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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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();
    }
    
    doThermalCoupling_ = true;
    if ( fabs(viscosity_) < 1e-6 ) {
      sprintf(painCave.errMsg, 
              "LangevinHullDynamics: The bath viscosity was set lower than\n"
              "\t1e-6 poise.  OpenMD is turning off the thermal coupling to\n"
              "\tthe bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doThermalCoupling_ = false;
    }

    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* sd;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;

    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {          
      for (sd = mol->beginIntegrableObject(j); 
           sd != NULL;
           sd = mol->nextIntegrableObject(j)) { 
        localSites_.push_back(sd);
      }
    }   
  }  
   
  void LangevinHullForceManager::postCalculation(){
  
    // 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(V3Zero);
      Vector3d dragForce(V3Zero);
      if (doThermalCoupling_) {
        randomForce = S * randNums[thisFacet++];
        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 / RealType(3.0);
          (*vertex)->addFrc(vertexForce);          
        }  
      }
    } 
    
    veloMunge->removeComDrift();
    veloMunge->removeAngularDrift();
    
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setVolume(surfaceMesh_->getVolume());    
    currSnapshot->setHullVolume(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:	1856
Committed:	Tue Apr 2 21:30:34 2013 UTC (12 years ago) by gezelter
File size:	9412 byte(s)
Log Message:	Bug fixes to get new parallel decomposition methods working without periodic boundary conditions. Updated volume in stats file correctly. LangevinHull fixes for low viscosity values.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#include <fstream>
43	#include <iostream>
44	#include "integrators/LangevinHullForceManager.hpp"
45	#include "utils/PhysicalConstants.hpp"
46	#include "math/ConvexHull.hpp"
47	#include "math/AlphaHull.hpp"
48	#include "math/Triangle.hpp"
49	#include "math/CholeskyDecomposition.hpp"
50	#ifdef IS_MPI
51	#include <mpi.h>
52	#endif
53
54	namespace OpenMD {
55
56	LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) : ForceManager(info) {
57
58	simParams = info->getSimParams();
59	veloMunge = new Velocitizer(info);
60
61	// Create Hull, Convex Hull for now, other options later.
62
63	stringToEnumMap_["Convex"] = hullConvex;
64	stringToEnumMap_["AlphaShape"] = hullAlphaShape;
65	stringToEnumMap_["Unknown"] = hullUnknown;
66
67	const std::string ht = simParams->getHULL_Method();
68
69
70
71	std::map<std::string, HullTypeEnum>::iterator iter;
72	iter = stringToEnumMap_.find(ht);
73	hullType_ = (iter == stringToEnumMap_.end()) ? LangevinHullForceManager::hullUnknown : iter->second;
74	if (hullType_ == hullUnknown) {
75	std::cerr << "WARNING! Hull Type Unknown!\n";
76	}
77
78	switch(hullType_) {
79	case hullConvex :
80	surfaceMesh_ = new ConvexHull();
81	break;
82	case hullAlphaShape :
83	surfaceMesh_ = new AlphaHull(simParams->getAlpha());
84	break;
85	case hullUnknown :
86	default :
87	break;
88	}
89	/* Check that the simulation has target pressure and target
90	temperature set */
91
92	if (!simParams->haveTargetTemp()) {
93	sprintf(painCave.errMsg,
94	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
95	"\twithout a targetTemp (K)!\n");
96	painCave.isFatal = 1;
97	painCave.severity = OPENMD_ERROR;
98	simError();
99	} else {
100	targetTemp_ = simParams->getTargetTemp();
101	}
102
103	if (!simParams->haveTargetPressure()) {
104	sprintf(painCave.errMsg,
105	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
106	"\twithout a targetPressure (atm)!\n");
107	painCave.isFatal = 1;
108	simError();
109	} else {
110	// Convert pressure from atm -> amu/(fs^2*Ang)
111	targetPressure_ = simParams->getTargetPressure() /
112	PhysicalConstants::pressureConvert;
113	}
114
115	if (simParams->getUsePeriodicBoundaryConditions()) {
116	sprintf(painCave.errMsg,
117	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
118	"\twith periodic boundary conditions!\n");
119	painCave.isFatal = 1;
120	simError();
121	}
122
123	if (!simParams->haveViscosity()) {
124	sprintf(painCave.errMsg,
125	"LangevinHullDynamics error: You can't use the Langevin Hull integrator\n"
126	"\twithout a viscosity!\n");
127	painCave.isFatal = 1;
128	painCave.severity = OPENMD_ERROR;
129	simError();
130	}else{
131	viscosity_ = simParams->getViscosity();
132	}
133
134	doThermalCoupling_ = true;
135	if ( fabs(viscosity_) < 1e-6 ) {
136	sprintf(painCave.errMsg,
137	"LangevinHullDynamics: The bath viscosity was set lower than\n"
138	"\t1e-6 poise. OpenMD is turning off the thermal coupling to\n"
139	"\tthe bath.\n");
140	painCave.isFatal = 0;
141	painCave.severity = OPENMD_INFO;
142	simError();
143	doThermalCoupling_ = false;
144	}
145
146	dt_ = simParams->getDt();
147
148	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
149
150	// Build a vector of integrable objects to determine if the are
151	// surface atoms
152	Molecule* mol;
153	StuntDouble* sd;
154	SimInfo::MoleculeIterator i;
155	Molecule::IntegrableObjectIterator j;
156
157	for (mol = info_->beginMolecule(i); mol != NULL;
158	mol = info_->nextMolecule(i)) {
159	for (sd = mol->beginIntegrableObject(j);
160	sd != NULL;
161	sd = mol->nextIntegrableObject(j)) {
162	localSites_.push_back(sd);
163	}
164	}
165	}
166
167	void LangevinHullForceManager::postCalculation(){
168
169	// Compute surface Mesh
170	surfaceMesh_->computeHull(localSites_);
171
172	// Get total area and number of surface stunt doubles
173	RealType area = surfaceMesh_->getArea();
174	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
175	int nTriangles = sMesh.size();
176
177	// Generate all of the necessary random forces
178	std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
179
180	// Loop over the mesh faces and apply external pressure to each
181	// of the faces
182	std::vector<Triangle>::iterator face;
183	std::vector<StuntDouble*>::iterator vertex;
184	int thisFacet = 0;
185	for (face = sMesh.begin(); face != sMesh.end(); ++face){
186	Triangle thisTriangle = *face;
187	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
188	RealType thisArea = thisTriangle.getArea();
189	Vector3d unitNormal = thisTriangle.getUnitNormal();
190	//unitNormal.normalize();
191	Vector3d centroid = thisTriangle.getCentroid();
192	Vector3d facetVel = thisTriangle.getFacetVelocity();
193	RealType thisMass = thisTriangle.getFacetMass();
194	Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
195
196	hydroTensor *= PhysicalConstants::viscoConvert;
197	Mat3x3d S;
198	CholeskyDecomposition(hydroTensor, S);
199
200	Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
201	PhysicalConstants::energyConvert;
202
203	Vector3d randomForce(V3Zero);
204	Vector3d dragForce(V3Zero);
205	if (doThermalCoupling_) {
206	randomForce = S * randNums[thisFacet++];
207	dragForce = -hydroTensor * facetVel;
208	}
209
210	Vector3d langevinForce = (extPressure + randomForce + dragForce);
211
212	// Apply triangle force to stuntdouble vertices
213	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
214	if ((*vertex) != NULL){
215	Vector3d vertexForce = langevinForce / RealType(3.0);
216	(*vertex)->addFrc(vertexForce);
217	}
218	}
219	}
220
221	veloMunge->removeComDrift();
222	veloMunge->removeAngularDrift();
223
224	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
225	currSnapshot->setVolume(surfaceMesh_->getVolume());
226	currSnapshot->setHullVolume(surfaceMesh_->getVolume());
227	ForceManager::postCalculation();
228	}
229
230
231	std::vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
232	RealType variance)
233	{
234
235	// zero fill the random vector before starting:
236	std::vector<Vector3d> gaussRand;
237	gaussRand.resize(nTriangles);
238	std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
239
240	#ifdef IS_MPI
241	if (worldRank == 0) {
242	#endif
243	for (int i = 0; i < nTriangles; i++) {
244	gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
245	gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
246	gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
247	}
248	#ifdef IS_MPI
249	}
250	#endif
251
252	// push these out to the other processors
253
254	#ifdef IS_MPI
255	if (worldRank == 0) {
256	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
257	} else {
258	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
259	}
260	#endif
261
262	return gaussRand;
263	}
264	}