src/integrators/SMIPDForceManager.cpp

/*
 * Copyright (c) 2008, 2009, 2010 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/AlphaHull.hpp"
#include "math/Triangle.hpp"
#include "math/CholeskyDecomposition.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {

  SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
    
    simParams = info->getSimParams();
    veloMunge = new Velocitizer(info);
    
    // Create Hull, Convex Hull for now, other options later.
    
    stringToEnumMap_["Convex"] = hullConvex;
    stringToEnumMap_["AlphaShape"] = hullAlphaShape;
    stringToEnumMap_["Unknown"] = hullUnknown;
    
    const std::string ht = simParams->getHULL_Method();
    
    
    
    std::map<std::string, HullTypeEnum>::iterator iter;
    iter = stringToEnumMap_.find(ht);
    hullType_ = (iter == stringToEnumMap_.end()) ? SMIPDForceManager::hullUnknown : iter->second;
    if (hullType_ == hullUnknown) {
      std::cerr << "WARNING! Hull Type Unknown!\n";
    }
    
    switch(hullType_) {
    case hullConvex :
      surfaceMesh_ = new ConvexHull();
      break;
    case hullAlphaShape :
      surfaceMesh_ = new AlphaHull(simParams->getAlpha());
      break;
    case hullUnknown :
    default :
      break;
    }
    /* 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(){
    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.getUnitNormal();
      //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();   
  }
  
  
  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:	1627
Committed:	Tue Sep 13 22:05:04 2011 UTC (13 years, 7 months ago) by gezelter
File size:	8864 byte(s)
Log Message:	Splitting out ifstrstream into a header and an implementation. This means that much of the code that depends on it can be compiled only once and the parallel I/O is concentrated into a few files. To do this, a number of files that relied on basic_ifstrstream to load the mpi header had to be modified to manage their own headers.
#	User	Rev	Content
1	chuckv	1293	/*
2	chuckv	1402	* Copyright (c) 2008, 2009, 2010 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	chuckv	1402	#include "math/AlphaHull.hpp"
47	chuckv	1293	#include "math/Triangle.hpp"
48	gezelter	1398	#include "math/CholeskyDecomposition.hpp"
49	gezelter	1627	#ifdef IS_MPI
50			#include <mpi.h>
51			#endif
52	chuckv	1293
53	gezelter	1390	namespace OpenMD {
54	gezelter	1324
55	gezelter	1344	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
56	chuckv	1402
57	chuckv	1293	simParams = info->getSimParams();
58	chuckv	1325	veloMunge = new Velocitizer(info);
59	chuckv	1293
60			// Create Hull, Convex Hull for now, other options later.
61	gezelter	1324
62	chuckv	1404	stringToEnumMap_["Convex"] = hullConvex;
63	chuckv	1402	stringToEnumMap_["AlphaShape"] = hullAlphaShape;
64			stringToEnumMap_["Unknown"] = hullUnknown;
65	chuckv	1293
66	chuckv	1402	const std::string ht = simParams->getHULL_Method();
67
68
69
70			std::map<std::string, HullTypeEnum>::iterator iter;
71			iter = stringToEnumMap_.find(ht);
72			hullType_ = (iter == stringToEnumMap_.end()) ? SMIPDForceManager::hullUnknown : iter->second;
73			if (hullType_ == hullUnknown) {
74			std::cerr << "WARNING! Hull Type Unknown!\n";
75			}
76
77			switch(hullType_) {
78			case hullConvex :
79			surfaceMesh_ = new ConvexHull();
80			break;
81			case hullAlphaShape :
82			surfaceMesh_ = new AlphaHull(simParams->getAlpha());
83			break;
84			case hullUnknown :
85			default :
86			break;
87			}
88	chuckv	1293	/* Check that the simulation has target pressure and target
89	chuckv	1325	temperature set */
90	chuckv	1323
91	chuckv	1293	if (!simParams->haveTargetTemp()) {
92	gezelter	1324	sprintf(painCave.errMsg,
93			"SMIPDynamics error: You can't use the SMIPD integrator\n"
94	gezelter	1357	"\twithout a targetTemp (K)!\n");
95	chuckv	1293	painCave.isFatal = 1;
96	gezelter	1390	painCave.severity = OPENMD_ERROR;
97	chuckv	1293	simError();
98			} else {
99			targetTemp_ = simParams->getTargetTemp();
100			}
101	chuckv	1323
102	chuckv	1293	if (!simParams->haveTargetPressure()) {
103	gezelter	1324	sprintf(painCave.errMsg,
104			"SMIPDynamics error: You can't use the SMIPD integrator\n"
105	gezelter	1357	"\twithout a targetPressure (atm)!\n");
106	chuckv	1293	painCave.isFatal = 1;
107			simError();
108			} else {
109	gezelter	1324	// Convert pressure from atm -> amu/(fs^2*Ang)
110			targetPressure_ = simParams->getTargetPressure() /
111	gezelter	1390	PhysicalConstants::pressureConvert;
112	chuckv	1293	}
113
114			if (simParams->getUsePeriodicBoundaryConditions()) {
115	gezelter	1324	sprintf(painCave.errMsg,
116			"SMIPDynamics error: You can't use the SMIPD integrator\n"
117	gezelter	1357	"\twith periodic boundary conditions!\n");
118	chuckv	1293	painCave.isFatal = 1;
119			simError();
120			}
121	gezelter	1324
122	gezelter	1398	if (!simParams->haveViscosity()) {
123	gezelter	1324	sprintf(painCave.errMsg,
124			"SMIPDynamics error: You can't use the SMIPD integrator\n"
125	gezelter	1398	"\twithout a viscosity!\n");
126	chuckv	1316	painCave.isFatal = 1;
127	gezelter	1390	painCave.severity = OPENMD_ERROR;
128	chuckv	1316	simError();
129	chuckv	1323	}else{
130	gezelter	1398	viscosity_ = simParams->getViscosity();
131	chuckv	1316	}
132	gezelter	1324
133	chuckv	1323	dt_ = simParams->getDt();
134	gezelter	1324
135	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
136	chuckv	1307
137	gezelter	1344	// Build a vector of integrable objects to determine if the are
138			// surface atoms
139	chuckv	1293	Molecule* mol;
140			StuntDouble* integrableObject;
141			SimInfo::MoleculeIterator i;
142	gezelter	1344	Molecule::IntegrableObjectIterator j;
143	chuckv	1323
144	gezelter	1324	for (mol = info_->beginMolecule(i); mol != NULL;
145			mol = info_->nextMolecule(i)) {
146			for (integrableObject = mol->beginIntegrableObject(j);
147			integrableObject != NULL;
148	chuckv	1293	integrableObject = mol->nextIntegrableObject(j)) {
149			localSites_.push_back(integrableObject);
150			}
151	gezelter	1324	}
152	chuckv	1293	}
153	chuckv	1325
154	gezelter	1464	void SMIPDForceManager::postCalculation(){
155	chuckv	1293	SimInfo::MoleculeIterator i;
156			Molecule::IntegrableObjectIterator j;
157			Molecule* mol;
158			StuntDouble* integrableObject;
159	chuckv	1325
160	gezelter	1324	// Compute surface Mesh
161	chuckv	1293	surfaceMesh_->computeHull(localSites_);
162	chuckv	1325
163	gezelter	1324	// Get total area and number of surface stunt doubles
164			RealType area = surfaceMesh_->getArea();
165	chuckv	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
166	chuckv	1307	int nTriangles = sMesh.size();
167
168	gezelter	1344	// Generate all of the necessary random forces
169	gezelter	1398	std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_);
170	gezelter	1344
171	chuckv	1325	// Loop over the mesh faces and apply external pressure to each
172			// of the faces
173	chuckv	1308	std::vector<Triangle>::iterator face;
174	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
175	gezelter	1344	int thisFacet = 0;
176	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
177	chuckv	1308	Triangle thisTriangle = *face;
178			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
179	chuckv	1316	RealType thisArea = thisTriangle.getArea();
180	chuckv	1404	Vector3d unitNormal = thisTriangle.getUnitNormal();
181			//unitNormal.normalize();
182	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
183	gezelter	1344	Vector3d facetVel = thisTriangle.getFacetVelocity();
184	gezelter	1355	RealType thisMass = thisTriangle.getFacetMass();
185	gezelter	1398	Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
186
187			hydroTensor *= PhysicalConstants::viscoConvert;
188			Mat3x3d S;
189			CholeskyDecomposition(hydroTensor, S);
190
191			Vector3d extPressure = -unitNormal * (targetPressure_ * thisArea) /
192			PhysicalConstants::energyConvert;
193	gezelter	1344
194	gezelter	1398	Vector3d randomForce = S * randNums[thisFacet++];
195			Vector3d dragForce = -hydroTensor * facetVel;
196	gezelter	1377
197	gezelter	1398	Vector3d langevinForce = (extPressure + randomForce + dragForce);
198	gezelter	1355
199	chuckv	1375	// Apply triangle force to stuntdouble vertices
200	chuckv	1325	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
201	chuckv	1375	if ((*vertex) != NULL){
202	gezelter	1344	Vector3d vertexForce = langevinForce / 3.0;
203			(*vertex)->addFrc(vertexForce);
204	chuckv	1307	}
205	chuckv	1293	}
206	chuckv	1302	}
207	gezelter	1355
208	chuckv	1325	veloMunge->removeComDrift();
209			veloMunge->removeAngularDrift();
210	gezelter	1355
211	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
212	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
213	gezelter	1464	ForceManager::postCalculation();
214	chuckv	1293	}
215	gezelter	1344
216	gezelter	1355
217	gezelter	1398	std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles,
218	gezelter	1344	RealType variance)
219			{
220	chuckv	1325
221	gezelter	1344	// zero fill the random vector before starting:
222	gezelter	1398	std::vector<Vector3d> gaussRand;
223	gezelter	1344	gaussRand.resize(nTriangles);
224	gezelter	1398	std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
225	chuckv	1325
226	gezelter	1344	#ifdef IS_MPI
227			if (worldRank == 0) {
228			#endif
229			for (int i = 0; i < nTriangles; i++) {
230	gezelter	1398	gaussRand[i][0] = randNumGen_.randNorm(0.0, variance);
231			gaussRand[i][1] = randNumGen_.randNorm(0.0, variance);
232			gaussRand[i][2] = randNumGen_.randNorm(0.0, variance);
233	gezelter	1344	}
234			#ifdef IS_MPI
235			}
236			#endif
237	chuckv	1325
238	gezelter	1344	// push these out to the other processors
239
240			#ifdef IS_MPI
241			if (worldRank == 0) {
242	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
243	gezelter	1344	} else {
244	gezelter	1398	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
245	gezelter	1344	}
246			#endif
247
248			return gaussRand;
249			}
250	chuckv	1293	}