igeom= 8
intin= 9
ithep= 11
+ ithep_pdb=51
irotam=12
+ irotam_pdb=52
itorp= 13
itordp= 23
ielep= 14
icsa_in=40
crc for ifc error 118
icsa_pdb=42
+C Lipidic input file for parameters range 60-79
+ iliptranpar=60
+C input file for transfer sidechain and peptide group inside the
+C lipidic environment if lipid is implicite
+
+C DNA input files for parameters range 80-99
+C Suger input files for parameters range 100-119
+C All-atom input files for parameters range 120-149
C
C Set default weights of the energy terms.
C
enddo
do i=1,ntyp
do j=1,ntyp
- aa(i,j)=0.0D0
- bb(i,j)=0.0D0
+ aa_aq(i,j)=0.0D0
+ bb_aq(i,j)=0.0D0
+ aa_lip(i,j)=0.0D0
+ bb_lip(i,j)=0.0D0
augm(i,j)=0.0D0
sigma(i,j)=0.0D0
r0(i,j)=0.0D0
rr0(i)=0.0D0
a0thet(i)=0.0D0
do j=1,2
- athet(j,i)=0.0D0
- bthet(j,i)=0.0D0
+ do ichir1=-1,1
+ do ichir2=-1,1
+ athet(j,i,ichir1,ichir2)=0.0D0
+ bthet(j,i,ichir1,ichir2)=0.0D0
+ enddo
+ enddo
enddo
do j=0,3
polthet(j,i)=0.0D0
enddo
nlob(ntyp1)=0
dsc(ntyp1)=0.0D0
- do i=1,maxtor
+ do i=-maxtor,maxtor
itortyp(i)=0
- do j=1,maxtor
+cc write (iout,*) "TU DOCHODZE",i,itortyp(i)
+ do iblock=1,2
+ do j=-maxtor,maxtor
do k=1,maxterm
- v1(k,j,i)=0.0D0
- v2(k,j,i)=0.0D0
+ v1(k,j,i,iblock)=0.0D0
+ v2(k,j,i,iblock)=0.0D0
enddo
enddo
enddo
+ enddo
+ do iblock=1,2
+ do i=-maxtor,maxtor
+ do j=-maxtor,maxtor
+ do k=-maxtor,maxtor
+ do l=1,maxtermd_1
+ v1c(1,l,i,j,k,iblock)=0.0D0
+ v1s(1,l,i,j,k,iblock)=0.0D0
+ v1c(2,l,i,j,k,iblock)=0.0D0
+ v1s(2,l,i,j,k,iblock)=0.0D0
+ enddo !l
+ do l=1,maxtermd_2
+ do m=1,maxtermd_2
+ v2c(m,l,i,j,k,iblock)=0.0D0
+ v2s(m,l,i,j,k,iblock)=0.0D0
+ enddo !m
+ enddo !l
+ enddo !k
+ enddo !j
+ enddo !i
+ enddo !iblock
+
do i=1,maxres
itype(i)=0
itel(i)=0
ihpb(i)=0
jhpb(i)=0
enddo
+C Initialize correlation arrays
+ do i=1,maxres
+ do k=1,2
+ b1(k,i)=0.0
+ b2(k,i)=0.0
+ b1tilde(k,i)=0.0
+c b2tilde(k,i)=0.0
+ do j=1,2
+C CC(j,k,i)=0.0
+C Ctilde(j,k,i)=0.0
+C DD(j,k,i)=0.0
+C Dtilde(j,k,i)=0.0
+ EE(j,k,i)=0.0
+ enddo
+ enddo
+ enddo
+ do i=-maxtor,maxtor
+ do k=1,2
+ do j=1,2
+ CC(j,k,i)=0.0
+ Ctilde(j,k,i)=0.0
+ DD(j,k,i)=0.0
+ Dtilde(j,k,i)=0.0
+ enddo
+ enddo
+ enddo
C
C Initialize timing.
C
C Initialize constants used to split the energy into long- and short-range
C components
C
- r_cut=2.0d0
- rlamb=0.3d0
+C r_cut=2.0d0
+C rlamb=0.3d0
#ifndef SPLITELE
nprint_ene=nprint_ene-1
#endif
include 'COMMON.NAMES'
include 'COMMON.FFIELD'
data restyp /
+ &'DD','DAU','DAI','DDB','DSM','DPR','DLY','DAR','DHI','DAS','DGL',
+ & 'DSG','DGN','DSN','DTH',
+ &'DYY','DAL','DTY','DTR','DVA','DLE','DIL','DPN','MED','DCY','ZER',
&'CYS','MET','PHE','ILE','LEU','VAL','TRP','TYR','ALA','GLY','THR',
- &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','D'/
+ &'SER','GLN','ASN','GLU','ASP','HIS','ARG','LYS','PRO','SME','DBZ',
+ &'AIB','ABU','D'/
data onelet /
+ &'z','z','z','z','z','p','k','r','h','d','e','n','q','s','t','g',
+ &'a','y','w','v','l','i','f','m','c','x',
&'C','M','F','I','L','V','W','Y','A','G','T',
- &'S','Q','N','E','D','H','R','K','P','X'/
+ &'S','Q','N','E','D','H','R','K','P','z','z','z','z','X'/
data potname /'LJ','LJK','BP','GB','GBV'/
data ename /
& "EVDW SC-SC","EVDW2 SC-p","EES p-p","ECORR4 ","ECORR5 ",
& "ECORR6 ","EELLO ","ETURN3 ","ETURN4 ","ETURN6 ",
& "EBE bend","ESC SCloc","ETORS ","ETORSD ","EHPB ","EVDWPP ",
- & "ESTR ","EVDW2_14 ","UCONST ", " ","ESCCOR"/
+ & "ESTR ","EVDW2_14 ","UCONST ", "EDIHC ","ESCCOR",
+ & "Eliptran","Eafmforce","Ehomology","ESAXS"/
data wname /
& "WSC","WSCP","WELEC","WCORR","WCORR5","WCORR6","WEL_LOC",
& "WTURN3","WTURN4","WTURN6","WANG","WSCLOC","WTOR","WTORD",
- & "WSTRAIN","WVDWPP","WBOND","SCAL14"," "," ","WSCCOR"/
- data nprint_ene /20/
+ & "WSTRAIN","WVDWPP","WBOND","SCAL14","WDIHCSN"," ","WSCCOR",
+ & "Wliptran","WAFM ","EHOMO","WSAXS"/
+ data nprint_ene /25/
data print_order/1,2,3,11,12,13,14,4,5,6,7,8,9,10,19,18,15,17,16,
- & 21,0/
+ & 21,24,22,23,20,25/
end
c---------------------------------------------------------------------------
subroutine init_int_table
call int_bounds(nres-2,ithet_start,ithet_end)
ithet_start=ithet_start+2
ithet_end=ithet_end+2
+ call int_bounds(nsaxs,isaxs_start,isaxs_end)
+c isaxs_start=isaxs_start+nnt-1
+c isaxs_end=isaxs_end+nnt-1
+ write (iout,*) me," isaxs_start",isaxs_start,
+ & " isaxs_end",isaxs_end
call int_bounds(nct-nnt-2,iturn3_start,iturn3_end)
iturn3_start=iturn3_start+nnt
iphi_start=iturn3_start+2
call int_bounds(nct-nnt,ibondp_start,ibondp_end)
ibondp_start=ibondp_start+nnt
ibondp_end=ibondp_end+nnt
+ call int_bounds(nres,ilip_start,ilip_end)
+ ilip_start=ilip_start
call int_bounds1(nres-1,ivec_start,ivec_end)
c print *,"Processor",myrank,fg_rank,fg_rank1,
c & " ivec_start",ivec_start," ivec_end",ivec_end
iaux=iphi1_end-iphi1_start+1
call MPI_Allgather(iaux,1,MPI_INTEGER,iphi1_count(0),1,
& MPI_INTEGER,FG_COMM,IERROR)
- do i=0,maxprocs-1
+ write (iout,*) "ielstart before zeroing out",max_fg_procs
+ call flush (iout)
+ do i=0,max_fg_procs-1
do j=1,maxres
ielstart_all(j,i)=0
ielend_all(j,i)=0
enddo
enddo
+ write (iout,*) "ielstart zeroed out"
+ call flush (iout)
call MPI_Allgather(iturn3_start,1,MPI_INTEGER,
& iturn3_start_all(0),1,MPI_INTEGER,FG_COMM,IERROR)
call MPI_Allgather(iturn4_start,1,MPI_INTEGER,
c write (iout,*) "Gather itask_cont_to ended"
c call flush(iout)
if (fg_rank.eq.king) then
+ if (me.eq.0 .or. .not. out1file) then
write (iout,*)"Contact receive task map (proc, #tasks, tasks)"
do i=0,nfgtasks-1
write (iout,'(20i4)') i,ntask_cont_from_all(i),
enddo
write (iout,*)
call flush(iout)
+ endif
C Check if every send will have a matching receive
ncheck_to=0
ncheck_from=0
ncheck_to=ncheck_to+ntask_cont_to_all(i)
ncheck_from=ncheck_from+ntask_cont_from_all(i)
enddo
- write (iout,*) "Control sums",ncheck_from,ncheck_to
+ if (me.eq.0 .or. .not. out1file)
+ & write (iout,*) "Control sums",ncheck_from,ncheck_to
if (ncheck_from.ne.ncheck_to) then
write (iout,*) "Error: #receive differs from #send."
write (iout,*) "Terminating program...!"
iphi1_end=nres
idihconstr_start=1
idihconstr_end=ndih_constr
+ isaxs_start=1
+ isaxs_end=nsaxs
iphid_start=iphi_start
iphid_end=iphi_end-1
itau_start=4
ibond_start=2
ibond_end=nres-1
ibondp_start=nnt
- ibondp_end=nct-1
+C ibondp_end=nct-1
+ ibondp_end=nct
ivec_start=1
ivec_end=nres-1
iset_start=3
iset_end=nres+1
iint_start=2
iint_end=nres-1
+ ilip_start=1
+ ilip_end=nres
#endif
return
end
include 'COMMON.SBRIDGE'
include 'COMMON.IOUNITS'
include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+c write(2,*)"hpb_partition: nhpb=",nhpb
#ifdef MPI
call int_bounds(nhpb,link_start,link_end)
- write (iout,*) 'Processor',fg_rank,' CG group',kolor,
+ if (.not. out1file)
+ & write (iout,*) 'Processor',fg_rank,' CG group',kolor,
& ' absolute rank',MyRank,
& ' nhpb',nhpb,' link_start=',link_start,
& ' link_end',link_end
link_start=1
link_end=nhpb
#endif
+c write(2,*)"hpb_partition: link_start=",nhpb," link_end=",link_end
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine homology_partition
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SETUP'
+ include 'COMMON.CONTROL'
+ include 'COMMON.MD'
+ include 'COMMON.INTERACT'
+cd write(iout,*)"homology_partition: lim_odl=",lim_odl,
+cd & " lim_dih",lim_dih
+#ifdef MPI
+ if (me.eq.king .or. .not. out1file) write (iout,*) "MPI"
+ call int_bounds(lim_odl,link_start_homo,link_end_homo)
+ call int_bounds(lim_dih,idihconstr_start_homo,
+ & idihconstr_end_homo)
+ idihconstr_start_homo=idihconstr_start_homo+nnt-1+3
+ idihconstr_end_homo=idihconstr_end_homo+nnt-1+3
+ if (me.eq.king .or. .not. out1file)
+ & write (iout,*) 'Processor',fg_rank,' CG group',kolor,
+ & ' absolute rank',MyRank,
+ & ' lim_odl',lim_odl,' link_start=',link_start_homo,
+ & ' link_end',link_end_homo,' lim_dih',lim_dih,
+ & ' idihconstr_start_homo',idihconstr_start_homo,
+ & ' idihconstr_end_homo',idihconstr_end_homo
+#else
+ write (iout,*) "Not MPI"
+ link_start_homo=1
+ link_end_homo=lim_odl
+ idihconstr_start_homo=nnt+3
+ idihconstr_end_homo=lim_dih+nnt-1+3
+ write (iout,*)
+ & ' lim_odl',lim_odl,' link_start=',link_start_homo,
+ & ' link_end',link_end_homo,' lim_dih',lim_dih,
+ & ' idihconstr_start_homo',idihconstr_start_homo,
+ & ' idihconstr_end_homo',idihconstr_end_homo
+#endif
+ return
+ end
+c------------------------------------------------------------------------------
+ subroutine NMRpeak_partition
+ implicit real*8 (a-h,o-z)
+ include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ include 'COMMON.SBRIDGE'
+ include 'COMMON.IOUNITS'
+ include 'COMMON.SETUP'
+#ifdef MPI
+ call int_bounds(npeak,link_start_peak,link_end_peak)
+ write (iout,*) 'Processor',fg_rank,' CG group',kolor,
+ & ' absolute rank',MyRank,
+ & ' npeak',npeak,' link_start_peak=',link_start_peak,
+ & ' link_end_peak',link_end_peak
+#else
+ link_start_peak=1
+ link_end_peak=npeak
+#endif
return
end
projects / unres.git / blobdiff