X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=blobdiff_plain;f=source%2Funres%2Fsrc_CSA_DiL%2Funres_csa.F;fp=source%2Funres%2Fsrc_CSA_DiL%2Funres_csa.F;h=0000000000000000000000000000000000000000;hp=ce55133fd77ed2d1cd6f026a933681aa8203ea8c;hb=2a226bfc86eabc6e4eae0c3ad1cbc3cb5417a05a;hpb=a0e685f844163003749ba91dfbf4644bcc8cfa30 diff --git a/source/unres/src_CSA_DiL/unres_csa.F b/source/unres/src_CSA_DiL/unres_csa.F deleted file mode 100644 index ce55133..0000000 --- a/source/unres/src_CSA_DiL/unres_csa.F +++ /dev/null @@ -1,556 +0,0 @@ -CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC -C C -C U N R E S C -C C -C Program to carry out conformational search of proteins in an united-residue C -C approximation. C -C C -CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - - -#ifdef MPI - include 'mpif.h' - include 'COMMON.SETUP' -#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' -c include 'COMMON.REMD' -c include 'COMMON.MD' - include 'COMMON.SBRIDGE' - double precision hrtime,mintime,sectime - character*64 text_mode_calc(-2:14) /'test', - & 'SC rotamer distribution', - & 'Energy evaluation or minimization', - & 'Regularization of PDB structure', - & 'Threading of a sequence on PDB structures', - & 'Monte Carlo (with minimization) ', - & 'Energy minimization of multiple conformations', - & 'Checking energy gradient', - & 'Entropic sampling Monte Carlo (with minimization)', - & 'Energy map', - & 'CSA calculations', - & 'Not used 9', - & 'Not used 10', - & 'Soft regularization of PDB structure', - & 'Mesoscopic molecular dynamics (MD) ', - & 'Not used 13', - & 'Replica exchange molecular dynamics (REMD)'/ - external ilen - -c call memmon_print_usage() - - call init_task - if (me.eq.king) - & write(iout,*)'### LAST MODIFIED 11/03/09 1:19PM by czarek' - if (me.eq.king) call cinfo -C Read force field parameters and job setup data - call readrtns - call flush(iout) -C - 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) -C -c if (modecalc.eq.-2) then -c call test -c stop -c else if (modecalc.eq.-1) then -c write(iout,*) "call check_sc_map next" -c call check_bond -c stop -c endif -#ifdef MPI - if (fg_rank.gt.0) then -C Fine-grain slaves just do energy and gradient components. - call ergastulum ! slave workhouse in Latin - else -#endif - if (modecalc.eq.0) then - call exec_eeval_or_minim -c else if (modecalc.eq.1) then -c call exec_regularize -c else if (modecalc.eq.2) then -c call exec_thread -c else if (modecalc.eq.3 .or. modecalc .eq.6) then -c call exec_MC - else if (modecalc.eq.4) then - call exec_mult_eeval_or_minim - else if (modecalc.eq.5) then - call exec_checkgrad -c else if (ModeCalc.eq.7) then -c call exec_map - else if (ModeCalc.eq.8) then - call exec_CSA -c else if (modecalc.eq.11) then -c call exec_softreg -c else if (modecalc.eq.12) then -c call exec_MD -c else if (modecalc.eq.14) then -c call exec_MREMD - else - write (iout,'(a)') 'This calculation type is not supported', - & ModeCalc - endif -#ifdef MPI - endif -C Finish task. - if (fg_rank.eq.0) call finish_task -c 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 -c--------------------------------------------------------------------------- - subroutine exec_eeval_or_minim - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SETUP' - 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' -c include 'COMMON.REMD' -c include 'COMMON.MD' - include 'COMMON.SBRIDGE' - common /srutu/ icall - double precision energy(0:n_ene) - double precision energy_long(0:n_ene),energy_short(0:n_ene) - double precision varia(maxvar) - if (indpdb.eq.0) call chainbuild -c time00=MPI_Wtime() - call chainbuild_cart -c if (split_ene) then -c print *,"Processor",myrank," after chainbuild" -c icall=1 -c call etotal_long(energy_long(0)) -c write (iout,*) "Printing long range energy" -c call enerprint(energy_long(0)) -c call etotal_short(energy_short(0)) -c write (iout,*) "Printing short range energy" -c call enerprint(energy_short(0)) -c do i=0,n_ene -c energy(i)=energy_long(i)+energy_short(i) -c write (iout,*) i,energy_long(i),energy_short(i),energy(i) -c enddo -c write (iout,*) "Printing long+short range energy" -c call enerprint(energy(0)) -c endif - call etotal(energy(0)) -c time_ene=MPI_Wtime()-time00 - write (iout,*) "Time for energy evaluation",time_ene - print *,"after etotal" - etota = energy(0) - etot =etota - call enerprint(energy(0)) -c call hairpin(.true.,nharp,iharp) -c call secondary2(.true.) - if (minim) then - - if (dccart) then - print *, 'Calling MINIM_DC' -c time1=MPI_WTIME() - call minim_dc(etot,iretcode,nfun) - else - if (indpdb.ne.0) then - call bond_regular - call chainbuild - endif - call geom_to_var(nvar,varia) - print *,'Calling MINIMIZE.' -c time1=MPI_WTIME() - call minimize(etot,varia,iretcode,nfun) - endif - print *,'SUMSL return code is',iretcode,' eval ',nfun -c evals=nfun/(MPI_WTIME()-time1) - print *,'# eval/s',evals - print *,'refstr=',refstr -c call hairpin(.true.,nharp,iharp) -c call secondary2(.true.) - call etotal(energy(0)) - etot = energy(0) - call enerprint(energy(0)) - - 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 - print *,'refstr=',refstr - if (refstr) call rms_nac_nnc(rms,frac,frac_nn,co,.true.) - call briefout(0,etot) - endif - if (outpdb) call pdbout(etot,titel(:32),ipdb) - if (outmol2) call mol2out(etot,titel(:32)) - return - end - - subroutine exec_checkgrad - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SETUP' - 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' -c include 'COMMON.REMD' - include 'COMMON.MD_' - include 'COMMON.SBRIDGE' - common /srutu/ icall - double precision energy(0:max_ene) -c do i=2,nres -c vbld(i)=vbld(i)+ran_number(-0.1d0,0.1d0) -c if (itype(i).ne.10) -c & vbld(i+nres)=vbld(i+nres)+ran_number(-0.001d0,0.001d0) -c enddo - if (indpdb.eq.0) call chainbuild -c do i=0,nres -c do j=1,3 -c dc(j,i)=dc(j,i)+ran_number(-0.2d0,0.2d0) -c enddo -c enddo -c do i=1,nres-1 -c if (itype(i).ne.10) then -c do j=1,3 -c dc(j,i+nres)=dc(j,i+nres)+ran_number(-0.2d0,0.2d0) -c enddo -c endif -c enddo -c do j=1,3 -c dc(j,0)=ran_number(-0.2d0,0.2d0) -c enddo - usampl=.true. - totT=1.d0 - eq_time=0.0d0 -c call read_fragments -c read(inp,*) t_bath -c call rescale_weights(t_bath) - 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 -c--------------------------------------------------------------------------- - subroutine exec_CSA -#ifdef MPI - include "mpif.h" -#endif - include 'DIMENSIONS' - include 'COMMON.IOUNITS' -C Conformational Space Annealling programmed by Jooyoung Lee. -C This method works only with parallel machines! -#ifdef MPI - call together -#else - write (iout,*) "CSA works on parallel machines only" -#endif - return - end -c--------------------------------------------------------------------------- -#ifdef MPI - subroutine exec_mult_eeval_or_minim - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'mpif.h' - integer muster(mpi_status_size) - include 'COMMON.SETUP' - 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.SBRIDGE' - double precision varia(maxvar) - integer ind(6) - double precision energy(0:n_ene) - logical eof - eof=.false. - - if(me.ne.king) then - call minim_mcmf - return - endif - - close (intin) - open(intin,file=intinname,status='old') - write (istat,'(a5,100a12)')"# ", - & (wname(print_order(i)),i=1,nprint_ene) - if (refstr) then - write (istat,'(a5,100a12)')"# ", - & (ename(print_order(i)),i=1,nprint_ene), - & "ETOT total","RMSD","nat.contact","nnt.contact", - & "cont.order","TMscore" - else - write (istat,'(a5,100a12)')"# ", - & (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) -c 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) - 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(0)) - call briefout(iconf,energy(0)) - call enerprint(energy(0)) - etot=energy(0) - if (refstr) then - call rms_nac_nnc(rms,frac,frac_nn,co,.true.) - call calc_tmscore(tm,.true.) - write (istat,'(i5,100(f12.3))') iconf, - & (energy(print_order(i)),i=1,nprint_ene),etot, - & rms,frac,frac_nn,co,tm - else - write (istat,'(i5,100(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 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) -c 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) - 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 - - n=n+1 - write (iout,*) 'Conformation #',iconf,' read' - 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) -c 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) -c 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) -c print *,'result received from worker ',man,' sending now' - - call var_to_geom(nvar,varia) - call chainbuild - call etotal(energy(0)) - iconf=ind(2) - write (iout,*) - write (iout,*) - write (iout,*) 'Conformation #',iconf," sumsl return code ", - & ind(5) - - etot=energy(0) - call enerprint(energy(0)) - call briefout(iconf,etot) - if (refstr) then - call rms_nac_nnc(rms,frac,frac_nn,co,.true.) - call calc_tmscore(tm,.true.) - write (istat,'(i5,100(f12.3))') iconf, - & (energy(print_order(i)),i=1,nprint_ene),etot, - & rms,frac,frac_nn,co,tm - else - write (istat,'(i5,100(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=11,err=11) time,ene - call read_x(intin,*11) -c 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) - 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 - n=n+1 - write (iout,*) 'Conformation #',iconf,' read' - 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(0)) - iconf=ind(2) - write (iout,*) - write (iout,*) - write (iout,*) 'Conformation #',iconf," sumsl return code ", - & ind(5) - - etot=energy(0) - call enerprint(energy(0)) - call briefout(iconf,etot) - if (refstr) then - call rms_nac_nnc(rms,frac,frac_nn,co,.true.) - call calc_tmscore(tm,.true.) - write (istat,'(i5,100(f12.3))') iconf, - & (energy(print_order(i)),i=1,nprint_ene),etot, - & rms,frac,frac_nn,co,tm - else - write (istat,'(i5,100(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 - return - end -#else - subroutine exec_mult_eeval_or_minim - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - write (iout,*) "Unsupported option in serial version" - return - end -#endif -c--------------------------------------------------------------------------- -