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();
    thermo = new Thermo(info);
    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 (K)!\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 (atm)!\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->haveThermalConductivity()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   without a thermalConductivity (W m^-1 K^-1)!\n");
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    }else{
      thermalConductivity_ = simParams->getThermalConductivity() * 
        OOPSEConstant::thermalConductivityConvert;
    }

    if (!simParams->haveThermalLength()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "   without a thermalLength (Angstroms)!\n");
      painCave.isFatal = 1;
      painCave.severity = OOPSE_ERROR;
      simError();
    }else{
      thermalLength_ = simParams->getThermalLength();
    }
    
    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<RealType>  randNums = genTriangleForces(nTriangles, variance_);

    RealType instaTemp = thermo->getTemperature();

    // 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();
      RealType thisMass = thisTriangle.getFacetMass();

      // gamma is the drag coefficient normal to the face of the triangle      
      RealType gamma = thermalConductivity_ * thisMass * thisArea  
        / (2.0 * thermalLength_ * OOPSEConstant::kB);
      
      gamma *= fabs(1.0 - targetTemp_/instaTemp);      
      
      RealType extPressure = - (targetPressure_ * thisArea) / 
        OOPSEConstant::energyConvert;

      RealType randomForce = randNums[thisFacet++] * 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));
          }
        }  
      }
    } 
    
    veloMunge->removeComDrift();
    veloMunge->removeAngularDrift();
    
    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::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
    } else {
      MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
    }
#endif
    
    return gaussRand;
  }
}
Revision:	3516
Committed:	Wed Jul 22 15:00:21 2009 UTC (16 years ago) by gezelter
File size:	8756 byte(s)
Log Message:	units for thermalConductivity, spelling error fixed
#	User	Rev	Content
1	chuckv	3450	/*
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	gezelter	3481
50	gezelter	3504	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
51
52	chuckv	3450	simParams = info->getSimParams();
53	gezelter	3515	thermo = new Thermo(info);
54	chuckv	3482	veloMunge = new Velocitizer(info);
55	chuckv	3450
56			// Create Hull, Convex Hull for now, other options later.
57	gezelter	3481
58	chuckv	3450	surfaceMesh_ = new ConvexHull();
59
60			/* Check that the simulation has target pressure and target
61	chuckv	3482	temperature set */
62	chuckv	3480
63	chuckv	3450	if (!simParams->haveTargetTemp()) {
64	gezelter	3481	sprintf(painCave.errMsg,
65			"SMIPDynamics error: You can't use the SMIPD integrator\n"
66	gezelter	3516	" without a targetTemp (K)!\n");
67	chuckv	3450	painCave.isFatal = 1;
68			painCave.severity = OOPSE_ERROR;
69			simError();
70			} else {
71			targetTemp_ = simParams->getTargetTemp();
72			}
73	chuckv	3480
74	chuckv	3450	if (!simParams->haveTargetPressure()) {
75	gezelter	3481	sprintf(painCave.errMsg,
76			"SMIPDynamics error: You can't use the SMIPD integrator\n"
77	gezelter	3516	" without a targetPressure (atm)!\n");
78	chuckv	3450	painCave.isFatal = 1;
79			simError();
80			} else {
81	gezelter	3481	// Convert pressure from atm -> amu/(fs^2*Ang)
82			targetPressure_ = simParams->getTargetPressure() /
83			OOPSEConstant::pressureConvert;
84	chuckv	3450	}
85
86			if (simParams->getUsePeriodicBoundaryConditions()) {
87	gezelter	3481	sprintf(painCave.errMsg,
88			"SMIPDynamics error: You can't use the SMIPD integrator\n"
89	gezelter	3515	" with periodic boundary conditions!\n");
90	chuckv	3450	painCave.isFatal = 1;
91			simError();
92			}
93	gezelter	3481
94	gezelter	3515	if (!simParams->haveThermalConductivity()) {
95	gezelter	3481	sprintf(painCave.errMsg,
96			"SMIPDynamics error: You can't use the SMIPD integrator\n"
97	gezelter	3516	" without a thermalConductivity (W m^-1 K^-1)!\n");
98	chuckv	3473	painCave.isFatal = 1;
99			painCave.severity = OOPSE_ERROR;
100			simError();
101	chuckv	3480	}else{
102	gezelter	3516	thermalConductivity_ = simParams->getThermalConductivity() *
103			OOPSEConstant::thermalConductivityConvert;
104	chuckv	3473	}
105	gezelter	3515
106			if (!simParams->haveThermalLength()) {
107			sprintf(painCave.errMsg,
108			"SMIPDynamics error: You can't use the SMIPD integrator\n"
109	gezelter	3516	" without a thermalLength (Angstroms)!\n");
110	gezelter	3515	painCave.isFatal = 1;
111			painCave.severity = OOPSE_ERROR;
112			simError();
113			}else{
114			thermalLength_ = simParams->getThermalLength();
115			}
116	gezelter	3481
117	chuckv	3480	dt_ = simParams->getDt();
118	gezelter	3481
119			variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
120	chuckv	3464
121	gezelter	3504	// Build a vector of integrable objects to determine if the are
122			// surface atoms
123	chuckv	3450	Molecule* mol;
124			StuntDouble* integrableObject;
125			SimInfo::MoleculeIterator i;
126	gezelter	3504	Molecule::IntegrableObjectIterator j;
127	chuckv	3480
128	gezelter	3481	for (mol = info_->beginMolecule(i); mol != NULL;
129			mol = info_->nextMolecule(i)) {
130			for (integrableObject = mol->beginIntegrableObject(j);
131			integrableObject != NULL;
132	chuckv	3450	integrableObject = mol->nextIntegrableObject(j)) {
133			localSites_.push_back(integrableObject);
134			}
135	gezelter	3481	}
136	chuckv	3450	}
137	chuckv	3482
138	chuckv	3450	void SMIPDForceManager::postCalculation(bool needStress){
139			SimInfo::MoleculeIterator i;
140			Molecule::IntegrableObjectIterator j;
141			Molecule* mol;
142			StuntDouble* integrableObject;
143	chuckv	3482
144	gezelter	3481	// Compute surface Mesh
145	chuckv	3450	surfaceMesh_->computeHull(localSites_);
146	chuckv	3482
147	gezelter	3481	// Get total area and number of surface stunt doubles
148			RealType area = surfaceMesh_->getArea();
149	chuckv	3482	int nSurfaceSDs = surfaceMesh_->getNs();
150	chuckv	3465	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
151	chuckv	3464	int nTriangles = sMesh.size();
152
153	gezelter	3504	// Generate all of the necessary random forces
154	gezelter	3515	std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_);
155	gezelter	3504
156	gezelter	3515	RealType instaTemp = thermo->getTemperature();
157
158	chuckv	3482	// Loop over the mesh faces and apply external pressure to each
159			// of the faces
160	chuckv	3465	std::vector<Triangle>::iterator face;
161	chuckv	3459	std::vector<StuntDouble*>::iterator vertex;
162	gezelter	3504	int thisFacet = 0;
163	chuckv	3450	for (face = sMesh.begin(); face != sMesh.end(); ++face){
164
165	chuckv	3465	Triangle thisTriangle = *face;
166			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
167	chuckv	3473	RealType thisArea = thisTriangle.getArea();
168	chuckv	3465	Vector3d unitNormal = thisTriangle.getNormal();
169	chuckv	3459	unitNormal.normalize();
170	chuckv	3465	Vector3d centroid = thisTriangle.getCentroid();
171	gezelter	3504	Vector3d facetVel = thisTriangle.getFacetVelocity();
172	gezelter	3515	RealType thisMass = thisTriangle.getFacetMass();
173	gezelter	3504
174	gezelter	3515	// gamma is the drag coefficient normal to the face of the triangle
175			RealType gamma = thermalConductivity_ * thisMass * thisArea
176	gezelter	3516	/ (2.0 * thermalLength_ * OOPSEConstant::kB);
177	gezelter	3515
178			gamma *= fabs(1.0 - targetTemp_/instaTemp);
179
180			RealType extPressure = - (targetPressure_ * thisArea) /
181			OOPSEConstant::energyConvert;
182	gezelter	3504
183	gezelter	3515	RealType randomForce = randNums[thisFacet++] * sqrt(gamma);
184			RealType dragForce = -gamma * dot(facetVel, unitNormal);
185	gezelter	3504
186	gezelter	3515	Vector3d langevinForce = (extPressure + randomForce + dragForce) *
187			unitNormal;
188
189	gezelter	3504	// Apply triangle force to stuntdouble vertices
190	chuckv	3482	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
191			if ((*vertex) != NULL){
192	gezelter	3504	Vector3d vertexForce = langevinForce / 3.0;
193			(*vertex)->addFrc(vertexForce);
194	chuckv	3482	if ((*vertex)->isDirectional()){
195	chuckv	3464	Vector3d vertexPos = (*vertex)->getPos();
196			Vector3d vertexCentroidVector = vertexPos - centroid;
197			(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce));
198			}
199			}
200	chuckv	3450	}
201	chuckv	3459	}
202	gezelter	3515
203	chuckv	3482	veloMunge->removeComDrift();
204			veloMunge->removeAngularDrift();
205	gezelter	3515
206	chuckv	3459	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
207	chuckv	3473	currSnapshot->setVolume(surfaceMesh_->getVolume());
208	chuckv	3459	ForceManager::postCalculation(needStress);
209	chuckv	3450	}
210	gezelter	3504
211	gezelter	3515
212			std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
213	gezelter	3504	RealType variance)
214			{
215	chuckv	3482
216	gezelter	3504	// zero fill the random vector before starting:
217	gezelter	3515	std::vector<RealType> gaussRand;
218	gezelter	3504	gaussRand.resize(nTriangles);
219	gezelter	3515	std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
220	chuckv	3482
221	gezelter	3504	#ifdef IS_MPI
222			if (worldRank == 0) {
223			#endif
224			for (int i = 0; i < nTriangles; i++) {
225	gezelter	3515	gaussRand[i] = randNumGen_.randNorm(0.0, variance);
226	gezelter	3504	}
227			#ifdef IS_MPI
228			}
229			#endif
230	chuckv	3482
231	gezelter	3504	// push these out to the other processors
232
233			#ifdef IS_MPI
234			if (worldRank == 0) {
235	gezelter	3515	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
236	gezelter	3504	} else {
237	gezelter	3515	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
238	gezelter	3504	}
239			#endif
240
241			return gaussRand;
242			}
243	chuckv	3450	}