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).
 */
 
#ifdef IS_MPI
#include <mpi.h>
#endif

#include "restraints/ThermoIntegrationForceManager.hpp"

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:	1938
Committed:	Thu Oct 31 15:32:17 2013 UTC (12 years ago) by gezelter
File size:	5979 byte(s)
Log Message:	Some MPI include re-ordering to work with the Intel MPI implementation.
#	Content
1	/*
2	* 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	* 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	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include "restraints/ThermoIntegrationForceManager.hpp"
48
49	namespace OpenMD {
50
51	ThermoIntegrationForceManager::ThermoIntegrationForceManager(SimInfo* info):
52	RestraintForceManager(info){
53	currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
54	simParam = info_->getSimParams();
55
56	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	"\t(lambda) was not specified. OpenMD will use a default\n"
64	"\tvalue of %f. To set lambda, use the \n"
65	"\tthermodynamicIntegrationLambda variable.\n",
66	tIntLambda_);
67	painCave.isFatal = 0;
68	simError();
69	}
70
71	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	"\texponent (k) was not specified. OpenMD will use a default\n"
79	"\tvalue of %f. To set k, use the thermodynamicIntegrationK\n"
80	"\tvariable.\n",
81	tIntK_);
82	painCave.isFatal = 0;
83	simError();
84	}
85
86	// build the scaling factor used to modulate the forces and torques
87	factor_ = pow(tIntLambda_, tIntK_);
88	}
89
90	ThermoIntegrationForceManager::~ThermoIntegrationForceManager(){
91	}
92
93	void ThermoIntegrationForceManager::calcForces(){
94	Snapshot* curSnapshot;
95	SimInfo::MoleculeIterator mi;
96	Molecule* mol;
97	Molecule::IntegrableObjectIterator ii;
98	StuntDouble* sd;
99	Vector3d frc;
100	Vector3d trq;
101	Mat3x3d tempTau;
102
103	// perform the standard calcForces first
104	ForceManager::calcForces();
105
106	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
107
108	// now scale forces and torques of all the sds
109
110	for (mol = info_->beginMolecule(mi); mol != NULL;
111	mol = info_->nextMolecule(mi)) {
112
113	for (sd = mol->beginIntegrableObject(ii); sd != NULL;
114	sd = mol->nextIntegrableObject(ii)) {
115
116	frc = sd->getFrc();
117	frc *= factor_;
118	sd->setFrc(frc);
119
120	if (sd->isDirectional()){
121	trq = sd->getTrq();
122	trq *= factor_;
123	sd->setTrq(trq);
124	}
125	}
126	}
127
128	// set rawPotential to be the unmodulated potential
129	lrPot_ = curSnapshot->getLongRangePotential();
130	curSnapshot->setRawPotential(lrPot_);
131
132	// modulate the potential and update the snapshot
133	lrPot_ *= factor_;
134	curSnapshot->setLongRangePotential(lrPot_);
135
136	// scale the pressure tensor
137	tempTau = curSnapshot->getStressTensor();
138	tempTau *= factor_;
139	curSnapshot->setStressTensor(tempTau);
140
141	// now, on to the applied restraining potentials (if needed):
142	RealType restPot_local = 0.0;
143	RealType vHarm_local = 0.0;
144
145	if (simParam->getUseRestraints()) {
146	// do restraints from RestraintForceManager:
147	restPot_local = doRestraints(1.0 - factor_);
148	vHarm_local = getUnscaledPotential();
149	}
150
151	#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	#else
159	lrPot_ += restPot_local;
160	vHarm_ = vHarm_local;
161	#endif
162
163	// give the final values to stats
164	curSnapshot->setLongRangePotential(lrPot_);
165	curSnapshot->setRestraintPotential(vHarm_);
166	}
167	}