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"
              "\t the 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());    
    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:	1855
Committed:	Tue Apr 2 18:31:51 2013 UTC (12 years, 1 month ago) by gezelter
File size:	9353 byte(s)
Log Message:	Fixed a bunch of bugs in CubicSpline debug sections, ForceMatrix Decomp computing costhetas for non-existent rotation matrices, Hidden accumulator counts, and SMIPD non-coupling
#	User	Rev	Content
1	gezelter	1629	/*
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1629	*/
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	gezelter	1855	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			"\t the bath.\n");
140			painCave.isFatal = 0;
141			painCave.severity = OPENMD_INFO;
142			simError();
143			doThermalCoupling_ = false;
144			}
145
146	gezelter	1629	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	gezelter	1767	StuntDouble* sd;
154	gezelter	1629	SimInfo::MoleculeIterator i;
155			Molecule::IntegrableObjectIterator j;
156
157			for (mol = info_->beginMolecule(i); mol != NULL;
158			mol = info_->nextMolecule(i)) {
159	gezelter	1767	for (sd = mol->beginIntegrableObject(j);
160			sd != NULL;
161			sd = mol->nextIntegrableObject(j)) {
162			localSites_.push_back(sd);
163	gezelter	1629	}
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	gezelter	1760
200	gezelter	1629	Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
201			PhysicalConstants::energyConvert;
202
203	gezelter	1855	Vector3d randomForce(V3Zero);
204			Vector3d dragForce(V3Zero);
205			if (doThermalCoupling_) {
206			randomForce = S * randNums[thisFacet++];
207			dragForce = -hydroTensor * facetVel;
208			}
209	gezelter	1629
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	gezelter	1668	Vector3d vertexForce = langevinForce / RealType(3.0);
216	gezelter	1629	(*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			ForceManager::postCalculation();
227			}
228
229
230			std::vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
231			RealType variance)
232			{
233
234			// zero fill the random vector before starting:
235			std::vector<Vector3d> gaussRand;
236			gaussRand.resize(nTriangles);
237			std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
238
239			#ifdef IS_MPI
240			if (worldRank == 0) {
241			#endif
242			for (int i = 0; i < nTriangles; i++) {
243			gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
244			gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
245			gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
246			}
247			#ifdef IS_MPI
248			}
249			#endif
250
251			// push these out to the other processors
252
253			#ifdef IS_MPI
254			if (worldRank == 0) {
255			MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
256			} else {
257			MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
258			}
259			#endif
260
261			return gaussRand;
262			}
263			}