int main (int argc, char *argv[])
//==========================================================================
{// begin routine
//==========================================================================
// Local Variables
int pi_beads,ip,natm_tot;
int iextended_on,num_nhc,len_nhc;
MDINTEGRATE mdintegrate;
MDATOMS mdatoms;
MDINTER mdinter;
MDINTRA mdintra;
GENERAL_DATA general_data;
CP cp;
// classes to read in position data for leanMD
MDCLATOMS_POS *mdclatoms_pos;
MDTHERM_POS therm_class;
MDTHERM_POS *therm_bead;
//=======================================================================
// I) Check for input file
if(argc < 2) {
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf("No input file specified\n");
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}//endif
//=======================================================================
// II) Invoke User Interface
parse(&mdintegrate,&mdatoms,&mdinter,&mdintra,&general_data,&cp,argv[1]);
//=======================================================================
// III) output state of classes
#define DEBUG_PARSE
#ifdef DEBUG_PARSE
mdintegrate.state_class_out();
mdatoms.state_class_out();
mdinter.state_class_out();
mdintra.state_class_out();
general_data.state_class_out();
cp.state_class_out();
#endif
//=======================================================================
// IV) Allocate classes, read the coordinates
pi_beads = (mdatoms.mdclatoms_info.pi_beads);
natm_tot = (mdatoms.mdclatoms_info.natm_tot);
iextended_on = (mdintegrate.mdtherm_info.iextended_on);
mdclatoms_pos = (MDCLATOMS_POS *)
cmalloc(pi_beads*sizeof(MDCLATOMS_POS),"main.C")-1;
for(ip=1;ip<=pi_beads;ip++){
mdclatoms_pos[ip].natm_tot = natm_tot;
mdclatoms_pos[ip].x = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].y = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].z = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vx =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vy =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vz =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
}// endfor
therm_bead = (MDTHERM_POS *)
cmalloc(pi_beads*sizeof(MDTHERM_POS),"main.C")-1;
if(iextended_on==1){
num_nhc = (mdintegrate.mdtherm_info.num_nhc);
len_nhc = (mdintegrate.mdtherm_info.len_nhc);
therm_class.num_nhc = num_nhc;
therm_class.len_nhc = len_nhc;
therm_class.x_nhc = cmall_mat(1,len_nhc,1,num_nhc,"main.C");
therm_class.v_nhc = cmall_mat(1,len_nhc,1,num_nhc,"main.C");
}// endif
read_coord(&mdintegrate,&mdatoms,&mdinter,&mdintra,&general_data,&cp,
mdclatoms_pos,&therm_class,therm_bead);
//=======================================================================
// V) Exit, stage left
fflush(stdout);
fflush(stderr);
exit(0);
return 0;
//----------------------------------------------------------------------
}//end routine
void control_mol_params(MDINTEGRATE *mdintegrate, MDATOMS *mdatoms,
MDINTER *mdinter, GENERAL_DATA *general_data,
MDINTRA *mdintra,CP *cp,
CLASS_PARSE *class_parse,CP_PARSE *cp_parse,
FREE_PARSE *free_parse,
FILENAME_PARSE *filename_parse)
/*==========================================================================*/
{ /*begin routine*/
/*========================================================================*/
/* Local variable declarations */
#include "../class_defs/allclass_strip_mdatoms.h"
#include "../class_defs/allclass_strip_mdintegrate.h"
#include "../class_defs/allclass_strip_mdinter.h"
#include "../class_defs/allclass_strip_mdintra.h"
#include "../class_defs/allclass_strip_gen.h"
#include "../class_defs/allclass_strip_cp.h"
int i,iii,jmol_typ,nmol_tot;
int nmol_typ,bond_free_num,bend_free_num,tors_free_num,rbar_sig_free_iopt;
int ifirst,nline,nfun_key;
int num_user,num_def,cp_on;
double now_memory;
char *fun_key;
int nhist,nhist_bar,nhist_sig,nfree,nsurf;
FILE *fp;
DICT_MOL dict_mol; /* Dictionaries and sizes */
DICT_WORD *word;
char *molsetname = filename_parse->molsetname;
double *text_mol;
double *text_nhc_mol;
int *mol_freeze_opt;
int *imol_nhc_opt;
int *nmol_jmol_typ;
int pi_beads = mdatoms->mdclatoms_info.pi_beads;
int iextend,ipress;
iextend = (general_data->genensopts.nvt
+general_data->genensopts.npt_i
+general_data->genensopts.npt_f
+general_data->genensopts.nst);
ipress = (general_data->genensopts.npt_i
+general_data->genensopts.npt_f);
cp_on = general_data->gensimopts.cp_min
+ general_data->gensimopts.cp_wave_min
+ general_data->gensimopts.cp_wave_min_pimd
+ general_data->gensimopts.cp
+ general_data->gensimopts.cp_wave
+ general_data->gensimopts.cp_pimd
+ general_data->gensimopts.cp_wave_pimd
+ general_data->gensimopts.debug_cp
+ general_data->gensimopts.debug_cp_pimd;
/*========================================================================*/
/* 0) Output to screen */
PRINTF("\n"); PRINT_LINE_STAR;
PRINTF("Reading molecular set up file %s\n",molsetname);
PRINT_LINE_DASH;PRINTF("\n");
/*========================================================================*/
/* I) Set up dictionaries and malloc temporaries */
ifirst = 1;
set_molset_fun_dict(&dict_mol.fun_dict,&dict_mol.num_fun_dict);
set_mol_dict(&dict_mol.mol_dict,&dict_mol.num_mol_dict,
iextend,class_parse->tau_nhc_def,
general_data->genstatepoint.t_ext,ifirst);
set_wave_dict(&dict_mol.wave_dict,&dict_mol.num_wave_dict,cp_parse);
set_bond_free_dict(&dict_mol.bond_free_dict,&dict_mol.num_bond_free_dict);
set_bend_free_dict(&dict_mol.bend_free_dict,&dict_mol.num_bend_free_dict);
set_tors_free_dict(&dict_mol.tors_free_dict,&dict_mol.num_tors_free_dict);
set_rbar_free_dict(&dict_mol.rbar_free_dict,&dict_mol.num_rbar_free_dict);
set_user_base_dict(&dict_mol.user_base_dict,&dict_mol.num_user_base_dict);
set_def_base_dict(&dict_mol.def_base_dict,&dict_mol.num_def_base_dict);
set_surf_dict(&dict_mol.surface_dict,&dict_mol.num_surface_dict);
num_user = dict_mol.num_user_base_dict;
num_def = dict_mol.num_def_base_dict;
word = (DICT_WORD *)cmalloc(sizeof(DICT_WORD),"control_mol_params");
fun_key = (char *)cmalloc(MAXWORD*sizeof(char),"control_mol_params");
/*========================================================================*/
/* II) Read the moleset file and count the molecule types */
/* and the free energy stuff */
nmol_typ = 0;
nline = 0;
nfun_key = 0;
bond_free_num = 0;
bend_free_num = 0;
tors_free_num = 0;
rbar_sig_free_iopt = 0;
nsurf = 0;
fp = cfopen((const char *) molsetname,"r");
while(get_fun_key_cnt(fp,fun_key,&nline,&nfun_key,molsetname)){
if(!strcasecmp(fun_key,"molecule_def")) {nmol_typ+=1;}
if(!strcasecmp(fun_key,"bond_free_def")){bond_free_num+=1;}
if(!strcasecmp(fun_key,"bend_free_def")){bend_free_num+=1;}
if(!strcasecmp(fun_key,"tors_free_def")){tors_free_num+=1;}
if(!strcasecmp(fun_key,"rbar_sig_free_def")){rbar_sig_free_iopt+=1;}
if(!strcasecmp(fun_key,"surface_def")){nsurf+=1;}
}/*endwhile*/
fclose(fp);
mdatom_maps->nmol_typ = nmol_typ;
mdintra->mdbond_free.num = bond_free_num;
mdintra->mdbend_free.num = bend_free_num;
mdintra->mdtors_free.num = tors_free_num;
mdintra->mdrbar_sig_free.iopt = rbar_sig_free_iopt ;
mdintra->mdrbar_sig_free.nfree = 0;
if((bond_free_num+bend_free_num+tors_free_num+rbar_sig_free_iopt)>1){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("Only one free energy definition permitted\n");
PRINTF("in set up file %s \n",molsetname);
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
#ifdef JUNK
int iperd = general_data->gencell.iperd;
if( (nsurf>0) && (iperd != 2)){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("Surface potentials permitted ONLY in systems with\n");
PRINTF("2D periodicity in set up file %s \n",molsetname);
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
#endif
mdsurface->isurf_on = nsurf;
//========================================================================
// III) Malloc molecular data storage and initialize
now_memory = (double)((nmol_typ)*(sizeof(int)*2))*1.e-06;
(*tot_memory) += now_memory;
PRINTF("Allocating molecular memory: %g Mbytes; Total memory: %g Mbytes\n",
now_memory,(*tot_memory));
mdatom_maps->nmol_jmol_typ =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
mdatom_maps->mol_typ =
(NAME *)cmalloc(nmol_typ*sizeof(NAME),"control_mol_params")-1;
mdatom_maps->nres_1mol_jmol_typ =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
mdatom_maps->jres_jmol_typ_strt =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->ionfo_opt =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->ires_bond_conv =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->tau_nhc_mol =
(double*)cmalloc(nmol_typ*sizeof(double),"control_mol_params")-1;
class_parse->text_nhc_mol =
(double*)cmalloc(nmol_typ*sizeof(double),"control_mol_params")-1;
class_parse->imol_nhc_opt =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->mol_freeze_opt =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->mol_hydrog_mass_opt =
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
class_parse->mol_hydrog_mass_val =
(double *)cmalloc(nmol_typ*sizeof(double),"control_mol_params")-1;
class_parse->mol_hydrog_con_opt=
(int *)cmalloc(nmol_typ*sizeof(int),"control_mol_params")-1;
filename_parse->mol_param_name =
(NAME *)cmalloc(nmol_typ*sizeof(NAME),"control_mol_params")-1;
filename_parse->user_intra_name=
(NAME *)cmalloc(num_user*sizeof(NAME),"control_mol_params")-1;
filename_parse->def_intra_name =
(NAME *)cmalloc(num_def*sizeof(NAME),"control_mol_params")-1;
if(bond_free_num>0){
mdintra->mdbond_free.file =
(char *)cmalloc(MAXWORD*sizeof(char),"control_mol_params");
free_parse->imoltyp_bond_free=
(int *) cmalloc(2*sizeof(int),"control_mol_params")-1;
free_parse->imol_bond_free =
(int *) cmalloc(2*sizeof(int),"control_mol_params")-1;
free_parse->ires_bond_free =
(int *) cmalloc(2*sizeof(int),"control_mol_params")-1;
free_parse->iatm_bond_free =
(int *) cmalloc(2*sizeof(int),"control_mol_params")-1;
}
if(bend_free_num>0){
mdintra->mdbend_free.file =
(char *)cmalloc(MAXWORD*sizeof(char),"control_mol_params");
free_parse->imoltyp_bend_free=
(int *) cmalloc(3*sizeof(int),"control_mol_params")-1;
free_parse->imol_bend_free =
(int *) cmalloc(3*sizeof(int),"control_mol_params")-1;
free_parse->ires_bend_free =
(int *) cmalloc(3*sizeof(int),"control_mol_params")-1;
free_parse->iatm_bend_free =
(int *) cmalloc(3*sizeof(int),"control_mol_params")-1;
}
if(tors_free_num>0){
mdintra->mdtors_free.file =
(char *)cmalloc(MAXWORD*sizeof(char),"control_mol_params");
free_parse->imoltyp_tors_free=
(int *) cmalloc(8*sizeof(int),"control_mol_params")-1;
free_parse->imol_tors_free =
(int *) cmalloc(8*sizeof(int),"control_mol_params")-1;
free_parse->ires_tors_free =
(int *) cmalloc(8*sizeof(int),"control_mol_params")-1;
free_parse->iatm_tors_free =
(int *) cmalloc(8*sizeof(int),"control_mol_params")-1;
}
if(rbar_sig_free_iopt>0){
mdintra->mdrbar_sig_free.file =
(char *)cmalloc(MAXWORD*sizeof(char),"control_mol_params");
}
mdclatoms_info->text_mol =
(double*)cmalloc(nmol_typ*sizeof(double),"control_mol_params")-1;
text_mol = mdclatoms_info->text_mol;
text_nhc_mol = class_parse->text_nhc_mol;
mol_freeze_opt = class_parse->mol_freeze_opt;
imol_nhc_opt = class_parse->imol_nhc_opt;
/*========================================================================*/
/* IV) Get molecular/CP setup information */
control_set_mol_params(mdatom_maps,&(cp->cpopts),
&(cp->cpcoeffs_info),cp_parse,class_parse,
mdintra,mdsurface,
filename_parse,free_parse,
&dict_mol,word,
fun_key,&nfun_key,iextend,
general_data->genstatepoint.t_ext,
ifirst,pi_beads);
if(tors_free_num==1){
tors_free_num = mdintra->mdtors_free.num; /* changed in above routine */
}/*endif*/
for(i=1; i<= nmol_typ; i++){
text_mol[i] = text_nhc_mol[i];
}/*endfor*/
/*========================================================================*/
/* V) Free some memory and malloc some other */
if(bond_free_num>0){
nhist = (mdintra->mdbond_free.nhist);
mdintra->mdbond_free.hist =
(double *)cmalloc(nhist*sizeof(double),"control_mol_params")-1;
}/*endif*/
if(bend_free_num>0){
nhist = (mdintra->mdbend_free.nhist);
mdintra->mdbend_free.hist =
(double *)cmalloc(nhist*sizeof(double),"control_mol_params")-1;
}/*endif*/
if(tors_free_num==1){
nhist = (mdintra->mdtors_free.nhist);
mdintra->mdtors_free.hist =
(double *)cmalloc(nhist*sizeof(double),"control_mol_params")-1;
}/*endif*/
if(tors_free_num==2){
nhist = (mdintra->mdtors_free.nhist);
mdintra->mdtors_free.hist_2d = cmall_mat(1,nhist,1,nhist,"control_mol_params");
}/*endif*/
if(rbar_sig_free_iopt>0){
nhist_bar = (mdintra->mdrbar_sig_free.nhist_bar);
nhist_sig = (mdintra->mdrbar_sig_free.nhist_sig);
nfree = (mdintra->mdrbar_sig_free.nfree);
mdintra->mdrbar_sig_free.hist =
cmall_mat(1,nhist_bar,1,nhist_sig,"control_mol_params");
mdintra->mdrbar_sig_free.hist_rn =
cmall_mat(1,nfree,1,nhist_bar,"control_mol_params");
}/*endif*/
cfree(fun_key,"control_mol_params");
cfree(word,"control_mol_params");
cfree(&dict_mol.fun_dict[1],"control_mol_params");
cfree(&dict_mol.mol_dict[1],"control_mol_params");
cfree(&dict_mol.wave_dict[1],"control_mol_params");
cfree(&dict_mol.bond_free_dict[1],"control_mol_params");
cfree(&dict_mol.bend_free_dict[1],"control_mol_params");
cfree(&dict_mol.tors_free_dict[1],"control_mol_params");
cfree(&dict_mol.rbar_free_dict[1],"control_mol_params");
cfree(&dict_mol.user_base_dict[1],"control_mol_params");
cfree(&dict_mol.def_base_dict[1],"control_mol_params");
for(jmol_typ=1;jmol_typ<=nmol_typ;jmol_typ++){
if((mol_freeze_opt[jmol_typ] > 0) && (ipress > 0)){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("No freezing allowed with NPT_I and NPT_F \n");
PRINTF("Ensembles \n");
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
if((mol_freeze_opt[jmol_typ]==1)&&(imol_nhc_opt[jmol_typ] > 0)){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("Do not use thermostating when freezing the \n");
PRINTF("whole molecule.(Use none option) \n");
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}/*endif*/
}/*endfor*/
/*========================================================================*/
/* Error check */
nmol_tot = 0;
nmol_jmol_typ = mdatom_maps->nmol_jmol_typ;
for(i=1;i<=nmol_typ;i++){nmol_tot+= nmol_jmol_typ[i];}
if(cp_on==1 && cp->cpopts.cp_dual_grid_opt >= 1){
if(cp_parse->cp_ecut_dual_grid > cp_parse->cp_ecut){
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
PRINTF("The small dense grid cutoff is less than the large sparse");
PRINTF("grid cutoff. This might work, but I doubut it\n");
PRINTF("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
FFLUSH(stdout);
EXIT(1);
}
}
/*========================================================================*/
/* VI) Done */
PRINTF("The class contains %d molecule types\n",nmol_typ);
PRINTF("\n");
PRINT_LINE_DASH;
PRINTF("Completed reading molecular set up file %s\n",molsetname);
PRINT_LINE_STAR;
PRINTF("\n");
/*------------------------------------------------------------------------*/
}/*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*/
