + | |
1487 | + | // extract componentList |
1488 | + | |
1489 | + | compList(); |
1490 | + | |
1491 | + | // calc the number of atoms, bond, bends, and torsions |
1492 | + | |
1493 | + | calcSysValues(); |
1494 | + | |
1495 | + | #ifdef IS_MPI |
1496 | + | // divide the molecules among the processors |
1497 | + | |
1498 | + | mpiMolDivide(); |
1499 | + | #endif //is_mpi |
1500 | + | |
1501 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1502 | + | |
1503 | + | makeSysArrays(); |
1504 | + | |
1505 | + | // make and initialize the molecules (all but atomic coordinates) |
1506 | + | |
1507 | + | makeMolecules(); |
1508 | + | |
1509 | + | for (k = 0; k < nInfo; k++){ |
1510 | + | info[k].identArray = new int[info[k].n_atoms]; |
1511 | + | for (i = 0; i < info[k].n_atoms; i++){ |
1512 | + | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1513 | + | } |
1514 | + | } |
1515 | + | } |
1516 | + | |
1517 | + | |
1518 | + | void SimSetup::createFF(void){ |
1519 | + | switch (ffCase){ |
1520 | + | case FF_DUFF: |
1521 | + | the_ff = new DUFF(); |
1522 | + | break; |
1523 | + | |
1524 | + | case FF_LJ: |
1525 | + | the_ff = new LJFF(); |
1526 | + | break; |
1527 | + | |
1528 | + | case FF_EAM: |
1529 | + | if (has_forcefield_variant) |
1530 | + | the_ff = new EAM_FF(forcefield_variant); |
1531 | + | else |
1532 | + | the_ff = new EAM_FF(); |
1533 | + | break; |
1534 | + | |
1535 | + | case FF_H2O: |
1536 | + | the_ff = new WATER(); |
1537 | + | break; |
1538 | + | |
1539 | + | default: |
1540 | + | sprintf(painCave.errMsg, |
1541 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1542 | + | painCave.isFatal = 1; |
1543 | + | simError(); |
1544 | + | } |
1545 | + | |
1546 | + | |
1547 | + | #ifdef IS_MPI |
1548 | + | strcpy(checkPointMsg, "ForceField creation successful"); |
1549 | + | MPIcheckPoint(); |
1550 | + | #endif // is_mpi |
1551 | + | } |
1552 | + | |
1553 | + | |
1554 | + | void SimSetup::compList(void){ |
1555 | + | int i; |
1556 | + | char* id; |
1557 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1558 | + | LinkedMolStamp* currentStamp = NULL; |
1559 | + | comp_stamps = new MoleculeStamp * [n_components]; |
1560 | + | bool haveCutoffGroups; |
1561 | + | |
1562 | + | haveCutoffGroups = false; |
1563 | + | |
1564 | + | // make an array of molecule stamps that match the components used. |
1565 | + | // also extract the used stamps out into a separate linked list |
1566 | + | |
1567 | + | for (i = 0; i < nInfo; i++){ |
1568 | + | info[i].nComponents = n_components; |
1569 | + | info[i].componentsNmol = components_nmol; |
1570 | + | info[i].compStamps = comp_stamps; |
1571 | + | info[i].headStamp = headStamp; |
1572 | + | } |
1573 | + | |
1574 | + | |
1575 | + | for (i = 0; i < n_components; i++){ |
1576 | + | id = the_components[i]->getType(); |
1577 | + | comp_stamps[i] = NULL; |
1578 | + | |
1579 | + | // check to make sure the component isn't already in the list |
1580 | + | |
1581 | + | comp_stamps[i] = headStamp->match(id); |
1582 | + | if (comp_stamps[i] == NULL){ |
1583 | + | // extract the component from the list; |
1584 | + | |
1585 | + | currentStamp = stamps->extractMolStamp(id); |
1586 | + | if (currentStamp == NULL){ |
1587 | + | sprintf(painCave.errMsg, |
1588 | + | "SimSetup error: Component \"%s\" was not found in the " |
1589 | + | "list of declared molecules\n", |
1590 | + | id); |
1591 | + | painCave.isFatal = 1; |
1592 | + | simError(); |
1593 | + | } |
1594 | + | |
1595 | + | headStamp->add(currentStamp); |
1596 | + | comp_stamps[i] = headStamp->match(id); |
1597 | + | } |
1598 | + | |
1599 | + | if(comp_stamps[i]->getNCutoffGroups() > 0) |
1600 | + | haveCutoffGroups = true; |
1601 | + | } |
1602 | + | |
1603 | + | for (i = 0; i < nInfo; i++) |
1604 | + | info[i].haveCutoffGroups = haveCutoffGroups; |
1605 | + | |
1606 | + | #ifdef IS_MPI |
1607 | + | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1608 | + | MPIcheckPoint(); |
1609 | + | #endif // is_mpi |
1610 | + | } |
1611 | + | |
1612 | + | void SimSetup::calcSysValues(void){ |
1613 | + | int i, j; |
1614 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1615 | + | |
1616 | + | int* molMembershipArray; |
1617 | + | CutoffGroupStamp* cg; |
1618 | + | |
1619 | + | tot_atoms = 0; |
1620 | + | tot_bonds = 0; |
1621 | + | tot_bends = 0; |
1622 | + | tot_torsions = 0; |
1623 | + | tot_rigid = 0; |
1624 | + | tot_groups = 0; |
1625 | + | for (i = 0; i < n_components; i++){ |
1626 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1627 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1628 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1629 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1630 | + | tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies(); |
1631 | + | |
1632 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1633 | + | atomsingroups = 0; |
1634 | + | for (j=0; j < ncutgroups; j++) { |
1635 | + | cg = comp_stamps[i]->getCutoffGroup(j); |
1636 | + | atomsingroups += cg->getNMembers(); |
1637 | + | } |
1638 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups; |
1639 | + | tot_groups += components_nmol[i] * ngroupsinstamp; |
1640 | + | } |
1641 | + | |
1642 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1643 | + | molMembershipArray = new int[tot_atoms]; |
1644 | + | |
1645 | + | for (i = 0; i < nInfo; i++){ |
1646 | + | info[i].n_atoms = tot_atoms; |
1647 | + | info[i].n_bonds = tot_bonds; |
1648 | + | info[i].n_bends = tot_bends; |
1649 | + | info[i].n_torsions = tot_torsions; |
1650 | + | info[i].n_SRI = tot_SRI; |
1651 | + | info[i].n_mol = tot_nmol; |
1652 | + | info[i].ngroup = tot_groups; |
1653 | + | info[i].molMembershipArray = molMembershipArray; |
1654 | + | } |
1655 | + | } |
1656 | + | |
1657 | + | #ifdef IS_MPI |
1658 | + | |
1659 | + | void SimSetup::mpiMolDivide(void){ |
1660 | + | int i, j, k; |
1661 | + | int localMol, allMol; |
1662 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1663 | + | int local_rigid, local_groups; |
1664 | + | vector<int> globalMolIndex; |
1665 | + | int ncutgroups, atomsingroups, ngroupsinstamp; |
1666 | + | CutoffGroupStamp* cg; |
1667 | + | |
1668 | + | mpiSim = new mpiSimulation(info); |
1669 | + | |
1670 | + | mpiSim->divideLabor(); |
1671 | + | globalAtomIndex = mpiSim->getGlobalAtomIndex(); |
1672 | + | globalGroupIndex = mpiSim->getGlobalGroupIndex(); |
1673 | + | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1674 | + | |
1675 | + | // set up the local variables |
1676 | + | |
1677 | + | mol2proc = mpiSim->getMolToProcMap(); |
1678 | + | molCompType = mpiSim->getMolComponentType(); |
1679 | + | |
1680 | + | allMol = 0; |
1681 | + | localMol = 0; |
1682 | + | local_atoms = 0; |
1683 | + | local_bonds = 0; |
1684 | + | local_bends = 0; |
1685 | + | local_torsions = 0; |
1686 | + | local_rigid = 0; |
1687 | + | local_groups = 0; |
1688 | + | globalAtomCounter = 0; |
1689 | + | |
1690 | + | for (i = 0; i < n_components; i++){ |
1691 | + | for (j = 0; j < components_nmol[i]; j++){ |
1692 | + | if (mol2proc[allMol] == worldRank){ |
1693 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1694 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1695 | + | local_bends += comp_stamps[i]->getNBends(); |
1696 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1697 | + | local_rigid += comp_stamps[i]->getNRigidBodies(); |
1698 | + | |
1699 | + | ncutgroups = comp_stamps[i]->getNCutoffGroups(); |
1700 | + | atomsingroups = 0; |
1701 | + | for (k=0; k < ncutgroups; k++) { |
1702 | + | cg = comp_stamps[i]->getCutoffGroup(k); |
1703 | + | atomsingroups += cg->getNMembers(); |
1704 | + | } |
1705 | + | ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + |
1706 | + | ncutgroups; |
1707 | + | local_groups += ngroupsinstamp; |
1708 | + | |
1709 | + | localMol++; |
1710 | + | } |
1711 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1712 | + | info[0].molMembershipArray[globalAtomCounter] = allMol; |
1713 | + | globalAtomCounter++; |
1714 | + | } |
1715 | + | |
1716 | + | allMol++; |
1717 | + | } |
1718 | + | } |
1719 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1720 | + | |
1721 | + | info[0].n_atoms = mpiSim->getNAtomsLocal(); |
1722 | + | |
1723 | + | if (local_atoms != info[0].n_atoms){ |
1724 | + | sprintf(painCave.errMsg, |
1725 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1726 | + | "\tlocalAtom (%d) are not equal.\n", |
1727 | + | info[0].n_atoms, local_atoms); |
1728 | + | painCave.isFatal = 1; |
1729 | + | simError(); |
1730 | + | } |
1731 | + | |
1732 | + | info[0].ngroup = mpiSim->getNGroupsLocal(); |
1733 | + | if (local_groups != info[0].ngroup){ |
1734 | + | sprintf(painCave.errMsg, |
1735 | + | "SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n" |
1736 | + | "\tlocalGroups (%d) are not equal.\n", |
1737 | + | info[0].ngroup, local_groups); |
1738 | + | painCave.isFatal = 1; |
1739 | + | simError(); |
1740 | + | } |
1741 | + | |
1742 | + | info[0].n_bonds = local_bonds; |
1743 | + | info[0].n_bends = local_bends; |
1744 | + | info[0].n_torsions = local_torsions; |
1745 | + | info[0].n_SRI = local_SRI; |
1746 | + | info[0].n_mol = localMol; |
1747 | + | |
1748 | + | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1749 | + | MPIcheckPoint(); |
1750 | + | } |
1751 | + | |
1752 | + | #endif // is_mpi |
1753 | + | |
1754 | + | |
1755 | + | void SimSetup::makeSysArrays(void){ |
1756 | + | |
1757 | + | #ifndef IS_MPI |
1758 | + | int k, j; |
1759 | + | #endif // is_mpi |
1760 | + | int i, l; |
1761 | + | |
1762 | + | Atom** the_atoms; |
1763 | + | Molecule* the_molecules; |
1764 | + | |
1765 | + | for (l = 0; l < nInfo; l++){ |
1766 | + | // create the atom and short range interaction arrays |
1767 | + | |
1768 | + | the_atoms = new Atom * [info[l].n_atoms]; |
1769 | + | the_molecules = new Molecule[info[l].n_mol]; |
1770 | + | int molIndex; |
1771 | + | |
1772 | + | // initialize the molecule's stampID's |
1773 | + | |
1774 | + | #ifdef IS_MPI |
1775 | + | |
1776 | + | |
1777 | + | molIndex = 0; |
1778 | + | for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
1779 | + | if (mol2proc[i] == worldRank){ |
1780 | + | the_molecules[molIndex].setStampID(molCompType[i]); |
1781 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1782 | + | the_molecules[molIndex].setGlobalIndex(i); |
1783 | + | molIndex++; |
1784 | + | } |
1785 | + | } |
1786 | + | |
1787 | + | #else // is_mpi |
1788 | + | |
1789 | + | molIndex = 0; |
1790 | + | globalAtomCounter = 0; |
1791 | + | for (i = 0; i < n_components; i++){ |
1792 | + | for (j = 0; j < components_nmol[i]; j++){ |
1793 | + | the_molecules[molIndex].setStampID(i); |
1794 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1795 | + | the_molecules[molIndex].setGlobalIndex(molIndex); |
1796 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1797 | + | info[l].molMembershipArray[globalAtomCounter] = molIndex; |
1798 | + | globalAtomCounter++; |
1799 | + | } |
1800 | + | molIndex++; |
1801 | + | } |
1802 | + | } |
1803 | + | |
1804 | + | |
1805 | + | #endif // is_mpi |
1806 | + | |
1807 | + | info[l].globalExcludes = new int; |
1808 | + | info[l].globalExcludes[0] = 0; |
1809 | + | |
1810 | + | // set the arrays into the SimInfo object |
1811 | + | |
1812 | + | info[l].atoms = the_atoms; |
1813 | + | info[l].molecules = the_molecules; |
1814 | + | info[l].nGlobalExcludes = 0; |
1815 | + | |
1816 | + | the_ff->setSimInfo(info); |
1817 | + | } |
1818 | + | } |
1819 | + | |
1820 | + | void SimSetup::makeIntegrator(void){ |
1821 | + | int k; |
1822 | + | |
1823 | + | NVE<Integrator<BaseIntegrator> >* myNVE = NULL; |
1824 | + | NVT<Integrator<BaseIntegrator> >* myNVT = NULL; |
1825 | + | NPTi<NPT<Integrator<BaseIntegrator> > >* myNPTi = NULL; |
1826 | + | NPTf<NPT<Integrator<BaseIntegrator> > >* myNPTf = NULL; |
1827 | + | NPTxyz<NPT<Integrator<BaseIntegrator> > >* myNPTxyz = NULL; |
1828 | + | |
1829 | + | for (k = 0; k < nInfo; k++){ |
1830 | + | switch (ensembleCase){ |
1831 | + | case NVE_ENS: |
1832 | + | if (globals->haveZconstraints()){ |
1833 | + | setupZConstraint(info[k]); |
1834 | + | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1835 | + | } |
1836 | + | else{ |
1837 | + | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1838 | + | } |
1839 | + | |
1840 | + | info->the_integrator = myNVE; |
1841 | + | break; |
1842 | + | |
1843 | + | case NVT_ENS: |
1844 | + | if (globals->haveZconstraints()){ |
1845 | + | setupZConstraint(info[k]); |
1846 | + | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1847 | + | } |
1848 | + | else |
1849 | + | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1850 | + | |
1851 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1852 | + | |
1853 | + | if (globals->haveTauThermostat()) |
1854 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1855 | + | else{ |
1856 | + | sprintf(painCave.errMsg, |
1857 | + | "SimSetup error: If you use the NVT\n" |
1858 | + | "\tensemble, you must set tauThermostat.\n"); |
1859 | + | painCave.isFatal = 1; |
1860 | + | simError(); |
1861 | + | } |
1862 | + | |
1863 | + | info->the_integrator = myNVT; |
1864 | + | break; |
1865 | + | |
1866 | + | case NPTi_ENS: |
1867 | + | if (globals->haveZconstraints()){ |
1868 | + | setupZConstraint(info[k]); |
1869 | + | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1870 | + | } |
1871 | + | else |
1872 | + | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1873 | + | |
1874 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1875 | + | |
1876 | + | if (globals->haveTargetPressure()) |
1877 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1878 | + | else{ |
1879 | + | sprintf(painCave.errMsg, |
1880 | + | "SimSetup error: If you use a constant pressure\n" |
1881 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1882 | + | painCave.isFatal = 1; |
1883 | + | simError(); |
1884 | + | } |
1885 | + | |
1886 | + | if (globals->haveTauThermostat()) |
1887 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1888 | + | else{ |
1889 | + | sprintf(painCave.errMsg, |
1890 | + | "SimSetup error: If you use an NPT\n" |
1891 | + | "\tensemble, you must set tauThermostat.\n"); |
1892 | + | painCave.isFatal = 1; |
1893 | + | simError(); |
1894 | + | } |
1895 | + | |
1896 | + | if (globals->haveTauBarostat()) |
1897 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1898 | + | else{ |
1899 | + | sprintf(painCave.errMsg, |
1900 | + | "SimSetup error: If you use an NPT\n" |
1901 | + | "\tensemble, you must set tauBarostat.\n"); |
1902 | + | painCave.isFatal = 1; |
1903 | + | simError(); |
1904 | + | } |
1905 | + | |
1906 | + | info->the_integrator = myNPTi; |
1907 | + | break; |
1908 | + | |
1909 | + | case NPTf_ENS: |
1910 | + | if (globals->haveZconstraints()){ |
1911 | + | setupZConstraint(info[k]); |
1912 | + | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1913 | + | } |
1914 | + | else |
1915 | + | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1916 | + | |
1917 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1918 | + | |
1919 | + | if (globals->haveTargetPressure()) |
1920 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1921 | + | else{ |
1922 | + | sprintf(painCave.errMsg, |
1923 | + | "SimSetup error: If you use a constant pressure\n" |
1924 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1925 | + | painCave.isFatal = 1; |
1926 | + | simError(); |
1927 | + | } |
1928 | + | |
1929 | + | if (globals->haveTauThermostat()) |
1930 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1931 | + | |
1932 | + | else{ |
1933 | + | sprintf(painCave.errMsg, |
1934 | + | "SimSetup error: If you use an NPT\n" |
1935 | + | "\tensemble, you must set tauThermostat.\n"); |
1936 | + | painCave.isFatal = 1; |
1937 | + | simError(); |
1938 | + | } |
1939 | + | |
1940 | + | if (globals->haveTauBarostat()) |
1941 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1942 | + | |
1943 | + | else{ |
1944 | + | sprintf(painCave.errMsg, |
1945 | + | "SimSetup error: If you use an NPT\n" |
1946 | + | "\tensemble, you must set tauBarostat.\n"); |
1947 | + | painCave.isFatal = 1; |
1948 | + | simError(); |
1949 | + | } |
1950 | + | |
1951 | + | info->the_integrator = myNPTf; |
1952 | + | break; |
1953 | + | |
1954 | + | case NPTxyz_ENS: |
1955 | + | if (globals->haveZconstraints()){ |
1956 | + | setupZConstraint(info[k]); |
1957 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1958 | + | } |
1959 | + | else |
1960 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1961 | + | |
1962 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1963 | + | |
1964 | + | if (globals->haveTargetPressure()) |
1965 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1966 | + | else{ |
1967 | + | sprintf(painCave.errMsg, |
1968 | + | "SimSetup error: If you use a constant pressure\n" |
1969 | + | "\tensemble, you must set targetPressure in the BASS file.\n"); |
1970 | + | painCave.isFatal = 1; |
1971 | + | simError(); |
1972 | + | } |
1973 | + | |
1974 | + | if (globals->haveTauThermostat()) |
1975 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1976 | + | else{ |
1977 | + | sprintf(painCave.errMsg, |
1978 | + | "SimSetup error: If you use an NPT\n" |
1979 | + | "\tensemble, you must set tauThermostat.\n"); |
1980 | + | painCave.isFatal = 1; |
1981 | + | simError(); |
1982 | + | } |
1983 | + | |
1984 | + | if (globals->haveTauBarostat()) |
1985 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1986 | + | else{ |
1987 | + | sprintf(painCave.errMsg, |
1988 | + | "SimSetup error: If you use an NPT\n" |
1989 | + | "\tensemble, you must set tauBarostat.\n"); |
1990 | + | painCave.isFatal = 1; |
1991 | + | simError(); |
1992 | + | } |
1993 | + | |
1994 | + | info->the_integrator = myNPTxyz; |
1995 | + | break; |
1996 | + | |
1997 | + | default: |
1998 | + | sprintf(painCave.errMsg, |
1999 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
2000 | + | painCave.isFatal = 1; |
2001 | + | simError(); |
2002 | + | } |
2003 | + | } |
2004 | + | } |
2005 | + | |
2006 | + | void SimSetup::initFortran(void){ |
2007 | + | info[0].refreshSim(); |
2008 | + | |
2009 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
2010 | + | the_ff->initForceField(LB_MIXING_RULE); |
2011 | + | } |
2012 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
2013 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
2014 | + | } |
2015 | + | else{ |
2016 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
2017 | + | info[0].mixingRule); |
2018 | + | painCave.isFatal = 1; |
2019 | + | simError(); |
2020 | + | } |
2021 | + | |
2022 | + | |
2023 | + | #ifdef IS_MPI |
2024 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
2025 | + | MPIcheckPoint(); |
2026 | + | #endif // is_mpi |
2027 | + | } |
2028 | + | |
2029 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
2030 | + | int nZConstraints; |
2031 | + | ZconStamp** zconStamp; |
2032 | + | |
2033 | + | if (globals->haveZconstraintTime()){ |
2034 | + | //add sample time of z-constraint into SimInfo's property list |
2035 | + | DoubleData* zconsTimeProp = new DoubleData(); |
2036 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
2037 | + | zconsTimeProp->setData(globals->getZconsTime()); |
2038 | + | theInfo.addProperty(zconsTimeProp); |
2039 | + | } |
2040 | + | else{ |
2041 | + | sprintf(painCave.errMsg, |
2042 | + | "ZConstraint error: If you use a ZConstraint,\n" |
2043 | + | "\tyou must set zconsTime.\n"); |
2044 | + | painCave.isFatal = 1; |
2045 | + | simError(); |
2046 | + | } |
2047 | + | |
2048 | + | //push zconsTol into siminfo, if user does not specify |
2049 | + | //value for zconsTol, a default value will be used |
2050 | + | DoubleData* zconsTol = new DoubleData(); |
2051 | + | zconsTol->setID(ZCONSTOL_ID); |
2052 | + | if (globals->haveZconsTol()){ |
2053 | + | zconsTol->setData(globals->getZconsTol()); |
2054 | + | } |
2055 | + | else{ |
2056 | + | double defaultZConsTol = 0.01; |
2057 | + | sprintf(painCave.errMsg, |
2058 | + | "ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
2059 | + | "\tOOPSE will use a default value of %f.\n" |
2060 | + | "\tTo set the tolerance, use the zconsTol variable.\n", |
2061 | + | defaultZConsTol); |
2062 | + | painCave.isFatal = 0; |
2063 | + | simError(); |
2064 | + | |
2065 | + | zconsTol->setData(defaultZConsTol); |
2066 | + | } |
2067 | + | theInfo.addProperty(zconsTol); |
2068 | + | |
2069 | + | //set Force Subtraction Policy |
2070 | + | StringData* zconsForcePolicy = new StringData(); |
2071 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
2072 | + | |
2073 | + | if (globals->haveZconsForcePolicy()){ |
2074 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
2075 | + | } |
2076 | + | else{ |
2077 | + | sprintf(painCave.errMsg, |
2078 | + | "ZConstraint Warning: No force subtraction policy was set.\n" |
2079 | + | "\tOOPSE will use PolicyByMass.\n" |
2080 | + | "\tTo set the policy, use the zconsForcePolicy variable.\n"); |
2081 | + | painCave.isFatal = 0; |
2082 | + | simError(); |
2083 | + | zconsForcePolicy->setData("BYMASS"); |
2084 | + | } |
2085 | + | |
2086 | + | theInfo.addProperty(zconsForcePolicy); |
2087 | + | |
2088 | + | //set zcons gap |
2089 | + | DoubleData* zconsGap = new DoubleData(); |
2090 | + | zconsGap->setID(ZCONSGAP_ID); |
2091 | + | |
2092 | + | if (globals->haveZConsGap()){ |
2093 | + | zconsGap->setData(globals->getZconsGap()); |
2094 | + | theInfo.addProperty(zconsGap); |
2095 | + | } |
2096 | + | |
2097 | + | //set zcons fixtime |
2098 | + | DoubleData* zconsFixtime = new DoubleData(); |
2099 | + | zconsFixtime->setID(ZCONSFIXTIME_ID); |
2100 | + | |
2101 | + | if (globals->haveZConsFixTime()){ |
2102 | + | zconsFixtime->setData(globals->getZconsFixtime()); |
2103 | + | theInfo.addProperty(zconsFixtime); |
2104 | + | } |
2105 | + | |
2106 | + | //set zconsUsingSMD |
2107 | + | IntData* zconsUsingSMD = new IntData(); |
2108 | + | zconsUsingSMD->setID(ZCONSUSINGSMD_ID); |
2109 | + | |
2110 | + | if (globals->haveZConsUsingSMD()){ |
2111 | + | zconsUsingSMD->setData(globals->getZconsUsingSMD()); |
2112 | + | theInfo.addProperty(zconsUsingSMD); |
2113 | + | } |
2114 | + | |
2115 | + | //Determine the name of ouput file and add it into SimInfo's property list |
2116 | + | //Be careful, do not use inFileName, since it is a pointer which |
2117 | + | //point to a string at master node, and slave nodes do not contain that string |
2118 | + | |
2119 | + | string zconsOutput(theInfo.finalName); |
2120 | + | |
2121 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
2122 | + | |
2123 | + | StringData* zconsFilename = new StringData(); |
2124 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
2125 | + | zconsFilename->setData(zconsOutput); |
2126 | + | |
2127 | + | theInfo.addProperty(zconsFilename); |
2128 | + | |
2129 | + | //setup index, pos and other parameters of z-constraint molecules |
2130 | + | nZConstraints = globals->getNzConstraints(); |
2131 | + | theInfo.nZconstraints = nZConstraints; |
2132 | + | |
2133 | + | zconStamp = globals->getZconStamp(); |
2134 | + | ZConsParaItem tempParaItem; |
2135 | + | |
2136 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
2137 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
2138 | + | |
2139 | + | for (int i = 0; i < nZConstraints; i++){ |
2140 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
2141 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
2142 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
2143 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
2144 | + | tempParaItem.havingCantVel = zconStamp[i]->haveCantVel(); |
2145 | + | tempParaItem.cantVel = zconStamp[i]->getCantVel(); |
2146 | + | zconsParaData->addItem(tempParaItem); |
2147 | + | } |
2148 | + | |
2149 | + | //check the uniqueness of index |
2150 | + | if(!zconsParaData->isIndexUnique()){ |
2151 | + | sprintf(painCave.errMsg, |
2152 | + | "ZConstraint Error: molIndex is not unique!\n"); |
2153 | + | painCave.isFatal = 1; |
2154 | + | simError(); |
2155 | + | } |
2156 | + | |
2157 | + | //sort the parameters by index of molecules |
2158 | + | zconsParaData->sortByIndex(); |
2159 | + | |
2160 | + | //push data into siminfo, therefore, we can retrieve later |
2161 | + | theInfo.addProperty(zconsParaData); |
2162 | + | } |
2163 | + | |
2164 | + | void SimSetup::makeMinimizer(){ |
2165 | + | |
2166 | + | OOPSEMinimizer* myOOPSEMinimizer; |
2167 | + | MinimizerParameterSet* param; |
2168 | + | char minimizerName[100]; |
2169 | + | |
2170 | + | for (int i = 0; i < nInfo; i++){ |
2171 | + | |
2172 | + | //prepare parameter set for minimizer |
2173 | + | param = new MinimizerParameterSet(); |
2174 | + | param->setDefaultParameter(); |
2175 | + | |
2176 | + | if (globals->haveMinimizer()){ |
2177 | + | param->setFTol(globals->getMinFTol()); |
2178 | + | } |
2179 | + | |
2180 | + | if (globals->haveMinGTol()){ |
2181 | + | param->setGTol(globals->getMinGTol()); |
2182 | + | } |
2183 | + | |
2184 | + | if (globals->haveMinMaxIter()){ |
2185 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2186 | + | } |
2187 | + | |
2188 | + | if (globals->haveMinWriteFrq()){ |
2189 | + | param->setMaxIteration(globals->getMinMaxIter()); |
2190 | + | } |
2191 | + | |
2192 | + | if (globals->haveMinWriteFrq()){ |
2193 | + | param->setWriteFrq(globals->getMinWriteFrq()); |
2194 | + | } |
2195 | + | |
2196 | + | if (globals->haveMinStepSize()){ |
2197 | + | param->setStepSize(globals->getMinStepSize()); |
2198 | + | } |
2199 | + | |
2200 | + | if (globals->haveMinLSMaxIter()){ |
2201 | + | param->setLineSearchMaxIteration(globals->getMinLSMaxIter()); |
2202 | + | } |
2203 | + | |
2204 | + | if (globals->haveMinLSTol()){ |
2205 | + | param->setLineSearchTol(globals->getMinLSTol()); |
2206 | + | } |
2207 | + | |
2208 | + | strcpy(minimizerName, globals->getMinimizer()); |
2209 | + | |
2210 | + | if (!strcasecmp(minimizerName, "CG")){ |
2211 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2212 | + | } |
2213 | + | else if (!strcasecmp(minimizerName, "SD")){ |
2214 | + | //myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param); |
2215 | + | myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param); |
2216 | + | } |
2217 | + | else{ |
2218 | + | sprintf(painCave.errMsg, |
2219 | + | "SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n"); |
2220 | + | painCave.isFatal = 0; |
2221 | + | simError(); |
2222 | + | |
2223 | + | myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param); |
2224 | + | } |
2225 | + | info[i].the_integrator = myOOPSEMinimizer; |
2226 | + | |
2227 | + | //store the minimizer into simInfo |
2228 | + | info[i].the_minimizer = myOOPSEMinimizer; |
2229 | + | info[i].has_minimizer = true; |
2230 | + | } |
2231 | + | |
2232 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |