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
        }
        
        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);
        
      } 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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	17310 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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	cli2	1360	MolecularRestraint* rest = new MolecularRestraint();
153
154			std::string restPre("mol_");
155			std::stringstream restName;
156			restName << restPre << molIndex;
157			rest->setRestraintName(restName.str());
158
159			if (stamp[i]->haveDisplacementSpringConstant()) {
160			rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
161			}
162			if (stamp[i]->haveTwistSpringConstant()) {
163			rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
164			}
165			if (stamp[i]->haveSwingXSpringConstant()) {
166			rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
167			}
168			if (stamp[i]->haveSwingYSpringConstant()) {
169			rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
170			}
171			if (stamp[i]->haveRestrainedTwistAngle()) {
172			rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle() * M_PI/180.0);
173			}
174			if (stamp[i]->haveRestrainedSwingYAngle()) {
175			rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle() * M_PI/180.0);
176			}
177			if (stamp[i]->haveRestrainedSwingXAngle()) {
178			rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0);
179			}
180	cli2	1364	if (stamp[i]->havePrint()) {
181			rest->setPrintRestraint(stamp[i]->getPrint());
182			}
183	cli2	1360
184			restraints_.push_back(rest);
185			mol->addProperty(new RestraintData("Restraint", rest));
186			restrainedMols_.push_back(mol);
187
188			} else if (myType.compare("OBJECT") == 0) {
189
190			std::string objectSelection;
191
192			if (!stamp[i]->haveObjectSelection()) {
193			sprintf(painCave.errMsg,
194			"Restraint Error: An object restraint was specified\n"
195			"\twithout providing a selection script in the\n"
196			"\tobjectSelection variable.\n");
197			painCave.isFatal = 1;
198			simError();
199			} else {
200			objectSelection = stamp[i]->getObjectSelection();
201			}
202
203			SelectionEvaluator evaluator(info);
204			SelectionManager seleMan(info);
205	cli2	1364
206	cli2	1360	evaluator.loadScriptString(objectSelection);
207			seleMan.setSelectionSet(evaluator.evaluate());
208			int selectionCount = seleMan.getSelectionCount();
209
210			sprintf(painCave.errMsg,
211			"Restraint Info: The specified restraint objectSelection,\n"
212			"\t\t%s\n"
213			"\twill result in %d integrable objects being\n"
214			"\trestrained.\n", objectSelection.c_str(), selectionCount);
215			painCave.isFatal = 0;
216			simError();
217
218			int selei;
219			StuntDouble* sd;
220
221			for (sd = seleMan.beginSelected(selei); sd != NULL;
222			sd = seleMan.nextSelected(selei)) {
223
224			ObjectRestraint* rest = new ObjectRestraint();
225
226			if (stamp[i]->haveDisplacementSpringConstant()) {
227			rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant());
228			}
229			if (stamp[i]->haveTwistSpringConstant()) {
230			rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant());
231			}
232			if (stamp[i]->haveSwingXSpringConstant()) {
233			rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant());
234			}
235			if (stamp[i]->haveSwingYSpringConstant()) {
236			rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant());
237			}
238			if (stamp[i]->haveRestrainedTwistAngle()) {
239			rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle());
240			}
241			if (stamp[i]->haveRestrainedSwingXAngle()) {
242			rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle());
243			}
244			if (stamp[i]->haveRestrainedSwingYAngle()) {
245			rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle());
246	cli2	1364	}
247			if (stamp[i]->havePrint()) {
248			rest->setPrintRestraint(stamp[i]->getPrint());
249			}
250
251	cli2	1360	restraints_.push_back(rest);
252			sd->addProperty(new RestraintData("Restraint", rest));
253			restrainedObjs_.push_back(sd);
254			}
255
256			}
257			}
258
259			// ThermodynamicIntegration subclasses RestraintForceManager, and there
260			// are times when it won't use restraints at all, so only open the
261			// restraint file if we are actually using restraints:
262
263			if (simParam->getUseRestraints()) {
264			std::string refFile = simParam->getRestraint_file();
265			RestReader* rr = new RestReader(info, refFile);
266
267			rr->readReferenceStructure();
268			}
269
270			restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest";
271			restOut = new RestWriter(info_, restOutput_.c_str(), restraints_);
272
273			if(!restOut){
274			sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n");
275			painCave.isFatal = 1;
276			simError();
277			}
278
279			// todo: figure out the scale factor. Right now, just scale them all to 1
280			std::vector<Restraint*>::const_iterator resti;
281			for(resti=restraints_.begin(); resti != restraints_.end(); ++resti){
282			(*resti)->setScaleFactor(1.0);
283			}
284			}
285
286			RestraintForceManager::~RestraintForceManager(){
287			if (restOut)
288			delete restOut;
289			}
290
291			void RestraintForceManager::init() {
292			currRestTime_ = currSnapshot_->getTime();
293			}
294
295			void RestraintForceManager::calcForces(bool needPotential, bool needStress){
296
297			ForceManager::calcForces(needPotential, needStress);
298			RealType restPot_local, restPot;
299
300			restPot_local = doRestraints(1.0);
301
302			#ifdef IS_MPI
303			MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1,
304			MPI::REALTYPE, MPI::SUM);
305			#else
306			restPot = restPot_local;
307			#endif
308			currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
309			currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot;
310			currSnapshot_->statData[Stats::VHARM] = restPot;
311
312			//write out forces and current positions of restrained molecules
313			if (currSnapshot_->getTime() >= currRestTime_){
314			restOut->writeRest(restInfo_);
315			currRestTime_ += restTime_;
316			}
317			}
318
319			RealType RestraintForceManager::doRestraints(RealType scalingFactor){
320			std::vector<Molecule*>::const_iterator rm;
321			GenericData* data;
322			Molecule::IntegrableObjectIterator ioi;
323			MolecularRestraint* mRest;
324			StuntDouble* sd;
325			RealType pTot;
326
327			std::vector<StuntDouble*>::const_iterator ro;
328			ObjectRestraint* oRest;
329
330			std::map<int, Restraint::RealPair> restInfo;
331
332			unscaledPotential_ = 0.0;
333
334			restInfo_.clear();
335
336			for(rm=restrainedMols_.begin(); rm != restrainedMols_.end(); ++rm){
337
338			// make sure this molecule (*rm) has a generic data for restraints:
339			data = (*rm)->getPropertyByName("Restraint");
340			if (data != NULL) {
341			// make sure we can reinterpret the generic data as restraint data:
342			RestraintData* restData= dynamic_cast<RestraintData*>(data);
343			if (restData != NULL) {
344			// make sure we can reinterpet the restraint data as a pointer to
345			// an MolecularRestraint:
346			mRest = dynamic_cast<MolecularRestraint*>(restData->getData());
347			if (mRest == NULL) {
348			sprintf( painCave.errMsg,
349			"Can not cast RestraintData to MolecularRestraint\n");
350	gezelter	1390	painCave.severity = OPENMD_ERROR;
351	cli2	1360	painCave.isFatal = 1;
352			simError();
353			}
354			} else {
355			sprintf( painCave.errMsg,
356			"Can not cast GenericData to RestraintData\n");
357	gezelter	1390	painCave.severity = OPENMD_ERROR;
358	cli2	1360	painCave.isFatal = 1;
359			simError();
360			}
361			} else {
362			sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
363	gezelter	1390	painCave.severity = OPENMD_ERROR;
364	cli2	1360	painCave.isFatal = 1;
365			simError();
366			}
367
368			// phew. At this point, we should have the pointer to the
369			// correct MolecularRestraint in the variable mRest.
370
371			Vector3d molCom = (*rm)->getCom();
372
373			std::vector<Vector3d> struc;
374			std::vector<Vector3d> forces;
375
376			for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL;
377			sd = (*rm)->nextIntegrableObject(ioi)) {
378			struc.push_back(sd->getPos());
379			}
380
381			mRest->setScaleFactor(scalingFactor);
382			mRest->calcForce(struc, molCom);
383			forces = mRest->getRestraintForces();
384			int index = 0;
385
386			for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL;
387			sd = (*rm)->nextIntegrableObject(ioi)) {
388			sd->addFrc(forces[index]);
389			struc.push_back(sd->getPos());
390			index++;
391			}
392
393			unscaledPotential_ += mRest->getUnscaledPotential();
394
395			restInfo = mRest->getRestraintInfo();
396	cli2	1364
397			// only collect data on restraints that we're going to print:
398			if (mRest->getPrintRestraint())
399			restInfo_.push_back(restInfo);
400	cli2	1360	}
401
402			for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){
403			// make sure this object (*ro) has a generic data for restraints:
404			data = (*ro)->getPropertyByName("Restraint");
405			if (data != NULL) {
406			// make sure we can reinterpret the generic data as restraint data:
407			RestraintData* restData= dynamic_cast<RestraintData*>(data);
408			if (restData != NULL) {
409			// make sure we can reinterpet the restraint data as a pointer to
410			// an ObjectRestraint:
411			oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
412			if (oRest == NULL) {
413			sprintf( painCave.errMsg,
414			"Can not cast RestraintData to ObjectRestraint\n");
415	gezelter	1390	painCave.severity = OPENMD_ERROR;
416	cli2	1360	painCave.isFatal = 1;
417			simError();
418			}
419			} else {
420			sprintf( painCave.errMsg,
421			"Can not cast GenericData to RestraintData\n");
422	gezelter	1390	painCave.severity = OPENMD_ERROR;
423	cli2	1360	painCave.isFatal = 1;
424			simError();
425			}
426			} else {
427			sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n");
428	gezelter	1390	painCave.severity = OPENMD_ERROR;
429	cli2	1360	painCave.isFatal = 1;
430			simError();
431			}
432
433			// phew. At this point, we should have the pointer to the
434			// correct Object restraint in the variable oRest.
435
436			oRest->setScaleFactor(scalingFactor);
437
438			Vector3d pos = (*ro)->getPos();
439
440			if ( (*ro)->isDirectional() ) {
441
442			// directional objects may have orientational restraints as well
443			// as positional, so get the rotation matrix first:
444
445			RotMat3x3d A = (*ro)->getA();
446			oRest->calcForce(pos, A);
447			(*ro)->addFrc(oRest->getRestraintForce());
448			(*ro)->addTrq(oRest->getRestraintTorque());
449			} else {
450
451			// plain vanilla positional restraints:
452
453			oRest->calcForce(pos);
454			(*ro)->addFrc(oRest->getRestraintForce());
455			}
456
457			unscaledPotential_ += oRest->getUnscaledPotential();
458
459			restInfo = oRest->getRestraintInfo();
460	cli2	1364
461			// only collect data on restraints that we're going to print:
462			if (oRest->getPrintRestraint())
463			restInfo_.push_back(restInfo);
464	cli2	1360	}
465
466			return unscaledPotential_ * scalingFactor;
467			}
468			}