void control_set_mol_params(ATOMMAPS *atommaps,CPOPTS *cpopts,
CPCOEFFS_INFO *cpcoeffs_info,CP_PARSE *cp_parse,
CLASS_PARSE *class_parse,
BONDED *bonded,SURFACE *surface,
FILENAME_PARSE *filename_parse,
FREE_PARSE *free_parse,
DICT_MOL *dict_mol,DICT_WORD *word,
char *fun_key,int *nfun_key,
int iextend,double t_ext,int ifirst,int pi_beads)
/*=======================================================================*/
{/*begin routine*/
/*=======================================================================*/
/* Local variable declarations */
int nline,nkey,i,num,ierr;
FILE *fp;
int *mol_ind_chk; /* Index check */
int *ifound;
int nmol_typ = atommaps->nmol_typ;
int *nmol_jmol_typ = atommaps->nmol_jmol_typ;
int *nres_1mol_jmol_typ = atommaps->nres_1mol_jmol_typ;
int num_fun_dict = dict_mol->num_fun_dict;
char *molsetname = filename_parse->molsetname;
int bond_free_num = bonded->bond_free.num;
int bend_free_num = bonded->bend_free.num;
int tors_free_num = bonded->tors_free.num;
int rbar_sig_free_iopt = bonded->rbar_sig_free.iopt;
int *imoltyp_rbar1_free;
int *imoltyp_rbar2_free;
int *imol_rbar1_free;
int *imol_rbar2_free;
int *ires_rbar1_free;
int *ires_rbar2_free;
int nbar_bond;
int *imoltyp_bond_free = free_parse->imoltyp_bond_free;
int *imol_bond_free = free_parse->imol_bond_free;
int *ires_bond_free = free_parse->ires_bond_free;
int *iatm_bond_free = free_parse->iatm_bond_free;
int *imoltyp_bend_free = free_parse->imoltyp_bend_free;
int *imol_bend_free = free_parse->imol_bend_free;
int *ires_bend_free = free_parse->ires_bend_free;
int *iatm_bend_free = free_parse->iatm_bend_free;
int *imoltyp_tors_free = free_parse->imoltyp_tors_free;
int *imol_tors_free = free_parse->imol_tors_free;
int *ires_tors_free = free_parse->ires_tors_free;
int *iatm_tors_free = free_parse->iatm_tors_free;
/*=======================================================================*/
/* 0) Set up molecular index checking memory */
mol_ind_chk = (int *) cmalloc(nmol_typ*sizeof(int))-1;
ifound = (int *) cmalloc(num_fun_dict*sizeof(int))-1;
for(i=1;i<=nmol_typ;i++){ mol_ind_chk[i]=0;}
for(i=1;i<=num_fun_dict;i++){ ifound[i]=0;}
/*=======================================================================*/
/* I) Fetch a valid functional key word from molset file */
fp = cfopen(molsetname,"r");
nline = 1;
*nfun_key = 0;
word->iuset = 0;
word->key_type = 0;
while(get_fun_key(fp,fun_key,&nline,nfun_key,molsetname)){
get_fun_key_index(fun_key,dict_mol->num_fun_dict,dict_mol->fun_dict,
nline,*nfun_key,molsetname,&num);
/*=======================================================================*/
/* II) Fetch the key words and key args of the functional key word */
/* and stick them into the correct dictionary */
if(num==1){
set_mol_dict(&(dict_mol->mol_dict),&(dict_mol->num_mol_dict),
iextend,class_parse->tau_nhc_def,t_ext,ifirst);
}
nkey=0;
while(get_word(fp,word,&nline,&nkey,*nfun_key,molsetname)){
switch(num){
case 1:
put_word_dict(word,dict_mol->mol_dict,dict_mol->num_mol_dict,
fun_key,nline,nkey,*nfun_key,molsetname);
break;
case 2:
put_word_dict(word,dict_mol->wave_dict,
dict_mol->num_wave_dict,fun_key,nline,nkey,
*nfun_key,molsetname);
break;
case 3:
put_word_dict(word,dict_mol->bond_free_dict,
dict_mol->num_bond_free_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 4:
put_word_dict(word,dict_mol->bend_free_dict,
dict_mol->num_bend_free_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 5:
put_word_dict(word,dict_mol->tors_free_dict,
dict_mol->num_tors_free_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 6:
put_word_dict(word,dict_mol->def_base_dict,
dict_mol->num_def_base_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 7:
put_word_dict(word,dict_mol->user_base_dict,
dict_mol->num_user_base_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 8:
put_word_dict(word,dict_mol->rbar_free_dict,
dict_mol->num_rbar_free_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
case 9:
put_word_dict(word,dict_mol->surface_dict,
dict_mol->num_surface_dict,fun_key,nline,
nkey,*nfun_key,molsetname);
break;
} /* end switch dictionary fills*/
} /* endwhile fetching keywords and keyargs*/
/*=====================================================================*/
/* III) Assign the key args of the key words to the appropriate */
/* program variables */
ifound[num]=1;
switch(num){
case 1:
set_mol_params(filename_parse,fun_key,dict_mol->mol_dict,
dict_mol->num_mol_dict,
class_parse,atommaps,mol_ind_chk,pi_beads);
break;
case 2:
set_wave_params(molsetname,fun_key,
dict_mol->wave_dict,dict_mol->num_wave_dict,
cpopts,cpcoeffs_info,cp_parse);
break;
case 3:
set_bond_free_params(molsetname,fun_key,
dict_mol->bond_free_dict,
dict_mol->num_bond_free_dict,
&(bonded->bond_free),free_parse,
atommaps->nmol_typ);
break;
case 4:
set_bend_free_params(molsetname,fun_key,
dict_mol->bend_free_dict,
dict_mol->num_bend_free_dict,
&(bonded->bend_free),free_parse,
atommaps->nmol_typ);
break;
case 5:
set_tors_free_params(molsetname,fun_key,
dict_mol->tors_free_dict,
dict_mol->num_tors_free_dict,
&(bonded->tors_free),free_parse,
atommaps->nmol_typ);
break;
case 6:
set_def_base_params(filename_parse,dict_mol->def_base_dict,
dict_mol->num_def_base_dict);
break;
case 7:
set_user_base_params(filename_parse,dict_mol->user_base_dict,
dict_mol->num_user_base_dict);
break;
case 8:
set_rbar_free_params(molsetname,fun_key,
dict_mol->rbar_free_dict,
dict_mol->num_rbar_free_dict,
&(bonded->rbar_sig_free),free_parse,
atommaps->nmol_typ);
break;
case 9:
set_surf_params(molsetname,fun_key,
dict_mol->surface_dict,
dict_mol->num_surface_dict,
surface);
break;
} /* end switch assigning dict stuff to variables */
} /*endwhile getting functional keywords data*/
/*=====================================================================*/
/* IV) Make sure everything that is required has been found */
/* if it hasn't either die or define defaults */
if(ifound[1]==0){
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf(" Required functional keyword %s not found \n",
dict_mol->fun_dict[1].keyword);
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}/*endif*/
if(ifound[6]==0){
set_def_base_params(filename_parse,dict_mol->def_base_dict,
dict_mol->num_def_base_dict);
}/*endif*/
if(ifound[7]==0){
set_user_base_params(filename_parse,dict_mol->user_base_dict,
dict_mol->num_user_base_dict);
}/*endif*/
/*=======================================================================*/
/* IV) Check indices */
for(i = 1;i<=nmol_typ;i++){
if(mol_ind_chk[i]!=1){
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@ \n");
printf("Molecule number %d specified %d times in file %s \n",
i,mol_ind_chk[i],molsetname);
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@ \n");
fflush(stdout);
exit(1);
}/*endif*/
} /*endfor*/
/*=======================================================================*/
/* V) Check free energy indices */
ierr = 0;
if(bond_free_num>0){
for(i=1;i<=2;i++){
if(imol_bond_free[i]>nmol_jmol_typ[imoltyp_bond_free[i]]){ierr=i;}
if(ires_bond_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_bond_free[i]],1))
{ierr=i;}
}/*endfor*/
}/*endif*/
if(bend_free_num>0){
for(i=1;i<=3;i++){
if(imol_bend_free[i]>nmol_jmol_typ[imoltyp_bend_free[i]]){ierr=i;}
if(ires_bend_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_bend_free[i]],1))
{ierr=i;}
}/*endfor*/
}/*endif*/
if(tors_free_num>0){tors_free_num=bonded->tors_free.num;}
if(tors_free_num==1){
for(i=1;i<=4;i++){
if(imol_tors_free[i]>nmol_jmol_typ[imoltyp_tors_free[i]]){ierr=i;}
if(ires_tors_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_tors_free[i]],1))
{ierr=i;}
}/*endfor*/
}/*endif*/
if(tors_free_num==2){
for(i=1;i<=8;i++){
if(imol_tors_free[i]>nmol_jmol_typ[imoltyp_tors_free[i]]){ierr=i;}
if(ires_tors_free[i]>MAX(nres_1mol_jmol_typ[imoltyp_tors_free[i]],1))
{ierr=i;}
}/*endfor*/
}/*endif*/
if(rbar_sig_free_iopt>0){
imoltyp_rbar1_free = free_parse->imoltyp_rbar1_free;
imoltyp_rbar2_free = free_parse->imoltyp_rbar2_free;
imol_rbar1_free = free_parse->imol_rbar1_free;
imol_rbar2_free = free_parse->imol_rbar2_free;
ires_rbar1_free = free_parse->ires_rbar1_free;
ires_rbar2_free = free_parse->ires_rbar2_free;
nbar_bond = free_parse->nbar_bond;
for(i=1;i<=nbar_bond;i++){
if(imol_rbar1_free[i]>nmol_jmol_typ[imoltyp_rbar1_free[i]]){ierr=1;}
if(imol_rbar2_free[i]>nmol_jmol_typ[imoltyp_rbar2_free[i]]){ierr=2;}
if(ires_rbar1_free[i]>
MAX(nres_1mol_jmol_typ[imoltyp_rbar1_free[i]],1)){ierr=1;}
if(ires_rbar2_free[i]>
MAX(nres_1mol_jmol_typ[imoltyp_rbar2_free[i]],1)){ierr=2;}
}/*endfor*/
}/*endif*/
if(ierr>0){
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf("Error specifing the %dth atom in a free energy def \n",ierr);
printf("in set up file %s \n",molsetname);
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}/*endif*/
/*=======================================================================*/
/* VI) Free memory */
cfree(&mol_ind_chk[1]);
cfree(&ifound[1]);
/*-----------------------------------------------------------------------*/
}/*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*/
