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Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 1185 by xsun, Fri Oct 5 19:02:09 2007 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41   #include <fstream>
42   #include <iostream>
43   #include "integrators/LDForceManager.hpp"
44   #include "math/CholeskyDecomposition.hpp"
45 < #include "utils/OOPSEConstant.hpp"
45 > #include "utils/PhysicalConstants.hpp"
46   #include "hydrodynamics/Sphere.hpp"
47   #include "hydrodynamics/Ellipsoid.hpp"
48 < #include "openbabel/mol.hpp"
48 > #include "utils/ElementsTable.hpp"
49  
50 < using namespace OpenBabel;
51 < namespace oopse {
50 > namespace OpenMD {
51  
52 <  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
52 >  LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53      simParams = info->getSimParams();
54      veloMunge = new Velocitizer(info);
55  
# Line 63 | Line 62 | namespace oopse {
62          sprintf( painCave.errMsg,
63                   "langevinBufferRadius must be specified "
64                   "when useSphericalBoundaryConditions is turned on.\n");
65 <        painCave.severity = OOPSE_ERROR;
65 >        painCave.severity = OPENMD_ERROR;
66          painCave.isFatal = 1;
67          simError();  
68        }
# Line 74 | Line 73 | namespace oopse {
73          sprintf( painCave.errMsg,
74                   "frozenBufferRadius must be specified "
75                   "when useSphericalBoundaryConditions is turned on.\n");
76 <        painCave.severity = OOPSE_ERROR;
76 >        painCave.severity = OPENMD_ERROR;
77          painCave.isFatal = 1;
78          simError();  
79        }
# Line 83 | Line 82 | namespace oopse {
82          sprintf( painCave.errMsg,
83                   "frozenBufferRadius has been set smaller than the "
84                   "langevinBufferRadius.  This is probably an error.\n");
85 <        painCave.severity = OOPSE_WARNING;
85 >        painCave.severity = OPENMD_WARNING;
86          painCave.isFatal = 0;
87          simError();  
88        }
# Line 118 | Line 117 | namespace oopse {
117          hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118        } else {              
119          sprintf( painCave.errMsg,
120 <                 "HydroPropFile must be set to a file name if Langevin\n"
121 <                 "\tDynamics is specified for rigidBodies which contain more\n"
122 <                 "\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
123 <        painCave.severity = OOPSE_ERROR;
120 >                 "HydroPropFile must be set to a file name if Langevin Dynamics\n"
121 >                 "\tis specified for rigidBodies which contain more than one atom\n"
122 >                 "\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
123 >        painCave.severity = OPENMD_ERROR;
124          painCave.isFatal = 1;
125          simError();  
126        }      
# Line 138 | Line 137 | namespace oopse {
137            } else {
138              sprintf( painCave.errMsg,
139                       "Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
140 <            painCave.severity = OOPSE_ERROR;
140 >            painCave.severity = OPENMD_ERROR;
141              painCave.isFatal = 1;
142              simError();  
143            }        
# Line 172 | Line 171 | namespace oopse {
171                  } else {
172                    sprintf( painCave.errMsg,
173                             "Can not cast GenericData to GayBerneParam\n");
174 <                  painCave.severity = OOPSE_ERROR;
174 >                  painCave.severity = OPENMD_ERROR;
175                    painCave.isFatal = 1;
176                    simError();  
177                  }
178                } else {
179                  sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180 <                painCave.severity = OOPSE_ERROR;
180 >                painCave.severity = OPENMD_ERROR;
181                  painCave.isFatal = 1;
182                  simError();    
183                }
# Line 193 | Line 192 | namespace oopse {
192                    } else {
193                      sprintf( painCave.errMsg,
194                               "Can not cast GenericData to LJParam\n");
195 <                    painCave.severity = OOPSE_ERROR;
195 >                    painCave.severity = OPENMD_ERROR;
196                      painCave.isFatal = 1;
197                      simError();          
198                    }      
199                  }
200                } else {
201 <                int obanum = etab.GetAtomicNum((atom->getType()).c_str());
202 <                if (obanum != 0) {
203 <                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
201 >                int aNum = etab.GetAtomicNum((atom->getType()).c_str());
202 >                if (aNum != 0) {
203 >                  currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
204                  } else {
205                    sprintf( painCave.errMsg,
206                             "Could not find atom type in default element.txt\n");
207 <                  painCave.severity = OOPSE_ERROR;
207 >                  painCave.severity = OPENMD_ERROR;
208                    painCave.isFatal = 1;
209                    simError();          
210                  }
211                }
212              }
213            }
214 +
215 +          if (!simParams->haveTargetTemp()) {
216 +            sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
217 +            painCave.isFatal = 1;
218 +            painCave.severity = OPENMD_ERROR;
219 +            simError();
220 +          }
221 +
222 +          if (!simParams->haveViscosity()) {
223 +            sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
224 +            painCave.isFatal = 1;
225 +            painCave.severity = OPENMD_ERROR;
226 +            simError();
227 +          }
228 +
229 +
230            HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
231            std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
232            if (iter != hydroPropMap.end())
# Line 224 | Line 239 | namespace oopse {
239          }
240        }
241      }
242 <    variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
242 >    variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
243    }  
244  
245    std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
# Line 250 | Line 265 | namespace oopse {
265      Molecule* mol;
266      StuntDouble* integrableObject;
267      RealType mass;
253 –    Vector3d vel;
268      Vector3d pos;
269      Vector3d frc;
270      Mat3x3d A;
# Line 262 | Line 276 | namespace oopse {
276      bool freezeMolecule;
277      int fdf;
278  
265 –
266 –
279      fdf = 0;
280  
281      for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
# Line 295 | Line 307 | namespace oopse {
307            fdf += integrableObject->freeze();
308          
309          if (doLangevinForces) {  
298 –          vel =integrableObject->getVel();
310            mass = integrableObject->getMass();
311            if (integrableObject->isDirectional()){
301 –            //calculate angular velocity in lab frame
302 –            Mat3x3d I = integrableObject->getI();
303 –            Vector3d angMom = integrableObject->getJ();
304 –            Vector3d omega;
305 –            
306 –            if (integrableObject->isLinear()) {
307 –              int linearAxis = integrableObject->linearAxis();
308 –              int l = (linearAxis +1 )%3;
309 –              int m = (linearAxis +2 )%3;
310 –              omega[l] = angMom[l] /I(l, l);
311 –              omega[m] = angMom[m] /I(m, m);
312 –              
313 –            } else {
314 –              omega[0] = angMom[0] /I(0, 0);
315 –              omega[1] = angMom[1] /I(1, 1);
316 –              omega[2] = angMom[2] /I(2, 2);
317 –            }
312  
313 <            //std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n";
313 >            // preliminaries for directional objects:
314  
321 –            //apply friction force and torque at center of resistance
315              A = integrableObject->getA();
316              Atrans = A.transpose();
317 <            //std::cerr << "A = " << integrableObject->getA() << "\n";
325 <            //std::cerr << "Atrans = " << A.transpose() << "\n\n";
326 <            Vector3d rcr = Atrans * hydroProps_[index]->getCOR();  
327 <            //std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n";
328 <            //std::cerr << "rcr = " << rcr << "\n\n";
329 <            Vector3d vcdLab = vel + cross(omega, rcr);
330 <        
331 <            //std::cerr << "velL = " << vel << "\n\n";
332 <            //std::cerr << "vcdL = " << vcdLab << "\n\n";
333 <            Vector3d vcdBody = A* vcdLab;
334 <            //std::cerr << "vcdB = " << vcdBody << "\n\n";
335 <            Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega);
317 >            Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();  
318  
337 –            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
338 –            //std::cerr << "ffB = " << frictionForceBody << "\n\n";
339 –            Vector3d frictionForceLab = Atrans*frictionForceBody;
340 –            //std::cerr << "ffL = " << frictionForceLab << "\n\n";
341 –            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
342 –            integrableObject->addFrc(frictionForceLab);
343 –            //std::cerr << "frc = " << integrableObject->getFrc() << "\n\n";
344 –            //std::cerr << "ome = " << omega << "\n\n";
345 –            Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega);
346 –            //std::cerr << "ftB = " << frictionTorqueBody << "\n\n";
347 –            Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
348 –            //std::cerr << "ftL = " << frictionTorqueLab << "\n\n";
349 –            //std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n";
350 –            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
351 –            integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
352 –            //std::cerr << "trq = " << integrableObject->getTrq() << "\n\n";
353 –
319              //apply random force and torque at center of resistance
320 +
321              Vector3d randomForceBody;
322              Vector3d randomTorqueBody;
323              genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
324 <            //std::cerr << "rfB = " << randomForceBody << "\n\n";
325 <            //std::cerr << "rtB = " << randomTorqueBody << "\n\n";
360 <            Vector3d randomForceLab = Atrans*randomForceBody;
361 <            Vector3d randomTorqueLab = Atrans* randomTorqueBody;
324 >            Vector3d randomForceLab = Atrans * randomForceBody;
325 >            Vector3d randomTorqueLab = Atrans * randomTorqueBody;
326              integrableObject->addFrc(randomForceLab);            
327 <            //std::cerr << "rfL = " << randomForceLab << "\n\n";
328 <            //std::cerr << "rtL = " << randomTorqueLab << "\n\n";
329 <            //std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n";
330 <            integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));            
327 >            integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));            
328 >
329 >            Mat3x3d I = integrableObject->getI();
330 >            Vector3d omegaBody;
331 >
332 >            // What remains contains velocity explicitly, but the velocity required
333 >            // is at the full step: v(t + h), while we have initially the velocity
334 >            // at the half step: v(t + h/2).  We need to iterate to converge the
335 >            // friction force and friction torque vectors.
336 >
337 >            // this is the velocity at the half-step:
338              
339 +            Vector3d vel =integrableObject->getVel();
340 +            Vector3d angMom = integrableObject->getJ();
341 +
342 +            //estimate velocity at full-step using everything but friction forces:          
343 +
344 +            frc = integrableObject->getFrc();
345 +            Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
346 +
347 +            Tb = integrableObject->lab2Body(integrableObject->getTrq());
348 +            Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;                            
349 +
350 +            Vector3d omegaLab;
351 +            Vector3d vcdLab;
352 +            Vector3d vcdBody;
353 +            Vector3d frictionForceBody;
354 +            Vector3d frictionForceLab(0.0);
355 +            Vector3d oldFFL;  // used to test for convergence
356 +            Vector3d frictionTorqueBody(0.0);
357 +            Vector3d oldFTB;  // used to test for convergence
358 +            Vector3d frictionTorqueLab;
359 +            RealType fdot;
360 +            RealType tdot;
361 +
362 +            //iteration starts here:
363 +
364 +            for (int k = 0; k < maxIterNum_; k++) {
365 +                            
366 +              if (integrableObject->isLinear()) {
367 +                int linearAxis = integrableObject->linearAxis();
368 +                int l = (linearAxis +1 )%3;
369 +                int m = (linearAxis +2 )%3;
370 +                omegaBody[l] = angMomStep[l] /I(l, l);
371 +                omegaBody[m] = angMomStep[m] /I(m, m);
372 +                
373 +              } else {
374 +                omegaBody[0] = angMomStep[0] /I(0, 0);
375 +                omegaBody[1] = angMomStep[1] /I(1, 1);
376 +                omegaBody[2] = angMomStep[2] /I(2, 2);
377 +              }
378 +              
379 +              omegaLab = Atrans * omegaBody;
380 +              
381 +              // apply friction force and torque at center of resistance
382 +              
383 +              vcdLab = velStep + cross(omegaLab, rcrLab);      
384 +              vcdBody = A * vcdLab;
385 +              frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
386 +              oldFFL = frictionForceLab;
387 +              frictionForceLab = Atrans * frictionForceBody;
388 +              oldFTB = frictionTorqueBody;
389 +              frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
390 +              frictionTorqueLab = Atrans * frictionTorqueBody;
391 +              
392 +              // re-estimate velocities at full-step using friction forces:
393 +              
394 +              velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
395 +              angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
396 +
397 +              // check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
398 +              
399 +              fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
400 +              tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
401 +              
402 +              if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
403 +                break; // iteration ends here
404 +            }
405 +
406 +            integrableObject->addFrc(frictionForceLab);
407 +            integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
408 +
409 +            
410            } else {
411              //spherical atom
412 <            Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
371 <            //std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n";
412 >
413              Vector3d randomForce;
414              Vector3d randomTorque;
415              genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
416 +            integrableObject->addFrc(randomForce);            
417 +
418 +            // What remains contains velocity explicitly, but the velocity required
419 +            // is at the full step: v(t + h), while we have initially the velocity
420 +            // at the half step: v(t + h/2).  We need to iterate to converge the
421 +            // friction force vector.
422 +
423 +            // this is the velocity at the half-step:
424              
425 <            integrableObject->addFrc(frictionForce+randomForce);            
425 >            Vector3d vel =integrableObject->getVel();
426 >
427 >            //estimate velocity at full-step using everything but friction forces:          
428 >
429 >            frc = integrableObject->getFrc();
430 >            Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
431 >
432 >            Vector3d frictionForce(0.0);
433 >            Vector3d oldFF;  // used to test for convergence
434 >            RealType fdot;
435 >
436 >            //iteration starts here:
437 >
438 >            for (int k = 0; k < maxIterNum_; k++) {
439 >
440 >              oldFF = frictionForce;                            
441 >              frictionForce = -hydroProps_[index]->getXitt() * velStep;
442 >
443 >              // re-estimate velocities at full-step using friction forces:
444 >              
445 >              velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
446 >
447 >              // check for convergence (if the vector has converged, fdot will be 1.0):
448 >              
449 >              fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
450 >              
451 >              if (fabs(1.0 - fdot) <= forceTolerance_)
452 >                break; // iteration ends here
453 >            }
454 >
455 >            integrableObject->addFrc(frictionForce);
456 >
457            }
458          }
459            
# Line 400 | Line 480 | void LDForceManager::genRandomForceAndTorque(Vector3d&
480      Z[0] = randNumGen_.randNorm(0, variance);
481      Z[1] = randNumGen_.randNorm(0, variance);
482      Z[2] = randNumGen_.randNorm(0, variance);
403 –    //Z[3] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
404 –    //Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
405 –    //Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI);
483      Z[3] = randNumGen_.randNorm(0, variance);
484      Z[4] = randNumGen_.randNorm(0, variance);
485      Z[5] = randNumGen_.randNorm(0, variance);
486      
410 –
487      generalForce = hydroProps_[index]->getS()*Z;
488      
489      force[0] = generalForce[0];

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