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

using namespace std;
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;

    switch(hullType_) {
    case hullConvex :
      surfaceMesh_ = new ConvexHull();
      break;
    case hullAlphaShape :
      surfaceMesh_ = new AlphaHull(simParams->getAlpha());
      break;
    case hullUnknown :
    default :
      sprintf(painCave.errMsg, 
              "LangevinHallForceManager: Unknown Hull_Method was requested!\n");
      painCave.isFatal = 1;
      simError();      
      break;
    }

    doThermalCoupling_ = true;
    doPressureCoupling_ = true;

    /* Check that the simulation has target pressure and target
       temperature set */    
    if (!simParams->haveTargetTemp()) {
      sprintf(painCave.errMsg, 
              "LangevinHullForceManager: no targetTemp (K) was set.\n"
              "\tOpenMD is turning off the thermal coupling to the bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doThermalCoupling_ = false;
    } else {
      targetTemp_ = simParams->getTargetTemp();
    }
    
    if (!simParams->haveTargetPressure()) {
      sprintf(painCave.errMsg, 
              "LangevinHullForceManager: no targetPressure (atm) was set.\n"
              "\tOpenMD is turning off the pressure coupling to the bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doPressureCoupling_ = false;
    } else {
      // Convert pressure from atm -> amu/(fs^2*Ang)
      targetPressure_ = simParams->getTargetPressure() / 
        PhysicalConstants::pressureConvert;
    }
   
    if (simParams->getUsePeriodicBoundaryConditions()) {
      sprintf(painCave.errMsg, 
              "LangevinHallForceManager: You can't use the Langevin Hull\n"
              "\tintegrator with periodic boundary conditions turned on!\n");
      painCave.isFatal = 1;
      simError();
    } 
    
    if (!simParams->haveViscosity()) {
      sprintf(painCave.errMsg, 
              "LangevinHullForceManager: no viscosity was set.\n"
              "\tOpenMD is turning off the thermal coupling to the bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doThermalCoupling_ = false;
    }else{
      viscosity_ = simParams->getViscosity();
    }
    
    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();
  
    if (doThermalCoupling_)
      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);
      }
    }
    
    // We need to make an initial guess at the bounding box in order
    // to compute long range forces in ForceMatrixDecomposition:

    // Compute surface Mesh
    surfaceMesh_->computeHull(localSites_);
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setBoundingBox(surfaceMesh_->getBoundingBox());
  }  
  
  void LangevinHullForceManager::postCalculation(){
  
    int nTriangles, thisFacet;
    RealType area, thisArea, thisMass;
    vector<Triangle> sMesh;
    Triangle thisTriangle;
    vector<Triangle>::iterator face;
    vector<StuntDouble*> vertexSDs;
    vector<StuntDouble*>::iterator vertex;

    Vector3d unitNormal, centroid, facetVel;
    Vector3d langevinForce, vertexForce;
    Vector3d extPressure, randomForce, dragForce;

    Mat3x3d hydroTensor, S;
    vector<Vector3d> randNums;

    // Compute surface Mesh
    surfaceMesh_->computeHull(localSites_);

    // Get total area and number of surface stunt doubles
    area = surfaceMesh_->getArea();
    sMesh = surfaceMesh_->getMesh();
    nTriangles = sMesh.size();

    if (doThermalCoupling_) {
      // Generate all of the necessary random forces
      randNums = genTriangleForces(nTriangles, variance_);
    }
    
    // Loop over the mesh faces
    thisFacet = 0;
    for (face = sMesh.begin(); face != sMesh.end(); ++face){
      thisTriangle = *face;
      vertexSDs = thisTriangle.getVertices();
      thisArea = thisTriangle.getArea(); 
      unitNormal = thisTriangle.getUnitNormal();
      centroid = thisTriangle.getCentroid();
      facetVel = thisTriangle.getFacetVelocity();
      thisMass = thisTriangle.getFacetMass();

      langevinForce = V3Zero;

      if (doPressureCoupling_) {
        extPressure = -unitNormal * (targetPressure_ * thisArea) /
          PhysicalConstants::energyConvert;
        langevinForce += extPressure;
      }

      if (doThermalCoupling_) {
        hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);      
        hydroTensor *= PhysicalConstants::viscoConvert;
        CholeskyDecomposition(hydroTensor, S);
        randomForce = S * randNums[thisFacet++];
        dragForce = -hydroTensor * facetVel;
        langevinForce += randomForce + dragForce;
      }
      
      // Apply triangle force to stuntdouble vertices
      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
        if ((*vertex) != NULL){
          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());
    // update the bounding box for use by ForceMatrixDecomposition:
    currSnapshot->setBoundingBox(surfaceMesh_->getBoundingBox());
    ForceManager::postCalculation();   
  }
    
  vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles, 
                                                               RealType var) {
    // zero fill the random vector before starting:
    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, var);
        gaussRand[i][1] = randNumGen_.randNorm(0.0, var);
        gaussRand[i][2] = randNumGen_.randNorm(0.0, var);
      }
#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:	1858
Committed:	Wed Apr 3 21:32:13 2013 UTC (12 years, 1 month ago) by gezelter
File size:	10364 byte(s)
Log Message:	Some bugfixes for cell-linked-list-style neighbor lists when the simulation doesn't use periodic boundary conditions. Cleaning up some of the Hull stuff while we're in there.
#	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	gezelter	1858	using namespace std;
55	gezelter	1629	namespace OpenMD {
56	gezelter	1858
57			LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) :
58			ForceManager(info) {
59	gezelter	1629
60			simParams = info->getSimParams();
61			veloMunge = new Velocitizer(info);
62
63			// Create Hull, Convex Hull for now, other options later.
64
65			stringToEnumMap_["Convex"] = hullConvex;
66			stringToEnumMap_["AlphaShape"] = hullAlphaShape;
67			stringToEnumMap_["Unknown"] = hullUnknown;
68
69			const std::string ht = simParams->getHULL_Method();
70
71			std::map<std::string, HullTypeEnum>::iterator iter;
72			iter = stringToEnumMap_.find(ht);
73	gezelter	1858	hullType_ = (iter == stringToEnumMap_.end()) ?
74			LangevinHullForceManager::hullUnknown : iter->second;
75
76	gezelter	1629	switch(hullType_) {
77			case hullConvex :
78			surfaceMesh_ = new ConvexHull();
79			break;
80			case hullAlphaShape :
81			surfaceMesh_ = new AlphaHull(simParams->getAlpha());
82			break;
83			case hullUnknown :
84			default :
85	gezelter	1858	sprintf(painCave.errMsg,
86			"LangevinHallForceManager: Unknown Hull_Method was requested!\n");
87			painCave.isFatal = 1;
88			simError();
89	gezelter	1629	break;
90			}
91	gezelter	1858
92			doThermalCoupling_ = true;
93			doPressureCoupling_ = true;
94
95	gezelter	1629	/* Check that the simulation has target pressure and target
96	gezelter	1858	temperature set */
97	gezelter	1629	if (!simParams->haveTargetTemp()) {
98			sprintf(painCave.errMsg,
99	gezelter	1858	"LangevinHullForceManager: no targetTemp (K) was set.\n"
100			"\tOpenMD is turning off the thermal coupling to the bath.\n");
101			painCave.isFatal = 0;
102			painCave.severity = OPENMD_INFO;
103	gezelter	1629	simError();
104	gezelter	1858	doThermalCoupling_ = false;
105	gezelter	1629	} else {
106			targetTemp_ = simParams->getTargetTemp();
107			}
108
109			if (!simParams->haveTargetPressure()) {
110			sprintf(painCave.errMsg,
111	gezelter	1858	"LangevinHullForceManager: no targetPressure (atm) was set.\n"
112			"\tOpenMD is turning off the pressure coupling to the bath.\n");
113			painCave.isFatal = 0;
114			painCave.severity = OPENMD_INFO;
115	gezelter	1629	simError();
116	gezelter	1858	doPressureCoupling_ = false;
117	gezelter	1629	} else {
118			// Convert pressure from atm -> amu/(fs^2*Ang)
119			targetPressure_ = simParams->getTargetPressure() /
120			PhysicalConstants::pressureConvert;
121			}
122
123			if (simParams->getUsePeriodicBoundaryConditions()) {
124			sprintf(painCave.errMsg,
125	gezelter	1858	"LangevinHallForceManager: You can't use the Langevin Hull\n"
126			"\tintegrator with periodic boundary conditions turned on!\n");
127	gezelter	1629	painCave.isFatal = 1;
128			simError();
129			}
130
131			if (!simParams->haveViscosity()) {
132			sprintf(painCave.errMsg,
133	gezelter	1858	"LangevinHullForceManager: no viscosity was set.\n"
134			"\tOpenMD is turning off the thermal coupling to the bath.\n");
135			painCave.isFatal = 0;
136			painCave.severity = OPENMD_INFO;
137	gezelter	1629	simError();
138	gezelter	1858	doThermalCoupling_ = false;
139	gezelter	1629	}else{
140			viscosity_ = simParams->getViscosity();
141			}
142
143	gezelter	1855	if ( fabs(viscosity_) < 1e-6 ) {
144			sprintf(painCave.errMsg,
145			"LangevinHullDynamics: The bath viscosity was set lower than\n"
146			"\t1e-6 poise. OpenMD is turning off the thermal coupling to\n"
147	gezelter	1856	"\tthe bath.\n");
148	gezelter	1855	painCave.isFatal = 0;
149			painCave.severity = OPENMD_INFO;
150			simError();
151			doThermalCoupling_ = false;
152			}
153
154	gezelter	1629	dt_ = simParams->getDt();
155
156	gezelter	1858	if (doThermalCoupling_)
157			variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
158	gezelter	1629
159			// Build a vector of integrable objects to determine if the are
160			// surface atoms
161			Molecule* mol;
162	gezelter	1767	StuntDouble* sd;
163	gezelter	1629	SimInfo::MoleculeIterator i;
164			Molecule::IntegrableObjectIterator j;
165	gezelter	1858
166	gezelter	1629	for (mol = info_->beginMolecule(i); mol != NULL;
167			mol = info_->nextMolecule(i)) {
168	gezelter	1767	for (sd = mol->beginIntegrableObject(j);
169			sd != NULL;
170			sd = mol->nextIntegrableObject(j)) {
171			localSites_.push_back(sd);
172	gezelter	1629	}
173	gezelter	1858	}
174
175			// We need to make an initial guess at the bounding box in order
176			// to compute long range forces in ForceMatrixDecomposition:
177
178			// Compute surface Mesh
179			surfaceMesh_->computeHull(localSites_);
180			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
181			currSnapshot->setBoundingBox(surfaceMesh_->getBoundingBox());
182	gezelter	1629	}
183	gezelter	1858
184	gezelter	1629	void LangevinHullForceManager::postCalculation(){
185
186	gezelter	1858	int nTriangles, thisFacet;
187			RealType area, thisArea, thisMass;
188			vector<Triangle> sMesh;
189			Triangle thisTriangle;
190			vector<Triangle>::iterator face;
191			vector<StuntDouble*> vertexSDs;
192			vector<StuntDouble*>::iterator vertex;
193
194			Vector3d unitNormal, centroid, facetVel;
195			Vector3d langevinForce, vertexForce;
196			Vector3d extPressure, randomForce, dragForce;
197
198			Mat3x3d hydroTensor, S;
199			vector<Vector3d> randNums;
200
201	gezelter	1629	// Compute surface Mesh
202			surfaceMesh_->computeHull(localSites_);
203
204			// Get total area and number of surface stunt doubles
205	gezelter	1858	area = surfaceMesh_->getArea();
206			sMesh = surfaceMesh_->getMesh();
207			nTriangles = sMesh.size();
208	gezelter	1629
209	gezelter	1858	if (doThermalCoupling_) {
210			// Generate all of the necessary random forces
211			randNums = genTriangleForces(nTriangles, variance_);
212			}
213
214			// Loop over the mesh faces
215			thisFacet = 0;
216	gezelter	1629	for (face = sMesh.begin(); face != sMesh.end(); ++face){
217	gezelter	1858	thisTriangle = *face;
218			vertexSDs = thisTriangle.getVertices();
219			thisArea = thisTriangle.getArea();
220			unitNormal = thisTriangle.getUnitNormal();
221			centroid = thisTriangle.getCentroid();
222			facetVel = thisTriangle.getFacetVelocity();
223			thisMass = thisTriangle.getFacetMass();
224	gezelter	1760
225	gezelter	1858	langevinForce = V3Zero;
226	gezelter	1629
227	gezelter	1858	if (doPressureCoupling_) {
228			extPressure = -unitNormal * (targetPressure_ * thisArea) /
229			PhysicalConstants::energyConvert;
230			langevinForce += extPressure;
231			}
232
233	gezelter	1855	if (doThermalCoupling_) {
234	gezelter	1858	hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
235			hydroTensor *= PhysicalConstants::viscoConvert;
236			CholeskyDecomposition(hydroTensor, S);
237	gezelter	1855	randomForce = S * randNums[thisFacet++];
238			dragForce = -hydroTensor * facetVel;
239	gezelter	1858	langevinForce += randomForce + dragForce;
240	gezelter	1855	}
241	gezelter	1629
242			// Apply triangle force to stuntdouble vertices
243			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
244			if ((*vertex) != NULL){
245	gezelter	1858	vertexForce = langevinForce / RealType(3.0);
246	gezelter	1629	(*vertex)->addFrc(vertexForce);
247			}
248			}
249			}
250
251			veloMunge->removeComDrift();
252			veloMunge->removeAngularDrift();
253
254			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
255	gezelter	1858	currSnapshot->setVolume(surfaceMesh_->getVolume());
256	gezelter	1856	currSnapshot->setHullVolume(surfaceMesh_->getVolume());
257	gezelter	1858	// update the bounding box for use by ForceMatrixDecomposition:
258			currSnapshot->setBoundingBox(surfaceMesh_->getBoundingBox());
259	gezelter	1629	ForceManager::postCalculation();
260			}
261
262	gezelter	1858	vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
263			RealType var) {
264	gezelter	1629	// zero fill the random vector before starting:
265	gezelter	1858	vector<Vector3d> gaussRand;
266	gezelter	1629	gaussRand.resize(nTriangles);
267			std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
268
269			#ifdef IS_MPI
270			if (worldRank == 0) {
271			#endif
272			for (int i = 0; i < nTriangles; i++) {
273	gezelter	1858	gaussRand[i][0] = randNumGen_.randNorm(0.0, var);
274			gaussRand[i][1] = randNumGen_.randNorm(0.0, var);
275			gaussRand[i][2] = randNumGen_.randNorm(0.0, var);
276	gezelter	1629	}
277			#ifdef IS_MPI
278			}
279			#endif
280
281			// push these out to the other processors
282
283			#ifdef IS_MPI
284			if (worldRank == 0) {
285			MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
286			} else {
287			MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
288			}
289			#endif
290
291			return gaussRand;
292			}
293			}