| 754 | 
  | 
    return maxCutoffRadius; | 
| 755 | 
  | 
} | 
| 756 | 
  | 
 | 
| 757 | 
< | 
void SimInfo::setupCutoff() { | 
| 758 | 
< | 
    double rcut_;  //cutoff radius | 
| 759 | 
< | 
    double rsw_; //switching radius | 
| 757 | 
> | 
void SimInfo::getCutoff(double& rcut, double& rsw) { | 
| 758 | 
  | 
     | 
| 759 | 
  | 
    if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { | 
| 760 | 
  | 
         | 
| 765 | 
  | 
                "\tfor the cutoffRadius.\n"); | 
| 766 | 
  | 
            painCave.isFatal = 0; | 
| 767 | 
  | 
            simError(); | 
| 768 | 
< | 
            rcut_ = 15.0; | 
| 768 | 
> | 
            rcut = 15.0; | 
| 769 | 
  | 
        } else{ | 
| 770 | 
< | 
            rcut_ = simParams_->getRcut(); | 
| 770 | 
> | 
            rcut = simParams_->getRcut(); | 
| 771 | 
  | 
        } | 
| 772 | 
  | 
 | 
| 773 | 
  | 
        if (!simParams_->haveRsw()){ | 
| 777 | 
  | 
                "\t0.95 * cutoffRadius for the switchingRadius\n"); | 
| 778 | 
  | 
            painCave.isFatal = 0; | 
| 779 | 
  | 
            simError(); | 
| 780 | 
< | 
            rsw_ = 0.95 * rcut_; | 
| 780 | 
> | 
            rsw = 0.95 * rcut; | 
| 781 | 
  | 
        } else{ | 
| 782 | 
< | 
            rsw_ = simParams_->getRsw(); | 
| 782 | 
> | 
            rsw = simParams_->getRsw(); | 
| 783 | 
  | 
        } | 
| 784 | 
  | 
 | 
| 785 | 
  | 
    } else { | 
| 787 | 
  | 
        //meta-data file, the maximum cutoff radius calculated from forcefiled will be used | 
| 788 | 
  | 
         | 
| 789 | 
  | 
        if (simParams_->haveRcut()) { | 
| 790 | 
< | 
            rcut_ = simParams_->getRcut(); | 
| 790 | 
> | 
            rcut = simParams_->getRcut(); | 
| 791 | 
  | 
        } else { | 
| 792 | 
  | 
            //set cutoff radius to the maximum cutoff radius based on atom types in the whole system | 
| 793 | 
< | 
            rcut_ = calcMaxCutoffRadius(); | 
| 793 | 
> | 
            rcut = calcMaxCutoffRadius(); | 
| 794 | 
  | 
        } | 
| 795 | 
  | 
 | 
| 796 | 
  | 
        if (simParams_->haveRsw()) { | 
| 797 | 
< | 
            rsw_  = simParams_->getRsw(); | 
| 797 | 
> | 
            rsw  = simParams_->getRsw(); | 
| 798 | 
  | 
        } else { | 
| 799 | 
< | 
            rsw_ = rcut_; | 
| 799 | 
> | 
            rsw = rcut; | 
| 800 | 
  | 
        } | 
| 801 | 
  | 
     | 
| 802 | 
  | 
    } | 
| 803 | 
< | 
         | 
| 803 | 
> | 
} | 
| 804 | 
> | 
 | 
| 805 | 
> | 
void SimInfo::setupCutoff() { | 
| 806 | 
> | 
    getCutoff(rcut_, rsw_);     | 
| 807 | 
  | 
    double rnblist = rcut_ + 1; // skin of neighbor list | 
| 808 | 
  | 
 | 
| 809 | 
  | 
    //Pass these cutoff radius etc. to fortran. This function should be called once and only once | 
| 835 | 
  | 
} | 
| 836 | 
  | 
 | 
| 837 | 
  | 
void SimInfo::setSnapshotManager(SnapshotManager* sman) { | 
| 838 | 
+ | 
    //if (sman_ == sman_) { | 
| 839 | 
+ | 
    //    return; | 
| 840 | 
+ | 
    //} | 
| 841 | 
+ | 
     | 
| 842 | 
+ | 
    //delete sman_; | 
| 843 | 
  | 
    sman_ = sman; | 
| 844 | 
  | 
 | 
| 845 | 
  | 
    Molecule* mol; |