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 "utils/OOPSEConstant.hpp"
#include "math/ConvexHull.hpp"
#include "math/Triangle.hpp"

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

    simParams = info->getSimParams();
    
    // 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_;

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;               

    // Build a vector of integrable objects to determine if the are
    // surface atoms

    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<RealType>  randNums = genTriangleForces(nTriangles, variance_);

    // Loop over the mesh faces and apply random force to each of the faces
    std::vector<Triangle>::iterator face;
    std::vector<StuntDouble*>::iterator vertex;
    int thisNumber = 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();
      RealType hydroLength = thisTriangle.getIncircleRadius() * 2.0 / 
        NumericConstant::PI;
      
      // gamma is the drag coefficient normal to the face of the triangle      
      RealType gamma = viscosity_ * hydroLength * 
        OOPSEConstant::viscoConvert;

      RealType extPressure = - (targetPressure_ * thisArea) / 
        OOPSEConstant::energyConvert;

      RealType randomForce = randNums[thisNumber++] * sqrt(gamma);
      RealType dragForce = -gamma * dot(facetVel, unitNormal);

      Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal;
      
      // 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));
          }
        }  
      }
    } 
    
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setVolume(surfaceMesh_->getVolume());    
    ForceManager::postCalculation(needStress);   
  }

  std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles, 
                                                             RealType variance) {

    // zero fill the random vector before starting:
    std::vector<RealType> gaussRand;
    gaussRand.resize(nTriangles);
    std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
   
#ifdef IS_MPI
    if (worldRank == 0) {
#endif
      for (int i = 0; i < nTriangles; i++) {
        gaussRand[i] = randNumGen_.randNorm(0.0, variance);
      }
#ifdef IS_MPI
    }
#endif

    // push these out to the other processors

#ifdef IS_MPI
    if (worldRank == 0) {
      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
    } else {
      MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
    }
#endif
   
    return gaussRand;
  }
}
Revision:	1324
Committed:	Wed Nov 26 14:26:17 2008 UTC (16 years, 5 months ago) by gezelter
Original Path:	*trunk/src/integrators/SMIPDForceManager.cpp*
File size:	8012 byte(s)
Log Message:	Cleaning up some cruft.
#	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			#include "utils/OOPSEConstant.hpp"
45			#include "math/ConvexHull.hpp"
46			#include "math/Triangle.hpp"
47
48			namespace oopse {
49	chuckv	1323
50	gezelter	1324	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
51
52	chuckv	1293	simParams = info->getSimParams();
53
54			// Create Hull, Convex Hull for now, other options later.
55	gezelter	1324
56	chuckv	1293	surfaceMesh_ = new ConvexHull();
57
58			/* Check that the simulation has target pressure and target
59			temperature set*/
60	chuckv	1323
61	chuckv	1293	if (!simParams->haveTargetTemp()) {
62	gezelter	1324	sprintf(painCave.errMsg,
63			"SMIPDynamics error: You can't use the SMIPD integrator\n"
64			" without a targetTemp!\n");
65	chuckv	1293	painCave.isFatal = 1;
66			painCave.severity = OOPSE_ERROR;
67			simError();
68			} else {
69			targetTemp_ = simParams->getTargetTemp();
70			}
71	chuckv	1323
72	chuckv	1293	if (!simParams->haveTargetPressure()) {
73	gezelter	1324	sprintf(painCave.errMsg,
74			"SMIPDynamics error: You can't use the SMIPD integrator\n"
75			" without a targetPressure!\n");
76	chuckv	1293	painCave.isFatal = 1;
77			simError();
78			} else {
79	gezelter	1324	// Convert pressure from atm -> amu/(fs^2*Ang)
80			targetPressure_ = simParams->getTargetPressure() /
81			OOPSEConstant::pressureConvert;
82	chuckv	1293	}
83
84			if (simParams->getUsePeriodicBoundaryConditions()) {
85	gezelter	1324	sprintf(painCave.errMsg,
86			"SMIPDynamics error: You can't use the SMIPD integrator\n"
87			" with periodic boundary conditions!\n");
88	chuckv	1293	painCave.isFatal = 1;
89			simError();
90			}
91	gezelter	1324
92	chuckv	1316	if (!simParams->haveViscosity()) {
93	gezelter	1324	sprintf(painCave.errMsg,
94			"SMIPDynamics error: You can't use the SMIPD integrator\n"
95			" without a viscosity!\n");
96	chuckv	1316	painCave.isFatal = 1;
97			painCave.severity = OOPSE_ERROR;
98			simError();
99	chuckv	1323	}else{
100			viscosity_ = simParams->getViscosity();
101	chuckv	1316	}
102	gezelter	1324
103	chuckv	1323	dt_ = simParams->getDt();
104	gezelter	1324
105			variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
106	chuckv	1307
107	chuckv	1293	Molecule* mol;
108			StuntDouble* integrableObject;
109			SimInfo::MoleculeIterator i;
110	gezelter	1324	Molecule::IntegrableObjectIterator j;
111	chuckv	1323
112	gezelter	1324	// Build a vector of integrable objects to determine if the are
113			// surface atoms
114	chuckv	1293
115	gezelter	1324	for (mol = info_->beginMolecule(i); mol != NULL;
116			mol = info_->nextMolecule(i)) {
117			for (integrableObject = mol->beginIntegrableObject(j);
118			integrableObject != NULL;
119	chuckv	1293	integrableObject = mol->nextIntegrableObject(j)) {
120			localSites_.push_back(integrableObject);
121			}
122	gezelter	1324	}
123	chuckv	1293	}
124	gezelter	1324
125	chuckv	1293	void SMIPDForceManager::postCalculation(bool needStress){
126			SimInfo::MoleculeIterator i;
127			Molecule::IntegrableObjectIterator j;
128			Molecule* mol;
129			StuntDouble* integrableObject;
130
131	gezelter	1324	// Compute surface Mesh
132	chuckv	1293	surfaceMesh_->computeHull(localSites_);
133	chuckv	1307
134	gezelter	1324	// Get total area and number of surface stunt doubles
135			RealType area = surfaceMesh_->getArea();
136			int nSurfaceSDs = surfaceMesh_->getNs();
137	chuckv	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
138	chuckv	1307	int nTriangles = sMesh.size();
139	gezelter	1324
140			// Generate all of the necessary random forces
141			std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_);
142	chuckv	1307
143	gezelter	1324	// Loop over the mesh faces and apply random force to each of the faces
144	chuckv	1308	std::vector<Triangle>::iterator face;
145	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
146			int thisNumber = 0;
147	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
148
149	chuckv	1308	Triangle thisTriangle = *face;
150			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
151	chuckv	1316	RealType thisArea = thisTriangle.getArea();
152	chuckv	1308	Vector3d unitNormal = thisTriangle.getNormal();
153	chuckv	1302	unitNormal.normalize();
154	gezelter	1324
155	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
156	chuckv	1316	Vector3d facetVel = thisTriangle.getFacetVelocity();
157	gezelter	1324	RealType hydroLength = thisTriangle.getIncircleRadius() * 2.0 /
158			NumericConstant::PI;
159
160			// gamma is the drag coefficient normal to the face of the triangle
161			RealType gamma = viscosity_ * hydroLength *
162			OOPSEConstant::viscoConvert;
163	chuckv	1304
164	gezelter	1324	RealType extPressure = - (targetPressure_ * thisArea) /
165			OOPSEConstant::energyConvert;
166	chuckv	1320
167	gezelter	1324	RealType randomForce = randNums[thisNumber++] * sqrt(gamma);
168			RealType dragForce = -gamma * dot(facetVel, unitNormal);
169	chuckv	1320
170	chuckv	1316	Vector3d langevinForce = (extPressure + randomForce + dragForce) * unitNormal;
171	chuckv	1307
172	gezelter	1324	// Apply triangle force to stuntdouble vertices
173			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex) {
174			if ((*vertex) != NULL) {
175			Vector3d vertexForce = langevinForce / 3.0;
176			(*vertex)->addFrc(vertexForce);
177			if ((*vertex)->isDirectional()) {
178	chuckv	1307	Vector3d vertexPos = (*vertex)->getPos();
179			Vector3d vertexCentroidVector = vertexPos - centroid;
180			(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
181			}
182			}
183	chuckv	1293	}
184	chuckv	1302	}
185	gezelter	1324
186	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
187	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
188	chuckv	1302	ForceManager::postCalculation(needStress);
189	chuckv	1293	}
190
191	gezelter	1324	std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
192			RealType variance) {
193	chuckv	1293
194			// zero fill the random vector before starting:
195			std::vector<RealType> gaussRand;
196			gaussRand.resize(nTriangles);
197			std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
198	gezelter	1324
199	chuckv	1293	#ifdef IS_MPI
200			if (worldRank == 0) {
201			#endif
202			for (int i = 0; i < nTriangles; i++) {
203	gezelter	1324	gaussRand[i] = randNumGen_.randNorm(0.0, variance);
204	chuckv	1293	}
205			#ifdef IS_MPI
206			}
207			#endif
208
209			// push these out to the other processors
210
211			#ifdef IS_MPI
212			if (worldRank == 0) {
213	gezelter	1324	MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
214	chuckv	1293	} else {
215	gezelter	1324	MPI_Bcast(&gaussRand[0], nTriangles, MPI_REALTYPE, 0, MPI_COMM_WORLD);
216	chuckv	1293	}
217			#endif
218	chuckv	1316
219	chuckv	1293	return gaussRand;
220			}
221			}