1 |
< |
/* |
1 |
> |
/* |
2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
3 |
|
* |
4 |
|
* The University of Notre Dame grants you ("Licensee") a |
49 |
|
|
50 |
|
#include "integrators/VelocityVerletIntegrator.hpp" |
51 |
|
#include "integrators/DLM.hpp" |
52 |
+ |
#include "utils/StringUtils.hpp" |
53 |
|
|
54 |
|
namespace oopse { |
55 |
< |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
55 |
> |
VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) { |
56 |
|
dt2 = 0.5 * dt; |
57 |
|
rotAlgo = new DLM(); |
58 |
|
rattle = new Rattle(info); |
59 |
< |
} |
60 |
< |
|
61 |
< |
VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
59 |
> |
} |
60 |
> |
|
61 |
> |
VelocityVerletIntegrator::~VelocityVerletIntegrator() { |
62 |
|
delete rotAlgo; |
63 |
|
delete rattle; |
64 |
< |
} |
65 |
< |
|
66 |
< |
void VelocityVerletIntegrator::initialize(){ |
67 |
< |
|
64 |
> |
} |
65 |
> |
|
66 |
> |
void VelocityVerletIntegrator::initialize(){ |
67 |
> |
|
68 |
|
forceMan_->init(); |
69 |
< |
|
69 |
> |
|
70 |
|
// remove center of mass drift velocity (in case we passed in a configuration |
71 |
|
// that was drifting |
72 |
|
velocitizer_->removeComDrift(); |
73 |
< |
|
73 |
> |
|
74 |
|
// initialize the forces before the first step |
75 |
|
calcForce(true, true); |
76 |
< |
|
76 |
> |
|
77 |
|
//execute constraint algorithm to make sure at the very beginning the system is constrained |
78 |
|
if (info_->getNGlobalConstraints() > 0) { |
79 |
< |
rattle->constraintA(); |
80 |
< |
calcForce(true, true); |
81 |
< |
rattle->constraintB(); |
82 |
< |
info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
79 |
> |
rattle->constraintA(); |
80 |
> |
calcForce(true, true); |
81 |
> |
rattle->constraintB(); |
82 |
> |
info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot |
83 |
|
} |
84 |
< |
|
84 |
> |
|
85 |
|
if (needVelocityScaling) { |
86 |
< |
velocitizer_->velocitize(targetScalingTemp); |
86 |
> |
velocitizer_->velocitize(targetScalingTemp); |
87 |
|
} |
88 |
|
|
89 |
|
dumpWriter = createDumpWriter(); |
90 |
+ |
|
91 |
|
statWriter = createStatWriter(); |
92 |
< |
|
93 |
< |
dumpWriter->writeDump(); |
94 |
< |
|
92 |
> |
|
93 |
> |
if (simParams->getUseSolidThermInt()) { |
94 |
> |
restWriter = createRestWriter(); |
95 |
> |
restWriter->writeZangle(); |
96 |
> |
} |
97 |
> |
|
98 |
> |
dumpWriter->writeDumpAndEor(); |
99 |
> |
|
100 |
> |
|
101 |
|
//save statistics, before writeStat, we must save statistics |
102 |
|
thermo.saveStat(); |
103 |
|
saveConservedQuantity(); |
104 |
|
statWriter->writeStat(currentSnapshot_->statData); |
105 |
< |
|
105 |
> |
|
106 |
|
currSample = sampleTime + currentSnapshot_->getTime(); |
107 |
|
currStatus = statusTime + currentSnapshot_->getTime();; |
108 |
< |
currThermal = thermalTime + + currentSnapshot_->getTime(); |
108 |
> |
currThermal = thermalTime + currentSnapshot_->getTime(); |
109 |
> |
if (needReset) { |
110 |
> |
currReset = resetTime + currentSnapshot_->getTime(); |
111 |
> |
} |
112 |
|
needPotential = false; |
113 |
|
needStress = false; |
114 |
< |
|
115 |
< |
} |
105 |
< |
|
106 |
< |
void VelocityVerletIntegrator::doIntegrate() { |
114 |
> |
|
115 |
> |
} |
116 |
|
|
117 |
< |
|
117 |
> |
void VelocityVerletIntegrator::doIntegrate() { |
118 |
> |
|
119 |
> |
|
120 |
|
initialize(); |
121 |
< |
|
121 |
> |
|
122 |
|
while (currentSnapshot_->getTime() < runTime) { |
123 |
< |
|
124 |
< |
preStep(); |
123 |
> |
|
124 |
> |
preStep(); |
125 |
> |
|
126 |
> |
integrateStep(); |
127 |
> |
|
128 |
> |
postStep(); |
129 |
> |
|
130 |
> |
} |
131 |
> |
|
132 |
> |
finalize(); |
133 |
> |
|
134 |
> |
} |
135 |
|
|
115 |
– |
integrateStep(); |
116 |
– |
|
117 |
– |
postStep(); |
136 |
|
|
137 |
+ |
void VelocityVerletIntegrator::preStep() { |
138 |
+ |
double difference = currentSnapshot_->getTime() + dt - currStatus; |
139 |
+ |
|
140 |
+ |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
141 |
+ |
needPotential = true; |
142 |
+ |
needStress = true; |
143 |
|
} |
144 |
+ |
|
145 |
+ |
} |
146 |
|
|
147 |
< |
finalize(); |
147 |
> |
void VelocityVerletIntegrator::postStep() { |
148 |
> |
|
149 |
> |
//save snapshot |
150 |
> |
info_->getSnapshotManager()->advance(); |
151 |
> |
|
152 |
> |
//increase time |
153 |
> |
currentSnapshot_->increaseTime(dt); |
154 |
> |
|
155 |
> |
if (needVelocityScaling) { |
156 |
> |
if (currentSnapshot_->getTime() >= currThermal) { |
157 |
> |
velocitizer_->velocitize(targetScalingTemp); |
158 |
> |
currThermal += thermalTime; |
159 |
> |
} |
160 |
> |
} |
161 |
> |
|
162 |
> |
if (currentSnapshot_->getTime() >= currSample) { |
163 |
> |
dumpWriter->writeDumpAndEor(); |
164 |
|
|
165 |
< |
} |
165 |
> |
if (simParams->getUseSolidThermInt()) |
166 |
> |
restWriter->writeZangle(); |
167 |
> |
|
168 |
> |
currSample += sampleTime; |
169 |
> |
} |
170 |
> |
|
171 |
> |
if (currentSnapshot_->getTime() >= currStatus) { |
172 |
> |
//save statistics, before writeStat, we must save statistics |
173 |
> |
thermo.saveStat(); |
174 |
> |
saveConservedQuantity(); |
175 |
> |
statWriter->writeStat(currentSnapshot_->statData); |
176 |
> |
|
177 |
> |
needPotential = false; |
178 |
> |
needStress = false; |
179 |
> |
currStatus += statusTime; |
180 |
> |
} |
181 |
|
|
182 |
+ |
if (needReset && currentSnapshot_->getTime() >= currReset) { |
183 |
+ |
resetIntegrator(); |
184 |
+ |
currReset += resetTime; |
185 |
+ |
} |
186 |
+ |
|
187 |
+ |
} |
188 |
|
|
126 |
– |
void VelocityVerletIntegrator::preStep() { |
127 |
– |
double difference = currentSnapshot_->getTime() + dt - currStatus; |
189 |
|
|
190 |
< |
if (difference > 0 || fabs(difference) < oopse::epsilon) { |
191 |
< |
needPotential = true; |
192 |
< |
needStress = true; |
193 |
< |
} |
194 |
< |
|
195 |
< |
} |
196 |
< |
|
197 |
< |
void VelocityVerletIntegrator::postStep() { |
198 |
< |
|
138 |
< |
//save snapshot |
139 |
< |
info_->getSnapshotManager()->advance(); |
140 |
< |
|
141 |
< |
//increase time |
142 |
< |
currentSnapshot_->increaseTime(dt); |
143 |
< |
|
144 |
< |
if (needVelocityScaling) { |
145 |
< |
if (currentSnapshot_->getTime() >= currThermal) { |
146 |
< |
velocitizer_->velocitize(targetScalingTemp); |
147 |
< |
currThermal += thermalTime; |
148 |
< |
} |
149 |
< |
} |
150 |
< |
|
151 |
< |
if (currentSnapshot_->getTime() >= currSample) { |
152 |
< |
dumpWriter->writeDump(); |
153 |
< |
currSample += sampleTime; |
154 |
< |
} |
155 |
< |
|
156 |
< |
if (currentSnapshot_->getTime() >= currStatus) { |
157 |
< |
//save statistics, before writeStat, we must save statistics |
158 |
< |
thermo.saveStat(); |
159 |
< |
saveConservedQuantity(); |
160 |
< |
statWriter->writeStat(currentSnapshot_->statData); |
161 |
< |
|
162 |
< |
needPotential = false; |
163 |
< |
needStress = false; |
164 |
< |
currStatus += statusTime; |
165 |
< |
} |
166 |
< |
|
167 |
< |
|
168 |
< |
} |
169 |
< |
|
170 |
< |
|
171 |
< |
void VelocityVerletIntegrator::finalize() { |
172 |
< |
|
173 |
< |
dumpWriter->writeDump(); |
174 |
< |
|
190 |
> |
void VelocityVerletIntegrator::finalize() { |
191 |
> |
dumpWriter->writeEor(); |
192 |
> |
|
193 |
> |
if (simParams->getUseSolidThermInt()) { |
194 |
> |
restWriter->writeZangle(); |
195 |
> |
delete restWriter; |
196 |
> |
restWriter = NULL; |
197 |
> |
} |
198 |
> |
|
199 |
|
delete dumpWriter; |
200 |
|
delete statWriter; |
201 |
< |
|
201 |
> |
|
202 |
|
dumpWriter = NULL; |
203 |
|
statWriter = NULL; |
204 |
< |
|
205 |
< |
} |
204 |
> |
|
205 |
> |
} |
206 |
|
|
207 |
< |
void VelocityVerletIntegrator::integrateStep() { |
208 |
< |
|
207 |
> |
void VelocityVerletIntegrator::integrateStep() { |
208 |
> |
|
209 |
|
moveA(); |
210 |
|
calcForce(needPotential, needStress); |
211 |
|
moveB(); |
212 |
< |
} |
212 |
> |
} |
213 |
|
|
214 |
|
|
215 |
< |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
216 |
< |
bool needStress) { |
215 |
> |
void VelocityVerletIntegrator::calcForce(bool needPotential, |
216 |
> |
bool needStress) { |
217 |
|
forceMan_->calcForces(needPotential, needStress); |
218 |
< |
} |
218 |
> |
} |
219 |
|
|
220 |
< |
DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
221 |
< |
return new DumpWriter(info_, info_->getDumpFileName()); |
222 |
< |
} |
220 |
> |
DumpWriter* VelocityVerletIntegrator::createDumpWriter() { |
221 |
> |
return new DumpWriter(info_); |
222 |
> |
} |
223 |
|
|
224 |
< |
StatWriter* VelocityVerletIntegrator::createStatWriter() { |
224 |
> |
StatWriter* VelocityVerletIntegrator::createStatWriter() { |
225 |
> |
// if solidThermInt is true, add extra information to the statfile |
226 |
> |
if (simParams->getUseSolidThermInt()){ |
227 |
> |
StatsBitSet mask; |
228 |
> |
mask.set(Stats::TIME); |
229 |
> |
mask.set(Stats::TOTAL_ENERGY); |
230 |
> |
mask.set(Stats::POTENTIAL_ENERGY); |
231 |
> |
mask.set(Stats::KINETIC_ENERGY); |
232 |
> |
mask.set(Stats::TEMPERATURE); |
233 |
> |
mask.set(Stats::PRESSURE); |
234 |
> |
mask.set(Stats::VOLUME); |
235 |
> |
mask.set(Stats::CONSERVED_QUANTITY); |
236 |
> |
mask.set(Stats::VRAW); |
237 |
> |
mask.set(Stats::VHARM); |
238 |
> |
return new StatWriter(info_->getStatFileName(), mask); |
239 |
> |
} |
240 |
> |
|
241 |
> |
if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){ |
242 |
> |
StatsBitSet mask; |
243 |
> |
mask.set(Stats::TIME); |
244 |
> |
mask.set(Stats::TOTAL_ENERGY); |
245 |
> |
mask.set(Stats::POTENTIAL_ENERGY); |
246 |
> |
mask.set(Stats::KINETIC_ENERGY); |
247 |
> |
mask.set(Stats::TEMPERATURE); |
248 |
> |
mask.set(Stats::PRESSURE); |
249 |
> |
mask.set(Stats::VOLUME); |
250 |
> |
mask.set(Stats::CONSERVED_QUANTITY); |
251 |
> |
mask.set(Stats::PRESSURE_TENSOR_X); |
252 |
> |
mask.set(Stats::PRESSURE_TENSOR_Y); |
253 |
> |
mask.set(Stats::PRESSURE_TENSOR_Z); |
254 |
> |
return new StatWriter(info_->getStatFileName(), mask); |
255 |
> |
} |
256 |
> |
|
257 |
|
return new StatWriter(info_->getStatFileName()); |
258 |
< |
} |
258 |
> |
} |
259 |
|
|
260 |
+ |
RestWriter* VelocityVerletIntegrator::createRestWriter(){ |
261 |
+ |
return new RestWriter(info_); |
262 |
+ |
} |
263 |
|
|
264 |
+ |
|
265 |
|
} //end namespace oopse |