ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/brains/SimInfo.cpp
(Generate patch)

Comparing trunk/src/brains/SimInfo.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 610 by chrisfen, Sun Sep 18 20:45:38 2005 UTC

# Line 52 | Line 52
52   #include "brains/SimInfo.hpp"
53   #include "math/Vector3.hpp"
54   #include "primitives/Molecule.hpp"
55 + #include "UseTheForce/fCutoffPolicy.h"
56 + #include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h"
57   #include "UseTheForce/doForces_interface.h"
58 + #include "UseTheForce/DarkSide/electrostatic_interface.h"
59   #include "UseTheForce/notifyCutoffs_interface.h"
60   #include "utils/MemoryUtils.hpp"
61   #include "utils/simError.h"
# Line 462 | Line 465 | namespace oopse {
465      //setup fortran force field
466      /** @deprecate */    
467      int isError = 0;
468 <    initFortranFF( &fInfo_.SIM_uses_RF , &isError );
468 >    
469 >    setupElectrostaticSummationMethod( isError );
470 >
471      if(isError){
472        sprintf( painCave.errMsg,
473                 "ForceField error: There was an error initializing the forceField in fortran.\n" );
# Line 511 | Line 516 | namespace oopse {
516      int useDipole = 0;
517      int useGayBerne = 0;
518      int useSticky = 0;
519 +    int useStickyPower = 0;
520      int useShape = 0;
521      int useFLARB = 0; //it is not in AtomType yet
522      int useDirectionalAtom = 0;    
523      int useElectrostatics = 0;
524      //usePBC and useRF are from simParams
525      int usePBC = simParams_->getPBC();
520 –    int useRF = simParams_->getUseRF();
526  
527      //loop over all of the atom types
528      for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
# Line 529 | Line 534 | namespace oopse {
534        useDipole |= (*i)->isDipole();
535        useGayBerne |= (*i)->isGayBerne();
536        useSticky |= (*i)->isSticky();
537 +      useStickyPower |= (*i)->isStickyPower();
538        useShape |= (*i)->isShape();
539      }
540  
541 <    if (useSticky || useDipole || useGayBerne || useShape) {
541 >    if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) {
542        useDirectionalAtom = 1;
543      }
544  
# Line 564 | Line 570 | namespace oopse {
570      temp = useSticky;
571      MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
572  
573 +    temp = useStickyPower;
574 +    MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
575 +    
576      temp = useGayBerne;
577      MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
578  
# Line 576 | Line 585 | namespace oopse {
585      temp = useFLARB;
586      MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
587  
579 –    temp = useRF;
580 –    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
581 –    
588   #endif
589  
590      fInfo_.SIM_uses_PBC = usePBC;    
# Line 588 | Line 594 | namespace oopse {
594      fInfo_.SIM_uses_Charges = useCharge;
595      fInfo_.SIM_uses_Dipoles = useDipole;
596      fInfo_.SIM_uses_Sticky = useSticky;
597 +    fInfo_.SIM_uses_StickyPower = useStickyPower;
598      fInfo_.SIM_uses_GayBerne = useGayBerne;
599      fInfo_.SIM_uses_EAM = useEAM;
600      fInfo_.SIM_uses_Shapes = useShape;
601      fInfo_.SIM_uses_FLARB = useFLARB;
595 –    fInfo_.SIM_uses_RF = useRF;
602  
603      if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
604  
# Line 824 | Line 830 | namespace oopse {
830      }
831    }
832  
833 <  void SimInfo::setupCutoff() {
833 >  void SimInfo::setupCutoff() {    
834      getCutoff(rcut_, rsw_);    
835      double rnblist = rcut_ + 1; // skin of neighbor list
836  
837      //Pass these cutoff radius etc. to fortran. This function should be called once and only once
838 <    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist);
838 >    
839 >    int cp =  TRADITIONAL_CUTOFF_POLICY;
840 >    if (simParams_->haveCutoffPolicy()) {
841 >      std::string myPolicy = simParams_->getCutoffPolicy();
842 >      if (myPolicy == "MIX") {
843 >        cp = MIX_CUTOFF_POLICY;
844 >      } else {
845 >        if (myPolicy == "MAX") {
846 >          cp = MAX_CUTOFF_POLICY;
847 >        } else {
848 >          if (myPolicy == "TRADITIONAL") {            
849 >            cp = TRADITIONAL_CUTOFF_POLICY;
850 >          } else {
851 >            // throw error        
852 >            sprintf( painCave.errMsg,
853 >                     "SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() );
854 >            painCave.isFatal = 1;
855 >            simError();
856 >          }    
857 >        }          
858 >      }
859 >    }
860 >    notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp);
861 >    // also send cutoff notification to electrostatics
862 >    setElectrostaticCutoffRadius(&rcut_);
863    }
864  
865 +  void SimInfo::setupElectrostaticSummationMethod( int isError ) {    
866 +    
867 +    int errorOut;
868 +    int esm =  NONE;
869 +    double alphaVal;
870 +    double dielectric;
871 +
872 +    errorOut = isError;
873 +    alphaVal = simParams_->getDampingAlpha();
874 +    dielectric = simParams_->getDielectric();
875 +
876 +    if (simParams_->haveElectrostaticSummationMethod()) {
877 +      std::string myMethod = simParams_->getElectrostaticSummationMethod();
878 +      if (myMethod == "NONE") {
879 +        esm = NONE;
880 +      } else {
881 +        if (myMethod == "UNDAMPED_WOLF") {
882 +          esm = UNDAMPED_WOLF;
883 +        } else {
884 +          if (myMethod == "DAMPED_WOLF") {            
885 +            esm = DAMPED_WOLF;
886 +            if (!simParams_->haveDampingAlpha()) {
887 +              //throw error
888 +              sprintf( painCave.errMsg,
889 +                       "SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Damped Wolf Method.", alphaVal);
890 +              painCave.isFatal = 0;
891 +              simError();
892 +            }
893 +          } else {
894 +            if (myMethod == "REACTION_FIELD") {
895 +              esm = REACTION_FIELD;
896 +            } else {
897 +              // throw error        
898 +              sprintf( painCave.errMsg,
899 +                       "SimInfo error: Unknown electrostaticSummationMethod. (Input file specified %s .)\n\telectrostaticSummationMethod must be one of: \"none\", \"undamped_wolf\", \"damped_wolf\", or \"reaction_field\".", myMethod.c_str() );
900 +              painCave.isFatal = 1;
901 +              simError();
902 +            }    
903 +          }          
904 +        }
905 +      }
906 +    }
907 +    // let's pass some summation method variables to fortran
908 +    setElectrostaticSummationMethod( &esm );
909 +    setDampedWolfAlpha( &alphaVal );
910 +    setReactionFieldDielectric( &dielectric );
911 +    initFortranFF( &esm, &errorOut );
912 +  }
913 +
914    void SimInfo::addProperty(GenericData* genData) {
915      properties_.addProperty(genData);  
916    }
# Line 939 | Line 1018 | namespace oopse {
1018  
1019      return o;
1020    }
1021 +  
1022 +  
1023 +   /*
1024 +   Returns center of mass and center of mass velocity in one function call.
1025 +   */
1026 +  
1027 +   void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){
1028 +      SimInfo::MoleculeIterator i;
1029 +      Molecule* mol;
1030 +      
1031 +    
1032 +      double totalMass = 0.0;
1033 +    
1034  
1035 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1036 +         double mass = mol->getMass();
1037 +         totalMass += mass;
1038 +         com += mass * mol->getCom();
1039 +         comVel += mass * mol->getComVel();          
1040 +      }  
1041 +      
1042 + #ifdef IS_MPI
1043 +      double tmpMass = totalMass;
1044 +      Vector3d tmpCom(com);  
1045 +      Vector3d tmpComVel(comVel);
1046 +      MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1047 +      MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1048 +      MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1049 + #endif
1050 +      
1051 +      com /= totalMass;
1052 +      comVel /= totalMass;
1053 +   }        
1054 +  
1055 +   /*
1056 +   Return intertia tensor for entire system and angular momentum Vector.
1057 +
1058 +
1059 +       [  Ixx -Ixy  -Ixz ]
1060 +  J =| -Iyx  Iyy  -Iyz |
1061 +       [ -Izx -Iyz   Izz ]
1062 +    */
1063 +
1064 +   void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){
1065 +      
1066 +
1067 +      double xx = 0.0;
1068 +      double yy = 0.0;
1069 +      double zz = 0.0;
1070 +      double xy = 0.0;
1071 +      double xz = 0.0;
1072 +      double yz = 0.0;
1073 +      Vector3d com(0.0);
1074 +      Vector3d comVel(0.0);
1075 +      
1076 +      getComAll(com, comVel);
1077 +      
1078 +      SimInfo::MoleculeIterator i;
1079 +      Molecule* mol;
1080 +      
1081 +      Vector3d thisq(0.0);
1082 +      Vector3d thisv(0.0);
1083 +
1084 +      double thisMass = 0.0;
1085 +    
1086 +      
1087 +      
1088 +  
1089 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
1090 +        
1091 +         thisq = mol->getCom()-com;
1092 +         thisv = mol->getComVel()-comVel;
1093 +         thisMass = mol->getMass();
1094 +         // Compute moment of intertia coefficients.
1095 +         xx += thisq[0]*thisq[0]*thisMass;
1096 +         yy += thisq[1]*thisq[1]*thisMass;
1097 +         zz += thisq[2]*thisq[2]*thisMass;
1098 +        
1099 +         // compute products of intertia
1100 +         xy += thisq[0]*thisq[1]*thisMass;
1101 +         xz += thisq[0]*thisq[2]*thisMass;
1102 +         yz += thisq[1]*thisq[2]*thisMass;
1103 +            
1104 +         angularMomentum += cross( thisq, thisv ) * thisMass;
1105 +            
1106 +      }  
1107 +      
1108 +      
1109 +      inertiaTensor(0,0) = yy + zz;
1110 +      inertiaTensor(0,1) = -xy;
1111 +      inertiaTensor(0,2) = -xz;
1112 +      inertiaTensor(1,0) = -xy;
1113 +      inertiaTensor(1,1) = xx + zz;
1114 +      inertiaTensor(1,2) = -yz;
1115 +      inertiaTensor(2,0) = -xz;
1116 +      inertiaTensor(2,1) = -yz;
1117 +      inertiaTensor(2,2) = xx + yy;
1118 +      
1119 + #ifdef IS_MPI
1120 +      Mat3x3d tmpI(inertiaTensor);
1121 +      Vector3d tmpAngMom;
1122 +      MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1123 +      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1124 + #endif
1125 +              
1126 +      return;
1127 +   }
1128 +
1129 +   //Returns the angular momentum of the system
1130 +   Vector3d SimInfo::getAngularMomentum(){
1131 +      
1132 +      Vector3d com(0.0);
1133 +      Vector3d comVel(0.0);
1134 +      Vector3d angularMomentum(0.0);
1135 +      
1136 +      getComAll(com,comVel);
1137 +      
1138 +      SimInfo::MoleculeIterator i;
1139 +      Molecule* mol;
1140 +      
1141 +      Vector3d thisr(0.0);
1142 +      Vector3d thisp(0.0);
1143 +      
1144 +      double thisMass;
1145 +      
1146 +      for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {        
1147 +        thisMass = mol->getMass();
1148 +        thisr = mol->getCom()-com;
1149 +        thisp = (mol->getComVel()-comVel)*thisMass;
1150 +        
1151 +        angularMomentum += cross( thisr, thisp );
1152 +        
1153 +      }  
1154 +      
1155 + #ifdef IS_MPI
1156 +      Vector3d tmpAngMom;
1157 +      MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1158 + #endif
1159 +      
1160 +      return angularMomentum;
1161 +   }
1162 +  
1163 +  
1164   }//end namespace oopse
1165  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines