src/integrators/SMIPDForceManager.cpp

/*
 * Copyright (c) 2008 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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
#include <fstream> 
#include <iostream>
#include "integrators/SMIPDForceManager.hpp"
#include "math/CholeskyDecomposition.hpp"
#include "utils/OOPSEConstant.hpp"
#include "math/ConvexHull.hpp"
#include "math/Triangle.hpp"

namespace oopse {

  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {

    simParams = info->getSimParams();
    veloMunge = new Velocitizer(info);
    
    // Create Hull, Convex Hull for now, other options later.
    
    surfaceMesh_ = new ConvexHull();
    
    /* 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"
              "   without a targetTemp!\n");      
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    } else {
      targetTemp_ = simParams->getTargetTemp();
    }
    
    if (!simParams->haveTargetPressure()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   without a targetPressure!\n");      
      painCave.isFatal = 1;
      simError();
    } else {
      // Convert pressure from atm -> amu/(fs^2*Ang)
      targetPressure_ = simParams->getTargetPressure() / 
        OOPSEConstant::pressureConvert;
    }
   
    if (simParams->getUsePeriodicBoundaryConditions()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   with periodic boundary conditions!\n");    
      painCave.isFatal = 1;
      simError();
    } 
    
    if (!simParams->haveViscosity()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   without a viscosity!\n");
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    }else{
      viscosity_ = simParams->getViscosity();
    }
    
    dt_ = simParams->getDt();
  
    variance_ = 2.0 * OOPSEConstant::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(bool needStress){
    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();
    int nSurfaceSDs = surfaceMesh_->getNs();
    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.getNormal();
      unitNormal.normalize();
      Vector3d centroid = thisTriangle.getCentroid();
      Vector3d facetVel = thisTriangle.getFacetVelocity();

      Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);

      hydroTensor *= OOPSEConstant::viscoConvert;
      Mat3x3d S;
      CholeskyDecomposition(hydroTensor, S);

      Vector3d extPressure = -unitNormal*(targetPressure_ * thisArea)/OOPSEConstant::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);          
          if ((*vertex)->isDirectional()){          
            Vector3d vertexPos = (*vertex)->getPos();
            Vector3d vertexCentroidVector = vertexPos - centroid;
            (*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
          }
        }  
      }
    } 
        
    veloMunge->removeComDrift();
    veloMunge->removeAngularDrift();

    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setVolume(surfaceMesh_->getVolume());    
    ForceManager::postCalculation(needStress);   
  }

  
  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
      RealType rx, ry, rz;
      for (int i = 0; i < nTriangles; i++) {
        rx = randNumGen_.randNorm(0.0, variance);
        ry = randNumGen_.randNorm(0.0, variance);
        rz = randNumGen_.randNorm(0.0, variance);
        gaussRand[i][0] = rx;
        gaussRand[i][1] = ry;
        gaussRand[i][2] = rz;
      }
#ifdef IS_MPI
    }
#endif
    
    // push these out to the other processors
    
#ifdef IS_MPI
    if (worldRank == 0) {
      MPI_Bcast(&gaussRand[0], nTriangles*3 , MPI_REALTYPE, 0, MPI_COMM_WORLD);
    } else {
      MPI_Bcast(&gaussRand[0], nTriangles*3, MPI_REALTYPE, 0, MPI_COMM_WORLD);
    }
#endif
    
    return gaussRand;
  }
}
Revision:	1344
Committed:	Wed May 13 22:27:29 2009 UTC (16 years, 5 months ago) by gezelter
File size:	8268 byte(s)
Log Message:	Adding boundary element hydrodynamics to SMIPD.
#	User	Rev	Content
1	chuckv	1293	/*
2			* Copyright (c) 2008 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. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include <fstream>
42			#include <iostream>
43			#include "integrators/SMIPDForceManager.hpp"
44	chuckv	1325	#include "math/CholeskyDecomposition.hpp"
45	chuckv	1293	#include "utils/OOPSEConstant.hpp"
46			#include "math/ConvexHull.hpp"
47			#include "math/Triangle.hpp"
48
49			namespace oopse {
50	gezelter	1324
51	gezelter	1344	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
52
53	chuckv	1293	simParams = info->getSimParams();
54	chuckv	1325	veloMunge = new Velocitizer(info);
55	chuckv	1293
56			// Create Hull, Convex Hull for now, other options later.
57	gezelter	1324
58	chuckv	1293	surfaceMesh_ = new ConvexHull();
59
60			/* Check that the simulation has target pressure and target
61	chuckv	1325	temperature set */
62	chuckv	1323
63	chuckv	1293	if (!simParams->haveTargetTemp()) {
64	gezelter	1324	sprintf(painCave.errMsg,
65			"SMIPDynamics error: You can't use the SMIPD integrator\n"
66			" without a targetTemp!\n");
67	chuckv	1293	painCave.isFatal = 1;
68			painCave.severity = OOPSE_ERROR;
69			simError();
70			} else {
71			targetTemp_ = simParams->getTargetTemp();
72			}
73	chuckv	1323
74	chuckv	1293	if (!simParams->haveTargetPressure()) {
75	gezelter	1324	sprintf(painCave.errMsg,
76			"SMIPDynamics error: You can't use the SMIPD integrator\n"
77			" without a targetPressure!\n");
78	chuckv	1293	painCave.isFatal = 1;
79			simError();
80			} else {
81	gezelter	1324	// Convert pressure from atm -> amu/(fs^2*Ang)
82			targetPressure_ = simParams->getTargetPressure() /
83			OOPSEConstant::pressureConvert;
84	chuckv	1293	}
85
86			if (simParams->getUsePeriodicBoundaryConditions()) {
87	gezelter	1324	sprintf(painCave.errMsg,
88			"SMIPDynamics error: You can't use the SMIPD integrator\n"
89			" with periodic boundary conditions!\n");
90	chuckv	1293	painCave.isFatal = 1;
91			simError();
92			}
93	gezelter	1324
94	chuckv	1316	if (!simParams->haveViscosity()) {
95	gezelter	1324	sprintf(painCave.errMsg,
96			"SMIPDynamics error: You can't use the SMIPD integrator\n"
97			" without a viscosity!\n");
98	chuckv	1316	painCave.isFatal = 1;
99			painCave.severity = OOPSE_ERROR;
100			simError();
101	chuckv	1323	}else{
102			viscosity_ = simParams->getViscosity();
103	chuckv	1316	}
104	gezelter	1324
105	chuckv	1323	dt_ = simParams->getDt();
106	gezelter	1324
107			variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
108	chuckv	1307
109	gezelter	1344	// Build a vector of integrable objects to determine if the are
110			// surface atoms
111	chuckv	1293	Molecule* mol;
112			StuntDouble* integrableObject;
113			SimInfo::MoleculeIterator i;
114	gezelter	1344	Molecule::IntegrableObjectIterator j;
115	chuckv	1323
116	gezelter	1324	for (mol = info_->beginMolecule(i); mol != NULL;
117			mol = info_->nextMolecule(i)) {
118			for (integrableObject = mol->beginIntegrableObject(j);
119			integrableObject != NULL;
120	chuckv	1293	integrableObject = mol->nextIntegrableObject(j)) {
121			localSites_.push_back(integrableObject);
122			}
123	gezelter	1324	}
124	chuckv	1293	}
125	chuckv	1325
126	chuckv	1293	void SMIPDForceManager::postCalculation(bool needStress){
127			SimInfo::MoleculeIterator i;
128			Molecule::IntegrableObjectIterator j;
129			Molecule* mol;
130			StuntDouble* integrableObject;
131	chuckv	1325
132	gezelter	1324	// Compute surface Mesh
133	chuckv	1293	surfaceMesh_->computeHull(localSites_);
134	chuckv	1325
135	gezelter	1324	// Get total area and number of surface stunt doubles
136			RealType area = surfaceMesh_->getArea();
137	chuckv	1325	int nSurfaceSDs = surfaceMesh_->getNs();
138	chuckv	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
139	chuckv	1307	int nTriangles = sMesh.size();
140
141	gezelter	1344	// Generate all of the necessary random forces
142			std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
143
144	chuckv	1325	// Loop over the mesh faces and apply external pressure to each
145			// of the faces
146	chuckv	1308	std::vector<Triangle>::iterator face;
147	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
148	gezelter	1344	int thisFacet = 0;
149	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
150
151	chuckv	1308	Triangle thisTriangle = *face;
152			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
153	chuckv	1316	RealType thisArea = thisTriangle.getArea();
154	chuckv	1308	Vector3d unitNormal = thisTriangle.getNormal();
155	chuckv	1302	unitNormal.normalize();
156	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
157	gezelter	1344	Vector3d facetVel = thisTriangle.getFacetVelocity();
158
159			Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
160
161			hydroTensor *= OOPSEConstant::viscoConvert;
162			Mat3x3d S;
163			CholeskyDecomposition(hydroTensor, S);
164
165			Vector3d extPressure = -unitNormal(targetPressure_ thisArea)/OOPSEConstant::energyConvert;
166			Vector3d randomForce = S * randNums[thisFacet++];
167			Vector3d dragForce = -hydroTensor * facetVel;
168
169			Vector3d langevinForce = (extPressure + randomForce + dragForce);
170
171			// Apply triangle force to stuntdouble vertices
172	chuckv	1325	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
173			if ((*vertex) != NULL){
174	gezelter	1344	Vector3d vertexForce = langevinForce / 3.0;
175			(*vertex)->addFrc(vertexForce);
176	chuckv	1325	if ((*vertex)->isDirectional()){
177	chuckv	1307	Vector3d vertexPos = (*vertex)->getPos();
178			Vector3d vertexCentroidVector = vertexPos - centroid;
179			(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
180			}
181			}
182	chuckv	1293	}
183	chuckv	1302	}
184	chuckv	1325
185			veloMunge->removeComDrift();
186			veloMunge->removeAngularDrift();
187
188	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
189	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
190	chuckv	1302	ForceManager::postCalculation(needStress);
191	chuckv	1293	}
192
193	gezelter	1344
194			std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles,
195			RealType variance)
196			{
197	chuckv	1325
198	gezelter	1344	// zero fill the random vector before starting:
199			std::vector<Vector3d> gaussRand;
200			gaussRand.resize(nTriangles);
201			std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
202	chuckv	1325
203	gezelter	1344	#ifdef IS_MPI
204			if (worldRank == 0) {
205			#endif
206			RealType rx, ry, rz;
207			for (int i = 0; i < nTriangles; i++) {
208			rx = randNumGen_.randNorm(0.0, variance);
209			ry = randNumGen_.randNorm(0.0, variance);
210			rz = randNumGen_.randNorm(0.0, variance);
211			gaussRand[i][0] = rx;
212			gaussRand[i][1] = ry;
213			gaussRand[i][2] = rz;
214			}
215			#ifdef IS_MPI
216			}
217			#endif
218	chuckv	1325
219	gezelter	1344	// push these out to the other processors
220
221			#ifdef IS_MPI
222			if (worldRank == 0) {
223			MPI_Bcast(&gaussRand[0], nTriangles*3 , MPI_REALTYPE, 0, MPI_COMM_WORLD);
224			} else {
225			MPI_Bcast(&gaussRand[0], nTriangles*3, MPI_REALTYPE, 0, MPI_COMM_WORLD);
226			}
227			#endif
228
229			return gaussRand;
230			}
231	chuckv	1293	}