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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 2508 by gezelter, Mon Dec 12 19:32:50 2005 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"
# Line 81 | Line 80 | namespace oopse {
80      return result;
81    }
82    
83 <  SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
84 <                   ForceField* ff, Globals* simParams) :
86 <    stamps_(stamps), forceField_(ff), simParams_(simParams),
83 >  SimInfo::SimInfo(ForceField* ff, Globals* simParams) :
84 >    forceField_(ff), simParams_(simParams),
85      ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0),
86      nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0),
87      nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0),
# Line 91 | Line 89 | namespace oopse {
89      nIntegrableObjects_(0),  nCutoffGroups_(0), nConstraints_(0),
90      sman_(NULL), fortranInitialized_(false) {
91  
94 –            
95 –      std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
92        MoleculeStamp* molStamp;
93        int nMolWithSameStamp;
94        int nCutoffAtoms = 0; // number of atoms belong to cutoff groups
# Line 100 | Line 96 | namespace oopse {
96        CutoffGroupStamp* cgStamp;    
97        RigidBodyStamp* rbStamp;
98        int nRigidAtoms = 0;
99 <    
100 <      for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
101 <        molStamp = i->first;
102 <        nMolWithSameStamp = i->second;
99 >      std::vector<Component*> components = simParams->getComponents();
100 >      
101 >      for (std::vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) {
102 >        molStamp = (*i)->getMoleculeStamp();
103 >        nMolWithSameStamp = (*i)->getNMol();
104          
105          addMoleculeStamp(molStamp, nMolWithSameStamp);
106  
107          //calculate atoms in molecules
108          nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;  
109  
113 –
110          //calculate atoms in cutoff groups
111          int nAtomsInGroups = 0;
112          int nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
113          
114          for (int j=0; j < nCutoffGroupsInStamp; j++) {
115 <          cgStamp = molStamp->getCutoffGroup(j);
115 >          cgStamp = molStamp->getCutoffGroupStamp(j);
116            nAtomsInGroups += cgStamp->getNMembers();
117          }
118  
# Line 129 | Line 125 | namespace oopse {
125          int nRigidBodiesInStamp = molStamp->getNRigidBodies();
126          
127          for (int j=0; j < nRigidBodiesInStamp; j++) {
128 <          rbStamp = molStamp->getRigidBody(j);
128 >          rbStamp = molStamp->getRigidBodyStamp(j);
129            nAtomsInRigidBodies += rbStamp->getNMembers();
130          }
131  
# Line 168 | Line 164 | namespace oopse {
164      }
165      molecules_.clear();
166        
171 –    delete stamps_;
167      delete sman_;
168      delete simParams_;
169      delete forceField_;
# Line 275 | Line 270 | namespace oopse {
270            }
271          }
272              
273 <      }//end for (integrableObject)
274 <    }// end for (mol)
273 >      }
274 >    }
275      
276      // n_constraints is local, so subtract them on each processor
277      ndf_local -= nConstraints_;
# Line 920 | Line 915 | namespace oopse {
915  
916  
917    }
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();
918  
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
919   #endif
920  
921 <    return maxCutoffRadius;
947 <  }
948 <
949 <  void SimInfo::getCutoff(double& rcut, double& rsw) {
921 >  void SimInfo::setupCutoff() {          
922      
923 <    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 <      }
964 <
965 <      if (!simParams_->haveSwitchingRadius()){
966 <        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 <      }
976 <
977 <    } else {
978 <      // if charge, dipole or reaction field is not used and the cutofff radius is not specified in
979 <      //meta-data file, the maximum cutoff radius calculated from forcefiled will be used
980 <        
981 <      if (simParams_->haveCutoffRadius()) {
982 <        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
1000 <
1001 <    //Pass these cutoff radius etc. to fortran. This function should be called once and only once
1002 <    
923 >    // Check the cutoff policy
924      int cp =  TRADITIONAL_CUTOFF_POLICY;
925      if (simParams_->haveCutoffPolicy()) {
926        std::string myPolicy = simParams_->getCutoffPolicy();
# Line 1021 | Line 942 | namespace oopse {
942            }    
943          }          
944        }
945 <    }
945 >    }          
946 >    notifyFortranCutoffPolicy(&cp);
947  
948 <
948 >    // Check the Skin Thickness for neighborlists
949 >    double skin;
950      if (simParams_->haveSkinThickness()) {
951 <      double skinThickness = simParams_->getSkinThickness();
952 <    }
951 >      skin = simParams_->getSkinThickness();
952 >      notifyFortranSkinThickness(&skin);
953 >    }            
954 >        
955 >    // Check if the cutoff was set explicitly:
956 >    if (simParams_->haveCutoffRadius()) {
957 >      rcut_ = simParams_->getCutoffRadius();
958 >      if (simParams_->haveSwitchingRadius()) {
959 >        rsw_  = simParams_->getSwitchingRadius();
960 >      } else {
961 >        rsw_ = rcut_;
962 >      }
963 >      notifyFortranCutoffs(&rcut_, &rsw_);
964 >      
965 >    } else {
966 >      
967 >      // For electrostatic atoms, we'll assume a large safe value:
968 >      if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) {
969 >        sprintf(painCave.errMsg,
970 >                "SimCreator Warning: No value was set for the cutoffRadius.\n"
971 >                "\tOOPSE will use a default value of 15.0 angstroms"
972 >                "\tfor the cutoffRadius.\n");
973 >        painCave.isFatal = 0;
974 >        simError();
975 >        rcut_ = 15.0;
976 >      
977 >        if (simParams_->haveElectrostaticSummationMethod()) {
978 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
979 >          toUpper(myMethod);
980 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
981 >            if (simParams_->haveSwitchingRadius()){
982 >              sprintf(painCave.errMsg,
983 >                      "SimInfo Warning: A value was set for the switchingRadius\n"
984 >                      "\teven though the electrostaticSummationMethod was\n"
985 >                      "\tset to %s\n", myMethod.c_str());
986 >              painCave.isFatal = 1;
987 >              simError();            
988 >            }
989 >          }
990 >        }
991 >      
992 >        if (simParams_->haveSwitchingRadius()){
993 >          rsw_ = simParams_->getSwitchingRadius();
994 >        } else {        
995 >          sprintf(painCave.errMsg,
996 >                  "SimCreator Warning: No value was set for switchingRadius.\n"
997 >                  "\tOOPSE will use a default value of\n"
998 >                  "\t0.85 * cutoffRadius for the switchingRadius\n");
999 >          painCave.isFatal = 0;
1000 >          simError();
1001 >          rsw_ = 0.85 * rcut_;
1002 >        }
1003 >        notifyFortranCutoffs(&rcut_, &rsw_);
1004 >      } else {
1005 >        // We didn't set rcut explicitly, and we don't have electrostatic atoms, so
1006 >        // We'll punt and let fortran figure out the cutoffs later.
1007 >        
1008 >        notifyFortranYouAreOnYourOwn();
1009  
1010 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
1011 <    // also send cutoff notification to electrostatics
1033 <    setElectrostaticCutoffRadius(&rcut_, &rsw_);
1010 >      }
1011 >    }
1012    }
1013  
1014    void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
# Line 1065 | Line 1043 | namespace oopse {
1043                } else {
1044                  // throw error        
1045                  sprintf( painCave.errMsg,
1046 <                         "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() );
1046 >                         "SimInfo error: Unknown electrostaticSummationMethod.\n"
1047 >                         "\t(Input file specified %s .)\n"
1048 >                         "\telectrostaticSummationMethod must be one of: \"none\",\n"
1049 >                         "\t\"shifted_potential\", \"shifted_force\", or \n"
1050 >                         "\t\"reaction_field\".\n", myMethod.c_str() );
1051                  painCave.isFatal = 1;
1052                  simError();
1053                }    
# Line 1086 | Line 1068 | namespace oopse {
1068            if (!simParams_->haveDampingAlpha()) {
1069              //throw error
1070              sprintf( painCave.errMsg,
1071 <                     "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used.", alphaVal);
1071 >                     "SimInfo warning: dampingAlpha was not specified in the input file.\n"
1072 >                     "\tA default value of %f (1/ang) will be used.\n", alphaVal);
1073              painCave.isFatal = 0;
1074              simError();
1075            }
1076          } else {
1077            // throw error        
1078            sprintf( painCave.errMsg,
1079 <                   "SimInfo error: Unknown electrostaticScreeningMethod. (Input file specified %s .)\n\telectrostaticScreeningMethod must be one of: \"undamped\" or \"damped\".", myScreen.c_str() );
1079 >                   "SimInfo error: Unknown electrostaticScreeningMethod.\n"
1080 >                   "\t(Input file specified %s .)\n"
1081 >                   "\telectrostaticScreeningMethod must be one of: \"undamped\"\n"
1082 >                   "or \"damped\".\n", myScreen.c_str() );
1083            painCave.isFatal = 1;
1084            simError();
1085          }
# Line 1101 | Line 1087 | namespace oopse {
1087      }
1088      
1089      // let's pass some summation method variables to fortran
1090 <    setElectrostaticSummationMethod( &esm );
1090 >    setElectrostaticSumMethod( &esm );
1091 >    setFortranElectrostaticMethod( &esm );
1092      setScreeningMethod( &sm );
1093      setDampingAlpha( &alphaVal );
1094      setReactionFieldDielectric( &dielectric );
1095 <    initFortranFF( &esm, &errorOut );
1095 >    initFortranFF( &errorOut );
1096    }
1097  
1098    void SimInfo::setupSwitchingFunction() {    

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