src/restraints/RestraintForceManager.cpp

/*
 * Copyright (c) 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 <cmath>
#include "restraints/RestraintForceManager.hpp"
#include "restraints/MolecularRestraint.hpp"
#include "restraints/ObjectRestraint.hpp"
#include "io/RestReader.hpp"
#include "utils/simError.h"
#include "utils/PhysicalConstants.hpp"
#include "utils/StringUtils.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif


namespace OpenMD {

  RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) {

    // order of affairs:
    //
    // 1) create restraints from the restraintStamps found in the MD
    // file.
    //
    // 2) Create RestraintReader to parse the input files for the ideal
    // structures.  This reader will set reference structures, and will 
    // calculate molecular centers of mass, etc.
    //
    // 3) sit around and wait for calcForces to be called.  When it comes, 
    // call the normal force manager calcForces, then loop through the 
    // restrained objects and do their restraint forces.

    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    Globals* simParam = info_->getSimParams();

    if (simParam->haveStatusTime()){      
      restTime_ = simParam->getStatusTime();
    } else {
      sprintf(painCave.errMsg,
              "Restraint warning: If you use restraints without setting\n"
              "\tstatusTime, no restraint data will be written to the rest\n"
              "\tfile.\n");
      painCave.isFatal = 0;
      simError();
      restTime_ = simParam->getRunTime();
    }

    int nRestraintStamps = simParam->getNRestraintStamps();
    std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps();

    for (int i = 0; i < nRestraintStamps; i++){

      std::string myType = toUpperCopy(stamp[i]->getType());

      if (myType.compare("MOLECULAR")==0){

        int molIndex;
        std::vector<Vector3d> ref;
        Vector3d refCom;

        if (!stamp[i]->haveMolIndex()) {
          sprintf(painCave.errMsg,
                  "Restraint Error: A molecular restraint was specified\n"
                  "\twithout providing a value for molIndex.\n");
          painCave.isFatal = 1;
          simError();      
        } else {
          molIndex = stamp[i]->getMolIndex();
        }
        
        if (molIndex < 0) {
          sprintf(painCave.errMsg,
                  "Restraint Error: A molecular restraint was specified\n"
                  "\twith a molIndex that was less than 0\n");
          painCave.isFatal = 1;
          simError();      
        }
        if (molIndex >= info_->getNGlobalMolecules()) {
          sprintf(painCave.errMsg,
                  "Restraint Error: A molecular restraint was specified with\n"
                  "\ta molIndex that was greater than the total number of molecules\n");
          painCave.isFatal = 1;
          simError();      
        }
       
        Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex);
        
        if (mol == NULL) {
#ifdef IS_MPI
          // getMoleculeByGlobalIndex returns a NULL in parallel if
          // this proc doesn't have the molecule.  Do a quick check to
          // make sure another processor is supposed to have it.
         
          int myrank = MPI::COMM_WORLD.Get_rank();
          if (info_->getMolToProc(molIndex) == myrank) {
            // If we were supposed to have it but got a null, then freak out.
#endif

            sprintf(painCave.errMsg,
                    "Restraint Error: A molecular restraint was specified, but\n"
                    "\tno molecule was found with global index %d.\n",
                    molIndex);
            painCave.isFatal = 1;
            simError();     

#ifdef IS_MPI
          }
#endif
        }
        

#ifdef IS_MPI
        // only handle this molecular restraint if this processor owns the
        // molecule
        int myrank = MPI::COMM_WORLD.Get_rank();
        if (info_->getMolToProc(molIndex) == myrank) {
#endif

        MolecularRestraint* rest = new MolecularRestraint();

        std::string restPre("mol_");
        std::stringstream restName;
        restName << restPre << molIndex;
        rest->setRestraintName(restName.str());
        
        if (stamp[i]->haveDisplacementSpringConstant()) {
          rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
        }                  
        if (stamp[i]->haveTwistSpringConstant()) {
          rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
        }        
        if (stamp[i]->haveSwingXSpringConstant()) {
          rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
        }
        if (stamp[i]->haveSwingYSpringConstant()) {
          rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
        }
        if (stamp[i]->haveRestrainedTwistAngle()) {
          rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle() * M_PI/180.0);
        }
        if (stamp[i]->haveRestrainedSwingYAngle()) {
          rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle() * M_PI/180.0);
        }
        if (stamp[i]->haveRestrainedSwingXAngle()) {
          rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0);
        }
        if (stamp[i]->havePrint()) {
          rest->setPrintRestraint(stamp[i]->getPrint());
        }

        restraints_.push_back(rest);
        mol->addProperty(new RestraintData("Restraint", rest));
        restrainedMols_.push_back(mol);
#ifdef IS_MPI
        }
#endif        
      } else if (myType.compare("OBJECT") == 0) {
        
        std::string objectSelection;

        if (!stamp[i]->haveObjectSelection()) {
          sprintf(painCave.errMsg,
                  "Restraint Error: An object restraint was specified\n"
                  "\twithout providing a selection script in the\n"
                  "\tobjectSelection variable.\n");
          painCave.isFatal = 1;
          simError();      
        } else {
          objectSelection = stamp[i]->getObjectSelection();
        }

        SelectionEvaluator evaluator(info);
        SelectionManager seleMan(info);
                
        evaluator.loadScriptString(objectSelection);
        seleMan.setSelectionSet(evaluator.evaluate());        
        int selectionCount = seleMan.getSelectionCount();
        
        sprintf(painCave.errMsg,
                "Restraint Info: The specified restraint objectSelection,\n"
                "\t\t%s\n"
                "\twill result in %d integrable objects being\n"
                "\trestrained.\n", objectSelection.c_str(), selectionCount);
        painCave.isFatal = 0;
        simError();                     

        int selei;
        StuntDouble* sd;

        for (sd = seleMan.beginSelected(selei); sd != NULL; 
             sd = seleMan.nextSelected(selei)) {
          
          ObjectRestraint* rest = new ObjectRestraint();
          
          if (stamp[i]->haveDisplacementSpringConstant()) {
            rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
          }                  
          if (stamp[i]->haveTwistSpringConstant()) {
            rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
          }        
          if (stamp[i]->haveSwingXSpringConstant()) {
            rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
          }
          if (stamp[i]->haveSwingYSpringConstant()) {
            rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
          }
          if (stamp[i]->haveRestrainedTwistAngle()) {
            rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle());
          }
          if (stamp[i]->haveRestrainedSwingXAngle()) {
            rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle());
          }
          if (stamp[i]->haveRestrainedSwingYAngle()) {
            rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle());
          }     
          if (stamp[i]->havePrint()) {
            rest->setPrintRestraint(stamp[i]->getPrint());
          }
    
          restraints_.push_back(rest);
          sd->addProperty(new RestraintData("Restraint", rest));
          restrainedObjs_.push_back(sd);                    
        }

      }
    }

    // ThermodynamicIntegration subclasses RestraintForceManager, and there
    // are times when it won't use restraints at all, so only open the
    // restraint file if we are actually using restraints:

    if (simParam->getUseRestraints()) {
      std::string refFile = simParam->getRestraint_file();
      RestReader* rr = new RestReader(info, refFile);

      rr->readReferenceStructure();
    }

    restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest";
    restOut = new RestWriter(info_, restOutput_.c_str(), restraints_);
    
    if(!restOut){
      sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n");
      painCave.isFatal = 1;
      simError();
    } 

    // todo: figure out the scale factor.  Right now, just scale them all to 1
    std::vector<Restraint*>::const_iterator resti;
    for(resti=restraints_.begin(); resti != restraints_.end(); ++resti){
      (*resti)->setScaleFactor(1.0);
    }
  }

  RestraintForceManager::~RestraintForceManager(){
    if (restOut)
      delete restOut;
  }

  void RestraintForceManager::init() {
    currRestTime_ = currSnapshot_->getTime();
  }

  void RestraintForceManager::calcForces(bool needPotential, bool needStress){

    ForceManager::calcForces(needPotential, needStress);    
    RealType restPot_local, restPot;

    restPot_local = doRestraints(1.0);

#ifdef IS_MPI    
    MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, 
                              MPI::REALTYPE, MPI::SUM);
#else
    restPot = restPot_local;
#endif
    currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
    currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot;
    currSnapshot_->statData[Stats::VHARM] = restPot;

    //write out forces and current positions of restrained molecules    
    if (currSnapshot_->getTime() >= currRestTime_){
      restOut->writeRest(restInfo_);
      currRestTime_ += restTime_;
    }
  }

  RealType RestraintForceManager::doRestraints(RealType scalingFactor){
    std::vector<Molecule*>::const_iterator rm;
    GenericData* data;
    Molecule::IntegrableObjectIterator ioi;
    MolecularRestraint* mRest;
    StuntDouble* sd;
    RealType pTot;

    std::vector<StuntDouble*>::const_iterator ro;
    ObjectRestraint* oRest;

    std::map<int, Restraint::RealPair> restInfo;

    unscaledPotential_ = 0.0;

    restInfo_.clear();

    for(rm=restrainedMols_.begin(); rm != restrainedMols_.end(); ++rm){

      // make sure this molecule (*rm) has a generic data for restraints:
      data = (*rm)->getPropertyByName("Restraint");
      if (data != NULL) {
        // make sure we can reinterpret the generic data as restraint data:
        RestraintData* restData= dynamic_cast<RestraintData*>(data);        
        if (restData != NULL) {
          // make sure we can reinterpet the restraint data as a pointer to
          // an MolecularRestraint:
          mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
          if (mRest == NULL) {
            sprintf( painCave.errMsg,
                     "Can not cast RestraintData to MolecularRestraint\n");
            painCave.severity = OPENMD_ERROR;
            painCave.isFatal = 1;
            simError();                      
          }
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to RestraintData\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();       
        }
      } else {
        sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }

      // phew.  At this point, we should have the pointer to the
      // correct MolecularRestraint in the variable mRest.

      Vector3d molCom = (*rm)->getCom();

      std::vector<Vector3d> struc;
      std::vector<Vector3d> forces;
      
      for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; 
          sd = (*rm)->nextIntegrableObject(ioi)) {        
        struc.push_back(sd->getPos());
      }

      mRest->setScaleFactor(scalingFactor);
      mRest->calcForce(struc, molCom);
      forces = mRest->getRestraintForces();
      int index = 0;

      for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; 
          sd = (*rm)->nextIntegrableObject(ioi)) {        
        sd->addFrc(forces[index]);
        struc.push_back(sd->getPos());
        index++;
      }
      
      unscaledPotential_ += mRest->getUnscaledPotential();

      restInfo = mRest->getRestraintInfo();

      // only collect data on restraints that we're going to print:
      if (mRest->getPrintRestraint()) 
        restInfo_.push_back(restInfo);
    }

    for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){
      // make sure this object (*ro) has a generic data for restraints:
      data = (*ro)->getPropertyByName("Restraint");
      if (data != NULL) {
        // make sure we can reinterpret the generic data as restraint data:
        RestraintData* restData= dynamic_cast<RestraintData*>(data);        
        if (restData != NULL) {
          // make sure we can reinterpet the restraint data as a pointer to
          // an ObjectRestraint:
          oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
          if (oRest == NULL) {
            sprintf( painCave.errMsg,
                     "Can not cast RestraintData to ObjectRestraint\n");
            painCave.severity = OPENMD_ERROR;
            painCave.isFatal = 1;
            simError();                      
          }
        } else {
          sprintf( painCave.errMsg,
                   "Can not cast GenericData to RestraintData\n");
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();       
        }
      } else {
        sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();          
      }
      
      // phew.  At this point, we should have the pointer to the
      // correct Object restraint in the variable oRest.

      oRest->setScaleFactor(scalingFactor);
      
      Vector3d pos = (*ro)->getPos();

      if ( (*ro)->isDirectional() ) {

        // directional objects may have orientational restraints as well
        // as positional, so get the rotation matrix first:

        RotMat3x3d A = (*ro)->getA();
        oRest->calcForce(pos, A);
        (*ro)->addFrc(oRest->getRestraintForce());
        (*ro)->addTrq(oRest->getRestraintTorque());
      } else {        

        // plain vanilla positional restraints:

        oRest->calcForce(pos);
        (*ro)->addFrc(oRest->getRestraintForce());
      }

      unscaledPotential_ += oRest->getUnscaledPotential();

      restInfo = oRest->getRestraintInfo();

      // only collect data on restraints that we're going to print:
      if (oRest->getPrintRestraint()) 
        restInfo_.push_back(restInfo);
    }

    return unscaledPotential_ * scalingFactor;
  }
}
Revision:	1398
Committed:	Tue Dec 8 22:17:02 2009 UTC (15 years, 4 months ago) by gezelter
Original Path:	*trunk/src/restraints/RestraintForceManager.cpp*
File size:	17562 byte(s)
Log Message:	Parallel bugfix in RestraintForceManager Reverted back to hydrodynamics on triangular plates for SMIPDForceManager Removed thermalLength and thermalConductivity keywords from Globals. Bug tracking in openmdformat (not yet resolved).
#	User	Rev	Content
1	cli2	1360	/*
2			* Copyright (c) 2009 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	cli2	1360	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	cli2	1360	* 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	cli2	1360	*/
41
42			#include <cmath>
43			#include "restraints/RestraintForceManager.hpp"
44			#include "restraints/MolecularRestraint.hpp"
45			#include "restraints/ObjectRestraint.hpp"
46			#include "io/RestReader.hpp"
47			#include "utils/simError.h"
48	gezelter	1390	#include "utils/PhysicalConstants.hpp"
49	cli2	1360	#include "utils/StringUtils.hpp"
50			#include "selection/SelectionEvaluator.hpp"
51			#include "selection/SelectionManager.hpp"
52			#ifdef IS_MPI
53			#include <mpi.h>
54			#endif
55
56
57	gezelter	1390	namespace OpenMD {
58	cli2	1360
59			RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) {
60
61			// order of affairs:
62			//
63			// 1) create restraints from the restraintStamps found in the MD
64			// file.
65			//
66			// 2) Create RestraintReader to parse the input files for the ideal
67			// structures. This reader will set reference structures, and will
68			// calculate molecular centers of mass, etc.
69			//
70			// 3) sit around and wait for calcForces to be called. When it comes,
71			// call the normal force manager calcForces, then loop through the
72			// restrained objects and do their restraint forces.
73
74			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
75			Globals* simParam = info_->getSimParams();
76
77			if (simParam->haveStatusTime()){
78			restTime_ = simParam->getStatusTime();
79			} else {
80			sprintf(painCave.errMsg,
81	cli2	1364	"Restraint warning: If you use restraints without setting\n"
82			"\tstatusTime, no restraint data will be written to the rest\n"
83	cli2	1360	"\tfile.\n");
84			painCave.isFatal = 0;
85			simError();
86			restTime_ = simParam->getRunTime();
87			}
88
89			int nRestraintStamps = simParam->getNRestraintStamps();
90			std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps();
91
92			for (int i = 0; i < nRestraintStamps; i++){
93
94			std::string myType = toUpperCopy(stamp[i]->getType());
95
96			if (myType.compare("MOLECULAR")==0){
97
98			int molIndex;
99			std::vector<Vector3d> ref;
100			Vector3d refCom;
101
102			if (!stamp[i]->haveMolIndex()) {
103			sprintf(painCave.errMsg,
104			"Restraint Error: A molecular restraint was specified\n"
105			"\twithout providing a value for molIndex.\n");
106			painCave.isFatal = 1;
107			simError();
108			} else {
109			molIndex = stamp[i]->getMolIndex();
110			}
111
112	gezelter	1366	if (molIndex < 0) {
113	cli2	1360	sprintf(painCave.errMsg,
114	gezelter	1366	"Restraint Error: A molecular restraint was specified\n"
115			"\twith a molIndex that was less than 0\n");
116	cli2	1360	painCave.isFatal = 1;
117			simError();
118			}
119	gezelter	1366	if (molIndex >= info_->getNGlobalMolecules()) {
120			sprintf(painCave.errMsg,
121			"Restraint Error: A molecular restraint was specified with\n"
122			"\ta molIndex that was greater than the total number of molecules\n");
123			painCave.isFatal = 1;
124			simError();
125			}
126
127			Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex);
128	cli2	1360
129	gezelter	1366	if (mol == NULL) {
130			#ifdef IS_MPI
131			// getMoleculeByGlobalIndex returns a NULL in parallel if
132			// this proc doesn't have the molecule. Do a quick check to
133			// make sure another processor is supposed to have it.
134
135			int myrank = MPI::COMM_WORLD.Get_rank();
136			if (info_->getMolToProc(molIndex) == myrank) {
137			// If we were supposed to have it but got a null, then freak out.
138			#endif
139
140			sprintf(painCave.errMsg,
141			"Restraint Error: A molecular restraint was specified, but\n"
142			"\tno molecule was found with global index %d.\n",
143			molIndex);
144			painCave.isFatal = 1;
145			simError();
146
147			#ifdef IS_MPI
148			}
149			#endif
150			}
151
152	gezelter	1398
153			#ifdef IS_MPI
154			// only handle this molecular restraint if this processor owns the
155			// molecule
156			int myrank = MPI::COMM_WORLD.Get_rank();
157			if (info_->getMolToProc(molIndex) == myrank) {
158			#endif
159
160	cli2	1360	MolecularRestraint* rest = new MolecularRestraint();
161
162			std::string restPre("mol_");
163			std::stringstream restName;
164			restName << restPre << molIndex;
165			rest->setRestraintName(restName.str());
166
167			if (stamp[i]->haveDisplacementSpringConstant()) {
168			rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
169			}
170			if (stamp[i]->haveTwistSpringConstant()) {
171			rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
172			}
173			if (stamp[i]->haveSwingXSpringConstant()) {
174			rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
175			}
176			if (stamp[i]->haveSwingYSpringConstant()) {
177			rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
178			}
179			if (stamp[i]->haveRestrainedTwistAngle()) {
180			rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle() * M_PI/180.0);
181			}
182			if (stamp[i]->haveRestrainedSwingYAngle()) {
183			rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle() * M_PI/180.0);
184			}
185			if (stamp[i]->haveRestrainedSwingXAngle()) {
186			rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0);
187			}
188	cli2	1364	if (stamp[i]->havePrint()) {
189			rest->setPrintRestraint(stamp[i]->getPrint());
190			}
191	cli2	1360
192			restraints_.push_back(rest);
193			mol->addProperty(new RestraintData("Restraint", rest));
194			restrainedMols_.push_back(mol);
195	gezelter	1398	#ifdef IS_MPI
196			}
197			#endif
198	cli2	1360	} else if (myType.compare("OBJECT") == 0) {
199
200			std::string objectSelection;
201
202			if (!stamp[i]->haveObjectSelection()) {
203			sprintf(painCave.errMsg,
204			"Restraint Error: An object restraint was specified\n"
205			"\twithout providing a selection script in the\n"
206			"\tobjectSelection variable.\n");
207			painCave.isFatal = 1;
208			simError();
209			} else {
210			objectSelection = stamp[i]->getObjectSelection();
211			}
212
213			SelectionEvaluator evaluator(info);
214			SelectionManager seleMan(info);
215	cli2	1364
216	cli2	1360	evaluator.loadScriptString(objectSelection);
217			seleMan.setSelectionSet(evaluator.evaluate());
218			int selectionCount = seleMan.getSelectionCount();
219
220			sprintf(painCave.errMsg,
221			"Restraint Info: The specified restraint objectSelection,\n"
222			"\t\t%s\n"
223			"\twill result in %d integrable objects being\n"
224			"\trestrained.\n", objectSelection.c_str(), selectionCount);
225			painCave.isFatal = 0;
226			simError();
227
228			int selei;
229			StuntDouble* sd;
230
231			for (sd = seleMan.beginSelected(selei); sd != NULL;
232			sd = seleMan.nextSelected(selei)) {
233
234			ObjectRestraint* rest = new ObjectRestraint();
235
236			if (stamp[i]->haveDisplacementSpringConstant()) {
237			rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
238			}
239			if (stamp[i]->haveTwistSpringConstant()) {
240			rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
241			}
242			if (stamp[i]->haveSwingXSpringConstant()) {
243			rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
244			}
245			if (stamp[i]->haveSwingYSpringConstant()) {
246			rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
247			}
248			if (stamp[i]->haveRestrainedTwistAngle()) {
249			rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle());
250			}
251			if (stamp[i]->haveRestrainedSwingXAngle()) {
252			rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle());
253			}
254			if (stamp[i]->haveRestrainedSwingYAngle()) {
255			rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle());
256	cli2	1364	}
257			if (stamp[i]->havePrint()) {
258			rest->setPrintRestraint(stamp[i]->getPrint());
259			}
260
261	cli2	1360	restraints_.push_back(rest);
262			sd->addProperty(new RestraintData("Restraint", rest));
263			restrainedObjs_.push_back(sd);
264			}
265
266			}
267			}
268
269			// ThermodynamicIntegration subclasses RestraintForceManager, and there
270			// are times when it won't use restraints at all, so only open the
271			// restraint file if we are actually using restraints:
272
273			if (simParam->getUseRestraints()) {
274			std::string refFile = simParam->getRestraint_file();
275			RestReader* rr = new RestReader(info, refFile);
276
277			rr->readReferenceStructure();
278			}
279
280			restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest";
281			restOut = new RestWriter(info_, restOutput_.c_str(), restraints_);
282
283			if(!restOut){
284			sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n");
285			painCave.isFatal = 1;
286			simError();
287			}
288
289			// todo: figure out the scale factor. Right now, just scale them all to 1
290			std::vector<Restraint*>::const_iterator resti;
291			for(resti=restraints_.begin(); resti != restraints_.end(); ++resti){
292			(*resti)->setScaleFactor(1.0);
293			}
294			}
295
296			RestraintForceManager::~RestraintForceManager(){
297			if (restOut)
298			delete restOut;
299			}
300
301			void RestraintForceManager::init() {
302			currRestTime_ = currSnapshot_->getTime();
303			}
304
305			void RestraintForceManager::calcForces(bool needPotential, bool needStress){
306
307			ForceManager::calcForces(needPotential, needStress);
308			RealType restPot_local, restPot;
309
310			restPot_local = doRestraints(1.0);
311
312			#ifdef IS_MPI
313			MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
314			MPI::REALTYPE, MPI::SUM);
315			#else
316			restPot = restPot_local;
317			#endif
318			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
319			currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot;
320			currSnapshot_->statData[Stats::VHARM] = restPot;
321
322			//write out forces and current positions of restrained molecules
323			if (currSnapshot_->getTime() >= currRestTime_){
324			restOut->writeRest(restInfo_);
325			currRestTime_ += restTime_;
326			}
327			}
328
329			RealType RestraintForceManager::doRestraints(RealType scalingFactor){
330			std::vector<Molecule*>::const_iterator rm;
331			GenericData* data;
332			Molecule::IntegrableObjectIterator ioi;
333			MolecularRestraint* mRest;
334			StuntDouble* sd;
335			RealType pTot;
336
337			std::vector<StuntDouble*>::const_iterator ro;
338			ObjectRestraint* oRest;
339
340			std::map<int, Restraint::RealPair> restInfo;
341
342			unscaledPotential_ = 0.0;
343
344			restInfo_.clear();
345
346			for(rm=restrainedMols_.begin(); rm != restrainedMols_.end(); ++rm){
347
348			// make sure this molecule (*rm) has a generic data for restraints:
349			data = (*rm)->getPropertyByName("Restraint");
350			if (data != NULL) {
351			// make sure we can reinterpret the generic data as restraint data:
352			RestraintData* restData= dynamic_cast<RestraintData*>(data);
353			if (restData != NULL) {
354			// make sure we can reinterpet the restraint data as a pointer to
355			// an MolecularRestraint:
356			mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
357			if (mRest == NULL) {
358			sprintf( painCave.errMsg,
359			"Can not cast RestraintData to MolecularRestraint\n");
360	gezelter	1390	painCave.severity = OPENMD_ERROR;
361	cli2	1360	painCave.isFatal = 1;
362			simError();
363			}
364			} else {
365			sprintf( painCave.errMsg,
366			"Can not cast GenericData to RestraintData\n");
367	gezelter	1390	painCave.severity = OPENMD_ERROR;
368	cli2	1360	painCave.isFatal = 1;
369			simError();
370			}
371			} else {
372			sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
373	gezelter	1390	painCave.severity = OPENMD_ERROR;
374	cli2	1360	painCave.isFatal = 1;
375			simError();
376			}
377
378			// phew. At this point, we should have the pointer to the
379			// correct MolecularRestraint in the variable mRest.
380
381			Vector3d molCom = (*rm)->getCom();
382
383			std::vector<Vector3d> struc;
384			std::vector<Vector3d> forces;
385
386			for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL;
387			sd = (*rm)->nextIntegrableObject(ioi)) {
388			struc.push_back(sd->getPos());
389			}
390
391			mRest->setScaleFactor(scalingFactor);
392			mRest->calcForce(struc, molCom);
393			forces = mRest->getRestraintForces();
394			int index = 0;
395
396			for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL;
397			sd = (*rm)->nextIntegrableObject(ioi)) {
398			sd->addFrc(forces[index]);
399			struc.push_back(sd->getPos());
400			index++;
401			}
402
403			unscaledPotential_ += mRest->getUnscaledPotential();
404
405			restInfo = mRest->getRestraintInfo();
406	cli2	1364
407			// only collect data on restraints that we're going to print:
408			if (mRest->getPrintRestraint())
409			restInfo_.push_back(restInfo);
410	cli2	1360	}
411
412			for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){
413			// make sure this object (*ro) has a generic data for restraints:
414			data = (*ro)->getPropertyByName("Restraint");
415			if (data != NULL) {
416			// make sure we can reinterpret the generic data as restraint data:
417			RestraintData* restData= dynamic_cast<RestraintData*>(data);
418			if (restData != NULL) {
419			// make sure we can reinterpet the restraint data as a pointer to
420			// an ObjectRestraint:
421			oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
422			if (oRest == NULL) {
423			sprintf( painCave.errMsg,
424			"Can not cast RestraintData to ObjectRestraint\n");
425	gezelter	1390	painCave.severity = OPENMD_ERROR;
426	cli2	1360	painCave.isFatal = 1;
427			simError();
428			}
429			} else {
430			sprintf( painCave.errMsg,
431			"Can not cast GenericData to RestraintData\n");
432	gezelter	1390	painCave.severity = OPENMD_ERROR;
433	cli2	1360	painCave.isFatal = 1;
434			simError();
435			}
436			} else {
437			sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
438	gezelter	1390	painCave.severity = OPENMD_ERROR;
439	cli2	1360	painCave.isFatal = 1;
440			simError();
441			}
442
443			// phew. At this point, we should have the pointer to the
444			// correct Object restraint in the variable oRest.
445
446			oRest->setScaleFactor(scalingFactor);
447
448			Vector3d pos = (*ro)->getPos();
449
450			if ( (*ro)->isDirectional() ) {
451
452			// directional objects may have orientational restraints as well
453			// as positional, so get the rotation matrix first:
454
455			RotMat3x3d A = (*ro)->getA();
456			oRest->calcForce(pos, A);
457			(*ro)->addFrc(oRest->getRestraintForce());
458			(*ro)->addTrq(oRest->getRestraintTorque());
459			} else {
460
461			// plain vanilla positional restraints:
462
463			oRest->calcForce(pos);
464			(*ro)->addFrc(oRest->getRestraintForce());
465			}
466
467			unscaledPotential_ += oRest->getUnscaledPotential();
468
469			restInfo = oRest->getRestraintInfo();
470	cli2	1364
471			// only collect data on restraints that we're going to print:
472			if (oRest->getPrintRestraint())
473			restInfo_.push_back(restInfo);
474	cli2	1360	}
475
476			return unscaledPotential_ * scalingFactor;
477			}
478			}