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root/group/trunk/OOPSE-2.0/src/brains/SimInfo.cpp
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Comparing trunk/OOPSE-2.0/src/brains/SimInfo.cpp (file contents):
Revision 2448 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 2552 by chrisfen, Thu Jan 12 16:47:25 2006 UTC

# Line 59 | Line 59
59   #include "UseTheForce/DarkSide/fSwitchingFunctionType.h"
60   #include "UseTheForce/doForces_interface.h"
61   #include "UseTheForce/DarkSide/electrostatic_interface.h"
62 – #include "UseTheForce/notifyCutoffs_interface.h"
62   #include "UseTheForce/DarkSide/switcheroo_interface.h"
63   #include "utils/MemoryUtils.hpp"
64   #include "utils/simError.h"
65   #include "selection/SelectionManager.hpp"
66 + #include "io/ForceFieldOptions.hpp"
67 + #include "UseTheForce/ForceField.hpp"
68  
69   #ifdef IS_MPI
70   #include "UseTheForce/mpiComponentPlan.h"
# Line 81 | Line 82 | namespace oopse {
82      return result;
83    }
84    
85 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
86 <                   ForceField* ff, Globals* simParams) :
86 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
85 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
86 >    forceField_(ff), simParams_(simParams),
87      ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
88      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
89      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
# Line 91 | Line 91 | namespace oopse {
91      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
92      sman_(NULL), fortranInitialized_(false) {
93  
94 –            
95 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
94        MoleculeStamp* molStamp;
95        int nMolWithSameStamp;
96        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 100 | Line 98 | namespace oopse {
98        CutoffGroupStamp* cgStamp;    
99        RigidBodyStamp* rbStamp;
100        int nRigidAtoms = 0;
101 <    
102 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
103 <        molStamp = i->first;
104 <        nMolWithSameStamp = i->second;
101 >      std::vector<Component*> components = simParams->getComponents();
102 >      
103 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
104 >        molStamp = (*i)->getMoleculeStamp();
105 >        nMolWithSameStamp = (*i)->getNMol();
106          
107          addMoleculeStamp(molStamp, nMolWithSameStamp);
108  
109          //calculate atoms in molecules
110          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
111  
113 –
112          //calculate atoms in cutoff groups
113          int nAtomsInGroups = 0;
114          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
115          
116          for (int j=0; j < nCutoffGroupsInStamp; j++) {
117 <          cgStamp = molStamp->getCutoffGroup(j);
117 >          cgStamp = molStamp->getCutoffGroupStamp(j);
118            nAtomsInGroups += cgStamp->getNMembers();
119          }
120  
# Line 129 | Line 127 | namespace oopse {
127          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
128          
129          for (int j=0; j < nRigidBodiesInStamp; j++) {
130 <          rbStamp = molStamp->getRigidBody(j);
130 >          rbStamp = molStamp->getRigidBodyStamp(j);
131            nAtomsInRigidBodies += rbStamp->getNMembers();
132          }
133  
# Line 168 | Line 166 | namespace oopse {
166      }
167      molecules_.clear();
168        
171 –    delete stamps_;
169      delete sman_;
170      delete simParams_;
171      delete forceField_;
# Line 275 | Line 272 | namespace oopse {
272            }
273          }
274              
275 <      }//end for (integrableObject)
276 <    }// end for (mol)
275 >      }
276 >    }
277      
278      // n_constraints is local, so subtract them on each processor
279      ndf_local -= nConstraints_;
# Line 920 | Line 917 | namespace oopse {
917  
918  
919    }
923 –
924 – #endif
925 –
926 –  double SimInfo::calcMaxCutoffRadius() {
927 –
928 –
929 –    std::set<AtomType*> atomTypes;
930 –    std::set<AtomType*>::iterator i;
931 –    std::vector<double> cutoffRadius;
932 –
933 –    //get the unique atom types
934 –    atomTypes = getUniqueAtomTypes();
920  
936 –    //query the max cutoff radius among these atom types
937 –    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
938 –      cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i));
939 –    }
940 –
941 –    double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end()));
942 – #ifdef IS_MPI
943 –    //pick the max cutoff radius among the processors
921   #endif
922  
923 <    return maxCutoffRadius;
947 <  }
948 <
949 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
923 >  void SimInfo::setupCutoff() {          
924      
925 <    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
952 <        
953 <      if (!simParams_->haveCutoffRadius()){
954 <        sprintf(painCave.errMsg,
955 <                "SimCreator Warning: No value was set for the cutoffRadius.\n"
956 <                "\tOOPSE will use a default value of 15.0 angstroms"
957 <                "\tfor the cutoffRadius.\n");
958 <        painCave.isFatal = 0;
959 <        simError();
960 <        rcut = 15.0;
961 <      } else{
962 <        rcut = simParams_->getCutoffRadius();
963 <      }
925 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
926  
927 <      if (!simParams_->haveSwitchingRadius()){
928 <        sprintf(painCave.errMsg,
967 <                "SimCreator Warning: No value was set for switchingRadius.\n"
968 <                "\tOOPSE will use a default value of\n"
969 <                "\t0.85 * cutoffRadius for the switchingRadius\n");
970 <        painCave.isFatal = 0;
971 <        simError();
972 <        rsw = 0.85 * rcut;
973 <      } else{
974 <        rsw = simParams_->getSwitchingRadius();
975 <      }
927 >    // Check the cutoff policy
928 >    int cp =  TRADITIONAL_CUTOFF_POLICY; // Set to traditional by default
929  
930 <    } else {
931 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
932 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
933 <        
934 <      if (simParams_->haveCutoffRadius()) {
935 <        rcut = simParams_->getCutoffRadius();
983 <      } else {
984 <        //set cutoff radius to the maximum cutoff radius based on atom types in the whole system
985 <        rcut = calcMaxCutoffRadius();
986 <      }
987 <
988 <      if (simParams_->haveSwitchingRadius()) {
989 <        rsw  = simParams_->getSwitchingRadius();
990 <      } else {
991 <        rsw = rcut;
992 <      }
993 <    
994 <    }
995 <  }
996 <
997 <  void SimInfo::setupCutoff() {    
998 <    getCutoff(rcut_, rsw_);    
999 <    double rnblist = rcut_ + 1; // skin of neighbor list
930 >    std::string myPolicy;
931 >    if (forceFieldOptions_.haveCutoffPolicy()){
932 >      myPolicy = forceFieldOptions_.getCutoffPolicy();
933 >    }else if (simParams_->haveCutoffPolicy()) {
934 >      myPolicy = simParams_->getCutoffPolicy();
935 >    }
936  
937 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002 <    
1003 <    int cp =  TRADITIONAL_CUTOFF_POLICY;
1004 <    if (simParams_->haveCutoffPolicy()) {
1005 <      std::string myPolicy = simParams_->getCutoffPolicy();
937 >    if (!myPolicy.empty()){
938        toUpper(myPolicy);
939        if (myPolicy == "MIX") {
940          cp = MIX_CUTOFF_POLICY;
# Line 1021 | Line 953 | namespace oopse {
953            }    
954          }          
955        }
956 <    }
956 >    }          
957 >    notifyFortranCutoffPolicy(&cp);
958  
959 <
959 >    // Check the Skin Thickness for neighborlists
960 >    double skin;
961      if (simParams_->haveSkinThickness()) {
962 <      double skinThickness = simParams_->getSkinThickness();
963 <    }
962 >      skin = simParams_->getSkinThickness();
963 >      notifyFortranSkinThickness(&skin);
964 >    }            
965 >        
966 >    // Check if the cutoff was set explicitly:
967 >    if (simParams_->haveCutoffRadius()) {
968 >      rcut_ = simParams_->getCutoffRadius();
969 >      if (simParams_->haveSwitchingRadius()) {
970 >        rsw_  = simParams_->getSwitchingRadius();
971 >      } else {
972 >        rsw_ = rcut_;
973 >      }
974 >      notifyFortranCutoffs(&rcut_, &rsw_);
975 >      
976 >    } else {
977 >      
978 >      // For electrostatic atoms, we'll assume a large safe value:
979 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
980 >        sprintf(painCave.errMsg,
981 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
982 >                "\tOOPSE will use a default value of 15.0 angstroms"
983 >                "\tfor the cutoffRadius.\n");
984 >        painCave.isFatal = 0;
985 >        simError();
986 >        rcut_ = 15.0;
987 >      
988 >        if (simParams_->haveElectrostaticSummationMethod()) {
989 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
990 >          toUpper(myMethod);
991 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
992 >            if (simParams_->haveSwitchingRadius()){
993 >              sprintf(painCave.errMsg,
994 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
995 >                      "\teven though the electrostaticSummationMethod was\n"
996 >                      "\tset to %s\n", myMethod.c_str());
997 >              painCave.isFatal = 1;
998 >              simError();            
999 >            }
1000 >          }
1001 >        }
1002 >      
1003 >        if (simParams_->haveSwitchingRadius()){
1004 >          rsw_ = simParams_->getSwitchingRadius();
1005 >        } else {        
1006 >          sprintf(painCave.errMsg,
1007 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
1008 >                  "\tOOPSE will use a default value of\n"
1009 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
1010 >          painCave.isFatal = 0;
1011 >          simError();
1012 >          rsw_ = 0.85 * rcut_;
1013 >        }
1014 >        notifyFortranCutoffs(&rcut_, &rsw_);
1015 >      } else {
1016 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1017 >        // We'll punt and let fortran figure out the cutoffs later.
1018 >        
1019 >        notifyFortranYouAreOnYourOwn();
1020  
1021 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1022 <    // also send cutoff notification to electrostatics
1033 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1021 >      }
1022 >    }
1023    }
1024  
1025    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 1065 | Line 1054 | namespace oopse {
1054                } else {
1055                  // throw error        
1056                  sprintf( painCave.errMsg,
1057 <                         "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"shifted_potential\", \"shifted_force\", or \"reaction_field\".", myMethod.c_str() );
1057 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1058 >                         "\t(Input file specified %s .)\n"
1059 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1060 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1061 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1062                  painCave.isFatal = 1;
1063                  simError();
1064                }    
# Line 1086 | Line 1079 | namespace oopse {
1079            if (!simParams_->haveDampingAlpha()) {
1080              //throw error
1081              sprintf( painCave.errMsg,
1082 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1082 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1083 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1084              painCave.isFatal = 0;
1085              simError();
1086            }
1087          } else {
1088            // throw error        
1089            sprintf( painCave.errMsg,
1090 <                   "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1090 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1091 >                   "\t(Input file specified %s .)\n"
1092 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1093 >                   "or \"damped\".\n", myScreen.c_str() );
1094            painCave.isFatal = 1;
1095            simError();
1096          }
# Line 1102 | Line 1099 | namespace oopse {
1099      
1100      // let's pass some summation method variables to fortran
1101      setElectrostaticSummationMethod( &esm );
1102 +    setFortranElectrostaticMethod( &esm );
1103      setScreeningMethod( &sm );
1104      setDampingAlpha( &alphaVal );
1105      setReactionFieldDielectric( &dielectric );
1106 <    initFortranFF( &esm, &errorOut );
1106 >    initFortranFF( &errorOut );
1107    }
1108  
1109    void SimInfo::setupSwitchingFunction() {    

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