decompiled_code:
void calcul_ickt_iso_md()
{
;
}

canonical_decompiled_code:
void func0()
{
;
}

original_code:
void calcul_ickt_iso_md(CLASS *class,GENERAL_DATA *general_data,
                     ANALYSIS *analysis)
{
  unsigned int nstep,nrun;
  unsigned int njump_ickt_iso;
  unsigned int nbpas_ickt_iso;
  unsigned int nnn_ickt_iso;
}

canonical_original_code:
void calcul_ickt_iso_md(struct class *class, struct general_data *general_data, struct analysis *analysis)
{
  unsigned int nstep; unsigned int nrun;
  unsigned int njump_ickt_iso;
  unsigned int nbpas_ickt_iso;
  unsigned int nnn_ickt_iso;
}

variable_types: struct analysis { struct info { int natm_real; int natm_ghost; int nmol_tot; int nmol_typ_real; int *nmol_jmol_typ_real; int *iatm_mol_typ_real; int *nmol_typ_atm_or_mol; double *masse_nmol_real; int nb_atm_typ_tot; int nb_atm_typ_ghost; int nb_atm_typ_real; int nb_atm_in_real_mol; int nb_mol_real_mol; int *natm_real_this_kind; int *natm_this_kind; int *natm_typ_real_or_ghost; int *map_atm_nb_to_atm_real_kind_nb; int *map_atm_nb_to_real_mol_or_atm; int *map_atm_nb_to_nmol_real_typ; int *nb_mol_real_jmol_typ; double *mass_real_mol; char (*name_real_mol)[50]; } info; struct pimd_bead { double **sc_op_x; double **sc_op_y; double **sc_op_z; double **sc_op_x2; double **sc_op_y2; double **sc_op_z2; double **sc_op_vx; double **sc_op_vy; double **sc_op_vz; double **sc_op_vx2; double **sc_op_vy2; double **sc_op_vz2; double ***bead_x; double ***bead_y; double ***bead_z; double ***bead_vx; double ***bead_vy; double ***bead_vz; } pimd_bead; struct rdf { int calcul_gr_on; int calcul_intra_on; int calcul_sq_from_gr_on; int njump; int periodic_write; int number_of_points; int nbk; double dr; double rmax; double dk; char *rdfname; int **iatm_pos; double *rbin; double *vol_diff; double ***rhist; double ***rhist_out; double ***gr; double ***sq; } rdf; struct velocorel { int calcul_atm_on; int ncor; int njump; int nwrite; int normalize; char *vovtname; char *output_kind; double **tmp_vtx; double **tmp_vty; double **tmp_vtz; double **vovtx; double **vovty; double **vovtz; int calcul_com_on; int ncor_com; int njump_com; int nwrite_com; int normalize_com; char *vovtname_com; char *output_kind_com; double **tmp_com_vtx; double **tmp_com_vty; double **tmp_com_vtz; double **com_vovtx; double **com_vovty; double **com_vovtz; } velocorel; struct msqdcorel { int calcul_atm_on; int ncor; int njump; char *msqdname; char *output_kind; double **tmp_msqdx; double **tmp_msqdy; double **tmp_msqdz; double **msqdx; double **msqdy; double **msqdz; } msqdcorel; struct eisf { int calcul_on; int eisf_on; } eisf; struct iikt_iso_corel { int calcul_on; int eisf_on; int ncor; int njump; int nbk_ask; int nb_kvecx; int nb_kvecy; int nb_kvecz; int full_iso; int calc_all_atm_typ; int natm_typ_calc; int natm_tot_calc; double kmin_ask; double kmax_ask; double kmin_calc_x; double kmin_calc_y; double kmin_calc_z; double dk_calc_x; double dk_calc_y; double dk_calc_z; int *natm_jmol_typ; int *map_calc_atm_on; int *map_calc_atm_typ; char *iikt_iso_name; char *output_kind; char (*list_atm_typ)[50]; double *kvec_x; double *kvec_y; double *kvec_z; double **tmp_0_tcosx; double **tmp_0_tcosy; double **tmp_0_tcosz; double **tmp_1_tcosx; double **tmp_1_tcosy; double **tmp_1_tcosz; double **tmp_0_tsinx; double **tmp_0_tsiny; double **tmp_0_tsinz; double **tmp_1_tsinx; double **tmp_1_tsiny; double **tmp_1_tsinz; double **ceisf_x; double **seisf_x; double **ceisf_y; double **seisf_y; double **ceisf_z; double **seisf_z; double **eisf_x; double **eisf_y; double **eisf_z; double ***ciikt_real_x; double ***ciikt_real_y; double ***ciikt_real_z; double ***ciikt_imag_x; double ***ciikt_imag_y; double ***ciikt_imag_z; } iikt_iso_corel; struct ickt_iso_corel { int calcul_on; int ncor; int njump; int nbk_ask; int nb_kvecx; int nb_kvecy; int nb_kvecz; int full_iso; double kmin_ask; double kmax_ask; double kmin_calc_x; double kmin_calc_y; double kmin_calc_z; double dk_calc_x; double dk_calc_y; double dk_calc_z; char *ickt_iso_name; double *kvec_x; double *kvec_y; double *kvec_z; double ***tmp_rho_real_x; double ***tmp_rho_real_y; double ***tmp_rho_real_z; double ***tmp_rho_imag_x; double ***tmp_rho_imag_y; double ***tmp_rho_imag_z; double ****cickt_real_x; double ****cickt_real_y; double ****cickt_real_z; double ****cickt_imag_x; double ****cickt_imag_y; double ****cickt_imag_z; } ickt_iso_corel; struct dip_self_corel { int calcul_on; int ncor; int njump; int normalize; char *momtname; char *output_kind; double **tmp_mx; double **tmp_my; double **tmp_mz; double **momtx; double **momty; double **momtz; } dip_self_corel; struct harmonic_analysis { int calcul_freq_on; int calcul_thermo_on; int calcul_spectra_on; int nfreqs; double delta; double *harm_freqs; } harmonic_analysis; } *

variable_types:
nstep
unsigned int

variable_types:
nrun
unsigned int

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 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 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 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 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 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 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 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 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; }


repo: TuckermanGroup/PINY

original_code:
void set_res_name_params(DICT_WORD res_name_dict[],int num_res_name_dict,
                         char fun_key[],char file_name[],NAME res_typ[],
                         int natm_jres_jmol_typ[],int jmol_typ,
                         int jres,int jres_off,
                         int ires_typ_jres_jmol_typ[])
{
  int num,i,index,index2;
  for(i=1;i<=num_res_name_dict;i++){
    if(res_name_dict[i].iuset==0 && res_name_dict[i].key_type==1){
      keyword_miss(res_name_dict,file_name,fun_key,i);}
  }
  index = 1;
  index2 = ires_typ_jres_jmol_typ[(jres+jres_off)];
  if(strcasecmp(res_typ[index2],res_name_dict[1].keyarg)!=0){
    keyarg_barf(res_name_dict,file_name,fun_key,index);}
  sscanf(res_name_dict[3].keyarg,"%d",&num);
  index = 3;
  if(num<0||num!=natm_jres_jmol_typ[(jres+jres_off)]){
    keyarg_barf(res_name_dict,file_name,fun_key,index);
  }
  natm_jres_jmol_typ[jres+jres_off] = num;
}

canonical_original_code:
void set_res_name_params(struct dict_word res_name_dict[], int num_res_name_dict, char fun_key[], char file_name[], char res_typ[][50], int natm_jres_jmol_typ[], int jmol_typ, int jres, int jres_off, int ires_typ_jres_jmol_typ[])
{
  int num; int i; int index; int index2;
  for(i=1;i<=num_res_name_dict;i++){
    if(res_name_dict[i].iuset==0 && res_name_dict[i].key_type==1){
      keyword_miss(res_name_dict,file_name,fun_key,i);}
  }
  index = 1;
  index2 = ires_typ_jres_jmol_typ[(jres+jres_off)];
  if(strcasecmp(res_typ[index2],res_name_dict[1].keyarg)!=0){
    keyarg_barf(res_name_dict,file_name,fun_key,index);}
  sscanf(res_name_dict[3].keyarg,"%d",&num);
  index = 3;
  if(num<0||num!=natm_jres_jmol_typ[(jres+jres_off)]){
    keyarg_barf(res_name_dict,file_name,fun_key,index);
  }
  natm_jres_jmol_typ[jres+jres_off] = num;
}

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

variable_types: jres int

variable_types: num int

variable_types: i int

variable_types: index int

return_type: void


nrerror

decompiled_code:
void __fastcall __noreturn nrerror(const char *a1)
{
fwrite("Numerical Recipes run-time error...\n", 1uLL, 0x24uLL, stderr);
fprintf(stderr, "%s\n", a1);
fwrite("...now exiting to system...\n", 1uLL, 0x1CuLL, stderr);
exit(1);
}

canonical_decompiled_code:
void __fastcall __noreturn func0(const char *a1)
{
fwrite("Numerical Recipes run-time error...\n", 1uLL, 0x24uLL, stderr);
fprintf(stderr, "%s\n", a1);
fwrite("...now exiting to system...\n", 1uLL, 0x1CuLL, stderr);
exit(1);
}

original_code:
void nrerror(char error_text[])
{
   fprintf(stderr,"Numerical Recipes run-time error...\n");
   fprintf(stderr,"%s\n",error_text);
   fprintf(stderr,"...now exiting to system...\n");
   exit(1);
}


dvector

decompiled_code:
char *__fastcall dvector(int a1, int a2)
{
char *v2; // rax

v2 = (char *)malloc(8LL * (a2 - a1 + 1));
if ( !v2 )
nrerror("allocation failure in dvector()");
return &v2[-8 * a1];
}

canonical_decompiled_code:
char *__fastcall func1(int a1, int a2)
{
char *v2; // rax

v2 = (char *)malloc(8LL * (a2 - a1 + 1));
if ( !v2 )
func0("allocation failure in dvector()");
return &v2[-8 * a1];
}

original_code:
double *dvector(int nl, int nh)
{
   double *v;
   v=(double *)malloc((size_t) ((nh-nl+1+0)*sizeof(double)));
   if (!v) nrerror("allocation failure in dvector()");
   return v-nl+0;
}

canonical_original_code:
double *dvector(int nl, int nh)
{
   double *v;
   v=(double *)malloc((unsigned long) ((nh-nl+1+0)*sizeof(double)));
   if (!v) nrerror("allocation failure in dvector()");
   return v-nl+0;
}

variable_types: nl int

variable_types: nh int

variable_types:
v
double *

return_type: double *


decompiled_code:
void __fastcall free_dvector(__int64 a1, int a2)
{
free((void *)(a1 + 8LL * a2));
}

canonical_decompiled_code:
void __fastcall func2(__int64 a1, int a2)
{
free((void *)(a1 + 8LL * a2));
}

original_code:
void free_dvector(double *v, int nl, int nh)
{
   free((v+nl-0));
}


decompiled_code:
void __fastcall free_dmatrix(__int64 a1, int a2, __int64 a3, int a4)
{
_QWORD *v4; // rbx

v4 = (_QWORD *)(a1 + 8LL * a2);
free((void *)(*v4 + 8LL * a4));
free(v4);
}

canonical_decompiled_code:
void __fastcall func3(__int64 a1, int a2, __int64 a3, int a4)
{
_QWORD *v4; // rbx

v4 = (_QWORD *)(a1 + 8LL * a2);
free((void *)(*v4 + 8LL * a4));
free(v4);
}

original_code:
void free_dmatrix(double **m, int nrl, int nrh, int ncl, int nch)
{
   free((char *)(m[nrl]+ncl-0));
   free((char *)(m+nrl-0));
}

variable_types:
m
double **

variable_types: nrl int

variable_types: nrh int

variable_types: ncl int

variable_types: nch int


decompiled_code:
void __fastcall free_d3tensor(__int64 a1, int a2, __int64 a3, int a4, __int64 a5, int a6)
{
_QWORD *v6; // rbx
__int64 v7; // rbp

v6 = (_QWORD *)(a1 + 8LL * a2);
v7 = 8LL * a4;
free((void *)(*(_QWORD *)(*v6 + v7) + 8LL * a6));
free((void *)(*v6 + v7));
free(v6);
}

canonical_decompiled_code:
void __fastcall func4(__int64 a1, int a2, __int64 a3, int a4, __int64 a5, int a6)
{
_QWORD *v6; // rbx
__int64 v7; // rbp

v6 = (_QWORD *)(a1 + 8LL * a2);
v7 = 8LL * a4;
free((void *)(*(_QWORD *)(*v6 + v7) + 8LL * a6));
free((void *)(*v6 + v7));
free(v6);
}

original_code:
void free_d3tensor(double ***t, int nrl, int nrh, int ncl, int nch,
   int ndl, int ndh)
{
   free((char *)(t[nrl][ncl]+ndl-0));
   free((char *)(t[nrl]+ncl-0));
   free((char *)(t+nrl-0));
}

variable_types:
t
double ***

variable_types: ndl int

variable_types: ndh int


original_code:
void int_NPTF_res(CLASS *class,BONDED *bonded,GENERAL_DATA *general_data)
   {
   int iflag;
   double dti2,dti;
   int ir_tra,ir_tor,ir_ter;
   int iii;
   int ix_respa = general_data->timeinfo.ix_respa;
   int int_res_ter = general_data->timeinfo.int_res_ter;
   int nres_tra = general_data->timeinfo.nres_tra;
   int nres_tor = general_data->timeinfo.nres_tor;
   int nres_ter = general_data->timeinfo.nres_ter;
   int nres_nhc = class->therm_info_class.nres_nhc;
   double dt = general_data->timeinfo.dt;
   dti = dt/((double)(nres_ter*nres_tor*nres_tra));
   dti2 = dti/2.0;
   switch(ix_respa){
     case 1:
       class->therm_info_class.wght = (double)(nres_tra*nres_tor*nres_ter);
       break;
     case 2:
       class->therm_info_class.wght = (double)(nres_tra*nres_tor);
       break;
     case 3:
       class->therm_info_class.wght = (double)(nres_tra);
       break;
     case 4:
       class->therm_info_class.wght = 1.0;
       break;
   }
   class->therm_info_class.dt_nhc = dti;
   class->therm_info_class.dti_nhc = dti/( (double)(nres_nhc) );
   set_yosh(class->therm_info_class.nyosh_nhc,
            class->therm_info_class.dti_nhc,
            class->therm_info_class.wdti,
            class->therm_info_class.wdti2,
            class->therm_info_class.wdti4,
            class->therm_info_class.wdti8,
            class->therm_info_class.wdti16);
   zero_constrt_iters(&(general_data->stat_avg));
   for(ir_ter=1;ir_ter<=nres_ter;ir_ter++){
     for(ir_tor=1;ir_tor<=nres_tor;ir_tor++){
       for(ir_tra=1;ir_tra<=nres_tra;ir_tra++){
        int_0_to_dt2_nptf(class,bonded,general_data,ir_tra,ir_tor,ir_ter,dti);
        (class->energy_ctrl.iget_full_inter) = 0;
        (class->energy_ctrl.iget_res_inter) = 0;
        (class->energy_ctrl.iget_full_intra) = 0;
        (class->energy_ctrl.iget_res_intra) = 1;
        if((ir_ter==nres_ter)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra))
             {(class->energy_ctrl.iget_full_inter) = 1;}
        if((int_res_ter==1)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra))
             {(class->energy_ctrl.iget_res_inter) = 1;}
        if(ir_tra==nres_tra)
             {(class->energy_ctrl.iget_full_intra) = 1;}
        energy_control(class,bonded,general_data);
       int_dt2_to_dt_nptf(class,bonded,general_data,ir_tra,ir_tor,ir_ter,dti);
        }
     }
   }
   iflag=2;
   int_final_class(class,bonded,general_data,iflag);
  }

canonical_original_code:
void int_NPTF_res(struct class *class, struct bonded *bonded, struct general_data *general_data)
   {
   int iflag;
   double dti2; double dti;
   int ir_tra; int ir_tor; int ir_ter;
   int iii;
   int ix_respa = general_data->timeinfo.ix_respa;
   int int_res_ter = general_data->timeinfo.int_res_ter;
   int nres_tra = general_data->timeinfo.nres_tra;
   int nres_tor = general_data->timeinfo.nres_tor;
   int nres_ter = general_data->timeinfo.nres_ter;
   int nres_nhc = class->therm_info_class.nres_nhc;
   double dt = general_data->timeinfo.dt;
   dti = dt/((double)(nres_ter*nres_tor*nres_tra));
   dti2 = dti/2.0;
   switch(ix_respa){
     case 1:
       class->therm_info_class.wght = (double)(nres_tra*nres_tor*nres_ter);
       break;
     case 2:
       class->therm_info_class.wght = (double)(nres_tra*nres_tor);
       break;
     case 3:
       class->therm_info_class.wght = (double)(nres_tra);
       break;
     case 4:
       class->therm_info_class.wght = 1.0;
       break;
   }
   class->therm_info_class.dt_nhc = dti;
   class->therm_info_class.dti_nhc = dti/( (double)(nres_nhc) );
   set_yosh(class->therm_info_class.nyosh_nhc,
            class->therm_info_class.dti_nhc,
            class->therm_info_class.wdti,
            class->therm_info_class.wdti2,
            class->therm_info_class.wdti4,
            class->therm_info_class.wdti8,
            class->therm_info_class.wdti16);
   zero_constrt_iters(&(general_data->stat_avg));
   for(ir_ter=1;ir_ter<=nres_ter;ir_ter++){
     for(ir_tor=1;ir_tor<=nres_tor;ir_tor++){
       for(ir_tra=1;ir_tra<=nres_tra;ir_tra++){
        int_0_to_dt2_nptf(class,bonded,general_data,ir_tra,ir_tor,ir_ter,dti);
        (class->energy_ctrl.iget_full_inter) = 0;
        (class->energy_ctrl.iget_res_inter) = 0;
        (class->energy_ctrl.iget_full_intra) = 0;
        (class->energy_ctrl.iget_res_intra) = 1;
        if((ir_ter==nres_ter)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra))
             {(class->energy_ctrl.iget_full_inter) = 1;}
        if((int_res_ter==1)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra))
             {(class->energy_ctrl.iget_res_inter) = 1;}
        if(ir_tra==nres_tra)
             {(class->energy_ctrl.iget_full_intra) = 1;}
        energy_control(class,bonded,general_data);
       int_dt2_to_dt_nptf(class,bonded,general_data,ir_tra,ir_tor,ir_ter,dti);
        }
     }
   }
   iflag=2;
   int_final_class(class,bonded,general_data,iflag);
  }

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: iflag int

variable_types: dti double

variable_types: iii int

variable_types: dt 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; }


original_code:
void int_NPTF_pimd(CLASS *class,BONDED *bonded,GENERAL_DATA *general_data,
                   ANALYSIS *analysis)
  {
  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 iii;
   int iflag;
   int ir_tra,ir_tor,ir_ter,ir_pimd;
   double dti;
   int pi_beads = class->clatoms_info.pi_beads;
   int pi_beads_proc = class->clatoms_info.pi_beads_proc;
   int comm_beads = class->communicate.comm_beads;
   int myid = class->communicate.myid;
   int ix_respa = general_data->timeinfo.ix_respa;
   int int_res_ter = general_data->timeinfo.int_res_ter;
   int nres_tra = general_data->timeinfo.nres_tra;
   int nres_tor = general_data->timeinfo.nres_tor;
   int nres_ter = general_data->timeinfo.nres_ter;
   int nres_pimd = general_data->timeinfo.nres_pimd;
   double dt = general_data->timeinfo.dt;
   int nres_nhc = class->therm_info_class.nres_nhc;
   int iperd = general_data->cell.iperd;
   int hmat_cons_typ = general_data->cell.hmat_cons_typ;
   int hmat_int_typ = general_data->cell.hmat_int_typ;
   double *vgmat = general_data->par_rahman.vgmat;
   double *hmat = general_data->cell.hmat;
   dti = dt/((double)(nres_ter*nres_tor*nres_tra*nres_pimd));
   if(general_data->timeinfo.ix_respa==1){
      class->therm_info_class.wght =
                     (double)(nres_pimd*nres_tra*nres_tor*nres_ter);
      class->therm_info_bead.wght =
                    (double)(nres_pimd*nres_tra*nres_tor*nres_ter);
   }
   if(ix_respa==2){
      class->therm_info_class.wght = (double)(nres_pimd*nres_tra*nres_tor);
      class->therm_info_bead.wght = (double)(nres_pimd*nres_tra*nres_tor);
   }
   if(ix_respa==3){
      class->therm_info_class.wght = (double)(nres_pimd*nres_tra);
      class->therm_info_bead.wght = (double)(nres_pimd*nres_tra);
   }
   if(ix_respa==4){
      class->therm_info_class.wght = (double)(nres_pimd);
      class->therm_info_bead.wght = (double)(nres_pimd);
   }
   if(ix_respa==5){
      class->therm_info_class.wght = 1.0;
      class->therm_info_bead.wght = 1.0;
   }
   class->therm_info_class.dt_nhc = dti;
   class->therm_info_bead.dt_nhc = dti;
   class->therm_info_class.dti_nhc = dti/( (double)(nres_nhc) );
   class->therm_info_bead.dti_nhc = dti/( (double)(nres_nhc) );
   set_yosh(class->therm_info_class.nyosh_nhc,
            class->therm_info_class.dti_nhc,
            class->therm_info_class.wdti,
            class->therm_info_class.wdti2,class->therm_info_class.wdti4,
            class->therm_info_class.wdti8,
            class->therm_info_class.wdti16);
   set_yosh(class->therm_info_bead.nyosh_nhc,
            class->therm_info_bead.dti_nhc,
            class->therm_info_bead.wdti,
            class->therm_info_bead.wdti2,class->therm_info_bead.wdti4,
            class->therm_info_bead.wdti8,
            class->therm_info_bead.wdti16);
   zero_constrt_iters(&(general_data->stat_avg));
   for(ir_ter=1;ir_ter<=nres_ter;ir_ter++){
      for(ir_tor=1;ir_tor<=nres_tor;ir_tor++){
        for(ir_tra=1;ir_tra<=nres_tra;ir_tra++){
        for(ir_pimd=1;ir_pimd<=nres_pimd;ir_pimd++){
          int_0_to_dt2_nptf_pimd(class,bonded,general_data,
                                 ir_tra,ir_tor,ir_ter,ir_pimd,dti);
          (class->energy_ctrl.iget_full_inter) = 0;
          (class->energy_ctrl.iget_res_inter) = 0;
          (class->energy_ctrl.iget_full_intra) = 0;
          (class->energy_ctrl.iget_res_intra) = 0;
          (class->energy_ctrl.iget_res_pimd) = 1;
          if((ir_ter==nres_ter)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra)
                               &&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_full_inter) = 1;}
          if((int_res_ter==1)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra)
                             &&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_res_inter) = 1;}
          if((ir_tra==nres_tra)&&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_full_intra) = 1;}
          if(ir_pimd == nres_pimd)
             {(class->energy_ctrl.iget_res_intra) = 1;}
          energy_control_pimd(class,bonded,general_data);
          int_dt2_to_dt_nptf_pimd(class,bonded,general_data,
                                  ir_tra,ir_tor,ir_ter,ir_pimd,dti);
        }
       }
     }
   }
    get_tvten_pimd(class,general_data);
    iflag = 2;
    nhc_vol_potkin_pimd(class,general_data,iflag);
   chck_constr_cell_mat(iperd,hmat_cons_typ,hmat_int_typ,vgmat,hmat,myid);
    }

canonical_original_code:
void int_NPTF_pimd(struct class *class, struct bonded *bonded, struct general_data *general_data, struct analysis *analysis)
  {
  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 iii;
   int iflag;
   int ir_tra; int ir_tor; int ir_ter; int ir_pimd;
   double dti;
   int pi_beads = class->clatoms_info.pi_beads;
   int pi_beads_proc = class->clatoms_info.pi_beads_proc;
   int comm_beads = class->communicate.comm_beads;
   int myid = class->communicate.myid;
   int ix_respa = general_data->timeinfo.ix_respa;
   int int_res_ter = general_data->timeinfo.int_res_ter;
   int nres_tra = general_data->timeinfo.nres_tra;
   int nres_tor = general_data->timeinfo.nres_tor;
   int nres_ter = general_data->timeinfo.nres_ter;
   int nres_pimd = general_data->timeinfo.nres_pimd;
   double dt = general_data->timeinfo.dt;
   int nres_nhc = class->therm_info_class.nres_nhc;
   int iperd = general_data->cell.iperd;
   int hmat_cons_typ = general_data->cell.hmat_cons_typ;
   int hmat_int_typ = general_data->cell.hmat_int_typ;
   double *vgmat = general_data->par_rahman.vgmat;
   double *hmat = general_data->cell.hmat;
   dti = dt/((double)(nres_ter*nres_tor*nres_tra*nres_pimd));
   if(general_data->timeinfo.ix_respa==1){
      class->therm_info_class.wght =
                     (double)(nres_pimd*nres_tra*nres_tor*nres_ter);
      class->therm_info_bead.wght =
                    (double)(nres_pimd*nres_tra*nres_tor*nres_ter);
   }
   if(ix_respa==2){
      class->therm_info_class.wght = (double)(nres_pimd*nres_tra*nres_tor);
      class->therm_info_bead.wght = (double)(nres_pimd*nres_tra*nres_tor);
   }
   if(ix_respa==3){
      class->therm_info_class.wght = (double)(nres_pimd*nres_tra);
      class->therm_info_bead.wght = (double)(nres_pimd*nres_tra);
   }
   if(ix_respa==4){
      class->therm_info_class.wght = (double)(nres_pimd);
      class->therm_info_bead.wght = (double)(nres_pimd);
   }
   if(ix_respa==5){
      class->therm_info_class.wght = 1.0;
      class->therm_info_bead.wght = 1.0;
   }
   class->therm_info_class.dt_nhc = dti;
   class->therm_info_bead.dt_nhc = dti;
   class->therm_info_class.dti_nhc = dti/( (double)(nres_nhc) );
   class->therm_info_bead.dti_nhc = dti/( (double)(nres_nhc) );
   set_yosh(class->therm_info_class.nyosh_nhc,
            class->therm_info_class.dti_nhc,
            class->therm_info_class.wdti,
            class->therm_info_class.wdti2,class->therm_info_class.wdti4,
            class->therm_info_class.wdti8,
            class->therm_info_class.wdti16);
   set_yosh(class->therm_info_bead.nyosh_nhc,
            class->therm_info_bead.dti_nhc,
            class->therm_info_bead.wdti,
            class->therm_info_bead.wdti2,class->therm_info_bead.wdti4,
            class->therm_info_bead.wdti8,
            class->therm_info_bead.wdti16);
   zero_constrt_iters(&(general_data->stat_avg));
   for(ir_ter=1;ir_ter<=nres_ter;ir_ter++){
      for(ir_tor=1;ir_tor<=nres_tor;ir_tor++){
        for(ir_tra=1;ir_tra<=nres_tra;ir_tra++){
        for(ir_pimd=1;ir_pimd<=nres_pimd;ir_pimd++){
          int_0_to_dt2_nptf_pimd(class,bonded,general_data,
                                 ir_tra,ir_tor,ir_ter,ir_pimd,dti);
          (class->energy_ctrl.iget_full_inter) = 0;
          (class->energy_ctrl.iget_res_inter) = 0;
          (class->energy_ctrl.iget_full_intra) = 0;
          (class->energy_ctrl.iget_res_intra) = 0;
          (class->energy_ctrl.iget_res_pimd) = 1;
          if((ir_ter==nres_ter)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra)
                               &&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_full_inter) = 1;}
          if((int_res_ter==1)&&(ir_tor==nres_tor)&&(ir_tra==nres_tra)
                             &&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_res_inter) = 1;}
          if((ir_tra==nres_tra)&&(ir_pimd==nres_pimd))
             {(class->energy_ctrl.iget_full_intra) = 1;}
          if(ir_pimd == nres_pimd)
             {(class->energy_ctrl.iget_res_intra) = 1;}
          energy_control_pimd(class,bonded,general_data);
          int_dt2_to_dt_nptf_pimd(class,bonded,general_data,
                                  ir_tra,ir_tor,ir_ter,ir_pimd,dti);
        }
       }
     }
   }
    get_tvten_pimd(class,general_data);
    iflag = 2;
    nhc_vol_potkin_pimd(class,general_data,iflag);
   chck_constr_cell_mat(iperd,hmat_cons_typ,hmat_int_typ,vgmat,hmat,myid);
    }

variable_types: struct analysis { struct info { int natm_real; int natm_ghost; int nmol_tot; int nmol_typ_real; int *nmol_jmol_typ_real; int *iatm_mol_typ_real; int *nmol_typ_atm_or_mol; double *masse_nmol_real; int nb_atm_typ_tot; int nb_atm_typ_ghost; int nb_atm_typ_real; int nb_atm_in_real_mol; int nb_mol_real_mol; int *natm_real_this_kind; int *natm_this_kind; int *natm_typ_real_or_ghost; int *map_atm_nb_to_atm_real_kind_nb; int *map_atm_nb_to_real_mol_or_atm; int *map_atm_nb_to_nmol_real_typ; int *nb_mol_real_jmol_typ; double *mass_real_mol; char (*name_real_mol)[50]; } info; struct pimd_bead { double **sc_op_x; double **sc_op_y; double **sc_op_z; double **sc_op_x2; double **sc_op_y2; double **sc_op_z2; double **sc_op_vx; double **sc_op_vy; double **sc_op_vz; double **sc_op_vx2; double **sc_op_vy2; double **sc_op_vz2; double ***bead_x; double ***bead_y; double ***bead_z; double ***bead_vx; double ***bead_vy; double ***bead_vz; } pimd_bead; struct rdf { int calcul_gr_on; int calcul_intra_on; int calcul_sq_from_gr_on; int njump; int periodic_write; int number_of_points; int nbk; double dr; double rmax; double dk; char *rdfname; int **iatm_pos; double *rbin; double *vol_diff; double ***rhist; double ***rhist_out; double ***gr; double ***sq; } rdf; struct velocorel { int calcul_atm_on; int ncor; int njump; int nwrite; int normalize; char *vovtname; char *output_kind; double **tmp_vtx; double **tmp_vty; double **tmp_vtz; double **vovtx; double **vovty; double **vovtz; int calcul_com_on; int ncor_com; int njump_com; int nwrite_com; int normalize_com; char *vovtname_com; char *output_kind_com; double **tmp_com_vtx; double **tmp_com_vty; double **tmp_com_vtz; double **com_vovtx; double **com_vovty; double **com_vovtz; } velocorel; struct msqdcorel { int calcul_atm_on; int ncor; int njump; char *msqdname; char *output_kind; double **tmp_msqdx; double **tmp_msqdy; double **tmp_msqdz; double **msqdx; double **msqdy; double **msqdz; } msqdcorel; struct eisf { int calcul_on; int eisf_on; } eisf; struct iikt_iso_corel { int calcul_on; int eisf_on; int ncor; int njump; int nbk_ask; int nb_kvecx; int nb_kvecy; int nb_kvecz; int full_iso; int calc_all_atm_typ; int natm_typ_calc; int natm_tot_calc; double kmin_ask; double kmax_ask; double kmin_calc_x; double kmin_calc_y; double kmin_calc_z; double dk_calc_x; double dk_calc_y; double dk_calc_z; int *natm_jmol_typ; int *map_calc_atm_on; int *map_calc_atm_typ; char *iikt_iso_name; char *output_kind; char (*list_atm_typ)[50]; double *kvec_x; double *kvec_y; double *kvec_z; double **tmp_0_tcosx; double **tmp_0_tcosy; double **tmp_0_tcosz; double **tmp_1_tcosx; double **tmp_1_tcosy; double **tmp_1_tcosz; double **tmp_0_tsinx; double **tmp_0_tsiny; double **tmp_0_tsinz; double **tmp_1_tsinx; double **tmp_1_tsiny; double **tmp_1_tsinz; double **ceisf_x; double **seisf_x; double **ceisf_y; double **seisf_y; double **ceisf_z; double **seisf_z; double **eisf_x; double **eisf_y; double **eisf_z; double ***ciikt_real_x; double ***ciikt_real_y; double ***ciikt_real_z; double ***ciikt_imag_x; double ***ciikt_imag_y; double ***ciikt_imag_z; } iikt_iso_corel; struct ickt_iso_corel { int calcul_on; int ncor; int njump; int nbk_ask; int nb_kvecx; int nb_kvecy; int nb_kvecz; int full_iso; double kmin_ask; double kmax_ask; double kmin_calc_x; double kmin_calc_y; double kmin_calc_z; double dk_calc_x; double dk_calc_y; double dk_calc_z; char *ickt_iso_name; double *kvec_x; double *kvec_y; double *kvec_z; double ***tmp_rho_real_x; double ***tmp_rho_real_y; double ***tmp_rho_real_z; double ***tmp_rho_imag_x; double ***tmp_rho_imag_y; double ***tmp_rho_imag_z; double ****cickt_real_x; double ****cickt_real_y; double ****cickt_real_z; double ****cickt_imag_x; double ****cickt_imag_y; double ****cickt_imag_z; } ickt_iso_corel; struct dip_self_corel { int calcul_on; int ncor; int njump; int normalize; char *momtname; char *output_kind; double **tmp_mx; double **tmp_my; double **tmp_mz; double **momtx; double **momty; double **momtz; } dip_self_corel; struct harmonic_analysis { int calcul_freq_on; int calcul_thermo_on; int calcul_spectra_on; int nfreqs; double delta; double *harm_freqs; } harmonic_analysis; } *

variable_types: myid int

variable_types: iperd int

variable_types:
vgmat
double *

variable_types:
hmat
double *

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 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 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 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 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 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; }