1 |
mmeineke |
558 |
#include <iostream> |
2 |
gezelter |
829 |
#include <stdlib.h> |
3 |
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#include <math.h> |
4 |
tim |
1234 |
#include "Rattle.hpp" |
5 |
tim |
1268 |
#include "Roll.hpp" |
6 |
mmeineke |
558 |
#ifdef IS_MPI |
7 |
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#include "mpiSimulation.hpp" |
8 |
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#include <unistd.h> |
9 |
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#endif //is_mpi |
10 |
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|
11 |
chuckv |
892 |
#ifdef PROFILE |
12 |
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#include "mdProfile.hpp" |
13 |
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#endif // profile |
14 |
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|
15 |
mmeineke |
558 |
#include "Integrator.hpp" |
16 |
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#include "simError.h" |
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18 |
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tim |
725 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
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ForceFields* the_ff){ |
21 |
mmeineke |
558 |
info = theInfo; |
22 |
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myFF = the_ff; |
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isFirst = 1; |
24 |
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25 |
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molecules = info->molecules; |
26 |
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nMols = info->n_mol; |
27 |
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28 |
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// give a little love back to the SimInfo object |
29 |
tim |
725 |
|
30 |
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if (info->the_integrator != NULL){ |
31 |
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delete info->the_integrator; |
32 |
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} |
33 |
tim |
837 |
|
34 |
mmeineke |
558 |
nAtoms = info->n_atoms; |
35 |
gezelter |
1097 |
integrableObjects = info->integrableObjects; |
36 |
tim |
1234 |
|
37 |
tim |
1452 |
consFramework = new RollFramework(info); |
38 |
tim |
1234 |
|
39 |
tim |
1268 |
if(consFramework == NULL){ |
40 |
tim |
1234 |
sprintf(painCave.errMsg, |
41 |
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"Integrator::Intergrator() Error: Memory allocation error for RattleFramework" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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/* |
47 |
mmeineke |
558 |
// check for constraints |
48 |
tim |
725 |
|
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constrainedA = NULL; |
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constrainedB = NULL; |
51 |
mmeineke |
558 |
constrainedDsqr = NULL; |
52 |
tim |
725 |
moving = NULL; |
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moved = NULL; |
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oldPos = NULL; |
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56 |
mmeineke |
558 |
nConstrained = 0; |
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checkConstraints(); |
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tim |
1234 |
*/ |
60 |
mmeineke |
558 |
} |
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tim |
725 |
template<typename T> Integrator<T>::~Integrator(){ |
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tim |
1268 |
if (consFramework != NULL) |
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delete consFramework; |
65 |
tim |
1234 |
/* |
66 |
tim |
725 |
if (nConstrained){ |
67 |
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; |
73 |
mmeineke |
558 |
} |
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tim |
1234 |
*/ |
75 |
mmeineke |
558 |
} |
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|
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tim |
1234 |
/* |
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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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|
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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; |
86 |
tim |
725 |
|
87 |
mmeineke |
558 |
SRI** theArray; |
88 |
tim |
725 |
for (int i = 0; i < nMols; i++){ |
89 |
tim |
1057 |
|
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theArray = (SRI * *) molecules[i].getMyBonds(); |
91 |
tim |
725 |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
92 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
93 |
mmeineke |
594 |
|
94 |
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()); |
99 |
mmeineke |
594 |
|
100 |
tim |
725 |
nConstrained++; |
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constrained = 0; |
102 |
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} |
103 |
mmeineke |
558 |
} |
104 |
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105 |
tim |
725 |
theArray = (SRI * *) molecules[i].getMyBends(); |
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for (int j = 0; j < molecules[i].getNBends(); j++){ |
107 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
108 |
tim |
725 |
|
109 |
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if (constrained){ |
110 |
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dummy_plug = theArray[j]->get_constraint(); |
111 |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
112 |
tim |
1268 |
temp_con[nConstrained].set_b(Dummy_plug->get_b()); |
113 |
tim |
725 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
114 |
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115 |
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nConstrained++; |
116 |
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constrained = 0; |
117 |
mmeineke |
558 |
} |
118 |
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} |
119 |
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120 |
tim |
725 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
121 |
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for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
122 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
123 |
tim |
725 |
|
124 |
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if (constrained){ |
125 |
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dummy_plug = theArray[j]->get_constraint(); |
126 |
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temp_con[nConstrained].set_a(dummy_plug->get_a()); |
127 |
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temp_con[nConstrained].set_b(dummy_plug->get_b()); |
128 |
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temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
129 |
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130 |
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nConstrained++; |
131 |
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constrained = 0; |
132 |
mmeineke |
558 |
} |
133 |
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} |
134 |
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} |
135 |
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136 |
tim |
1057 |
|
137 |
tim |
725 |
if (nConstrained > 0){ |
138 |
mmeineke |
558 |
isConstrained = 1; |
139 |
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140 |
tim |
725 |
if (constrainedA != NULL) |
141 |
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delete[] constrainedA; |
142 |
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if (constrainedB != NULL) |
143 |
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delete[] constrainedB; |
144 |
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if (constrainedDsqr != NULL) |
145 |
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delete[] constrainedDsqr; |
146 |
mmeineke |
558 |
|
147 |
tim |
725 |
constrainedA = new int[nConstrained]; |
148 |
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constrainedB = new int[nConstrained]; |
149 |
mmeineke |
558 |
constrainedDsqr = new double[nConstrained]; |
150 |
tim |
725 |
|
151 |
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for (int i = 0; i < nConstrained; i++){ |
152 |
mmeineke |
558 |
constrainedA[i] = temp_con[i].get_a(); |
153 |
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constrainedB[i] = temp_con[i].get_b(); |
154 |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
155 |
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} |
156 |
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157 |
tim |
725 |
|
158 |
chrisfen |
999 |
// save oldAtoms to check for lode balancing later on. |
159 |
tim |
725 |
|
160 |
mmeineke |
558 |
oldAtoms = nAtoms; |
161 |
tim |
725 |
|
162 |
mmeineke |
558 |
moving = new int[nAtoms]; |
163 |
tim |
725 |
moved = new int[nAtoms]; |
164 |
mmeineke |
558 |
|
165 |
tim |
725 |
oldPos = new double[nAtoms * 3]; |
166 |
mmeineke |
558 |
} |
167 |
tim |
725 |
|
168 |
mmeineke |
558 |
delete[] temp_con; |
169 |
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} |
170 |
tim |
1234 |
*/ |
171 |
mmeineke |
558 |
|
172 |
tim |
725 |
template<typename T> void Integrator<T>::integrate(void){ |
173 |
mmeineke |
558 |
|
174 |
tim |
725 |
double runTime = info->run_time; |
175 |
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double sampleTime = info->sampleTime; |
176 |
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double statusTime = info->statusTime; |
177 |
mmeineke |
558 |
double thermalTime = info->thermalTime; |
178 |
mmeineke |
746 |
double resetTime = info->resetTime; |
179 |
mmeineke |
558 |
|
180 |
gezelter |
1178 |
double difference; |
181 |
mmeineke |
558 |
double currSample; |
182 |
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double currThermal; |
183 |
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double currStatus; |
184 |
mmeineke |
746 |
double currReset; |
185 |
tim |
837 |
|
186 |
mmeineke |
558 |
int calcPot, calcStress; |
187 |
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188 |
tim |
725 |
tStats = new Thermo(info); |
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statOut = new StatWriter(info); |
190 |
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dumpOut = new DumpWriter(info); |
191 |
mmeineke |
558 |
|
192 |
mmeineke |
561 |
atoms = info->atoms; |
193 |
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194 |
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dt = info->dt; |
195 |
mmeineke |
558 |
dt2 = 0.5 * dt; |
196 |
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197 |
mmeineke |
784 |
readyCheck(); |
198 |
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199 |
tim |
1127 |
// remove center of mass drift velocity (in case we passed in a configuration |
200 |
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// that was drifting |
201 |
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tStats->removeCOMdrift(); |
202 |
tim |
1452 |
//tStats->removeAngularMomentum(); |
203 |
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|
204 |
chrisfen |
1180 |
// initialize the retraints if necessary |
205 |
chrisfen |
1212 |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
206 |
chrisfen |
1180 |
myFF->initRestraints(); |
207 |
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} |
208 |
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209 |
mmeineke |
558 |
// initialize the forces before the first step |
210 |
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211 |
tim |
677 |
calcForce(1, 1); |
212 |
tim |
1234 |
|
213 |
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//execute constraint algorithm to make sure at the very beginning the system is constrained |
214 |
tim |
1284 |
//consFramework->doPreConstraint(); |
215 |
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//consFramework->doConstrainA(); |
216 |
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//calcForce(1, 1); |
217 |
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//consFramework->doConstrainB(); |
218 |
tim |
1035 |
|
219 |
tim |
725 |
if (info->setTemp){ |
220 |
tim |
677 |
thermalize(); |
221 |
mmeineke |
558 |
} |
222 |
tim |
725 |
|
223 |
mmeineke |
558 |
calcPot = 0; |
224 |
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calcStress = 0; |
225 |
mmeineke |
711 |
currSample = sampleTime + info->getTime(); |
226 |
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currThermal = thermalTime+ info->getTime(); |
227 |
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currStatus = statusTime + info->getTime(); |
228 |
mmeineke |
746 |
currReset = resetTime + info->getTime(); |
229 |
mmeineke |
558 |
|
230 |
tim |
725 |
dumpOut->writeDump(info->getTime()); |
231 |
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statOut->writeStat(info->getTime()); |
232 |
mmeineke |
559 |
|
233 |
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234 |
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#ifdef IS_MPI |
235 |
tim |
725 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
236 |
mmeineke |
559 |
MPIcheckPoint(); |
237 |
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#endif // is_mpi |
238 |
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|
239 |
tim |
1113 |
while (info->getTime() < runTime && !stopIntegrator()){ |
240 |
gezelter |
1178 |
difference = info->getTime() + dt - currStatus; |
241 |
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if (difference > 0 || fabs(difference) < 1e-4 ){ |
242 |
mmeineke |
558 |
calcPot = 1; |
243 |
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calcStress = 1; |
244 |
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} |
245 |
mmeineke |
561 |
|
246 |
chuckv |
892 |
#ifdef PROFILE |
247 |
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startProfile( pro1 ); |
248 |
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#endif |
249 |
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|
250 |
tim |
725 |
integrateStep(calcPot, calcStress); |
251 |
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|
252 |
chuckv |
892 |
#ifdef PROFILE |
253 |
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endProfile( pro1 ); |
254 |
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255 |
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startProfile( pro2 ); |
256 |
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#endif // profile |
257 |
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|
258 |
mmeineke |
643 |
info->incrTime(dt); |
259 |
mmeineke |
558 |
|
260 |
tim |
725 |
if (info->setTemp){ |
261 |
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if (info->getTime() >= currThermal){ |
262 |
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thermalize(); |
263 |
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currThermal += thermalTime; |
264 |
mmeineke |
558 |
} |
265 |
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} |
266 |
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|
267 |
tim |
725 |
if (info->getTime() >= currSample){ |
268 |
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dumpOut->writeDump(info->getTime()); |
269 |
mmeineke |
558 |
currSample += sampleTime; |
270 |
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} |
271 |
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272 |
tim |
725 |
if (info->getTime() >= currStatus){ |
273 |
tim |
837 |
statOut->writeStat(info->getTime()); |
274 |
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calcPot = 0; |
275 |
mmeineke |
558 |
calcStress = 0; |
276 |
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currStatus += statusTime; |
277 |
tim |
837 |
} |
278 |
mmeineke |
559 |
|
279 |
mmeineke |
746 |
if (info->resetIntegrator){ |
280 |
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if (info->getTime() >= currReset){ |
281 |
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this->resetIntegrator(); |
282 |
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currReset += resetTime; |
283 |
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} |
284 |
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} |
285 |
chuckv |
892 |
|
286 |
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#ifdef PROFILE |
287 |
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endProfile( pro2 ); |
288 |
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#endif //profile |
289 |
mmeineke |
746 |
|
290 |
mmeineke |
559 |
#ifdef IS_MPI |
291 |
tim |
725 |
strcpy(checkPointMsg, "successfully took a time step."); |
292 |
mmeineke |
559 |
MPIcheckPoint(); |
293 |
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#endif // is_mpi |
294 |
mmeineke |
558 |
} |
295 |
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|
296 |
chrisfen |
1180 |
// dump out a file containing the omega values for the final configuration |
297 |
chrisfen |
1212 |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
298 |
chrisfen |
1180 |
myFF->dumpzAngle(); |
299 |
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300 |
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301 |
mmeineke |
561 |
delete dumpOut; |
302 |
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delete statOut; |
303 |
mmeineke |
558 |
} |
304 |
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|
305 |
tim |
725 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
306 |
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int calcStress){ |
307 |
mmeineke |
558 |
// Position full step, and velocity half step |
308 |
chuckv |
892 |
|
309 |
|
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#ifdef PROFILE |
310 |
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startProfile(pro3); |
311 |
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#endif //profile |
312 |
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|
313 |
tim |
1234 |
//save old state (position, velocity etc) |
314 |
tim |
1268 |
consFramework->doPreConstraint(); |
315 |
mmeineke |
558 |
|
316 |
chuckv |
892 |
#ifdef PROFILE |
317 |
|
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endProfile(pro3); |
318 |
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319 |
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startProfile(pro4); |
320 |
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#endif // profile |
321 |
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|
322 |
mmeineke |
558 |
moveA(); |
323 |
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|
324 |
chuckv |
892 |
#ifdef PROFILE |
325 |
|
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endProfile(pro4); |
326 |
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327 |
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startProfile(pro5); |
328 |
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#endif//profile |
329 |
tim |
725 |
|
330 |
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|
331 |
mmeineke |
614 |
#ifdef IS_MPI |
332 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
333 |
mmeineke |
614 |
MPIcheckPoint(); |
334 |
|
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#endif // is_mpi |
335 |
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|
336 |
mmeineke |
558 |
// calc forces |
337 |
tim |
725 |
calcForce(calcPot, calcStress); |
338 |
mmeineke |
558 |
|
339 |
mmeineke |
614 |
#ifdef IS_MPI |
340 |
tim |
725 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
341 |
mmeineke |
614 |
MPIcheckPoint(); |
342 |
|
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#endif // is_mpi |
343 |
|
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|
344 |
chuckv |
892 |
#ifdef PROFILE |
345 |
|
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endProfile( pro5 ); |
346 |
tim |
725 |
|
347 |
chuckv |
892 |
startProfile( pro6 ); |
348 |
|
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#endif //profile |
349 |
|
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|
350 |
tim |
1452 |
consFramework->doPreConstraint(); |
351 |
|
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|
352 |
mmeineke |
558 |
// finish the velocity half step |
353 |
tim |
725 |
|
354 |
mmeineke |
558 |
moveB(); |
355 |
tim |
725 |
|
356 |
chuckv |
892 |
#ifdef PROFILE |
357 |
|
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endProfile(pro6); |
358 |
|
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#endif // profile |
359 |
tim |
725 |
|
360 |
mmeineke |
614 |
#ifdef IS_MPI |
361 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
362 |
mmeineke |
614 |
MPIcheckPoint(); |
363 |
|
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#endif // is_mpi |
364 |
mmeineke |
558 |
} |
365 |
|
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|
366 |
|
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|
367 |
tim |
725 |
template<typename T> void Integrator<T>::moveA(void){ |
368 |
gezelter |
1097 |
size_t i, j; |
369 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
370 |
gezelter |
600 |
double Tb[3], ji[3]; |
371 |
|
|
double vel[3], pos[3], frc[3]; |
372 |
|
|
double mass; |
373 |
chrisfen |
1187 |
double omega; |
374 |
gezelter |
1097 |
|
375 |
|
|
for (i = 0; i < integrableObjects.size() ; i++){ |
376 |
|
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integrableObjects[i]->getVel(vel); |
377 |
|
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integrableObjects[i]->getPos(pos); |
378 |
|
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integrableObjects[i]->getFrc(frc); |
379 |
|
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|
380 |
|
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mass = integrableObjects[i]->getMass(); |
381 |
mmeineke |
558 |
|
382 |
tim |
725 |
for (j = 0; j < 3; j++){ |
383 |
gezelter |
600 |
// velocity half step |
384 |
tim |
725 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
385 |
gezelter |
600 |
// position whole step |
386 |
|
|
pos[j] += dt * vel[j]; |
387 |
|
|
} |
388 |
mmeineke |
594 |
|
389 |
gezelter |
1097 |
integrableObjects[i]->setVel(vel); |
390 |
|
|
integrableObjects[i]->setPos(pos); |
391 |
gezelter |
600 |
|
392 |
gezelter |
1097 |
if (integrableObjects[i]->isDirectional()){ |
393 |
mmeineke |
558 |
|
394 |
|
|
// get and convert the torque to body frame |
395 |
mmeineke |
597 |
|
396 |
gezelter |
1097 |
integrableObjects[i]->getTrq(Tb); |
397 |
|
|
integrableObjects[i]->lab2Body(Tb); |
398 |
tim |
725 |
|
399 |
mmeineke |
558 |
// get the angular momentum, and propagate a half step |
400 |
gezelter |
600 |
|
401 |
gezelter |
1097 |
integrableObjects[i]->getJ(ji); |
402 |
gezelter |
600 |
|
403 |
tim |
725 |
for (j = 0; j < 3; j++) |
404 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
405 |
tim |
725 |
|
406 |
gezelter |
1097 |
this->rotationPropagation( integrableObjects[i], ji ); |
407 |
gezelter |
600 |
|
408 |
gezelter |
1097 |
integrableObjects[i]->setJ(ji); |
409 |
tim |
1452 |
|
410 |
tim |
725 |
} |
411 |
mmeineke |
558 |
} |
412 |
mmeineke |
768 |
|
413 |
tim |
1268 |
consFramework->doConstrainA(); |
414 |
mmeineke |
558 |
} |
415 |
|
|
|
416 |
|
|
|
417 |
tim |
725 |
template<typename T> void Integrator<T>::moveB(void){ |
418 |
gezelter |
600 |
int i, j; |
419 |
|
|
double Tb[3], ji[3]; |
420 |
|
|
double vel[3], frc[3]; |
421 |
|
|
double mass; |
422 |
mmeineke |
558 |
|
423 |
gezelter |
1097 |
for (i = 0; i < integrableObjects.size(); i++){ |
424 |
|
|
integrableObjects[i]->getVel(vel); |
425 |
|
|
integrableObjects[i]->getFrc(frc); |
426 |
mmeineke |
558 |
|
427 |
gezelter |
1097 |
mass = integrableObjects[i]->getMass(); |
428 |
gezelter |
600 |
|
429 |
mmeineke |
558 |
// velocity half step |
430 |
tim |
725 |
for (j = 0; j < 3; j++) |
431 |
|
|
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
432 |
gezelter |
600 |
|
433 |
gezelter |
1097 |
integrableObjects[i]->setVel(vel); |
434 |
mmeineke |
597 |
|
435 |
gezelter |
1097 |
if (integrableObjects[i]->isDirectional()){ |
436 |
tim |
725 |
|
437 |
tim |
837 |
// get and convert the torque to body frame |
438 |
gezelter |
600 |
|
439 |
gezelter |
1097 |
integrableObjects[i]->getTrq(Tb); |
440 |
|
|
integrableObjects[i]->lab2Body(Tb); |
441 |
gezelter |
600 |
|
442 |
|
|
// get the angular momentum, and propagate a half step |
443 |
|
|
|
444 |
gezelter |
1097 |
integrableObjects[i]->getJ(ji); |
445 |
gezelter |
600 |
|
446 |
tim |
725 |
for (j = 0; j < 3; j++) |
447 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
448 |
mmeineke |
597 |
|
449 |
tim |
725 |
|
450 |
gezelter |
1097 |
integrableObjects[i]->setJ(ji); |
451 |
mmeineke |
558 |
} |
452 |
tim |
1452 |
|
453 |
mmeineke |
558 |
} |
454 |
mmeineke |
768 |
|
455 |
tim |
1268 |
consFramework->doConstrainB(); |
456 |
mmeineke |
558 |
} |
457 |
|
|
|
458 |
tim |
1234 |
/* |
459 |
tim |
725 |
template<typename T> void Integrator<T>::preMove(void){ |
460 |
gezelter |
600 |
int i, j; |
461 |
|
|
double pos[3]; |
462 |
mmeineke |
558 |
|
463 |
tim |
725 |
if (nConstrained){ |
464 |
|
|
for (i = 0; i < nAtoms; i++){ |
465 |
|
|
atoms[i]->getPos(pos); |
466 |
mmeineke |
561 |
|
467 |
tim |
725 |
for (j = 0; j < 3; j++){ |
468 |
|
|
oldPos[3 * i + j] = pos[j]; |
469 |
gezelter |
600 |
} |
470 |
|
|
} |
471 |
tim |
725 |
} |
472 |
gezelter |
600 |
} |
473 |
|
|
|
474 |
tim |
645 |
template<typename T> void Integrator<T>::constrainA(){ |
475 |
mmeineke |
787 |
int i, j; |
476 |
mmeineke |
558 |
int done; |
477 |
gezelter |
600 |
double posA[3], posB[3]; |
478 |
|
|
double velA[3], velB[3]; |
479 |
mmeineke |
572 |
double pab[3]; |
480 |
|
|
double rab[3]; |
481 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
482 |
mmeineke |
558 |
double rma, rmb; |
483 |
|
|
double dx, dy, dz; |
484 |
mmeineke |
561 |
double rpab; |
485 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
486 |
|
|
double diffsq; |
487 |
|
|
double gab; |
488 |
|
|
int iteration; |
489 |
|
|
|
490 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
491 |
mmeineke |
558 |
moving[i] = 0; |
492 |
tim |
725 |
moved[i] = 1; |
493 |
mmeineke |
558 |
} |
494 |
mmeineke |
567 |
|
495 |
mmeineke |
558 |
iteration = 0; |
496 |
|
|
done = 0; |
497 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
498 |
mmeineke |
558 |
done = 1; |
499 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
500 |
mmeineke |
558 |
a = constrainedA[i]; |
501 |
|
|
b = constrainedB[i]; |
502 |
mmeineke |
563 |
|
503 |
tim |
725 |
ax = (a * 3) + 0; |
504 |
|
|
ay = (a * 3) + 1; |
505 |
|
|
az = (a * 3) + 2; |
506 |
mmeineke |
563 |
|
507 |
tim |
725 |
bx = (b * 3) + 0; |
508 |
|
|
by = (b * 3) + 1; |
509 |
|
|
bz = (b * 3) + 2; |
510 |
|
|
|
511 |
|
|
if (moved[a] || moved[b]){ |
512 |
|
|
atoms[a]->getPos(posA); |
513 |
|
|
atoms[b]->getPos(posB); |
514 |
|
|
|
515 |
|
|
for (j = 0; j < 3; j++) |
516 |
gezelter |
600 |
pab[j] = posA[j] - posB[j]; |
517 |
mmeineke |
567 |
|
518 |
tim |
725 |
//periodic boundary condition |
519 |
mmeineke |
567 |
|
520 |
tim |
725 |
info->wrapVector(pab); |
521 |
mmeineke |
572 |
|
522 |
tim |
725 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
523 |
mmeineke |
558 |
|
524 |
tim |
725 |
rabsq = constrainedDsqr[i]; |
525 |
|
|
diffsq = rabsq - pabsq; |
526 |
mmeineke |
567 |
|
527 |
tim |
725 |
// the original rattle code from alan tidesley |
528 |
|
|
if (fabs(diffsq) > (tol * rabsq * 2)){ |
529 |
|
|
rab[0] = oldPos[ax] - oldPos[bx]; |
530 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
531 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
532 |
mmeineke |
558 |
|
533 |
tim |
725 |
info->wrapVector(rab); |
534 |
mmeineke |
567 |
|
535 |
tim |
725 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
536 |
mmeineke |
558 |
|
537 |
tim |
725 |
rpabsq = rpab * rpab; |
538 |
mmeineke |
558 |
|
539 |
mmeineke |
563 |
|
540 |
tim |
725 |
if (rpabsq < (rabsq * -diffsq)){ |
541 |
mmeineke |
558 |
#ifdef IS_MPI |
542 |
tim |
725 |
a = atoms[a]->getGlobalIndex(); |
543 |
|
|
b = atoms[b]->getGlobalIndex(); |
544 |
mmeineke |
558 |
#endif //is_mpi |
545 |
tim |
725 |
sprintf(painCave.errMsg, |
546 |
|
|
"Constraint failure in constrainA at atom %d and %d.\n", a, |
547 |
|
|
b); |
548 |
|
|
painCave.isFatal = 1; |
549 |
|
|
simError(); |
550 |
|
|
} |
551 |
mmeineke |
558 |
|
552 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
553 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
554 |
mmeineke |
567 |
|
555 |
tim |
725 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
556 |
mmeineke |
567 |
|
557 |
mmeineke |
572 |
dx = rab[0] * gab; |
558 |
|
|
dy = rab[1] * gab; |
559 |
|
|
dz = rab[2] * gab; |
560 |
mmeineke |
558 |
|
561 |
tim |
725 |
posA[0] += rma * dx; |
562 |
|
|
posA[1] += rma * dy; |
563 |
|
|
posA[2] += rma * dz; |
564 |
mmeineke |
558 |
|
565 |
tim |
725 |
atoms[a]->setPos(posA); |
566 |
mmeineke |
558 |
|
567 |
tim |
725 |
posB[0] -= rmb * dx; |
568 |
|
|
posB[1] -= rmb * dy; |
569 |
|
|
posB[2] -= rmb * dz; |
570 |
gezelter |
600 |
|
571 |
tim |
725 |
atoms[b]->setPos(posB); |
572 |
gezelter |
600 |
|
573 |
mmeineke |
558 |
dx = dx / dt; |
574 |
|
|
dy = dy / dt; |
575 |
|
|
dz = dz / dt; |
576 |
|
|
|
577 |
tim |
725 |
atoms[a]->getVel(velA); |
578 |
mmeineke |
558 |
|
579 |
tim |
725 |
velA[0] += rma * dx; |
580 |
|
|
velA[1] += rma * dy; |
581 |
|
|
velA[2] += rma * dz; |
582 |
mmeineke |
558 |
|
583 |
tim |
725 |
atoms[a]->setVel(velA); |
584 |
gezelter |
600 |
|
585 |
tim |
725 |
atoms[b]->getVel(velB); |
586 |
gezelter |
600 |
|
587 |
tim |
725 |
velB[0] -= rmb * dx; |
588 |
|
|
velB[1] -= rmb * dy; |
589 |
|
|
velB[2] -= rmb * dz; |
590 |
gezelter |
600 |
|
591 |
tim |
725 |
atoms[b]->setVel(velB); |
592 |
gezelter |
600 |
|
593 |
tim |
725 |
moving[a] = 1; |
594 |
|
|
moving[b] = 1; |
595 |
|
|
done = 0; |
596 |
|
|
} |
597 |
mmeineke |
558 |
} |
598 |
|
|
} |
599 |
tim |
725 |
|
600 |
|
|
for (i = 0; i < nAtoms; i++){ |
601 |
mmeineke |
558 |
moved[i] = moving[i]; |
602 |
|
|
moving[i] = 0; |
603 |
|
|
} |
604 |
|
|
|
605 |
|
|
iteration++; |
606 |
|
|
} |
607 |
|
|
|
608 |
tim |
725 |
if (!done){ |
609 |
|
|
sprintf(painCave.errMsg, |
610 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n", |
611 |
|
|
iteration); |
612 |
mmeineke |
558 |
painCave.isFatal = 1; |
613 |
|
|
simError(); |
614 |
|
|
} |
615 |
mmeineke |
768 |
|
616 |
mmeineke |
558 |
} |
617 |
|
|
|
618 |
tim |
725 |
template<typename T> void Integrator<T>::constrainB(void){ |
619 |
mmeineke |
787 |
int i, j; |
620 |
mmeineke |
558 |
int done; |
621 |
gezelter |
600 |
double posA[3], posB[3]; |
622 |
|
|
double velA[3], velB[3]; |
623 |
mmeineke |
558 |
double vxab, vyab, vzab; |
624 |
mmeineke |
572 |
double rab[3]; |
625 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
626 |
mmeineke |
558 |
double rma, rmb; |
627 |
|
|
double dx, dy, dz; |
628 |
mmeineke |
787 |
double rvab; |
629 |
mmeineke |
558 |
double gab; |
630 |
|
|
int iteration; |
631 |
|
|
|
632 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
633 |
mmeineke |
558 |
moving[i] = 0; |
634 |
|
|
moved[i] = 1; |
635 |
|
|
} |
636 |
|
|
|
637 |
|
|
done = 0; |
638 |
mmeineke |
561 |
iteration = 0; |
639 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
640 |
mmeineke |
567 |
done = 1; |
641 |
|
|
|
642 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
643 |
mmeineke |
558 |
a = constrainedA[i]; |
644 |
|
|
b = constrainedB[i]; |
645 |
|
|
|
646 |
tim |
725 |
ax = (a * 3) + 0; |
647 |
|
|
ay = (a * 3) + 1; |
648 |
|
|
az = (a * 3) + 2; |
649 |
mmeineke |
563 |
|
650 |
tim |
725 |
bx = (b * 3) + 0; |
651 |
|
|
by = (b * 3) + 1; |
652 |
|
|
bz = (b * 3) + 2; |
653 |
mmeineke |
563 |
|
654 |
tim |
725 |
if (moved[a] || moved[b]){ |
655 |
|
|
atoms[a]->getVel(velA); |
656 |
|
|
atoms[b]->getVel(velB); |
657 |
mmeineke |
558 |
|
658 |
tim |
725 |
vxab = velA[0] - velB[0]; |
659 |
|
|
vyab = velA[1] - velB[1]; |
660 |
|
|
vzab = velA[2] - velB[2]; |
661 |
gezelter |
600 |
|
662 |
tim |
725 |
atoms[a]->getPos(posA); |
663 |
|
|
atoms[b]->getPos(posB); |
664 |
gezelter |
600 |
|
665 |
tim |
725 |
for (j = 0; j < 3; j++) |
666 |
gezelter |
600 |
rab[j] = posA[j] - posB[j]; |
667 |
mmeineke |
558 |
|
668 |
tim |
725 |
info->wrapVector(rab); |
669 |
mmeineke |
558 |
|
670 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
671 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
672 |
mmeineke |
558 |
|
673 |
tim |
725 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
674 |
gezelter |
600 |
|
675 |
tim |
725 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
676 |
gezelter |
600 |
|
677 |
tim |
725 |
if (fabs(gab) > tol){ |
678 |
|
|
dx = rab[0] * gab; |
679 |
|
|
dy = rab[1] * gab; |
680 |
|
|
dz = rab[2] * gab; |
681 |
|
|
|
682 |
|
|
velA[0] += rma * dx; |
683 |
|
|
velA[1] += rma * dy; |
684 |
|
|
velA[2] += rma * dz; |
685 |
|
|
|
686 |
|
|
atoms[a]->setVel(velA); |
687 |
|
|
|
688 |
|
|
velB[0] -= rmb * dx; |
689 |
|
|
velB[1] -= rmb * dy; |
690 |
|
|
velB[2] -= rmb * dz; |
691 |
|
|
|
692 |
|
|
atoms[b]->setVel(velB); |
693 |
|
|
|
694 |
|
|
moving[a] = 1; |
695 |
|
|
moving[b] = 1; |
696 |
|
|
done = 0; |
697 |
|
|
} |
698 |
mmeineke |
558 |
} |
699 |
|
|
} |
700 |
|
|
|
701 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
702 |
mmeineke |
558 |
moved[i] = moving[i]; |
703 |
|
|
moving[i] = 0; |
704 |
|
|
} |
705 |
tim |
725 |
|
706 |
mmeineke |
558 |
iteration++; |
707 |
|
|
} |
708 |
|
|
|
709 |
tim |
725 |
if (!done){ |
710 |
|
|
sprintf(painCave.errMsg, |
711 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n", |
712 |
|
|
iteration); |
713 |
mmeineke |
558 |
painCave.isFatal = 1; |
714 |
|
|
simError(); |
715 |
tim |
725 |
} |
716 |
mmeineke |
558 |
} |
717 |
tim |
1234 |
*/ |
718 |
mmeineke |
778 |
template<typename T> void Integrator<T>::rotationPropagation |
719 |
gezelter |
1097 |
( StuntDouble* sd, double ji[3] ){ |
720 |
mmeineke |
778 |
|
721 |
|
|
double angle; |
722 |
|
|
double A[3][3], I[3][3]; |
723 |
tim |
1118 |
int i, j, k; |
724 |
mmeineke |
778 |
|
725 |
|
|
// use the angular velocities to propagate the rotation matrix a |
726 |
|
|
// full time step |
727 |
|
|
|
728 |
gezelter |
1097 |
sd->getA(A); |
729 |
|
|
sd->getI(I); |
730 |
tim |
837 |
|
731 |
tim |
1118 |
if (sd->isLinear()) { |
732 |
|
|
i = sd->linearAxis(); |
733 |
|
|
j = (i+1)%3; |
734 |
|
|
k = (i+2)%3; |
735 |
|
|
|
736 |
|
|
angle = dt2 * ji[j] / I[j][j]; |
737 |
|
|
this->rotate( k, i, angle, ji, A ); |
738 |
|
|
|
739 |
|
|
angle = dt * ji[k] / I[k][k]; |
740 |
|
|
this->rotate( i, j, angle, ji, A); |
741 |
|
|
|
742 |
|
|
angle = dt2 * ji[j] / I[j][j]; |
743 |
|
|
this->rotate( k, i, angle, ji, A ); |
744 |
|
|
|
745 |
|
|
} else { |
746 |
gezelter |
1125 |
// rotate about the x-axis |
747 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
748 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
749 |
|
|
|
750 |
|
|
// rotate about the y-axis |
751 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
752 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
753 |
|
|
|
754 |
|
|
// rotate about the z-axis |
755 |
|
|
angle = dt * ji[2] / I[2][2]; |
756 |
chrisfen |
1187 |
sd->addZangle(angle); |
757 |
gezelter |
1125 |
this->rotate( 0, 1, angle, ji, A); |
758 |
|
|
|
759 |
|
|
// rotate about the y-axis |
760 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
761 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
762 |
|
|
|
763 |
|
|
// rotate about the x-axis |
764 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
765 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
766 |
|
|
|
767 |
tim |
1118 |
} |
768 |
gezelter |
1097 |
sd->setA( A ); |
769 |
mmeineke |
778 |
} |
770 |
|
|
|
771 |
tim |
725 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
772 |
|
|
double angle, double ji[3], |
773 |
|
|
double A[3][3]){ |
774 |
|
|
int i, j, k; |
775 |
mmeineke |
558 |
double sinAngle; |
776 |
|
|
double cosAngle; |
777 |
|
|
double angleSqr; |
778 |
|
|
double angleSqrOver4; |
779 |
|
|
double top, bottom; |
780 |
|
|
double rot[3][3]; |
781 |
|
|
double tempA[3][3]; |
782 |
|
|
double tempJ[3]; |
783 |
|
|
|
784 |
|
|
// initialize the tempA |
785 |
|
|
|
786 |
tim |
725 |
for (i = 0; i < 3; i++){ |
787 |
|
|
for (j = 0; j < 3; j++){ |
788 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
789 |
mmeineke |
558 |
} |
790 |
|
|
} |
791 |
|
|
|
792 |
|
|
// initialize the tempJ |
793 |
|
|
|
794 |
tim |
725 |
for (i = 0; i < 3; i++) |
795 |
|
|
tempJ[i] = ji[i]; |
796 |
|
|
|
797 |
mmeineke |
558 |
// initalize rot as a unit matrix |
798 |
|
|
|
799 |
|
|
rot[0][0] = 1.0; |
800 |
|
|
rot[0][1] = 0.0; |
801 |
|
|
rot[0][2] = 0.0; |
802 |
|
|
|
803 |
|
|
rot[1][0] = 0.0; |
804 |
|
|
rot[1][1] = 1.0; |
805 |
|
|
rot[1][2] = 0.0; |
806 |
tim |
725 |
|
807 |
mmeineke |
558 |
rot[2][0] = 0.0; |
808 |
|
|
rot[2][1] = 0.0; |
809 |
|
|
rot[2][2] = 1.0; |
810 |
tim |
725 |
|
811 |
mmeineke |
558 |
// use a small angle aproximation for sin and cosine |
812 |
|
|
|
813 |
tim |
725 |
angleSqr = angle * angle; |
814 |
mmeineke |
558 |
angleSqrOver4 = angleSqr / 4.0; |
815 |
|
|
top = 1.0 - angleSqrOver4; |
816 |
|
|
bottom = 1.0 + angleSqrOver4; |
817 |
|
|
|
818 |
|
|
cosAngle = top / bottom; |
819 |
|
|
sinAngle = angle / bottom; |
820 |
|
|
|
821 |
|
|
rot[axes1][axes1] = cosAngle; |
822 |
|
|
rot[axes2][axes2] = cosAngle; |
823 |
|
|
|
824 |
|
|
rot[axes1][axes2] = sinAngle; |
825 |
|
|
rot[axes2][axes1] = -sinAngle; |
826 |
tim |
725 |
|
827 |
mmeineke |
558 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
828 |
tim |
725 |
|
829 |
|
|
for (i = 0; i < 3; i++){ |
830 |
mmeineke |
558 |
ji[i] = 0.0; |
831 |
tim |
725 |
for (k = 0; k < 3; k++){ |
832 |
mmeineke |
558 |
ji[i] += rot[i][k] * tempJ[k]; |
833 |
|
|
} |
834 |
|
|
} |
835 |
|
|
|
836 |
tim |
837 |
// rotate the Rotation matrix acording to: |
837 |
mmeineke |
558 |
// A[][] = A[][] * transpose(rot[][]) |
838 |
|
|
|
839 |
|
|
|
840 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
841 |
mmeineke |
558 |
// calculation as: |
842 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
843 |
|
|
|
844 |
tim |
725 |
for (i = 0; i < 3; i++){ |
845 |
|
|
for (j = 0; j < 3; j++){ |
846 |
gezelter |
600 |
A[j][i] = 0.0; |
847 |
tim |
725 |
for (k = 0; k < 3; k++){ |
848 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
849 |
mmeineke |
558 |
} |
850 |
|
|
} |
851 |
|
|
} |
852 |
|
|
} |
853 |
tim |
677 |
|
854 |
tim |
725 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
855 |
|
|
myFF->doForces(calcPot, calcStress); |
856 |
tim |
677 |
} |
857 |
|
|
|
858 |
|
|
template<typename T> void Integrator<T>::thermalize(){ |
859 |
tim |
725 |
tStats->velocitize(); |
860 |
tim |
677 |
} |
861 |
tim |
763 |
|
862 |
|
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
863 |
|
|
return tStats->getTotalE(); |
864 |
mmeineke |
768 |
} |
865 |
tim |
837 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
866 |
|
|
//By default, return a null string |
867 |
|
|
//The reason we use string instead of char* is that if we use char*, we will |
868 |
|
|
//return a pointer point to local variable which might cause problem |
869 |
|
|
return string(); |
870 |
|
|
} |
871 |
tim |
1452 |
|
872 |
|
|
|
873 |
|
|
template<typename T> void Integrator<T>::printQuaternion(StuntDouble* sd){ |
874 |
|
|
Mat4x4d S; |
875 |
|
|
double I[3][3]; |
876 |
|
|
Vector4d j4; |
877 |
|
|
Vector3d j; |
878 |
|
|
Vector3d tempJ; |
879 |
|
|
Vector4d qdot; |
880 |
|
|
Vector4d omega4; |
881 |
|
|
Mat4x4d I4; |
882 |
|
|
Quaternion q; |
883 |
|
|
double I0; |
884 |
|
|
Vector4d p_qua; |
885 |
|
|
|
886 |
|
|
if (sd->isDirectional()){ |
887 |
|
|
sd->getQ(q.vec); |
888 |
|
|
sd->getI(I); |
889 |
|
|
sd->getJ(j.vec); |
890 |
|
|
|
891 |
|
|
//omega4[0] = 0.0; |
892 |
|
|
//omega4[1] = j[0]/I[0][0]; |
893 |
|
|
//omega4[2] = j[1]/I[1][1]; |
894 |
|
|
//omega4[3] = j[2]/I[2][2]; |
895 |
|
|
|
896 |
|
|
//S = getS(q); |
897 |
|
|
//qdot = 0.5 * S * omega4; |
898 |
|
|
|
899 |
|
|
//I0 = (qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2])/(qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3]); |
900 |
|
|
|
901 |
|
|
//I4.element[0][0] = I0; |
902 |
|
|
//I4.element[1][1] = I[0][0]; |
903 |
|
|
//I4.element[2][2] = I[1][1]; |
904 |
|
|
//I4.element[3][3] = I[2][2]; |
905 |
|
|
|
906 |
|
|
S = getS(q); |
907 |
|
|
j4[0] = 0.0; |
908 |
|
|
j4[1] = j[0]; |
909 |
|
|
j4[2] = j[1]; |
910 |
|
|
j4[3] = j[2]; |
911 |
|
|
|
912 |
|
|
p_qua = 2 * S * j4; |
913 |
|
|
|
914 |
|
|
j4 = 0.5 * S.transpose() * p_qua; |
915 |
|
|
//cout << "q0^2 + q1^2 + q2^2 + q3^2 = " << q[0]*q[0] + q[1]*q[1] + q[2]*q[2] + q[3]*q[3] << endl; |
916 |
|
|
//cout << "q0*q0dot + q1*q1dot + q2 *q2dot + q3*q3dot = " <<q[0]*qdot[0] + q[1]*qdot[1] + q[2]*qdot[2] + q[3]*qdot[3] << endl; |
917 |
|
|
//cout << "q1*q1dot* Ixx + q2*q2dot* Iyy + q3 *q3dot* Izz = " << qdot[1] * q[1] * I[0][0] + qdot[2] * q[2] * I[1][1] + qdot[3] * q[3] * I[2][2] << endl; |
918 |
|
|
//cout << "q1*q1dot + q2 *q2dot + q3*q3dot = " << qdot[1] * q[1]+ qdot[2] * q[2] + qdot[3] * q[3] << endl; |
919 |
|
|
//cout << "I0 = " << I0 << endl; |
920 |
|
|
cout << "p_qua[0] = " << p_qua[0] << endl; |
921 |
|
|
} |
922 |
|
|
} |
923 |
|
|
|
924 |
|
|
template<typename T> Mat4x4d Integrator<T>::getS(const Quaternion& q){ |
925 |
|
|
Mat4x4d result; |
926 |
|
|
|
927 |
|
|
result.element[0][0] = q.x; |
928 |
|
|
result.element[0][1] = -q.y; |
929 |
|
|
result.element[0][2] = -q.z; |
930 |
|
|
result.element[0][3] = -q.w; |
931 |
|
|
|
932 |
|
|
result.element[1][0] = q.y; |
933 |
|
|
result.element[1][1] = q.x; |
934 |
|
|
result.element[1][2] = -q.w; |
935 |
|
|
result.element[1][3] = q.z; |
936 |
|
|
|
937 |
|
|
result.element[2][0] = q.z; |
938 |
|
|
result.element[2][1] = q.w; |
939 |
|
|
result.element[2][2] = q.x; |
940 |
|
|
result.element[2][3] = -q.y; |
941 |
|
|
|
942 |
|
|
result.element[3][0] = q.w; |
943 |
|
|
result.element[3][1] = -q.z; |
944 |
|
|
result.element[3][2] = q.y; |
945 |
|
|
result.element[3][3] = q.x; |
946 |
|
|
|
947 |
|
|
return result; |
948 |
|
|
} |
949 |
|
|
|