original_code:
void energy_control_final(CLASS *class, BONDED *bonded,
                          GENERAL_DATA *general_data)
   {
  int MPI_INT = 1;
  int MPI_DOUBLE = 1;
  int MPI_CHAR = 1;
  int MPI_MAX = 1;
  int MPI_SUM = 1;
  int MPI_ANY_TAG = 1;
  int MPI_ANY_SOURCE = 1;
  int *MPI_BOTTOM = {0};
  int i,iii,igloc,iver_get,ip,iup,j,igo;
  double *fx, *fy, *fz, temp;
  double *fxt, *fyt, *fzt;
  double *fxtemp = class->ewd_scr.x;
  double *fytemp = class->ewd_scr.y;
  double *fztemp = class->ewd_scr.z;
  int nfreeze = class->atommaps.nfreeze;
  int *freeze_map = class->atommaps.freeze_map;
  int pimd_freez_typ = class->atommaps.pimd_freez_typ;
  int nfree = class->clatoms_info.nfree;
  int pi_beads = class->clatoms_info.pi_beads;
  int pi_beads_proc = class->clatoms_info.pi_beads_proc;
  int pi_beads_proc_st= class->clatoms_info.pi_beads_proc_st;
  int *recv_count_atm = class->class_comm_forc_pkg.recv_count_atm;
  int myatm_start = class->clatoms_info.myatm_start;
  int myatm_end = class->clatoms_info.myatm_end;
  int np_beads = class->communicate.np_beads;
  int np_states = class->communicate.np_states;
  int np_tot = class->communicate.np;
  int np_forc = class->communicate.np_forc;
  int myid = class->communicate.myid_forc;
  int myid_state = class->communicate.myid_state;
  int myid_bead = class->communicate.myid_bead;
  int comm_forc = class->communicate.comm_forc;
  int world = class->communicate.world;
  int comm_beads = class->communicate.comm_beads;
  int iget_full_inter = class->energy_ctrl.iget_full_inter;
  int iget_res_inter = class->energy_ctrl.iget_res_inter;
  double *pvten_temp = general_data->ptens.pvten_tmp;
  double *pvten_tot = general_data->ptens.pvten_tot;
  double *pvten = general_data->ptens.pvten;
  double t_ext = general_data->statepoint.t_ext;
  double volume = general_data->cell.vol;
  int hmat_int_typ = general_data->cell.hmat_int_typ;
  int npt_i = general_data->ensopts.npt_i;
  int npt_f = general_data->ensopts.npt_f;
  int pimd_on;
  pimd_on = general_data->simopts.pimd
                        +general_data->simopts.debug_pimd
                        +general_data->simopts.cp_pimd
                        +general_data->simopts.cp_wave_pimd
                        +general_data->simopts.cp_wave_min_pimd
                        +general_data->simopts.debug_cp_pimd;
  ("energy control final");
  iver_get = 0;
  if( (pimd_on==1) && (iget_full_inter==1) ){iver_get = 1;}
  if(iget_full_inter==1){
    general_data->stat_avg.press_kin = (nfree*t_ext)/(3.0*315777.0*volume);
  }
  if(np_tot > 1){
    if((np_beads>1)||((pimd_on==1)&&(np_states>1||np_forc>1))){
      for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
      Allreduce(&(pvten_tot[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
      for(i=1;i<=9;i++){pvten_tot[i] = pvten_temp[i];}
      if(np_states>1||np_forc>1){
        for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
        Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
        for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
      }else{
        if(myid_state==0){
          for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
          Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,
                                                              comm_beads);
          for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
        }
      }
    }else{
      if( (np_forc>1) || (np_states>1) ){
        for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
        Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
        for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
      }
    }
  }
  if(myid_state == 0 || np_forc > 0){
    if(npt_i==1){
     box_force_iso(general_data->par_rahman.fgmat_p,
                 &(general_data->baro.f_lnv_p),
                   general_data->ptens.pvten,general_data->ptens.pvten_inc,
                   general_data->statepoint.pext,general_data->cell.vol,
                   bonded->constrnt.iconstrnt);
    }
    if(npt_f==1){
      box_force_flex(general_data->par_rahman.fgmat_p,
                     general_data->ptens.pvten,general_data->ptens.pvten_inc,
                     general_data->statepoint.pext,
                     general_data->statepoint.stens_ext,
                     bonded->constrnt.iconstrnt,&(general_data->cell));
    }
  }
  if(myid_state == 0 || np_forc > 0){
    for(ip=1;ip<=pi_beads_proc;ip++){
      distrib_ghost_force(&(class->clatoms_info),&(class->clatoms_pos[ip]),
                          &(class->ghost_atoms),iver_get);
    }
  }
  if(myid_state == 0 || np_forc > 1){
    if(nfreeze > 0) {
      iup = 1; igo=0;
      if(pimd_freez_typ==2){iup=pi_beads_proc;igo=1;}
      if(pimd_freez_typ==1 && pi_beads_proc_st==1){igo=1;}
      if(igo==1){
        for(ip=1;ip<=iup;ip++){
          fx = class->clatoms_pos[ip].fx;
          fy = class->clatoms_pos[ip].fy;
          fz = class->clatoms_pos[ip].fz;
          if(pi_beads > 1) {
             fxt = class->clatoms_pos[ip].fxt;
             fyt = class->clatoms_pos[ip].fyt;
             fzt = class->clatoms_pos[ip].fzt;
          }
          for(i=1;i <= nfreeze;i++){
            igloc = freeze_map[i];
            fx[igloc] = 0.0;
            fy[igloc] = 0.0;
            fz[igloc] = 0.0;
            if(pi_beads > 1) {
               fxt[igloc] = 0.0;
               fyt[igloc] = 0.0;
               fzt[igloc] = 0.0;
            }
          }
        }
      }
    }
  }
  if( (iget_full_inter+iget_res_inter)>=1){
    if(np_forc>1&&pimd_on==0){
      for(ip=1;ip<=pi_beads_proc;ip++){
        fx = class->clatoms_pos[ip].fx;
        fy = class->clatoms_pos[ip].fy;
        fz = class->clatoms_pos[ip].fz;
        Reduce_scatter(&fx[1],&fxtemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        Reduce_scatter(&fy[1],&fytemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        Reduce_scatter(&fz[1],&fztemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        for(i=myatm_start;i<=myatm_end;i++){
          fx[i] = fxtemp[i];
          fy[i] = fytemp[i];
          fz[i] = fztemp[i];
        }
      }
    }
  }
  ("energy control final");
   }

canonical_original_code:
void energy_control_final(struct class *class, struct bonded *bonded, struct general_data *general_data)
   {
  int MPI_INT = 1;
  int MPI_DOUBLE = 1;
  int MPI_CHAR = 1;
  int MPI_MAX = 1;
  int MPI_SUM = 1;
  int MPI_ANY_TAG = 1;
  int MPI_ANY_SOURCE = 1;
  int *MPI_BOTTOM = {0};
  int i; int iii; int igloc; int iver_get; int ip; int iup; int j; int igo;
  double *fx; double *fy; double *fz; double temp;
  double *fxt; double *fyt; double *fzt;
  double *fxtemp = class->ewd_scr.x;
  double *fytemp = class->ewd_scr.y;
  double *fztemp = class->ewd_scr.z;
  int nfreeze = class->atommaps.nfreeze;
  int *freeze_map = class->atommaps.freeze_map;
  int pimd_freez_typ = class->atommaps.pimd_freez_typ;
  int nfree = class->clatoms_info.nfree;
  int pi_beads = class->clatoms_info.pi_beads;
  int pi_beads_proc = class->clatoms_info.pi_beads_proc;
  int pi_beads_proc_st = class->clatoms_info.pi_beads_proc_st;
  int *recv_count_atm = class->class_comm_forc_pkg.recv_count_atm;
  int myatm_start = class->clatoms_info.myatm_start;
  int myatm_end = class->clatoms_info.myatm_end;
  int np_beads = class->communicate.np_beads;
  int np_states = class->communicate.np_states;
  int np_tot = class->communicate.np;
  int np_forc = class->communicate.np_forc;
  int myid = class->communicate.myid_forc;
  int myid_state = class->communicate.myid_state;
  int myid_bead = class->communicate.myid_bead;
  int comm_forc = class->communicate.comm_forc;
  int world = class->communicate.world;
  int comm_beads = class->communicate.comm_beads;
  int iget_full_inter = class->energy_ctrl.iget_full_inter;
  int iget_res_inter = class->energy_ctrl.iget_res_inter;
  double *pvten_temp = general_data->ptens.pvten_tmp;
  double *pvten_tot = general_data->ptens.pvten_tot;
  double *pvten = general_data->ptens.pvten;
  double t_ext = general_data->statepoint.t_ext;
  double volume = general_data->cell.vol;
  int hmat_int_typ = general_data->cell.hmat_int_typ;
  int npt_i = general_data->ensopts.npt_i;
  int npt_f = general_data->ensopts.npt_f;
  int pimd_on;
  pimd_on = general_data->simopts.pimd
                        +general_data->simopts.debug_pimd
                        +general_data->simopts.cp_pimd
                        +general_data->simopts.cp_wave_pimd
                        +general_data->simopts.cp_wave_min_pimd
                        +general_data->simopts.debug_cp_pimd;
  ("energy control final");
  iver_get = 0;
  if( (pimd_on==1) && (iget_full_inter==1) ){iver_get = 1;}
  if(iget_full_inter==1){
    general_data->stat_avg.press_kin = (nfree*t_ext)/(3.0*315777.0*volume);
  }
  if(np_tot > 1){
    if((np_beads>1)||((pimd_on==1)&&(np_states>1||np_forc>1))){
      for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
      Allreduce(&(pvten_tot[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
      for(i=1;i<=9;i++){pvten_tot[i] = pvten_temp[i];}
      if(np_states>1||np_forc>1){
        for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
        Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
        for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
      }else{
        if(myid_state==0){
          for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
          Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,
                                                              comm_beads);
          for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
        }
      }
    }else{
      if( (np_forc>1) || (np_states>1) ){
        for(i=1;i<=9;i++){pvten_temp[i]=0.0;}
        Allreduce(&(pvten[1]),&(pvten_temp[1]),9,MPI_DOUBLE,MPI_SUM,0,world);
        for(i=1;i<=9;i++){pvten[i] = pvten_temp[i];}
      }
    }
  }
  if(myid_state == 0 || np_forc > 0){
    if(npt_i==1){
     box_force_iso(general_data->par_rahman.fgmat_p,
                 &(general_data->baro.f_lnv_p),
                   general_data->ptens.pvten,general_data->ptens.pvten_inc,
                   general_data->statepoint.pext,general_data->cell.vol,
                   bonded->constrnt.iconstrnt);
    }
    if(npt_f==1){
      box_force_flex(general_data->par_rahman.fgmat_p,
                     general_data->ptens.pvten,general_data->ptens.pvten_inc,
                     general_data->statepoint.pext,
                     general_data->statepoint.stens_ext,
                     bonded->constrnt.iconstrnt,&(general_data->cell));
    }
  }
  if(myid_state == 0 || np_forc > 0){
    for(ip=1;ip<=pi_beads_proc;ip++){
      distrib_ghost_force(&(class->clatoms_info),&(class->clatoms_pos[ip]),
                          &(class->ghost_atoms),iver_get);
    }
  }
  if(myid_state == 0 || np_forc > 1){
    if(nfreeze > 0) {
      iup = 1; igo=0;
      if(pimd_freez_typ==2){iup=pi_beads_proc;igo=1;}
      if(pimd_freez_typ==1 && pi_beads_proc_st==1){igo=1;}
      if(igo==1){
        for(ip=1;ip<=iup;ip++){
          fx = class->clatoms_pos[ip].fx;
          fy = class->clatoms_pos[ip].fy;
          fz = class->clatoms_pos[ip].fz;
          if(pi_beads > 1) {
             fxt = class->clatoms_pos[ip].fxt;
             fyt = class->clatoms_pos[ip].fyt;
             fzt = class->clatoms_pos[ip].fzt;
          }
          for(i=1;i <= nfreeze;i++){
            igloc = freeze_map[i];
            fx[igloc] = 0.0;
            fy[igloc] = 0.0;
            fz[igloc] = 0.0;
            if(pi_beads > 1) {
               fxt[igloc] = 0.0;
               fyt[igloc] = 0.0;
               fzt[igloc] = 0.0;
            }
          }
        }
      }
    }
  }
  if( (iget_full_inter+iget_res_inter)>=1){
    if(np_forc>1&&pimd_on==0){
      for(ip=1;ip<=pi_beads_proc;ip++){
        fx = class->clatoms_pos[ip].fx;
        fy = class->clatoms_pos[ip].fy;
        fz = class->clatoms_pos[ip].fz;
        Reduce_scatter(&fx[1],&fxtemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        Reduce_scatter(&fy[1],&fytemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        Reduce_scatter(&fz[1],&fztemp[myatm_start],&recv_count_atm[1],
                       MPI_DOUBLE,MPI_SUM,comm_forc);
        for(i=myatm_start;i<=myatm_end;i++){
          fx[i] = fxtemp[i];
          fy[i] = fytemp[i];
          fz[i] = fztemp[i];
        }
      }
    }
  }
  ("energy control final");
   }

variable_types: struct class { struct clatoms_info { int natm_tot; int pi_beads; int pi_beads_proc; int pi_beads_proc_st; int pi_beads_proc_end; int nfree; int nfree_pimd; int nchrg; int pi_beads_full_ter; int pi_beads_res_ter; int pi_beads_full_tra; int pi_beads_res_tra; int cg_reset_flag; int natm_mall; int nchrg_mall; int hess_calc; int natm_proc; int N_H2; int i_H2_start; int nab_initio; int myatm_start; double gamma_adb; double wght_pimd; double pi_temperature; double pi_beads_full_ter_wght; double pi_beads_res_ter_wght; double pi_beads_full_tra_wght; double pi_beads_res_tra_wght; double rcut_spread; double mass_sc_fact; int *ip_lab; int *ichrg; int *cp_vlnc_up; int *cp_atm_flag; double *mass; double *q; double *alp_pol; double *b_neut; double *roll_sc; double *text_atm; double *text_mol; double *xold; double *prekf; double *xmod; double alp_ewd; } clatoms_info; struct clatoms_tran { int pi_beads_proc; int pi_atm_proc; int pi_atm_proc_use; int pi_proc_rem; int nwork; int *sendcounts; int *senddspls; int *ifax; double *rat1_stag; double *path_eig; double *work; double *work3; double *x_trans; double *x_temp; double *xt_temp; } clatoms_tran; struct clatoms_pos { double *mass; double *x; double *vx; double *fx; double *fxt; double *fxm; double *hess_xx; } *clatoms_pos; struct ghost_atoms { int nghost_tot; int natm_comp_max; int nghost_mall; int nghost_old; int ncomp_mall; int ncomp_old; int *ighost_map; int *natm_comp; int **iatm_comp; double **coef; } ghost_atoms; struct atommaps { int nmol_typ; int nres_typ; int natm_typ; int nfreeze; int nfreeze_mall; int natm_typ_mall; int nres_typ_max; int nres_max; int nres_tot; int nres_sum; int pimd_freez_typ; char (*atm_typ)[50]; char (*res_typ)[50]; char (*mol_typ)[50]; int *nmol_jmol_typ; int *nres_1mol_jmol_typ; int *jatm_jmol_typ_strt; int *jres_jmol_typ_strt; int *ires_typ_jres_jmol_typ; int *jatm_jres_1mol_jmol_typ_strt; int *natm_1mol_jmol_typ; int *natm_jres_jmol_typ; int *nfree_1mol_jmol_typ; int *nfree_jres_jmol_typ; int *icons_jmol_typ; int *icons_jres_jmol_typ; int *natm_jmol_typ; int *iatm_mol_typ; int *iatm_res_typ; int *iatm_atm_typ; int *iatm_atm_typ_nl; int *iatm_atm_typ_nl_rev; int *imap_atm_typ_nl; int *imap_atm_typ_nl_gh; int *iatm_mol_num; int *iatm_proc_num; int *iatm_res_num; int *ighost_flag; int *freeze_flag; int *freeze_map; int *atom_label; int *cp_atm_lst; } atommaps; struct therm_info { int num_nhc; int len_nhc; int nres_nhc; int nyosh_nhc; int therm_typ; int num_nhc_proc; int num_nhc_share; int mytherm_start; double dt_nhc; int *inhc_x; int *itherm_nshare; double *ditherm_nshare_i; int *map_share; double *text_nhc; double *wdti; double **mass_nhc; } therm_info_class; struct therm_info therm_info_bead; struct therm_pos { double **x_nhc; double x_nhc_tot; } therm_class; struct therm_pos *therm_bead; struct vel_samp_class { int ivel_smpl_on; int ivel_scale_on; int nvx_smpl; int nvx_scale; int nvnhc_smpl; int iseed; double qseed; } vel_samp_class; struct energy_ctrl { int pme_on; int int_res_ter; int isep_vvdw; int iswit_vdw; int block_std_on; int iget_pe_real_inter_freq; int iget_pe_real_inter; int itime; int iget_full_inter; int iget_full_intra; int iget_full_pimd; } energy_ctrl; struct nbr_list { int iver; int ilnk; int nolst; int brnch_root_list_opt; double *x0; struct verlist { int iver_init; int iver_fill; int nolst_ver_update; int jver_pad; int nmem_min_lst; int nver_lst; int nver_lst_res; int nver_lst_now; int nver_lst_now_res; int *nter; int *jter; int *jver_off; int *nter_res; int *jter_res; int *jver_off_res; double mem_safe; } verlist; struct lnklist { int ilnk_init; int lnk_for_odd; int ncell_div_avg; int lnk_excl_safe; int lnk_vol_safe; int ncell_a; int natm_cell_max; int lnk_list_dim; int nshft_lnk; int nshft_lnk_res; double vol_lnk_map; double rcut_max; int *lnk_list; int *ishft_a; int *iexl_chk; int *ishft_a_res; int *iexl_chk_res; int *natm_cell; double *shft_wght; double *shft_wght_res; double *hmat_lnk; } lnklist; struct brnch_root { int nbrnch_tot; int nroot_tot; int natm_add_tot; int nbrnch_root_max; double brnch_root_dist_max; double cutdif_min_brnch_root; double cutdif_min_brnch_brnch; double cutdif_min_brnch_root_res; double cutdif_min_brnch_brnch_res; double r2_nocheck_dist; double r2_nocheck_dist_res; double cutskin_bb_min; double cutskin_bb_min_res; int *brnch_atm_list; int *brnch_atm_root; int *root_atm_list; int *root_atm_map; int *brnch_atm_map; int *nbrnch_of_root_big; int *nbrnch_of_root; int **ibrnch_of_root; int *natm_add; int *iatm_add; int *iatm_add_off; } brnch_root; } nbr_list; struct interact { int nsplin; int iswit_vdw; int dielectric_opt; int ishave_opt; int nter_typ; int nsplin_tot; int ninter_mall; int nsplin_mall_tot; int *inter_map_index; double dielectric_rheal; double dielectric_cut; double dielectric_eps; double brnch_root_skin; double skin; double brnch_root_cut; double rheal_res; double pten_inter_guess; double pten_kin_guess; double clong; double clong_res; double spread_now; double spread_lnk; double brnch_root_skin_lnk; double cutoff_max; double *cutoff; double *cutoff_res; double *cutti; double *cutskin; double *cutskin_res; double *cutskin_root; double *cutskin_root_res; double *vcut_coul; double *rmin_spl; double *dr_spl; double *cv0; double *cdv0; double *cv0_c; double *cdv0_c; } interact; struct int_scr { double v_lnv; double *x; double *vx; double *gx; double **x_nhc; double *vgmat; double *x_vol_nhc; double *sc; double *sc_temp; double *atm_kin; double *step_up; struct therm_scr { double *sc; double *atm_kin; } *therm_scr; } int_scr; struct ewd_scr { double *q; double *x; double *fx; double *heli; double *cossc; double *fx2; double *temp; double *helr_now; } ewd_scr; struct for_scr { int nlen; int nsplin_t; int num_brk; int intact; double wght_lnk; double wght_ter; double wght_ter_res; double wght_tra; double wght_tra_res; double wght_pimd; int *j_indext; int *i_indext2; int *j_lnk; int *j_index; int *num_brk_i; int *iexcl; int *index_atm; } for_scr; double tot_memory; struct part_mesh { int pme_on; int kmax_pme; int n_interp; int pme_res_on; int kmax_pme_res; int n_interp_res; int pme_para_opt; int nlen_pme; int nktot_pme; int ngrid_a; int nktot_pme_res; int ngrid_a_res; int ninterp_mall; int ninterp_tot_mall; int *iatemp; int *nc; int **igrid_a; int **igrid_now; double ecut; double ecut_res; double *bweight_tot_res; double *bweight_tot; double *qgrid; double *qgrid_scr; double *qgrid_tmp_real; double *qgrid_tmp_imag; double *frac_a; double *aj; double **ua; double **mn_a; double **dmn_a; double **qgrid_now; } part_mesh; struct surface { int isurf_on; int natm_typ; int nsplin_surf; int nsplin_tot; double zheal; double surface_height; double *surface_pot; double *surface_forc; double *zcut_off; double *dz_spl; double *dzi_spl; double *zmin_spl; char surface_type[50]; } surface; struct communicate { int np_beads; int myid; int myid_bead_forc; int myid_bead; int myid_bead_prime; int myid_state; int myid_forc; int myid_forc_source; int myid_forc_target; int world; int comm_beads; int comm_beads_forc; int comm_states; int comm_forc; int comm_forc_source; int comm_forc_target; int comm_faux; } communicate; struct class_comm_forc_pkg { int num_proc; int myid; int myatm_start; int mytherm_start; int *displs_atm; int *displs_therm; int comm; int world; double dbl_num_proc; struct class_plimpton_ind { int num_proc_source; int num_proc_target; int myid_source; int myid_target; int natoms_tot; int *index_src; int *index_src_even; int *index_src_odd; int *index_trg; int *index_trg_even; int *index_trg_odd; int *displs_atm_trg; int *displs_atm_src; int *src_odd_end; int *src_even_end; int *trg_odd_end; int *trg_even_end; int *src_odd_begin; int *src_even_begin; int *trg_odd_begin; int *trg_even_begin; int my_src_odd_counts; int my_src_even_counts; int my_trg_odd_counts; int my_trg_even_counts; int *my_src_odd; int *my_src_even; int *my_trg_odd; int *my_trg_even; int **jmax; int *jmin; int **imax; int source; int target; } plimpton_ind; } class_comm_forc_pkg; } *

variable_types: struct bonded { struct bond { int npow; int ntyp_pow; int ncon; int ntyp_con; int nbond_pow_mall; int nbond_typ_pow_mall; int nbond_con_mall; int nbond_typ_con_mall; int block_pow_on; int ncon_tot; int ncon_max; int nblock_pow; int nblock_con; int *j1_pow; int *jtyp_pow; int *j1_con; int *jtyp_con; int *iblock_pow_size; int *iblock_pow_conflict_1; int *iblock_con_size; int *iblock_con_conflict_1; double *eq_pow; double *eq_pow_res; double *c_0; double *dc_0; double *al_con; double *eq_con; } bond; struct grp_bond_con { int num_33; int num_21; int num_43; int ntyp_33; int num_23; int ntyp_23; int num_46; int ntyp_46; int max_iter; int ngrp_21_mall; int ngrp_33_mall; int ngrp_43_mall; int ngrp_23_mall; int ngrp_46_mall; int ngrp_typ_21_mall; int ngrp_typ_33_mall; int ngrp_typ_43_mall; int ngrp_typ_23_mall; int ngrp_typ_46_mall; int num_21_tot; double tol; int *j1_33; int *j1_21; int *j2_43; int *jtyp_33; int *j1_23; int *jtyp_23; int *j1_46; int *jtyp_46; double **al_33; double **al_23; double **al_21; double **eq_21; double **al_46; int ncons_gather_tot; int ncons_gather; int ncons_gather_max; int *ind_gather_fwd; int *ind_gather_bck; int *ind_gather_scr; } grp_bond_con; struct grp_bond_watts { int num_33; int num_33_tot; int ntyp_33; int ngrp_33_mall; int ngrp_typ_33_mall; int *j1_33; int *jtyp_33; double *cos_thet0_2; double **eq_33; double **c_0_33; double **c_4_33; double **dc_0_33; double **dc_4_33; } grp_bond_watts; struct constrnt { int iconstrnt; int iroll; int max_iter; double tolshake; double tolratl; } constrnt; struct bond_free { int num; int j1; int npow; int nhist; double fk; double eq; double del; double rmin; double rmax; char *file; double *hist; } bond_free; struct bend { int npow; int ntyp_pow; int ncon; int ntyp_con; int nbend_pow_mall; int nbend_typ_pow_mall; int nbend_con_mall; int nbend_typ_con_mall; int block_pow_on; int ncon_tot; int nblock_pow; int nblock_con; int *j1_pow; int *jtyp_pow; int *j1_con; int *jtyp_con; int *iblock_pow_size; int *iblock_pow_conflict_1; int *iblock_pow_conflict_3; int *iblock_con_size; int *iblock_con_conflict_1; int *iblock_con_conflict_3; double *eq_pow; double *c_0; double *s_0; double *dc_0; double *ds_0; double *al_con; double *eq_con; } bend; struct bend_free { int num; int j1; int npow; int nhist; double fk; double eq; double del; char *file; double *hist; } bend_free; struct bend_bnd { int num; int ntyp; int nbend_bnd_mall; int nbend_bnd_typ_mall; int block_on; int nblock; int *j1; int *jtyp; int *iblock_size; int *iblock_conflict_1; int *iblock_conflict_3; double *eq_bond; double *eq_bend; double *cbond_0; double *dcbond_0; double *cbend_0; double *sbend_0; double *dcbend_0; double *dsbend_0; } bend_bnd; struct tors { int npow; int ntyp_pow; int nimpr; int ncon; int ntyp_con; int ntors_pow_mall; int ntors_typ_pow_mall; int ntors_con_mall; int ntors_typ_con_mall; int block_pow_on; int block_con_on; int ncon_tot; int nblock_pow; int nblock_con; int *j1_pow; int *jtyp_pow; int *j1_con; int *jtyp_con; int *iblock_pow_size; int *iblock_pow_conflict_1; int *iblock_pow_conflict_3; int *iblock_con_size; int *iblock_con_conflict_1; int *iblock_con_conflict_3; double *c_0; double *s_0; double *dc_0; double *ds_0; double *eq_pow; double *al_con; double *eq_con; } tors; struct tors_free { int num; int npow; int nhist; int j1[3]; double fk; double eq[3]; double del; char *file; double *hist; double **hist_2d; } tors_free; struct rbar_sig_free { int nfree; int nhist_bar; int iopt; int *j1; double fk_bar; double fk_sigma; double eq_bar; double eq_sigma; double del_bar; double rmin; double smin; double rnfree; double **hist; double **hist_rn; char *file; } rbar_sig_free; struct onfo { int num; int ntyp; int nonfo_mall; int nonfo_typ_mall; int block_on; int nblock; int *j1; int *jtyp; int *iblock_size; int *iblock_conflict_1; double *feps; double *s6; double *sc; } onfo; struct ecor { int nsplin; int num; int block_on; int nblock; int nktot_res; int necor_mall; double alp_ewd; double ecut; double rmin_spl; double rmax_spl; double dr_spl; int *j1; int *iblock_size; int *iblock_conflict_1; double *cv0; } ecor; struct excl { int nlst; int nlst_root; int num_cp; int *num; int *j; int *j_off; int *j1_cp; } excl; struct intra_scr { int nlen; double wght_ter; double wght_ter_res; double wght_tra; double wght_tra_res; double int_res_inter; int *iatm_typ; int *jatm_typ; double *vpot; double *p11; double *p21; double *p31; double *x1; double *x2; double *x3; double *x4; double *x5; double *x6; double *x7; double *x8; double *fx1; double *fx2; double *fx3; double *fx4; double *dx12; double *dx13; double *dx23; double *dx42; double *dx43; double *dx56; double *dx57; double *dx67; double *dx86; double *dx87; double *c_0; double *dc_0; double *ds_0; double *s_0; double *eq; double *m1; double *vx1; double *vx2; double *sc_1; double *sc; double *q1; double *rmin; double *dri; double *vcut_coul; double *del_r; double *swit; double *cutoff_res; } intra_scr; } *

variable_types: struct general_data { struct simopts { int md; int pimd; int minimize; int cp; int cp_pimd; int cp_wave; int cp_wave_pimd; int cp_wave_min_pimd; int cp_min; int cp_wave_min; int debug; int debug_pimd; int debug_cp; int debug_cp_pimd; int pi_beads; int pi_md_typ; int initial_spread_opt; int anneal_opt; double ann_rate; double ann_start_temp; double ann_target_temp; } simopts; struct minopts { int min_std; int min_cg; int min_diis; int diis_hist_len; int cp_min_std; int cp_min_cg; int cp_min_diis; int cp_diis_hist_len; int cp_cg_line_min_len; int min_atm_com_fix_opt; double tol_coef; double tol_atom; } minopts; struct ensopts { int nve; } ensopts; struct filenames { char *iname; char *dname; char *dnamec; char *cpname; char *ksname; char *elfname; char *cvname; char *ccname; char *cpparname; char *centname; char *forcename; int low_lim_par; int high_lim_par; int iwrite_screen; int iwrite_inst; int iwrite_dump; int iwrite_kseigs; int iwrite_confv; int iwrite_confp; int iwrite_par_confp; int iwrite_confc; int iwrite_path_cent; int ifile_open; int iwrite_conf_binary; int iwrite_units; int iwrite_atm_for; int iwrite_elf; } filenames; struct statepoint { double pext; } statepoint; struct cell { int iperd; int intra_perds; int cubic_box_flag; int hmat_int_typ; int hmat_cons_typ; int imov_cp_box; double vol; double vol_cp; double vol0; double area; double alpha_conv_dual; double *hmat; double *hmat_ewd; double *hmat_cp; double *cp_box_center; double *cp_box_center_rel; double *cp_vbox_center; double *cp_fbox_center; } cell; struct timeinfo { int ntime; int ix_respa; int int_res_ter; int nres_ter; int int_res_tor; int int_res_pimd; int iget_pe_real_inter_freq; int exit_flag; double dt; } timeinfo; struct baro { int len_nhc; double x_lnv; double v_lnv_glob; double v_lnv_g; double f_lnv_p; double vol; double mass_lnv; double c2_lnv; double roll_scv; double roll_scg; double roll_scg0; double x_lnv_o; double v_lnv_g_wght; double area; double *x_vol_nhc; double *f_vol_nhc; double *hmato; } baro; struct par_rahman { double vol; double mass_hm; double c1_hm; double roll_scg; double roll_scg0; double area; double *vgmat; double *vgmat_glob; double *fgmat_p; double *roll_mtv; double *roll_mtvv; double *vtemps; double *vexpdt; double *vtempx; double *hmat_t; double *fv1; double *vgmat_g_wght; } par_rahman; struct ptens { double *tvten; double *pvten; double *pvten_inc; double *pvten_tmp_res; double *pvten_inc_t1; double *pvten_inc_a; double *pvten_inc_old; double *count_inc; double *pvten_inc_glob; double *pvten_mode; } ptens; struct stat_avg { int nexclt; int iter_shake; int iswit_vdw; int itime_update; int iter_shake_cp; int write_cp_atm_flag; double vintert; double vintrat; double vsurft; double vbondt; double vbend_bndt; double vbend_bnd_bond; double vbondt_watts; double vreal; double vvdw; double vlong; double vbond_free; double vbar_free; double kinet; double kinet_v; double vol; double kinet_nhc; double kinet_nhc_bead; double aikinet_nhc_bead; double akinet_nhc_bead; double vpot_v; double vpotnhc; double aiter_shake; double iter_23; double aiter_23; double aiter_21; double iter_23r; double aiter_23r; double aiter_21r; double acella; double aicella; double acellab; double aicellab; double apress; double press_inter; double apress_inter; double apress_intra; double press_kin; double apress_kin; double econv0; double cp_kconv0; double cpu1; double updates; double kinet_cp_up; double kinet_cp_dn; double kinet_cp; double kinet_nhc_cp; double vpotnhc_cp; double cp_ehart; double cp_eext; double cp_exc; double cp_muxc; double cp_eke; double cp_enl; double aiter_shake_cp; double maxfc; double pi_ke_prim; double api_ke_prim; double aipi_ke_prim; double kin_harm; double *apten; double fc_mag_up; double fc_max_up; double fatm_max; double count_diag_srot; double econv_now; double isokconv; } stat_avg; struct ewald { int nsplin_g; int nktot; int nktot_res; int nktot_mall; int nktot_res_mall; int nkc_max; int nkb_max; double alp_ewd; double self_erf; double ecut; double ecut_clus; double alp_clus; double gs_max; int *kastr; int *ibrk1; int *kastr_res; int *ibrk1_res; double *clus_corr_r; double *clus_corr_r_res; double *cvgs_2d0; double *vgc_1d_y; } ewald; struct para_fft_pkg3d { int nktot; int ncoef_use; int nfft_size; int nfft; int igeneric_opt; int scale_opt; int len_ifax; int nwork1; double ecut; int comm; int num_proc; int *map_proc; int *recv_counts_rho; int *recv_counts_coef; int *map_pme_dn; int *recvcounts_pme_dn; int *sendcounts_pme_dn; int *map_pme_up; int *recvcounts_pme_up; int *sendcounts_pme_up; int ndata_kc; int nkf3; int str_fft_kc_proc; int ska_fft_kc_proc; int skb_fft_kc_proc; int *sendcounts_fft_kc; int *recvcounts_fft_kc; int *sum_fft_kc_proc; int nka_fft_kc; int *ka_fft_kc; int *ifax_c_f; double *work_1c_f; double *work_1c_r; int ndata_kb; int nkf2; int str_fft_kb_proc; int ska_fft_kb_proc; int skc_fft_kb_proc; int *ska_fft_kb_proc_all; int *skc_fft_kb_proc_all; int *sendcounts_fft_kb; int *recvcounts_fft_kb; int *sum_fft_kb_proc; int *ifax_b_f; double *work_1b_f; double *work_1b_r; int ndata_ka; int nkf1; int str_fft_ka_proc; int skb_fft_ka_proc; int skc_fft_ka_proc; int *skb_fft_ka_proc_all; int *skc_fft_ka_proc_all; int *sendcounts_fft_ka; int *recvcounts_fft_ka; int *ifax_a_f; double *work_1a_f; double *work_1a_r; int *send_counts_row_big_small; int *recv_counts_row_big_small; int *sdispls_row_big_small; int *rdispls_row_big_small; int *send_counts_dual_map; int *recv_counts_dual_map; int *sdispls_dual_map; int *rdispls_dual_map; int *send_counts_row_big_small_upack; int *recv_counts_row_big_small_upack; int *sdispls_row_big_small_upack; int *rdispls_row_big_small_upack; int *send_counts_dual_map_upack; int *recv_counts_dual_map_upack; int *sdispls_dual_map_upack; int *rdispls_dual_map_upack; int *send_counts_ioff_big_small; int *recv_counts_ioff_big_small; int *sdispls_ioff_big_small; int *rdispls_ioff_big_small; } pme_fft_pkg; struct para_fft_pkg3d pme_res_fft_pkg; int error_check_on; } *

variable_types: igloc int

variable_types: ip int

variable_types: iup int

variable_types: j int

variable_types: igo int

variable_types:
fx
double *

variable_types:
fy
double *

variable_types:
fz
double *

variable_types: temp double

variable_types:
fxt
double *

variable_types:
fyt
double *

variable_types:
fzt
double *

variable_types:
fxtemp
double *

variable_types:
fytemp
double *

variable_types:
fztemp
double *

variable_types: nfreeze int

variable_types: nfree int

variable_types: myid int

variable_types: world int

variable_types: volume double

user_defined_types: struct class { struct clatoms_info clatoms_info; struct clatoms_tran clatoms_tran; struct clatoms_pos *clatoms_pos; struct ghost_atoms ghost_atoms; struct atommaps atommaps; struct therm_info therm_info_class; struct therm_info therm_info_bead; struct therm_pos therm_class; struct therm_pos *therm_bead; struct vel_samp_class vel_samp_class; struct energy_ctrl energy_ctrl; struct nbr_list nbr_list; struct interact interact; struct int_scr int_scr; struct ewd_scr ewd_scr; struct for_scr for_scr; double tot_memory; struct part_mesh part_mesh; struct surface surface; struct communicate communicate; struct class_comm_forc_pkg class_comm_forc_pkg; }

user_defined_types: struct bonded { struct bond bond; struct grp_bond_con grp_bond_con; struct grp_bond_watts grp_bond_watts; struct constrnt constrnt; struct bond_free bond_free; struct bend bend; struct bend_free bend_free; struct bend_bnd bend_bnd; struct tors tors; struct tors_free tors_free; struct rbar_sig_free rbar_sig_free; struct onfo onfo; struct ecor ecor; struct excl excl; struct intra_scr intra_scr; }

user_defined_types: struct general_data { struct simopts simopts; struct minopts minopts; struct ensopts ensopts; struct filenames filenames; struct statepoint statepoint; struct cell cell; struct timeinfo timeinfo; struct baro baro; struct par_rahman par_rahman; struct ptens ptens; struct stat_avg stat_avg; struct ewald ewald; struct para_fft_pkg3d pme_fft_pkg; struct para_fft_pkg3d pme_res_fft_pkg; int error_check_on; }

user_defined_types: struct nbr_list { int iver; int ilnk; int nolst; int brnch_root_list_opt; double *x0; struct verlist verlist; struct lnklist lnklist; struct brnch_root brnch_root; }

user_defined_types: struct int_scr { double v_lnv; double *x; double *vx; double *gx; double **x_nhc; double *vgmat; double *x_vol_nhc; double *sc; double *sc_temp; double *atm_kin; double *step_up; struct therm_scr *therm_scr; }

user_defined_types: struct class_comm_forc_pkg { int num_proc; int myid; int myatm_start; int mytherm_start; int *displs_atm; int *displs_therm; int comm; int world; double dbl_num_proc; struct class_plimpton_ind plimpton_ind; }


repo: TuckermanGroup/PINY

original_code:
void set_ghost(GHOST_ATOMS *ghost_atoms,CLATOMS_INFO *clatoms_info,
               ATOMMAPS *atommaps,
               BUILD_INTRA *build_intra,DICT_WORD *atm_dict,
               int num_atm_dict,
               char *filename,char *fun_key,int iatm_ind)
{
   int nstrip=5,imask;
   int numg[6],index,i;
   double anumg[6];
   int nghost_old,ncomp_old,nghost;
   int nghost_new,ncomp_new,ncomp,iii;
   ncomp = 0;index=16;
   for(i=1;i<=nstrip;i++){
     if(atm_dict[index].iuset==0){break;}
      ncomp = i;
      strcpy(build_intra->strip1,atm_dict[index].keyarg);
      parse_ghost(build_intra->strip1,build_intra->strip2,&numg[i],&anumg[i]);
      index++;
   }
   index = 16;
   for(i=1;i<=ncomp;i++){
      if((numg[i]<=0)||(numg[i]>build_intra->natmind_1res_now)){
                     keyarg_barf(atm_dict,filename,fun_key,index);}
      imask = build_intra->mask_atm[numg[i]];
      if(imask==0){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("You have managed to nuke one of the atoms making \n");
        printf("up a ghost atom without nuking the ghost atom, \n");
        printf("itself, in residue file  %s\n",filename);
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
      }
      numg[i] = build_intra->index_atm[numg[i]];
      if(numg[i]>build_intra->natm_1res_now||numg[i]<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
      numg[i] += clatoms_info->natm_tot;
      index++;
   }
   if(ncomp>0){
       ghost_atoms->nghost_tot++;
       build_intra->nghost_now++;
       nghost = ghost_atoms->nghost_tot;
       if(nghost > build_intra->nghost_tot_max){
           nghost_old = build_intra->nghost_tot_max;
           ncomp_old = 5;
           build_intra->nghost_tot_max+=100;
           nghost_new = build_intra->nghost_tot_max;
           ncomp_new = 5;
           ghost_atoms->ighost_map = (int *) crealloc(
                                     &(ghost_atoms->ighost_map)[1],
                                       nghost_new*sizeof(int))-1;
           ghost_atoms->natm_comp = (int *) crealloc(
                                     &(ghost_atoms->natm_comp)[1],
                                       nghost_new*sizeof(int))-1;
           ghost_atoms->ighost_map = (int *) crealloc(
                                   &(ghost_atoms->ighost_map)[1],
                                     nghost_new*sizeof(int))-1;
           ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
                                                    1,ncomp_old,1,nghost_old,
                                                    1,ncomp_new,1,nghost_new);
           ghost_atoms->coef = creall_mat(ghost_atoms->coef,
                                                1,ncomp_old,1,nghost_old,
                                                1,ncomp_new,1,nghost_new);
        }
   }
   if(ncomp>5){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("You have managed to use too many ghost_defs!!!\n");
        printf("Technical support was too tired to do the  \n");
        printf("heinous work necessary to support an arbitray number.\n");
        printf("Wait for the next upgrade you power tool.      \n");
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
   }
   if(ncomp>0){
     atommaps->ighost_flag[iatm_ind] = nghost;
     ghost_atoms->natm_comp_max = (((ghost_atoms->natm_comp_max)>(ncomp))?(ghost_atoms->natm_comp_max):(ncomp));
     ghost_atoms->ighost_map[nghost] = iatm_ind;
     ghost_atoms->natm_comp[nghost] = ncomp;
     for(i=1;i<=ncomp;i++){
       ghost_atoms->iatm_comp[i][nghost] = numg[i];
       ghost_atoms->coef[i][nghost] = anumg[i];
     }
   }
}

canonical_original_code:
void set_ghost(struct ghost_atoms *ghost_atoms, struct clatoms_info *clatoms_info, struct atommaps *atommaps, struct build_intra *build_intra, struct dict_word *atm_dict, int num_atm_dict, char *filename, char *fun_key, int iatm_ind)
{
   int nstrip = 5; int imask;
   int numg[6]; int index; int i;
   double anumg[6];
   int nghost_old; int ncomp_old; int nghost;
   int nghost_new; int ncomp_new; int ncomp; int iii;
   ncomp = 0;index=16;
   for(i=1;i<=nstrip;i++){
     if(atm_dict[index].iuset==0){break;}
      ncomp = i;
      strcpy(build_intra->strip1,atm_dict[index].keyarg);
      parse_ghost(build_intra->strip1,build_intra->strip2,&numg[i],&anumg[i]);
      index++;
   }
   index = 16;
   for(i=1;i<=ncomp;i++){
      if((numg[i]<=0)||(numg[i]>build_intra->natmind_1res_now)){
                     keyarg_barf(atm_dict,filename,fun_key,index);}
      imask = build_intra->mask_atm[numg[i]];
      if(imask==0){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("You have managed to nuke one of the atoms making \n");
        printf("up a ghost atom without nuking the ghost atom, \n");
        printf("itself, in residue file  %s\n",filename);
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
      }
      numg[i] = build_intra->index_atm[numg[i]];
      if(numg[i]>build_intra->natm_1res_now||numg[i]<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
      numg[i] += clatoms_info->natm_tot;
      index++;
   }
   if(ncomp>0){
       ghost_atoms->nghost_tot++;
       build_intra->nghost_now++;
       nghost = ghost_atoms->nghost_tot;
       if(nghost > build_intra->nghost_tot_max){
           nghost_old = build_intra->nghost_tot_max;
           ncomp_old = 5;
           build_intra->nghost_tot_max+=100;
           nghost_new = build_intra->nghost_tot_max;
           ncomp_new = 5;
           ghost_atoms->ighost_map = (int *) crealloc(
                                     &(ghost_atoms->ighost_map)[1],
                                       nghost_new*sizeof(int))-1;
           ghost_atoms->natm_comp = (int *) crealloc(
                                     &(ghost_atoms->natm_comp)[1],
                                       nghost_new*sizeof(int))-1;
           ghost_atoms->ighost_map = (int *) crealloc(
                                   &(ghost_atoms->ighost_map)[1],
                                     nghost_new*sizeof(int))-1;
           ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
                                                    1,ncomp_old,1,nghost_old,
                                                    1,ncomp_new,1,nghost_new);
           ghost_atoms->coef = creall_mat(ghost_atoms->coef,
                                                1,ncomp_old,1,nghost_old,
                                                1,ncomp_new,1,nghost_new);
        }
   }
   if(ncomp>5){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("You have managed to use too many ghost_defs!!!\n");
        printf("Technical support was too tired to do the  \n");
        printf("heinous work necessary to support an arbitray number.\n");
        printf("Wait for the next upgrade you power tool.      \n");
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
   }
   if(ncomp>0){
     atommaps->ighost_flag[iatm_ind] = nghost;
     ghost_atoms->natm_comp_max = (((ghost_atoms->natm_comp_max)>(ncomp))?(ghost_atoms->natm_comp_max):(ncomp));
     ghost_atoms->ighost_map[nghost] = iatm_ind;
     ghost_atoms->natm_comp[nghost] = ncomp;
     for(i=1;i<=ncomp;i++){
       ghost_atoms->iatm_comp[i][nghost] = numg[i];
       ghost_atoms->coef[i][nghost] = anumg[i];
     }
   }
}

variable_types: struct ghost_atoms { int nghost_tot; int natm_comp_max; int nghost_mall; int nghost_old; int ncomp_mall; int ncomp_old; int *ighost_map; int *natm_comp; int **iatm_comp; double **coef; } *

variable_types: struct clatoms_info { int natm_tot; int pi_beads; int pi_beads_proc; int pi_beads_proc_st; int pi_beads_proc_end; int nfree; int nfree_pimd; int nchrg; int pi_beads_full_ter; int pi_beads_res_ter; int pi_beads_full_tra; int pi_beads_res_tra; int cg_reset_flag; int natm_mall; int nchrg_mall; int hess_calc; int natm_proc; int N_H2; int i_H2_start; int nab_initio; int myatm_start; double gamma_adb; double wght_pimd; double pi_temperature; double pi_beads_full_ter_wght; double pi_beads_res_ter_wght; double pi_beads_full_tra_wght; double pi_beads_res_tra_wght; double rcut_spread; double mass_sc_fact; int *ip_lab; int *ichrg; int *cp_vlnc_up; int *cp_atm_flag; double *mass; double *q; double *alp_pol; double *b_neut; double *roll_sc; double *text_atm; double *text_mol; double *xold; double *prekf; double *xmod; double alp_ewd; } *

variable_types: struct atommaps { int nmol_typ; int nres_typ; int natm_typ; int nfreeze; int nfreeze_mall; int natm_typ_mall; int nres_typ_max; int nres_max; int nres_tot; int nres_sum; int pimd_freez_typ; char (*atm_typ)[50]; char (*res_typ)[50]; char (*mol_typ)[50]; int *nmol_jmol_typ; int *nres_1mol_jmol_typ; int *jatm_jmol_typ_strt; int *jres_jmol_typ_strt; int *ires_typ_jres_jmol_typ; int *jatm_jres_1mol_jmol_typ_strt; int *natm_1mol_jmol_typ; int *natm_jres_jmol_typ; int *nfree_1mol_jmol_typ; int *nfree_jres_jmol_typ; int *icons_jmol_typ; int *icons_jres_jmol_typ; int *natm_jmol_typ; int *iatm_mol_typ; int *iatm_res_typ; int *iatm_atm_typ; int *iatm_atm_typ_nl; int *iatm_atm_typ_nl_rev; int *imap_atm_typ_nl; int *imap_atm_typ_nl_gh; int *iatm_mol_num; int *iatm_proc_num; int *iatm_res_num; int *ighost_flag; int *freeze_flag; int *freeze_map; int *atom_label; int *cp_atm_lst; } *

variable_types: struct build_intra { struct bond_site { char bond_site_name[5][50]; int branch_1[5]; int branch_2[5]; int valence; int improper_ind[5]; } *bond_site; int *mask_atm; int *index_atm; int *iatm_ind_chk; int *ires_ind_chk; int natm_1res_pure_now; int natm_tot_max; int nfreeze_max; int nfreeze_now; int natm_1res_now; int natm_1res_max; int natmind_1res_now; int natmind_1res_max; int nghost_now; int nghost_tot_max; int nbond_pow_max; int nbond_con_max; int nbond_nul_max; int nbond_typ_pow_max; int nbond_typ_con_max; struct CBOND { char atm1[50]; } *cbond_typ_pow; struct CBOND *cbond_typ_con; struct CBOND *cbond_typ_now; int nbend_pow_max; int nbend_con_max; int nbend_nul_max; int nbend_typ_pow_max; int nbend_typ_con_max; struct CBEND { char atm1[50]; } *cbend_typ_pow; struct CBEND *cbend_typ_con; struct CBEND *cbend_typ_now; int ntors_pow_max; int ntors_con_max; int ntors_nul_max; int ntors_typ_pow_max; int ntors_typ_con_max; struct CTORS { char atm1[50]; } *ctors_typ_pow; struct CTORS *ctors_typ_con; struct CTORS *ctors_typ_now; int nonfo_max; int nonfo_nul_max; int nonfo_typ_max; struct CBOND *confo_typ; struct CBOND *confo_typ_now; int nbend_bnd_max; int nbend_bnd_typ_max; struct CBEND *cbend_bnd_typ; struct CBEND *cbend_bnd_typ_now; int ngrp_33_max; int ngrp_watt_33_max; int ngrp_21_max; int ngrp_43_max; int ngrp_23_max; int ngrp_46_max; int ngrp_typ_21_max; int ngrp_typ_43_max; int ngrp_typ_33_max; int ngrp_typ_watt_33_max; int ngrp_typ_23_max; int ngrp_typ_46_max; struct CGRP_CONS { char atm1[50]; } *cgrp_typ_now; struct CGRP_CONS *cgrp_typ_21; struct CGRP_CONS *cgrp_typ_43; struct CGRP_CONS *cgrp_typ_33; struct CGRP_CONS *cgrp_typ_watt_33; struct CGRP_CONS *cgrp_typ_23; struct CGRP_CONS *cgrp_typ_46; int natm_typ_max; int nres_typ_max; char *strip1; int *ibend_bnd_typ_pure; int *ibend_bnd_typ_map; } *

variable_types: struct dict_word { int iflag; char keyword[50]; char error_mes[100]; } *

variable_types:
filename
char *

variable_types: nstrip int

variable_types: imask int

variable_types:
numg
int [6]

variable_types: index int

variable_types: i int

variable_types:
anumg
double [6]

variable_types: nghost int

variable_types: ncomp int

variable_types: iii int

return_type: void

user_defined_types: struct build_intra { struct bond_site *bond_site; int *mask_atm; int *index_atm; int *iatm_ind_chk; int *ires_ind_chk; int natm_1res_pure_now; int natm_tot_max; int nfreeze_max; int nfreeze_now; int natm_1res_now; int natm_1res_max; int natmind_1res_now; int natmind_1res_max; int nghost_now; int nghost_tot_max; int nbond_pow_max; int nbond_con_max; int nbond_nul_max; int nbond_typ_pow_max; int nbond_typ_con_max; struct CBOND *cbond_typ_pow; struct CBOND *cbond_typ_con; struct CBOND *cbond_typ_now; int nbend_pow_max; int nbend_con_max; int nbend_nul_max; int nbend_typ_pow_max; int nbend_typ_con_max; struct CBEND *cbend_typ_pow; struct CBEND *cbend_typ_con; struct CBEND *cbend_typ_now; int ntors_pow_max; int ntors_con_max; int ntors_nul_max; int ntors_typ_pow_max; int ntors_typ_con_max; struct CTORS *ctors_typ_pow; struct CTORS *ctors_typ_con; struct CTORS *ctors_typ_now; int nonfo_max; int nonfo_nul_max; int nonfo_typ_max; struct CBOND *confo_typ; struct CBOND *confo_typ_now; int nbend_bnd_max; int nbend_bnd_typ_max; struct CBEND *cbend_bnd_typ; struct CBEND *cbend_bnd_typ_now; int ngrp_33_max; int ngrp_watt_33_max; int ngrp_21_max; int ngrp_43_max; int ngrp_23_max; int ngrp_46_max; int ngrp_typ_21_max; int ngrp_typ_43_max; int ngrp_typ_33_max; int ngrp_typ_watt_33_max; int ngrp_typ_23_max; int ngrp_typ_46_max; struct CGRP_CONS *cgrp_typ_now; struct CGRP_CONS *cgrp_typ_21; struct CGRP_CONS *cgrp_typ_43; struct CGRP_CONS *cgrp_typ_33; struct CGRP_CONS *cgrp_typ_watt_33; struct CGRP_CONS *cgrp_typ_23; struct CGRP_CONS *cgrp_typ_46; int natm_typ_max; int nres_typ_max; char *strip1; int *ibend_bnd_typ_pure; int *ibend_bnd_typ_map; }


decompiled_code:
__int64 __fastcall set_atm_params(__int64 a1, int a2, __int64 a3, const char *a4, int a5, int a6, int a7, __int64 a8, __int64 a9, __int64 a10, int *a11)
{
__int64 v11; // r15
_DWORD *v13; // rbp
int i; // er12
__int64 result; // rax
int v16; // eax
int v17; // ebp
__int64 v18; // rbp
unsigned int v19; // eax
unsigned int v20; // edx
unsigned int v21; // eax
unsigned int v22; // esi
unsigned int v23; // ecx
unsigned int v24; // eax
unsigned int v25; // edx
unsigned int v26; // eax
unsigned int v27; // edx
unsigned int v28; // eax
unsigned int v29; // edx
unsigned int v30; // eax
unsigned int v31; // edx
unsigned int v32; // eax
int v33; // er12
int v34; // er14
int v35; // er13
const char *v36; // r12
int v37; // er14
int v38; // ebp
int v39; // eax
int v40; // eax
double v45; // [rsp+20h] [rbp-98h] BYREF
unsigned int v46; // [rsp+28h] [rbp-90h] BYREF
int v47; // [rsp+2Ch] [rbp-8Ch] BYREF
unsigned int v48; // [rsp+30h] [rbp-88h] BYREF
unsigned int v49; // [rsp+34h] [rbp-84h] BYREF
unsigned int v50; // [rsp+38h] [rbp-80h] BYREF
unsigned int v51; // [rsp+3Ch] [rbp-7Ch] BYREF
char src[120]; // [rsp+40h] [rbp-78h] BYREF

v11 = a1;
if ( a2 > 0 )
{
v13 = (_DWORD *)(a1 + 216);
for ( i = 1; i <= a2; ++i )
{
if ( !*v13 && v13[1] == 1 )
keyword_miss(a1, a4, a3, (unsigned int)i);
v13 += 53;
}
}
_isoc99_sscanf(a1 + 486, "%d", &v47);
if ( *(_DWORD *)(a9 + 64) < v47 || v47 < 0 )
keyarg_barf(a1, a4, a3, 2LL);
result = v47;
if ( *(int *)(*(_QWORD *)(a9 + 8) + 4LL * v47) > 0 )
{
v16 = *(_DWORD *)(*(_QWORD *)(a9 + 16) + 4LL * v47);
v47 = v16;
if ( v16 > *(_DWORD *)(a9 + 56) || v16 < 0 )
keyarg_barf(a1, a4, a3, 2LL);
++*(_DWORD *)(*(_QWORD *)(a9 + 24) + 4LL * v47);
v17 = v47;
v47 += *(_DWORD *)a10;
_isoc99_sscanf(a1 + 698, "%lg", &v45);
if ( v45 <= 0.0 )
keyarg_barf(a1, a4, a3, 3LL);
*(double *)(*(_QWORD *)(a10 + 200) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 910, "%lg", &v45);
*(double *)(*(_QWORD *)(a10 + 208) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1122, "%lg", &v45);
if ( v45 < 0.0 )
keyarg_barf(a1, a4, a3, 5LL);
*(double *)(*(_QWORD *)(a10 + 216) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1334, "%lg", &v45);
*(double *)(*(_QWORD *)(a10 + 224) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1546, "%d", &v51);
v18 = 316LL * v17;
v19 = v51;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 292) = v51;
if ( v19 > 6 )
keyarg_barf(a1, a4, a3, 7LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 1758));
parse_improp(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), &v46, &v50, &v49, &v48);
v20 = v46;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 300) = v46 + 1;
v21 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 304) = v50 + 1;
v22 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 308) = v49 + 1;
v23 = v48;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 312) = v48 + 1;
v24 = v23 + v22 + v20 + v21;
if ( v24 && v24 != 6 )
keyarg_barf(a1, a4, a3, 8LL);
if ( v48 + v49 + v46 + v50 == 6
&& (v49 > 3
|| v50 > 3
|| v46 > 3
|| v49 == v48
|| v50 == v48
|| v46 == v48
|| v50 == v49
|| v46 == v49
|| v46 == v50
|| v48 > 3) )
{
keyarg_barf(a1, a4, a3, 8LL);
}
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 1970));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 50), src);
v25 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 256) = v50;
v26 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 276) = v49;
if ( v26 + 1 > 7 || v25 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 9LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2182));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 100), src);
v27 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 260) = v50;
v28 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 280) = v49;
if ( v28 + 1 > 7 || v27 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 10LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2394));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 150), src);
v29 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 264) = v50;
v30 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 284) = v49;
if ( v30 + 1 > 7 || v29 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 11LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2606));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 200), src);
v31 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 268) = v50;
v32 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 288) = v49;
if ( v32 + 1 > 7 || v31 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 12LL);
_isoc99_sscanf(a1 + 2818, "%d", &v51);
*(_DWORD *)(*(_QWORD *)(a10 + 176) + 4LL * v47) = v51;
_isoc99_sscanf(a1 + 3030, "%d", &v51);
*(_DWORD *)(*(_QWORD *)(a10 + 184) + 4LL * v47) = v51;
if ( *(_DWORD *)(a1 + 2760) == 1 && !*(_DWORD *)(a1 + 2972) )
*(_DWORD *)(*(_QWORD *)(a10 + 184) + 4LL * v47) = *(_DWORD *)(*(_QWORD *)(a10 + 176) + 4LL * v47);
if ( !strcasecmp((const char *)(a1 + 3242), "yes") )
*(_DWORD *)(*(_QWORD *)(a10 + 192) + 4LL * v47) = 1;
if ( !strcasecmp((const char *)(a1 + 3242), "no") )
*(_DWORD *)(*(_QWORD *)(a10 + 192) + 4LL * v47) = 0;
*(_DWORD *)(*(_QWORD *)(a8 + 256) + 4LL * v47) = 0;
if ( *(_DWORD *)(a1 + 3396) )
set_ghost(a11, (_DWORD *)a10, a8, a9, a1, (unsigned int)a2, a4, a3, v47);
v33 = 0;
if ( !strcasecmp((const char *)(a1 + 4514), "standard") )
{
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 0;
v33 = 1;
}
if ( !strcasecmp((const char *)(a1 + 4514), "backbone") )
{
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 1;
if ( strcasecmp((const char *)(a1 + 4514), "sidechain") )
goto LABEL_48;
}
else if ( strcasecmp((const char *)(a1 + 4514), "sidechain") )
{
if ( !v33 )
keyarg_barf(a1, a4, a3, 21LL);
LABEL_48:
v34 = *(_DWORD *)(a8 + 8);
v35 = v34 + 1;
if ( v34 <= 0 )
{
v39 = *(_DWORD *)(a9 + 384);
if ( v39 >= v35 )
goto LABEL_67;
}
else
{
v36 = (const char *)(*(_QWORD *)(a8 + 48) + 50LL);
v37 = v34 + 1;
v38 = 1;
do
{
if ( !strcasecmp((const char *)(a1 + 274), v36) )
v35 = v38;
++v38;
v36 += 50;
}
while ( v38 != v37 );
v11 = a1;
v39 = *(_DWORD *)(a9 + 384);
if ( v39 >= v35 )
{
LABEL_54:
if ( *(_DWORD *)(a8 + 8) + 1 != v35 )
{
LABEL_55:
*(_DWORD *)(*(_QWORD *)(a8 + 176) + 4LL * v47) = a5;
*(_DWORD *)(*(_QWORD *)(a8 + 232) + 4LL * v47) = 1;
*(_DWORD *)(*(_QWORD *)(a8 + 248) + 4LL * v47) = a6;
*(_DWORD *)(*(_QWORD *)(a8 + 192) + 4LL * v47) = v35;
result = *(_QWORD *)(a8 + 184);
*(_DWORD *)(result + 4LL * v47) = *(_DWORD *)(*(_QWORD *)(a8 + 104) + 4LL * (a7 + a6));
return result;
}
LABEL_67:
*(_DWORD *)(a8 + 8) = v35;
strcpy((char *)(*(_QWORD *)(a8 + 48) + 50LL * v35), (const char *)(v11 + 274));
goto LABEL_55;
}
}
v40 = v39 + 100;
*(_DWORD *)(a9 + 384) = v40;
*(_QWORD *)(a8 + 48) = crealloc(*(_QWORD *)(a8 + 48) + 50LL, 50LL * v40) - 50;
goto LABEL_54;
}
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 2;
goto LABEL_48;
}
return result;
}

canonical_decompiled_code:
__int64 __fastcall func1(__int64 a1, int a2, __int64 a3, const char *a4, int a5, int a6, int a7, __int64 a8, __int64 a9, __int64 a10, int *a11)
{
__int64 v11; // r15
_DWORD *v13; // rbp
int i; // er12
__int64 result; // rax
int v16; // eax
int v17; // ebp
__int64 v18; // rbp
unsigned int v19; // eax
unsigned int v20; // edx
unsigned int v21; // eax
unsigned int v22; // esi
unsigned int v23; // ecx
unsigned int v24; // eax
unsigned int v25; // edx
unsigned int v26; // eax
unsigned int v27; // edx
unsigned int v28; // eax
unsigned int v29; // edx
unsigned int v30; // eax
unsigned int v31; // edx
unsigned int v32; // eax
int v33; // er12
int v34; // er14
int v35; // er13
const char *v36; // r12
int v37; // er14
int v38; // ebp
int v39; // eax
int v40; // eax
double v45; // [rsp+20h] [rbp-98h] BYREF
unsigned int v46; // [rsp+28h] [rbp-90h] BYREF
int v47; // [rsp+2Ch] [rbp-8Ch] BYREF
unsigned int v48; // [rsp+30h] [rbp-88h] BYREF
unsigned int v49; // [rsp+34h] [rbp-84h] BYREF
unsigned int v50; // [rsp+38h] [rbp-80h] BYREF
unsigned int v51; // [rsp+3Ch] [rbp-7Ch] BYREF
char src[120]; // [rsp+40h] [rbp-78h] BYREF

v11 = a1;
if ( a2 > 0 )
{
v13 = (_DWORD *)(a1 + 216);
for ( i = 1; i <= a2; ++i )
{
if ( !*v13 && v13[1] == 1 )
keyword_miss(a1, a4, a3, (unsigned int)i);
v13 += 53;
}
}
_isoc99_sscanf(a1 + 486, "%d", &v47);
if ( *(_DWORD *)(a9 + 64) < v47 || v47 < 0 )
keyarg_barf(a1, a4, a3, 2LL);
result = v47;
if ( *(int *)(*(_QWORD *)(a9 + 8) + 4LL * v47) > 0 )
{
v16 = *(_DWORD *)(*(_QWORD *)(a9 + 16) + 4LL * v47);
v47 = v16;
if ( v16 > *(_DWORD *)(a9 + 56) || v16 < 0 )
keyarg_barf(a1, a4, a3, 2LL);
++*(_DWORD *)(*(_QWORD *)(a9 + 24) + 4LL * v47);
v17 = v47;
v47 += *(_DWORD *)a10;
_isoc99_sscanf(a1 + 698, "%lg", &v45);
if ( v45 <= 0.0 )
keyarg_barf(a1, a4, a3, 3LL);
*(double *)(*(_QWORD *)(a10 + 200) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 910, "%lg", &v45);
*(double *)(*(_QWORD *)(a10 + 208) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1122, "%lg", &v45);
if ( v45 < 0.0 )
keyarg_barf(a1, a4, a3, 5LL);
*(double *)(*(_QWORD *)(a10 + 216) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1334, "%lg", &v45);
*(double *)(*(_QWORD *)(a10 + 224) + 8LL * v47) = v45;
_isoc99_sscanf(a1 + 1546, "%d", &v51);
v18 = 316LL * v17;
v19 = v51;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 292) = v51;
if ( v19 > 6 )
keyarg_barf(a1, a4, a3, 7LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 1758));
parse_improp(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), &v46, &v50, &v49, &v48);
v20 = v46;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 300) = v46 + 1;
v21 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 304) = v50 + 1;
v22 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 308) = v49 + 1;
v23 = v48;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 312) = v48 + 1;
v24 = v23 + v22 + v20 + v21;
if ( v24 && v24 != 6 )
keyarg_barf(a1, a4, a3, 8LL);
if ( v48 + v49 + v46 + v50 == 6
&& (v49 > 3
|| v50 > 3
|| v46 > 3
|| v49 == v48
|| v50 == v48
|| v46 == v48
|| v50 == v49
|| v46 == v49
|| v46 == v50
|| v48 > 3) )
{
keyarg_barf(a1, a4, a3, 8LL);
}
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 1970));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 50), src);
v25 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 256) = v50;
v26 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 276) = v49;
if ( v26 + 1 > 7 || v25 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 9LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2182));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 100), src);
v27 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 260) = v50;
v28 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 280) = v49;
if ( v28 + 1 > 7 || v27 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 10LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2394));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 150), src);
v29 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 264) = v50;
v30 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 284) = v49;
if ( v30 + 1 > 7 || v29 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 11LL);
strcpy(*(char **)(a9 + 392), (const char *)(a1 + 2606));
parse_bond_site(*(_QWORD *)(a9 + 392), *(_QWORD *)(a9 + 400), src, &v50, &v49);
strcpy((char *)(*(_QWORD *)a9 + v18 + 200), src);
v31 = v50;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 268) = v50;
v32 = v49;
*(_DWORD *)(*(_QWORD *)a9 + v18 + 288) = v49;
if ( v32 + 1 > 7 || v31 + 1 > 7 || !src[0] )
keyarg_barf(a1, a4, a3, 12LL);
_isoc99_sscanf(a1 + 2818, "%d", &v51);
*(_DWORD *)(*(_QWORD *)(a10 + 176) + 4LL * v47) = v51;
_isoc99_sscanf(a1 + 3030, "%d", &v51);
*(_DWORD *)(*(_QWORD *)(a10 + 184) + 4LL * v47) = v51;
if ( *(_DWORD *)(a1 + 2760) == 1 && !*(_DWORD *)(a1 + 2972) )
*(_DWORD *)(*(_QWORD *)(a10 + 184) + 4LL * v47) = *(_DWORD *)(*(_QWORD *)(a10 + 176) + 4LL * v47);
if ( !strcasecmp((const char *)(a1 + 3242), "yes") )
*(_DWORD *)(*(_QWORD *)(a10 + 192) + 4LL * v47) = 1;
if ( !strcasecmp((const char *)(a1 + 3242), "no") )
*(_DWORD *)(*(_QWORD *)(a10 + 192) + 4LL * v47) = 0;
*(_DWORD *)(*(_QWORD *)(a8 + 256) + 4LL * v47) = 0;
if ( *(_DWORD *)(a1 + 3396) )
func0(a11, (_DWORD *)a10, a8, a9, a1, (unsigned int)a2, a4, a3, v47);
v33 = 0;
if ( !strcasecmp((const char *)(a1 + 4514), "standard") )
{
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 0;
v33 = 1;
}
if ( !strcasecmp((const char *)(a1 + 4514), "backbone") )
{
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 1;
if ( strcasecmp((const char *)(a1 + 4514), "sidechain") )
goto LABEL_48;
}
else if ( strcasecmp((const char *)(a1 + 4514), "sidechain") )
{
if ( !v33 )
keyarg_barf(a1, a4, a3, 21LL);
LABEL_48:
v34 = *(_DWORD *)(a8 + 8);
v35 = v34 + 1;
if ( v34 <= 0 )
{
v39 = *(_DWORD *)(a9 + 384);
if ( v39 >= v35 )
goto LABEL_67;
}
else
{
v36 = (const char *)(*(_QWORD *)(a8 + 48) + 50LL);
v37 = v34 + 1;
v38 = 1;
do
{
if ( !strcasecmp((const char *)(a1 + 274), v36) )
v35 = v38;
++v38;
v36 += 50;
}
while ( v38 != v37 );
v11 = a1;
v39 = *(_DWORD *)(a9 + 384);
if ( v39 >= v35 )
{
LABEL_54:
if ( *(_DWORD *)(a8 + 8) + 1 != v35 )
{
LABEL_55:
*(_DWORD *)(*(_QWORD *)(a8 + 176) + 4LL * v47) = a5;
*(_DWORD *)(*(_QWORD *)(a8 + 232) + 4LL * v47) = 1;
*(_DWORD *)(*(_QWORD *)(a8 + 248) + 4LL * v47) = a6;
*(_DWORD *)(*(_QWORD *)(a8 + 192) + 4LL * v47) = v35;
result = *(_QWORD *)(a8 + 184);
*(_DWORD *)(result + 4LL * v47) = *(_DWORD *)(*(_QWORD *)(a8 + 104) + 4LL * (a7 + a6));
return result;
}
LABEL_67:
*(_DWORD *)(a8 + 8) = v35;
strcpy((char *)(*(_QWORD *)(a8 + 48) + 50LL * v35), (const char *)(v11 + 274));
goto LABEL_55;
}
}
v40 = v39 + 100;
*(_DWORD *)(a9 + 384) = v40;
*(_QWORD *)(a8 + 48) = crealloc(*(_QWORD *)(a8 + 48) + 50LL, 50LL * v40) - 50;
goto LABEL_54;
}
*(_DWORD *)(*(_QWORD *)(a8 + 280) + 4LL * v47) = 2;
goto LABEL_48;
}
return result;
}

original_code:
void set_atm_params(DICT_WORD atm_dict[],int num_atm_dict,
                    char fun_key[],char filename[],
                    int jmol_typ,int jres, int jres_off,ATOMMAPS *atommaps,
                    BUILD_INTRA *build_intra,CLATOMS_INFO *clatoms_info,
                    GHOST_ATOMS *ghost_atoms)
{
  NAME site;
  int i,iii,num,num2,num3,num4,iatm_ind,imask,index,num1;
  int itype,iatm_ind_sm,ifound;
  double dnum;
  for(i=1;i<=num_atm_dict;i++){
    if(atm_dict[i].iuset==0 && atm_dict[i].key_type==1){
      keyword_miss(atm_dict,filename,fun_key,i);}
  }
  sscanf(atm_dict[2].keyarg,"%d",&iatm_ind);
  index = 2;
  if(iatm_ind>build_intra->natmind_1res_now||iatm_ind<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
  imask = build_intra->mask_atm[iatm_ind];
  if(imask>0){
    iatm_ind = (build_intra->index_atm)[iatm_ind];
    if(iatm_ind>build_intra->natm_1res_now||iatm_ind<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
    build_intra->iatm_ind_chk[iatm_ind]++;
    iatm_ind_sm = iatm_ind;
    iatm_ind = iatm_ind + clatoms_info->natm_tot;
     sscanf(atm_dict[3].keyarg,"%lg",&dnum);
     index = 3;
     if(dnum<=0.0){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     clatoms_info->mass[iatm_ind] = dnum;
     sscanf(atm_dict[4].keyarg,"%lg",&dnum);
     clatoms_info->q[iatm_ind] = dnum;
     sscanf(atm_dict[5].keyarg,"%lg",&dnum);
     index = 5;
     if(dnum<0.0){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     clatoms_info->alp_pol[iatm_ind] = dnum;
     sscanf(atm_dict[6].keyarg,"%lg",&dnum);
     clatoms_info->b_neut[iatm_ind] = dnum;
     sscanf(atm_dict[7].keyarg,"%d",&num);
     build_intra->bond_site[iatm_ind_sm].valence = num;
     index = 7;
     if(num<0||num>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     strcpy(build_intra->strip1,atm_dict[8].keyarg);
     parse_improp(build_intra->strip1,build_intra->strip2,&num1,&num2,&num3,
                                                                      &num4);
     build_intra->bond_site[iatm_ind_sm].improper_ind[1]=num1+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[2]=num2+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[3]=num3+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[4]=num4+1;
     index = 8;
     if((num1+num2+num3+num4)!=0&&(num1+num2+num3+num4)!=6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     if((num1+num2+num3+num4)==6){
      if(num1<0||num1>3||num2<0||num2>3||num3<0||num3>3||num4<0||num4>3||
         num1==num2||num1==num3||num2==num3||num1==num4||num2==num4||
         num3==num4){
       keyarg_barf(atm_dict,filename,fun_key,index);}}
     strcpy(build_intra->strip1,atm_dict[9].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[1],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[1] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[1] = num3;
     index = 9;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     strcpy(build_intra->strip1,atm_dict[10].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[2],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[2] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[2] = num3;
     index = 10;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     strcpy(build_intra->strip1,atm_dict[11].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[3],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[3] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[3] = num3;
     index = 11;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     strcpy(build_intra->strip1,atm_dict[12].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[4],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[4] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[4] = num3;
     index = 12;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     sscanf(atm_dict[13].keyarg,"%d",&num);
     clatoms_info->cp_vlnc_up[iatm_ind] = num;
     sscanf(atm_dict[14].keyarg,"%d",&num);
     clatoms_info->cp_vlnc_dn[iatm_ind] = num;
     if(atm_dict[13].iuset == 1 && atm_dict[14].iuset == 0){
      clatoms_info->cp_vlnc_dn[iatm_ind] = clatoms_info->cp_vlnc_up[iatm_ind];
     }
     ifound = 0;
     if(strcasecmp(atm_dict[15].keyarg,"yes")==0){
       ifound=1;clatoms_info->cp_atm_flag[iatm_ind] = 1;
     }
     if(strcasecmp(atm_dict[15].keyarg,"no")==0){
       ifound=1;clatoms_info->cp_atm_flag[iatm_ind] = 0;
     }
     atommaps->ighost_flag[iatm_ind] = 0;
     if(atm_dict[16].iuset!=0){
      set_ghost(ghost_atoms,clatoms_info,atommaps,build_intra,
               atm_dict,num_atm_dict,
               filename,fun_key,iatm_ind);
     }
     index = 16+5;
     ifound = 0;
     if(strcasecmp(atm_dict[index].keyarg,"standard")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 0;
     }
     if(strcasecmp(atm_dict[index].keyarg,"backbone")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 1;
     }
     if(strcasecmp(atm_dict[index].keyarg,"sidechain")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 2;
     }
    if(ifound==0){
     keyarg_barf(atm_dict,filename,fun_key,index);
    }
     itype = atommaps->natm_typ + 1;
     for(i=1;i<=atommaps->natm_typ;i++){
       if(strcasecmp(atm_dict[1].keyarg,atommaps->atm_typ[i])==0)
         itype=i;
     }
     if(itype>build_intra->natm_typ_max){
       build_intra->natm_typ_max+=100;
       atommaps->atm_typ = (NAME *)
         crealloc(&(atommaps->atm_typ[1]),
                  (build_intra->natm_typ_max)*sizeof(NAME))-1;
     }
     if(itype==atommaps->natm_typ+1){
       atommaps->natm_typ+=1;
       strcpy(atommaps->atm_typ[itype],atm_dict[1].keyarg);
     }
     atommaps->iatm_mol_typ[iatm_ind] = jmol_typ;
     atommaps->iatm_mol_num[iatm_ind] = 1;
     atommaps->iatm_res_num[iatm_ind] = jres;
     atommaps->iatm_atm_typ[iatm_ind] = itype;
     atommaps->iatm_res_typ[iatm_ind] =
                        atommaps->ires_typ_jres_jmol_typ[jres+jres_off];
   }
}

canonical_original_code:
void set_atm_params(struct dict_word atm_dict[], int num_atm_dict, char fun_key[], char filename[], int jmol_typ, int jres, int jres_off, struct atommaps *atommaps, struct build_intra *build_intra, struct clatoms_info *clatoms_info, struct ghost_atoms *ghost_atoms)
{
  char site[50];
  int i; int iii; int num; int num2; int num3; int num4; int iatm_ind; int imask; int index; int num1;
  int itype; int iatm_ind_sm; int ifound;
  double dnum;
  for(i=1;i<=num_atm_dict;i++){
    if(atm_dict[i].iuset==0 && atm_dict[i].key_type==1){
      keyword_miss(atm_dict,filename,fun_key,i);}
  }
  sscanf(atm_dict[2].keyarg,"%d",&iatm_ind);
  index = 2;
  if(iatm_ind>build_intra->natmind_1res_now||iatm_ind<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
  imask = build_intra->mask_atm[iatm_ind];
  if(imask>0){
    iatm_ind = (build_intra->index_atm)[iatm_ind];
    if(iatm_ind>build_intra->natm_1res_now||iatm_ind<0){
             keyarg_barf(atm_dict,filename,fun_key,index);}
    build_intra->iatm_ind_chk[iatm_ind]++;
    iatm_ind_sm = iatm_ind;
    iatm_ind = iatm_ind + clatoms_info->natm_tot;
     sscanf(atm_dict[3].keyarg,"%lg",&dnum);
     index = 3;
     if(dnum<=0.0){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     clatoms_info->mass[iatm_ind] = dnum;
     sscanf(atm_dict[4].keyarg,"%lg",&dnum);
     clatoms_info->q[iatm_ind] = dnum;
     sscanf(atm_dict[5].keyarg,"%lg",&dnum);
     index = 5;
     if(dnum<0.0){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     clatoms_info->alp_pol[iatm_ind] = dnum;
     sscanf(atm_dict[6].keyarg,"%lg",&dnum);
     clatoms_info->b_neut[iatm_ind] = dnum;
     sscanf(atm_dict[7].keyarg,"%d",&num);
     build_intra->bond_site[iatm_ind_sm].valence = num;
     index = 7;
     if(num<0||num>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     strcpy(build_intra->strip1,atm_dict[8].keyarg);
     parse_improp(build_intra->strip1,build_intra->strip2,&num1,&num2,&num3,
                                                                      &num4);
     build_intra->bond_site[iatm_ind_sm].improper_ind[1]=num1+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[2]=num2+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[3]=num3+1;
     build_intra->bond_site[iatm_ind_sm].improper_ind[4]=num4+1;
     index = 8;
     if((num1+num2+num3+num4)!=0&&(num1+num2+num3+num4)!=6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     if((num1+num2+num3+num4)==6){
      if(num1<0||num1>3||num2<0||num2>3||num3<0||num3>3||num4<0||num4>3||
         num1==num2||num1==num3||num2==num3||num1==num4||num2==num4||
         num3==num4){
       keyarg_barf(atm_dict,filename,fun_key,index);}}
     strcpy(build_intra->strip1,atm_dict[9].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[1],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[1] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[1] = num3;
     index = 9;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     strcpy(build_intra->strip1,atm_dict[10].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[2],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[2] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[2] = num3;
     index = 10;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);
     }
     strcpy(build_intra->strip1,atm_dict[11].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[3],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[3] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[3] = num3;
     index = 11;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     strcpy(build_intra->strip1,atm_dict[12].keyarg);
     parse_bond_site(build_intra->strip1,build_intra->strip2,site,&num2,&num3);
     strcpy(build_intra->bond_site[iatm_ind_sm].bond_site_name[4],site);
     build_intra->bond_site[iatm_ind_sm].branch_1[4] = num2;
     build_intra->bond_site[iatm_ind_sm].branch_2[4] = num3;
     index = 12;
     if(strlen(site)==0||num2<-1||num3<-1||num2>6||num3>6){
       keyarg_barf(atm_dict,filename,fun_key,index);}
     sscanf(atm_dict[13].keyarg,"%d",&num);
     clatoms_info->cp_vlnc_up[iatm_ind] = num;
     sscanf(atm_dict[14].keyarg,"%d",&num);
     clatoms_info->cp_vlnc_dn[iatm_ind] = num;
     if(atm_dict[13].iuset == 1 && atm_dict[14].iuset == 0){
      clatoms_info->cp_vlnc_dn[iatm_ind] = clatoms_info->cp_vlnc_up[iatm_ind];
     }
     ifound = 0;
     if(strcasecmp(atm_dict[15].keyarg,"yes")==0){
       ifound=1;clatoms_info->cp_atm_flag[iatm_ind] = 1;
     }
     if(strcasecmp(atm_dict[15].keyarg,"no")==0){
       ifound=1;clatoms_info->cp_atm_flag[iatm_ind] = 0;
     }
     atommaps->ighost_flag[iatm_ind] = 0;
     if(atm_dict[16].iuset!=0){
      set_ghost(ghost_atoms,clatoms_info,atommaps,build_intra,
               atm_dict,num_atm_dict,
               filename,fun_key,iatm_ind);
     }
     index = 16+5;
     ifound = 0;
     if(strcasecmp(atm_dict[index].keyarg,"standard")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 0;
     }
     if(strcasecmp(atm_dict[index].keyarg,"backbone")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 1;
     }
     if(strcasecmp(atm_dict[index].keyarg,"sidechain")==0){
       ifound=1;atommaps->atom_label[iatm_ind] = 2;
     }
    if(ifound==0){
     keyarg_barf(atm_dict,filename,fun_key,index);
    }
     itype = atommaps->natm_typ + 1;
     for(i=1;i<=atommaps->natm_typ;i++){
       if(strcasecmp(atm_dict[1].keyarg,atommaps->atm_typ[i])==0)
         itype=i;
     }
     if(itype>build_intra->natm_typ_max){
       build_intra->natm_typ_max+=100;
       atommaps->atm_typ = (char (*)[50])
         crealloc(&(atommaps->atm_typ[1]),
                  (build_intra->natm_typ_max)*sizeof(NAME))-1;
     }
     if(itype==atommaps->natm_typ+1){
       atommaps->natm_typ+=1;
       strcpy(atommaps->atm_typ[itype],atm_dict[1].keyarg);
     }
     atommaps->iatm_mol_typ[iatm_ind] = jmol_typ;
     atommaps->iatm_mol_num[iatm_ind] = 1;
     atommaps->iatm_res_num[iatm_ind] = jres;
     atommaps->iatm_atm_typ[iatm_ind] = itype;
     atommaps->iatm_res_typ[iatm_ind] =
                        atommaps->ires_typ_jres_jmol_typ[jres+jres_off];
   }
}

variable_types: struct dict_word { int iflag; char keyword[50]; char error_mes[100]; } []

variable_types:
filename
char []

variable_types: jres int

variable_types:
site
char [50]

variable_types: num int

variable_types: itype int

variable_types: ifound int

variable_types: dnum double

user_defined_types: struct atommaps { int nmol_typ; int nres_typ; int natm_typ; int nfreeze; int nfreeze_mall; int natm_typ_mall; int nres_typ_max; int nres_max; int nres_tot; int nres_sum; int pimd_freez_typ; char (*atm_typ)[50]; char (*res_typ)[50]; char (*mol_typ)[50]; int *nmol_jmol_typ; int *nres_1mol_jmol_typ; int *jatm_jmol_typ_strt; int *jres_jmol_typ_strt; int *ires_typ_jres_jmol_typ; int *jatm_jres_1mol_jmol_typ_strt; int *natm_1mol_jmol_typ; int *natm_jres_jmol_typ; int *nfree_1mol_jmol_typ; int *nfree_jres_jmol_typ; int *icons_jmol_typ; int *icons_jres_jmol_typ; int *natm_jmol_typ; int *iatm_mol_typ; int *iatm_res_typ; int *iatm_atm_typ; int *iatm_atm_typ_nl; int *iatm_atm_typ_nl_rev; int *imap_atm_typ_nl; int *imap_atm_typ_nl_gh; int *iatm_mol_num; int *iatm_proc_num; int *iatm_res_num; int *ighost_flag; int *freeze_flag; int *freeze_map; int *atom_label; int *cp_atm_lst; }

user_defined_types: struct clatoms_info { int natm_tot; int pi_beads; int pi_beads_proc; int pi_beads_proc_st; int pi_beads_proc_end; int nfree; int nfree_pimd; int nchrg; int pi_beads_full_ter; int pi_beads_res_ter; int pi_beads_full_tra; int pi_beads_res_tra; int cg_reset_flag; int natm_mall; int nchrg_mall; int hess_calc; int natm_proc; int N_H2; int i_H2_start; int nab_initio; int myatm_start; double gamma_adb; double wght_pimd; double pi_temperature; double pi_beads_full_ter_wght; double pi_beads_res_ter_wght; double pi_beads_full_tra_wght; double pi_beads_res_tra_wght; double rcut_spread; double mass_sc_fact; int *ip_lab; int *ichrg; int *cp_vlnc_up; int *cp_atm_flag; double *mass; double *q; double *alp_pol; double *b_neut; double *roll_sc; double *text_atm; double *text_mol; double *xold; double *prekf; double *xmod; double alp_ewd; }

user_defined_types: struct ghost_atoms { int nghost_tot; int natm_comp_max; int nghost_mall; int nghost_old; int ncomp_mall; int ncomp_old; int *ighost_map; int *natm_comp; int **iatm_comp; double **coef; }

user_defined_types: struct bond_site { char bond_site_name[5][50]; int branch_1[5]; int branch_2[5]; int valence; int improper_ind[5]; }