ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/integrators/LDForceManager.cpp
(Generate patch)

Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 1293 by chuckv, Sun Sep 14 01:32:26 2008 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 "utils/ElementsTable.hpp"
49  
50 < namespace oopse {
50 > namespace OpenMD {
51  
52    LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53      simParams = info->getSimParams();
# Line 62 | 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 73 | 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 82 | 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 120 | Line 120 | namespace oopse {
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 = OOPSE_ERROR;
123 >        painCave.severity = OPENMD_ERROR;
124          painCave.isFatal = 1;
125          simError();  
126        }      
# Line 137 | 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 171 | 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 192 | 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                    }      
# Line 204 | Line 204 | namespace oopse {
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                  }
# Line 215 | Line 215 | namespace oopse {
215            if (!simParams->haveTargetTemp()) {
216              sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
217              painCave.isFatal = 1;
218 <            painCave.severity = OOPSE_ERROR;
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 = OOPSE_ERROR;
225 >            painCave.severity = OPENMD_ERROR;
226              simError();
227            }
228  
# Line 239 | 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 342 | Line 342 | namespace oopse {
342              //estimate velocity at full-step using everything but friction forces:          
343  
344              frc = integrableObject->getFrc();
345 <            Vector3d velStep = vel + (dt2_ /mass * OOPSEConstant::energyConvert) * frc;
345 >            Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
346  
347              Tb = integrableObject->lab2Body(integrableObject->getTrq());
348 <            Vector3d angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * Tb;                            
348 >            Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;                            
349  
350              Vector3d omegaLab;
351              Vector3d vcdLab;
# Line 391 | Line 391 | namespace oopse {
391                
392                // re-estimate velocities at full-step using friction forces:
393                
394 <              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForceLab);
395 <              angMomStep = angMom + (dt2_ * OOPSEConstant::energyConvert) * (Tb + frictionTorqueBody);
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                
# Line 427 | Line 427 | namespace oopse {
427              //estimate velocity at full-step using everything but friction forces:          
428  
429              frc = integrableObject->getFrc();
430 <            Vector3d velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * frc;
430 >            Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
431  
432              Vector3d frictionForce(0.0);
433              Vector3d oldFF;  // used to test for convergence
# Line 442 | Line 442 | namespace oopse {
442  
443                // re-estimate velocities at full-step using friction forces:
444                
445 <              velStep = vel + (dt2_ / mass * OOPSEConstant::energyConvert) * (frc + frictionForce);
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                

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines