decompiled_code:
__int64 __fastcall analysis_pimd(_DWORD *a1, __int64 a2, __int64 a3, _DWORD *a4)
{
unsigned int v5; // er14
int v6; // er13
__int64 result; // rax

v5 = a1[822];
v6 = a1[814];
if ( *(_DWORD *)(a2 + 500) == 1 )
result = prelim_analysis(a1, a2, a4);
if ( a4[72] == 1 )
result = calcul_gr(a1, a2, a4);
if ( !a1[813] )
{
if ( a4[102] != 1 || (result = calcul_vovt_atm(a1, a2, a4), !a1[813]) )
{
if ( a4[168] == 1 )
result = calcul_iikt_iso_cmd(a1, a2, a4);
}
}
if ( v6 > 1 )
result = Barrier(v5);
return result;
}

canonical_decompiled_code:
__int64 __fastcall func0(_DWORD *a1, __int64 a2, __int64 a3, _DWORD *a4)
{
unsigned int v5; // er14
int v6; // er13
__int64 result; // rax

v5 = a1[822];
v6 = a1[814];
if ( *(_DWORD *)(a2 + 500) == 1 )
result = prelim_analysis(a1, a2, a4);
if ( a4[72] == 1 )
result = calcul_gr(a1, a2, a4);
if ( !a1[813] )
{
if ( a4[102] != 1 || (result = calcul_vovt_atm(a1, a2, a4), !a1[813]) )
{
if ( a4[168] == 1 )
result = calcul_iikt_iso_cmd(a1, a2, a4);
}
}
if ( v6 > 1 )
result = Barrier(v5);
return result;
}

original_code:
void analysis_pimd(CLASS *class,GENERAL_DATA *general_data,
     BONDED *bonded, ANALYSIS *analysis)
{
   int world = class->communicate.world;
  int num_proc = class->communicate.np;
  if (general_data->timeinfo.itime==1)
  {
   prelim_analysis(class,general_data,analysis);
  };
  if (analysis->rdf.calcul_gr_on==1)
  {
   calcul_gr(class,general_data,analysis);
  };
  if (class->communicate.myid==0)
  {
   if (analysis->velocorel.calcul_atm_on==1)
   {
    calcul_vovt_atm(class,general_data,analysis);
   };
  };
  if(class->communicate.myid==0)
  {
   if (analysis->iikt_iso_corel.calcul_on==1)
   {
    calcul_iikt_iso_cmd(class,general_data,analysis);
   };
  };
  if(num_proc>1){ Barrier(world); }
}

canonical_original_code:
void analysis_pimd(struct class *class, struct general_data *general_data, struct bonded *bonded, struct analysis *analysis)
{
   int world = class->communicate.world;
  int num_proc = class->communicate.np;
  if (general_data->timeinfo.itime==1)
  {
   prelim_analysis(class,general_data,analysis);
  };
  if (analysis->rdf.calcul_gr_on==1)
  {
   calcul_gr(class,general_data,analysis);
  };
  if (class->communicate.myid==0)
  {
   if (analysis->velocorel.calcul_atm_on==1)
   {
    calcul_vovt_atm(class,general_data,analysis);
   };
  };
  if(class->communicate.myid==0)
  {
   if (analysis->iikt_iso_corel.calcul_on==1)
   {
    calcul_iikt_iso_cmd(class,general_data,analysis);
   };
  };
  if(num_proc>1){ Barrier(world); }
}

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; } *

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 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 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 analysis { struct info info; struct pimd_bead pimd_bead; struct rdf rdf; struct velocorel velocorel; struct msqdcorel msqdcorel; struct eisf eisf; struct iikt_iso_corel iikt_iso_corel; struct ickt_iso_corel ickt_iso_corel; struct dip_self_corel dip_self_corel; struct harmonic_analysis harmonic_analysis; }

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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }


repo: TuckermanGroup/PINY

original_code:
void set_bend_bnd_params(DICT_WORD intra_dict[],int num_intra_dict,
                         char *fun_key,char *file_name,int jmol_typ,
                         CLATOMS_INFO *clatoms_info,ATOMMAPS *atommaps,
                         BEND_BND *bend_bnd,BEND *bend,
                         NULL_INTER_PARSE *null_inter_parse,
                         BUILD_INTRA *build_intra, int iresidue,int ires_off)
{
  int num,index,ifound,igo;
  int itype1,itype2,itype3;
  int iatm_ind1,iatm_ind2,iatm_ind3;
  int imask1,imask2,imask3;
  int i,itype;
  for(i=1;i<=3;i++){
    if(intra_dict[i].iuset==0 && intra_dict[i].key_type==1){
      keyword_miss(intra_dict,file_name,fun_key,i);
    }
  }
  index = 1;
  sscanf(intra_dict[1].keyarg,"%d",&num);
  iatm_ind1 = num;
  if(iatm_ind1>build_intra->natmind_1res_now||iatm_ind1<0){
            keyarg_barf(intra_dict,file_name,fun_key,index);}
  imask1 = build_intra->mask_atm[iatm_ind1];
  if(imask1>0)iatm_ind1 = build_intra->index_atm[iatm_ind1];
  index = 2;
  sscanf(intra_dict[2].keyarg,"%d",&num);
  iatm_ind2 = num;
  if(iatm_ind2>build_intra->natmind_1res_now||iatm_ind2<0){
    keyarg_barf(intra_dict,file_name,fun_key,index);
  }
  imask2 = build_intra->mask_atm[iatm_ind2];
  if(imask2>0)iatm_ind2 = build_intra->index_atm[iatm_ind2];
  index = 3;
  sscanf(intra_dict[3].keyarg,"%d",&num);
  iatm_ind3 = num;
  if(iatm_ind3>build_intra->natmind_1res_now||iatm_ind3<0){
            keyarg_barf(intra_dict,file_name,fun_key,index);}
  imask3 = build_intra->mask_atm[iatm_ind3];
  if(imask3>0)iatm_ind3 = build_intra->index_atm[iatm_ind3];
  index = 5;
  ifound = 0;
  if(strcasecmp(intra_dict[5].keyarg,"on")==0) {ifound = 1;}
  if(strcasecmp(intra_dict[5].keyarg,"con")==0){ifound = 2;}
  if(strcasecmp(intra_dict[5].keyarg,"off")==0){ifound = 3;}
  if(ifound==0){
    keyarg_barf(intra_dict,file_name,fun_key,index);
  }
  if(ifound == 2 && clatoms_info->pi_beads>1){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("Constraints not implemented under  \n");
        printf(" path integral dynamics.            \n");
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
  }
  igo = imask1*imask2*imask3;
  if(igo==1){
    itype1 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind1)];
    itype2 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind2)];
    itype3 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind3)];
    strcpy(build_intra->cbend_bnd_typ_now->atm1,atommaps->atm_typ[itype1]);
    strcpy(build_intra->cbend_bnd_typ_now->atm2,atommaps->atm_typ[itype2]);
    strcpy(build_intra->cbend_bnd_typ_now->atm3,atommaps->atm_typ[itype3]);
    strcpy(build_intra->cbend_bnd_typ_now->label,intra_dict[6].keyarg);
  }
  if(ifound==1&&igo==1){
    if(bend_bnd->num+1 > build_intra->nbend_bnd_max){
      build_intra->nbend_bnd_max += 100;
      bend_bnd->j1 =(int*)crealloc(&(bend_bnd->j1)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->j2 =(int*)crealloc(&(bend_bnd->j2)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->j3 =(int*)crealloc(&(bend_bnd->j3)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->jtyp=(int*)crealloc(&(bend_bnd->jtyp)[1],
                                    build_intra->nbend_bnd_max*sizeof(int))-1;
    }
    itype = bend_bnd->ntyp+1;
    for(i=1;i<=bend_bnd->ntyp;i++){
      if((strcasecmp(build_intra->cbend_bnd_typ[i].atm1,
                     build_intra->cbend_bnd_typ_now->atm1)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm2,
                       build_intra->cbend_bnd_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm3,
                       build_intra->cbend_bnd_typ_now->atm3)==0)
  &&(strcasecmp(build_intra->cbend_bnd_typ[i].label,
         build_intra->cbend_bnd_typ_now->label)==0)) {itype=i;}
      if((strcasecmp(build_intra->cbend_bnd_typ[i].atm1,
                     build_intra->cbend_bnd_typ_now->atm3)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm2,
                       build_intra->cbend_bnd_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm3,
                       build_intra->cbend_bnd_typ_now->atm1)==0)
  &&(strcasecmp(build_intra->cbend_bnd_typ[i].label,
         build_intra->cbend_bnd_typ_now->label)==0)) {itype=i;}
    }
    if(itype>build_intra->nbend_bnd_typ_max){
      build_intra->nbend_bnd_typ_max += 100;
      build_intra->cbend_bnd_typ =
        (CBEND *) crealloc(&build_intra->cbend_bnd_typ[1],
                           build_intra->nbend_bnd_typ_max*sizeof(CBEND))-1;
    }
    if(itype==bend_bnd->ntyp+1){
      bend_bnd->ntyp++;
      strcpy(build_intra->cbend_bnd_typ[itype].atm1,
             build_intra->cbend_bnd_typ_now->atm1);
      strcpy(build_intra->cbend_bnd_typ[itype].atm2,
             build_intra->cbend_bnd_typ_now->atm2);
      strcpy(build_intra->cbend_bnd_typ[itype].atm3,
             build_intra->cbend_bnd_typ_now->atm3);
      strcpy(build_intra->cbend_bnd_typ[itype].label,
             build_intra->cbend_bnd_typ_now->label);
    }
    bend_bnd->num += 1;
    bend_bnd->j1[bend_bnd->num] = iatm_ind1 + clatoms_info->natm_tot;
    bend_bnd->j2[bend_bnd->num] = iatm_ind2 + clatoms_info->natm_tot;
    bend_bnd->j3[bend_bnd->num] = iatm_ind3 + clatoms_info->natm_tot;
    bend_bnd->jtyp[bend_bnd->num] = itype;
  }
  if(ifound==2&&igo==1){
    ires_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
    atommaps->nfree_jres_jmol_typ[ires_off+iresidue] -= 1;
    atommaps->icons_jres_jmol_typ[ires_off+iresidue] = 1;
    if(bend->ncon+1 > build_intra->nbend_con_max){
      build_intra->nbend_con_max += 100;
      bend->j1_con = (int *)crealloc(&(bend->j1_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
      bend->j2_con = (int *)crealloc(&(bend->j2_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
      bend->jtyp_con=(int *)crealloc(&(bend->jtyp_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
    }
    itype = (bend->ntyp_con)+1;
    for(i=1;i<=bend->ntyp_con;i++){
      if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
       build_intra->cbend_typ_now->atm1)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
         build_intra->cbend_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
         build_intra->cbend_typ_now->atm3)==0)
  &&(strcasecmp(build_intra->cbend_typ_con[i].label,
         build_intra->cbend_typ_now->label)==0)){itype=i;}
      if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
       build_intra->cbend_typ_now->atm3)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
         build_intra->cbend_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
         build_intra->cbend_typ_now->atm1)==0)
  &&(strcasecmp(build_intra->cbend_typ_con[i].label,
         build_intra->cbend_typ_now->label)==0)){itype=i;}
    }
    if(itype>build_intra->nbend_typ_con_max){
      build_intra->nbend_typ_con_max += 100;
      build_intra->cbend_typ_con = (CBEND *)
 crealloc(&(build_intra->cbend_typ_con[1]),
   build_intra->nbend_typ_con_max*sizeof(CBEND))-1;
    }
    if(itype==(bend->ntyp_con)+1){
      bend->ntyp_con+=1;
      strcpy(build_intra->cbend_typ_con[itype].atm1,
      build_intra->cbend_typ_now->atm1);
      strcpy(build_intra->cbend_typ_con[itype].atm2,
      build_intra->cbend_typ_now->atm2);
      strcpy(build_intra->cbend_typ_con[itype].atm3,
      build_intra->cbend_typ_now->atm3);
      strcpy(build_intra->cbend_typ_con[itype].label,
      build_intra->cbend_typ_now->label);
    }
    bend->ncon += 1;
    bend->j1_con[bend->ncon] = iatm_ind1 + clatoms_info->natm_tot;
    bend->j2_con[bend->ncon] = iatm_ind2 + clatoms_info->natm_tot;
    bend->j3_con[bend->ncon] = iatm_ind3 + clatoms_info->natm_tot;
    bend->jtyp_con[bend->ncon] = itype;
    if((atommaps->ighost_flag[bend->j1_con[bend->ncon]]!=0)||
       (atommaps->ighost_flag[bend->j2_con[bend->ncon]]!=0)||
       (atommaps->ighost_flag[bend->j3_con[bend->ncon]]!=0)){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("Ghost atoms are not permitted in constrained bends\n");
        printf("in molecule index %d in residue index %d in file %s\n",
                jmol_typ,iresidue,file_name);
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
    }
  }
  if(ifound==3&&igo==1){
    if(null_inter_parse->nbend_nul+1 > build_intra->nbend_nul_max){
      build_intra->nbend_nul_max += 100;
      null_inter_parse->jbend1_nul =
 (int *) crealloc(&(null_inter_parse->jbend1_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
      null_inter_parse->jbend2_nul =
 (int *) crealloc(&(null_inter_parse->jbend2_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
      null_inter_parse->jbend3_nul =
 (int *) crealloc(&(null_inter_parse->jbend3_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
    }
    null_inter_parse->nbend_nul += 1;
    (null_inter_parse->jbend1_nul)[null_inter_parse->nbend_nul] =
                       iatm_ind1 + clatoms_info->natm_tot;
    (null_inter_parse->jbend2_nul)[null_inter_parse->nbend_nul] =
                              iatm_ind2 + clatoms_info->natm_tot;
    (null_inter_parse->jbend3_nul)[null_inter_parse->nbend_nul] =
                              iatm_ind3 + clatoms_info->natm_tot;
  }
}

canonical_original_code:
void set_bend_bnd_params(struct dict_word intra_dict[], int num_intra_dict, char *fun_key, char *file_name, int jmol_typ, struct clatoms_info *clatoms_info, struct atommaps *atommaps, struct bend_bnd *bend_bnd, struct bend *bend, struct null_inter_parse *null_inter_parse, struct build_intra *build_intra, int iresidue, int ires_off)
{
  int num; int index; int ifound; int igo;
  int itype1; int itype2; int itype3;
  int iatm_ind1; int iatm_ind2; int iatm_ind3;
  int imask1; int imask2; int imask3;
  int i; int itype;
  for(i=1;i<=3;i++){
    if(intra_dict[i].iuset==0 && intra_dict[i].key_type==1){
      keyword_miss(intra_dict,file_name,fun_key,i);
    }
  }
  index = 1;
  sscanf(intra_dict[1].keyarg,"%d",&num);
  iatm_ind1 = num;
  if(iatm_ind1>build_intra->natmind_1res_now||iatm_ind1<0){
            keyarg_barf(intra_dict,file_name,fun_key,index);}
  imask1 = build_intra->mask_atm[iatm_ind1];
  if(imask1>0)iatm_ind1 = build_intra->index_atm[iatm_ind1];
  index = 2;
  sscanf(intra_dict[2].keyarg,"%d",&num);
  iatm_ind2 = num;
  if(iatm_ind2>build_intra->natmind_1res_now||iatm_ind2<0){
    keyarg_barf(intra_dict,file_name,fun_key,index);
  }
  imask2 = build_intra->mask_atm[iatm_ind2];
  if(imask2>0)iatm_ind2 = build_intra->index_atm[iatm_ind2];
  index = 3;
  sscanf(intra_dict[3].keyarg,"%d",&num);
  iatm_ind3 = num;
  if(iatm_ind3>build_intra->natmind_1res_now||iatm_ind3<0){
            keyarg_barf(intra_dict,file_name,fun_key,index);}
  imask3 = build_intra->mask_atm[iatm_ind3];
  if(imask3>0)iatm_ind3 = build_intra->index_atm[iatm_ind3];
  index = 5;
  ifound = 0;
  if(strcasecmp(intra_dict[5].keyarg,"on")==0) {ifound = 1;}
  if(strcasecmp(intra_dict[5].keyarg,"con")==0){ifound = 2;}
  if(strcasecmp(intra_dict[5].keyarg,"off")==0){ifound = 3;}
  if(ifound==0){
    keyarg_barf(intra_dict,file_name,fun_key,index);
  }
  if(ifound == 2 && clatoms_info->pi_beads>1){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("Constraints not implemented under  \n");
        printf(" path integral dynamics.            \n");
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
  }
  igo = imask1*imask2*imask3;
  if(igo==1){
    itype1 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind1)];
    itype2 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind2)];
    itype3 = atommaps->iatm_atm_typ[(clatoms_info->natm_tot+iatm_ind3)];
    strcpy(build_intra->cbend_bnd_typ_now->atm1,atommaps->atm_typ[itype1]);
    strcpy(build_intra->cbend_bnd_typ_now->atm2,atommaps->atm_typ[itype2]);
    strcpy(build_intra->cbend_bnd_typ_now->atm3,atommaps->atm_typ[itype3]);
    strcpy(build_intra->cbend_bnd_typ_now->label,intra_dict[6].keyarg);
  }
  if(ifound==1&&igo==1){
    if(bend_bnd->num+1 > build_intra->nbend_bnd_max){
      build_intra->nbend_bnd_max += 100;
      bend_bnd->j1 =(int *)crealloc(&(bend_bnd->j1)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->j2 =(int *)crealloc(&(bend_bnd->j2)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->j3 =(int *)crealloc(&(bend_bnd->j3)[1],
                                   build_intra->nbend_bnd_max*sizeof(int))-1;
      bend_bnd->jtyp=(int *)crealloc(&(bend_bnd->jtyp)[1],
                                    build_intra->nbend_bnd_max*sizeof(int))-1;
    }
    itype = bend_bnd->ntyp+1;
    for(i=1;i<=bend_bnd->ntyp;i++){
      if((strcasecmp(build_intra->cbend_bnd_typ[i].atm1,
                     build_intra->cbend_bnd_typ_now->atm1)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm2,
                       build_intra->cbend_bnd_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm3,
                       build_intra->cbend_bnd_typ_now->atm3)==0)
  &&(strcasecmp(build_intra->cbend_bnd_typ[i].label,
         build_intra->cbend_bnd_typ_now->label)==0)) {itype=i;}
      if((strcasecmp(build_intra->cbend_bnd_typ[i].atm1,
                     build_intra->cbend_bnd_typ_now->atm3)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm2,
                       build_intra->cbend_bnd_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_bnd_typ[i].atm3,
                       build_intra->cbend_bnd_typ_now->atm1)==0)
  &&(strcasecmp(build_intra->cbend_bnd_typ[i].label,
         build_intra->cbend_bnd_typ_now->label)==0)) {itype=i;}
    }
    if(itype>build_intra->nbend_bnd_typ_max){
      build_intra->nbend_bnd_typ_max += 100;
      build_intra->cbend_bnd_typ =
        (struct CBEND *) crealloc(&build_intra->cbend_bnd_typ[1],
                           build_intra->nbend_bnd_typ_max*sizeof(CBEND))-1;
    }
    if(itype==bend_bnd->ntyp+1){
      bend_bnd->ntyp++;
      strcpy(build_intra->cbend_bnd_typ[itype].atm1,
             build_intra->cbend_bnd_typ_now->atm1);
      strcpy(build_intra->cbend_bnd_typ[itype].atm2,
             build_intra->cbend_bnd_typ_now->atm2);
      strcpy(build_intra->cbend_bnd_typ[itype].atm3,
             build_intra->cbend_bnd_typ_now->atm3);
      strcpy(build_intra->cbend_bnd_typ[itype].label,
             build_intra->cbend_bnd_typ_now->label);
    }
    bend_bnd->num += 1;
    bend_bnd->j1[bend_bnd->num] = iatm_ind1 + clatoms_info->natm_tot;
    bend_bnd->j2[bend_bnd->num] = iatm_ind2 + clatoms_info->natm_tot;
    bend_bnd->j3[bend_bnd->num] = iatm_ind3 + clatoms_info->natm_tot;
    bend_bnd->jtyp[bend_bnd->num] = itype;
  }
  if(ifound==2&&igo==1){
    ires_off = atommaps->jres_jmol_typ_strt[jmol_typ]-1;
    atommaps->nfree_jres_jmol_typ[ires_off+iresidue] -= 1;
    atommaps->icons_jres_jmol_typ[ires_off+iresidue] = 1;
    if(bend->ncon+1 > build_intra->nbend_con_max){
      build_intra->nbend_con_max += 100;
      bend->j1_con = (int *)crealloc(&(bend->j1_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
      bend->j2_con = (int *)crealloc(&(bend->j2_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
      bend->jtyp_con=(int *)crealloc(&(bend->jtyp_con)[1],
         build_intra->nbend_con_max*sizeof(int))-1;
    }
    itype = (bend->ntyp_con)+1;
    for(i=1;i<=bend->ntyp_con;i++){
      if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
       build_intra->cbend_typ_now->atm1)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
         build_intra->cbend_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
         build_intra->cbend_typ_now->atm3)==0)
  &&(strcasecmp(build_intra->cbend_typ_con[i].label,
         build_intra->cbend_typ_now->label)==0)){itype=i;}
      if((strcasecmp(build_intra->cbend_typ_con[i].atm1,
       build_intra->cbend_typ_now->atm3)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm2,
         build_intra->cbend_typ_now->atm2)==0)
         &&(strcasecmp(build_intra->cbend_typ_con[i].atm3,
         build_intra->cbend_typ_now->atm1)==0)
  &&(strcasecmp(build_intra->cbend_typ_con[i].label,
         build_intra->cbend_typ_now->label)==0)){itype=i;}
    }
    if(itype>build_intra->nbend_typ_con_max){
      build_intra->nbend_typ_con_max += 100;
      build_intra->cbend_typ_con = (struct CBEND *)
 crealloc(&(build_intra->cbend_typ_con[1]),
   build_intra->nbend_typ_con_max*sizeof(CBEND))-1;
    }
    if(itype==(bend->ntyp_con)+1){
      bend->ntyp_con+=1;
      strcpy(build_intra->cbend_typ_con[itype].atm1,
      build_intra->cbend_typ_now->atm1);
      strcpy(build_intra->cbend_typ_con[itype].atm2,
      build_intra->cbend_typ_now->atm2);
      strcpy(build_intra->cbend_typ_con[itype].atm3,
      build_intra->cbend_typ_now->atm3);
      strcpy(build_intra->cbend_typ_con[itype].label,
      build_intra->cbend_typ_now->label);
    }
    bend->ncon += 1;
    bend->j1_con[bend->ncon] = iatm_ind1 + clatoms_info->natm_tot;
    bend->j2_con[bend->ncon] = iatm_ind2 + clatoms_info->natm_tot;
    bend->j3_con[bend->ncon] = iatm_ind3 + clatoms_info->natm_tot;
    bend->jtyp_con[bend->ncon] = itype;
    if((atommaps->ighost_flag[bend->j1_con[bend->ncon]]!=0)||
       (atommaps->ighost_flag[bend->j2_con[bend->ncon]]!=0)||
       (atommaps->ighost_flag[bend->j3_con[bend->ncon]]!=0)){
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        printf("Ghost atoms are not permitted in constrained bends\n");
        printf("in molecule index %d in residue index %d in file %s\n",
                jmol_typ,iresidue,file_name);
        printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
        fflush(stdout);
        exit(1);
    }
  }
  if(ifound==3&&igo==1){
    if(null_inter_parse->nbend_nul+1 > build_intra->nbend_nul_max){
      build_intra->nbend_nul_max += 100;
      null_inter_parse->jbend1_nul =
 (int *) crealloc(&(null_inter_parse->jbend1_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
      null_inter_parse->jbend2_nul =
 (int *) crealloc(&(null_inter_parse->jbend2_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
      null_inter_parse->jbend3_nul =
 (int *) crealloc(&(null_inter_parse->jbend3_nul)[1],
    build_intra->nbend_nul_max*sizeof(int))-1;
    }
    null_inter_parse->nbend_nul += 1;
    (null_inter_parse->jbend1_nul)[null_inter_parse->nbend_nul] =
                       iatm_ind1 + clatoms_info->natm_tot;
    (null_inter_parse->jbend2_nul)[null_inter_parse->nbend_nul] =
                              iatm_ind2 + clatoms_info->natm_tot;
    (null_inter_parse->jbend3_nul)[null_inter_parse->nbend_nul] =
                              iatm_ind3 + clatoms_info->natm_tot;
  }
}

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

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 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; } *

variable_types: 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; } *

variable_types: struct null_inter_parse { int nbond_nul; int ntors_nul; int *jbond1_nul; int *jbend1_nul; int *jtors1_nul; int *jonfo1_nul; } *

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: iresidue int

variable_types: num int

variable_types: index int

variable_types: ifound int

variable_types: igo int

variable_types: i int

variable_types: itype 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; }


original_code:
void min_CG(CLASS *class,BONDED *bonded,GENERAL_DATA *general_data,int ireset)
{
    int i,ipart,ifirst=1;
    int natm_tot;
    double dt,tol_glob,dt22,dt2;
    double dtsm,dtsm2;
    double gamma;
    double fovlap_old;
    static double fovlap;
    double *zeta;
   int min_atm_com_fix_opt = general_data->minopts.min_atm_com_fix_opt;
   double *clatoms_x = class->clatoms_pos[1].x;
   double *clatoms_y = class->clatoms_pos[1].y;
   double *clatoms_z = class->clatoms_pos[1].z;
   double *clatoms_vx = class->clatoms_pos[1].vx;
   double *clatoms_vy = class->clatoms_pos[1].vy;
   double *clatoms_vz = class->clatoms_pos[1].vz;
   double *clatoms_fx = class->clatoms_pos[1].fx;
   double *clatoms_fy = class->clatoms_pos[1].fy;
   double *clatoms_fz = class->clatoms_pos[1].fz;
   double *chx = class->clatoms_pos[1].vx;
   double *chy = class->clatoms_pos[1].vy;
   double *chz = class->clatoms_pos[1].vz;
   double *clatoms_mass = class->clatoms_info.mass;
   double *clatoms_xold = class->clatoms_info.xold;
   double *clatoms_yold = class->clatoms_info.yold;
   double *clatoms_zold = class->clatoms_info.zold;
    (class->energy_ctrl.int_res_tra) = 0;
    (class->energy_ctrl.int_res_ter) = 0;
    dt = (general_data->timeinfo.dt);
    dt2 = dt/2.0;
    dt22 = dt*dt/2.0;
    dtsm = .01;
    dtsm2 = dtsm/2.0;
    general_data->stat_avg.iter_shake = 0;
    general_data->stat_avg.iter_ratl = 0;
    natm_tot = class->clatoms_info.natm_tot;
    zeta = (double *) cmalloc(natm_tot*sizeof(double))-1;
   if(ireset == 1){
     for(i=1;i<=natm_tot; i++){
      chx[i] = 0.0;
      chy[i] = 0.0;
      chz[i] = 0.0;
     }
     gamma = 0.0;
     fovlap = 1.0;
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_xold[ipart] = clatoms_x[ipart];
      clatoms_yold[ipart] = clatoms_y[ipart];
      clatoms_zold[ipart] = clatoms_z[ipart];
              }
    (class->energy_ctrl.iget_full_inter)= 1;
    (class->energy_ctrl.iget_res_inter) = 0;
    (class->energy_ctrl.iget_full_intra)= 1;
    (class->energy_ctrl.iget_res_intra) = 0;
    energy_control(class,bonded,general_data);
    if(min_atm_com_fix_opt==1){
       proj_com_out(class->clatoms_info.natm_tot,
                    clatoms_fx,clatoms_fy,clatoms_fz);
    }
   if((bonded->constrnt.iconstrnt)==1){
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      (clatoms_vx)[ipart] += (clatoms_fx)[ipart]*dtsm2/((clatoms_mass)[ipart]);
      (clatoms_vy)[ipart] += (clatoms_fy)[ipart]*dtsm2/((clatoms_mass)[ipart]);
      (clatoms_vz)[ipart] += (clatoms_fz)[ipart]*dtsm2/((clatoms_mass)[ipart]);
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] += clatoms_vx[ipart]*dtsm;
      clatoms_y[ipart] += clatoms_vy[ipart]*dtsm;
      clatoms_z[ipart] += clatoms_vz[ipart]*dtsm;
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_vx[ipart] = 0.0;
      clatoms_vy[ipart] = 0.0;
      clatoms_vz[ipart] = 0.0;
    }
    init_constraint(bonded,&(general_data->ptens));
    (bonded->constrnt.iroll) = 0;
     shake_control(bonded,&(class->clatoms_info),&(class->clatoms_pos[1]),
                  &(general_data->cell),&(general_data->ptens),
                  &(general_data->statepoint),
                  &(general_data->baro),&(general_data->par_rahman),
                  &(general_data->stat_avg),dt,&tol_glob,ifirst,
                  &(class->class_comm_forc_pkg),&(class->ewd_scr));
   for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_fx[ipart] += clatoms_vx[ipart]*clatoms_mass[ipart]/dtsm2;
      clatoms_fy[ipart] += clatoms_vy[ipart]*clatoms_mass[ipart]/dtsm2;
      clatoms_fz[ipart] += clatoms_vz[ipart]*clatoms_mass[ipart]/dtsm2;
              }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] = clatoms_xold[ipart];
      clatoms_y[ipart] = clatoms_yold[ipart];
      clatoms_z[ipart] = clatoms_zold[ipart];
    }
   }
   fovlap_old = fovlap;
   fovlap = 0.0;
   for(i=1;i<=natm_tot;i++){
    fovlap += clatoms_fx[i]*clatoms_fx[i]
            + clatoms_fy[i]*clatoms_fy[i]
            + clatoms_fz[i]*clatoms_fz[i];
   }
   if(ireset != 1) {gamma = fovlap/fovlap_old;}
     for(i=1;i<=natm_tot; i++){
      chx[i] = clatoms_fx[i] + gamma*chx[i];
      chy[i] = clatoms_fy[i] + gamma*chy[i];
      chz[i] = clatoms_fz[i] + gamma*chz[i];
     }
   for(i=1;i<=natm_tot;i++) {
    zeta[i] = dt/clatoms_mass[i];
   }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] = clatoms_xold[ipart] + zeta[ipart]*chx[ipart];
      clatoms_y[ipart] = clatoms_yold[ipart] + zeta[ipart]*chy[ipart];
      clatoms_z[ipart] = clatoms_zold[ipart] + zeta[ipart]*chz[ipart];
              }
    if((bonded->constrnt.iconstrnt)==1){
         (bonded->constrnt.iroll) = 0;
         init_constraint(bonded,&(general_data->ptens));
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_vx[ipart] = 0.0;
      clatoms_vy[ipart] = 0.0;
      clatoms_vz[ipart] = 0.0;
              }
         shake_control(bonded,&(class->clatoms_info),&(class->clatoms_pos[1]),
                      &(general_data->cell),&(general_data->ptens),
                      &(general_data->statepoint),
                      &(general_data->baro),&(general_data->par_rahman),
                      &(general_data->stat_avg),dt,&tol_glob,ifirst,
                      &(class->class_comm_forc_pkg),&(class->ewd_scr));
           }
   get_ghost_pos(&(class->clatoms_info),&(class->clatoms_pos[1]),
                 &(class->ghost_atoms));
    (class->energy_ctrl.iget_full_inter)= 1;
    (class->energy_ctrl.iget_res_inter) = 0;
    (class->energy_ctrl.iget_full_intra)= 1;
    (class->energy_ctrl.iget_res_intra) = 0;
    energy_control(class,bonded,general_data);
   cfree(&(zeta[1]));
               }

canonical_original_code:
void min_CG(struct class *class, struct bonded *bonded, struct general_data *general_data, int ireset)
{
    int i; int ipart; int ifirst = 1;
    int natm_tot;
    double dt; double tol_glob; double dt22; double dt2;
    double dtsm; double dtsm2;
    double gamma;
    double fovlap_old;
    static double fovlap;
    double *zeta;
   int min_atm_com_fix_opt = general_data->minopts.min_atm_com_fix_opt;
   double *clatoms_x = class->clatoms_pos[1].x;
   double *clatoms_y = class->clatoms_pos[1].y;
   double *clatoms_z = class->clatoms_pos[1].z;
   double *clatoms_vx = class->clatoms_pos[1].vx;
   double *clatoms_vy = class->clatoms_pos[1].vy;
   double *clatoms_vz = class->clatoms_pos[1].vz;
   double *clatoms_fx = class->clatoms_pos[1].fx;
   double *clatoms_fy = class->clatoms_pos[1].fy;
   double *clatoms_fz = class->clatoms_pos[1].fz;
   double *chx = class->clatoms_pos[1].vx;
   double *chy = class->clatoms_pos[1].vy;
   double *chz = class->clatoms_pos[1].vz;
   double *clatoms_mass = class->clatoms_info.mass;
   double *clatoms_xold = class->clatoms_info.xold;
   double *clatoms_yold = class->clatoms_info.yold;
   double *clatoms_zold = class->clatoms_info.zold;
    (class->energy_ctrl.int_res_tra) = 0;
    (class->energy_ctrl.int_res_ter) = 0;
    dt = (general_data->timeinfo.dt);
    dt2 = dt/2.0;
    dt22 = dt*dt/2.0;
    dtsm = .01;
    dtsm2 = dtsm/2.0;
    general_data->stat_avg.iter_shake = 0;
    general_data->stat_avg.iter_ratl = 0;
    natm_tot = class->clatoms_info.natm_tot;
    zeta = (double *) cmalloc(natm_tot*sizeof(double))-1;
   if(ireset == 1){
     for(i=1;i<=natm_tot; i++){
      chx[i] = 0.0;
      chy[i] = 0.0;
      chz[i] = 0.0;
     }
     gamma = 0.0;
     fovlap = 1.0;
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_xold[ipart] = clatoms_x[ipart];
      clatoms_yold[ipart] = clatoms_y[ipart];
      clatoms_zold[ipart] = clatoms_z[ipart];
              }
    (class->energy_ctrl.iget_full_inter)= 1;
    (class->energy_ctrl.iget_res_inter) = 0;
    (class->energy_ctrl.iget_full_intra)= 1;
    (class->energy_ctrl.iget_res_intra) = 0;
    energy_control(class,bonded,general_data);
    if(min_atm_com_fix_opt==1){
       proj_com_out(class->clatoms_info.natm_tot,
                    clatoms_fx,clatoms_fy,clatoms_fz);
    }
   if((bonded->constrnt.iconstrnt)==1){
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      (clatoms_vx)[ipart] += (clatoms_fx)[ipart]*dtsm2/((clatoms_mass)[ipart]);
      (clatoms_vy)[ipart] += (clatoms_fy)[ipart]*dtsm2/((clatoms_mass)[ipart]);
      (clatoms_vz)[ipart] += (clatoms_fz)[ipart]*dtsm2/((clatoms_mass)[ipart]);
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] += clatoms_vx[ipart]*dtsm;
      clatoms_y[ipart] += clatoms_vy[ipart]*dtsm;
      clatoms_z[ipart] += clatoms_vz[ipart]*dtsm;
    }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_vx[ipart] = 0.0;
      clatoms_vy[ipart] = 0.0;
      clatoms_vz[ipart] = 0.0;
    }
    init_constraint(bonded,&(general_data->ptens));
    (bonded->constrnt.iroll) = 0;
     shake_control(bonded,&(class->clatoms_info),&(class->clatoms_pos[1]),
                  &(general_data->cell),&(general_data->ptens),
                  &(general_data->statepoint),
                  &(general_data->baro),&(general_data->par_rahman),
                  &(general_data->stat_avg),dt,&tol_glob,ifirst,
                  &(class->class_comm_forc_pkg),&(class->ewd_scr));
   for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_fx[ipart] += clatoms_vx[ipart]*clatoms_mass[ipart]/dtsm2;
      clatoms_fy[ipart] += clatoms_vy[ipart]*clatoms_mass[ipart]/dtsm2;
      clatoms_fz[ipart] += clatoms_vz[ipart]*clatoms_mass[ipart]/dtsm2;
              }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] = clatoms_xold[ipart];
      clatoms_y[ipart] = clatoms_yold[ipart];
      clatoms_z[ipart] = clatoms_zold[ipart];
    }
   }
   fovlap_old = fovlap;
   fovlap = 0.0;
   for(i=1;i<=natm_tot;i++){
    fovlap += clatoms_fx[i]*clatoms_fx[i]
            + clatoms_fy[i]*clatoms_fy[i]
            + clatoms_fz[i]*clatoms_fz[i];
   }
   if(ireset != 1) {gamma = fovlap/fovlap_old;}
     for(i=1;i<=natm_tot; i++){
      chx[i] = clatoms_fx[i] + gamma*chx[i];
      chy[i] = clatoms_fy[i] + gamma*chy[i];
      chz[i] = clatoms_fz[i] + gamma*chz[i];
     }
   for(i=1;i<=natm_tot;i++) {
    zeta[i] = dt/clatoms_mass[i];
   }
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_x[ipart] = clatoms_xold[ipart] + zeta[ipart]*chx[ipart];
      clatoms_y[ipart] = clatoms_yold[ipart] + zeta[ipart]*chy[ipart];
      clatoms_z[ipart] = clatoms_zold[ipart] + zeta[ipart]*chz[ipart];
              }
    if((bonded->constrnt.iconstrnt)==1){
         (bonded->constrnt.iroll) = 0;
         init_constraint(bonded,&(general_data->ptens));
    for(ipart=1;ipart<=(class->clatoms_info.natm_tot);ipart++){
      clatoms_vx[ipart] = 0.0;
      clatoms_vy[ipart] = 0.0;
      clatoms_vz[ipart] = 0.0;
              }
         shake_control(bonded,&(class->clatoms_info),&(class->clatoms_pos[1]),
                      &(general_data->cell),&(general_data->ptens),
                      &(general_data->statepoint),
                      &(general_data->baro),&(general_data->par_rahman),
                      &(general_data->stat_avg),dt,&tol_glob,ifirst,
                      &(class->class_comm_forc_pkg),&(class->ewd_scr));
           }
   get_ghost_pos(&(class->clatoms_info),&(class->clatoms_pos[1]),
                 &(class->ghost_atoms));
    (class->energy_ctrl.iget_full_inter)= 1;
    (class->energy_ctrl.iget_res_inter) = 0;
    (class->energy_ctrl.iget_full_intra)= 1;
    (class->energy_ctrl.iget_res_intra) = 0;
    energy_control(class,bonded,general_data);
   cfree(&(zeta[1]));
               }

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: ireset int

variable_types: ipart int

variable_types: ifirst int

variable_types: dt double

variable_types: dtsm double

variable_types: gamma double

variable_types: fovlap double

variable_types:
zeta
double *

variable_types:
chx
double *

variable_types:
chy
double *

variable_types:
chz
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 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 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; }

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 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 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; }

user_defined_types: struct therm_pos { double **x_nhc; double x_nhc_tot; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: struct ewd_scr { double *q; double *x; double *fx; double *heli; double *cossc; double *fx2; double *temp; double *helr_now; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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]; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: struct constrnt { int iconstrnt; int iroll; int max_iter; double tolshake; double tolratl; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: struct bend_free { int num; int j1; int npow; int nhist; double fk; double eq; double del; char *file; double *hist; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: struct excl { int nlst; int nlst_root; int num_cp; int *num; int *j; int *j_off; int *j1_cp; }

user_defined_types: 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; }

user_defined_types: struct clatoms_pos { double *mass; double *x; double *vx; double *fx; double *fxt; double *fxm; double *hess_xx; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: 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; }

user_defined_types: struct therm_scr { double *sc; double *atm_kin; }