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Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 106 | Line 107 | namespace OpenMD{
107  
108      /**
109       * Sets the global index of this stuntDouble.
110 <     * @param new global index to be set
110 >     * @param index new global index to be set
111       */
112      void setGlobalIndex(int index) {
113        globalIndex_ = index;
# Line 567 | Line 568 | namespace OpenMD{
568      void setEuler(const Vector3d& euler, int snapshotNo) {
569        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = euler;
570      }
571 <      
572 <    /**
573 <     * Returns the previous unit vectors of this stuntDouble
574 <     * @return the unit vectors of this stuntDouble
571 >
572 >    /**
573 >     * Returns the previous dipole vector of this stuntDouble
574 >     * @return the dipole vector of this stuntDouble
575       */    
576 <    RotMat3x3d getPrevElectroFrame() {
577 <      return ((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_];
576 >    Vector3d getPrevDipole() {
577 >      return ((snapshotMan_->getPrevSnapshot())->*storage_).dipole[localIndex_];
578      }
579 <      
579 >    
580      /**
581 <     * Returns the current unit vectors of this stuntDouble
582 <     * @return the unit vectors of this stuntDouble
581 >     * Returns the current dipole vector of this stuntDouble
582 >     * @return the dipole vector of this stuntDouble
583       */    
584 <    RotMat3x3d getElectroFrame() {
585 <      return ((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_];
584 >    Vector3d getDipole() {
585 >      return ((snapshotMan_->getCurrentSnapshot())->*storage_).dipole[localIndex_];
586      }
587 <
587 >    
588      /**
589 <     * Returns the unit vectors of this stuntDouble in specified snapshot
589 >     * Returns the dipole vector of this stuntDouble in specified snapshot
590       *
591 <     * @return the unit vectors of this stuntDouble
591 >     * @return the dipole vector of this stuntDouble
592       * @param snapshotNo
593       */    
594 <    RotMat3x3d getElectroFrame(int snapshotNo) {
595 <      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_];
594 >    Vector3d getDipole(int snapshotNo) {
595 >      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).dipole[localIndex_];
596      }
597  
598 +
599      /**
600 +     * Returns the previous quadrupole tensor of this stuntDouble
601 +     * @return the quadrupole tensor of this stuntDouble
602 +     */    
603 +    Mat3x3d getPrevQuadrupole() {
604 +      return ((snapshotMan_->getPrevSnapshot())->*storage_).quadrupole[localIndex_];
605 +    }
606 +    
607 +    /**
608 +     * Returns the current quadrupole tensor of this stuntDouble
609 +     * @return the quadrupole tensor of this stuntDouble
610 +     */    
611 +    Mat3x3d getQuadrupole() {
612 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).quadrupole[localIndex_];
613 +    }
614 +    
615 +    /**
616 +     * Returns the quadrupole tensor of this stuntDouble in specified snapshot
617 +     *
618 +     * @return the quadrupole tensor of this stuntDouble
619 +     * @param snapshotNo
620 +     */    
621 +    Mat3x3d getQuadrupole(int snapshotNo) {
622 +      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).quadrupole[localIndex_];
623 +    }
624 +        
625 +    /**
626       * Returns the previous force of this stuntDouble
627       * @return the force of this stuntDouble
628       */    
# Line 848 | Line 876 | namespace OpenMD{
876        ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).particlePot[localIndex_] += particlePot;
877      }      
878  
851 –
879      /**
880 <     * Returns the previous z-angle of this stuntDouble
881 <     * @return the z-angle of this stuntDouble
880 >     * Returns the previous fluctuating charge of this stuntDouble
881 >     * @return the fluctuating charge of this stuntDouble
882       */    
883 <    RealType getPrevZangle() {
884 <      return ((snapshotMan_->getPrevSnapshot())->*storage_).zAngle[localIndex_];
883 >    RealType getPrevFlucQPos() {
884 >      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_];
885      }
886        
887      /**
888 <     * Returns the current z-angle of this stuntDouble
889 <     * @return the z-angle of this stuntDouble
888 >     * Returns the current fluctuating charge of this stuntDouble
889 >     * @return the fluctuating charge of this stuntDouble
890       */    
891 <    RealType getZangle() {
892 <      return ((snapshotMan_->getCurrentSnapshot())->*storage_).zAngle[localIndex_];
891 >    RealType getFlucQPos() {
892 >      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_];
893      }
894  
895      /**
896 <     * Returns the z-angle of this stuntDouble in specified snapshot
897 <     * @return the z-angle of this stuntDouble
896 >     * Returns the fluctuating charge of this stuntDouble in specified snapshot
897 >     * @return the fluctuating charge of this stuntDouble
898       * @param snapshotNo
899       */    
900 <    RealType getZangle(int snapshotNo) {
901 <      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).zAngle[localIndex_];
900 >    RealType getFlucQPos(int snapshotNo) {
901 >      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_];
902      }
903  
904      /**
905 <     * Sets  the previous z-angle of this stuntDouble
906 <     * @param angle  new z-angle
907 <     * @see #getZangle
905 >     * Sets  the previous fluctuating charge of this stuntDouble
906 >     * @param charge  new fluctuating charge
907 >     * @see #getFlucQPos
908       */        
909 <    void setPrevZangle(RealType angle) {
910 <      ((snapshotMan_->getPrevSnapshot())->*storage_).zAngle[localIndex_] = angle;
909 >    void setPrevFlucQPos(RealType charge) {
910 >      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_] = charge;
911      }
912        
913      /**
914 <     * Sets  the current z-angle of this stuntDouble
915 <     * @param angle  new z-angle
914 >     * Sets  the current fluctuating charge of this stuntDouble
915 >     * @param charge  new fluctuating charge
916       */        
917 <    void setZangle(RealType angle) {
918 <      ((snapshotMan_->getCurrentSnapshot())->*storage_).zAngle[localIndex_] = angle;
917 >    void setFlucQPos(RealType charge) {
918 >      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_] = charge;
919      }
920  
921      /**
922 <     * Sets  the z-angle of this stuntDouble in specified snapshot
923 <     * @param angle z-angle to be set
922 >     * Sets  the fluctuating charge of this stuntDouble in specified snapshot
923 >     * @param charge fluctuating charge to be set
924       * @param snapshotNo
925 <     * @see #getZangle
925 >     * @see #getFlucQPos
926       */        
927 <    void setZangle(RealType angle, int snapshotNo) {
928 <      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).zAngle[localIndex_] = angle;
927 >    void setFlucQPos(RealType charge, int snapshotNo) {
928 >      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_] = charge;
929      }
930  
931      /**
932 <     * Adds z-angle into the previous z-angle of this stuntDouble
933 <     * @param angle  new z-angle
934 <     * @see #getZangle
932 >     * Adds fluctuating charge into the previous fluctuating charge of this stuntDouble
933 >     * @param charge  new fluctuating charge
934 >     * @see #getFlucQPos
935       */        
936 <    void addPrevZangle(RealType angle) {
937 <      ((snapshotMan_->getPrevSnapshot())->*storage_).zAngle[localIndex_] += angle;
936 >    void addPrevFlucQPos(RealType charge) {
937 >      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQPos[localIndex_] += charge;
938      }
939        
940      /**
941 <     * Adds z-angle into the current z-angle of this stuntDouble
942 <     * @param angle  new z-angle
941 >     * Adds fluctuating charge into the current fluctuating charge of this stuntDouble
942 >     * @param charge  new fluctuating charge
943       */        
944 <    void addZangle(RealType angle) {
945 <      ((snapshotMan_->getCurrentSnapshot())->*storage_).zAngle[localIndex_] += angle;
944 >    void addFlucQPos(RealType charge) {
945 >      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQPos[localIndex_] += charge;
946      }
947  
948      /**
949 <     * Adds z-angle into the z-angle of this stuntDouble in specified snapshot
950 <     * @param angle z-angle to be add
949 >     * Adds fluctuating charge into the fluctuating charge of this stuntDouble in specified snapshot
950 >     * @param charge fluctuating charge to be add
951       * @param snapshotNo
952 <     * @see #getZangle
952 >     * @see #getFlucQPos
953       */        
954 <    void addZangle(RealType angle, int snapshotNo) {
955 <      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).zAngle[localIndex_] += angle;
954 >    void addflucQPos(RealType charge, int snapshotNo) {
955 >      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQPos[localIndex_] += charge;
956      }      
957  
958 +
959 +    /**
960 +     * Returns the previous charge velocity of this stuntDouble
961 +     * @return the charge velocity of this stuntDouble
962 +     */    
963 +    RealType getPrevFlucQVel() {
964 +      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_];
965 +    }
966 +      
967 +    /**
968 +     * Returns the current charge velocity of this stuntDouble
969 +     * @return the charge velocity of this stuntDouble
970 +     */    
971 +    RealType getFlucQVel() {
972 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_];
973 +    }
974 +
975 +    /**
976 +     * Returns the charge velocity of this stuntDouble in specified snapshot
977 +     * @return the charge velocity of this stuntDouble
978 +     * @param snapshotNo
979 +     */    
980 +    RealType getFlucQVel(int snapshotNo) {
981 +      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_];
982 +    }
983 +
984 +    /**
985 +     * Sets  the previous charge velocity of this stuntDouble
986 +     * @param cvel  new charge velocity
987 +     * @see #getFlucQVel
988 +     */        
989 +    void setPrevFlucQVel(RealType cvel) {
990 +      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_] = cvel;
991 +    }
992 +      
993 +    /**
994 +     * Sets  the current charge velocity of this stuntDouble
995 +     * @param cvel  new charge velocity
996 +     */        
997 +    void setFlucQVel(RealType cvel) {
998 +      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_] = cvel;
999 +    }
1000 +
1001 +    /**
1002 +     * Sets  the charge velocity of this stuntDouble in specified snapshot
1003 +     * @param cvel charge velocity to be set
1004 +     * @param snapshotNo
1005 +     * @see #getFlucQVel
1006 +     */        
1007 +    void setFlucQVel(RealType cvel, int snapshotNo) {
1008 +      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_] = cvel;
1009 +    }
1010 +
1011 +    /**
1012 +     * Adds charge velocity into the previous charge velocity of this stuntDouble
1013 +     * @param cvel  new charge velocity
1014 +     * @see #getFlucQVel
1015 +     */        
1016 +    void addPrevFlucQVel(RealType cvel) {
1017 +      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQVel[localIndex_] += cvel;
1018 +    }
1019 +      
1020 +    /**
1021 +     * Adds charge velocity into the current charge velocity of this stuntDouble
1022 +     * @param cvel  new charge velocity
1023 +     */        
1024 +    void addFlucQVel(RealType cvel) {
1025 +      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQVel[localIndex_] += cvel;
1026 +    }
1027 +
1028 +    /**
1029 +     * Adds charge velocity into the charge velocity of this stuntDouble in specified snapshot
1030 +     * @param cvel charge velocity to be add
1031 +     * @param snapshotNo
1032 +     * @see #getFlucQVel
1033 +     */        
1034 +    void addflucQVel(RealType cvel, int snapshotNo) {
1035 +      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQVel[localIndex_] += cvel;
1036 +    }      
1037 +
1038 +
1039 +    /**
1040 +     * Returns the previous charge force of this stuntDouble
1041 +     * @return the charge force of this stuntDouble
1042 +     */    
1043 +    RealType getPrevFlucQFrc() {
1044 +      return ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_];
1045 +    }
1046 +      
1047 +    /**
1048 +     * Returns the current charge force of this stuntDouble
1049 +     * @return the charge force of this stuntDouble
1050 +     */    
1051 +    RealType getFlucQFrc() {
1052 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_];
1053 +    }
1054 +
1055 +    /**
1056 +     * Returns the charge force of this stuntDouble in specified snapshot
1057 +     * @return the charge force of this stuntDouble
1058 +     * @param snapshotNo
1059 +     */    
1060 +    RealType getFlucQFrc(int snapshotNo) {
1061 +      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_];
1062 +    }
1063 +
1064 +    /**
1065 +     * Sets  the previous charge force of this stuntDouble
1066 +     * @param cfrc  new charge force
1067 +     * @see #getFlucQFrc
1068 +     */        
1069 +    void setPrevFlucQFrc(RealType cfrc) {
1070 +      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_] = cfrc;
1071 +    }
1072 +      
1073 +    /**
1074 +     * Sets  the current charge force of this stuntDouble
1075 +     * @param cfrc  new charge force
1076 +     */        
1077 +    void setFlucQFrc(RealType cfrc) {
1078 +      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_] = cfrc;
1079 +    }
1080 +
1081 +    /**
1082 +     * Sets  the charge force of this stuntDouble in specified snapshot
1083 +     * @param cfrc charge force to be set
1084 +     * @param snapshotNo
1085 +     * @see #getFlucQFrc
1086 +     */        
1087 +    void setFlucQFrc(RealType cfrc, int snapshotNo) {
1088 +      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_] = cfrc;
1089 +    }
1090 +
1091 +    /**
1092 +     * Adds charge force into the previous charge force of this stuntDouble
1093 +     * @param cfrc   charge force to be added
1094 +     * @see #getFlucQFrc
1095 +     */        
1096 +    void addPrevFlucQFrc(RealType cfrc) {
1097 +      ((snapshotMan_->getPrevSnapshot())->*storage_).flucQFrc[localIndex_] += cfrc;
1098 +    }
1099 +      
1100 +    /**
1101 +     * Adds charge force into the current charge force of this stuntDouble
1102 +     * @param cfrc   charge force to be added
1103 +     */        
1104 +    void addFlucQFrc(RealType cfrc) {
1105 +      ((snapshotMan_->getCurrentSnapshot())->*storage_).flucQFrc[localIndex_] += cfrc;
1106 +    }
1107 +
1108 +    /**
1109 +     * Adds charge force into the charge force of this stuntDouble in specified snapshot
1110 +     * @param cfrc charge force to be added
1111 +     * @param snapshotNo
1112 +     * @see #getFlucQFrc
1113 +     */        
1114 +    void addflucQFrc(RealType cfrc, int snapshotNo) {
1115 +      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).flucQFrc[localIndex_] += cfrc;
1116 +    }      
1117 +
1118 +
1119 +    /**
1120 +     * Returns the previous electric field of this stuntDouble
1121 +     * @return the electric field of this stuntDouble
1122 +     */    
1123 +    Vector3d getPrevElectricField() {
1124 +      return ((snapshotMan_->getPrevSnapshot())->*storage_).electricField[localIndex_];
1125 +    }
1126 +      
1127 +    /**
1128 +     * Returns the current electric field of this stuntDouble
1129 +     * @return the electric field of this stuntDouble
1130 +     */    
1131 +    Vector3d getElectricField() {
1132 +      return ((snapshotMan_->getCurrentSnapshot())->*storage_).electricField[localIndex_];
1133 +    }
1134 +
1135 +    /**
1136 +     * Returns the electric field of this stuntDouble in specified snapshot
1137 +     * @return the electric field of this stuntDouble
1138 +     * @param snapshotNo
1139 +     */    
1140 +    Vector3d getElectricField(int snapshotNo) {
1141 +      return ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electricField[localIndex_];
1142 +    }
1143 +
1144 +    /**
1145 +     * Sets  the previous electric field of this stuntDouble
1146 +     * @param pos  new electric field
1147 +     * @see #getElectricField
1148 +     */        
1149 +    void setPrevElectricField(const Vector3d& pos) {
1150 +      ((snapshotMan_->getPrevSnapshot())->*storage_).electricField[localIndex_] = pos;
1151 +    }
1152 +      
1153 +    /**
1154 +     * Sets  the current electric field of this stuntDouble
1155 +     * @param pos  new electric field
1156 +     */        
1157 +    void setElectricField(const Vector3d& pos) {
1158 +      DataStorage&  data = snapshotMan_->getCurrentSnapshot()->*storage_;
1159 +      data.electricField[localIndex_] = pos;
1160 +      //((snapshotMan_->getCurrentSnapshot())->*storage_).electricField[localIndex_] = pos;
1161 +    }
1162 +
1163 +    /**
1164 +     * Sets  the electric field of this stuntDouble in specified snapshot
1165 +     * @param pos electric field to be set
1166 +     * @param snapshotNo
1167 +     * @see #getElectricField
1168 +     */        
1169 +    void setElectricField(const Vector3d& pos, int snapshotNo) {
1170 +
1171 +      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electricField[localIndex_] = pos;
1172 +
1173 +    }
1174 +
1175 +
1176      /** Set the force of this stuntDouble to zero */
1177      void zeroForcesAndTorques();
1178      /**

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