src/integrators/LangevinHullForceManager.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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#include <fstream> 
#include <iostream>
#include "integrators/LangevinHullForceManager.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

using namespace std;
namespace OpenMD {
  
  LangevinHullForceManager::LangevinHullForceManager(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()) ? 
      LangevinHullForceManager::hullUnknown : iter->second;

    switch(hullType_) {
    case hullConvex :
      surfaceMesh_ = new ConvexHull();
      break;
    case hullAlphaShape :
      surfaceMesh_ = new AlphaHull(simParams->getAlpha());
      break;
    case hullUnknown :
    default :
      sprintf(painCave.errMsg, 
              "LangevinHallForceManager: Unknown Hull_Method was requested!\n");
      painCave.isFatal = 1;
      simError();      
      break;
    }

    doThermalCoupling_ = true;
    doPressureCoupling_ = true;

    /* Check that the simulation has target pressure and target
       temperature set */    
    if (!simParams->haveTargetTemp()) {
      sprintf(painCave.errMsg, 
              "LangevinHullForceManager: no targetTemp (K) was set.\n"
              "\tOpenMD is turning off the thermal coupling to the bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doThermalCoupling_ = false;
    } else {
      targetTemp_ = simParams->getTargetTemp();

      if (!simParams->haveViscosity()) {
        sprintf(painCave.errMsg, 
                "LangevinHullForceManager: no viscosity was set.\n"
                "\tOpenMD is turning off the thermal coupling to the bath.\n");
        painCave.isFatal = 0;
        painCave.severity = OPENMD_INFO;
        simError();      
        doThermalCoupling_ = false;
      }else{
        viscosity_ = simParams->getViscosity();
        if ( fabs(viscosity_) < 1e-6 ) {
          sprintf(painCave.errMsg, 
                  "LangevinHullDynamics: The bath viscosity was set lower\n"
                  "\tthan 1e-6 poise.  OpenMD is turning off the thermal\n"
                  "\tcoupling to the bath.\n");
          painCave.isFatal = 0;
          painCave.severity = OPENMD_INFO;
          simError();
          doThermalCoupling_ = false;
        }      
      }      
    }
    if (!simParams->haveTargetPressure()) {
      sprintf(painCave.errMsg, 
              "LangevinHullForceManager: no targetPressure (atm) was set.\n"
              "\tOpenMD is turning off the pressure coupling to the bath.\n");
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      doPressureCoupling_ = false;
    } else {
      // Convert pressure from atm -> amu/(fs^2*Ang)
      targetPressure_ = simParams->getTargetPressure() / 
        PhysicalConstants::pressureConvert;
    }
    if (simParams->getUsePeriodicBoundaryConditions()) {
      sprintf(painCave.errMsg, 
              "LangevinHallForceManager: You can't use the Langevin Hull\n"
              "\tintegrator with periodic boundary conditions turned on!\n");
      painCave.isFatal = 1;
      simError();
    } 

    dt_ = simParams->getDt();

    if (doThermalCoupling_)
      variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;

    // Build a vector of integrable objects to determine if the are
    // surface atoms
    Molecule* mol;
    StuntDouble* sd;
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {          
      for (sd = mol->beginIntegrableObject(j); 
           sd != NULL;
           sd = mol->nextIntegrableObject(j)) { 
        localSites_.push_back(sd);
      }
    }
    
    // We need to make an initial guess at the bounding box in order
    // to compute long range forces in ForceMatrixDecomposition:

    // Compute surface Mesh
    surfaceMesh_->computeHull(localSites_);
  }  

  LangevinHullForceManager::~LangevinHullForceManager() { 
    delete surfaceMesh_;
    delete veloMunge;
  }
  
  void LangevinHullForceManager::postCalculation(){
  
    int nTriangles, thisFacet;
    RealType area, thisArea, thisMass;
    vector<Triangle> sMesh;
    Triangle thisTriangle;
    vector<Triangle>::iterator face;
    vector<StuntDouble*> vertexSDs;
    vector<StuntDouble*>::iterator vertex;

    Vector3d unitNormal, centroid, facetVel;
    Vector3d langevinForce, vertexForce;
    Vector3d extPressure, randomForce, dragForce;

    Mat3x3d hydroTensor, S;
    vector<Vector3d> randNums;

    // Compute surface Mesh
    surfaceMesh_->computeHull(localSites_);
    // Get total area and number of surface stunt doubles
    area = surfaceMesh_->getArea();
    sMesh = surfaceMesh_->getMesh();
    nTriangles = sMesh.size();

    if (doThermalCoupling_) {
      // Generate all of the necessary random forces
      randNums = genTriangleForces(nTriangles, variance_);
    }
    
    // Loop over the mesh faces
    thisFacet = 0;
    for (face = sMesh.begin(); face != sMesh.end(); ++face){
      thisTriangle = *face;
      vertexSDs = thisTriangle.getVertices();
      thisArea = thisTriangle.getArea(); 
      unitNormal = thisTriangle.getUnitNormal();
      centroid = thisTriangle.getCentroid();
      facetVel = thisTriangle.getFacetVelocity();
      thisMass = thisTriangle.getFacetMass();

      langevinForce = V3Zero;

      if (doPressureCoupling_) {
        extPressure = -unitNormal * (targetPressure_ * thisArea) /
          PhysicalConstants::energyConvert;
        langevinForce += extPressure;
      }

      if (doThermalCoupling_) {
        hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);      
        hydroTensor *= PhysicalConstants::viscoConvert;
        CholeskyDecomposition(hydroTensor, S);
        randomForce = S * randNums[thisFacet++];
        dragForce = -hydroTensor * facetVel;
        langevinForce += randomForce + dragForce;
      }
      
      // Apply triangle force to stuntdouble vertices
      for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
        if ((*vertex) != NULL){
          vertexForce = langevinForce / RealType(3.0);
          (*vertex)->addFrc(vertexForce);          
        }  
      }
    } 
    
    veloMunge->removeComDrift();
    veloMunge->removeAngularDrift();
    
    Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot->setVolume(surfaceMesh_->getVolume());   
    currSnapshot->setHullVolume(surfaceMesh_->getVolume());
    ForceManager::postCalculation();   
  }
    
  vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles, 
                                                               RealType var) {
    // zero fill the random vector before starting:
    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, var);
        gaussRand[i][1] = randNumGen_.randNorm(0.0, var);
        gaussRand[i][2] = randNumGen_.randNorm(0.0, var);
      }
#ifdef IS_MPI
    }
#endif
    
    // push these out to the other processors
    
#ifdef IS_MPI
    // Same command on all nodes:
    MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
#endif
    
    return gaussRand;
  }
}
Revision:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	10164 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	User	Rev	Content
1	gezelter	1629	/*
2			* Copyright (c) 2008, 2009, 2010 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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1629	*/
42			#include <fstream>
43			#include <iostream>
44			#include "integrators/LangevinHullForceManager.hpp"
45			#include "utils/PhysicalConstants.hpp"
46			#include "math/ConvexHull.hpp"
47			#include "math/AlphaHull.hpp"
48			#include "math/Triangle.hpp"
49			#include "math/CholeskyDecomposition.hpp"
50			#ifdef IS_MPI
51			#include <mpi.h>
52			#endif
53
54	gezelter	1858	using namespace std;
55	gezelter	1629	namespace OpenMD {
56	gezelter	1858
57			LangevinHullForceManager::LangevinHullForceManager(SimInfo* info) :
58			ForceManager(info) {
59	gezelter	1866
60	gezelter	1629	simParams = info->getSimParams();
61			veloMunge = new Velocitizer(info);
62
63			// Create Hull, Convex Hull for now, other options later.
64
65			stringToEnumMap_["Convex"] = hullConvex;
66			stringToEnumMap_["AlphaShape"] = hullAlphaShape;
67			stringToEnumMap_["Unknown"] = hullUnknown;
68
69			const std::string ht = simParams->getHULL_Method();
70
71			std::map<std::string, HullTypeEnum>::iterator iter;
72			iter = stringToEnumMap_.find(ht);
73	gezelter	1858	hullType_ = (iter == stringToEnumMap_.end()) ?
74			LangevinHullForceManager::hullUnknown : iter->second;
75
76	gezelter	1629	switch(hullType_) {
77			case hullConvex :
78			surfaceMesh_ = new ConvexHull();
79			break;
80			case hullAlphaShape :
81			surfaceMesh_ = new AlphaHull(simParams->getAlpha());
82			break;
83			case hullUnknown :
84			default :
85	gezelter	1858	sprintf(painCave.errMsg,
86			"LangevinHallForceManager: Unknown Hull_Method was requested!\n");
87			painCave.isFatal = 1;
88			simError();
89	gezelter	1629	break;
90			}
91	gezelter	1858
92			doThermalCoupling_ = true;
93			doPressureCoupling_ = true;
94
95	gezelter	1629	/* Check that the simulation has target pressure and target
96	gezelter	1858	temperature set */
97	gezelter	1629	if (!simParams->haveTargetTemp()) {
98			sprintf(painCave.errMsg,
99	gezelter	1858	"LangevinHullForceManager: no targetTemp (K) was set.\n"
100			"\tOpenMD is turning off the thermal coupling to the bath.\n");
101			painCave.isFatal = 0;
102			painCave.severity = OPENMD_INFO;
103	gezelter	1629	simError();
104	gezelter	1858	doThermalCoupling_ = false;
105	gezelter	1629	} else {
106			targetTemp_ = simParams->getTargetTemp();
107	gezelter	1866
108			if (!simParams->haveViscosity()) {
109			sprintf(painCave.errMsg,
110			"LangevinHullForceManager: no viscosity was set.\n"
111			"\tOpenMD is turning off the thermal coupling to the bath.\n");
112			painCave.isFatal = 0;
113			painCave.severity = OPENMD_INFO;
114			simError();
115			doThermalCoupling_ = false;
116			}else{
117			viscosity_ = simParams->getViscosity();
118			if ( fabs(viscosity_) < 1e-6 ) {
119			sprintf(painCave.errMsg,
120			"LangevinHullDynamics: The bath viscosity was set lower\n"
121			"\tthan 1e-6 poise. OpenMD is turning off the thermal\n"
122			"\tcoupling to the bath.\n");
123			painCave.isFatal = 0;
124			painCave.severity = OPENMD_INFO;
125			simError();
126			doThermalCoupling_ = false;
127			}
128			}
129	gezelter	1629	}
130			if (!simParams->haveTargetPressure()) {
131			sprintf(painCave.errMsg,
132	gezelter	1858	"LangevinHullForceManager: no targetPressure (atm) was set.\n"
133			"\tOpenMD is turning off the pressure coupling to the bath.\n");
134			painCave.isFatal = 0;
135			painCave.severity = OPENMD_INFO;
136	gezelter	1629	simError();
137	gezelter	1858	doPressureCoupling_ = false;
138	gezelter	1629	} else {
139			// Convert pressure from atm -> amu/(fs^2*Ang)
140			targetPressure_ = simParams->getTargetPressure() /
141			PhysicalConstants::pressureConvert;
142			}
143			if (simParams->getUsePeriodicBoundaryConditions()) {
144			sprintf(painCave.errMsg,
145	gezelter	1858	"LangevinHallForceManager: You can't use the Langevin Hull\n"
146			"\tintegrator with periodic boundary conditions turned on!\n");
147	gezelter	1629	painCave.isFatal = 1;
148			simError();
149			}
150	gezelter	1855
151	gezelter	1629	dt_ = simParams->getDt();
152	gezelter	1866
153	gezelter	1858	if (doThermalCoupling_)
154			variance_ = 2.0 * PhysicalConstants::kb * targetTemp_ / dt_;
155	gezelter	1629
156			// Build a vector of integrable objects to determine if the are
157			// surface atoms
158			Molecule* mol;
159	gezelter	1767	StuntDouble* sd;
160	gezelter	1629	SimInfo::MoleculeIterator i;
161			Molecule::IntegrableObjectIterator j;
162	gezelter	1858
163	gezelter	1629	for (mol = info_->beginMolecule(i); mol != NULL;
164			mol = info_->nextMolecule(i)) {
165	gezelter	1767	for (sd = mol->beginIntegrableObject(j);
166			sd != NULL;
167			sd = mol->nextIntegrableObject(j)) {
168			localSites_.push_back(sd);
169	gezelter	1629	}
170	gezelter	1858	}
171
172			// We need to make an initial guess at the bounding box in order
173			// to compute long range forces in ForceMatrixDecomposition:
174
175			// Compute surface Mesh
176			surfaceMesh_->computeHull(localSites_);
177	gezelter	1629	}
178	gezelter	1867
179			LangevinHullForceManager::~LangevinHullForceManager() {
180			delete surfaceMesh_;
181	gezelter	1868	delete veloMunge;
182	gezelter	1867	}
183	gezelter	1858
184	gezelter	1629	void LangevinHullForceManager::postCalculation(){
185
186	gezelter	1858	int nTriangles, thisFacet;
187			RealType area, thisArea, thisMass;
188			vector<Triangle> sMesh;
189			Triangle thisTriangle;
190			vector<Triangle>::iterator face;
191			vector<StuntDouble*> vertexSDs;
192			vector<StuntDouble*>::iterator vertex;
193
194			Vector3d unitNormal, centroid, facetVel;
195			Vector3d langevinForce, vertexForce;
196			Vector3d extPressure, randomForce, dragForce;
197
198			Mat3x3d hydroTensor, S;
199			vector<Vector3d> randNums;
200
201	gezelter	1629	// Compute surface Mesh
202			surfaceMesh_->computeHull(localSites_);
203			// Get total area and number of surface stunt doubles
204	gezelter	1858	area = surfaceMesh_->getArea();
205			sMesh = surfaceMesh_->getMesh();
206			nTriangles = sMesh.size();
207	gezelter	1629
208	gezelter	1858	if (doThermalCoupling_) {
209			// Generate all of the necessary random forces
210			randNums = genTriangleForces(nTriangles, variance_);
211			}
212
213			// Loop over the mesh faces
214			thisFacet = 0;
215	gezelter	1629	for (face = sMesh.begin(); face != sMesh.end(); ++face){
216	gezelter	1858	thisTriangle = *face;
217			vertexSDs = thisTriangle.getVertices();
218			thisArea = thisTriangle.getArea();
219			unitNormal = thisTriangle.getUnitNormal();
220			centroid = thisTriangle.getCentroid();
221			facetVel = thisTriangle.getFacetVelocity();
222			thisMass = thisTriangle.getFacetMass();
223	gezelter	1760
224	gezelter	1858	langevinForce = V3Zero;
225	gezelter	1629
226	gezelter	1858	if (doPressureCoupling_) {
227			extPressure = -unitNormal * (targetPressure_ * thisArea) /
228			PhysicalConstants::energyConvert;
229			langevinForce += extPressure;
230			}
231
232	gezelter	1855	if (doThermalCoupling_) {
233	gezelter	1858	hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_);
234			hydroTensor *= PhysicalConstants::viscoConvert;
235			CholeskyDecomposition(hydroTensor, S);
236	gezelter	1855	randomForce = S * randNums[thisFacet++];
237			dragForce = -hydroTensor * facetVel;
238	gezelter	1858	langevinForce += randomForce + dragForce;
239	gezelter	1855	}
240	gezelter	1629
241			// Apply triangle force to stuntdouble vertices
242			for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){
243			if ((*vertex) != NULL){
244	gezelter	1858	vertexForce = langevinForce / RealType(3.0);
245	gezelter	1629	(*vertex)->addFrc(vertexForce);
246			}
247			}
248			}
249
250			veloMunge->removeComDrift();
251			veloMunge->removeAngularDrift();
252
253			Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
254	gezelter	1858	currSnapshot->setVolume(surfaceMesh_->getVolume());
255	gezelter	1856	currSnapshot->setHullVolume(surfaceMesh_->getVolume());
256	gezelter	1629	ForceManager::postCalculation();
257			}
258
259	gezelter	1858	vector<Vector3d> LangevinHullForceManager::genTriangleForces(int nTriangles,
260			RealType var) {
261	gezelter	1629	// zero fill the random vector before starting:
262	gezelter	1858	vector<Vector3d> gaussRand;
263	gezelter	1629	gaussRand.resize(nTriangles);
264			std::fill(gaussRand.begin(), gaussRand.end(), V3Zero);
265
266			#ifdef IS_MPI
267			if (worldRank == 0) {
268			#endif
269			for (int i = 0; i < nTriangles; i++) {
270	gezelter	1858	gaussRand[i][0] = randNumGen_.randNorm(0.0, var);
271			gaussRand[i][1] = randNumGen_.randNorm(0.0, var);
272			gaussRand[i][2] = randNumGen_.randNorm(0.0, var);
273	gezelter	1629	}
274			#ifdef IS_MPI
275			}
276			#endif
277
278			// push these out to the other processors
279
280			#ifdef IS_MPI
281	gezelter	1874	// Same command on all nodes:
282			MPI::COMM_WORLD.Bcast(&gaussRand[0], nTriangles*3, MPI::REALTYPE, 0);
283	gezelter	1629	#endif
284
285			return gaussRand;
286			}
287			}