+++ /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