| 1 |
< |
#include <iostream> |
| 2 |
< |
#include <stdlib.h> |
| 3 |
< |
#include <math.h> |
| 4 |
< |
#ifdef IS_MPI |
| 5 |
< |
#include "brains/mpiSimulation.hpp" |
| 6 |
< |
#include <unistd.h> |
| 7 |
< |
#endif //is_mpi |
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< |
|
| 9 |
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#ifdef PROFILE |
| 10 |
< |
#include "profiling/mdProfile.hpp" |
| 11 |
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#endif // profile |
| 12 |
< |
|
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
| 20 |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
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* notice, this list of conditions and the following disclaimer in the |
| 23 |
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* documentation and/or other materials provided with the |
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* distribution. |
| 25 |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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> |
*/ |
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> |
|
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> |
#include "brains/Snapshot.hpp" |
| 43 |
|
#include "integrators/Integrator.hpp" |
| 44 |
|
#include "utils/simError.h" |
| 45 |
+ |
namespace oopse { |
| 46 |
+ |
Integrator::Integrator(SimInfo* info) |
| 47 |
+ |
: info_(info), forceMan_(NULL) , needPotential(false), needStress(false), |
| 48 |
+ |
needReset(false), velocitizer_(NULL), needVelocityScaling(false), |
| 49 |
+ |
rnemd_(NULL), useRNEMD(false), |
| 50 |
+ |
dumpWriter(NULL), statWriter(NULL), thermo(info), |
| 51 |
+ |
currentSnapshot_(info->getSnapshotManager()->getCurrentSnapshot()) { |
| 52 |
|
|
| 53 |
+ |
simParams = info->getSimParams(); |
| 54 |
|
|
| 55 |
< |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
| 56 |
< |
ForceFields* the_ff){ |
| 57 |
< |
info = theInfo; |
| 58 |
< |
myFF = the_ff; |
| 59 |
< |
isFirst = 1; |
| 55 |
> |
if (simParams->haveDt()) { |
| 56 |
> |
dt = simParams->getDt(); |
| 57 |
> |
} else { |
| 58 |
> |
sprintf(painCave.errMsg, |
| 59 |
> |
"Integrator Error: dt is not set\n"); |
| 60 |
> |
painCave.isFatal = 1; |
| 61 |
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simError(); |
| 62 |
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} |
| 63 |
> |
|
| 64 |
> |
if (simParams->haveRunTime()) { |
| 65 |
> |
runTime = simParams->getRunTime(); |
| 66 |
> |
} else { |
| 67 |
> |
sprintf(painCave.errMsg, |
| 68 |
> |
"Integrator Error: runTime is not set\n"); |
| 69 |
> |
painCave.isFatal = 1; |
| 70 |
> |
simError(); |
| 71 |
> |
} |
| 72 |
> |
// set the status, sample, and thermal kick times |
| 73 |
> |
if (simParams->haveSampleTime()){ |
| 74 |
> |
sampleTime = simParams->getSampleTime(); |
| 75 |
> |
statusTime = sampleTime; |
| 76 |
> |
} else{ |
| 77 |
> |
sampleTime = simParams->getRunTime(); |
| 78 |
> |
statusTime = sampleTime; |
| 79 |
> |
} |
| 80 |
|
|
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molecules = info->molecules; |
| 82 |
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nMols = info->n_mol; |
| 81 |
> |
if (simParams->haveStatusTime()){ |
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statusTime = simParams->getStatusTime(); |
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} |
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|
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// give a little love back to the SimInfo object |
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> |
if (simParams->haveThermalTime()){ |
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> |
thermalTime = simParams->getThermalTime(); |
| 87 |
> |
} else { |
| 88 |
> |
thermalTime = simParams->getRunTime(); |
| 89 |
> |
} |
| 90 |
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|
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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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|
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nAtoms = info->n_atoms; |
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integrableObjects = info->integrableObjects; |
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|
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|
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// check for constraints |
| 37 |
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|
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constrainedA = NULL; |
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constrainedB = NULL; |
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constrainedDsqr = NULL; |
| 41 |
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moving = NULL; |
| 42 |
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moved = NULL; |
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oldPos = NULL; |
| 44 |
< |
|
| 45 |
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nConstrained = 0; |
| 46 |
< |
|
| 47 |
< |
checkConstraints(); |
| 48 |
< |
|
| 49 |
< |
} |
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< |
|
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< |
template<typename T> Integrator<T>::~Integrator(){ |
| 52 |
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|
| 53 |
< |
if (nConstrained){ |
| 54 |
< |
delete[] constrainedA; |
| 55 |
< |
delete[] constrainedB; |
| 56 |
< |
delete[] constrainedDsqr; |
| 57 |
< |
delete[] moving; |
| 58 |
< |
delete[] moved; |
| 59 |
< |
delete[] oldPos; |
| 60 |
< |
} |
| 61 |
< |
|
| 62 |
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} |
| 63 |
< |
|
| 64 |
< |
|
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template<typename T> void Integrator<T>::checkConstraints(void){ |
| 66 |
< |
isConstrained = 0; |
| 67 |
< |
|
| 68 |
< |
Constraint* temp_con; |
| 69 |
< |
Constraint* dummy_plug; |
| 70 |
< |
temp_con = new Constraint[info->n_SRI]; |
| 71 |
< |
nConstrained = 0; |
| 72 |
< |
int constrained = 0; |
| 73 |
< |
|
| 74 |
< |
SRI** theArray; |
| 75 |
< |
for (int i = 0; i < nMols; i++){ |
| 76 |
< |
|
| 77 |
< |
theArray = (SRI * *) molecules[i].getMyBonds(); |
| 78 |
< |
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
| 79 |
< |
constrained = theArray[j]->is_constrained(); |
| 80 |
< |
|
| 81 |
< |
if (constrained){ |
| 82 |
< |
dummy_plug = theArray[j]->get_constraint(); |
| 83 |
< |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 84 |
< |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
| 85 |
< |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 86 |
< |
|
| 87 |
< |
nConstrained++; |
| 88 |
< |
constrained = 0; |
| 91 |
> |
if (!simParams->getUseInitalTime()) { |
| 92 |
> |
currentSnapshot_->setTime(0.0); |
| 93 |
|
} |
| 90 |
– |
} |
| 94 |
|
|
| 95 |
< |
theArray = (SRI * *) molecules[i].getMyBends(); |
| 96 |
< |
for (int j = 0; j < molecules[i].getNBends(); j++){ |
| 97 |
< |
constrained = theArray[j]->is_constrained(); |
| 95 |
< |
|
| 96 |
< |
if (constrained){ |
| 97 |
< |
dummy_plug = theArray[j]->get_constraint(); |
| 98 |
< |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 99 |
< |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
| 100 |
< |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 101 |
< |
|
| 102 |
< |
nConstrained++; |
| 103 |
< |
constrained = 0; |
| 95 |
> |
if (simParams->haveResetTime()) { |
| 96 |
> |
needReset = true; |
| 97 |
> |
resetTime = simParams->getResetTime(); |
| 98 |
|
} |
| 105 |
– |
} |
| 99 |
|
|
| 107 |
– |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
| 108 |
– |
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
| 109 |
– |
constrained = theArray[j]->is_constrained(); |
| 100 |
|
|
| 101 |
< |
if (constrained){ |
| 102 |
< |
dummy_plug = theArray[j]->get_constraint(); |
| 103 |
< |
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
| 104 |
< |
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
| 105 |
< |
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
| 106 |
< |
|
| 107 |
< |
nConstrained++; |
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< |
constrained = 0; |
| 101 |
> |
if (simParams->haveUseRNEMD()) { |
| 102 |
> |
if (simParams->getUseRNEMD()) { |
| 103 |
> |
useRNEMD = simParams->getUseRNEMD(); |
| 104 |
> |
if (simParams->haveRNEMD_swapTime()) { |
| 105 |
> |
RNEMD_swapTime = simParams->getRNEMD_swapTime(); |
| 106 |
> |
} |
| 107 |
> |
} |
| 108 |
|
} |
| 109 |
< |
} |
| 110 |
< |
} |
| 109 |
> |
|
| 110 |
> |
// Create a default ForceManager: If the subclass wants to use |
| 111 |
> |
// a different ForceManager, use setForceManager |
| 112 |
> |
forceMan_ = new ForceManager(info); |
| 113 |
> |
|
| 114 |
> |
// check for the temperature set flag (velocity scaling) |
| 115 |
> |
if (simParams->haveTempSet()) { |
| 116 |
> |
needVelocityScaling = simParams->getTempSet(); |
| 117 |
|
|
| 118 |
+ |
if (simParams->haveTargetTemp()) { |
| 119 |
+ |
targetScalingTemp = simParams->getTargetTemp(); |
| 120 |
+ |
} |
| 121 |
+ |
else { |
| 122 |
+ |
sprintf(painCave.errMsg, |
| 123 |
+ |
"Integrator Error: Target Temperature is not set\n"); |
| 124 |
+ |
painCave.isFatal = 1; |
| 125 |
+ |
simError(); |
| 126 |
|
|
| 127 |
< |
if (nConstrained > 0){ |
| 128 |
< |
isConstrained = 1; |
| 126 |
< |
|
| 127 |
< |
if (constrainedA != NULL) |
| 128 |
< |
delete[] constrainedA; |
| 129 |
< |
if (constrainedB != NULL) |
| 130 |
< |
delete[] constrainedB; |
| 131 |
< |
if (constrainedDsqr != NULL) |
| 132 |
< |
delete[] constrainedDsqr; |
| 133 |
< |
|
| 134 |
< |
constrainedA = new int[nConstrained]; |
| 135 |
< |
constrainedB = new int[nConstrained]; |
| 136 |
< |
constrainedDsqr = new double[nConstrained]; |
| 137 |
< |
|
| 138 |
< |
for (int i = 0; i < nConstrained; i++){ |
| 139 |
< |
constrainedA[i] = temp_con[i].get_a(); |
| 140 |
< |
constrainedB[i] = temp_con[i].get_b(); |
| 141 |
< |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
| 142 |
< |
} |
| 143 |
< |
|
| 144 |
< |
|
| 145 |
< |
// save oldAtoms to check for lode balancing later on. |
| 146 |
< |
|
| 147 |
< |
oldAtoms = nAtoms; |
| 148 |
< |
|
| 149 |
< |
moving = new int[nAtoms]; |
| 150 |
< |
moved = new int[nAtoms]; |
| 151 |
< |
|
| 152 |
< |
oldPos = new double[nAtoms * 3]; |
| 153 |
< |
} |
| 154 |
< |
|
| 155 |
< |
delete[] temp_con; |
| 156 |
< |
} |
| 157 |
< |
|
| 158 |
< |
|
| 159 |
< |
template<typename T> void Integrator<T>::integrate(void){ |
| 160 |
< |
|
| 161 |
< |
double runTime = info->run_time; |
| 162 |
< |
double sampleTime = info->sampleTime; |
| 163 |
< |
double statusTime = info->statusTime; |
| 164 |
< |
double thermalTime = info->thermalTime; |
| 165 |
< |
double resetTime = info->resetTime; |
| 166 |
< |
|
| 167 |
< |
double difference; |
| 168 |
< |
double currSample; |
| 169 |
< |
double currThermal; |
| 170 |
< |
double currStatus; |
| 171 |
< |
double currReset; |
| 172 |
< |
|
| 173 |
< |
int calcPot, calcStress; |
| 174 |
< |
int i; |
| 175 |
< |
int localIndex; |
| 176 |
< |
|
| 177 |
< |
#ifdef IS_MPI |
| 178 |
< |
int which_node; |
| 179 |
< |
#endif // is_mpi |
| 180 |
< |
|
| 181 |
< |
vector<StuntDouble*> particles; |
| 182 |
< |
string inAngle; |
| 183 |
< |
|
| 184 |
< |
tStats = new Thermo(info); |
| 185 |
< |
statOut = new StatWriter(info); |
| 186 |
< |
dumpOut = new DumpWriter(info); |
| 187 |
< |
|
| 188 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
| 189 |
< |
restOut = new RestraintWriter(info); |
| 190 |
< |
initRestraints = new RestraintReader(info); |
| 191 |
< |
} |
| 192 |
< |
|
| 193 |
< |
atoms = info->atoms; |
| 194 |
< |
|
| 195 |
< |
dt = info->dt; |
| 196 |
< |
dt2 = 0.5 * dt; |
| 197 |
< |
|
| 198 |
< |
readyCheck(); |
| 199 |
< |
|
| 200 |
< |
// remove center of mass drift velocity (in case we passed in a configuration |
| 201 |
< |
// that was drifting |
| 202 |
< |
tStats->removeCOMdrift(); |
| 203 |
< |
|
| 204 |
< |
// initialize the retraints if necessary |
| 205 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt) { |
| 206 |
< |
initRestraints->zeroZangle(); |
| 207 |
< |
inAngle = info->zAngleName + "_in"; |
| 208 |
< |
initRestraints->readZangle(inAngle.c_str()); |
| 209 |
< |
initRestraints->readIdealCrystal(); |
| 210 |
< |
} |
| 211 |
< |
|
| 212 |
< |
// initialize the forces before the first step |
| 213 |
< |
calcForce(1, 1); |
| 214 |
< |
|
| 215 |
< |
//execute constraint algorithm to make sure at the very beginning the system is constrained |
| 216 |
< |
if(nConstrained){ |
| 217 |
< |
preMove(); |
| 218 |
< |
constrainA(); |
| 219 |
< |
calcForce(1, 1); |
| 220 |
< |
constrainB(); |
| 221 |
< |
} |
| 222 |
< |
|
| 223 |
< |
if (info->setTemp){ |
| 224 |
< |
thermalize(); |
| 225 |
< |
} |
| 226 |
< |
|
| 227 |
< |
calcPot = 0; |
| 228 |
< |
calcStress = 0; |
| 229 |
< |
currSample = sampleTime + info->getTime(); |
| 230 |
< |
currThermal = thermalTime+ info->getTime(); |
| 231 |
< |
currStatus = statusTime + info->getTime(); |
| 232 |
< |
currReset = resetTime + info->getTime(); |
| 233 |
< |
|
| 234 |
< |
dumpOut->writeDump(info->getTime()); |
| 235 |
< |
statOut->writeStat(info->getTime()); |
| 236 |
< |
restOut->writeZangle(info->getTime()); |
| 237 |
< |
|
| 238 |
< |
#ifdef IS_MPI |
| 239 |
< |
strcpy(checkPointMsg, "The integrator is ready to go."); |
| 240 |
< |
MPIcheckPoint(); |
| 241 |
< |
#endif // is_mpi |
| 242 |
< |
|
| 243 |
< |
while (info->getTime() < runTime && !stopIntegrator()){ |
| 244 |
< |
difference = info->getTime() + dt - currStatus; |
| 245 |
< |
if (difference > 0 || fabs(difference) < 1e-4 ){ |
| 246 |
< |
calcPot = 1; |
| 247 |
< |
calcStress = 1; |
| 248 |
< |
} |
| 249 |
< |
|
| 250 |
< |
#ifdef PROFILE |
| 251 |
< |
startProfile( pro1 ); |
| 252 |
< |
#endif |
| 127 |
> |
} |
| 128 |
> |
} |
| 129 |
|
|
| 130 |
< |
integrateStep(calcPot, calcStress); |
| 131 |
< |
|
| 132 |
< |
#ifdef PROFILE |
| 133 |
< |
endProfile( pro1 ); |
| 134 |
< |
|
| 135 |
< |
startProfile( pro2 ); |
| 260 |
< |
#endif // profile |
| 261 |
< |
|
| 262 |
< |
info->incrTime(dt); |
| 263 |
< |
|
| 264 |
< |
if (info->setTemp){ |
| 265 |
< |
if (info->getTime() >= currThermal){ |
| 266 |
< |
thermalize(); |
| 267 |
< |
currThermal += thermalTime; |
| 268 |
< |
} |
| 269 |
< |
} |
| 270 |
< |
|
| 271 |
< |
if (info->getTime() >= currSample){ |
| 272 |
< |
dumpOut->writeDump(info->getTime()); |
| 273 |
< |
// write a zAng file to coincide with each dump or eor file |
| 274 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt) |
| 275 |
< |
restOut->writeZangle(info->getTime()); |
| 276 |
< |
currSample += sampleTime; |
| 277 |
< |
} |
| 278 |
< |
|
| 279 |
< |
if (info->getTime() >= currStatus){ |
| 280 |
< |
statOut->writeStat(info->getTime()); |
| 281 |
< |
calcPot = 0; |
| 282 |
< |
calcStress = 0; |
| 283 |
< |
currStatus += statusTime; |
| 284 |
< |
} |
| 285 |
< |
|
| 286 |
< |
if (info->resetIntegrator){ |
| 287 |
< |
if (info->getTime() >= currReset){ |
| 288 |
< |
this->resetIntegrator(); |
| 289 |
< |
currReset += resetTime; |
| 290 |
< |
} |
| 291 |
< |
} |
| 292 |
< |
|
| 293 |
< |
#ifdef PROFILE |
| 294 |
< |
endProfile( pro2 ); |
| 295 |
< |
#endif //profile |
| 296 |
< |
|
| 297 |
< |
#ifdef IS_MPI |
| 298 |
< |
strcpy(checkPointMsg, "successfully took a time step."); |
| 299 |
< |
MPIcheckPoint(); |
| 300 |
< |
#endif // is_mpi |
| 301 |
< |
} |
| 302 |
< |
|
| 303 |
< |
dumpOut->writeFinal(info->getTime()); |
| 304 |
< |
|
| 305 |
< |
// write the file containing the omega values of the final configuration |
| 306 |
< |
if (info->useSolidThermInt && !info->useLiquidThermInt){ |
| 307 |
< |
restOut->writeZangle(info->getTime()); |
| 308 |
< |
restOut->writeZangle(info->getTime(), inAngle.c_str()); |
| 309 |
< |
} |
| 310 |
< |
|
| 311 |
< |
delete dumpOut; |
| 312 |
< |
delete statOut; |
| 313 |
< |
} |
| 314 |
< |
|
| 315 |
< |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
| 316 |
< |
int calcStress){ |
| 317 |
< |
// Position full step, and velocity half step |
| 318 |
< |
|
| 319 |
< |
#ifdef PROFILE |
| 320 |
< |
startProfile(pro3); |
| 321 |
< |
#endif //profile |
| 322 |
< |
|
| 323 |
< |
//save old state (position, velocity etc) |
| 324 |
< |
preMove(); |
| 325 |
< |
#ifdef PROFILE |
| 326 |
< |
endProfile(pro3); |
| 327 |
< |
|
| 328 |
< |
startProfile(pro4); |
| 329 |
< |
#endif // profile |
| 330 |
< |
|
| 331 |
< |
moveA(); |
| 332 |
< |
|
| 333 |
< |
#ifdef PROFILE |
| 334 |
< |
endProfile(pro4); |
| 335 |
< |
|
| 336 |
< |
startProfile(pro5); |
| 337 |
< |
#endif//profile |
| 338 |
< |
|
| 339 |
< |
|
| 340 |
< |
#ifdef IS_MPI |
| 341 |
< |
strcpy(checkPointMsg, "Succesful moveA\n"); |
| 342 |
< |
MPIcheckPoint(); |
| 343 |
< |
#endif // is_mpi |
| 344 |
< |
|
| 345 |
< |
// calc forces |
| 346 |
< |
calcForce(calcPot, calcStress); |
| 347 |
< |
|
| 348 |
< |
#ifdef IS_MPI |
| 349 |
< |
strcpy(checkPointMsg, "Succesful doForces\n"); |
| 350 |
< |
MPIcheckPoint(); |
| 351 |
< |
#endif // is_mpi |
| 352 |
< |
|
| 353 |
< |
#ifdef PROFILE |
| 354 |
< |
endProfile( pro5 ); |
| 355 |
< |
|
| 356 |
< |
startProfile( pro6 ); |
| 357 |
< |
#endif //profile |
| 358 |
< |
|
| 359 |
< |
// finish the velocity half step |
| 360 |
< |
|
| 361 |
< |
moveB(); |
| 362 |
< |
|
| 363 |
< |
#ifdef PROFILE |
| 364 |
< |
endProfile(pro6); |
| 365 |
< |
#endif // profile |
| 366 |
< |
|
| 367 |
< |
#ifdef IS_MPI |
| 368 |
< |
strcpy(checkPointMsg, "Succesful moveB\n"); |
| 369 |
< |
MPIcheckPoint(); |
| 370 |
< |
#endif // is_mpi |
| 371 |
< |
} |
| 372 |
< |
|
| 373 |
< |
|
| 374 |
< |
template<typename T> void Integrator<T>::moveA(void){ |
| 375 |
< |
size_t i, j; |
| 376 |
< |
DirectionalAtom* dAtom; |
| 377 |
< |
double Tb[3], ji[3]; |
| 378 |
< |
double vel[3], pos[3], frc[3]; |
| 379 |
< |
double mass; |
| 380 |
< |
double omega; |
| 381 |
< |
|
| 382 |
< |
for (i = 0; i < integrableObjects.size() ; i++){ |
| 383 |
< |
integrableObjects[i]->getVel(vel); |
| 384 |
< |
integrableObjects[i]->getPos(pos); |
| 385 |
< |
integrableObjects[i]->getFrc(frc); |
| 386 |
< |
// std::cerr << "f = " << frc[0] << "\t" << frc[1] << "\t" << frc[2] << "\n"; |
| 387 |
< |
|
| 388 |
< |
mass = integrableObjects[i]->getMass(); |
| 389 |
< |
|
| 390 |
< |
for (j = 0; j < 3; j++){ |
| 391 |
< |
// velocity half step |
| 392 |
< |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 393 |
< |
// position whole step |
| 394 |
< |
pos[j] += dt * vel[j]; |
| 130 |
> |
// Create a default a velocitizer: If the subclass wants to use |
| 131 |
> |
// a different velocitizer, use setVelocitizer |
| 132 |
> |
velocitizer_ = new Velocitizer(info); |
| 133 |
> |
// Create a default a RNEMD. |
| 134 |
> |
rnemd_ = new RNEMD(info); |
| 135 |
> |
|
| 136 |
|
} |
| 137 |
|
|
| 138 |
< |
integrableObjects[i]->setVel(vel); |
| 139 |
< |
integrableObjects[i]->setPos(pos); |
| 140 |
< |
|
| 141 |
< |
|
| 401 |
< |
if (integrableObjects[i]->isDirectional()){ |
| 402 |
< |
|
| 403 |
< |
// get and convert the torque to body frame |
| 404 |
< |
|
| 405 |
< |
integrableObjects[i]->getTrq(Tb); |
| 406 |
< |
|
| 407 |
< |
// std::cerr << "t = " << Tb[0] << "\t" << Tb[1] << "\t" << Tb[2] << "\n"; |
| 408 |
< |
integrableObjects[i]->lab2Body(Tb); |
| 409 |
< |
|
| 410 |
< |
// get the angular momentum, and propagate a half step |
| 411 |
< |
|
| 412 |
< |
integrableObjects[i]->getJ(ji); |
| 413 |
< |
|
| 414 |
< |
for (j = 0; j < 3; j++) |
| 415 |
< |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 416 |
< |
|
| 417 |
< |
this->rotationPropagation( integrableObjects[i], ji ); |
| 418 |
< |
|
| 419 |
< |
integrableObjects[i]->setJ(ji); |
| 420 |
< |
} |
| 421 |
< |
} |
| 422 |
< |
|
| 423 |
< |
if(nConstrained) |
| 424 |
< |
constrainA(); |
| 425 |
< |
} |
| 426 |
< |
|
| 427 |
< |
|
| 428 |
< |
template<typename T> void Integrator<T>::moveB(void){ |
| 429 |
< |
int i, j; |
| 430 |
< |
double Tb[3], ji[3]; |
| 431 |
< |
double vel[3], frc[3]; |
| 432 |
< |
double mass; |
| 433 |
< |
|
| 434 |
< |
for (i = 0; i < integrableObjects.size(); i++){ |
| 435 |
< |
integrableObjects[i]->getVel(vel); |
| 436 |
< |
integrableObjects[i]->getFrc(frc); |
| 437 |
< |
|
| 438 |
< |
mass = integrableObjects[i]->getMass(); |
| 439 |
< |
|
| 440 |
< |
// velocity half step |
| 441 |
< |
for (j = 0; j < 3; j++) |
| 442 |
< |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
| 443 |
< |
|
| 444 |
< |
integrableObjects[i]->setVel(vel); |
| 445 |
< |
|
| 446 |
< |
if (integrableObjects[i]->isDirectional()){ |
| 447 |
< |
|
| 448 |
< |
// get and convert the torque to body frame |
| 449 |
< |
|
| 450 |
< |
integrableObjects[i]->getTrq(Tb); |
| 451 |
< |
integrableObjects[i]->lab2Body(Tb); |
| 452 |
< |
|
| 453 |
< |
// get the angular momentum, and propagate a half step |
| 454 |
< |
|
| 455 |
< |
integrableObjects[i]->getJ(ji); |
| 456 |
< |
|
| 457 |
< |
for (j = 0; j < 3; j++) |
| 458 |
< |
ji[j] += (dt2 * Tb[j]) * eConvert; |
| 459 |
< |
|
| 460 |
< |
|
| 461 |
< |
integrableObjects[i]->setJ(ji); |
| 462 |
< |
} |
| 463 |
< |
} |
| 464 |
< |
|
| 465 |
< |
if(nConstrained) |
| 466 |
< |
constrainB(); |
| 467 |
< |
} |
| 468 |
< |
|
| 469 |
< |
|
| 470 |
< |
template<typename T> void Integrator<T>::preMove(void){ |
| 471 |
< |
int i, j; |
| 472 |
< |
double pos[3]; |
| 473 |
< |
|
| 474 |
< |
if (nConstrained){ |
| 475 |
< |
for (i = 0; i < nAtoms; i++){ |
| 476 |
< |
atoms[i]->getPos(pos); |
| 477 |
< |
|
| 478 |
< |
for (j = 0; j < 3; j++){ |
| 479 |
< |
oldPos[3 * i + j] = pos[j]; |
| 480 |
< |
} |
| 481 |
< |
} |
| 482 |
< |
} |
| 483 |
< |
} |
| 484 |
< |
|
| 485 |
< |
template<typename T> void Integrator<T>::constrainA(){ |
| 486 |
< |
int i, j; |
| 487 |
< |
int done; |
| 488 |
< |
double posA[3], posB[3]; |
| 489 |
< |
double velA[3], velB[3]; |
| 490 |
< |
double pab[3]; |
| 491 |
< |
double rab[3]; |
| 492 |
< |
int a, b, ax, ay, az, bx, by, bz; |
| 493 |
< |
double rma, rmb; |
| 494 |
< |
double dx, dy, dz; |
| 495 |
< |
double rpab; |
| 496 |
< |
double rabsq, pabsq, rpabsq; |
| 497 |
< |
double diffsq; |
| 498 |
< |
double gab; |
| 499 |
< |
int iteration; |
| 500 |
< |
|
| 501 |
< |
for (i = 0; i < nAtoms; i++){ |
| 502 |
< |
moving[i] = 0; |
| 503 |
< |
moved[i] = 1; |
| 504 |
< |
} |
| 505 |
< |
|
| 506 |
< |
iteration = 0; |
| 507 |
< |
done = 0; |
| 508 |
< |
while (!done && (iteration < maxIteration)){ |
| 509 |
< |
done = 1; |
| 510 |
< |
for (i = 0; i < nConstrained; i++){ |
| 511 |
< |
a = constrainedA[i]; |
| 512 |
< |
b = constrainedB[i]; |
| 513 |
< |
|
| 514 |
< |
ax = (a * 3) + 0; |
| 515 |
< |
ay = (a * 3) + 1; |
| 516 |
< |
az = (a * 3) + 2; |
| 517 |
< |
|
| 518 |
< |
bx = (b * 3) + 0; |
| 519 |
< |
by = (b * 3) + 1; |
| 520 |
< |
bz = (b * 3) + 2; |
| 521 |
< |
|
| 522 |
< |
if (moved[a] || moved[b]){ |
| 523 |
< |
atoms[a]->getPos(posA); |
| 524 |
< |
atoms[b]->getPos(posB); |
| 525 |
< |
|
| 526 |
< |
for (j = 0; j < 3; j++) |
| 527 |
< |
pab[j] = posA[j] - posB[j]; |
| 528 |
< |
|
| 529 |
< |
//periodic boundary condition |
| 530 |
< |
|
| 531 |
< |
info->wrapVector(pab); |
| 532 |
< |
|
| 533 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 534 |
< |
|
| 535 |
< |
rabsq = constrainedDsqr[i]; |
| 536 |
< |
diffsq = rabsq - pabsq; |
| 537 |
< |
|
| 538 |
< |
// the original rattle code from alan tidesley |
| 539 |
< |
if (fabs(diffsq) > (tol * rabsq * 2)){ |
| 540 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 541 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
| 542 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
| 543 |
< |
|
| 544 |
< |
info->wrapVector(rab); |
| 545 |
< |
|
| 546 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 547 |
< |
|
| 548 |
< |
rpabsq = rpab * rpab; |
| 549 |
< |
|
| 550 |
< |
|
| 551 |
< |
if (rpabsq < (rabsq * -diffsq)){ |
| 552 |
< |
#ifdef IS_MPI |
| 553 |
< |
a = atoms[a]->getGlobalIndex(); |
| 554 |
< |
b = atoms[b]->getGlobalIndex(); |
| 555 |
< |
#endif //is_mpi |
| 556 |
< |
sprintf(painCave.errMsg, |
| 557 |
< |
"Constraint failure in constrainA at atom %d and %d.\n", a, |
| 558 |
< |
b); |
| 559 |
< |
painCave.isFatal = 1; |
| 560 |
< |
simError(); |
| 561 |
< |
} |
| 562 |
< |
|
| 563 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 564 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 565 |
< |
|
| 566 |
< |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 567 |
< |
|
| 568 |
< |
dx = rab[0] * gab; |
| 569 |
< |
dy = rab[1] * gab; |
| 570 |
< |
dz = rab[2] * gab; |
| 571 |
< |
|
| 572 |
< |
posA[0] += rma * dx; |
| 573 |
< |
posA[1] += rma * dy; |
| 574 |
< |
posA[2] += rma * dz; |
| 575 |
< |
|
| 576 |
< |
atoms[a]->setPos(posA); |
| 577 |
< |
|
| 578 |
< |
posB[0] -= rmb * dx; |
| 579 |
< |
posB[1] -= rmb * dy; |
| 580 |
< |
posB[2] -= rmb * dz; |
| 581 |
< |
|
| 582 |
< |
atoms[b]->setPos(posB); |
| 583 |
< |
|
| 584 |
< |
dx = dx / dt; |
| 585 |
< |
dy = dy / dt; |
| 586 |
< |
dz = dz / dt; |
| 587 |
< |
|
| 588 |
< |
atoms[a]->getVel(velA); |
| 589 |
< |
|
| 590 |
< |
velA[0] += rma * dx; |
| 591 |
< |
velA[1] += rma * dy; |
| 592 |
< |
velA[2] += rma * dz; |
| 593 |
< |
|
| 594 |
< |
atoms[a]->setVel(velA); |
| 595 |
< |
|
| 596 |
< |
atoms[b]->getVel(velB); |
| 597 |
< |
|
| 598 |
< |
velB[0] -= rmb * dx; |
| 599 |
< |
velB[1] -= rmb * dy; |
| 600 |
< |
velB[2] -= rmb * dz; |
| 601 |
< |
|
| 602 |
< |
atoms[b]->setVel(velB); |
| 603 |
< |
|
| 604 |
< |
moving[a] = 1; |
| 605 |
< |
moving[b] = 1; |
| 606 |
< |
done = 0; |
| 607 |
< |
} |
| 608 |
< |
} |
| 609 |
< |
} |
| 610 |
< |
|
| 611 |
< |
for (i = 0; i < nAtoms; i++){ |
| 612 |
< |
moved[i] = moving[i]; |
| 613 |
< |
moving[i] = 0; |
| 614 |
< |
} |
| 615 |
< |
|
| 616 |
< |
iteration++; |
| 617 |
< |
} |
| 618 |
< |
|
| 619 |
< |
if (!done){ |
| 620 |
< |
sprintf(painCave.errMsg, |
| 621 |
< |
"Constraint failure in constrainA, too many iterations: %d\n", |
| 622 |
< |
iteration); |
| 623 |
< |
painCave.isFatal = 1; |
| 624 |
< |
simError(); |
| 625 |
< |
} |
| 626 |
< |
|
| 627 |
< |
} |
| 628 |
< |
|
| 629 |
< |
template<typename T> void Integrator<T>::constrainB(void){ |
| 630 |
< |
int i, j; |
| 631 |
< |
int done; |
| 632 |
< |
double posA[3], posB[3]; |
| 633 |
< |
double velA[3], velB[3]; |
| 634 |
< |
double vxab, vyab, vzab; |
| 635 |
< |
double rab[3]; |
| 636 |
< |
int a, b, ax, ay, az, bx, by, bz; |
| 637 |
< |
double rma, rmb; |
| 638 |
< |
double dx, dy, dz; |
| 639 |
< |
double rvab; |
| 640 |
< |
double gab; |
| 641 |
< |
int iteration; |
| 642 |
< |
|
| 643 |
< |
for (i = 0; i < nAtoms; i++){ |
| 644 |
< |
moving[i] = 0; |
| 645 |
< |
moved[i] = 1; |
| 646 |
< |
} |
| 647 |
< |
|
| 648 |
< |
done = 0; |
| 649 |
< |
iteration = 0; |
| 650 |
< |
while (!done && (iteration < maxIteration)){ |
| 651 |
< |
done = 1; |
| 652 |
< |
|
| 653 |
< |
for (i = 0; i < nConstrained; i++){ |
| 654 |
< |
a = constrainedA[i]; |
| 655 |
< |
b = constrainedB[i]; |
| 656 |
< |
|
| 657 |
< |
ax = (a * 3) + 0; |
| 658 |
< |
ay = (a * 3) + 1; |
| 659 |
< |
az = (a * 3) + 2; |
| 660 |
< |
|
| 661 |
< |
bx = (b * 3) + 0; |
| 662 |
< |
by = (b * 3) + 1; |
| 663 |
< |
bz = (b * 3) + 2; |
| 664 |
< |
|
| 665 |
< |
if (moved[a] || moved[b]){ |
| 666 |
< |
atoms[a]->getVel(velA); |
| 667 |
< |
atoms[b]->getVel(velB); |
| 668 |
< |
|
| 669 |
< |
vxab = velA[0] - velB[0]; |
| 670 |
< |
vyab = velA[1] - velB[1]; |
| 671 |
< |
vzab = velA[2] - velB[2]; |
| 672 |
< |
|
| 673 |
< |
atoms[a]->getPos(posA); |
| 674 |
< |
atoms[b]->getPos(posB); |
| 675 |
< |
|
| 676 |
< |
for (j = 0; j < 3; j++) |
| 677 |
< |
rab[j] = posA[j] - posB[j]; |
| 678 |
< |
|
| 679 |
< |
info->wrapVector(rab); |
| 680 |
< |
|
| 681 |
< |
rma = 1.0 / atoms[a]->getMass(); |
| 682 |
< |
rmb = 1.0 / atoms[b]->getMass(); |
| 683 |
< |
|
| 684 |
< |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
| 685 |
< |
|
| 686 |
< |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
| 687 |
< |
|
| 688 |
< |
if (fabs(gab) > tol){ |
| 689 |
< |
dx = rab[0] * gab; |
| 690 |
< |
dy = rab[1] * gab; |
| 691 |
< |
dz = rab[2] * gab; |
| 692 |
< |
|
| 693 |
< |
velA[0] += rma * dx; |
| 694 |
< |
velA[1] += rma * dy; |
| 695 |
< |
velA[2] += rma * dz; |
| 696 |
< |
|
| 697 |
< |
atoms[a]->setVel(velA); |
| 698 |
< |
|
| 699 |
< |
velB[0] -= rmb * dx; |
| 700 |
< |
velB[1] -= rmb * dy; |
| 701 |
< |
velB[2] -= rmb * dz; |
| 702 |
< |
|
| 703 |
< |
atoms[b]->setVel(velB); |
| 704 |
< |
|
| 705 |
< |
moving[a] = 1; |
| 706 |
< |
moving[b] = 1; |
| 707 |
< |
done = 0; |
| 708 |
< |
} |
| 709 |
< |
} |
| 710 |
< |
} |
| 711 |
< |
|
| 712 |
< |
for (i = 0; i < nAtoms; i++){ |
| 713 |
< |
moved[i] = moving[i]; |
| 714 |
< |
moving[i] = 0; |
| 715 |
< |
} |
| 716 |
< |
|
| 717 |
< |
iteration++; |
| 718 |
< |
} |
| 719 |
< |
|
| 720 |
< |
if (!done){ |
| 721 |
< |
sprintf(painCave.errMsg, |
| 722 |
< |
"Constraint failure in constrainB, too many iterations: %d\n", |
| 723 |
< |
iteration); |
| 724 |
< |
painCave.isFatal = 1; |
| 725 |
< |
simError(); |
| 726 |
< |
} |
| 727 |
< |
} |
| 728 |
< |
|
| 729 |
< |
template<typename T> void Integrator<T>::rotationPropagation |
| 730 |
< |
( StuntDouble* sd, double ji[3] ){ |
| 731 |
< |
|
| 732 |
< |
double angle; |
| 733 |
< |
double A[3][3], I[3][3]; |
| 734 |
< |
int i, j, k; |
| 735 |
< |
|
| 736 |
< |
// use the angular velocities to propagate the rotation matrix a |
| 737 |
< |
// full time step |
| 738 |
< |
|
| 739 |
< |
sd->getA(A); |
| 740 |
< |
sd->getI(I); |
| 741 |
< |
|
| 742 |
< |
if (sd->isLinear()) { |
| 743 |
< |
|
| 744 |
< |
i = sd->linearAxis(); |
| 745 |
< |
j = (i+1)%3; |
| 746 |
< |
k = (i+2)%3; |
| 747 |
< |
|
| 748 |
< |
angle = dt2 * ji[j] / I[j][j]; |
| 749 |
< |
this->rotate( k, i, angle, ji, A ); |
| 750 |
< |
|
| 751 |
< |
angle = dt * ji[k] / I[k][k]; |
| 752 |
< |
this->rotate( i, j, angle, ji, A); |
| 753 |
< |
|
| 754 |
< |
angle = dt2 * ji[j] / I[j][j]; |
| 755 |
< |
this->rotate( k, i, angle, ji, A ); |
| 756 |
< |
|
| 757 |
< |
} else { |
| 758 |
< |
// rotate about the x-axis |
| 759 |
< |
angle = dt2 * ji[0] / I[0][0]; |
| 760 |
< |
this->rotate( 1, 2, angle, ji, A ); |
| 138 |
> |
Integrator::~Integrator(){ |
| 139 |
> |
delete forceMan_; |
| 140 |
> |
delete velocitizer_; |
| 141 |
> |
delete rnemd_; |
| 142 |
|
|
| 143 |
< |
// rotate about the y-axis |
| 144 |
< |
angle = dt2 * ji[1] / I[1][1]; |
| 764 |
< |
this->rotate( 2, 0, angle, ji, A ); |
| 765 |
< |
|
| 766 |
< |
// rotate about the z-axis |
| 767 |
< |
angle = dt * ji[2] / I[2][2]; |
| 768 |
< |
sd->addZangle(angle); |
| 769 |
< |
this->rotate( 0, 1, angle, ji, A); |
| 770 |
< |
|
| 771 |
< |
// rotate about the y-axis |
| 772 |
< |
angle = dt2 * ji[1] / I[1][1]; |
| 773 |
< |
this->rotate( 2, 0, angle, ji, A ); |
| 774 |
< |
|
| 775 |
< |
// rotate about the x-axis |
| 776 |
< |
angle = dt2 * ji[0] / I[0][0]; |
| 777 |
< |
this->rotate( 1, 2, angle, ji, A ); |
| 778 |
< |
|
| 143 |
> |
delete dumpWriter; |
| 144 |
> |
delete statWriter; |
| 145 |
|
} |
| 780 |
– |
sd->setA( A ); |
| 781 |
– |
} |
| 146 |
|
|
| 783 |
– |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
| 784 |
– |
double angle, double ji[3], |
| 785 |
– |
double A[3][3]){ |
| 786 |
– |
int i, j, k; |
| 787 |
– |
double sinAngle; |
| 788 |
– |
double cosAngle; |
| 789 |
– |
double angleSqr; |
| 790 |
– |
double angleSqrOver4; |
| 791 |
– |
double top, bottom; |
| 792 |
– |
double rot[3][3]; |
| 793 |
– |
double tempA[3][3]; |
| 794 |
– |
double tempJ[3]; |
| 147 |
|
|
| 796 |
– |
// initialize the tempA |
| 797 |
– |
|
| 798 |
– |
for (i = 0; i < 3; i++){ |
| 799 |
– |
for (j = 0; j < 3; j++){ |
| 800 |
– |
tempA[j][i] = A[i][j]; |
| 801 |
– |
} |
| 802 |
– |
} |
| 803 |
– |
|
| 804 |
– |
// initialize the tempJ |
| 805 |
– |
|
| 806 |
– |
for (i = 0; i < 3; i++) |
| 807 |
– |
tempJ[i] = ji[i]; |
| 808 |
– |
|
| 809 |
– |
// initalize rot as a unit matrix |
| 810 |
– |
|
| 811 |
– |
rot[0][0] = 1.0; |
| 812 |
– |
rot[0][1] = 0.0; |
| 813 |
– |
rot[0][2] = 0.0; |
| 814 |
– |
|
| 815 |
– |
rot[1][0] = 0.0; |
| 816 |
– |
rot[1][1] = 1.0; |
| 817 |
– |
rot[1][2] = 0.0; |
| 818 |
– |
|
| 819 |
– |
rot[2][0] = 0.0; |
| 820 |
– |
rot[2][1] = 0.0; |
| 821 |
– |
rot[2][2] = 1.0; |
| 822 |
– |
|
| 823 |
– |
// use a small angle aproximation for sin and cosine |
| 824 |
– |
|
| 825 |
– |
angleSqr = angle * angle; |
| 826 |
– |
angleSqrOver4 = angleSqr / 4.0; |
| 827 |
– |
top = 1.0 - angleSqrOver4; |
| 828 |
– |
bottom = 1.0 + angleSqrOver4; |
| 829 |
– |
|
| 830 |
– |
cosAngle = top / bottom; |
| 831 |
– |
sinAngle = angle / bottom; |
| 832 |
– |
|
| 833 |
– |
rot[axes1][axes1] = cosAngle; |
| 834 |
– |
rot[axes2][axes2] = cosAngle; |
| 835 |
– |
|
| 836 |
– |
rot[axes1][axes2] = sinAngle; |
| 837 |
– |
rot[axes2][axes1] = -sinAngle; |
| 838 |
– |
|
| 839 |
– |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
| 840 |
– |
|
| 841 |
– |
for (i = 0; i < 3; i++){ |
| 842 |
– |
ji[i] = 0.0; |
| 843 |
– |
for (k = 0; k < 3; k++){ |
| 844 |
– |
ji[i] += rot[i][k] * tempJ[k]; |
| 845 |
– |
} |
| 846 |
– |
} |
| 847 |
– |
|
| 848 |
– |
// rotate the Rotation matrix acording to: |
| 849 |
– |
// A[][] = A[][] * transpose(rot[][]) |
| 850 |
– |
|
| 851 |
– |
|
| 852 |
– |
// NOte for as yet unknown reason, we are performing the |
| 853 |
– |
// calculation as: |
| 854 |
– |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
| 855 |
– |
|
| 856 |
– |
for (i = 0; i < 3; i++){ |
| 857 |
– |
for (j = 0; j < 3; j++){ |
| 858 |
– |
A[j][i] = 0.0; |
| 859 |
– |
for (k = 0; k < 3; k++){ |
| 860 |
– |
A[j][i] += tempA[i][k] * rot[j][k]; |
| 861 |
– |
} |
| 862 |
– |
} |
| 863 |
– |
} |
| 148 |
|
} |
| 149 |
|
|
| 866 |
– |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
| 867 |
– |
myFF->doForces(calcPot, calcStress); |
| 868 |
– |
} |
| 869 |
– |
|
| 870 |
– |
template<typename T> void Integrator<T>::thermalize(){ |
| 871 |
– |
tStats->velocitize(); |
| 872 |
– |
} |
| 873 |
– |
|
| 874 |
– |
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
| 875 |
– |
return tStats->getTotalE(); |
| 876 |
– |
} |
| 877 |
– |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
| 878 |
– |
//By default, return a null string |
| 879 |
– |
//The reason we use string instead of char* is that if we use char*, we will |
| 880 |
– |
//return a pointer point to local variable which might cause problem |
| 881 |
– |
return string(); |
| 882 |
– |
} |
