timlim=60.0D0*timlim
safety = 60.0d0*safety
modecalc=0
+ call readi(controlcard,"INTER_LIST_UPDATE",imatupdate,100)
call reada(controlcard,"T_BATH",t_bath,300.0d0)
minim=(index(controlcard,'MINIMIZE').gt.0)
dccart=(index(controlcard,'CART').gt.0)
overlapsc=(index(controlcard,'OVERLAP').gt.0)
overlapsc=.not.overlapsc
- searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
- searchsc=.not.searchsc
+ searchsc=(index(controlcard,'SEARCHSC').gt.0 .and.
+ & index(controlcard,'NOSEARCHSC').eq.0)
sideadd=(index(controlcard,'SIDEADD').gt.0)
energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
mremd_dec=(index(controlcard,'MREMD_DEC').gt.0)
call reada(controlcard,'BOXX',boxxsize,100.0d0)
call reada(controlcard,'BOXY',boxysize,100.0d0)
call reada(controlcard,'BOXZ',boxzsize,100.0d0)
+ write(iout,*) "Periodic box dimensions",boxxsize,boxysize,boxzsize
c Cutoff range for interactions
- call reada(controlcard,"R_CUT",r_cut,15.0d0)
+ call reada(controlcard,"R_CUT_INT",r_cut_int,25.0d0)
+ call reada(controlcard,"R_CUT_RESPA",r_cut_respa,2.0d0)
call reada(controlcard,"LAMBDA",rlamb,0.3d0)
+ write (iout,*) "Cutoff on interactions",r_cut_int
+ write (iout,*)
+ & "Cutoff in switching short and long range interactions in RESPA",
+ & r_cut_respa
+ write (iout,*) "lambda in switch function",rlamb
call reada(controlcard,"LIPTHICK",lipthick,0.0d0)
call reada(controlcard,"LIPAQBUF",lipbufthick,0.0d0)
if (lipthick.gt.0.0d0) then
& "Initial time step of numerical integration:",d_time,
& " natural units"
write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
+ write (iout,'(a60,f10.5,a)') "Cutoff on interactions",r_cut_int,
+ & " A"
+ write(iout,'(a60,i5)')"Frequency of updating interaction list",
+ & imatupdate
if (RESPA) then
write (iout,'(2a,i4,a)')
& "A-MTS algorithm used; initial time step for fast-varying",
& " short-range forces split into",ntime_split," steps."
write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
- & r_cut," lambda",rlamb
+ & r_cut_respa," lambda",rlamb
endif
write (iout,'(2a,f10.5)')
& "Maximum acceleration threshold to reduce the time step",
character*24 model_ki_dist, model_ki_angle
character*500 controlcard
integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec,
- & ik,iistart,iishift
+ & ik,iistart
integer ilen
external ilen
- logical liiflag
+ logical liiflag,lfirst
+ integer i01,i10
c
c FP - Nov. 2014 Temporary specifications for new vars
c
enddo
lim_odl=ii
endif
+c write (iout,*) "Distance restraints set"
+c call flush(iout)
c
c Theta, dihedral and SC retraints
c
enddo
lim_dih=nct-nnt-2
endif
+c write (iout,*) "Dihedral angle restraints set"
+c call flush(iout)
if (waga_theta.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_theta,status='old')
c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i)
enddo
endif
+c write (iout,*) "Angle restraints set"
+c call flush(iout)
if (waga_d.gt.0.0d0) then
c open (ientin,file=tpl_k_sigma_d,status='old')
enddo
endif
enddo
+c write (iout,*) "SC restraints set"
+c call flush(iout)
c
c remove distance restraints not used in any model from the list
c shift data in all arrays
c
+c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct
if (waga_dist.ne.0.0d0) then
ii=0
liiflag=.true.
+ lfirst=.true.
do i=nnt,nct-2
do j=i+2,nct
ii=ii+1
- if (ii_in_use(ii).eq.0.and.liiflag) then
+c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0
+c & .and. distal.le.dist2_cut ) then
+c write (iout,*) "i",i," j",j," ii",ii
+c call flush(iout)
+ if (ii_in_use(ii).eq.0.and.liiflag.or.
+ & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then
liiflag=.false.
- iistart=ii
+ i10=ii
+ if (lfirst) then
+ lfirst=.false.
+ iistart=ii
+ else
+ if(i10.eq.lim_odl) i10=i10+1
+ do ki=0,i10-i01-1
+ ires_homo(iistart+ki)=ires_homo(ki+i01)
+ jres_homo(iistart+ki)=jres_homo(ki+i01)
+ ii_in_use(iistart+ki)=ii_in_use(ki+i01)
+ do k=1,constr_homology
+ odl(k,iistart+ki)=odl(k,ki+i01)
+ sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01)
+ l_homo(k,iistart+ki)=l_homo(k,ki+i01)
+ enddo
+ enddo
+ iistart=iistart+i10-i01
+ endif
endif
- if (ii_in_use(ii).ne.0.and..not.liiflag.or.
- & .not.liiflag.and.ii.eq.lim_odl) then
- if (ii.eq.lim_odl) then
- iishift=ii-iistart+1
- else
- iishift=ii-iistart
- endif
+ if (ii_in_use(ii).ne.0.and..not.liiflag) then
+ i01=ii
liiflag=.true.
- do ki=iistart,lim_odl-iishift
- ires_homo(ki)=ires_homo(ki+iishift)
- jres_homo(ki)=jres_homo(ki+iishift)
- ii_in_use(ki)=ii_in_use(ki+iishift)
- do k=1,constr_homology
- odl(k,ki)=odl(k,ki+iishift)
- sigma_odl(k,ki)=sigma_odl(k,ki+iishift)
- l_homo(k,ki)=l_homo(k,ki+iishift)
- enddo
- enddo
- ii=ii-iishift
- lim_odl=lim_odl-iishift
endif
enddo
enddo
+ lim_odl=iistart-1
endif
-
+c write (iout,*) "Removing distances completed"
+c call flush(iout)
endif ! .not. klapaucjusz
if (constr_homology.gt.0) call homology_partition
+c write (iout,*) "After homology_partition"
+c call flush(iout)
if (constr_homology.gt.0) call init_int_table
-c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
-c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c write (iout,*) "After init_int_table"
+c call flush(iout)
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
c
c Print restraints
c
enddo
enddo
call int_from_cart(.true.,.false.)
- call sc_loc_geom(.true.)
+ call sc_loc_geom(.false.)
do i=1,nres
thetaref(i)=theta(i)
phiref(i)=phi(i)
projects / unres.git / blobdiff