--- /dev/null
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+! !
+! U N R E S !
+! !
+! Program to carry out conformational search of proteins in an united-residue !
+! approximation. !
+! !
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ program unres
+
+ use io_units
+ use control_data
+ use control, only:tcpu
+ use io_base, only:ilen
+ use geometry, only:chainbuild
+ use control, only:dajczas
+ use check_bond_
+ use energy
+ use compare, only: test
+ use map_
+ use MDyn
+ use MPI_
+ use io, only:readrtns
+
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+#ifdef MPI
+ use MPI_data ! include 'COMMON.SETUP'
+ implicit none
+ include 'mpif.h'
+ integer :: ierr
+#else
+ use MPI_data, only: me,king
+ implicit none
+#endif
+! include 'COMMON.TIME1'
+! include 'COMMON.INTERACT'
+! include 'COMMON.NAMES'
+! include 'COMMON.GEO'
+! include 'COMMON.HEADER'
+! include 'COMMON.CONTROL'
+! include 'COMMON.CONTACTS'
+! include 'COMMON.CHAIN'
+! include 'COMMON.VAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.FFIELD'
+! include 'COMMON.REMD'
+! include 'COMMON.MD'
+! include 'COMMON.SBRIDGE'
+
+ real(kind=8) :: hrtime,mintime,sectime
+ character(len=64) :: text_mode_calc(-2:14)
+ text_mode_calc(-2) = 'test'
+ text_mode_calc(-1) = 'cos'
+ text_mode_calc(0) = 'Energy evaluation or minimization'
+ text_mode_calc(1) = 'Regularization of PDB structure'
+ text_mode_calc(2) = 'Threading of a sequence on PDB structures'
+ text_mode_calc(3) = 'Monte Carlo (with minimization) '
+ text_mode_calc(4) = 'Energy minimization of multiple conformations'
+ text_mode_calc(5) = 'Checking energy gradient'
+ text_mode_calc(6) = 'Entropic sampling Monte Carlo (with minimization)'
+ text_mode_calc(7) = 'Energy map'
+ text_mode_calc(8) = 'CSA calculations'
+ text_mode_calc(9) = 'Not used 9'
+ text_mode_calc(10) = 'Not used 10'
+ text_mode_calc(11) = 'Soft regularization of PDB structure'
+ text_mode_calc(12) = 'Mesoscopic molecular dynamics (MD) '
+ text_mode_calc(13) = 'Not used 13'
+ text_mode_calc(14) = 'Replica exchange molecular dynamics (REMD)'
+! external ilen
+! call memmon_print_usage()
+
+ call init_task
+ if (me.eq.king) &
+ write(iout,*)'### LAST MODIFIED 09/03/15 15:32PM by EL'
+ if (me.eq.king) call cinfo
+! Read force field parameters and job setup data
+ call readrtns
+ call flush(iout)
+!
+ if (me.eq.king .or. .not. out1file) then
+ write (iout,'(2a/)') &
+ text_mode_calc(modecalc)(:ilen(text_mode_calc(modecalc))), &
+ ' calculation.'
+ if (minim) write (iout,'(a)') &
+ 'Conformations will be energy-minimized.'
+ write (iout,'(80(1h*)/)')
+ endif
+ call flush(iout)
+!
+ if (modecalc.eq.-2) then
+ call test
+ stop
+ else if (modecalc.eq.-1) then
+ write(iout,*) "call check_sc_map next"
+ call check_bond
+ stop
+ endif
+!elwrite(iout,*)"!!!!!!!!!!!!!!!!! in unres"
+
+#ifdef MPI
+ if (fg_rank.gt.0) then
+! Fine-grain slaves just do energy and gradient components.
+ call ergastulum ! slave workhouse in Latin
+ else
+#endif
+ if (modecalc.eq.0) then
+!write(iout,*)"!!!!!!!!!!!!!!!!! in unres"
+
+ call exec_eeval_or_minim
+!write(iout,*)"!!!!!!!!!!!!!!!!! in unres"
+
+ else if (modecalc.eq.1) then
+ call exec_regularize
+ else if (modecalc.eq.2) then
+ call exec_thread
+ else if (modecalc.eq.3 .or. modecalc .eq.6) then
+ call exec_MC
+ else if (modecalc.eq.4) then
+ call exec_mult_eeval_or_minim
+ else if (modecalc.eq.5) then
+ call exec_checkgrad
+!write(iout,*) "check grad dwa razy"
+!el call exec_checkgrad
+ else if (ModeCalc.eq.7) then
+ call exec_map
+ else if (ModeCalc.eq.8) then
+ call exec_CSA
+ else if (modecalc.eq.11) then
+ call exec_softreg
+ else if (modecalc.eq.12) then
+ call exec_MD
+ else if (modecalc.eq.14) then
+ call exec_MREMD
+ else
+ write (iout,'(a)') 'This calculation type is not supported',&
+ ModeCalc
+ endif
+!elwrite(iout,*)"!!!!!!!!!!!!!!!!!"
+
+#ifdef MPI
+ endif
+! Finish task.
+ if (fg_rank.eq.0) call finish_task
+! call memmon_print_usage()
+#ifdef TIMING
+ call print_detailed_timing
+#endif
+ call MPI_Finalize(ierr)
+ stop 'Bye Bye...'
+#else
+ call dajczas(tcpu(),hrtime,mintime,sectime)
+ stop '********** Program terminated normally.'
+#endif
+
+ end program !UNRES
+!-----------------------------------------------------------------------------
+!
+!-----------------------------------------------------------------------------
+ subroutine exec_MD
+ use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL'
+ use geometry, only:chainbuild
+ use MDyn
+ use io_units !include 'COMMON.IOUNITS'
+! use io_common
+ implicit none
+! include 'DIMENSIONS'
+#ifdef MPI
+ include "mpif.h"
+#endif
+ call alloc_MD_arrays
+ if (me.eq.king .or. .not. out1file) &
+ write (iout,*) "Calling chainbuild"
+ call chainbuild
+ call MD
+ return
+ end subroutine exec_MD
+!---------------------------------------------------------------------------
+ subroutine exec_MREMD
+ use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL'
+ use io_units !include 'COMMON.IOUNITS'
+! use io_common
+ use REMD_data !include 'COMMON.REMD'
+ use geometry, only:chainbuild
+ use MREMDyn
+
+ implicit none
+! include 'DIMENSIONS'
+#ifdef MPI
+ include "mpif.h"
+#endif
+
+ integer :: i
+ call alloc_MD_arrays
+ call alloc_MREMD_arrays
+
+ if (me.eq.king .or. .not. out1file) &
+ write (iout,*) "Calling chainbuild"
+ call chainbuild
+ if (me.eq.king .or. .not. out1file) &
+ write (iout,*) "Calling REMD"
+ if (remd_mlist) then
+ call MREMD
+ else
+ do i=1,nrep
+ remd_m(i)=1
+ enddo
+ call MREMD
+ endif
+ return
+ end subroutine exec_MREMD
+!-----------------------------------------------------------------------------
+ subroutine exec_eeval_or_minim
+ use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL''COMMON.TIME1''COMMON.NAMES''COMMON.HEADER'
+ use io_units !include 'COMMON.IOUNITS'
+ use names
+! use energy !include 'COMMON.INTERACT''COMMON.CONTACTS''COMMON.VAR''COMMON.FFIELD' 'COMMON.SBRIDGE'
+ use geometry_data !include 'COMMON.GEO''COMMON.CHAIN'
+! use REMD !include 'COMMON.REMD'
+! use MD !include 'COMMON.MD'
+
+ use energy_data
+
+ use io_base
+ use geometry, only:chainbuild
+ use energy
+ use compare, only:alloc_compare_arrays,hairpin,secondary2,rms_nac_nnc
+ use minimm, only:minimize,minim_dc,sc_move
+ use compare_data !el
+ use comm_srutu
+ implicit none
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ integer :: i
+!el common /srutu/ icall
+ real(kind=8) :: energy_(0:n_ene)
+ real(kind=8) :: energy_long(0:n_ene),energy_short(0:n_ene)
+ real(kind=8) :: varia(6*nres) !(maxvar) (maxvar=6*maxres)
+ real(kind=8) :: time00, evals, etota, etot, time_ene, time1
+ integer :: nharp,nft_sc,iretcode,nfun
+ integer,dimension(4,nres/3) :: iharp !(4,nres/3)(4,maxres/3)
+ logical :: fail
+ real(kind=8) :: rms,frac,frac_nn,co
+
+ integer :: j,k
+ call alloc_compare_arrays
+ if (indpdb.eq.0) call chainbuild
+#ifdef MPI
+ time00=MPI_Wtime()
+#endif
+ call chainbuild_cart
+! write(iout,*)"in exec_eeval or minimim",split_ene
+! do j=1,2*nres+2
+! write(iout,*)"cccccc",j,(c(i,j),i=1,3)
+! write(iout,*)"dcccccc",j,(dc(i,j),i=1,3)
+! enddo
+ if (split_ene) then
+! write(iout,*)"in exec_eeval or minimim"
+
+ print *,"Processor",myrank," after chainbuild"
+ icall=1
+!elwrite(iout,*)"in exec_eeval or minimim"
+
+ call etotal_long(energy_long)
+ write (iout,*) "Printing long range energy"
+ call enerprint(energy_long)
+!elwrite(iout,*)"in exec_eeval or minimim"
+
+ call etotal_short(energy_short)
+ write (iout,*) "Printing short range energy"
+ call enerprint(energy_short)
+ do i=0,n_ene
+ energy_(i)=energy_long(i)+energy_short(i)
+ write (iout,*) i,energy_long(i),energy_short(i),energy_(i)
+ enddo
+ write (iout,*) "Printing long+short range energy"
+ call enerprint(energy_)
+ endif
+
+ call etotal(energy_)
+!elwrite(iout,*)"after etotal in exec_eev"
+#ifdef MPI
+ time_ene=MPI_Wtime()-time00
+#endif
+ write (iout,*) "Time for energy evaluation",time_ene
+ print *,"after etotal"
+ etota = energy_(0)
+ etot = etota
+ call enerprint(energy_)
+!write(iout,*)"after enerprint"
+ call hairpin(.true.,nharp,iharp)
+!write(iout,*) "after hairpin"!,hfrag(1,1)
+ call secondary2(.true.)
+!write(iout,*) "after secondary2"
+ if (minim) then
+!rc overlap test
+!elwrite(iout,*) "after secondary2 minim",minim
+ if (overlapsc) then
+ print *, 'Calling OVERLAP_SC'
+!write(iout,*) 'Calling OVERLAP_SC'
+ call overlap_sc(fail)
+!write(iout,*) 'after Calling OVERLAP_SC'
+ endif
+
+ if (searchsc) then
+ call sc_move(2,nres-1,10,1d10,nft_sc,etot)
+ print *,'SC_move',nft_sc,etot
+ write(iout,*) 'SC_move',nft_sc,etot
+ endif
+
+ if (dccart) then
+!write(iout,*) 'CART calling minim_dc', nvar
+ print *, 'Calling MINIM_DC'
+#ifdef MPI
+ time1=MPI_WTIME()
+#endif
+! call check_ecartint !el
+ call minim_dc(etot,iretcode,nfun)
+! call check_ecartint !el
+ else
+!write(iout,*) "indpdb",indpdb
+ if (indpdb.ne.0) then
+!write(iout,*) 'if indpdb', indpdb
+ call bond_regular
+ call chainbuild
+ endif
+ call geom_to_var(nvar,varia)
+!write(iout,*) 'po geom to var; calling minimize', nvar
+ print *,'Calling MINIMIZE.'
+#ifdef MPI
+ time1=MPI_WTIME()
+#endif
+! call check_eint
+! call exec_checkgrad !el
+ call minimize(etot,varia,iretcode,nfun)
+! call check_eint
+! call exec_checkgrad !el
+ endif
+ print *,'SUMSL return code is',iretcode,' eval ',nfun
+#ifdef MPI
+ evals=nfun/(MPI_WTIME()-time1)
+#endif
+ print *,'# eval/s',evals
+ print *,'refstr=',refstr
+ call hairpin(.true.,nharp,iharp)
+ call secondary2(.true.)
+ call etotal(energy_)
+ etot = energy_(0)
+ call enerprint(energy_)
+
+ call intout
+ call briefout(0,etot)
+ if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (iout,'(a,i3)') 'SUMSL return code:',iretcode
+ write (iout,'(a,i20)') '# of energy evaluations:',nfun+1
+ write (iout,'(a,f16.3)')'# of energy evaluations/sec:',evals
+ else
+!elwrite(iout,*) "after secondary2 minim",minim
+ print *,'refstr=',refstr
+ if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+!elwrite(iout,*) "rms_nac"
+!elwrite(iout,*) "before briefout"
+ call briefout(0,etot)
+!elwrite(iout,*) "after briefout"
+ endif
+ if (outpdb) call pdbout(etot,titel(:32),ipdb)
+ if (outmol2) call mol2out(etot,titel(:32))
+!elwrite(iout,*) "after exec_eeval_or_minim"
+ return
+ end subroutine exec_eeval_or_minim
+!-----------------------------------------------------------------------------
+ subroutine exec_regularize
+! use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL''COMMON.TIME1''COMMON.NAMES''COMMON.HEADER'
+ use io_units !include 'COMMON.IOUNITS'
+ use names
+ use energy_data !include 'COMMON.INTERACT''COMMON.CONTACTS''COMMON.VAR''COMMON.FFIELD' 'COMMON.SBRIDGE'
+ use geometry_data !include 'COMMON.GEO''COMMON.CHAIN'
+ ! use REMD !include 'COMMON.REMD'
+! use MD !include 'COMMON.MD'
+ use regularize_
+ use compare
+ implicit none
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+ real(kind=8) :: energy_(0:n_ene)
+ real(kind=8) :: etot
+ real(kind=8) :: rms,frac,frac_nn,co
+ integer :: iretcode
+
+ call alloc_compare_arrays
+ call gen_dist_constr
+ call sc_conf
+ call intout
+ call regularize(nct-nnt+1,etot,rms,cref(1,nnt,1),iretcode)
+ call etotal(energy_)
+ energy_(0)=energy_(0)-energy_(14)
+ etot=energy_(0)
+ call enerprint(energy_)
+ call intout
+ call briefout(0,etot)
+ if (outpdb) call pdbout(etot,titel(:32),ipdb)
+ if (outmol2) call mol2out(etot,titel(:32))
+ if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (iout,'(a,i3)') 'SUMSL return code:',iretcode
+ return
+ end subroutine exec_regularize
+!-----------------------------------------------------------------------------
+ subroutine exec_thread
+! use MPI_data !include 'COMMON.SETUP'
+ use compare
+ implicit none
+! include 'DIMENSIONS'
+#ifdef MP
+ include "mpif.h"
+#endif
+ call alloc_compare_arrays
+ call thread_seq
+ return
+ end subroutine exec_thread
+!-----------------------------------------------------------------------------
+ subroutine exec_MC
+! use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL'
+ use geometry_data
+ use energy_data
+ use mcm_md
+ implicit none
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+ character(len=10) :: nodeinfo
+ real(kind=8) :: varia(6*nres) !(maxvar) (maxvar=6*maxres)
+ integer :: ipar
+#ifdef MPI
+ include "mpif.h"
+#endif
+ call alloc_MCM_arrays
+ call mcm_setup
+ if (minim) then
+#ifdef MPI
+ if (modecalc.eq.3) then
+ call do_mcm(ipar)
+ else
+ call entmcm
+ endif
+#else
+ if (modecalc.eq.3) then
+ call do_mcm(ipar)
+ else
+ call entmcm
+ endif
+#endif
+ else
+ call monte_carlo
+ endif
+ return
+ end subroutine exec_MC
+!-----------------------------------------------------------------------------
+ subroutine exec_mult_eeval_or_minim
+ use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL''COMMON.TIME1''COMMON.NAMES''COMMON.HEADER'
+ use io_units !include 'COMMON.IOUNITS'
+ use names
+ use energy_data !include 'COMMON.INTERACT''COMMON.CONTACTS''COMMON.VAR''COMMON.FFIELD' 'COMMON.SBRIDGE'
+ use geometry_data !include 'COMMON.GEO''COMMON.CHAIN'
+! use REMD !include 'COMMON.REMD'
+! use MD !include 'COMMON.MD'
+ use io_base
+ use geometry, only:chainbuild,geom_to_var,int_from_cart1,var_to_geom
+ use energy, only:etotal,enerprint
+ use compare, only:rms_nac_nnc
+ use minimm, only:minimize!,minim_mcmf
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+#ifdef MPI
+ use minimm, only:minim_mcmf
+ implicit none
+ include 'mpif.h'
+ integer :: ierror,ierr
+ real(kind=8) :: man
+ real(kind=8),dimension(mpi_status_size) :: muster
+#else
+ implicit none
+#endif
+ real(kind=8) :: varia(6*nres) !(maxvar) (maxvar=6*maxres)
+ integer,dimension(6) :: ind
+ real(kind=8) :: energy_(0:n_ene)
+ logical :: eof
+ real(kind=8) :: etot,ene0
+ integer :: mm,imm,nft,n,iconf,nmin,i,iretcode,nfun,it,&
+ nf_mcmf,j
+ real(kind=8) :: rms,frac,frac_nn,co,time,ene
+
+ eof=.false.
+#ifdef MPI
+ if(me.ne.king) then
+ call minim_mcmf
+ return
+ endif
+
+ close (intin)
+ open(intin,file=intinname,status='old')
+ write (istat,'(a5,20a12)')"# ",&
+ (wname(print_order(i)),i=1,nprint_ene)
+ if (refstr) then
+ write (istat,'(a5,20a12)')"# ",&
+ (ename(print_order(i)),i=1,nprint_ene),&
+ "ETOT total","RMSD","nat.contact","nnt.contact"
+ else
+ write (istat,'(a5,20a12)')"# ",&
+ (ename(print_order(i)),i=1,nprint_ene),"ETOT total"
+ endif
+
+ if (.not.minim) then
+ do while (.not. eof)
+ if (read_cart) then
+ read (intin,'(e15.10,e15.5)',end=1100,err=1100) time,ene
+ call read_x(intin,*11)
+#ifdef MPI
+! Broadcast the order to compute internal coordinates to the slaves.
+ if (nfgtasks.gt.1) &
+ call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
+#endif
+ call int_from_cart1(.false.)
+ else
+ read (intin,'(i5)',end=1100,err=1100) iconf
+ call read_angles(intin,*11)
+ call geom_to_var(nvar,varia)
+ call chainbuild
+ endif
+ write (iout,'(a,i7)') 'Conformation #',iconf
+ call etotal(energy_)
+ call briefout(iconf,energy_(0))
+ call enerprint(energy_)
+ etot=energy_(0)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (istat,'(i5,20(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot,&
+ rms,frac,frac_nn,co
+!jlee end
+ else
+ write (istat,'(i5,16(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot
+ endif
+ enddo
+1100 continue
+ goto 1101
+ endif
+
+ mm=0
+ imm=0
+ nft=0
+ ene0=0.0d0
+ n=0
+ iconf=0
+! do n=1,nzsc
+ do while (.not. eof)
+ mm=mm+1
+ if (mm.lt.nodes) then
+ if (read_cart) then
+ read (intin,'(e15.10,e15.5)',end=11,err=11) time,ene
+ call read_x(intin,*11)
+#ifdef MPI
+! Broadcast the order to compute internal coordinates to the slaves.
+ if (nfgtasks.gt.1) &
+ call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
+#endif
+ call int_from_cart1(.false.)
+ else
+ read (intin,'(i5)',end=11,err=11) iconf
+ call read_angles(intin,*11)
+ call geom_to_var(nvar,varia)
+ call chainbuild
+ endif
+ write (iout,'(a,i7)') 'Conformation #',iconf
+ n=n+1
+ imm=imm+1
+ ind(1)=1
+ ind(2)=n
+ ind(3)=0
+ ind(4)=0
+ ind(5)=0
+ ind(6)=0
+ ene0=0.0d0
+ call mpi_send(ind,6,mpi_integer,mm,idint,CG_COMM,&
+ ierr)
+ call mpi_send(varia,nvar,mpi_double_precision,mm,&
+ idreal,CG_COMM,ierr)
+ call mpi_send(ene0,1,mpi_double_precision,mm,&
+ idreal,CG_COMM,ierr)
+! print *,'task ',n,' sent to worker ',mm,nvar
+ else
+ call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint,&
+ CG_COMM,muster,ierr)
+ man=muster(mpi_source)
+! print *,'receiving result from worker ',man,' (',iii1,iii,')'
+ call mpi_recv(varia,nvar,mpi_double_precision,&
+ man,idreal,CG_COMM,muster,ierr)
+ call mpi_recv(ene,1,&
+ mpi_double_precision,man,idreal,&
+ CG_COMM,muster,ierr)
+ call mpi_recv(ene0,1,&
+ mpi_double_precision,man,idreal,&
+ CG_COMM,muster,ierr)
+! print *,'result received from worker ',man,' sending now'
+
+ call var_to_geom(nvar,varia)
+ call chainbuild
+ call etotal(energy_)
+ iconf=ind(2)
+ write (iout,*)
+ write (iout,*)
+ write (iout,'(a,2i7)') 'Conformation #',iconf,ind(5)
+
+ etot=energy_(0)
+ call enerprint(energy_)
+ call briefout(it,etot)
+! if (minim) call briefout(it,etot)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (istat,'(i5,19(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot,&
+ rms,frac,frac_nn,co
+ else
+ write (istat,'(i5,15(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot
+ endif
+
+ imm=imm-1
+ if (read_cart) then
+ read (intin,'(e15.10,e15.5)',end=1101,err=1101) time,ene
+ call read_x(intin,*11)
+#ifdef MPI
+! Broadcast the order to compute internal coordinates to the slaves.
+ if (nfgtasks.gt.1) &
+ call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
+#endif
+ call int_from_cart1(.false.)
+ else
+ read (intin,'(i5)',end=1101,err=1101) iconf
+ call read_angles(intin,*11)
+ call geom_to_var(nvar,varia)
+ call chainbuild
+ endif
+ n=n+1
+ imm=imm+1
+ ind(1)=1
+ ind(2)=n
+ ind(3)=0
+ ind(4)=0
+ ind(5)=0
+ ind(6)=0
+ call mpi_send(ind,6,mpi_integer,man,idint,CG_COMM,&
+ ierr)
+ call mpi_send(varia,nvar,mpi_double_precision,man,&
+ idreal,CG_COMM,ierr)
+ call mpi_send(ene0,1,mpi_double_precision,man,&
+ idreal,CG_COMM,ierr)
+ nf_mcmf=nf_mcmf+ind(4)
+ nmin=nmin+1
+ endif
+ enddo
+11 continue
+ do j=1,imm
+ call mpi_recv(ind,6,mpi_integer,mpi_any_source,idint,&
+ CG_COMM,muster,ierr)
+ man=muster(mpi_source)
+ call mpi_recv(varia,nvar,mpi_double_precision,&
+ man,idreal,CG_COMM,muster,ierr)
+ call mpi_recv(ene,1,&
+ mpi_double_precision,man,idreal,&
+ CG_COMM,muster,ierr)
+ call mpi_recv(ene0,1,&
+ mpi_double_precision,man,idreal,&
+ CG_COMM,muster,ierr)
+
+ call var_to_geom(nvar,varia)
+ call chainbuild
+ call etotal(energy_)
+ iconf=ind(2)
+ write (iout,*)
+ write (iout,*)
+ write (iout,'(a,2i7)') 'Conformation #',iconf,ind(5)
+
+ etot=energy_(0)
+ call enerprint(energy_)
+ call briefout(it,etot)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (istat,'(i5,19(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot,&
+ rms,frac,frac_nn,co
+ else
+ write (istat,'(i5,15(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot
+ endif
+ nmin=nmin+1
+ enddo
+1101 continue
+ do i=1, nodes-1
+ ind(1)=0
+ ind(2)=0
+ ind(3)=0
+ ind(4)=0
+ ind(5)=0
+ ind(6)=0
+ call mpi_send(ind,6,mpi_integer,i,idint,CG_COMM,&
+ ierr)
+ enddo
+#else
+ close (intin)
+ open(intin,file=intinname,status='old')
+ write (istat,'(a5,20a12)')"# ",&
+ (wname(print_order(i)),i=1,nprint_ene)
+ write (istat,'("# ",20(1pe12.4))') &
+ (weights(print_order(i)),i=1,nprint_ene)
+ if (refstr) then
+ write (istat,'(a5,20a12)')"# ",&
+ (ename(print_order(i)),i=1,nprint_ene),&
+ "ETOT total","RMSD","nat.contact","nnt.contact"
+ else
+ write (istat,'(a5,14a12)')"# ",&
+ (ename(print_order(i)),i=1,nprint_ene),"ETOT total"
+ endif
+ do while (.not. eof)
+ if (read_cart) then
+ read (intin,'(e15.10,e15.5)',end=11,err=11) time,ene
+ call read_x(intin,*11)
+#ifdef MPI
+! Broadcast the order to compute internal coordinates to the slaves.
+ if (nfgtasks.gt.1) &
+ call MPI_Bcast(6,1,MPI_INTEGER,king,FG_COMM,IERROR)
+#endif
+ call int_from_cart1(.false.)
+ else
+ read (intin,'(i5)',end=11,err=11) iconf
+ call read_angles(intin,*11)
+ call geom_to_var(nvar,varia)
+ call chainbuild
+ endif
+ write (iout,'(a,i7)') 'Conformation #',iconf
+ if (minim) call minimize(etot,varia,iretcode,nfun)
+ call etotal(energy_)
+
+ etot=energy_(0)
+ call enerprint(energy_)
+ if (minim) call briefout(it,etot)
+ if (refstr) then
+ call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ write (istat,'(i5,18(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),&
+ etot,rms,frac,frac_nn,co
+!jlee end
+ else
+ write (istat,'(i5,14(f12.3))') iconf,&
+ (energy_(print_order(i)),i=1,nprint_ene),etot
+ endif
+ enddo
+ 11 continue
+#endif
+ return
+ end subroutine exec_mult_eeval_or_minim
+!-----------------------------------------------------------------------------
+ subroutine exec_checkgrad
+! use MPI_data !include 'COMMON.SETUP'
+ use control_data !include 'COMMON.CONTROL''COMMON.TIME1''COMMON.NAMES''COMMON.HEADER'
+ use io_units !include 'COMMON.IOUNITS'
+!el use energy_data, only:icall !include 'COMMON.INTERACT''COMMON.CONTACTS''COMMON.VAR''COMMON.FFIELD' 'COMMON.SBRIDGE'
+ use geometry_data !include 'COMMON.GEO''COMMON.CHAIN'
+! use REMD !include 'COMMON.REMD'
+ use MD_data !include 'COMMON.MD'
+ use io_base, only:intout
+ use io_config, only:read_fragments
+ use geometry
+ use energy
+ use comm_srutu
+ implicit none
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+#ifdef MPI
+ include 'mpif.h'
+#endif
+!el integer :: icall
+!el common /srutu/ icall
+ real(kind=8) :: energy_(0:max_ene)
+ real(kind=8) :: etot
+ integer :: i
+! do i=2,nres
+! vbld(i)=vbld(i)+ran_number(-0.1d0,0.1d0)
+! if (itype(i).ne.10)
+! & vbld(i+nres)=vbld(i+nres)+ran_number(-0.001d0,0.001d0)
+! enddo
+ if (indpdb.eq.0) call chainbuild
+! do i=0,nres
+! do j=1,3
+! dc(j,i)=dc(j,i)+ran_number(-0.2d0,0.2d0)
+! enddo
+! enddo
+! do i=1,nres-1
+! if (itype(i).ne.10) then
+! do j=1,3
+! dc(j,i+nres)=dc(j,i+nres)+ran_number(-0.2d0,0.2d0)
+! enddo
+! endif
+! enddo
+! do j=1,3
+! dc(j,0)=ran_number(-0.2d0,0.2d0)
+! enddo
+ usampl=.true.
+ totT=1.d0
+ eq_time=0.0d0
+ call read_fragments
+ call chainbuild_cart
+ call cartprint
+ call intout
+ icall=1
+ call etotal(energy_(0))
+ etot = energy_(0)
+ call enerprint(energy_(0))
+ write (iout,*) "Uconst",Uconst," Uconst_back",uconst_back
+ print *,'icheckgrad=',icheckgrad
+ goto (10,20,30) icheckgrad
+ 10 call check_ecartint
+ return
+ 20 call check_cartgrad
+ return
+ 30 call check_eint
+ return
+ end subroutine exec_checkgrad
+!-----------------------------------------------------------------------------
+ subroutine exec_map
+! use map_data
+ use map_
+ use io_config, only:map_read
+ implicit none
+! Energy maps
+ call alloc_map_arrays
+ call map_read
+ call map
+ return
+ end subroutine exec_map
+!-----------------------------------------------------------------------------
+ subroutine exec_CSA
+
+ use io_units !include 'COMMON.IOUNITS'
+ use CSA
+
+ implicit none
+#ifdef MPI
+ include "mpif.h"
+#endif
+! include 'DIMENSIONS'
+! Conformational Space Annealling programmed by Jooyoung Lee.
+! This method works only with parallel machines!
+#ifdef MPI
+ call alloc_CSA_arrays
+ call together
+#else
+ write (iout,*) "CSA works on parallel machines only"
+#endif
+ return
+ end subroutine exec_CSA
+!-----------------------------------------------------------------------------
+ subroutine exec_softreg
+ use io_units !include 'COMMON.IOUNITS'
+ use control_data !include 'COMMON.CONTROL'
+ use energy_data
+ use io_base, only:intout,briefout
+ use geometry, only:chainbuild
+ use energy
+ use compare
+ implicit none
+! include 'DIMENSIONS'
+ real(kind=8) :: energy_(0:n_ene)
+!el local variables
+ real(kind=8) :: rms,frac,frac_nn,co,etot
+ logical :: debug
+
+ call alloc_compare_arrays
+ call chainbuild
+ call etotal(energy_)
+ call enerprint(energy_)
+ if (.not.lsecondary) then
+ write(iout,*) 'Calling secondary structure recognition'
+ call secondary2(debug)
+ else
+ write(iout,*) 'Using secondary structure supplied in pdb'
+ endif
+
+ call softreg
+
+ call etotal(energy_)
+ etot=energy_(0)
+ call enerprint(energy_)
+ call intout
+ call briefout(0,etot)
+ call secondary2(.true.)
+ if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.)
+ return
+ end subroutine exec_softreg
+!-----------------------------------------------------------------------------
+! minimize_p.F
+!-----------------------------------------------------------------------------
+!el#ifdef MPI
+ subroutine ergastulum
+
+! implicit real*8 (a-h,o-z)
+! include 'DIMENSIONS'
+ use MD_data
+ use energy
+ use MDyn, only:setup_fricmat
+ use REMD, only:fricmat_mult,ginv_mult
+#ifdef MPI
+ include "mpif.h"
+#endif
+! include 'COMMON.SETUP'
+! include 'COMMON.DERIV'
+! include 'COMMON.VAR'
+! include 'COMMON.IOUNITS'
+! include 'COMMON.FFIELD'
+! include 'COMMON.INTERACT'
+! include 'COMMON.MD'
+! include 'COMMON.TIME1'
+ real(kind=8),dimension(6*nres) :: z,d_a_tmp !(maxres6) maxres6=6*maxres
+ real(kind=8) :: edum(0:n_ene),time_order(0:10)
+!el real(kind=8),dimension(2*nres,2*nres) :: Gcopy !(maxres2,maxres2) maxres2=2*maxres
+!el common /przechowalnia/ Gcopy
+ integer :: icall = 0
+
+!el local variables
+ real(kind=8) :: time00
+ integer :: iorder,i,j,nres2,ierr,ierror
+ nres2=2*nres
+ if(.not.allocated(Gcopy)) allocate(Gcopy(nres2,nres2))
+! common.MD
+ if(.not.allocated(Ginv)) allocate(Ginv(nres2,nres2)) !(maxres2,maxres2)
+! common /mdpmpi/
+ if(.not.allocated(ng_start)) allocate(ng_start(0:nfgtasks-1))
+ if(.not.allocated(ng_counts)) allocate(ng_counts(0:nfgtasks-1))
+ if(.not.allocated(nginv_counts)) allocate(nginv_counts(0:nfgtasks-1)) !(0:MaxProcs-1)
+ if(.not.allocated(nginv_start)) allocate(nginv_start(0:nfgtasks)) !(0:MaxProcs)
+
+ if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2)) !maxres2=2*maxres
+
+! Workers wait for variables and NF, and NFL from the boss
+ iorder=0
+ do while (iorder.ge.0)
+! write (*,*) 'Processor',fg_rank,' CG group',kolor,
+! & ' receives order from Master'
+ time00=MPI_Wtime()
+ call MPI_Bcast(iorder,1,MPI_INTEGER,king,FG_COMM,IERR)
+ time_Bcast=time_Bcast+MPI_Wtime()-time00
+ if (icall.gt.4 .and. iorder.ge.0) &
+ time_order(iorder)=time_order(iorder)+MPI_Wtime()-time00
+ icall=icall+1
+! write (*,*)
+! & 'Processor',fg_rank,' completed receive MPI_BCAST order',iorder
+ if (iorder.eq.0) then
+ call zerograd
+ call etotal(edum)
+! write (2,*) "After etotal"
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! call flush(2)
+ else if (iorder.eq.2) then
+ call zerograd
+ call etotal_short(edum)
+! write (2,*) "After etotal_short"
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! call flush(2)
+ else if (iorder.eq.3) then
+ call zerograd
+ call etotal_long(edum)
+! write (2,*) "After etotal_long"
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! call flush(2)
+ else if (iorder.eq.1) then
+ call sum_gradient
+! write (2,*) "After sum_gradient"
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! call flush(2)
+ else if (iorder.eq.4) then
+ call ginv_mult(z,d_a_tmp)
+ else if (iorder.eq.5) then
+! Setup MD things for a slave
+ dimen=(nct-nnt+1)+nside
+ dimen1=(nct-nnt)+(nct-nnt+1)
+ dimen3=dimen*3
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! call flush(2)
+ call int_bounds(dimen,igmult_start,igmult_end)
+ igmult_start=igmult_start-1
+ call MPI_Allgather(3*igmult_start,1,MPI_INTEGER,&
+ ng_start(0),1,MPI_INTEGER,FG_COMM,IERROR)
+ my_ng_count=igmult_end-igmult_start
+ call MPI_Allgather(3*my_ng_count,1,MPI_INTEGER,ng_counts(0),1,&
+ MPI_INTEGER,FG_COMM,IERROR)
+ write (2,*) "ng_start",(ng_start(i),i=0,nfgtasks-1) !sp
+! write (2,*) "ng_counts",(ng_counts(i),i=0,nfgtasks-1)
+ myginv_ng_count=nres2*my_ng_count !el maxres2
+! write (2,*) "igmult_start",igmult_start," igmult_end",
+! & igmult_end," my_ng_count",my_ng_count
+! call flush(2)
+ call MPI_Allgather(nres2*igmult_start,1,MPI_INTEGER,& !el maxres2
+ nginv_start(0),1,MPI_INTEGER,FG_COMM,IERROR)
+ call MPI_Allgather(myginv_ng_count,1,MPI_INTEGER,&
+ nginv_counts(0),1,MPI_INTEGER,FG_COMM,IERROR)
+! write (2,*) "nginv_start",(nginv_start(i),i=0,nfgtasks-1)
+! write (2,*) "nginv_counts",(nginv_counts(i),i=0,nfgtasks-1)
+! call flush(2)
+! call MPI_Barrier(FG_COMM,IERROR)
+ time00=MPI_Wtime()
+ call MPI_Scatterv(ginv(1,1),nginv_counts(0),&
+ nginv_start(0),MPI_DOUBLE_PRECISION,gcopy(1,1),&
+ myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
+#ifdef TIMING
+ time_scatter_ginv=time_scatter_ginv+MPI_Wtime()-time00
+#endif
+ do i=1,dimen
+ do j=1,2*my_ng_count
+ ginv(j,i)=gcopy(i,j)
+ enddo
+ enddo
+! write (2,*) "dimen",dimen," dimen3",dimen3
+! write (2,*) "End MD setup"
+! call flush(2)
+! write (iout,*) "My chunk of ginv_block"
+! call MATOUT2(my_ng_count,dimen3,maxres2,maxers2,ginv_block)
+ else if (iorder.eq.6) then
+ call int_from_cart1(.false.)
+ else if (iorder.eq.7) then
+ call chainbuild_cart
+ else if (iorder.eq.8) then
+ call intcartderiv
+ else if (iorder.eq.9) then
+ call fricmat_mult(z,d_a_tmp)
+ else if (iorder.eq.10) then
+ call setup_fricmat
+ endif
+ enddo
+ write (*,*) 'Processor',fg_rank,' CG group',kolor,&
+ ' absolute rank',myrank,' leves ERGASTULUM.'
+ write(*,*)'Processor',fg_rank,' wait times for respective orders',&
+ (' order[',i,']',time_order(i),i=0,10)
+ return
+ end subroutine ergastulum
projects / unres4.git / blobdiff