src/integrators/LangevinHullForceManager.cpp

/*
 * Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#include <fstream> 
#include <iostream>
#include "integrators/LangevinHullForceManager.hpp"
#include "utils/PhysicalConstants.hpp"
#include "math/ConvexHull.hpp"
#include "math/AlphaHull.hpp"
#include "math/Triangle.hpp"
#include "math/CholeskyDecomposition.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {

  LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) : ForceManager(info) {
    
    simParams = info->getSimParams();
    veloMunge = new Velocitizer(info);
    
    // Create Hull, Convex Hull for now, other options later.
    
    stringToEnumMap_["Convex"] = hullConvex;
    stringToEnumMap_["AlphaShape"] = hullAlphaShape;
    stringToEnumMap_["Unknown"] = hullUnknown;
    
    const std::string ht = simParams->getHULL_Method();
    
    
    
    std::map<std::string, HullTypeEnum>::iterator iter;
    iter = stringToEnumMap_.find(ht);
    hullType_ = (iter == stringToEnumMap_.end()) ? LangevinHullForceManager::hullUnknown : iter->second;
    if (hullType_ == hullUnknown) {
      std::cerr << "WARNING! Hull Type Unknown!\n";
    }
    
    switch(hullType_) {
    case hullConvex :
      surfaceMesh_ = new ConvexHull();
      break;
    case hullAlphaShape :
      surfaceMesh_ = new AlphaHull(simParams->getAlpha());
      break;
    case hullUnknown :
    default :
      break;
    }
    /* Check that the simulation has target pressure and target
       temperature set */
    
    if (!simParams->haveTargetTemp()) {
      sprintf(painCave.errMsg, 
              "LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
              "\twithout a targetTemp (K)!\n");      
      painCave.isFatal = 1;
      painCave.severity = OPENMD_ERROR;
      simError();
    } else {
      targetTemp_ = simParams->getTargetTemp();
    }
    
    if (!simParams->haveTargetPressure()) {
      sprintf(painCave.errMsg, 
              "LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
              "\twithout a targetPressure (atm)!\n");      
      painCave.isFatal = 1;
      simError();
    } else {
      // Convert pressure from atm -> amu/(fs^2*Ang)
      targetPressure_ = simParams->getTargetPressure() / 
        PhysicalConstants::pressureConvert;
    }
   
    if (simParams->getUsePeriodicBoundaryConditions()) {
      sprintf(painCave.errMsg, 
              "LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
              "\twith periodic boundary conditions!\n");    
      painCave.isFatal = 1;
      simError();
    } 
    
    if (!simParams->haveViscosity()) {
      sprintf(painCave.errMsg, 
              "LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
              "\twithout a viscosity!\n");
      painCave.isFatal = 1;
      painCave.severity = OPENMD_ERROR;
      simError();
    }else{
      viscosity_ = simParams->getViscosity();
    }
    
    dt_ = simParams->getDt();
  
    variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;

    // Build a vector of integrable objects to determine if the are
    // surface atoms
    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {          
      for (integrableObject = mol->beginIntegrableObject(j); 
           integrableObject != NULL;
           integrableObject = mol->nextIntegrableObject(j)) {   
        localSites_.push_back(integrableObject);
      }
    }   
  }  
   
  void LangevinHullForceManager::postCalculation(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* integrableObject;
  
    // Compute surface Mesh
    surfaceMesh_->computeHull(localSites_);

    // Get total area and number of surface stunt doubles
    RealType area = surfaceMesh_->getArea();
    std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
    int nTriangles = sMesh.size();

    // Generate all of the necessary random forces
    std::vector<Vector3d>  randNums = genTriangleForces(nTriangles, variance_);

    // Loop over the mesh faces and apply external pressure to each 
    // of the faces
    std::vector<Triangle>::iterator face;
    std::vector<StuntDouble*>::iterator vertex;
    int thisFacet = 0;
    for (face = sMesh.begin(); face != sMesh.end(); ++face){
      Triangle thisTriangle = *face;
      std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
      RealType thisArea = thisTriangle.getArea(); 
      Vector3d unitNormal = thisTriangle.getUnitNormal();
      //unitNormal.normalize();
      Vector3d centroid = thisTriangle.getCentroid();
      Vector3d facetVel = thisTriangle.getFacetVelocity();
      RealType thisMass = thisTriangle.getFacetMass();
      Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
      
      hydroTensor *= PhysicalConstants::viscoConvert;
      Mat3x3d S;
      CholeskyDecomposition(hydroTensor, S);
      
      Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
        PhysicalConstants::energyConvert;

      Vector3d randomForce = S * randNums[thisFacet++];
      Vector3d dragForce = -hydroTensor * facetVel;

      Vector3d langevinForce = (extPressure + randomForce + dragForce);
      
      // Apply triangle force to stuntdouble vertices
      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
        if ((*vertex) != NULL){
          Vector3d vertexForce = langevinForce / 3.0;
          (*vertex)->addFrc(vertexForce);          
        }  
      }
    } 
    
    veloMunge->removeComDrift();
    veloMunge->removeAngularDrift();
    
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setVolume(surfaceMesh_->getVolume());    
    ForceManager::postCalculation();   
  }
  
  
  std::vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles, 
                                                             RealType variance)
  {
    
    // zero fill the random vector before starting:
    std::vector<Vector3d> gaussRand;
    gaussRand.resize(nTriangles);
    std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif
      for (int i = 0; i < nTriangles; i++) {
        gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
        gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
        gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
      }
#ifdef IS_MPI
    }
#endif
    
    // push these out to the other processors
    
#ifdef IS_MPI
    if (worldRank == 0) {
      MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
    } else {
      MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
    }
#endif
    
    return gaussRand;
  }
}
Revision:	1629
Committed:	Wed Sep 14 21:15:17 2011 UTC (13 years, 7 months ago) by gezelter
File size:	8970 byte(s)
Log Message:	Merging changes from old branch into development branch
#	Content
1	/*
2	* Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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/LangevinHullForceManager.hpp"
44	#include "utils/PhysicalConstants.hpp"
45	#include "math/ConvexHull.hpp"
46	#include "math/AlphaHull.hpp"
47	#include "math/Triangle.hpp"
48	#include "math/CholeskyDecomposition.hpp"
49	#ifdef IS_MPI
50	#include <mpi.h>
51	#endif
52
53	namespace OpenMD {
54
55	LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) : ForceManager(info) {
56
57	simParams = info->getSimParams();
58	veloMunge = new Velocitizer(info);
59
60	// Create Hull, Convex Hull for now, other options later.
61
62	stringToEnumMap_["Convex"] = hullConvex;
63	stringToEnumMap_["AlphaShape"] = hullAlphaShape;
64	stringToEnumMap_["Unknown"] = hullUnknown;
65
66	const std::string ht = simParams->getHULL_Method();
67
68
69
70	std::map<std::string, HullTypeEnum>::iterator iter;
71	iter = stringToEnumMap_.find(ht);
72	hullType_ = (iter == stringToEnumMap_.end()) ? LangevinHullForceManager::hullUnknown : iter->second;
73	if (hullType_ == hullUnknown) {
74	std::cerr << "WARNING! Hull Type Unknown!\n";
75	}
76
77	switch(hullType_) {
78	case hullConvex :
79	surfaceMesh_ = new ConvexHull();
80	break;
81	case hullAlphaShape :
82	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
83	break;
84	case hullUnknown :
85	default :
86	break;
87	}
88	/* Check that the simulation has target pressure and target
89	temperature set */
90
91	if (!simParams->haveTargetTemp()) {
92	sprintf(painCave.errMsg,
93	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
94	"\twithout a targetTemp (K)!\n");
95	painCave.isFatal = 1;
96	painCave.severity = OPENMD_ERROR;
97	simError();
98	} else {
99	targetTemp_ = simParams->getTargetTemp();
100	}
101
102	if (!simParams->haveTargetPressure()) {
103	sprintf(painCave.errMsg,
104	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
105	"\twithout a targetPressure (atm)!\n");
106	painCave.isFatal = 1;
107	simError();
108	} else {
109	// Convert pressure from atm -> amu/(fs^2*Ang)
110	targetPressure_ = simParams->getTargetPressure() /
111	PhysicalConstants::pressureConvert;
112	}
113
114	if (simParams->getUsePeriodicBoundaryConditions()) {
115	sprintf(painCave.errMsg,
116	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
117	"\twith periodic boundary conditions!\n");
118	painCave.isFatal = 1;
119	simError();
120	}
121
122	if (!simParams->haveViscosity()) {
123	sprintf(painCave.errMsg,
124	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
125	"\twithout a viscosity!\n");
126	painCave.isFatal = 1;
127	painCave.severity = OPENMD_ERROR;
128	simError();
129	}else{
130	viscosity_ = simParams->getViscosity();
131	}
132
133	dt_ = simParams->getDt();
134
135	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
136
137	// Build a vector of integrable objects to determine if the are
138	// surface atoms
139	Molecule* mol;
140	StuntDouble* integrableObject;
141	SimInfo::MoleculeIterator i;
142	Molecule::IntegrableObjectIterator j;
143
144	for (mol = info_->beginMolecule(i); mol != NULL;
145	mol = info_->nextMolecule(i)) {
146	for (integrableObject = mol->beginIntegrableObject(j);
147	integrableObject != NULL;
148	integrableObject = mol->nextIntegrableObject(j)) {
149	localSites_.push_back(integrableObject);
150	}
151	}
152	}
153
154	void LangevinHullForceManager::postCalculation(){
155	SimInfo::MoleculeIterator i;
156	Molecule::IntegrableObjectIterator j;
157	Molecule* mol;
158	StuntDouble* integrableObject;
159
160	// Compute surface Mesh
161	surfaceMesh_->computeHull(localSites_);
162
163	// Get total area and number of surface stunt doubles
164	RealType area = surfaceMesh_->getArea();
165	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
166	int nTriangles = sMesh.size();
167
168	// Generate all of the necessary random forces
169	std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
170
171	// Loop over the mesh faces and apply external pressure to each
172	// of the faces
173	std::vector<Triangle>::iterator face;
174	std::vector<StuntDouble*>::iterator vertex;
175	int thisFacet = 0;
176	for (face = sMesh.begin(); face != sMesh.end(); ++face){
177	Triangle thisTriangle = *face;
178	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
179	RealType thisArea = thisTriangle.getArea();
180	Vector3d unitNormal = thisTriangle.getUnitNormal();
181	//unitNormal.normalize();
182	Vector3d centroid = thisTriangle.getCentroid();
183	Vector3d facetVel = thisTriangle.getFacetVelocity();
184	RealType thisMass = thisTriangle.getFacetMass();
185	Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
186
187	hydroTensor *= PhysicalConstants::viscoConvert;
188	Mat3x3d S;
189	CholeskyDecomposition(hydroTensor, S);
190
191	Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
192	PhysicalConstants::energyConvert;
193
194	Vector3d randomForce = S * randNums[thisFacet++];
195	Vector3d dragForce = -hydroTensor * facetVel;
196
197	Vector3d langevinForce = (extPressure + randomForce + dragForce);
198
199	// Apply triangle force to stuntdouble vertices
200	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
201	if ((*vertex) != NULL){
202	Vector3d vertexForce = langevinForce / 3.0;
203	(*vertex)->addFrc(vertexForce);
204	}
205	}
206	}
207
208	veloMunge->removeComDrift();
209	veloMunge->removeAngularDrift();
210
211	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212	currSnapshot->setVolume(surfaceMesh_->getVolume());
213	ForceManager::postCalculation();
214	}
215
216
217	std::vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
218	RealType variance)
219	{
220
221	// zero fill the random vector before starting:
222	std::vector<Vector3d> gaussRand;
223	gaussRand.resize(nTriangles);
224	std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
225
226	#ifdef IS_MPI
227	if (worldRank == 0) {
228	#endif
229	for (int i = 0; i < nTriangles; i++) {
230	gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
231	gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
232	gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
233	}
234	#ifdef IS_MPI
235	}
236	#endif
237
238	// push these out to the other processors
239
240	#ifdef IS_MPI
241	if (worldRank == 0) {
242	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
243	} else {
244	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
245	}
246	#endif
247
248	return gaussRand;
249	}
250	}