src/restraints/ThermoIntegrationForceManager.cpp

/*
 * Copyright (c) 2005 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 "restraints/ThermoIntegrationForceManager.hpp"

#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {
  
  ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info): 
    RestraintForceManager(info){
    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    simParam = info_->getSimParams();
    
    if (simParam->haveThermodynamicIntegrationLambda()){
      tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
    }
    else{
      tIntLambda_ = 1.0;
      sprintf(painCave.errMsg,
              "ThermoIntegration error: the transformation parameter\n"
              "\t(lambda) was not specified. OpenMD will use a default\n"
              "\tvalue of %f. To set lambda, use the \n"
              "\tthermodynamicIntegrationLambda variable.\n",
              tIntLambda_);
      painCave.isFatal = 0;
      simError();
    }
    
    if (simParam->haveThermodynamicIntegrationK()){
      tIntK_ = simParam->getThermodynamicIntegrationK();
    }
    else{
      tIntK_ = 1.0;
      sprintf(painCave.errMsg,
              "ThermoIntegration Warning: the tranformation parameter\n"
              "\texponent (k) was not specified. OpenMD will use a default\n"
              "\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
              "\tvariable.\n",
              tIntK_);
      painCave.isFatal = 0;
      simError();      
    }
    
    // build the scaling factor used to modulate the forces and torques
    factor_ = pow(tIntLambda_, tIntK_);
  }
  
  ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
  }
  
  void ThermoIntegrationForceManager::calcForces(){
    Snapshot* curSnapshot;
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::IntegrableObjectIterator ii;
    StuntDouble* integrableObject;
    Vector3d frc;
    Vector3d trq;
    Mat3x3d tempTau;
    
    // perform the standard calcForces first
    ForceManager::calcForces();
    
    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();

    // now scale forces and torques of all the integrableObjects
      
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      for (integrableObject = mol->beginIntegrableObject(ii); 
           integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) {
        frc = integrableObject->getFrc();
        frc *= factor_;
        integrableObject->setFrc(frc);
        
        if (integrableObject->isDirectional()){
          trq = integrableObject->getTrq();
          trq *= factor_;
          integrableObject->setTrq(trq);
        }
      }
    }
    
    // set vraw to be the unmodulated potential
    lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
    curSnapshot->statData[Stats::VRAW] = lrPot_;
    
    // modulate the potential and update the snapshot
    lrPot_ *= factor_;
    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
    
    // scale the pressure tensor
    tempTau = curSnapshot->statData.getTau();
    tempTau *= factor_;
    curSnapshot->statData.setTau(tempTau);

    // now, on to the applied restraining potentials (if needed):
    RealType restPot_local = 0.0;
    RealType vHarm_local = 0.0;
    
    if (simParam->getUseRestraints()) {
      // do restraints from RestraintForceManager:
      //restPot_local = doRestraints(1.0 - factor_);     
      restPot_local = doRestraints(1.0 - factor_);      
      vHarm_local = getUnscaledPotential();
    }
      
#ifdef IS_MPI
    RealType restPot;
    MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, 
                              MPI::REALTYPE, MPI::SUM);
    MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1, 
                              MPI::REALTYPE, MPI::SUM);         
    lrPot_ += restPot;
#else
    lrPot_ += restPot_local;
    vHarm_ = vHarm_local;
#endif

    // give the final values to stats
    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
    curSnapshot->statData[Stats::VHARM] = vHarm_;
  }  
}
Revision:	1464
Committed:	Fri Jul 9 19:29:05 2010 UTC (14 years, 9 months ago) by gezelter
Original Path:	*trunk/src/restraints/ThermoIntegrationForceManager.cpp*
File size:	6170 byte(s)
Log Message:	removing cruft (atom numbers, do_pot, do_stress) from many modules and force managers
#	User	Rev	Content
1	gezelter	507	/*
2	chrisfen	417	* Copyright (c) 2005 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chrisfen	417	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chrisfen	417	* 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	chrisfen	417	*/
41
42	cli2	1360
43	chrisfen	417	#include "restraints/ThermoIntegrationForceManager.hpp"
44
45	chrisfen	1028	#ifdef IS_MPI
46			#include <mpi.h>
47	cli2	1360	#endif
48	chrisfen	1028
49	gezelter	1390	namespace OpenMD {
50	chrisfen	417
51			ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
52	cli2	1360	RestraintForceManager(info){
53			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54			simParam = info_->getSimParams();
55	chrisfen	417
56	cli2	1360	if (simParam->haveThermodynamicIntegrationLambda()){
57			tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
58			}
59			else{
60			tIntLambda_ = 1.0;
61			sprintf(painCave.errMsg,
62			"ThermoIntegration error: the transformation parameter\n"
63	gezelter	1390	"\t(lambda) was not specified. OpenMD will use a default\n"
64	cli2	1360	"\tvalue of %f. To set lambda, use the \n"
65			"\tthermodynamicIntegrationLambda variable.\n",
66			tIntLambda_);
67			painCave.isFatal = 0;
68			simError();
69			}
70	chrisfen	417
71	cli2	1360	if (simParam->haveThermodynamicIntegrationK()){
72			tIntK_ = simParam->getThermodynamicIntegrationK();
73			}
74			else{
75			tIntK_ = 1.0;
76			sprintf(painCave.errMsg,
77			"ThermoIntegration Warning: the tranformation parameter\n"
78	gezelter	1390	"\texponent (k) was not specified. OpenMD will use a default\n"
79	cli2	1360	"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
80			"\tvariable.\n",
81			tIntK_);
82			painCave.isFatal = 0;
83			simError();
84			}
85	chrisfen	417
86	cli2	1360	// build the scaling factor used to modulate the forces and torques
87			factor_ = pow(tIntLambda_, tIntK_);
88			}
89	chrisfen	417
90			ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
91			}
92
93	gezelter	1464	void ThermoIntegrationForceManager::calcForces(){
94	chrisfen	417	Snapshot* curSnapshot;
95			SimInfo::MoleculeIterator mi;
96			Molecule* mol;
97			Molecule::IntegrableObjectIterator ii;
98			StuntDouble* integrableObject;
99			Vector3d frc;
100			Vector3d trq;
101	chrisfen	423	Mat3x3d tempTau;
102	chrisfen	417
103			// perform the standard calcForces first
104	gezelter	1464	ForceManager::calcForces();
105	chrisfen	417
106	chrisfen	419	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
107
108	chrisfen	417	// now scale forces and torques of all the integrableObjects
109
110			for (mol = info_->beginMolecule(mi); mol != NULL;
111			mol = info_->nextMolecule(mi)) {
112			for (integrableObject = mol->beginIntegrableObject(ii);
113			integrableObject != NULL;
114			integrableObject = mol->nextIntegrableObject(ii)) {
115			frc = integrableObject->getFrc();
116			frc *= factor_;
117			integrableObject->setFrc(frc);
118
119			if (integrableObject->isDirectional()){
120			trq = integrableObject->getTrq();
121			trq *= factor_;
122			integrableObject->setTrq(trq);
123			}
124			}
125			}
126	cli2	1360
127	chrisfen	420	// set vraw to be the unmodulated potential
128			lrPot_ = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL];
129			curSnapshot->statData[Stats::VRAW] = lrPot_;
130	chrisfen	417
131	chrisfen	420	// modulate the potential and update the snapshot
132			lrPot_ *= factor_;
133			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
134
135	chrisfen	423	// scale the pressure tensor
136			tempTau = curSnapshot->statData.getTau();
137			tempTau *= factor_;
138			curSnapshot->statData.setTau(tempTau);
139	cli2	1360
140			// now, on to the applied restraining potentials (if needed):
141			RealType restPot_local = 0.0;
142			RealType vHarm_local = 0.0;
143
144			if (simParam->getUseRestraints()) {
145			// do restraints from RestraintForceManager:
146			//restPot_local = doRestraints(1.0 - factor_);
147			restPot_local = doRestraints(1.0 - factor_);
148			vHarm_local = getUnscaledPotential();
149			}
150	chrisfen	417
151	cli2	1360	#ifdef IS_MPI
152			RealType restPot;
153			MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
154			MPI::REALTYPE, MPI::SUM);
155			MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1,
156			MPI::REALTYPE, MPI::SUM);
157			lrPot_ += restPot;
158	chrisfen	1028	#else
159	cli2	1360	lrPot_ += restPot_local;
160			vHarm_ = vHarm_local;
161			#endif
162	chrisfen	1028
163	cli2	1360	// give the final values to stats
164			curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot_;
165			curSnapshot->statData[Stats::VHARM] = vHarm_;
166			}
167	chrisfen	417	}