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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 

#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* sd;
    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 sds
      
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {

      for (sd = mol->beginIntegrableObject(ii); sd != NULL; 
           sd = mol->nextIntegrableObject(ii)) {

        frc = sd->getFrc();
        frc *= factor_;
        sd->setFrc(frc);
        
        if (sd->isDirectional()){
          trq = sd->getTrq();
          trq *= factor_;
          sd->setTrq(trq);
        }
      }
    }
    
    // set rawPotential to be the unmodulated potential
    lrPot_ = curSnapshot->getLongRangePotential();
    curSnapshot->setRawPotential(lrPot_);
    
    // modulate the potential and update the snapshot
    lrPot_ *= factor_;
    curSnapshot->setLongRangePotential(lrPot_);
    
    // scale the pressure tensor
    tempTau = curSnapshot->getStressTensor();
    tempTau *= factor_;
    curSnapshot->setStressTensor(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_);      
      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->setLongRangePotential(lrPot_);
    curSnapshot->setRestraintPotential(vHarm_);
  }  
}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	5980 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chrisfen	417	*/
42
43	cli2	1360
44	chrisfen	417	#include "restraints/ThermoIntegrationForceManager.hpp"
45
46	chrisfen	1028	#ifdef IS_MPI
47			#include <mpi.h>
48	cli2	1360	#endif
49	chrisfen	1028
50	gezelter	1390	namespace OpenMD {
51	chrisfen	417
52			ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
53	cli2	1360	RestraintForceManager(info){
54			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
55			simParam = info_->getSimParams();
56	chrisfen	417
57	cli2	1360	if (simParam->haveThermodynamicIntegrationLambda()){
58			tIntLambda_ = simParam->getThermodynamicIntegrationLambda();
59			}
60			else{
61			tIntLambda_ = 1.0;
62			sprintf(painCave.errMsg,
63			"ThermoIntegration error: the transformation parameter\n"
64	gezelter	1390	"\t(lambda) was not specified. OpenMD will use a default\n"
65	cli2	1360	"\tvalue of %f. To set lambda, use the \n"
66			"\tthermodynamicIntegrationLambda variable.\n",
67			tIntLambda_);
68			painCave.isFatal = 0;
69			simError();
70			}
71	chrisfen	417
72	cli2	1360	if (simParam->haveThermodynamicIntegrationK()){
73			tIntK_ = simParam->getThermodynamicIntegrationK();
74			}
75			else{
76			tIntK_ = 1.0;
77			sprintf(painCave.errMsg,
78			"ThermoIntegration Warning: the tranformation parameter\n"
79	gezelter	1390	"\texponent (k) was not specified. OpenMD will use a default\n"
80	cli2	1360	"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
81			"\tvariable.\n",
82			tIntK_);
83			painCave.isFatal = 0;
84			simError();
85			}
86	chrisfen	417
87	cli2	1360	// build the scaling factor used to modulate the forces and torques
88			factor_ = pow(tIntLambda_, tIntK_);
89			}
90	chrisfen	417
91			ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
92			}
93
94	gezelter	1464	void ThermoIntegrationForceManager::calcForces(){
95	chrisfen	417	Snapshot* curSnapshot;
96			SimInfo::MoleculeIterator mi;
97			Molecule* mol;
98			Molecule::IntegrableObjectIterator ii;
99	gezelter	1782	StuntDouble* sd;
100	chrisfen	417	Vector3d frc;
101			Vector3d trq;
102	chrisfen	423	Mat3x3d tempTau;
103	chrisfen	417
104			// perform the standard calcForces first
105	gezelter	1464	ForceManager::calcForces();
106	chrisfen	417
107	chrisfen	419	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
108
109	gezelter	1782	// now scale forces and torques of all the sds
110	chrisfen	417
111			for (mol = info_->beginMolecule(mi); mol != NULL;
112			mol = info_->nextMolecule(mi)) {
113	gezelter	1782
114			for (sd = mol->beginIntegrableObject(ii); sd != NULL;
115			sd = mol->nextIntegrableObject(ii)) {
116
117			frc = sd->getFrc();
118	chrisfen	417	frc *= factor_;
119	gezelter	1782	sd->setFrc(frc);
120	chrisfen	417
121	gezelter	1782	if (sd->isDirectional()){
122			trq = sd->getTrq();
123	chrisfen	417	trq *= factor_;
124	gezelter	1782	sd->setTrq(trq);
125	chrisfen	417	}
126			}
127			}
128	cli2	1360
129	gezelter	1782	// set rawPotential to be the unmodulated potential
130			lrPot_ = curSnapshot->getLongRangePotential();
131			curSnapshot->setRawPotential(lrPot_);
132	chrisfen	417
133	chrisfen	420	// modulate the potential and update the snapshot
134			lrPot_ *= factor_;
135	gezelter	1782	curSnapshot->setLongRangePotential(lrPot_);
136	chrisfen	420
137	chrisfen	423	// scale the pressure tensor
138	gezelter	1782	tempTau = curSnapshot->getStressTensor();
139	chrisfen	423	tempTau *= factor_;
140	gezelter	1782	curSnapshot->setStressTensor(tempTau);
141	cli2	1360
142			// now, on to the applied restraining potentials (if needed):
143			RealType restPot_local = 0.0;
144			RealType vHarm_local = 0.0;
145
146			if (simParam->getUseRestraints()) {
147			// do restraints from RestraintForceManager:
148			restPot_local = doRestraints(1.0 - factor_);
149			vHarm_local = getUnscaledPotential();
150			}
151	chrisfen	417
152	cli2	1360	#ifdef IS_MPI
153			RealType restPot;
154			MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
155			MPI::REALTYPE, MPI::SUM);
156			MPI::COMM_WORLD.Allreduce(&vHarm_local, &vHarm_, 1,
157			MPI::REALTYPE, MPI::SUM);
158			lrPot_ += restPot;
159	chrisfen	1028	#else
160	cli2	1360	lrPot_ += restPot_local;
161			vHarm_ = vHarm_local;
162			#endif
163	chrisfen	1028
164	cli2	1360	// give the final values to stats
165	gezelter	1782	curSnapshot->setLongRangePotential(lrPot_);
166			curSnapshot->setRestraintPotential(vHarm_);
167	cli2	1360	}
168	chrisfen	417	}