src/integrators/SMIPDForceManager.cpp

/*
 * Copyright (c) 2008, 2009 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();
    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"
              "\twithout 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"
              "\twithout 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"
              "\twith periodic boundary conditions!\n");    
      painCave.isFatal = 1;
      simError();
    } 
    
    if (!simParams->haveThermalConductivity()) {
      sprintf(painCave.errMsg, 
              "SMIPDynamics error: You can't use the SMIPD integrator\n"
              "\twithout 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"
              "\twithout 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();
    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 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);
      
      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;
          //          std::cout << "Adding force: " << facetVel << " to global id: " << (*vertex)->getGlobalIndex() << std::endl; 
          (*vertex)->addFrc(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:	1375
Committed:	Tue Oct 20 20:05:56 2009 UTC (15 years, 6 months ago) by chuckv
File size:	8478 byte(s)
Log Message:	Re-write of convex hull.
#	Content
1	/*
2	* Copyright (c) 2008, 2009 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
50	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
51
52	simParams = info->getSimParams();
53	veloMunge = new Velocitizer(info);
54
55	// Create Hull, Convex Hull for now, other options later.
56
57	surfaceMesh_ = new ConvexHull();
58
59	/* Check that the simulation has target pressure and target
60	temperature set */
61
62	if (!simParams->haveTargetTemp()) {
63	sprintf(painCave.errMsg,
64	"SMIPDynamics error: You can't use the SMIPD integrator\n"
65	"\twithout a targetTemp (K)!\n");
66	painCave.isFatal = 1;
67	painCave.severity = OOPSE_ERROR;
68	simError();
69	} else {
70	targetTemp_ = simParams->getTargetTemp();
71	}
72
73	if (!simParams->haveTargetPressure()) {
74	sprintf(painCave.errMsg,
75	"SMIPDynamics error: You can't use the SMIPD integrator\n"
76	"\twithout a targetPressure (atm)!\n");
77	painCave.isFatal = 1;
78	simError();
79	} else {
80	// Convert pressure from atm -> amu/(fs^2*Ang)
81	targetPressure_ = simParams->getTargetPressure() /
82	OOPSEConstant::pressureConvert;
83	}
84
85	if (simParams->getUsePeriodicBoundaryConditions()) {
86	sprintf(painCave.errMsg,
87	"SMIPDynamics error: You can't use the SMIPD integrator\n"
88	"\twith periodic boundary conditions!\n");
89	painCave.isFatal = 1;
90	simError();
91	}
92
93	if (!simParams->haveThermalConductivity()) {
94	sprintf(painCave.errMsg,
95	"SMIPDynamics error: You can't use the SMIPD integrator\n"
96	"\twithout a thermalConductivity (W m^-1 K^-1)!\n");
97	painCave.isFatal = 1;
98	painCave.severity = OOPSE_ERROR;
99	simError();
100	}else{
101	thermalConductivity_ = simParams->getThermalConductivity() *
102	OOPSEConstant::thermalConductivityConvert;
103	}
104
105	if (!simParams->haveThermalLength()) {
106	sprintf(painCave.errMsg,
107	"SMIPDynamics error: You can't use the SMIPD integrator\n"
108	"\twithout a thermalLength (Angstroms)!\n");
109	painCave.isFatal = 1;
110	painCave.severity = OOPSE_ERROR;
111	simError();
112	}else{
113	thermalLength_ = simParams->getThermalLength();
114	}
115
116	dt_ = simParams->getDt();
117
118	variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_;
119
120	// Build a vector of integrable objects to determine if the are
121	// surface atoms
122	Molecule* mol;
123	StuntDouble* integrableObject;
124	SimInfo::MoleculeIterator i;
125	Molecule::IntegrableObjectIterator j;
126
127	for (mol = info_->beginMolecule(i); mol != NULL;
128	mol = info_->nextMolecule(i)) {
129	for (integrableObject = mol->beginIntegrableObject(j);
130	integrableObject != NULL;
131	integrableObject = mol->nextIntegrableObject(j)) {
132	localSites_.push_back(integrableObject);
133	}
134	}
135	}
136
137	void SMIPDForceManager::postCalculation(bool needStress){
138	SimInfo::MoleculeIterator i;
139	Molecule::IntegrableObjectIterator j;
140	Molecule* mol;
141	StuntDouble* integrableObject;
142
143	// Compute surface Mesh
144
145	surfaceMesh_->computeHull(localSites_);
146
147	// Get total area and number of surface stunt doubles
148	RealType area = surfaceMesh_->getArea();
149	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
150	int nTriangles = sMesh.size();
151
152	// Generate all of the necessary random forces
153	std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_);
154
155	// Loop over the mesh faces and apply external pressure to each
156	// of the faces
157	std::vector<Triangle>::iterator face;
158	std::vector<StuntDouble*>::iterator vertex;
159	int thisFacet = 0;
160	for (face = sMesh.begin(); face != sMesh.end(); ++face){
161
162	Triangle thisTriangle = *face;
163	std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
164	RealType thisArea = thisTriangle.getArea();
165	Vector3d unitNormal = thisTriangle.getNormal();
166	unitNormal.normalize();
167	Vector3d centroid = thisTriangle.getCentroid();
168	Vector3d facetVel = thisTriangle.getFacetVelocity();
169	RealType thisMass = thisTriangle.getFacetMass();
170
171	// gamma is the drag coefficient normal to the face of the triangle
172	RealType gamma = thermalConductivity_ * thisMass * thisArea
173	/ (2.0 * thermalLength_ * OOPSEConstant::kB);
174
175	RealType extPressure = - (targetPressure_ * thisArea) /
176	OOPSEConstant::energyConvert;
177
178	RealType randomForce = randNums[thisFacet++] * sqrt(gamma);
179	RealType dragForce = -gamma * dot(facetVel, unitNormal);
180
181	Vector3d langevinForce = (extPressure + randomForce + dragForce) *
182	unitNormal;
183
184	// Apply triangle force to stuntdouble vertices
185	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
186	if ((*vertex) != NULL){
187	Vector3d vertexForce = langevinForce / 3.0;
188	// std::cout << "Adding force: " << facetVel << " to global id: " << (*vertex)->getGlobalIndex() << std::endl;
189	(*vertex)->addFrc(vertexForce);
190	}
191	}
192	}
193
194	veloMunge->removeComDrift();
195	veloMunge->removeAngularDrift();
196
197	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
198	currSnapshot->setVolume(surfaceMesh_->getVolume());
199	ForceManager::postCalculation(needStress);
200	}
201
202
203	std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
204	RealType variance)
205	{
206
207	// zero fill the random vector before starting:
208	std::vector<RealType> gaussRand;
209	gaussRand.resize(nTriangles);
210	std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
211
212	#ifdef IS_MPI
213	if (worldRank == 0) {
214	#endif
215	for (int i = 0; i < nTriangles; i++) {
216	gaussRand[i] = randNumGen_.randNorm(0.0, variance);
217	}
218	#ifdef IS_MPI
219	}
220	#endif
221
222	// push these out to the other processors
223
224	#ifdef IS_MPI
225	if (worldRank == 0) {
226	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
227	} else {
228	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
229	}
230	#endif
231
232	return gaussRand;
233	}
234	}