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. 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/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.
    
    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 = 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(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<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();
      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(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
      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:	1398
Committed:	Tue Dec 8 22:17:02 2009 UTC (15 years, 4 months ago) by gezelter
Original Path:	*trunk/src/integrators/SMIPDForceManager.cpp*
File size:	8083 byte(s)
Log Message:	Parallel bugfix in RestraintForceManager Reverted back to hydrodynamics on triangular plates for SMIPDForceManager Removed thermalLength and thermalConductivity keywords from Globals. Bug tracking in openmdformat (not yet resolved).
#	User	Rev	Content
1	chuckv	1293	/*
2	chuckv	1375	* Copyright (c) 2008, 2009 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			#include "math/Triangle.hpp"
47	gezelter	1398	#include "math/CholeskyDecomposition.hpp"
48	chuckv	1293
49	gezelter	1390	namespace OpenMD {
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	gezelter	1357	"\twithout a targetTemp (K)!\n");
67	chuckv	1293	painCave.isFatal = 1;
68	gezelter	1390	painCave.severity = OPENMD_ERROR;
69	chuckv	1293	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	gezelter	1357	"\twithout a targetPressure (atm)!\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	gezelter	1390	PhysicalConstants::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	gezelter	1357	"\twith periodic boundary conditions!\n");
90	chuckv	1293	painCave.isFatal = 1;
91			simError();
92			}
93	gezelter	1324
94	gezelter	1398	if (!simParams->haveViscosity()) {
95	gezelter	1324	sprintf(painCave.errMsg,
96			"SMIPDynamics error: You can't use the SMIPD integrator\n"
97	gezelter	1398	"\twithout a viscosity!\n");
98	chuckv	1316	painCave.isFatal = 1;
99	gezelter	1390	painCave.severity = OPENMD_ERROR;
100	chuckv	1316	simError();
101	chuckv	1323	}else{
102	gezelter	1398	viscosity_ = simParams->getViscosity();
103	chuckv	1316	}
104	gezelter	1324
105	chuckv	1323	dt_ = simParams->getDt();
106	gezelter	1324
107	gezelter	1390	variance_ = 2.0 * PhysicalConstants::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	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
138	chuckv	1307	int nTriangles = sMesh.size();
139
140	gezelter	1344	// Generate all of the necessary random forces
141	gezelter	1398	std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
142	gezelter	1344
143	chuckv	1325	// Loop over the mesh faces and apply external pressure to each
144			// of the faces
145	chuckv	1308	std::vector<Triangle>::iterator face;
146	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
147	gezelter	1344	int thisFacet = 0;
148	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
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	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
155	gezelter	1344	Vector3d facetVel = thisTriangle.getFacetVelocity();
156	gezelter	1355	RealType thisMass = thisTriangle.getFacetMass();
157	gezelter	1398	Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
158
159			hydroTensor *= PhysicalConstants::viscoConvert;
160			Mat3x3d S;
161			CholeskyDecomposition(hydroTensor, S);
162
163			Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
164			PhysicalConstants::energyConvert;
165	gezelter	1344
166	gezelter	1398	Vector3d randomForce = S * randNums[thisFacet++];
167			Vector3d dragForce = -hydroTensor * facetVel;
168	gezelter	1377
169	gezelter	1398	Vector3d langevinForce = (extPressure + randomForce + dragForce);
170	gezelter	1355
171	chuckv	1375	// Apply triangle force to stuntdouble vertices
172	chuckv	1325	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
173	chuckv	1375	if ((*vertex) != NULL){
174	gezelter	1344	Vector3d vertexForce = langevinForce / 3.0;
175			(*vertex)->addFrc(vertexForce);
176	chuckv	1307	}
177	chuckv	1293	}
178	chuckv	1302	}
179	gezelter	1355
180	chuckv	1325	veloMunge->removeComDrift();
181			veloMunge->removeAngularDrift();
182	gezelter	1355
183	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
184	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
185	chuckv	1302	ForceManager::postCalculation(needStress);
186	chuckv	1293	}
187	gezelter	1344
188	gezelter	1355
189	gezelter	1398	std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles,
190	gezelter	1344	RealType variance)
191			{
192	chuckv	1325
193	gezelter	1344	// zero fill the random vector before starting:
194	gezelter	1398	std::vector<Vector3d> gaussRand;
195	gezelter	1344	gaussRand.resize(nTriangles);
196	gezelter	1398	std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
197	chuckv	1325
198	gezelter	1344	#ifdef IS_MPI
199			if (worldRank == 0) {
200			#endif
201			for (int i = 0; i < nTriangles; i++) {
202	gezelter	1398	gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
203			gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
204			gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
205	gezelter	1344	}
206			#ifdef IS_MPI
207			}
208			#endif
209	chuckv	1325
210	gezelter	1344	// push these out to the other processors
211
212			#ifdef IS_MPI
213			if (worldRank == 0) {
214	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
215	gezelter	1344	} else {
216	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
217	gezelter	1344	}
218			#endif
219
220			return gaussRand;
221			}
222	chuckv	1293	}