1 |
mmeineke |
558 |
#include <iostream> |
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gezelter |
829 |
#include <stdlib.h> |
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#include <math.h> |
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mmeineke |
558 |
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#ifdef IS_MPI |
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#include "mpiSimulation.hpp" |
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#include <unistd.h> |
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#endif //is_mpi |
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chuckv |
892 |
#ifdef PROFILE |
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#include "mdProfile.hpp" |
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#endif // profile |
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mmeineke |
558 |
#include "Integrator.hpp" |
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#include "simError.h" |
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tim |
725 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
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ForceFields* the_ff){ |
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mmeineke |
558 |
info = theInfo; |
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myFF = the_ff; |
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isFirst = 1; |
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molecules = info->molecules; |
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nMols = info->n_mol; |
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// give a little love back to the SimInfo object |
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tim |
725 |
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if (info->the_integrator != NULL){ |
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delete info->the_integrator; |
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} |
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tim |
837 |
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mmeineke |
558 |
nAtoms = info->n_atoms; |
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// check for constraints |
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tim |
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constrainedA = NULL; |
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constrainedB = NULL; |
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mmeineke |
558 |
constrainedDsqr = NULL; |
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tim |
725 |
moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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mmeineke |
558 |
nConstrained = 0; |
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checkConstraints(); |
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} |
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tim |
725 |
template<typename T> Integrator<T>::~Integrator(){ |
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if (nConstrained){ |
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mmeineke |
558 |
delete[] constrainedA; |
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delete[] constrainedB; |
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delete[] constrainedDsqr; |
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delete[] moving; |
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delete[] moved; |
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mmeineke |
561 |
delete[] oldPos; |
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mmeineke |
558 |
} |
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} |
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tim |
725 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
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mmeineke |
558 |
isConstrained = 0; |
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tim |
725 |
Constraint* temp_con; |
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Constraint* dummy_plug; |
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mmeineke |
558 |
temp_con = new Constraint[info->n_SRI]; |
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nConstrained = 0; |
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int constrained = 0; |
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tim |
725 |
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mmeineke |
558 |
SRI** theArray; |
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tim |
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for (int i = 0; i < nMols; i++){ |
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theArray = (SRI * *) molecules[i].getMyBonds(); |
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for (int j = 0; j < molecules[i].getNBonds(); j++){ |
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mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
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mmeineke |
594 |
|
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tim |
725 |
if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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mmeineke |
594 |
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tim |
725 |
nConstrained++; |
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constrained = 0; |
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} |
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mmeineke |
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} |
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tim |
725 |
theArray = (SRI * *) molecules[i].getMyBends(); |
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for (int j = 0; j < molecules[i].getNBends(); j++){ |
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mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
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tim |
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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nConstrained++; |
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constrained = 0; |
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mmeineke |
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} |
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} |
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tim |
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theArray = (SRI * *) molecules[i].getMyTorsions(); |
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for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
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mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
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tim |
725 |
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if (constrained){ |
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
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nConstrained++; |
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constrained = 0; |
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mmeineke |
558 |
} |
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} |
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} |
116 |
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117 |
tim |
725 |
if (nConstrained > 0){ |
118 |
mmeineke |
558 |
isConstrained = 1; |
119 |
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120 |
tim |
725 |
if (constrainedA != NULL) |
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delete[] constrainedA; |
122 |
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if (constrainedB != NULL) |
123 |
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delete[] constrainedB; |
124 |
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if (constrainedDsqr != NULL) |
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delete[] constrainedDsqr; |
126 |
mmeineke |
558 |
|
127 |
tim |
725 |
constrainedA = new int[nConstrained]; |
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constrainedB = new int[nConstrained]; |
129 |
mmeineke |
558 |
constrainedDsqr = new double[nConstrained]; |
130 |
tim |
725 |
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for (int i = 0; i < nConstrained; i++){ |
132 |
mmeineke |
558 |
constrainedA[i] = temp_con[i].get_a(); |
133 |
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constrainedB[i] = temp_con[i].get_b(); |
134 |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
136 |
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137 |
tim |
725 |
|
138 |
chrisfen |
999 |
// save oldAtoms to check for lode balancing later on. |
139 |
tim |
725 |
|
140 |
mmeineke |
558 |
oldAtoms = nAtoms; |
141 |
tim |
725 |
|
142 |
mmeineke |
558 |
moving = new int[nAtoms]; |
143 |
tim |
725 |
moved = new int[nAtoms]; |
144 |
mmeineke |
558 |
|
145 |
tim |
725 |
oldPos = new double[nAtoms * 3]; |
146 |
mmeineke |
558 |
} |
147 |
tim |
725 |
|
148 |
mmeineke |
558 |
delete[] temp_con; |
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} |
150 |
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152 |
tim |
725 |
template<typename T> void Integrator<T>::integrate(void){ |
153 |
mmeineke |
558 |
|
154 |
tim |
725 |
double runTime = info->run_time; |
155 |
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double sampleTime = info->sampleTime; |
156 |
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double statusTime = info->statusTime; |
157 |
mmeineke |
558 |
double thermalTime = info->thermalTime; |
158 |
mmeineke |
746 |
double resetTime = info->resetTime; |
159 |
mmeineke |
558 |
|
160 |
mmeineke |
746 |
|
161 |
mmeineke |
558 |
double currSample; |
162 |
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double currThermal; |
163 |
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double currStatus; |
164 |
mmeineke |
746 |
double currReset; |
165 |
tim |
837 |
|
166 |
mmeineke |
558 |
int calcPot, calcStress; |
167 |
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168 |
tim |
725 |
tStats = new Thermo(info); |
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statOut = new StatWriter(info); |
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dumpOut = new DumpWriter(info); |
171 |
mmeineke |
558 |
|
172 |
mmeineke |
561 |
atoms = info->atoms; |
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174 |
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dt = info->dt; |
175 |
mmeineke |
558 |
dt2 = 0.5 * dt; |
176 |
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177 |
mmeineke |
784 |
readyCheck(); |
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179 |
mmeineke |
558 |
// initialize the forces before the first step |
180 |
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tim |
677 |
calcForce(1, 1); |
182 |
tim |
781 |
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183 |
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if (nConstrained){ |
184 |
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preMove(); |
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constrainA(); |
186 |
tim |
837 |
calcForce(1, 1); |
187 |
tim |
781 |
constrainB(); |
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} |
189 |
mmeineke |
843 |
|
190 |
tim |
725 |
if (info->setTemp){ |
191 |
tim |
677 |
thermalize(); |
192 |
mmeineke |
558 |
} |
193 |
tim |
725 |
|
194 |
mmeineke |
558 |
calcPot = 0; |
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calcStress = 0; |
196 |
mmeineke |
711 |
currSample = sampleTime + info->getTime(); |
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currThermal = thermalTime+ info->getTime(); |
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currStatus = statusTime + info->getTime(); |
199 |
mmeineke |
746 |
currReset = resetTime + info->getTime(); |
200 |
mmeineke |
558 |
|
201 |
tim |
725 |
dumpOut->writeDump(info->getTime()); |
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statOut->writeStat(info->getTime()); |
203 |
mmeineke |
559 |
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#ifdef IS_MPI |
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tim |
725 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
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mmeineke |
559 |
MPIcheckPoint(); |
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#endif // is_mpi |
209 |
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210 |
tim |
725 |
while (info->getTime() < runTime){ |
211 |
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if ((info->getTime() + dt) >= currStatus){ |
212 |
mmeineke |
558 |
calcPot = 1; |
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calcStress = 1; |
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} |
215 |
mmeineke |
561 |
|
216 |
chuckv |
892 |
#ifdef PROFILE |
217 |
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startProfile( pro1 ); |
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#endif |
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220 |
tim |
725 |
integrateStep(calcPot, calcStress); |
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222 |
chuckv |
892 |
#ifdef PROFILE |
223 |
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endProfile( pro1 ); |
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startProfile( pro2 ); |
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#endif // profile |
227 |
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228 |
mmeineke |
643 |
info->incrTime(dt); |
229 |
mmeineke |
558 |
|
230 |
tim |
725 |
if (info->setTemp){ |
231 |
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if (info->getTime() >= currThermal){ |
232 |
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thermalize(); |
233 |
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currThermal += thermalTime; |
234 |
mmeineke |
558 |
} |
235 |
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} |
236 |
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237 |
tim |
725 |
if (info->getTime() >= currSample){ |
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dumpOut->writeDump(info->getTime()); |
239 |
mmeineke |
558 |
currSample += sampleTime; |
240 |
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} |
241 |
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242 |
tim |
725 |
if (info->getTime() >= currStatus){ |
243 |
tim |
837 |
statOut->writeStat(info->getTime()); |
244 |
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calcPot = 0; |
245 |
mmeineke |
558 |
calcStress = 0; |
246 |
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currStatus += statusTime; |
247 |
tim |
837 |
} |
248 |
mmeineke |
559 |
|
249 |
mmeineke |
746 |
if (info->resetIntegrator){ |
250 |
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if (info->getTime() >= currReset){ |
251 |
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this->resetIntegrator(); |
252 |
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currReset += resetTime; |
253 |
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} |
254 |
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} |
255 |
chuckv |
892 |
|
256 |
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#ifdef PROFILE |
257 |
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endProfile( pro2 ); |
258 |
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#endif //profile |
259 |
mmeineke |
746 |
|
260 |
mmeineke |
559 |
#ifdef IS_MPI |
261 |
tim |
725 |
strcpy(checkPointMsg, "successfully took a time step."); |
262 |
mmeineke |
559 |
MPIcheckPoint(); |
263 |
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#endif // is_mpi |
264 |
mmeineke |
558 |
} |
265 |
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266 |
mmeineke |
561 |
delete dumpOut; |
267 |
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delete statOut; |
268 |
mmeineke |
558 |
} |
269 |
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270 |
tim |
725 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
271 |
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int calcStress){ |
272 |
mmeineke |
558 |
// Position full step, and velocity half step |
273 |
chuckv |
892 |
|
274 |
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#ifdef PROFILE |
275 |
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startProfile(pro3); |
276 |
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#endif //profile |
277 |
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278 |
tim |
725 |
preMove(); |
279 |
mmeineke |
558 |
|
280 |
chuckv |
892 |
#ifdef PROFILE |
281 |
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endProfile(pro3); |
282 |
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283 |
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startProfile(pro4); |
284 |
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#endif // profile |
285 |
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286 |
mmeineke |
558 |
moveA(); |
287 |
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288 |
chuckv |
892 |
#ifdef PROFILE |
289 |
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endProfile(pro4); |
290 |
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291 |
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startProfile(pro5); |
292 |
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#endif//profile |
293 |
tim |
725 |
|
294 |
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295 |
mmeineke |
614 |
#ifdef IS_MPI |
296 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
297 |
mmeineke |
614 |
MPIcheckPoint(); |
298 |
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#endif // is_mpi |
299 |
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300 |
tim |
725 |
|
301 |
mmeineke |
558 |
// calc forces |
302 |
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303 |
tim |
725 |
calcForce(calcPot, calcStress); |
304 |
mmeineke |
558 |
|
305 |
mmeineke |
614 |
#ifdef IS_MPI |
306 |
tim |
725 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
307 |
mmeineke |
614 |
MPIcheckPoint(); |
308 |
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#endif // is_mpi |
309 |
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310 |
chuckv |
892 |
#ifdef PROFILE |
311 |
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endProfile( pro5 ); |
312 |
tim |
725 |
|
313 |
chuckv |
892 |
startProfile( pro6 ); |
314 |
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#endif //profile |
315 |
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|
316 |
mmeineke |
558 |
// finish the velocity half step |
317 |
tim |
725 |
|
318 |
mmeineke |
558 |
moveB(); |
319 |
tim |
725 |
|
320 |
chuckv |
892 |
#ifdef PROFILE |
321 |
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endProfile(pro6); |
322 |
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#endif // profile |
323 |
tim |
725 |
|
324 |
mmeineke |
614 |
#ifdef IS_MPI |
325 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
326 |
mmeineke |
614 |
MPIcheckPoint(); |
327 |
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#endif // is_mpi |
328 |
mmeineke |
558 |
} |
329 |
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330 |
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|
331 |
tim |
725 |
template<typename T> void Integrator<T>::moveA(void){ |
332 |
gezelter |
600 |
int i, j; |
333 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
334 |
gezelter |
600 |
double Tb[3], ji[3]; |
335 |
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double vel[3], pos[3], frc[3]; |
336 |
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double mass; |
337 |
mmeineke |
558 |
|
338 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
339 |
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atoms[i]->getVel(vel); |
340 |
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atoms[i]->getPos(pos); |
341 |
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atoms[i]->getFrc(frc); |
342 |
mmeineke |
567 |
|
343 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
344 |
mmeineke |
594 |
|
345 |
tim |
725 |
for (j = 0; j < 3; j++){ |
346 |
gezelter |
600 |
// velocity half step |
347 |
tim |
725 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
348 |
gezelter |
600 |
// position whole step |
349 |
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pos[j] += dt * vel[j]; |
350 |
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} |
351 |
mmeineke |
594 |
|
352 |
tim |
725 |
atoms[i]->setVel(vel); |
353 |
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atoms[i]->setPos(pos); |
354 |
gezelter |
600 |
|
355 |
tim |
725 |
if (atoms[i]->isDirectional()){ |
356 |
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dAtom = (DirectionalAtom *) atoms[i]; |
357 |
mmeineke |
558 |
|
358 |
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// get and convert the torque to body frame |
359 |
mmeineke |
597 |
|
360 |
tim |
725 |
dAtom->getTrq(Tb); |
361 |
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dAtom->lab2Body(Tb); |
362 |
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|
363 |
mmeineke |
558 |
// get the angular momentum, and propagate a half step |
364 |
gezelter |
600 |
|
365 |
tim |
725 |
dAtom->getJ(ji); |
366 |
gezelter |
600 |
|
367 |
tim |
725 |
for (j = 0; j < 3; j++) |
368 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
369 |
tim |
725 |
|
370 |
mmeineke |
778 |
this->rotationPropagation( dAtom, ji ); |
371 |
gezelter |
600 |
|
372 |
tim |
725 |
dAtom->setJ(ji); |
373 |
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} |
374 |
mmeineke |
558 |
} |
375 |
mmeineke |
768 |
|
376 |
|
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if (nConstrained){ |
377 |
|
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constrainA(); |
378 |
|
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} |
379 |
mmeineke |
558 |
} |
380 |
|
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|
381 |
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|
382 |
tim |
725 |
template<typename T> void Integrator<T>::moveB(void){ |
383 |
gezelter |
600 |
int i, j; |
384 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
385 |
gezelter |
600 |
double Tb[3], ji[3]; |
386 |
|
|
double vel[3], frc[3]; |
387 |
|
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double mass; |
388 |
mmeineke |
558 |
|
389 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
390 |
|
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atoms[i]->getVel(vel); |
391 |
|
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atoms[i]->getFrc(frc); |
392 |
mmeineke |
558 |
|
393 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
394 |
|
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|
395 |
mmeineke |
558 |
// velocity half step |
396 |
tim |
725 |
for (j = 0; j < 3; j++) |
397 |
|
|
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
398 |
gezelter |
600 |
|
399 |
tim |
725 |
atoms[i]->setVel(vel); |
400 |
mmeineke |
597 |
|
401 |
tim |
725 |
if (atoms[i]->isDirectional()){ |
402 |
|
|
dAtom = (DirectionalAtom *) atoms[i]; |
403 |
|
|
|
404 |
tim |
837 |
// get and convert the torque to body frame |
405 |
gezelter |
600 |
|
406 |
tim |
725 |
dAtom->getTrq(Tb); |
407 |
|
|
dAtom->lab2Body(Tb); |
408 |
gezelter |
600 |
|
409 |
|
|
// get the angular momentum, and propagate a half step |
410 |
|
|
|
411 |
tim |
725 |
dAtom->getJ(ji); |
412 |
gezelter |
600 |
|
413 |
tim |
725 |
for (j = 0; j < 3; j++) |
414 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
415 |
mmeineke |
597 |
|
416 |
tim |
725 |
|
417 |
|
|
dAtom->setJ(ji); |
418 |
mmeineke |
558 |
} |
419 |
|
|
} |
420 |
mmeineke |
768 |
|
421 |
|
|
if (nConstrained){ |
422 |
|
|
constrainB(); |
423 |
|
|
} |
424 |
mmeineke |
558 |
} |
425 |
|
|
|
426 |
tim |
725 |
template<typename T> void Integrator<T>::preMove(void){ |
427 |
gezelter |
600 |
int i, j; |
428 |
|
|
double pos[3]; |
429 |
mmeineke |
558 |
|
430 |
tim |
725 |
if (nConstrained){ |
431 |
|
|
for (i = 0; i < nAtoms; i++){ |
432 |
|
|
atoms[i]->getPos(pos); |
433 |
mmeineke |
561 |
|
434 |
tim |
725 |
for (j = 0; j < 3; j++){ |
435 |
|
|
oldPos[3 * i + j] = pos[j]; |
436 |
gezelter |
600 |
} |
437 |
|
|
} |
438 |
tim |
725 |
} |
439 |
gezelter |
600 |
} |
440 |
|
|
|
441 |
tim |
645 |
template<typename T> void Integrator<T>::constrainA(){ |
442 |
mmeineke |
787 |
int i, j; |
443 |
mmeineke |
558 |
int done; |
444 |
gezelter |
600 |
double posA[3], posB[3]; |
445 |
|
|
double velA[3], velB[3]; |
446 |
mmeineke |
572 |
double pab[3]; |
447 |
|
|
double rab[3]; |
448 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
449 |
mmeineke |
558 |
double rma, rmb; |
450 |
|
|
double dx, dy, dz; |
451 |
mmeineke |
561 |
double rpab; |
452 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
453 |
|
|
double diffsq; |
454 |
|
|
double gab; |
455 |
|
|
int iteration; |
456 |
|
|
|
457 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
458 |
mmeineke |
558 |
moving[i] = 0; |
459 |
tim |
725 |
moved[i] = 1; |
460 |
mmeineke |
558 |
} |
461 |
mmeineke |
567 |
|
462 |
mmeineke |
558 |
iteration = 0; |
463 |
|
|
done = 0; |
464 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
465 |
mmeineke |
558 |
done = 1; |
466 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
467 |
mmeineke |
558 |
a = constrainedA[i]; |
468 |
|
|
b = constrainedB[i]; |
469 |
mmeineke |
563 |
|
470 |
tim |
725 |
ax = (a * 3) + 0; |
471 |
|
|
ay = (a * 3) + 1; |
472 |
|
|
az = (a * 3) + 2; |
473 |
mmeineke |
563 |
|
474 |
tim |
725 |
bx = (b * 3) + 0; |
475 |
|
|
by = (b * 3) + 1; |
476 |
|
|
bz = (b * 3) + 2; |
477 |
|
|
|
478 |
|
|
if (moved[a] || moved[b]){ |
479 |
|
|
atoms[a]->getPos(posA); |
480 |
|
|
atoms[b]->getPos(posB); |
481 |
|
|
|
482 |
|
|
for (j = 0; j < 3; j++) |
483 |
gezelter |
600 |
pab[j] = posA[j] - posB[j]; |
484 |
mmeineke |
567 |
|
485 |
tim |
725 |
//periodic boundary condition |
486 |
mmeineke |
567 |
|
487 |
tim |
725 |
info->wrapVector(pab); |
488 |
mmeineke |
572 |
|
489 |
tim |
725 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
490 |
mmeineke |
558 |
|
491 |
tim |
725 |
rabsq = constrainedDsqr[i]; |
492 |
|
|
diffsq = rabsq - pabsq; |
493 |
mmeineke |
567 |
|
494 |
tim |
725 |
// the original rattle code from alan tidesley |
495 |
|
|
if (fabs(diffsq) > (tol * rabsq * 2)){ |
496 |
|
|
rab[0] = oldPos[ax] - oldPos[bx]; |
497 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
498 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
499 |
mmeineke |
558 |
|
500 |
tim |
725 |
info->wrapVector(rab); |
501 |
mmeineke |
567 |
|
502 |
tim |
725 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
503 |
mmeineke |
558 |
|
504 |
tim |
725 |
rpabsq = rpab * rpab; |
505 |
mmeineke |
558 |
|
506 |
mmeineke |
563 |
|
507 |
tim |
725 |
if (rpabsq < (rabsq * -diffsq)){ |
508 |
mmeineke |
558 |
#ifdef IS_MPI |
509 |
tim |
725 |
a = atoms[a]->getGlobalIndex(); |
510 |
|
|
b = atoms[b]->getGlobalIndex(); |
511 |
mmeineke |
558 |
#endif //is_mpi |
512 |
tim |
725 |
sprintf(painCave.errMsg, |
513 |
|
|
"Constraint failure in constrainA at atom %d and %d.\n", a, |
514 |
|
|
b); |
515 |
|
|
painCave.isFatal = 1; |
516 |
|
|
simError(); |
517 |
|
|
} |
518 |
mmeineke |
558 |
|
519 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
520 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
521 |
mmeineke |
567 |
|
522 |
tim |
725 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
523 |
mmeineke |
567 |
|
524 |
mmeineke |
572 |
dx = rab[0] * gab; |
525 |
|
|
dy = rab[1] * gab; |
526 |
|
|
dz = rab[2] * gab; |
527 |
mmeineke |
558 |
|
528 |
tim |
725 |
posA[0] += rma * dx; |
529 |
|
|
posA[1] += rma * dy; |
530 |
|
|
posA[2] += rma * dz; |
531 |
mmeineke |
558 |
|
532 |
tim |
725 |
atoms[a]->setPos(posA); |
533 |
mmeineke |
558 |
|
534 |
tim |
725 |
posB[0] -= rmb * dx; |
535 |
|
|
posB[1] -= rmb * dy; |
536 |
|
|
posB[2] -= rmb * dz; |
537 |
gezelter |
600 |
|
538 |
tim |
725 |
atoms[b]->setPos(posB); |
539 |
gezelter |
600 |
|
540 |
mmeineke |
558 |
dx = dx / dt; |
541 |
|
|
dy = dy / dt; |
542 |
|
|
dz = dz / dt; |
543 |
|
|
|
544 |
tim |
725 |
atoms[a]->getVel(velA); |
545 |
mmeineke |
558 |
|
546 |
tim |
725 |
velA[0] += rma * dx; |
547 |
|
|
velA[1] += rma * dy; |
548 |
|
|
velA[2] += rma * dz; |
549 |
mmeineke |
558 |
|
550 |
tim |
725 |
atoms[a]->setVel(velA); |
551 |
gezelter |
600 |
|
552 |
tim |
725 |
atoms[b]->getVel(velB); |
553 |
gezelter |
600 |
|
554 |
tim |
725 |
velB[0] -= rmb * dx; |
555 |
|
|
velB[1] -= rmb * dy; |
556 |
|
|
velB[2] -= rmb * dz; |
557 |
gezelter |
600 |
|
558 |
tim |
725 |
atoms[b]->setVel(velB); |
559 |
gezelter |
600 |
|
560 |
tim |
725 |
moving[a] = 1; |
561 |
|
|
moving[b] = 1; |
562 |
|
|
done = 0; |
563 |
|
|
} |
564 |
mmeineke |
558 |
} |
565 |
|
|
} |
566 |
tim |
725 |
|
567 |
|
|
for (i = 0; i < nAtoms; i++){ |
568 |
mmeineke |
558 |
moved[i] = moving[i]; |
569 |
|
|
moving[i] = 0; |
570 |
|
|
} |
571 |
|
|
|
572 |
|
|
iteration++; |
573 |
|
|
} |
574 |
|
|
|
575 |
tim |
725 |
if (!done){ |
576 |
|
|
sprintf(painCave.errMsg, |
577 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n", |
578 |
|
|
iteration); |
579 |
mmeineke |
558 |
painCave.isFatal = 1; |
580 |
|
|
simError(); |
581 |
|
|
} |
582 |
mmeineke |
768 |
|
583 |
mmeineke |
558 |
} |
584 |
|
|
|
585 |
tim |
725 |
template<typename T> void Integrator<T>::constrainB(void){ |
586 |
mmeineke |
787 |
int i, j; |
587 |
mmeineke |
558 |
int done; |
588 |
gezelter |
600 |
double posA[3], posB[3]; |
589 |
|
|
double velA[3], velB[3]; |
590 |
mmeineke |
558 |
double vxab, vyab, vzab; |
591 |
mmeineke |
572 |
double rab[3]; |
592 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
593 |
mmeineke |
558 |
double rma, rmb; |
594 |
|
|
double dx, dy, dz; |
595 |
mmeineke |
787 |
double rvab; |
596 |
mmeineke |
558 |
double gab; |
597 |
|
|
int iteration; |
598 |
|
|
|
599 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
600 |
mmeineke |
558 |
moving[i] = 0; |
601 |
|
|
moved[i] = 1; |
602 |
|
|
} |
603 |
|
|
|
604 |
|
|
done = 0; |
605 |
mmeineke |
561 |
iteration = 0; |
606 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
607 |
mmeineke |
567 |
done = 1; |
608 |
|
|
|
609 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
610 |
mmeineke |
558 |
a = constrainedA[i]; |
611 |
|
|
b = constrainedB[i]; |
612 |
|
|
|
613 |
tim |
725 |
ax = (a * 3) + 0; |
614 |
|
|
ay = (a * 3) + 1; |
615 |
|
|
az = (a * 3) + 2; |
616 |
mmeineke |
563 |
|
617 |
tim |
725 |
bx = (b * 3) + 0; |
618 |
|
|
by = (b * 3) + 1; |
619 |
|
|
bz = (b * 3) + 2; |
620 |
mmeineke |
563 |
|
621 |
tim |
725 |
if (moved[a] || moved[b]){ |
622 |
|
|
atoms[a]->getVel(velA); |
623 |
|
|
atoms[b]->getVel(velB); |
624 |
mmeineke |
558 |
|
625 |
tim |
725 |
vxab = velA[0] - velB[0]; |
626 |
|
|
vyab = velA[1] - velB[1]; |
627 |
|
|
vzab = velA[2] - velB[2]; |
628 |
gezelter |
600 |
|
629 |
tim |
725 |
atoms[a]->getPos(posA); |
630 |
|
|
atoms[b]->getPos(posB); |
631 |
gezelter |
600 |
|
632 |
tim |
725 |
for (j = 0; j < 3; j++) |
633 |
gezelter |
600 |
rab[j] = posA[j] - posB[j]; |
634 |
mmeineke |
558 |
|
635 |
tim |
725 |
info->wrapVector(rab); |
636 |
mmeineke |
558 |
|
637 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
638 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
639 |
mmeineke |
558 |
|
640 |
tim |
725 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
641 |
gezelter |
600 |
|
642 |
tim |
725 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
643 |
gezelter |
600 |
|
644 |
tim |
725 |
if (fabs(gab) > tol){ |
645 |
|
|
dx = rab[0] * gab; |
646 |
|
|
dy = rab[1] * gab; |
647 |
|
|
dz = rab[2] * gab; |
648 |
|
|
|
649 |
|
|
velA[0] += rma * dx; |
650 |
|
|
velA[1] += rma * dy; |
651 |
|
|
velA[2] += rma * dz; |
652 |
|
|
|
653 |
|
|
atoms[a]->setVel(velA); |
654 |
|
|
|
655 |
|
|
velB[0] -= rmb * dx; |
656 |
|
|
velB[1] -= rmb * dy; |
657 |
|
|
velB[2] -= rmb * dz; |
658 |
|
|
|
659 |
|
|
atoms[b]->setVel(velB); |
660 |
|
|
|
661 |
|
|
moving[a] = 1; |
662 |
|
|
moving[b] = 1; |
663 |
|
|
done = 0; |
664 |
|
|
} |
665 |
mmeineke |
558 |
} |
666 |
|
|
} |
667 |
|
|
|
668 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
669 |
mmeineke |
558 |
moved[i] = moving[i]; |
670 |
|
|
moving[i] = 0; |
671 |
|
|
} |
672 |
tim |
725 |
|
673 |
mmeineke |
558 |
iteration++; |
674 |
|
|
} |
675 |
|
|
|
676 |
tim |
725 |
if (!done){ |
677 |
|
|
sprintf(painCave.errMsg, |
678 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n", |
679 |
|
|
iteration); |
680 |
mmeineke |
558 |
painCave.isFatal = 1; |
681 |
|
|
simError(); |
682 |
tim |
725 |
} |
683 |
mmeineke |
558 |
} |
684 |
|
|
|
685 |
mmeineke |
778 |
template<typename T> void Integrator<T>::rotationPropagation |
686 |
|
|
( DirectionalAtom* dAtom, double ji[3] ){ |
687 |
|
|
|
688 |
|
|
double angle; |
689 |
|
|
double A[3][3], I[3][3]; |
690 |
|
|
|
691 |
|
|
// use the angular velocities to propagate the rotation matrix a |
692 |
|
|
// full time step |
693 |
|
|
|
694 |
|
|
dAtom->getA(A); |
695 |
|
|
dAtom->getI(I); |
696 |
tim |
837 |
|
697 |
|
|
// rotate about the x-axis |
698 |
mmeineke |
778 |
angle = dt2 * ji[0] / I[0][0]; |
699 |
tim |
837 |
this->rotate( 1, 2, angle, ji, A ); |
700 |
|
|
|
701 |
mmeineke |
778 |
// rotate about the y-axis |
702 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
703 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
704 |
tim |
837 |
|
705 |
mmeineke |
778 |
// rotate about the z-axis |
706 |
|
|
angle = dt * ji[2] / I[2][2]; |
707 |
|
|
this->rotate( 0, 1, angle, ji, A); |
708 |
tim |
837 |
|
709 |
mmeineke |
778 |
// rotate about the y-axis |
710 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
711 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
712 |
tim |
837 |
|
713 |
mmeineke |
778 |
// rotate about the x-axis |
714 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
715 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
716 |
tim |
837 |
|
717 |
|
|
dAtom->setA( A ); |
718 |
mmeineke |
778 |
} |
719 |
|
|
|
720 |
tim |
725 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
721 |
|
|
double angle, double ji[3], |
722 |
|
|
double A[3][3]){ |
723 |
|
|
int i, j, k; |
724 |
mmeineke |
558 |
double sinAngle; |
725 |
|
|
double cosAngle; |
726 |
|
|
double angleSqr; |
727 |
|
|
double angleSqrOver4; |
728 |
|
|
double top, bottom; |
729 |
|
|
double rot[3][3]; |
730 |
|
|
double tempA[3][3]; |
731 |
|
|
double tempJ[3]; |
732 |
|
|
|
733 |
|
|
// initialize the tempA |
734 |
|
|
|
735 |
tim |
725 |
for (i = 0; i < 3; i++){ |
736 |
|
|
for (j = 0; j < 3; j++){ |
737 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
738 |
mmeineke |
558 |
} |
739 |
|
|
} |
740 |
|
|
|
741 |
|
|
// initialize the tempJ |
742 |
|
|
|
743 |
tim |
725 |
for (i = 0; i < 3; i++) |
744 |
|
|
tempJ[i] = ji[i]; |
745 |
|
|
|
746 |
mmeineke |
558 |
// initalize rot as a unit matrix |
747 |
|
|
|
748 |
|
|
rot[0][0] = 1.0; |
749 |
|
|
rot[0][1] = 0.0; |
750 |
|
|
rot[0][2] = 0.0; |
751 |
|
|
|
752 |
|
|
rot[1][0] = 0.0; |
753 |
|
|
rot[1][1] = 1.0; |
754 |
|
|
rot[1][2] = 0.0; |
755 |
tim |
725 |
|
756 |
mmeineke |
558 |
rot[2][0] = 0.0; |
757 |
|
|
rot[2][1] = 0.0; |
758 |
|
|
rot[2][2] = 1.0; |
759 |
tim |
725 |
|
760 |
mmeineke |
558 |
// use a small angle aproximation for sin and cosine |
761 |
|
|
|
762 |
tim |
725 |
angleSqr = angle * angle; |
763 |
mmeineke |
558 |
angleSqrOver4 = angleSqr / 4.0; |
764 |
|
|
top = 1.0 - angleSqrOver4; |
765 |
|
|
bottom = 1.0 + angleSqrOver4; |
766 |
|
|
|
767 |
|
|
cosAngle = top / bottom; |
768 |
|
|
sinAngle = angle / bottom; |
769 |
|
|
|
770 |
|
|
rot[axes1][axes1] = cosAngle; |
771 |
|
|
rot[axes2][axes2] = cosAngle; |
772 |
|
|
|
773 |
|
|
rot[axes1][axes2] = sinAngle; |
774 |
|
|
rot[axes2][axes1] = -sinAngle; |
775 |
tim |
725 |
|
776 |
mmeineke |
558 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
777 |
tim |
725 |
|
778 |
|
|
for (i = 0; i < 3; i++){ |
779 |
mmeineke |
558 |
ji[i] = 0.0; |
780 |
tim |
725 |
for (k = 0; k < 3; k++){ |
781 |
mmeineke |
558 |
ji[i] += rot[i][k] * tempJ[k]; |
782 |
|
|
} |
783 |
|
|
} |
784 |
|
|
|
785 |
tim |
837 |
// rotate the Rotation matrix acording to: |
786 |
mmeineke |
558 |
// A[][] = A[][] * transpose(rot[][]) |
787 |
|
|
|
788 |
|
|
|
789 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
790 |
mmeineke |
558 |
// calculation as: |
791 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
792 |
|
|
|
793 |
tim |
725 |
for (i = 0; i < 3; i++){ |
794 |
|
|
for (j = 0; j < 3; j++){ |
795 |
gezelter |
600 |
A[j][i] = 0.0; |
796 |
tim |
725 |
for (k = 0; k < 3; k++){ |
797 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
798 |
mmeineke |
558 |
} |
799 |
|
|
} |
800 |
|
|
} |
801 |
|
|
} |
802 |
tim |
677 |
|
803 |
tim |
725 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
804 |
|
|
myFF->doForces(calcPot, calcStress); |
805 |
tim |
677 |
} |
806 |
|
|
|
807 |
|
|
template<typename T> void Integrator<T>::thermalize(){ |
808 |
tim |
725 |
tStats->velocitize(); |
809 |
tim |
677 |
} |
810 |
tim |
763 |
|
811 |
|
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
812 |
|
|
return tStats->getTotalE(); |
813 |
mmeineke |
768 |
} |
814 |
tim |
837 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
815 |
|
|
//By default, return a null string |
816 |
|
|
//The reason we use string instead of char* is that if we use char*, we will |
817 |
|
|
//return a pointer point to local variable which might cause problem |
818 |
|
|
return string(); |
819 |
|
|
} |