void reallocate_intra_list(CLATOMS_INFO *clatoms_info,GHOST_ATOMS *ghost_atoms,
ATOMMAPS *atommaps,
BUILD_INTRA *build_intra,BONDED *bonded,
NULL_INTER_PARSE *null_inter_parse,
int jmol_typ,
int nbond_pow_add,int nbond_con_add,int nbond_null_add,
int nbend_pow_add,int nbend_con_add,int nbend_null_add,
int ntors_pow_add,int ntors_con_add,int ntors_null_add,
int nonfo_add,int nonfo_null_add,int nbend_bnd_add,
int natm_add,int nghost_add,int nfreeze_add,int ngrp_43_add,
int ngrp_33_add,int ngrp_watt_33_add,int ngrp_21_add,
int ngrp_23_add,int ngrp_46_add)
/*==========================================================================*/
/* Begin routine */
{ /*begin routine */
/*==========================================================================*/
int nmol,nmol1,mem_add_now,iii;
int nfreeze_old,nfreeze_new;
int nghost_new,nghost_old,ncomp_new,ncomp_old;
/*==========================================================================*/
/* I) Reallocate the atoms */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*natm_add;
if(clatoms_info->natm_tot+nmol1 > build_intra->natm_tot_max){
mem_add_now = clatoms_info->natm_tot+nmol1 - build_intra->natm_tot_max;
build_intra->natm_tot_max += MAX(mem_add_now,NMEM_MIN);
clatoms_info->mass = (double *)crealloc(&((clatoms_info->mass[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->q = (double *)crealloc(&((clatoms_info->q[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->cp_vlnc_up = (int *)crealloc(&((clatoms_info->cp_vlnc_up[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->cp_vlnc_dn = (int *)crealloc(&((clatoms_info->cp_vlnc_dn[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->cp_atm_flag = (int *)crealloc(&((clatoms_info->cp_atm_flag[1])),
build_intra->natm_tot_max*
sizeof(int))-1;
clatoms_info->alp_pol = (double *)crealloc(&((clatoms_info->alp_pol[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->b_neut = (double *)crealloc(&((clatoms_info->b_neut[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
clatoms_info->text_atm =(double *)crealloc(&((clatoms_info->text_atm[1])),
build_intra->natm_tot_max*
sizeof(double))-1;
atommaps->iatm_mol_typ = (int *) crealloc(&(atommaps->iatm_mol_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_atm_typ = (int *) crealloc(&(atommaps->iatm_atm_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_res_typ = (int *) crealloc(&(atommaps->iatm_res_typ[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_mol_num = (int *) crealloc(&(atommaps->iatm_mol_num[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->iatm_res_num = (int *) crealloc(&(atommaps->iatm_res_num[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->ighost_flag = (int *)crealloc(&(atommaps->ighost_flag[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->freeze_flag = (int *)crealloc(&(atommaps->freeze_flag[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
atommaps->atom_label = (int *)crealloc(&(atommaps->atom_label[1]),
build_intra->natm_tot_max*
sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the ghosts */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nghost_add;
if(ghost_atoms->nghost_tot+nmol1 > build_intra->nghost_tot_max){
nghost_old = build_intra->nghost_tot_max;
ncomp_old = NCOEF_GHOST_MAX;
build_intra->nghost_tot_max+=
MAX((ghost_atoms->nghost_tot+nmol1-build_intra->nghost_tot_max),NMEM_MIN);
nghost_new = build_intra->nghost_tot_max;
ncomp_new = NCOEF_GHOST_MAX;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],
nghost_new*sizeof(int))-1;
ghost_atoms->natm_comp = (int *) crealloc(
&(ghost_atoms->natm_comp)[1],
nghost_new*sizeof(int))-1;
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new);
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new);
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the freeze */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nfreeze_add;
if(atommaps->nfreeze+nmol1 > build_intra->nfreeze_max){
nfreeze_old = build_intra->nfreeze_max;
build_intra->nfreeze_max+=
MAX((atommaps->nfreeze+nmol1-build_intra->nfreeze_max),NMEM_MIN);
nfreeze_new = build_intra->nfreeze_max;
atommaps->freeze_map = (int *) crealloc(
&(atommaps->freeze_map)[1],
nfreeze_new*sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
/* I) Reallocate the grpcons */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_21_add;
if(bonded->grp_bond_con.num_21+nmol1 > build_intra->ngrp_21_max){
build_intra->ngrp_21_max +=
MAX((bonded->grp_bond_con.num_21+nmol1-build_intra->ngrp_21_max),NMEM_MIN);
bonded->grp_bond_con.j1_21 =
(int *) crealloc(&(bonded->grp_bond_con.j1_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
bonded->grp_bond_con.j2_21 =
(int *) crealloc(&(bonded->grp_bond_con.j2_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_21 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_21)[1],
build_intra->ngrp_21_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_23_add;
if(bonded->grp_bond_con.num_23+nmol1 > build_intra->ngrp_23_max){
build_intra->ngrp_23_max +=
MAX((bonded->grp_bond_con.num_23+nmol1-build_intra->ngrp_23_max),NMEM_MIN);
bonded->grp_bond_con.j1_23 =
(int *) crealloc(&(bonded->grp_bond_con.j1_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.j2_23 =
(int *) crealloc(&(bonded->grp_bond_con.j2_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.j3_23 =
(int *) crealloc(&(bonded->grp_bond_con.j3_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_23 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_23)[1],
build_intra->ngrp_23_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_33_add;
if(bonded->grp_bond_con.num_33+nmol1 > build_intra->ngrp_33_max){
build_intra->ngrp_33_max +=
MAX((bonded->grp_bond_con.num_33+nmol1-build_intra->ngrp_33_max),NMEM_MIN);
bonded->grp_bond_con.j1_33 =
(int *) crealloc(&(bonded->grp_bond_con.j1_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.j2_33 =
(int *) crealloc(&(bonded->grp_bond_con.j2_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.j3_33 =
(int *) crealloc(&(bonded->grp_bond_con.j3_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_33)[1],
build_intra->ngrp_33_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_watt_33_add;
if(bonded->grp_bond_watts.num_33+nmol1 > build_intra->ngrp_watt_33_max){
build_intra->ngrp_watt_33_max +=
MAX((bonded->grp_bond_watts.num_33+nmol1-build_intra->ngrp_watt_33_max),
NMEM_MIN);
bonded->grp_bond_watts.j1_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j1_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.j2_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j2_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.j3_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j3_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
bonded->grp_bond_watts.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_watts.jtyp_33)[1],
build_intra->ngrp_watt_33_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_43_add;
if(bonded->grp_bond_con.num_43+nmol1 > build_intra->ngrp_43_max){
build_intra->ngrp_43_max +=
MAX((bonded->grp_bond_con.num_43+nmol1-build_intra->ngrp_43_max),NMEM_MIN);
bonded->grp_bond_con.j1_43 =
(int *) crealloc(&(bonded->grp_bond_con.j1_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j2_43 =
(int *) crealloc(&(bonded->grp_bond_con.j2_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j3_43 =
(int *) crealloc(&(bonded->grp_bond_con.j3_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.j4_43 =
(int *) crealloc(&(bonded->grp_bond_con.j4_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_43 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_43)[1],
build_intra->ngrp_43_max*sizeof(int))-1;
}/*endif*/
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*ngrp_46_add;
if(bonded->grp_bond_con.num_46+nmol1 > build_intra->ngrp_46_max){
build_intra->ngrp_46_max +=
MAX((bonded->grp_bond_con.num_46+nmol1-build_intra->ngrp_46_max),NMEM_MIN);
bonded->grp_bond_con.j1_46 =
(int *) crealloc(&(bonded->grp_bond_con.j1_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j2_46 =
(int *) crealloc(&(bonded->grp_bond_con.j2_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j3_46 =
(int *) crealloc(&(bonded->grp_bond_con.j3_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.j4_46 =
(int *) crealloc(&(bonded->grp_bond_con.j4_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
bonded->grp_bond_con.jtyp_46 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_46)[1],
build_intra->ngrp_46_max*sizeof(int))-1;
}/*endif*/
/*===========================================================================*/
/* I) Reallocate the bonds */
nmol = atommaps->nmol_jmol_typ[jmol_typ];
nmol1 = (nmol-1)*nbond_pow_add;
if(bonded->bond.npow+nmol1 > build_intra->nbond_pow_max){
build_intra->nbond_pow_max +=
MAX((bonded->bond.npow+nmol1-build_intra->nbond_pow_max),NMEM_MIN);
bonded->bond.j1_pow = (int *)crealloc(&(bonded->bond.j1_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
bonded->bond.j2_pow = (int *)crealloc(&(bonded->bond.j2_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
bonded->bond.jtyp_pow=(int *)crealloc(&(bonded->bond.jtyp_pow)[1],
build_intra->nbond_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbond_con_add;
if(bonded->bond.ncon+nmol1 > build_intra->nbond_con_max){
build_intra->nbond_con_max +=
MAX((bonded->bond.ncon+nmol1-build_intra->nbond_con_max),NMEM_MIN);
bonded->bond.j1_con = (int *)crealloc(&(bonded->bond.j1_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
bonded->bond.j2_con = (int *)crealloc(&(bonded->bond.j2_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
bonded->bond.jtyp_con=(int *)crealloc(&(bonded->bond.jtyp_con)[1],
build_intra->nbond_con_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbond_null_add;
if((null_inter_parse->nbond_nul)+nmol1 > build_intra->nbond_nul_max) {
build_intra->nbond_nul_max +=
MAX((null_inter_parse->nbond_nul+nmol1-build_intra->nbond_nul_max),NMEM_MIN);
null_inter_parse->jbond1_nul =
(int *) crealloc(&(null_inter_parse->jbond1_nul)[1],
build_intra->nbond_nul_max*sizeof(int))-1;
null_inter_parse->jbond2_nul =
(int *) crealloc(&(null_inter_parse->jbond2_nul)[1],
build_intra->nbond_nul_max*sizeof(int))-1;
} /*endif*/
/*====================================================================*/
/* II) Reallocate the bends */
nmol1 = (nmol-1)*nbend_pow_add;
if(bonded->bend.npow+nmol1 > build_intra->nbend_pow_max){
build_intra->nbend_pow_max +=
MAX((bonded->bend.npow+nmol1-build_intra->nbend_pow_max),NMEM_MIN);
bonded->bend.j1_pow =(int*)crealloc(&(bonded->bend.j1_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.j2_pow =(int*)crealloc(&(bonded->bend.j2_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.j3_pow =(int*)crealloc(&(bonded->bend.j3_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
bonded->bend.jtyp_pow=(int*)crealloc(&(bonded->bend.jtyp_pow)[1],
build_intra->nbend_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbend_con_add;
if(bonded->bend.ncon+nmol1 > build_intra->nbend_con_max){
build_intra->nbend_con_max +=
MAX((bonded->bend.ncon+nmol1-build_intra->nbend_con_max),NMEM_MIN);
bonded->bend.j1_con = (int *)crealloc(&(bonded->bend.j1_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bonded->bend.j2_con = (int *)crealloc(&(bonded->bend.j2_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
bonded->bend.jtyp_con=(int *)crealloc(&(bonded->bend.jtyp_con)[1],
build_intra->nbend_con_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nbend_null_add;
if(null_inter_parse->nbend_nul+nmol1 > build_intra->nbend_nul_max){
build_intra->nbend_nul_max +=
MAX((null_inter_parse->nbend_nul+nmol1-build_intra->nbend_nul_max),NMEM_MIN);
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;
} /*endif*/
/*====================================================================*/
/* IV) Reallocate the torsions */
nmol1 = (nmol-1)*ntors_pow_add;
if((bonded->tors.npow)+nmol1 > build_intra->ntors_pow_max){
build_intra->ntors_pow_max +=
MAX((bonded->tors.npow+nmol1-build_intra->ntors_pow_max),NMEM_MIN);
bonded->tors.j1_pow =(int*)crealloc(&(bonded->tors.j1_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j2_pow =(int*)crealloc(&(bonded->tors.j2_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j3_pow =(int*)crealloc(&(bonded->tors.j3_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.j4_pow =(int*)crealloc(&(bonded->tors.j4_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
bonded->tors.jtyp_pow=(int*)crealloc(&(bonded->tors.jtyp_pow)[1],
build_intra->ntors_pow_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*ntors_con_add;
if(bonded->tors.ncon+nmol1 > build_intra->ntors_con_max){
build_intra->ntors_con_max +=
MAX((bonded->tors.ncon+nmol1-build_intra->ntors_con_max),NMEM_MIN);
bonded->tors.j1_con = (int *) crealloc(&(bonded->tors.j1_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j2_con = (int *) crealloc(&(bonded->tors.j2_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j3_con = (int *) crealloc(&(bonded->tors.j3_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.j4_con = (int *) crealloc(&(bonded->tors.j4_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
bonded->tors.jtyp_con=(int *) crealloc(&(bonded->tors.jtyp_con)[1],
build_intra->ntors_con_max*sizeof(int))-1;
} /* endif */
nmol1 = (nmol-1)*ntors_null_add;
if(null_inter_parse->ntors_nul+nmol1 > build_intra->ntors_nul_max){
build_intra->ntors_nul_max +=
MAX((null_inter_parse->ntors_nul+nmol1-build_intra->ntors_nul_max),NMEM_MIN);
null_inter_parse->jtors1_nul =
(int *) crealloc(&(null_inter_parse->jtors1_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors2_nul =
(int *) crealloc(&(null_inter_parse->jtors2_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors3_nul =
(int *) crealloc(&(null_inter_parse->jtors3_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
null_inter_parse->jtors4_nul =
(int *) crealloc(&(null_inter_parse->jtors4_nul[1]),
build_intra->ntors_nul_max*sizeof(int))-1;
} /*endif*/
/*====================================================================*/
/* V) Reallocate the torsions */
nmol1 = (nmol-1)*nonfo_add;
if(bonded->onfo.num+nmol1 > build_intra->nonfo_max){
build_intra->nonfo_max +=
MAX((bonded->onfo.num+nmol1-build_intra->nonfo_max),NMEM_MIN);
bonded->onfo.j1 =(int *) crealloc(&(bonded->onfo.j1)[1],
build_intra->nonfo_max*sizeof(int))-1;
bonded->onfo.j2 =(int *) crealloc(&(bonded->onfo.j2)[1],
build_intra->nonfo_max*sizeof(int))-1;
bonded->onfo.jtyp =(int *) crealloc(&(bonded->onfo.jtyp)[1],
build_intra->nonfo_max*sizeof(int))-1;
}/*endif*/
nmol1 = (nmol-1)*nonfo_null_add;
if(null_inter_parse->nonfo_nul+nmol1 > build_intra->nonfo_nul_max){
build_intra->nonfo_nul_max +=
MAX((null_inter_parse->nonfo_nul+nmol1-build_intra->nonfo_nul_max),NMEM_MIN);
null_inter_parse->jonfo1_nul =
(int *) crealloc(&(null_inter_parse->jonfo1_nul)[1],
build_intra->nonfo_nul_max*sizeof(int))-1;
null_inter_parse->jonfo2_nul =
(int *) crealloc(&(null_inter_parse->jonfo2_nul)[1],
build_intra->nonfo_nul_max*sizeof(int))-1;
}/*endif*/
/*====================================================================*/
/* VI) Reallocate the Uri-Bradleys */
nmol1 = (nmol-1)*nbend_bnd_add;
if(bonded->bend_bnd.num+nmol1 > build_intra->nbend_bnd_max){
mem_add_now = bonded->bend_bnd.num+nmol1-build_intra->nbend_bnd_max;
build_intra->nbend_bnd_max += MAX(mem_add_now,NMEM_MIN);
bonded->bend_bnd.j1 =(int*)crealloc(&(bonded->bend_bnd.j1)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.j2 =(int*)crealloc(&(bonded->bend_bnd.j2)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.j3 =(int*)crealloc(&(bonded->bend_bnd.j3)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
bonded->bend_bnd.jtyp=(int*)crealloc(&(bonded->bend_bnd.jtyp)[1],
build_intra->nbend_bnd_max*sizeof(int))-1;
}/*endif*/
/*==========================================================================*/
} /*end routine*/
void set_ghost(MDGHOST_ATOMS *ghost_atoms,MDCLATOMS_INFO *clatoms_info,
MDATOM_MAPS *atommaps,BUILD_INTRA *build_intra,
DICT_WORD *atm_dict,int num_atm_dict,
char *filename,char *fun_key,int iatm_ind)
/*==========================================================================*/
{ /*begin routine*/
/*==========================================================================*/
/* Local Variables */
int nstrip=NCOEF_GHOST_MAX,imask;
int numg[NCOEF_GHOST_MAX1],index,i;
double anumg[NCOEF_GHOST_MAX1];
int nghost_old,ncomp_old,nghost;
int nghost_new,ncomp_new,ncomp,iii;
/*==========================================================================*/
/* I) Strip out indices of Ghost atoms */
ncomp = 0;index=16; /*INDEX for GHOST*/
for(i=1;i<=nstrip;i++){
if(atm_dict[index].iuset==0){break;}
ncomp = i;
strcpy(build_intra->strip1,atm_dict[index].keyarg);
parse_ghost(build_intra->strip1,build_intra->strip2,&numg[i],&anumg[i]);
index++;
}/*endfor*/
/*==========================================================================*/
/* II) Check Mask of indices making up Ghost atoms and rejigger them*/
index = 16;
for(i=1;i<=ncomp;i++){
if((numg[i]<=0)||(numg[i]>build_intra->natmind_1res_now)){
keyarg_barf(atm_dict,filename,fun_key,index);}
imask = build_intra->mask_atm[numg[i]];
if(imask==0){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("You have managed to nuke one of the atoms making \n");
PRINTF("up a ghost atom without nuking the ghost atom, \n");
PRINTF("itself, in residue file %s\n",filename);
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
numg[i] = build_intra->index_atm[numg[i]];
if(numg[i]>build_intra->natm_1res_now||numg[i]<0){
keyarg_barf(atm_dict,filename,fun_key,index);}
numg[i] += clatoms_info->natm_tot;
index++;
}/*endfor*/
/*==========================================================================*/
/* III) Memory allocation */
if(ncomp>0){
ghost_atoms->nghost_tot++;
build_intra->nghost_now++;
nghost = ghost_atoms->nghost_tot;
if(nghost > build_intra->nghost_tot_max){
nghost_old = build_intra->nghost_tot_max;
ncomp_old = NCOEF_GHOST_MAX;
build_intra->nghost_tot_max+=NMEM_MIN;
nghost_new = build_intra->nghost_tot_max;
ncomp_new = NCOEF_GHOST_MAX;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->natm_comp = (int *) crealloc(
&(ghost_atoms->natm_comp)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->ighost_map = (int *) crealloc(
&(ghost_atoms->ighost_map)[1],nghost_new*sizeof(int),"set_ghost")-1;
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new,"set_ghost");
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old,1,nghost_old,
1,ncomp_new,1,nghost_new,"set_ghost");
}/*endif*/
}/*endif*/
if(ncomp>NCOEF_GHOST_MAX){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("You have managed to use too many ghost_defs!!!\n");
PRINTF("Technical support was too tired to do the \n");
PRINTF("heinous work necessary to support an arbitray number.\n");
PRINTF("Wait for the next upgrade you power tool. \n");
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
/*==========================================================================*/
/* IV) Assign Ghosts parameters */
if(ncomp>0){
ghost_atoms->ighost_flag[iatm_ind] = nghost;
ghost_atoms->natm_comp_max = MAX(ghost_atoms->natm_comp_max,ncomp);
ghost_atoms->ighost_map[nghost] = iatm_ind;
ghost_atoms->natm_comp[nghost] = ncomp;
for(i=1;i<=ncomp;i++){
ghost_atoms->iatm_comp[i][nghost] = numg[i];
ghost_atoms->coef[i][nghost] = anumg[i];
}/*endfor*/
}/*endif*/
/*--------------------------------------------------------------------------*/
}/*end routine */
void close_intra_params(CLATOMS_INFO *clatoms_info,CLATOMS_POS *clatoms_pos,
GHOST_ATOMS *ghost_atoms,
ATOMMAPS *atommaps,
BUILD_INTRA *build_intra,
BONDED *bonded,
NULL_INTER_PARSE *null_inter_parse,
double *tot_memory,SIMOPTS *simopts,int np_forc)
/*=======================================================================*/
/* Begin routine */
{/*begin routine*/
/*=======================================================================*/
/* Local Variables */
int i,ntyp_pow,iii,nsec,inow,know;
double now_memory;
int natm_typ_mall;
int natm_mall;
int nghost_mall;
int nfreeze_mall;
int ncomp_mall;
int nchrg_mall;
int ngrp_21_mall;
int ngrp_typ_21_mall;
int ngrp_33_mall;
int ngrp_typ_33_mall;
int ngrp_watt_33_mall;
int ngrp_typ_watt_33_mall;
int ngrp_43_mall;
int ngrp_typ_43_mall;
int ngrp_23_mall;
int ngrp_typ_23_mall;
int ngrp_46_mall;
int ngrp_typ_46_mall;
int nbond_pow_mall;
int nbond_typ_pow_mall;
int nbond_con_mall;
int nbond_typ_con_mall;
int nbend_pow_mall;
int nbend_typ_pow_mall;
int nbend_con_mall;
int nbend_typ_con_mall;
int nbend_bnd_mall;
int nbend_bnd_typ_mall;
int ntors_pow_mall;
int ntors_typ_pow_mall;
int ntors_con_mall;
int ntors_typ_con_mall;
int nonfo_mall;
int nonfo_typ_mall;
int pimd_on;
int nghost_old,nfreeze_old,ncomp_old;
int pi_beads = clatoms_info->pi_beads;
int pimd_freez_typ = atommaps->pimd_freez_typ;
/*======================================================================*/
/* 0) Make the length of each vector an odd number */
nghost_old = build_intra->nghost_tot_max;
nfreeze_old = build_intra->nfreeze_max;
ncomp_old = NCOEF_GHOST_MAX;
natm_mall = clatoms_info->natm_tot;
natm_typ_mall = atommaps->natm_typ;
nghost_mall = ghost_atoms->nghost_tot;
nfreeze_mall = atommaps->nfreeze;
ncomp_mall = ghost_atoms->natm_comp_max;
ngrp_21_mall = bonded->grp_bond_con.num_21;
ngrp_33_mall = bonded->grp_bond_con.num_33;
ngrp_watt_33_mall = bonded->grp_bond_watts.num_33;
ngrp_43_mall = bonded->grp_bond_con.num_43;
ngrp_23_mall = bonded->grp_bond_con.num_23;
ngrp_46_mall = bonded->grp_bond_con.num_46;
ngrp_typ_21_mall = bonded->grp_bond_con.ntyp_21;
ngrp_typ_33_mall = bonded->grp_bond_con.ntyp_33;
ngrp_typ_watt_33_mall = bonded->grp_bond_watts.ntyp_33;
ngrp_typ_43_mall = bonded->grp_bond_con.ntyp_43;
ngrp_typ_23_mall = bonded->grp_bond_con.ntyp_23;
ngrp_typ_46_mall = bonded->grp_bond_con.ntyp_46;
nbond_pow_mall = bonded->bond.npow;
nbond_typ_pow_mall = bonded->bond.ntyp_pow;
nbond_con_mall = bonded->bond.ncon;
nbond_typ_con_mall = bonded->bond.ntyp_con;
nbend_pow_mall = bonded->bend.npow;
nbend_typ_pow_mall = bonded->bend.ntyp_pow;
nbend_con_mall = bonded->bend.ncon;
nbend_typ_con_mall = bonded->bend.ntyp_con;
nbend_bnd_mall = bonded->bend_bnd.num;
nbend_bnd_typ_mall = bonded->bend_bnd.ntyp;
ntors_pow_mall = bonded->tors.npow;
ntors_typ_pow_mall = bonded->tors.ntyp_pow;
ntors_con_mall = bonded->tors.ncon;
ntors_typ_con_mall = bonded->tors.ntyp_con;
nonfo_mall = bonded->onfo.num;
nonfo_typ_mall = bonded->onfo.ntyp;
if((natm_mall % 2)==0){natm_mall += 1;}
nsec=natm_mall/np_forc;
if((natm_mall%np_forc)!=0){nsec++;}
natm_mall = nsec*np_forc;
if((natm_typ_mall % 2)==0){natm_typ_mall += 1;}
if(((nghost_mall % 2)==0)
&&(nghost_mall !=0)){nghost_mall++;}
if(((nfreeze_mall % 2)==0)
&&(nfreeze_mall !=0)){nfreeze_mall++;}
if(((ncomp_mall % 2)==0)
&&(ncomp_mall !=0)){ncomp_mall++;}
if(((ngrp_21_mall % 2)==0)
&&(ngrp_21_mall !=0)){ngrp_21_mall++;}
if(((ngrp_33_mall % 2)==0)
&&(ngrp_33_mall !=0)){ngrp_33_mall++;}
if(((ngrp_watt_33_mall % 2)==0)
&&(ngrp_watt_33_mall !=0)){ngrp_watt_33_mall++;}
if(((ngrp_43_mall % 2)==0)
&&(ngrp_43_mall !=0)){ngrp_43_mall++;}
if(((ngrp_23_mall % 2)==0)
&&(ngrp_23_mall !=0)){ngrp_23_mall++;}
if(((ngrp_46_mall % 2)==0)
&&(ngrp_46_mall !=0)){ngrp_46_mall++;}
if(((ngrp_typ_21_mall % 2)==0)
&&(ngrp_typ_21_mall !=0)){ngrp_typ_21_mall++;}
if(((ngrp_typ_33_mall % 2)==0)
&&(ngrp_typ_33_mall !=0)){ngrp_typ_33_mall++;}
if(((ngrp_typ_watt_33_mall % 2)==0)
&&(ngrp_typ_watt_33_mall !=0)){ngrp_typ_watt_33_mall++;}
if(((ngrp_typ_43_mall % 2)==0)
&&(ngrp_typ_43_mall !=0)){ngrp_typ_43_mall++;}
if(((ngrp_typ_23_mall % 2)==0)
&&(ngrp_typ_23_mall !=0)){ngrp_typ_23_mall++;}
if(((ngrp_typ_46_mall % 2)==0)
&&(ngrp_typ_46_mall !=0)){ngrp_typ_46_mall++;}
if(((nbond_pow_mall % 2)==0)
&&(nbond_pow_mall !=0)){nbond_pow_mall += 1;}
if(((nbond_typ_pow_mall % 2)==0)
&&(nbond_typ_pow_mall !=0)){nbond_typ_pow_mall+= 1;}
if(((nbond_con_mall % 2)==0)
&&(nbond_con_mall !=0)){nbond_pow_mall += 1;}
if(((nbond_typ_con_mall % 2)==0)
&&(nbond_typ_con_mall !=0)){nbond_typ_pow_mall+= 1;}
if(((nbend_pow_mall % 2)==0)
&&(nbend_pow_mall !=0)){nbend_pow_mall += 1;}
if(((nbend_typ_pow_mall % 2)==0)
&&(nbend_typ_pow_mall !=0)){nbend_typ_pow_mall+= 1;}
if(((nbend_con_mall % 2)==0)
&&(nbend_con_mall !=0)){nbend_pow_mall += 1;}
if(((nbend_typ_con_mall % 2)==0)
&&(nbend_typ_con_mall !=0)){nbend_typ_pow_mall+= 1;}
if(((nbend_bnd_mall % 2)==0)
&&(nbend_bnd_mall !=0)){nbend_bnd_mall += 1;}
if(((nbend_bnd_typ_mall % 2)==0)
&&(nbend_bnd_typ_mall !=0)){nbend_bnd_typ_mall+= 1;}
if(((ntors_pow_mall % 2)==0)
&&(ntors_pow_mall !=0)){ntors_pow_mall += 1;}
if(((ntors_typ_pow_mall % 2)==0)
&&(ntors_typ_pow_mall !=0)){ntors_typ_pow_mall+= 1;}
if(((ntors_con_mall % 2)==0)
&&(ntors_con_mall !=0)){ntors_pow_mall += 1;}
if(((ntors_typ_con_mall % 2)==0)
&&(ntors_typ_con_mall !=0)){ntors_typ_pow_mall+= 1;}
if(((nonfo_mall % 2)==0)
&&(nonfo_mall !=0)){nonfo_mall += 1;}
if(((nonfo_typ_mall % 2)==0)
&&(nonfo_typ_mall !=0)){nonfo_typ_mall += 1;}
/*======================================================================*/
/* I) Atm stuff: Note constrain flag set here */
/* and charged atoms are counted */
bonded->constrnt.iconstrnt=0;
if(bonded->bond.ncon > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_21 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_23 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_33 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_watts.num_33 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_43 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->grp_bond_con.num_46 > 0) bonded->constrnt.iconstrnt=1;
if(bonded->bend.ncon > 0) bonded->constrnt.iconstrnt=1;
if(bonded->tors.ncon > 0) bonded->constrnt.iconstrnt=1;
clatoms_info->ichrg = (int *)cmalloc(natm_mall*sizeof(int))-1;
clatoms_info->nfree = 0;
clatoms_info->nfree_pimd = 0;
for(i=1;i<=atommaps->nmol_typ;i++){
inow = atommaps->nfree_1mol_jmol_typ[i]
*atommaps->nmol_jmol_typ[i];
know = 3*atommaps->natm_1mol_jmol_typ[i]
*atommaps->nmol_jmol_typ[i];
clatoms_info->nfree += inow;
if(pimd_freez_typ==2){
clatoms_info->nfree_pimd += inow*pi_beads;
}else{
clatoms_info->nfree_pimd += (inow + know*(pi_beads-1));
}/*endif*/
}/*endfor*/
clatoms_info->nchrg = 0;
for(i=1;i<=clatoms_info->natm_tot;i++){
clatoms_info->mass[i] *= PROT_MASS;
if(clatoms_info->q[i] != 0) {
clatoms_info->nchrg++;
clatoms_info->ichrg[(clatoms_info->nchrg)] = i;
}
}
nchrg_mall = clatoms_info->nchrg;
if((nchrg_mall % 2)==0){nchrg_mall += 1;}
now_memory = ((double)(((natm_mall)*sizeof(double)*13+sizeof(int)*4)+
natm_typ_mall*(sizeof(double)*0+sizeof(int)*25))
*1.e-06);
*tot_memory += now_memory;
printf("Atom allocation: %g Mbytes; Total memory: %g Mbytes\n",
now_memory,*tot_memory);
atommaps->atm_typ = (NAME *)crealloc(&(atommaps->atm_typ)[1],
natm_typ_mall*sizeof(NAME))-1;
clatoms_info->mass = (double *)crealloc(&(clatoms_info->mass)[1],
natm_mall*sizeof(double))-1;
clatoms_info->q = (double *)crealloc(&(clatoms_info->q)[1],
natm_mall*sizeof(double))-1;
clatoms_info->cp_vlnc_up = (int *)crealloc(&(clatoms_info->cp_vlnc_up)[1],
natm_mall*sizeof(int))-1;
clatoms_info->cp_vlnc_dn = (int *)crealloc(&(clatoms_info->cp_vlnc_dn)[1],
natm_mall*sizeof(int))-1;
clatoms_info->cp_atm_flag = (int *)crealloc(&(clatoms_info->cp_atm_flag)[1],
natm_mall*sizeof(int))-1;
clatoms_info->ichrg = (int *)crealloc(&(clatoms_info->ichrg)[1],
nchrg_mall*sizeof(int))-1;
clatoms_info->alp_pol = (double *)crealloc(&(clatoms_info->alp_pol)[1],
natm_mall*sizeof(double))-1;
clatoms_info->b_neut = (double *)crealloc(&(clatoms_info->b_neut)[1],
natm_mall*sizeof(double))-1;
clatoms_info->text_atm = (double *)crealloc(&(clatoms_info->text_atm)[1],
natm_mall*sizeof(double))-1;
atommaps->iatm_mol_typ = (int *)crealloc(&(atommaps->iatm_mol_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_atm_typ = (int *)crealloc(&(atommaps->iatm_atm_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_res_typ = (int *)crealloc(&(atommaps->iatm_res_typ)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_mol_num = (int *)crealloc(&(atommaps->iatm_mol_num)[1],
natm_mall*sizeof(int))-1;
atommaps->iatm_res_num = (int *)crealloc(&(atommaps->iatm_res_num)[1],
natm_mall*sizeof(int))-1;
pimd_on = simopts->pimd + simopts->cp_pimd
+ simopts->cp_wave_pimd + simopts->cp_wave_min_pimd
+ simopts->debug_pimd + simopts->debug_cp_pimd;
clatoms_info->xold= (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->yold= (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->zold= (double *)cmalloc(natm_mall*sizeof(double))-1;
if(pi_beads>1||pimd_on==1){
clatoms_info->xmod = (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->ymod = (double *)cmalloc(natm_mall*sizeof(double))-1;
clatoms_info->zmod = (double *)cmalloc(natm_mall*sizeof(double))-1;
}/*endif*/
if(clatoms_info->pi_beads>1||pimd_on==1){
clatoms_info->prekf = (double *)cmalloc(natm_mall*sizeof(double))-1;
}
clatoms_info->roll_sc = (double *)cmalloc(natm_mall*sizeof(double))-1;
/*========================================================================*/
/* I) Ghost_atm stuff */
ghost_atoms->ighost_map = (int *) crealloc(&(ghost_atoms->ighost_map)[1],
nghost_mall*sizeof(int))-1;
ghost_atoms->natm_comp = (int *) crealloc(&(ghost_atoms->natm_comp)[1],
nghost_mall*sizeof(int))-1;
atommaps->ighost_flag = (int *) crealloc(&(atommaps->ighost_flag)[1],
natm_mall*sizeof(int))-1;
/* need to set up reallocate matrix */
ghost_atoms->iatm_comp = creall_int_mat(ghost_atoms->iatm_comp,
1,ncomp_old ,1,nghost_old,
1,ncomp_mall,1,nghost_mall);
ghost_atoms->coef = creall_mat(ghost_atoms->coef,
1,ncomp_old ,1,nghost_old,
1,ncomp_mall,1,nghost_mall);
/*========================================================================*/
/* I) Freeze_atm stuff */
atommaps->freeze_map = (int *) crealloc(&(atommaps->freeze_map)[1],
nfreeze_mall*sizeof(int))-1;
atommaps->freeze_flag = (int *) crealloc(&(atommaps->freeze_flag)[1],
natm_mall*sizeof(int))-1;
atommaps->atom_label = (int *) crealloc(&(atommaps->atom_label)[1],
natm_mall*sizeof(int))-1;
/*========================================================================*/
/* II) Grp constrnts */
bonded->grp_bond_con.j1_21 =
(int *)crealloc(&(bonded->grp_bond_con.j1_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_21 =
(int *) crealloc(&(bonded->grp_bond_con.j2_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_21 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_21)[1],
ngrp_21_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_33 =
(int *)crealloc(&(bonded->grp_bond_con.j1_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_33 =
(int *) crealloc(&(bonded->grp_bond_con.j2_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_33 =
(int *) crealloc(&(bonded->grp_bond_con.j3_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_33)[1],
ngrp_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j1_33 =
(int *)crealloc(&(bonded->grp_bond_watts.j1_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j2_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j2_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.j3_33 =
(int *) crealloc(&(bonded->grp_bond_watts.j3_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.jtyp_33 =
(int *) crealloc(&(bonded->grp_bond_watts.jtyp_33)[1],
ngrp_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_23 =
(int *) crealloc(&(bonded->grp_bond_con.j1_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_23 =
(int *) crealloc(&(bonded->grp_bond_con.j2_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_23 =
(int *) crealloc(&(bonded->grp_bond_con.j3_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_23 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_23)[1],
ngrp_23_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_43 =
(int *)crealloc(&(bonded->grp_bond_con.j1_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_43 =
(int *) crealloc(&(bonded->grp_bond_con.j2_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_43 =
(int *) crealloc(&(bonded->grp_bond_con.j3_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j4_43 =
(int *) crealloc(&(bonded->grp_bond_con.j4_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_43 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_43)[1],
ngrp_43_mall*sizeof(int))-1;
bonded->grp_bond_con.j1_46 =
(int *) crealloc(&(bonded->grp_bond_con.j1_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j2_46 =
(int *) crealloc(&(bonded->grp_bond_con.j2_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j3_46 =
(int *) crealloc(&(bonded->grp_bond_con.j3_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.j4_46 =
(int *) crealloc(&(bonded->grp_bond_con.j4_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.jtyp_46 =
(int *) crealloc(&(bonded->grp_bond_con.jtyp_46)[1],
ngrp_46_mall*sizeof(int))-1;
bonded->grp_bond_con.al_21 = cmall_mat(1,1,1,ngrp_21_mall);
bonded->grp_bond_con.al_33 = cmall_mat(1,3,1,ngrp_33_mall);
bonded->grp_bond_con.al_43 = cmall_mat(1,3,1,ngrp_43_mall);
bonded->grp_bond_con.al_23 = cmall_mat(1,2,1,ngrp_23_mall);
bonded->grp_bond_con.al_46 = cmall_mat(1,6,1,ngrp_46_mall);
bonded->grp_bond_con.eq_21 = cmall_mat(1,1,1,ngrp_typ_21_mall);
bonded->grp_bond_con.eq_33 = cmall_mat(1,3,1,ngrp_typ_33_mall);
bonded->grp_bond_watts.eq_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_con.eq_43 = cmall_mat(1,3,1,ngrp_typ_43_mall);
bonded->grp_bond_con.eq_23 = cmall_mat(1,2,1,ngrp_typ_23_mall);
bonded->grp_bond_con.eq_46 = cmall_mat(1,6,1,ngrp_typ_46_mall);
bonded->grp_bond_watts.cos_thet0_2 =
(double *)malloc(ngrp_typ_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.sin_thet0_2 =
(double *)malloc(ngrp_typ_watt_33_mall*sizeof(int))-1;
bonded->grp_bond_watts.c_0_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_1_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_2_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_3_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_4_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_5_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.c_6_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_0_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_1_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_2_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_3_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_4_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_5_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
bonded->grp_bond_watts.dc_6_33 = cmall_mat(1,3,1,ngrp_typ_watt_33_mall);
/*======================================================================*/
/* II) Bonds */
now_memory = ((nbond_pow_mall)*(sizeof(double)*0+sizeof(int)*3)+
(nbond_con_mall)*(sizeof(double)*1 + sizeof(int)*3)+
(nbond_typ_pow_mall)*(sizeof(double)*14+ sizeof(int)*0 )+
(nbond_typ_con_mall)*(sizeof(double)*1 + sizeof(int)*0)+
(nbend_pow_mall)*(sizeof(double)*0 + sizeof(int)*4)+
(nbend_typ_pow_mall)*(sizeof(double)*29+ sizeof(int)*0)+
(nbend_con_mall)*(sizeof(double)*1 + sizeof(int)*4)+
(nbend_typ_con_mall)*(sizeof(double)*1 + sizeof(int)*0)+
(nbend_bnd_mall)*(sizeof(double)*0 + sizeof(int)*4)+
(nbend_bnd_typ_mall)*(sizeof(double)*44 + sizeof(int)*0)+
(ntors_pow_mall)*(sizeof(double)*0 + sizeof(int)*5)+
(ntors_con_mall)*(sizeof(double)*1 + sizeof(int)*5)+
(ntors_typ_pow_mall)*(sizeof(double)*30 + sizeof(int)*0)+
(nonfo_mall)*(sizeof(double)*0 + sizeof(int)*3)+
(nonfo_typ_mall)*(sizeof(double)*3 + sizeof(int)*0)
)*1.e-06;
*tot_memory += now_memory;
printf("Intramolecular allocation: %g Mbytes; Total memory: %g Mbytes\n",
now_memory,*tot_memory);
ntyp_pow = nbond_typ_pow_mall;
bonded->bond.j1_pow = (int *) crealloc(&(bonded->bond.j1_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.j2_pow = (int *) crealloc(&(bonded->bond.j2_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.jtyp_pow = (int *)crealloc(&(bonded->bond.jtyp_pow)[1],
nbond_pow_mall*sizeof(int))-1;
bonded->bond.j1_con = (int *) crealloc(&(bonded->bond.j1_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.j2_con = (int *) crealloc(&(bonded->bond.j2_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.jtyp_con = (int *)crealloc(&(bonded->bond.jtyp_con)[1],
nbond_con_mall*sizeof(int))-1;
bonded->bond.al_con = (double *)cmalloc(nbond_con_mall*sizeof(double))-1;
bonded->bond.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.eq_pow_res = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bond.eq_con = (double *)cmalloc(nbond_typ_con_mall
*sizeof(double))-1;
null_inter_parse->jbond1_nul= (int *)
crealloc(&(null_inter_parse->jbond1_nul)[1],
null_inter_parse->nbond_nul*sizeof(int))-1;
null_inter_parse->jbond2_nul= (int *)
crealloc(&(null_inter_parse->jbond2_nul)[1],
null_inter_parse->nbond_nul*sizeof(int))-1;
/*=======================================================================*/
/* III) Bends */
ntyp_pow = nbend_typ_pow_mall;
bonded->bend.j1_pow = (int *) crealloc(&(bonded->bend.j1_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j2_pow = (int *) crealloc(&(bonded->bend.j2_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j3_pow = (int *) crealloc(&(bonded->bend.j3_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.jtyp_pow = (int *)crealloc(&(bonded->bend.jtyp_pow)[1],
nbend_pow_mall*sizeof(int))-1;
bonded->bend.j1_con = (int *) crealloc(&(bonded->bend.j1_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.j2_con = (int *) crealloc(&(bonded->bend.j2_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.j3_con = (int *) crealloc(&(bonded->bend.j3_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.jtyp_con = (int *)crealloc(&(bonded->bend.jtyp_con)[1],
nbend_con_mall*sizeof(int))-1;
bonded->bend.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.s_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.ds_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->bend.eq_con = (double *)cmalloc(nbend_typ_con_mall
*sizeof(double))-1;
bonded->bend.al_con = (double *)cmalloc(nbend_con_mall
*sizeof(double))-1;
null_inter_parse->jbend1_nul= (int *)
crealloc(&(null_inter_parse->jbend1_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
null_inter_parse->jbend2_nul= (int *)
crealloc(&(null_inter_parse->jbend2_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
null_inter_parse->jbend3_nul= (int *)
crealloc(&(null_inter_parse->jbend3_nul)[1],
null_inter_parse->nbend_nul*sizeof(int))-1;
/*=======================================================================*/
/* III) Bend_bnds */
bonded->bend_bnd.j1 = (int *) crealloc(&(bonded->bend_bnd.j1)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.j2 = (int *) crealloc(&(bonded->bend_bnd.j2)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.j3 = (int *) crealloc(&(bonded->bend_bnd.j3)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.jtyp = (int *)crealloc(&(bonded->bend_bnd.jtyp)[1],
nbend_bnd_mall*sizeof(int))-1;
bonded->bend_bnd.eq_bond = (double *)cmalloc(nbend_bnd_typ_mall*
sizeof(double))-1;
bonded->bend_bnd.eq_bend = (double *)cmalloc(nbend_bnd_typ_mall*
sizeof(double))-1;
bonded->bend_bnd.cbond_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbond_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbond_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.cbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.sbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dcbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_0 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_1 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_2 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_3 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_4 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_5 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
bonded->bend_bnd.dsbend_6 = (double *)cmalloc(nbend_bnd_typ_mall
*sizeof(double))-1;
/*======================================================================*/
/* IV) Tors */
ntyp_pow = ntors_typ_pow_mall;
bonded->tors.j1_pow = (int *) crealloc(&(bonded->tors.j1_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j2_pow = (int *) crealloc(&(bonded->tors.j2_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j3_pow = (int *) crealloc(&(bonded->tors.j3_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j4_pow = (int *) crealloc(&(bonded->tors.j4_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.jtyp_pow = (int *)crealloc(&(bonded->tors.jtyp_pow)[1],
ntors_pow_mall*sizeof(int))-1;
bonded->tors.j1_con = (int *) crealloc(&(bonded->tors.j1_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j2_con = (int *) crealloc(&(bonded->tors.j2_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j3_con = (int *) crealloc(&(bonded->tors.j3_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.j4_con = (int *) crealloc(&(bonded->tors.j4_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.jtyp_con = (int *)crealloc(&(bonded->tors.jtyp_con)[1],
ntors_con_mall*sizeof(int))-1;
bonded->tors.al_con = (double *)cmalloc(ntors_con_mall
*sizeof(double))-1;
bonded->tors.eq_pow = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.c_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.s_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.dc_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_0 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_1 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_2 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_3 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_4 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_5 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.ds_6 = (double *)cmalloc(ntyp_pow*sizeof(double))-1;
bonded->tors.eq_con = (double *)cmalloc(ntors_typ_pow_mall
*sizeof(double))-1;
null_inter_parse->jtors1_nul= (int *)
crealloc(&(null_inter_parse->jtors1_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors2_nul= (int *)
crealloc(&(null_inter_parse->jtors2_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors3_nul= (int *)
crealloc(&(null_inter_parse->jtors3_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
null_inter_parse->jtors4_nul= (int *)
crealloc(&(null_inter_parse->jtors4_nul)[1],
null_inter_parse->ntors_nul*sizeof(int))-1;
/*=======================================================================*/
/* V) Onfo */
bonded->onfo.j1 = (int *) crealloc(&(bonded->onfo.j1)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.j2 = (int *) crealloc(&(bonded->onfo.j2)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.jtyp = (int *) crealloc(&(bonded->onfo.jtyp)[1],
nonfo_mall*sizeof(int))-1;
bonded->onfo.feps = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
bonded->onfo.s6 = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
bonded->onfo.sc = (double *)cmalloc(nonfo_typ_mall*sizeof(double))-1;
null_inter_parse->jonfo1_nul= (int *)
crealloc(&(null_inter_parse->jonfo1_nul)[1],
null_inter_parse->nonfo_nul*sizeof(int))-1;
null_inter_parse->jonfo2_nul = (int *)
crealloc(&(null_inter_parse->jonfo2_nul)[1],
null_inter_parse->nonfo_nul*sizeof(int))-1;
/*=======================================================================*/
/* V) Assign mall variables */
clatoms_info->natm_mall = natm_mall;
clatoms_info->nchrg_mall = nchrg_mall;
ghost_atoms->nghost_mall = nghost_mall;
ghost_atoms->ncomp_mall = ncomp_mall;
atommaps->nfreeze_mall = nfreeze_mall;
atommaps->natm_typ_mall = natm_typ_mall;
bonded->bond.nbond_pow_mall = nbond_pow_mall;
bonded->bond.nbond_typ_pow_mall = nbond_typ_pow_mall;
bonded->bond.nbond_con_mall = nbond_con_mall;
bonded->bond.nbond_typ_con_mall = nbond_typ_con_mall;
bonded->grp_bond_con.ngrp_21_mall = ngrp_21_mall;
bonded->grp_bond_watts.ngrp_33_mall = ngrp_watt_33_mall;
bonded->grp_bond_con.ngrp_33_mall = ngrp_33_mall;
bonded->grp_bond_con.ngrp_43_mall = ngrp_43_mall;
bonded->grp_bond_con.ngrp_23_mall = ngrp_23_mall;
bonded->grp_bond_con.ngrp_46_mall = ngrp_46_mall;
bonded->grp_bond_con.ngrp_typ_21_mall = ngrp_typ_21_mall;
bonded->grp_bond_con.ngrp_typ_33_mall = ngrp_typ_33_mall;
bonded->grp_bond_watts.ngrp_typ_33_mall = ngrp_typ_watt_33_mall;
bonded->grp_bond_con.ngrp_typ_43_mall = ngrp_typ_43_mall;
bonded->grp_bond_con.ngrp_typ_23_mall = ngrp_typ_23_mall;
bonded->grp_bond_con.ngrp_typ_46_mall = ngrp_typ_46_mall;
bonded->bend.nbend_con_mall = nbend_con_mall;
bonded->bend.nbend_typ_con_mall = nbend_typ_con_mall;
bonded->bend.nbend_pow_mall = nbend_pow_mall;
bonded->bend.nbend_typ_pow_mall = nbend_typ_pow_mall;
bonded->bend_bnd.nbend_bnd_mall = nbend_bnd_mall;
bonded->bend_bnd.nbend_bnd_typ_mall = nbend_bnd_typ_mall;
bonded->tors.ntors_pow_mall = ntors_pow_mall;
bonded->tors.ntors_typ_pow_mall = ntors_typ_pow_mall;
bonded->tors.ntors_con_mall = ntors_con_mall;
bonded->tors.ntors_typ_con_mall = ntors_typ_con_mall;
bonded->onfo.nonfo_mall = nonfo_mall;
bonded->onfo.nonfo_typ_mall = nonfo_typ_mall;
/*-----------------------------------------------------------------------*/
}/*end routine*/
