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root/OpenMD/branches/development/src/brains/SimInfo.cpp
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Comparing branches/development/src/brains/SimInfo.cpp (file contents):
Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC vs.
Revision 1530 by gezelter, Tue Dec 28 21:47:55 2010 UTC

# Line 55 | Line 55
55   #include "primitives/Molecule.hpp"
56   #include "primitives/StuntDouble.hpp"
57   #include "UseTheForce/fCutoffPolicy.h"
58 – #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
58   #include "UseTheForce/doForces_interface.h"
59   #include "UseTheForce/DarkSide/neighborLists_interface.h"
61 – #include "UseTheForce/DarkSide/switcheroo_interface.h"
60   #include "utils/MemoryUtils.hpp"
61   #include "utils/simError.h"
62   #include "selection/SelectionManager.hpp"
63   #include "io/ForceFieldOptions.hpp"
64   #include "UseTheForce/ForceField.hpp"
65 < #include "nonbonded/InteractionManager.hpp"
65 > #include "nonbonded/SwitchingFunction.hpp"
66  
67  
68   #ifdef IS_MPI
# Line 656 | Line 654 | namespace OpenMD {
654      molStampIds_.insert(molStampIds_.end(), nmol, curStampId);
655    }
656  
659 –  void SimInfo::update() {
657  
658 <    setupSimType();
659 <    setupCutoffRadius();
660 <    setupSwitchingRadius();
661 <    setupCutoffMethod();
662 <    setupSkinThickness();
663 <    setupSwitchingFunction();
664 <    setupAccumulateBoxDipole();
658 >  /**
659 >   * update
660 >   *
661 >   *  Performs the global checks and variable settings after the objects have been
662 >   *  created.
663 >   *
664 >   */
665 >  void SimInfo::update() {
666 >    
667 >    setupSimVariables();
668 >    setupCutoffs();
669 >    setupSwitching();
670 >    setupElectrostatics();
671 >    setupNeighborlists();
672  
673   #ifdef IS_MPI
674      setupFortranParallel();
# Line 684 | Line 688 | namespace OpenMD {
688      Atom* atom;
689      set<AtomType*> atomTypes;
690      
691 <    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
688 <      
691 >    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {      
692        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
693          atomTypes.insert(atom->getAtomType());
694 <      }
695 <      
693 <    }
694 <    
694 >      }      
695 >    }    
696      return atomTypes;        
697    }
698  
699    /**
700 <   * setupCutoffRadius
700 >   * setupCutoffs
701 >   *
702 >   * Sets the values of cutoffRadius and cutoffMethod
703     *
704 +   * cutoffRadius : realType
705     *  If the cutoffRadius was explicitly set, use that value.
706     *  If the cutoffRadius was not explicitly set:
707     *      Are there electrostatic atoms?  Use 12.0 Angstroms.
708     *      No electrostatic atoms?  Poll the atom types present in the
709     *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
710     *      Use the maximum suggested value that was found.
711 +   *
712 +   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
713 +   *      If cutoffMethod was explicitly set, use that choice.
714 +   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
715     */
716 <  void SimInfo::setupCutoffRadius() {
716 >  void SimInfo::setupCutoffs() {
717      
718      if (simParams_->haveCutoffRadius()) {
719        cutoffRadius_ = simParams_->getCutoffRadius();
720      } else {      
721        if (usesElectrostaticAtoms_) {
722          sprintf(painCave.errMsg,
723 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
723 >                "SimInfo: No value was set for the cutoffRadius.\n"
724                  "\tOpenMD will use a default value of 12.0 angstroms"
725                  "\tfor the cutoffRadius.\n");
726          painCave.isFatal = 0;
727 +        painCave.severity = OPENMD_INFO;
728          simError();
729          cutoffRadius_ = 12.0;
730        } else {
# Line 728 | Line 737 | namespace OpenMD {
737            cutoffRadius_ = max(thisCut, cutoffRadius_);
738          }
739          sprintf(painCave.errMsg,
740 <                "SimInfo Warning: No value was set for the cutoffRadius.\n"
740 >                "SimInfo: No value was set for the cutoffRadius.\n"
741                  "\tOpenMD will use %lf angstroms.\n",
742                  cutoffRadius_);
743          painCave.isFatal = 0;
744 +        painCave.severity = OPENMD_INFO;
745          simError();
746        }            
747      }
748  
749      InteractionManager::Instance()->setCutoffRadius(cutoffRadius_);
750 +
751 +    map<string, CutoffMethod> stringToCutoffMethod;
752 +    stringToCutoffMethod["HARD"] = HARD;
753 +    stringToCutoffMethod["SWITCHING_FUNCTION"] = SWITCHING_FUNCTION;
754 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
755 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
756 +  
757 +    if (simParams_->haveCutoffMethod()) {
758 +      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
759 +      map<string, CutoffMethod>::iterator i;
760 +      i = stringToCutoffMethod.find(cutMeth);
761 +      if (i == stringToCutoffMethod.end()) {
762 +        sprintf(painCave.errMsg,
763 +                "SimInfo: Could not find chosen cutoffMethod %s\n"
764 +                "\tShould be one of: "
765 +                "HARD, SWITCHING_FUNCTION, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
766 +                cutMeth.c_str());
767 +        painCave.isFatal = 1;
768 +        painCave.severity = OPENMD_ERROR;
769 +        simError();
770 +      } else {
771 +        cutoffMethod_ = i->second;
772 +      }
773 +    } else {
774 +      sprintf(painCave.errMsg,
775 +              "SimInfo: No value was set for the cutoffMethod.\n"
776 +              "\tOpenMD will use SHIFTED_FORCE.\n");
777 +        painCave.isFatal = 0;
778 +        painCave.severity = OPENMD_INFO;
779 +        simError();
780 +        cutoffMethod_ = SHIFTED_FORCE;        
781 +    }
782 +
783 +    InteractionManager::Instance()->setCutoffMethod(cutoffMethod_);
784    }
785    
786    /**
787 <   * setupSwitchingRadius
787 >   * setupSwitching
788     *
789 +   * Sets the values of switchingRadius and
790     *  If the switchingRadius was explicitly set, use that value (but check it)
791     *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
792     */
793 <  void SimInfo::setupSwitchingRadius() {
793 >  void SimInfo::setupSwitching() {
794      
795      if (simParams_->haveSwitchingRadius()) {
796        switchingRadius_ = simParams_->getSwitchingRadius();
797        if (switchingRadius_ > cutoffRadius_) {        
798          sprintf(painCave.errMsg,
799 <                "SimInfo Error: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
799 >                "SimInfo: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
800                  switchingRadius_, cutoffRadius_);
801          painCave.isFatal = 1;
802 +        painCave.severity = OPENMD_ERROR;
803          simError();
758 –
804        }
805      } else {      
806        switchingRadius_ = 0.85 * cutoffRadius_;
807        sprintf(painCave.errMsg,
808 <              "SimInfo Warning: No value was set for the switchingRadius.\n"
808 >              "SimInfo: No value was set for the switchingRadius.\n"
809                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
810                "\tswitchingRadius = %f. for this simulation\n", switchingRadius_);
811        painCave.isFatal = 0;
812 +      painCave.severity = OPENMD_WARNING;
813        simError();
814 <    }            
814 >    }          
815 >  
816      InteractionManager::Instance()->setSwitchingRadius(switchingRadius_);
817 +
818 +    SwitchingFunctionType ft;
819 +    
820 +    if (simParams_->haveSwitchingFunctionType()) {
821 +      string funcType = simParams_->getSwitchingFunctionType();
822 +      toUpper(funcType);
823 +      if (funcType == "CUBIC") {
824 +        ft = cubic;
825 +      } else {
826 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
827 +          ft = fifth_order_poly;
828 +        } else {
829 +          // throw error        
830 +          sprintf( painCave.errMsg,
831 +                   "SimInfo : Unknown switchingFunctionType. (Input file specified %s .)\n"
832 +                   "\tswitchingFunctionType must be one of: "
833 +                   "\"cubic\" or \"fifth_order_polynomial\".",
834 +                   funcType.c_str() );
835 +          painCave.isFatal = 1;
836 +          painCave.severity = OPENMD_ERROR;
837 +          simError();
838 +        }          
839 +      }
840 +    }
841 +
842 +    InteractionManager::Instance()->setSwitchingFunctionType(ft);
843    }
844  
845    /**
# Line 992 | Line 1065 | namespace OpenMD {
1065  
1066  
1067    void SimInfo::setupSwitchingFunction() {    
995 –    int ft = CUBIC;
996 –    
997 –    if (simParams_->haveSwitchingFunctionType()) {
998 –      string funcType = simParams_->getSwitchingFunctionType();
999 –      toUpper(funcType);
1000 –      if (funcType == "CUBIC") {
1001 –        ft = CUBIC;
1002 –      } else {
1003 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
1004 –          ft = FIFTH_ORDER_POLY;
1005 –        } else {
1006 –          // throw error        
1007 –          sprintf( painCave.errMsg,
1008 –                   "SimInfo error: Unknown switchingFunctionType. (Input file specified %s .)\n\tswitchingFunctionType must be one of: \"cubic\" or \"fifth_order_polynomial\".", funcType.c_str() );
1009 –          painCave.isFatal = 1;
1010 –          simError();
1011 –        }          
1012 –      }
1013 –    }
1068  
1015 –    // send switching function notification to switcheroo
1016 –    setFunctionType(&ft);
1017 –
1069    }
1070  
1071    void SimInfo::setupAccumulateBoxDipole() {    

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