src/integrators/SMIPDForceManager.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/SMIPDForceManager.hpp"
#include "utils/PhysicalConstants.hpp"
#include "math/ConvexHull.hpp"
#include "math/AlphaHull.hpp"
#include "math/Triangle.hpp"
#include "math/CholeskyDecomposition.hpp"

namespace OpenMD {

  SMIPDForceManager::SMIPDForceManager(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()) ? SMIPDForceManager::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, 
              "SMIPDynamics error: You can't use the SMIPD 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, 
              "SMIPDynamics error: You can't use the SMIPD 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, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "\twith periodic boundary conditions!\n");    
      painCave.isFatal = 1;
      simError();
    } 
    
    if (!simParams->haveViscosity()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD 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 SMIPDForceManager::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> SMIPDForceManager::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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	8826 byte(s)
Log Message:	Creating busticated version of OpenMD
#	User	Rev	Content
1	chuckv	1293	/*
2	chuckv	1402	* Copyright (c) 2008, 2009, 2010 The University of Notre Dame. All Rights Reserved.
3	chuckv	1293	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chuckv	1293	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chuckv	1293	* 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	gezelter	1390	*
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	chuckv	1293	*/
41			#include <fstream>
42			#include <iostream>
43			#include "integrators/SMIPDForceManager.hpp"
44	gezelter	1390	#include "utils/PhysicalConstants.hpp"
45	chuckv	1293	#include "math/ConvexHull.hpp"
46	chuckv	1402	#include "math/AlphaHull.hpp"
47	chuckv	1293	#include "math/Triangle.hpp"
48	gezelter	1398	#include "math/CholeskyDecomposition.hpp"
49	chuckv	1293
50	gezelter	1390	namespace OpenMD {
51	gezelter	1324
52	gezelter	1344	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
53	chuckv	1402
54	chuckv	1293	simParams = info->getSimParams();
55	chuckv	1325	veloMunge = new Velocitizer(info);
56	chuckv	1293
57			// Create Hull, Convex Hull for now, other options later.
58	gezelter	1324
59	chuckv	1404	stringToEnumMap_["Convex"] = hullConvex;
60	chuckv	1402	stringToEnumMap_["AlphaShape"] = hullAlphaShape;
61			stringToEnumMap_["Unknown"] = hullUnknown;
62	chuckv	1293
63	chuckv	1402	const std::string ht = simParams->getHULL_Method();
64
65
66
67			std::map<std::string, HullTypeEnum>::iterator iter;
68			iter = stringToEnumMap_.find(ht);
69			hullType_ = (iter == stringToEnumMap_.end()) ? SMIPDForceManager::hullUnknown : iter->second;
70			if (hullType_ == hullUnknown) {
71			std::cerr << "WARNING! Hull Type Unknown!\n";
72			}
73
74			switch(hullType_) {
75			case hullConvex :
76			surfaceMesh_ = new ConvexHull();
77			break;
78			case hullAlphaShape :
79			surfaceMesh_ = new AlphaHull(simParams->getAlpha());
80			break;
81			case hullUnknown :
82			default :
83			break;
84			}
85	chuckv	1293	/* Check that the simulation has target pressure and target
86	chuckv	1325	temperature set */
87	chuckv	1323
88	chuckv	1293	if (!simParams->haveTargetTemp()) {
89	gezelter	1324	sprintf(painCave.errMsg,
90			"SMIPDynamics error: You can't use the SMIPD integrator\n"
91	gezelter	1357	"\twithout a targetTemp (K)!\n");
92	chuckv	1293	painCave.isFatal = 1;
93	gezelter	1390	painCave.severity = OPENMD_ERROR;
94	chuckv	1293	simError();
95			} else {
96			targetTemp_ = simParams->getTargetTemp();
97			}
98	chuckv	1323
99	chuckv	1293	if (!simParams->haveTargetPressure()) {
100	gezelter	1324	sprintf(painCave.errMsg,
101			"SMIPDynamics error: You can't use the SMIPD integrator\n"
102	gezelter	1357	"\twithout a targetPressure (atm)!\n");
103	chuckv	1293	painCave.isFatal = 1;
104			simError();
105			} else {
106	gezelter	1324	// Convert pressure from atm -> amu/(fs^2*Ang)
107			targetPressure_ = simParams->getTargetPressure() /
108	gezelter	1390	PhysicalConstants::pressureConvert;
109	chuckv	1293	}
110
111			if (simParams->getUsePeriodicBoundaryConditions()) {
112	gezelter	1324	sprintf(painCave.errMsg,
113			"SMIPDynamics error: You can't use the SMIPD integrator\n"
114	gezelter	1357	"\twith periodic boundary conditions!\n");
115	chuckv	1293	painCave.isFatal = 1;
116			simError();
117			}
118	gezelter	1324
119	gezelter	1398	if (!simParams->haveViscosity()) {
120	gezelter	1324	sprintf(painCave.errMsg,
121			"SMIPDynamics error: You can't use the SMIPD integrator\n"
122	gezelter	1398	"\twithout a viscosity!\n");
123	chuckv	1316	painCave.isFatal = 1;
124	gezelter	1390	painCave.severity = OPENMD_ERROR;
125	chuckv	1316	simError();
126	chuckv	1323	}else{
127	gezelter	1398	viscosity_ = simParams->getViscosity();
128	chuckv	1316	}
129	gezelter	1324
130	chuckv	1323	dt_ = simParams->getDt();
131	gezelter	1324
132	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
133	chuckv	1307
134	gezelter	1344	// Build a vector of integrable objects to determine if the are
135			// surface atoms
136	chuckv	1293	Molecule* mol;
137			StuntDouble* integrableObject;
138			SimInfo::MoleculeIterator i;
139	gezelter	1344	Molecule::IntegrableObjectIterator j;
140	chuckv	1323
141	gezelter	1324	for (mol = info_->beginMolecule(i); mol != NULL;
142			mol = info_->nextMolecule(i)) {
143			for (integrableObject = mol->beginIntegrableObject(j);
144			integrableObject != NULL;
145	chuckv	1293	integrableObject = mol->nextIntegrableObject(j)) {
146			localSites_.push_back(integrableObject);
147			}
148	gezelter	1324	}
149	chuckv	1293	}
150	chuckv	1325
151	gezelter	1464	void SMIPDForceManager::postCalculation(){
152	chuckv	1293	SimInfo::MoleculeIterator i;
153			Molecule::IntegrableObjectIterator j;
154			Molecule* mol;
155			StuntDouble* integrableObject;
156	chuckv	1325
157	gezelter	1324	// Compute surface Mesh
158	chuckv	1293	surfaceMesh_->computeHull(localSites_);
159	chuckv	1325
160	gezelter	1324	// Get total area and number of surface stunt doubles
161			RealType area = surfaceMesh_->getArea();
162	chuckv	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
163	chuckv	1307	int nTriangles = sMesh.size();
164
165	gezelter	1344	// Generate all of the necessary random forces
166	gezelter	1398	std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
167	gezelter	1344
168	chuckv	1325	// Loop over the mesh faces and apply external pressure to each
169			// of the faces
170	chuckv	1308	std::vector<Triangle>::iterator face;
171	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
172	gezelter	1344	int thisFacet = 0;
173	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
174	chuckv	1308	Triangle thisTriangle = *face;
175			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
176	chuckv	1316	RealType thisArea = thisTriangle.getArea();
177	chuckv	1404	Vector3d unitNormal = thisTriangle.getUnitNormal();
178			//unitNormal.normalize();
179	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
180	gezelter	1344	Vector3d facetVel = thisTriangle.getFacetVelocity();
181	gezelter	1355	RealType thisMass = thisTriangle.getFacetMass();
182	gezelter	1398	Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
183
184			hydroTensor *= PhysicalConstants::viscoConvert;
185			Mat3x3d S;
186			CholeskyDecomposition(hydroTensor, S);
187
188			Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
189			PhysicalConstants::energyConvert;
190	gezelter	1344
191	gezelter	1398	Vector3d randomForce = S * randNums[thisFacet++];
192			Vector3d dragForce = -hydroTensor * facetVel;
193	gezelter	1377
194	gezelter	1398	Vector3d langevinForce = (extPressure + randomForce + dragForce);
195	gezelter	1355
196	chuckv	1375	// Apply triangle force to stuntdouble vertices
197	chuckv	1325	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
198	chuckv	1375	if ((*vertex) != NULL){
199	gezelter	1344	Vector3d vertexForce = langevinForce / 3.0;
200			(*vertex)->addFrc(vertexForce);
201	chuckv	1307	}
202	chuckv	1293	}
203	chuckv	1302	}
204	gezelter	1355
205	chuckv	1325	veloMunge->removeComDrift();
206			veloMunge->removeAngularDrift();
207	gezelter	1355
208	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
209	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
210	gezelter	1464	ForceManager::postCalculation();
211	chuckv	1293	}
212	gezelter	1344
213	gezelter	1355
214	gezelter	1398	std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles,
215	gezelter	1344	RealType variance)
216			{
217	chuckv	1325
218	gezelter	1344	// zero fill the random vector before starting:
219	gezelter	1398	std::vector<Vector3d> gaussRand;
220	gezelter	1344	gaussRand.resize(nTriangles);
221	gezelter	1398	std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
222	chuckv	1325
223	gezelter	1344	#ifdef IS_MPI
224			if (worldRank == 0) {
225			#endif
226			for (int i = 0; i < nTriangles; i++) {
227	gezelter	1398	gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
228			gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
229			gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
230	gezelter	1344	}
231			#ifdef IS_MPI
232			}
233			#endif
234	chuckv	1325
235	gezelter	1344	// push these out to the other processors
236
237			#ifdef IS_MPI
238			if (worldRank == 0) {
239	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
240	gezelter	1344	} else {
241	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
242	gezelter	1344	}
243			#endif
244
245			return gaussRand;
246			}
247	chuckv	1293	}