1 |
#include <iostream>
|
2 |
#include <stdlib.h>
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3 |
#include <math.h>
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4 |
#ifdef IS_MPI
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5 |
#include "brains/mpiSimulation.hpp"
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6 |
#include <unistd.h>
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7 |
#endif //is_mpi
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8 |
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9 |
#ifdef PROFILE
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10 |
#include "profiling/mdProfile.hpp"
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#endif // profile
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12 |
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13 |
#include "integrators/Integrator.hpp"
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14 |
#include "utils/simError.h"
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15 |
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16 |
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17 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo,
|
18 |
ForceFields* the_ff){
|
19 |
info = theInfo;
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20 |
myFF = the_ff;
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21 |
isFirst = 1;
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22 |
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23 |
molecules = info->molecules;
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24 |
nMols = info->n_mol;
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25 |
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26 |
// give a little love back to the SimInfo object
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27 |
|
28 |
if (info->the_integrator != NULL){
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29 |
delete info->the_integrator;
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30 |
}
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31 |
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32 |
nAtoms = info->n_atoms;
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33 |
integrableObjects = info->integrableObjects;
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34 |
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35 |
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36 |
// check for constraints
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37 |
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38 |
constrainedA = NULL;
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39 |
constrainedB = NULL;
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40 |
constrainedDsqr = NULL;
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41 |
moving = NULL;
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42 |
moved = NULL;
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43 |
oldPos = NULL;
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44 |
|
45 |
nConstrained = 0;
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46 |
|
47 |
checkConstraints();
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48 |
|
49 |
}
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50 |
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51 |
template<typename T> Integrator<T>::~Integrator(){
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52 |
|
53 |
if (nConstrained){
|
54 |
delete[] constrainedA;
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55 |
delete[] constrainedB;
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56 |
delete[] constrainedDsqr;
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57 |
delete[] moving;
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58 |
delete[] moved;
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59 |
delete[] oldPos;
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}
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61 |
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62 |
}
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63 |
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64 |
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65 |
template<typename T> void Integrator<T>::checkConstraints(void){
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66 |
isConstrained = 0;
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67 |
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68 |
Constraint* temp_con;
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69 |
Constraint* dummy_plug;
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70 |
temp_con = new Constraint[info->n_SRI];
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71 |
nConstrained = 0;
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72 |
int constrained = 0;
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73 |
|
74 |
SRI** theArray;
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75 |
for (int i = 0; i < nMols; i++){
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76 |
|
77 |
theArray = (SRI * *) molecules[i].getMyBonds();
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78 |
for (int j = 0; j < molecules[i].getNBonds(); j++){
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79 |
constrained = theArray[j]->is_constrained();
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80 |
|
81 |
if (constrained){
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82 |
dummy_plug = theArray[j]->get_constraint();
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83 |
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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85 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
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86 |
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87 |
nConstrained++;
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constrained = 0;
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}
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}
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91 |
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92 |
theArray = (SRI * *) molecules[i].getMyBends();
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for (int j = 0; j < molecules[i].getNBends(); j++){
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constrained = theArray[j]->is_constrained();
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95 |
|
96 |
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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100 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
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101 |
|
102 |
nConstrained++;
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103 |
constrained = 0;
|
104 |
}
|
105 |
}
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106 |
|
107 |
theArray = (SRI * *) molecules[i].getMyTorsions();
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108 |
for (int j = 0; j < molecules[i].getNTorsions(); j++){
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109 |
constrained = theArray[j]->is_constrained();
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110 |
|
111 |
if (constrained){
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112 |
dummy_plug = theArray[j]->get_constraint();
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113 |
temp_con[nConstrained].set_a(dummy_plug->get_a());
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114 |
temp_con[nConstrained].set_b(dummy_plug->get_b());
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115 |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
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116 |
|
117 |
nConstrained++;
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118 |
constrained = 0;
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}
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120 |
}
|
121 |
}
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122 |
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123 |
|
124 |
if (nConstrained > 0){
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125 |
isConstrained = 1;
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126 |
|
127 |
if (constrainedA != NULL)
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128 |
delete[] constrainedA;
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129 |
if (constrainedB != NULL)
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130 |
delete[] constrainedB;
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131 |
if (constrainedDsqr != NULL)
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delete[] constrainedDsqr;
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133 |
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134 |
constrainedA = new int[nConstrained];
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constrainedB = new int[nConstrained];
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136 |
constrainedDsqr = new double[nConstrained];
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137 |
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138 |
for (int i = 0; i < nConstrained; i++){
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139 |
constrainedA[i] = temp_con[i].get_a();
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140 |
constrainedB[i] = temp_con[i].get_b();
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141 |
constrainedDsqr[i] = temp_con[i].get_dsqr();
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142 |
}
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144 |
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145 |
// save oldAtoms to check for lode balancing later on.
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146 |
|
147 |
oldAtoms = nAtoms;
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148 |
|
149 |
moving = new int[nAtoms];
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150 |
moved = new int[nAtoms];
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151 |
|
152 |
oldPos = new double[nAtoms * 3];
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153 |
}
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154 |
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155 |
delete[] temp_con;
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156 |
}
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157 |
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158 |
|
159 |
template<typename T> void Integrator<T>::integrate(void){
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160 |
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161 |
double runTime = info->run_time;
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162 |
double sampleTime = info->sampleTime;
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163 |
double statusTime = info->statusTime;
|
164 |
double thermalTime = info->thermalTime;
|
165 |
double resetTime = info->resetTime;
|
166 |
|
167 |
double difference;
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168 |
double currSample;
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169 |
double currThermal;
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170 |
double currStatus;
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171 |
double currReset;
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172 |
|
173 |
int calcPot, calcStress;
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174 |
|
175 |
tStats = new Thermo(info);
|
176 |
statOut = new StatWriter(info);
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177 |
dumpOut = new DumpWriter(info);
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178 |
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179 |
atoms = info->atoms;
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180 |
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181 |
dt = info->dt;
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182 |
dt2 = 0.5 * dt;
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183 |
|
184 |
readyCheck();
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185 |
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186 |
// remove center of mass drift velocity (in case we passed in a configuration
|
187 |
// that was drifting
|
188 |
tStats->removeCOMdrift();
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189 |
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190 |
// initialize the retraints if necessary
|
191 |
if (info->useSolidThermInt && !info->useLiquidThermInt) {
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192 |
myFF->initRestraints();
|
193 |
}
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194 |
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195 |
// initialize the forces before the first step
|
196 |
|
197 |
calcForce(1, 1);
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198 |
|
199 |
//execute constraint algorithm to make sure at the very beginning the system is constrained
|
200 |
if(nConstrained){
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201 |
preMove();
|
202 |
constrainA();
|
203 |
calcForce(1, 1);
|
204 |
constrainB();
|
205 |
}
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206 |
|
207 |
if (info->setTemp){
|
208 |
thermalize();
|
209 |
}
|
210 |
|
211 |
calcPot = 0;
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212 |
calcStress = 0;
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213 |
currSample = sampleTime + info->getTime();
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214 |
currThermal = thermalTime+ info->getTime();
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215 |
currStatus = statusTime + info->getTime();
|
216 |
currReset = resetTime + info->getTime();
|
217 |
|
218 |
dumpOut->writeDump(info->getTime());
|
219 |
statOut->writeStat(info->getTime());
|
220 |
|
221 |
|
222 |
#ifdef IS_MPI
|
223 |
strcpy(checkPointMsg, "The integrator is ready to go.");
|
224 |
MPIcheckPoint();
|
225 |
#endif // is_mpi
|
226 |
|
227 |
while (info->getTime() < runTime && !stopIntegrator()){
|
228 |
difference = info->getTime() + dt - currStatus;
|
229 |
if (difference > 0 || fabs(difference) < 1e-4 ){
|
230 |
calcPot = 1;
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231 |
calcStress = 1;
|
232 |
}
|
233 |
|
234 |
#ifdef PROFILE
|
235 |
startProfile( pro1 );
|
236 |
#endif
|
237 |
|
238 |
integrateStep(calcPot, calcStress);
|
239 |
|
240 |
#ifdef PROFILE
|
241 |
endProfile( pro1 );
|
242 |
|
243 |
startProfile( pro2 );
|
244 |
#endif // profile
|
245 |
|
246 |
info->incrTime(dt);
|
247 |
|
248 |
if (info->setTemp){
|
249 |
if (info->getTime() >= currThermal){
|
250 |
thermalize();
|
251 |
currThermal += thermalTime;
|
252 |
}
|
253 |
}
|
254 |
|
255 |
if (info->getTime() >= currSample){
|
256 |
dumpOut->writeDump(info->getTime());
|
257 |
currSample += sampleTime;
|
258 |
}
|
259 |
|
260 |
if (info->getTime() >= currStatus){
|
261 |
statOut->writeStat(info->getTime());
|
262 |
calcPot = 0;
|
263 |
calcStress = 0;
|
264 |
currStatus += statusTime;
|
265 |
}
|
266 |
|
267 |
if (info->resetIntegrator){
|
268 |
if (info->getTime() >= currReset){
|
269 |
this->resetIntegrator();
|
270 |
currReset += resetTime;
|
271 |
}
|
272 |
}
|
273 |
|
274 |
#ifdef PROFILE
|
275 |
endProfile( pro2 );
|
276 |
#endif //profile
|
277 |
|
278 |
#ifdef IS_MPI
|
279 |
strcpy(checkPointMsg, "successfully took a time step.");
|
280 |
MPIcheckPoint();
|
281 |
#endif // is_mpi
|
282 |
}
|
283 |
|
284 |
dumpOut->writeFinal(info->getTime());
|
285 |
|
286 |
// dump out a file containing the omega values for the final configuration
|
287 |
if (info->useSolidThermInt && !info->useLiquidThermInt)
|
288 |
myFF->dumpzAngle();
|
289 |
|
290 |
|
291 |
delete dumpOut;
|
292 |
delete statOut;
|
293 |
}
|
294 |
|
295 |
template<typename T> void Integrator<T>::integrateStep(int calcPot,
|
296 |
int calcStress){
|
297 |
// Position full step, and velocity half step
|
298 |
|
299 |
#ifdef PROFILE
|
300 |
startProfile(pro3);
|
301 |
#endif //profile
|
302 |
|
303 |
//save old state (position, velocity etc)
|
304 |
preMove();
|
305 |
#ifdef PROFILE
|
306 |
endProfile(pro3);
|
307 |
|
308 |
startProfile(pro4);
|
309 |
#endif // profile
|
310 |
|
311 |
moveA();
|
312 |
|
313 |
#ifdef PROFILE
|
314 |
endProfile(pro4);
|
315 |
|
316 |
startProfile(pro5);
|
317 |
#endif//profile
|
318 |
|
319 |
|
320 |
#ifdef IS_MPI
|
321 |
strcpy(checkPointMsg, "Succesful moveA\n");
|
322 |
MPIcheckPoint();
|
323 |
#endif // is_mpi
|
324 |
|
325 |
// calc forces
|
326 |
calcForce(calcPot, calcStress);
|
327 |
|
328 |
#ifdef IS_MPI
|
329 |
strcpy(checkPointMsg, "Succesful doForces\n");
|
330 |
MPIcheckPoint();
|
331 |
#endif // is_mpi
|
332 |
|
333 |
#ifdef PROFILE
|
334 |
endProfile( pro5 );
|
335 |
|
336 |
startProfile( pro6 );
|
337 |
#endif //profile
|
338 |
|
339 |
// finish the velocity half step
|
340 |
|
341 |
moveB();
|
342 |
|
343 |
#ifdef PROFILE
|
344 |
endProfile(pro6);
|
345 |
#endif // profile
|
346 |
|
347 |
#ifdef IS_MPI
|
348 |
strcpy(checkPointMsg, "Succesful moveB\n");
|
349 |
MPIcheckPoint();
|
350 |
#endif // is_mpi
|
351 |
}
|
352 |
|
353 |
|
354 |
template<typename T> void Integrator<T>::moveA(void){
|
355 |
size_t i, j;
|
356 |
DirectionalAtom* dAtom;
|
357 |
Vector3d Tb;
|
358 |
Vector3d ji;
|
359 |
Vector3d vel;
|
360 |
Vector3d pos;
|
361 |
Vector3d frc;
|
362 |
double mass;
|
363 |
double omega;
|
364 |
|
365 |
for (i = 0; i < integrableObjects.size() ; i++){
|
366 |
vel = integrableObjects[i]->getVel();
|
367 |
pos = integrableObjects[i]->getPos();
|
368 |
integrableObjects[i]->getFrc(frc);
|
369 |
|
370 |
mass = integrableObjects[i]->getMass();
|
371 |
|
372 |
for (j = 0; j < 3; j++){
|
373 |
// velocity half step
|
374 |
vel[j] += (dt2 * frc[j] / mass) * eConvert;
|
375 |
// position whole step
|
376 |
pos[j] += dt * vel[j];
|
377 |
}
|
378 |
|
379 |
integrableObjects[i]->setVel(vel);
|
380 |
integrableObjects[i]->setPos(pos);
|
381 |
|
382 |
if (integrableObjects[i]->isDirectional()){
|
383 |
|
384 |
// get and convert the torque to body frame
|
385 |
|
386 |
Tb = integrableObjects[i]->getTrq();
|
387 |
integrableObjects[i]->lab2Body(Tb);
|
388 |
|
389 |
// get the angular momentum, and propagate a half step
|
390 |
|
391 |
ji = integrableObjects[i]->getJ();
|
392 |
|
393 |
for (j = 0; j < 3; j++)
|
394 |
ji[j] += (dt2 * Tb[j]) * eConvert;
|
395 |
|
396 |
this->rotationPropagation( integrableObjects[i], ji );
|
397 |
|
398 |
integrableObjects[i]->setJ(ji);
|
399 |
}
|
400 |
}
|
401 |
|
402 |
if(nConstrained)
|
403 |
constrainA();
|
404 |
}
|
405 |
|
406 |
|
407 |
template<typename T> void Integrator<T>::moveB(void){
|
408 |
int i, j;
|
409 |
double Tb[3], ji[3];
|
410 |
double vel[3], frc[3];
|
411 |
double mass;
|
412 |
|
413 |
for (i = 0; i < integrableObjects.size(); i++){
|
414 |
vel = integrableObjects[i]->getVel();
|
415 |
integrableObjects[i]->getFrc(frc);
|
416 |
|
417 |
mass = integrableObjects[i]->getMass();
|
418 |
|
419 |
// velocity half step
|
420 |
for (j = 0; j < 3; j++)
|
421 |
vel[j] += (dt2 * frc[j] / mass) * eConvert;
|
422 |
|
423 |
integrableObjects[i]->setVel(vel);
|
424 |
|
425 |
if (integrableObjects[i]->isDirectional()){
|
426 |
|
427 |
// get and convert the torque to body frame
|
428 |
|
429 |
Tb = integrableObjects[i]->getTrq();
|
430 |
integrableObjects[i]->lab2Body(Tb);
|
431 |
|
432 |
// get the angular momentum, and propagate a half step
|
433 |
|
434 |
ji = integrableObjects[i]->getJ();
|
435 |
|
436 |
for (j = 0; j < 3; j++)
|
437 |
ji[j] += (dt2 * Tb[j]) * eConvert;
|
438 |
|
439 |
|
440 |
integrableObjects[i]->setJ(ji);
|
441 |
}
|
442 |
}
|
443 |
|
444 |
if(nConstrained)
|
445 |
constrainB();
|
446 |
}
|
447 |
|
448 |
|
449 |
template<typename T> void Integrator<T>::preMove(void){
|
450 |
int i, j;
|
451 |
double pos[3];
|
452 |
|
453 |
if (nConstrained){
|
454 |
for (i = 0; i < nAtoms; i++){
|
455 |
pos = atoms[i]->getPos();
|
456 |
|
457 |
for (j = 0; j < 3; j++){
|
458 |
oldPos[3 * i + j] = pos[j];
|
459 |
}
|
460 |
}
|
461 |
}
|
462 |
}
|
463 |
|
464 |
template<typename T> void Integrator<T>::constrainA(){
|
465 |
int i, j;
|
466 |
int done;
|
467 |
double posA[3], posB[3];
|
468 |
double velA[3], velB[3];
|
469 |
double pab[3];
|
470 |
double rab[3];
|
471 |
int a, b, ax, ay, az, bx, by, bz;
|
472 |
double rma, rmb;
|
473 |
double dx, dy, dz;
|
474 |
double rpab;
|
475 |
double rabsq, pabsq, rpabsq;
|
476 |
double diffsq;
|
477 |
double gab;
|
478 |
int iteration;
|
479 |
|
480 |
for (i = 0; i < nAtoms; i++){
|
481 |
moving[i] = 0;
|
482 |
moved[i] = 1;
|
483 |
}
|
484 |
|
485 |
iteration = 0;
|
486 |
done = 0;
|
487 |
while (!done && (iteration < maxIteration)){
|
488 |
done = 1;
|
489 |
for (i = 0; i < nConstrained; i++){
|
490 |
a = constrainedA[i];
|
491 |
b = constrainedB[i];
|
492 |
|
493 |
ax = (a * 3) + 0;
|
494 |
ay = (a * 3) + 1;
|
495 |
az = (a * 3) + 2;
|
496 |
|
497 |
bx = (b * 3) + 0;
|
498 |
by = (b * 3) + 1;
|
499 |
bz = (b * 3) + 2;
|
500 |
|
501 |
if (moved[a] || moved[b]){
|
502 |
posA = atoms[a]->getPos();
|
503 |
posB = atoms[b]->getPos();
|
504 |
|
505 |
for (j = 0; j < 3; j++)
|
506 |
pab[j] = posA[j] - posB[j];
|
507 |
|
508 |
//periodic boundary condition
|
509 |
|
510 |
info->wrapVector(pab);
|
511 |
|
512 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2];
|
513 |
|
514 |
rabsq = constrainedDsqr[i];
|
515 |
diffsq = rabsq - pabsq;
|
516 |
|
517 |
// the original rattle code from alan tidesley
|
518 |
if (fabs(diffsq) > (tol * rabsq * 2)){
|
519 |
rab[0] = oldPos[ax] - oldPos[bx];
|
520 |
rab[1] = oldPos[ay] - oldPos[by];
|
521 |
rab[2] = oldPos[az] - oldPos[bz];
|
522 |
|
523 |
info->wrapVector(rab);
|
524 |
|
525 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2];
|
526 |
|
527 |
rpabsq = rpab * rpab;
|
528 |
|
529 |
|
530 |
if (rpabsq < (rabsq * -diffsq)){
|
531 |
#ifdef IS_MPI
|
532 |
a = atoms[a]->getGlobalIndex();
|
533 |
b = atoms[b]->getGlobalIndex();
|
534 |
#endif //is_mpi
|
535 |
sprintf(painCave.errMsg,
|
536 |
"Constraint failure in constrainA at atom %d and %d.\n", a,
|
537 |
b);
|
538 |
painCave.isFatal = 1;
|
539 |
simError();
|
540 |
}
|
541 |
|
542 |
rma = 1.0 / atoms[a]->getMass();
|
543 |
rmb = 1.0 / atoms[b]->getMass();
|
544 |
|
545 |
gab = diffsq / (2.0 * (rma + rmb) * rpab);
|
546 |
|
547 |
dx = rab[0] * gab;
|
548 |
dy = rab[1] * gab;
|
549 |
dz = rab[2] * gab;
|
550 |
|
551 |
posA[0] += rma * dx;
|
552 |
posA[1] += rma * dy;
|
553 |
posA[2] += rma * dz;
|
554 |
|
555 |
atoms[a]->setPos(posA);
|
556 |
|
557 |
posB[0] -= rmb * dx;
|
558 |
posB[1] -= rmb * dy;
|
559 |
posB[2] -= rmb * dz;
|
560 |
|
561 |
atoms[b]->setPos(posB);
|
562 |
|
563 |
dx = dx / dt;
|
564 |
dy = dy / dt;
|
565 |
dz = dz / dt;
|
566 |
|
567 |
velA = atoms[a]->getVel();
|
568 |
|
569 |
velA[0] += rma * dx;
|
570 |
velA[1] += rma * dy;
|
571 |
velA[2] += rma * dz;
|
572 |
|
573 |
atoms[a]->setVel(velA);
|
574 |
|
575 |
velB = atoms[b]->getVel();
|
576 |
|
577 |
velB[0] -= rmb * dx;
|
578 |
velB[1] -= rmb * dy;
|
579 |
velB[2] -= rmb * dz;
|
580 |
|
581 |
atoms[b]->setVel(velB);
|
582 |
|
583 |
moving[a] = 1;
|
584 |
moving[b] = 1;
|
585 |
done = 0;
|
586 |
}
|
587 |
}
|
588 |
}
|
589 |
|
590 |
for (i = 0; i < nAtoms; i++){
|
591 |
moved[i] = moving[i];
|
592 |
moving[i] = 0;
|
593 |
}
|
594 |
|
595 |
iteration++;
|
596 |
}
|
597 |
|
598 |
if (!done){
|
599 |
sprintf(painCave.errMsg,
|
600 |
"Constraint failure in constrainA, too many iterations: %d\n",
|
601 |
iteration);
|
602 |
painCave.isFatal = 1;
|
603 |
simError();
|
604 |
}
|
605 |
|
606 |
}
|
607 |
|
608 |
template<typename T> void Integrator<T>::constrainB(void){
|
609 |
int i, j;
|
610 |
int done;
|
611 |
double posA[3], posB[3];
|
612 |
double velA[3], velB[3];
|
613 |
double vxab, vyab, vzab;
|
614 |
double rab[3];
|
615 |
int a, b, ax, ay, az, bx, by, bz;
|
616 |
double rma, rmb;
|
617 |
double dx, dy, dz;
|
618 |
double rvab;
|
619 |
double gab;
|
620 |
int iteration;
|
621 |
|
622 |
for (i = 0; i < nAtoms; i++){
|
623 |
moving[i] = 0;
|
624 |
moved[i] = 1;
|
625 |
}
|
626 |
|
627 |
done = 0;
|
628 |
iteration = 0;
|
629 |
while (!done && (iteration < maxIteration)){
|
630 |
done = 1;
|
631 |
|
632 |
for (i = 0; i < nConstrained; i++){
|
633 |
a = constrainedA[i];
|
634 |
b = constrainedB[i];
|
635 |
|
636 |
ax = (a * 3) + 0;
|
637 |
ay = (a * 3) + 1;
|
638 |
az = (a * 3) + 2;
|
639 |
|
640 |
bx = (b * 3) + 0;
|
641 |
by = (b * 3) + 1;
|
642 |
bz = (b * 3) + 2;
|
643 |
|
644 |
if (moved[a] || moved[b]){
|
645 |
velA = atoms[a]->getVel();
|
646 |
velB = atoms[b]->getVel();
|
647 |
|
648 |
vxab = velA[0] - velB[0];
|
649 |
vyab = velA[1] - velB[1];
|
650 |
vzab = velA[2] - velB[2];
|
651 |
|
652 |
posA = atoms[a]->getPos();
|
653 |
posB = atoms[b]->getPos();
|
654 |
|
655 |
for (j = 0; j < 3; j++)
|
656 |
rab[j] = posA[j] - posB[j];
|
657 |
|
658 |
info->wrapVector(rab);
|
659 |
|
660 |
rma = 1.0 / atoms[a]->getMass();
|
661 |
rmb = 1.0 / atoms[b]->getMass();
|
662 |
|
663 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab;
|
664 |
|
665 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]);
|
666 |
|
667 |
if (fabs(gab) > tol){
|
668 |
dx = rab[0] * gab;
|
669 |
dy = rab[1] * gab;
|
670 |
dz = rab[2] * gab;
|
671 |
|
672 |
velA[0] += rma * dx;
|
673 |
velA[1] += rma * dy;
|
674 |
velA[2] += rma * dz;
|
675 |
|
676 |
atoms[a]->setVel(velA);
|
677 |
|
678 |
velB[0] -= rmb * dx;
|
679 |
velB[1] -= rmb * dy;
|
680 |
velB[2] -= rmb * dz;
|
681 |
|
682 |
atoms[b]->setVel(velB);
|
683 |
|
684 |
moving[a] = 1;
|
685 |
moving[b] = 1;
|
686 |
done = 0;
|
687 |
}
|
688 |
}
|
689 |
}
|
690 |
|
691 |
for (i = 0; i < nAtoms; i++){
|
692 |
moved[i] = moving[i];
|
693 |
moving[i] = 0;
|
694 |
}
|
695 |
|
696 |
iteration++;
|
697 |
}
|
698 |
|
699 |
if (!done){
|
700 |
sprintf(painCave.errMsg,
|
701 |
"Constraint failure in constrainB, too many iterations: %d\n",
|
702 |
iteration);
|
703 |
painCave.isFatal = 1;
|
704 |
simError();
|
705 |
}
|
706 |
}
|
707 |
|
708 |
template<typename T> void Integrator<T>::rotationPropagation
|
709 |
( StuntDouble* sd, double ji[3] ){
|
710 |
|
711 |
double angle;
|
712 |
double A[3][3], I[3][3];
|
713 |
int i, j, k;
|
714 |
|
715 |
// use the angular velocities to propagate the rotation matrix a
|
716 |
// full time step
|
717 |
|
718 |
sd->getA(A);
|
719 |
sd->getI(I);
|
720 |
|
721 |
if (sd->isLinear()) {
|
722 |
i = sd->linearAxis();
|
723 |
j = (i+1)%3;
|
724 |
k = (i+2)%3;
|
725 |
|
726 |
angle = dt2 * ji[j] / I[j][j];
|
727 |
this->rotate( k, i, angle, ji, A );
|
728 |
|
729 |
angle = dt * ji[k] / I[k][k];
|
730 |
this->rotate( i, j, angle, ji, A);
|
731 |
|
732 |
angle = dt2 * ji[j] / I[j][j];
|
733 |
this->rotate( k, i, angle, ji, A );
|
734 |
|
735 |
} else {
|
736 |
// rotate about the x-axis
|
737 |
angle = dt2 * ji[0] / I[0][0];
|
738 |
this->rotate( 1, 2, angle, ji, A );
|
739 |
|
740 |
// rotate about the y-axis
|
741 |
angle = dt2 * ji[1] / I[1][1];
|
742 |
this->rotate( 2, 0, angle, ji, A );
|
743 |
|
744 |
// rotate about the z-axis
|
745 |
angle = dt * ji[2] / I[2][2];
|
746 |
sd->addZangle(angle);
|
747 |
this->rotate( 0, 1, angle, ji, A);
|
748 |
|
749 |
// rotate about the y-axis
|
750 |
angle = dt2 * ji[1] / I[1][1];
|
751 |
this->rotate( 2, 0, angle, ji, A );
|
752 |
|
753 |
// rotate about the x-axis
|
754 |
angle = dt2 * ji[0] / I[0][0];
|
755 |
this->rotate( 1, 2, angle, ji, A );
|
756 |
|
757 |
}
|
758 |
sd->setA( A );
|
759 |
}
|
760 |
|
761 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2,
|
762 |
double angle, double ji[3],
|
763 |
double A[3][3]){
|
764 |
int i, j, k;
|
765 |
double sinAngle;
|
766 |
double cosAngle;
|
767 |
double angleSqr;
|
768 |
double angleSqrOver4;
|
769 |
double top, bottom;
|
770 |
double rot[3][3];
|
771 |
double tempA[3][3];
|
772 |
double tempJ[3];
|
773 |
|
774 |
// initialize the tempA
|
775 |
|
776 |
for (i = 0; i < 3; i++){
|
777 |
for (j = 0; j < 3; j++){
|
778 |
tempA[j][i] = A[i][j];
|
779 |
}
|
780 |
}
|
781 |
|
782 |
// initialize the tempJ
|
783 |
|
784 |
for (i = 0; i < 3; i++)
|
785 |
tempJ[i] = ji[i];
|
786 |
|
787 |
// initalize rot as a unit matrix
|
788 |
|
789 |
rot[0][0] = 1.0;
|
790 |
rot[0][1] = 0.0;
|
791 |
rot[0][2] = 0.0;
|
792 |
|
793 |
rot[1][0] = 0.0;
|
794 |
rot[1][1] = 1.0;
|
795 |
rot[1][2] = 0.0;
|
796 |
|
797 |
rot[2][0] = 0.0;
|
798 |
rot[2][1] = 0.0;
|
799 |
rot[2][2] = 1.0;
|
800 |
|
801 |
// use a small angle aproximation for sin and cosine
|
802 |
|
803 |
angleSqr = angle * angle;
|
804 |
angleSqrOver4 = angleSqr / 4.0;
|
805 |
top = 1.0 - angleSqrOver4;
|
806 |
bottom = 1.0 + angleSqrOver4;
|
807 |
|
808 |
cosAngle = top / bottom;
|
809 |
sinAngle = angle / bottom;
|
810 |
|
811 |
rot[axes1][axes1] = cosAngle;
|
812 |
rot[axes2][axes2] = cosAngle;
|
813 |
|
814 |
rot[axes1][axes2] = sinAngle;
|
815 |
rot[axes2][axes1] = -sinAngle;
|
816 |
|
817 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[]
|
818 |
|
819 |
for (i = 0; i < 3; i++){
|
820 |
ji[i] = 0.0;
|
821 |
for (k = 0; k < 3; k++){
|
822 |
ji[i] += rot[i][k] * tempJ[k];
|
823 |
}
|
824 |
}
|
825 |
|
826 |
// rotate the Rotation matrix acording to:
|
827 |
// A[][] = A[][] * transpose(rot[][])
|
828 |
|
829 |
|
830 |
// NOte for as yet unknown reason, we are performing the
|
831 |
// calculation as:
|
832 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][])
|
833 |
|
834 |
for (i = 0; i < 3; i++){
|
835 |
for (j = 0; j < 3; j++){
|
836 |
A[j][i] = 0.0;
|
837 |
for (k = 0; k < 3; k++){
|
838 |
A[j][i] += tempA[i][k] * rot[j][k];
|
839 |
}
|
840 |
}
|
841 |
}
|
842 |
}
|
843 |
|
844 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){
|
845 |
myFF->doForces(calcPot, calcStress);
|
846 |
}
|
847 |
|
848 |
template<typename T> void Integrator<T>::thermalize(){
|
849 |
tStats->velocitize();
|
850 |
}
|
851 |
|
852 |
template<typename T> double Integrator<T>::getConservedQuantity(void){
|
853 |
return tStats->getTotalE();
|
854 |
}
|
855 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){
|
856 |
//By default, return a null string
|
857 |
//The reason we use string instead of char* is that if we use char*, we will
|
858 |
//return a pointer point to local variable which might cause problem
|
859 |
return string();
|
860 |
}
|