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 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.
#	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	using namespace std;
55	namespace OpenMD {
56
57	LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) :
58	ForceManager(info) {
59
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	hullType_ = (iter == stringToEnumMap_.end()) ?
74	LangevinHullForceManager::hullUnknown : iter->second;
75
76	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	sprintf(painCave.errMsg,
86	"LangevinHallForceManager: Unknown Hull_Method was requested!\n");
87	painCave.isFatal = 1;
88	simError();
89	break;
90	}
91
92	doThermalCoupling_ = true;
93	doPressureCoupling_ = true;
94
95	/* Check that the simulation has target pressure and target
96	temperature set */
97	if (!simParams->haveTargetTemp()) {
98	sprintf(painCave.errMsg,
99	"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	simError();
104	doThermalCoupling_ = false;
105	} else {
106	targetTemp_ = simParams->getTargetTemp();
107	}
108
109	if (!simParams->haveTargetPressure()) {
110	sprintf(painCave.errMsg,
111	"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	simError();
116	doPressureCoupling_ = false;
117	} 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	"LangevinHallForceManager: You can't use the Langevin Hull\n"
126	"\tintegrator with periodic boundary conditions turned on!\n");
127	painCave.isFatal = 1;
128	simError();
129	}
130
131	if (!simParams->haveViscosity()) {
132	sprintf(painCave.errMsg,
133	"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	simError();
138	doThermalCoupling_ = false;
139	}else{
140	viscosity_ = simParams->getViscosity();
141	}
142
143	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	"\tthe bath.\n");
148	painCave.isFatal = 0;
149	painCave.severity = OPENMD_INFO;
150	simError();
151	doThermalCoupling_ = false;
152	}
153
154	dt_ = simParams->getDt();
155
156	if (doThermalCoupling_)
157	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
158
159	// Build a vector of integrable objects to determine if the are
160	// surface atoms
161	Molecule* mol;
162	StuntDouble* sd;
163	SimInfo::MoleculeIterator i;
164	Molecule::IntegrableObjectIterator j;
165
166	for (mol = info_->beginMolecule(i); mol != NULL;
167	mol = info_->nextMolecule(i)) {
168	for (sd = mol->beginIntegrableObject(j);
169	sd != NULL;
170	sd = mol->nextIntegrableObject(j)) {
171	localSites_.push_back(sd);
172	}
173	}
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	}
183
184	void LangevinHullForceManager::postCalculation(){
185
186	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	// Compute surface Mesh
202	surfaceMesh_->computeHull(localSites_);
203
204	// Get total area and number of surface stunt doubles
205	area = surfaceMesh_->getArea();
206	sMesh = surfaceMesh_->getMesh();
207	nTriangles = sMesh.size();
208
209	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	for (face = sMesh.begin(); face != sMesh.end(); ++face){
217	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
225	langevinForce = V3Zero;
226
227	if (doPressureCoupling_) {
228	extPressure = -unitNormal * (targetPressure_ * thisArea) /
229	PhysicalConstants::energyConvert;
230	langevinForce += extPressure;
231	}
232
233	if (doThermalCoupling_) {
234	hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
235	hydroTensor *= PhysicalConstants::viscoConvert;
236	CholeskyDecomposition(hydroTensor, S);
237	randomForce = S * randNums[thisFacet++];
238	dragForce = -hydroTensor * facetVel;
239	langevinForce += randomForce + dragForce;
240	}
241
242	// Apply triangle force to stuntdouble vertices
243	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
244	if ((*vertex) != NULL){
245	vertexForce = langevinForce / RealType(3.0);
246	(*vertex)->addFrc(vertexForce);
247	}
248	}
249	}
250
251	veloMunge->removeComDrift();
252	veloMunge->removeAngularDrift();
253
254	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
255	currSnapshot->setVolume(surfaceMesh_->getVolume());
256	currSnapshot->setHullVolume(surfaceMesh_->getVolume());
257	// update the bounding box for use by ForceMatrixDecomposition:
258	currSnapshot->setBoundingBox(surfaceMesh_->getBoundingBox());
259	ForceManager::postCalculation();
260	}
261
262	vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
263	RealType var) {
264	// zero fill the random vector before starting:
265	vector<Vector3d> gaussRand;
266	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	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	}
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	}