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"

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->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 = OPENMD_ERROR;
      simError();
    }else{
      thermalConductivity_ = simParams->getThermalConductivity() * 
        PhysicalConstants::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 = OPENMD_ERROR;
      simError();
    }else{
      thermalLength_ = simParams->getThermalLength();
    }
    
    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<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();
      //      Mat3x3d hydroTens = thisTriangle.computeHydrodynamicTensor(viscosity);

      // gamma is the drag coefficient normal to the face of the triangle      
      RealType gamma = thermalConductivity_ * thisMass * thisArea 
        / (2.0 * thermalLength_ * PhysicalConstants::kB);

      RealType extPressure = - (targetPressure_ * thisArea) / 
        PhysicalConstants::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);          
        }  
      }
    } 
    
    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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/integrators/SMIPDForceManager.cpp*
File size:	8487 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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
48	gezelter	1390	namespace OpenMD {
49	gezelter	1324
50	gezelter	1344	SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) {
51
52	chuckv	1293	simParams = info->getSimParams();
53	chuckv	1325	veloMunge = new Velocitizer(info);
54	chuckv	1293
55			// Create Hull, Convex Hull for now, other options later.
56	gezelter	1324
57	chuckv	1293	surfaceMesh_ = new ConvexHull();
58
59			/* Check that the simulation has target pressure and target
60	chuckv	1325	temperature set */
61	chuckv	1323
62	chuckv	1293	if (!simParams->haveTargetTemp()) {
63	gezelter	1324	sprintf(painCave.errMsg,
64			"SMIPDynamics error: You can't use the SMIPD integrator\n"
65	gezelter	1357	"\twithout a targetTemp (K)!\n");
66	chuckv	1293	painCave.isFatal = 1;
67	gezelter	1390	painCave.severity = OPENMD_ERROR;
68	chuckv	1293	simError();
69			} else {
70			targetTemp_ = simParams->getTargetTemp();
71			}
72	chuckv	1323
73	chuckv	1293	if (!simParams->haveTargetPressure()) {
74	gezelter	1324	sprintf(painCave.errMsg,
75			"SMIPDynamics error: You can't use the SMIPD integrator\n"
76	gezelter	1357	"\twithout a targetPressure (atm)!\n");
77	chuckv	1293	painCave.isFatal = 1;
78			simError();
79			} else {
80	gezelter	1324	// Convert pressure from atm -> amu/(fs^2*Ang)
81			targetPressure_ = simParams->getTargetPressure() /
82	gezelter	1390	PhysicalConstants::pressureConvert;
83	chuckv	1293	}
84
85			if (simParams->getUsePeriodicBoundaryConditions()) {
86	gezelter	1324	sprintf(painCave.errMsg,
87			"SMIPDynamics error: You can't use the SMIPD integrator\n"
88	gezelter	1357	"\twith periodic boundary conditions!\n");
89	chuckv	1293	painCave.isFatal = 1;
90			simError();
91			}
92	gezelter	1324
93	gezelter	1355	if (!simParams->haveThermalConductivity()) {
94	gezelter	1324	sprintf(painCave.errMsg,
95			"SMIPDynamics error: You can't use the SMIPD integrator\n"
96	gezelter	1357	"\twithout a thermalConductivity (W m^-1 K^-1)!\n");
97	chuckv	1316	painCave.isFatal = 1;
98	gezelter	1390	painCave.severity = OPENMD_ERROR;
99	chuckv	1316	simError();
100	chuckv	1323	}else{
101	gezelter	1356	thermalConductivity_ = simParams->getThermalConductivity() *
102	gezelter	1390	PhysicalConstants::thermalConductivityConvert;
103	chuckv	1316	}
104	gezelter	1355
105			if (!simParams->haveThermalLength()) {
106			sprintf(painCave.errMsg,
107			"SMIPDynamics error: You can't use the SMIPD integrator\n"
108	gezelter	1357	"\twithout a thermalLength (Angstroms)!\n");
109	gezelter	1355	painCave.isFatal = 1;
110	gezelter	1390	painCave.severity = OPENMD_ERROR;
111	gezelter	1355	simError();
112			}else{
113			thermalLength_ = simParams->getThermalLength();
114			}
115	gezelter	1324
116	chuckv	1323	dt_ = simParams->getDt();
117	gezelter	1324
118	gezelter	1390	variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
119	chuckv	1307
120	gezelter	1344	// Build a vector of integrable objects to determine if the are
121			// surface atoms
122	chuckv	1293	Molecule* mol;
123			StuntDouble* integrableObject;
124			SimInfo::MoleculeIterator i;
125	gezelter	1344	Molecule::IntegrableObjectIterator j;
126	chuckv	1323
127	gezelter	1324	for (mol = info_->beginMolecule(i); mol != NULL;
128			mol = info_->nextMolecule(i)) {
129			for (integrableObject = mol->beginIntegrableObject(j);
130			integrableObject != NULL;
131	chuckv	1293	integrableObject = mol->nextIntegrableObject(j)) {
132			localSites_.push_back(integrableObject);
133			}
134	gezelter	1324	}
135	chuckv	1293	}
136	chuckv	1325
137	chuckv	1293	void SMIPDForceManager::postCalculation(bool needStress){
138			SimInfo::MoleculeIterator i;
139			Molecule::IntegrableObjectIterator j;
140			Molecule* mol;
141			StuntDouble* integrableObject;
142	chuckv	1325
143	gezelter	1324	// Compute surface Mesh
144	chuckv	1293	surfaceMesh_->computeHull(localSites_);
145	chuckv	1325
146	gezelter	1324	// Get total area and number of surface stunt doubles
147			RealType area = surfaceMesh_->getArea();
148	chuckv	1308	std::vector<Triangle> sMesh = surfaceMesh_->getMesh();
149	chuckv	1307	int nTriangles = sMesh.size();
150
151	gezelter	1344	// Generate all of the necessary random forces
152	gezelter	1355	std::vector<RealType> randNums = genTriangleForces(nTriangles, variance_);
153	gezelter	1344
154	chuckv	1325	// Loop over the mesh faces and apply external pressure to each
155			// of the faces
156	chuckv	1308	std::vector<Triangle>::iterator face;
157	chuckv	1302	std::vector<StuntDouble*>::iterator vertex;
158	gezelter	1344	int thisFacet = 0;
159	chuckv	1293	for (face = sMesh.begin(); face != sMesh.end(); ++face){
160	chuckv	1308	Triangle thisTriangle = *face;
161			std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices();
162	chuckv	1316	RealType thisArea = thisTriangle.getArea();
163	chuckv	1308	Vector3d unitNormal = thisTriangle.getNormal();
164	chuckv	1302	unitNormal.normalize();
165	chuckv	1308	Vector3d centroid = thisTriangle.getCentroid();
166	gezelter	1344	Vector3d facetVel = thisTriangle.getFacetVelocity();
167	gezelter	1355	RealType thisMass = thisTriangle.getFacetMass();
168	gezelter	1390	// Mat3x3d hydroTens = thisTriangle.computeHydrodynamicTensor(viscosity);
169	gezelter	1344
170	gezelter	1355	// gamma is the drag coefficient normal to the face of the triangle
171	gezelter	1357	RealType gamma = thermalConductivity_ * thisMass * thisArea
172	gezelter	1390	/ (2.0 * thermalLength_ * PhysicalConstants::kB);
173	gezelter	1377
174	gezelter	1355	RealType extPressure = - (targetPressure_ * thisArea) /
175	gezelter	1390	PhysicalConstants::energyConvert;
176	gezelter	1355	RealType randomForce = randNums[thisFacet++] * sqrt(gamma);
177			RealType dragForce = -gamma * dot(facetVel, unitNormal);
178	gezelter	1344
179	gezelter	1355	Vector3d langevinForce = (extPressure + randomForce + dragForce) *
180			unitNormal;
181
182	chuckv	1375	// Apply triangle force to stuntdouble vertices
183	chuckv	1325	for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
184	chuckv	1375	if ((*vertex) != NULL){
185	gezelter	1344	Vector3d vertexForce = langevinForce / 3.0;
186			(*vertex)->addFrc(vertexForce);
187	chuckv	1307	}
188	chuckv	1293	}
189	chuckv	1302	}
190	gezelter	1355
191	chuckv	1325	veloMunge->removeComDrift();
192			veloMunge->removeAngularDrift();
193	gezelter	1355
194	chuckv	1302	Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
195	chuckv	1316	currSnapshot->setVolume(surfaceMesh_->getVolume());
196	chuckv	1302	ForceManager::postCalculation(needStress);
197	chuckv	1293	}
198	gezelter	1344
199	gezelter	1355
200			std::vector<RealType> SMIPDForceManager::genTriangleForces(int nTriangles,
201	gezelter	1344	RealType variance)
202			{
203	chuckv	1325
204	gezelter	1344	// zero fill the random vector before starting:
205	gezelter	1355	std::vector<RealType> gaussRand;
206	gezelter	1344	gaussRand.resize(nTriangles);
207	gezelter	1355	std::fill(gaussRand.begin(), gaussRand.end(), 0.0);
208	chuckv	1325
209	gezelter	1344	#ifdef IS_MPI
210			if (worldRank == 0) {
211			#endif
212			for (int i = 0; i < nTriangles; i++) {
213	gezelter	1355	gaussRand[i] = randNumGen_.randNorm(0.0, variance);
214	gezelter	1344	}
215			#ifdef IS_MPI
216			}
217			#endif
218	chuckv	1325
219	gezelter	1344	// push these out to the other processors
220
221			#ifdef IS_MPI
222			if (worldRank == 0) {
223	gezelter	1355	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
224	gezelter	1344	} else {
225	gezelter	1355	MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles, MPI::REALTYPE, 0);
226	gezelter	1344	}
227			#endif
228
229			return gaussRand;
230			}
231	chuckv	1293	}