X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fsrc_MD%2Fsrc%2Freadrtns_CSA.F;fp=source%2Funres%2Fsrc_MD%2Fsrc%2Freadrtns_CSA.F;h=0000000000000000000000000000000000000000;hb=0a11a2c4ccee14ed99ae44f2565b270ba8d4bbb6;hp=50f794f61293c4249d32f5f4a062c70f65935e31;hpb=5eb407964903815242c59de10960f42761139e10;p=unres.git diff --git a/source/unres/src_MD/src/readrtns_CSA.F b/source/unres/src_MD/src/readrtns_CSA.F deleted file mode 100644 index 50f794f..0000000 --- a/source/unres/src_MD/src/readrtns_CSA.F +++ /dev/null @@ -1,2585 +0,0 @@ - subroutine readrtns - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SETUP' - include 'COMMON.CONTROL' - include 'COMMON.SBRIDGE' - include 'COMMON.IOUNITS' - logical file_exist -C Read force-field parameters except weights - call parmread -C Read job setup parameters - call read_control -C Read control parameters for energy minimzation if required - if (minim) call read_minim -C Read MCM control parameters if required - if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread -C Read MD control parameters if reqjuired - if (modecalc.eq.12) call read_MDpar -C Read MREMD control parameters if required - if (modecalc.eq.14) then - call read_MDpar - call read_REMDpar - endif -C Read MUCA control parameters if required - if (lmuca) call read_muca -C Read CSA control parameters if required (from fort.40 if exists -C otherwise from general input file) - if (modecalc.eq.8) then - inquire (file="fort.40",exist=file_exist) - if (.not.file_exist) call csaread - endif -cfmc if (modecalc.eq.10) call mcmfread -C Read molecule information, molecule geometry, energy-term weights, and -C restraints if requested - call molread -C Print restraint information -#ifdef MPI - if (.not. out1file .or. me.eq.king) then -#endif - if (nhpb.gt.nss) - &write (iout,'(a,i5,a)') "The following",nhpb-nss, - & " distance constraints have been imposed" - do i=nss+1,nhpb - write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i) - enddo -#ifdef MPI - endif -#endif -c print *,"Processor",myrank," leaves READRTNS" - return - end -C------------------------------------------------------------------------------- - subroutine read_control -C -C Read contorl data -C - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MP - include 'mpif.h' - logical OKRandom, prng_restart - real*8 r1 -#endif - include 'COMMON.IOUNITS' - include 'COMMON.TIME1' - include 'COMMON.THREAD' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.MCM' - include 'COMMON.MAP' - include 'COMMON.HEADER' - include 'COMMON.CSA' - include 'COMMON.CHAIN' - include 'COMMON.MUCA' - include 'COMMON.MD' - include 'COMMON.FFIELD' - include 'COMMON.SETUP' - COMMON /MACHSW/ KDIAG,ICORFL,IXDR - character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/ - character*80 ucase - character*320 controlcard - - nglob_csa=0 - eglob_csa=1d99 - nmin_csa=0 - read (INP,'(a)') titel - call card_concat(controlcard) -c out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0 -c print *,"Processor",me," fg_rank",fg_rank," out1file",out1file - call reada(controlcard,'SEED',seed,0.0D0) - call random_init(seed) -C Set up the time limit (caution! The time must be input in minutes!) - read_cart=index(controlcard,'READ_CART').gt.0 - call readi(controlcard,'CONSTR_DIST',constr_dist,0) - call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours - unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0 - call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes - call reada(controlcard,'RMSDBC',rmsdbc,3.0D0) - call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0) - call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0) - call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0) - call reada(controlcard,'DRMS',drms,0.1D0) - if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then - write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc - write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1 - write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max - write (iout,'(a,f10.1)')'DRMS = ',drms - write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm - write (iout,'(a,f10.1)') 'Time limit (min):',timlim - endif - call readi(controlcard,'NZ_START',nz_start,0) - call readi(controlcard,'NZ_END',nz_end,0) - call readi(controlcard,'IZ_SC',iz_sc,0) - timlim=60.0D0*timlim - safety = 60.0d0*safety - timem=timlim - modecalc=0 - 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 - sideadd=(index(controlcard,'SIDEADD').gt.0) - energy_dec=(index(controlcard,'ENERGY_DEC').gt.0) - outpdb=(index(controlcard,'PDBOUT').gt.0) - outmol2=(index(controlcard,'MOL2OUT').gt.0) - pdbref=(index(controlcard,'PDBREF').gt.0) - refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0) - indpdb=index(controlcard,'PDBSTART') - extconf=(index(controlcard,'EXTCONF').gt.0) - call readi(controlcard,'IPRINT',iprint,0) - call readi(controlcard,'MAXGEN',maxgen,10000) - call readi(controlcard,'MAXOVERLAP',maxoverlap,1000) - call readi(controlcard,"KDIAG",kdiag,0) - call readi(controlcard,"RESCALE_MODE",rescale_mode,1) - if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) - & write (iout,*) "RESCALE_MODE",rescale_mode - split_ene=index(controlcard,'SPLIT_ENE').gt.0 - if (index(controlcard,'REGULAR').gt.0.0D0) then - call reada(controlcard,'WEIDIS',weidis,0.1D0) - modecalc=1 - refstr=.true. - endif - if (index(controlcard,'CHECKGRAD').gt.0) then - modecalc=5 - if (index(controlcard,'CART').gt.0) then - icheckgrad=1 - elseif (index(controlcard,'CARINT').gt.0) then - icheckgrad=2 - else - icheckgrad=3 - endif - elseif (index(controlcard,'THREAD').gt.0) then - modecalc=2 - call readi(controlcard,'THREAD',nthread,0) - if (nthread.gt.0) then - call reada(controlcard,'WEIDIS',weidis,0.1D0) - else - if (fg_rank.eq.0) - & write (iout,'(a)')'A number has to follow the THREAD keyword.' - stop 'Error termination in Read_Control.' - endif - else if (index(controlcard,'MCMA').gt.0) then - modecalc=3 - else if (index(controlcard,'MCEE').gt.0) then - modecalc=6 - else if (index(controlcard,'MULTCONF').gt.0) then - modecalc=4 - else if (index(controlcard,'MAP').gt.0) then - modecalc=7 - call readi(controlcard,'MAP',nmap,0) - else if (index(controlcard,'CSA').gt.0) then - modecalc=8 -crc else if (index(controlcard,'ZSCORE').gt.0) then -crc -crc ZSCORE is rm from UNRES, modecalc=9 is available -crc -crc modecalc=9 -cfcm else if (index(controlcard,'MCMF').gt.0) then -cfmc modecalc=10 - else if (index(controlcard,'SOFTREG').gt.0) then - modecalc=11 - else if (index(controlcard,'CHECK_BOND').gt.0) then - modecalc=-1 - else if (index(controlcard,'TEST').gt.0) then - modecalc=-2 - else if (index(controlcard,'MD').gt.0) then - modecalc=12 - else if (index(controlcard,'RE ').gt.0) then - modecalc=14 - endif - - lmuca=index(controlcard,'MUCA').gt.0 - call readi(controlcard,'MUCADYN',mucadyn,0) - call readi(controlcard,'MUCASMOOTH',muca_smooth,0) - if (lmuca .and. (me.eq.king .or. .not.out1file )) - & then - write (iout,*) 'MUCADYN=',mucadyn - write (iout,*) 'MUCASMOOTH=',muca_smooth - endif - - iscode=index(controlcard,'ONE_LETTER') - indphi=index(controlcard,'PHI') - indback=index(controlcard,'BACK') - iranconf=index(controlcard,'RAND_CONF') - i2ndstr=index(controlcard,'USE_SEC_PRED') - gradout=index(controlcard,'GRADOUT').gt.0 - gnorm_check=index(controlcard,'GNORM_CHECK').gt.0 - - if(me.eq.king.or..not.out1file) - & write (iout,'(2a)') diagmeth(kdiag), - & ' routine used to diagonalize matrices.' - return - end -c-------------------------------------------------------------------------- - subroutine read_REMDpar -C -C Read REMD settings -C - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.TIME1' - include 'COMMON.MD' -#ifndef LANG0 - include 'COMMON.LANGEVIN' -#else - include 'COMMON.LANGEVIN.lang0' -#endif - include 'COMMON.INTERACT' - include 'COMMON.NAMES' - include 'COMMON.GEO' - include 'COMMON.REMD' - include 'COMMON.CONTROL' - include 'COMMON.SETUP' - character*80 ucase - character*320 controlcard - character*3200 controlcard1 - integer iremd_m_total - - if(me.eq.king.or..not.out1file) - & write (iout,*) "REMD setup" - - call card_concat(controlcard) - call readi(controlcard,"NREP",nrep,3) - call readi(controlcard,"NSTEX",nstex,1000) - call reada(controlcard,"RETMIN",retmin,10.0d0) - call reada(controlcard,"RETMAX",retmax,1000.0d0) - mremdsync=(index(controlcard,'SYNC').gt.0) - call readi(controlcard,"NSYN",i_sync_step,100) - restart1file=(index(controlcard,'REST1FILE').gt.0) - traj1file=(index(controlcard,'TRAJ1FILE').gt.0) - call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1) - if(max_cache_traj_use.gt.max_cache_traj) - & max_cache_traj_use=max_cache_traj - if(me.eq.king.or..not.out1file) then -cd if (traj1file) then -crc caching is in testing - NTWX is not ignored -cd write (iout,*) "NTWX value is ignored" -cd write (iout,*) " trajectory is stored to one file by master" -cd write (iout,*) " before exchange at NSTEX intervals" -cd endif - write (iout,*) "NREP= ",nrep - write (iout,*) "NSTEX= ",nstex - write (iout,*) "SYNC= ",mremdsync - write (iout,*) "NSYN= ",i_sync_step - write (iout,*) "TRAJCACHE= ",max_cache_traj_use - endif - - t_exchange_only=(index(controlcard,'TONLY').gt.0) - call readi(controlcard,"HREMD",hremd,0) - if((me.eq.king.or..not.out1file).and.hremd.gt.0) then - write (iout,*) "Hamiltonian REMD with ",hremd," sets of weights" - endif - if(usampl.and.hremd.gt.0) then - write (iout,'(//a)') - & "========== ERROR: USAMPL and HREMD cannot be used together" -#ifdef MPI - call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE) -#endif - stop - endif - - - remd_tlist=.false. - if (index(controlcard,'TLIST').gt.0) then - remd_tlist=.true. - call card_concat(controlcard1) - read(controlcard1,*) (remd_t(i),i=1,nrep) - if(me.eq.king.or..not.out1file) - & write (iout,*)'tlist',(remd_t(i),i=1,nrep) - endif - remd_mlist=.false. - if (index(controlcard,'MLIST').gt.0) then - remd_mlist=.true. - call card_concat(controlcard1) - read(controlcard1,*) (remd_m(i),i=1,nrep) - if(me.eq.king.or..not.out1file) then - write (iout,*)'mlist',(remd_m(i),i=1,nrep) - iremd_m_total=0 - do i=1,nrep - iremd_m_total=iremd_m_total+remd_m(i) - enddo - if(hremd.gt.1)then - write (iout,*) 'Total number of replicas ', - & iremd_m_total*hremd - else - write (iout,*) 'Total number of replicas ',iremd_m_total - endif - endif - endif - if(me.eq.king.or..not.out1file) - & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup " - return - end -c-------------------------------------------------------------------------- - subroutine read_MDpar -C -C Read MD settings -C - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.TIME1' - include 'COMMON.MD' -#ifndef LANG0 - include 'COMMON.LANGEVIN' -#else - include 'COMMON.LANGEVIN.lang0' -#endif - include 'COMMON.INTERACT' - include 'COMMON.NAMES' - include 'COMMON.GEO' - include 'COMMON.SETUP' - include 'COMMON.CONTROL' - include 'COMMON.SPLITELE' - character*80 ucase - character*320 controlcard - - call card_concat(controlcard) - call readi(controlcard,"NSTEP",n_timestep,1000000) - call readi(controlcard,"NTWE",ntwe,100) - call readi(controlcard,"NTWX",ntwx,1000) - call reada(controlcard,"DT",d_time,1.0d-1) - call reada(controlcard,"DVMAX",dvmax,2.0d1) - call reada(controlcard,"DAMAX",damax,1.0d1) - call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1) - call readi(controlcard,"LANG",lang,0) - RESPA = index(controlcard,"RESPA") .gt. 0 - call readi(controlcard,"NTIME_SPLIT",ntime_split,1) - ntime_split0=ntime_split - call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64) - ntime_split0=ntime_split - call reada(controlcard,"R_CUT",r_cut,2.0d0) - call reada(controlcard,"LAMBDA",rlamb,0.3d0) - rest = index(controlcard,"REST").gt.0 - tbf = index(controlcard,"TBF").gt.0 - tnp = index(controlcard,"NOSEPOINCARE99").gt.0 - tnp1 = index(controlcard,"NOSEPOINCARE01").gt.0 - tnh = index(controlcard,"NOSEHOOVER96").gt.0 - if (RESPA.and.tnh)then - xiresp = index(controlcard,"XIRESP").gt.0 - endif - call reada(controlcard,"Q_NP",Q_np,0.1d0) - usampl = index(controlcard,"USAMPL").gt.0 - - mdpdb = index(controlcard,"MDPDB").gt.0 - call reada(controlcard,"T_BATH",t_bath,300.0d0) - call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1) - call reada(controlcard,"EQ_TIME",eq_time,1.0d+4) - call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000) - if (count_reset_moment.eq.0) count_reset_moment=1000000000 - call readi(controlcard,"RESET_VEL",count_reset_vel,1000) - reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0 - reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0 - if (count_reset_vel.eq.0) count_reset_vel=1000000000 - large = index(controlcard,"LARGE").gt.0 - print_compon = index(controlcard,"PRINT_COMPON").gt.0 - rattle = index(controlcard,"RATTLE").gt.0 -c if performing umbrella sampling, fragments constrained are read from the fragment file - nset=0 - if(usampl) then - call read_fragments - endif - - if(me.eq.king.or..not.out1file) then - write (iout,*) - write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run " - write (iout,*) - write (iout,'(a)') "The units are:" - write (iout,'(a)') "positions: angstrom, time: 48.9 fs" - write (iout,'(2a)') "velocity: angstrom/(48.9 fs),", - & " acceleration: angstrom/(48.9 fs)**2" - write (iout,'(a)') "energy: kcal/mol, temperature: K" - write (iout,*) - write (iout,'(a60,i10)') "Number of time steps:",n_timestep - write (iout,'(a60,f10.5,a)') - & "Initial time step of numerical integration:",d_time, - & " natural units" - write (iout,'(60x,f10.5,a)') d_time*48.9," fs" - 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 - endif - write (iout,'(2a,f10.5)') - & "Maximum acceleration threshold to reduce the time step", - & "/increase split number:",damax - write (iout,'(2a,f10.5)') - & "Maximum predicted energy drift to reduce the timestep", - & "/increase split number:",edriftmax - write (iout,'(a60,f10.5)') - & "Maximum velocity threshold to reduce velocities:",dvmax - write (iout,'(a60,i10)') "Frequency of property output:",ntwe - write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx - if (rattle) write (iout,'(a60)') - & "Rattle algorithm used to constrain the virtual bonds" - endif - reset_fricmat=1000 - if (lang.gt.0) then - call reada(controlcard,"ETAWAT",etawat,0.8904d0) - call reada(controlcard,"RWAT",rwat,1.4d0) - call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2) - surfarea=index(controlcard,"SURFAREA").gt.0 - call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000) - if(me.eq.king.or..not.out1file)then - write (iout,'(/a,$)') "Langevin dynamics calculation" - if (lang.eq.1) then - write (iout,'(a/)') - & " with direct integration of Langevin equations" - else if (lang.eq.2) then - write (iout,'(a/)') " with TINKER stochasic MD integrator" - else if (lang.eq.3) then - write (iout,'(a/)') " with Ciccotti's stochasic MD integrator" - else if (lang.eq.4) then - write (iout,'(a/)') " in overdamped mode" - else - write (iout,'(//a,i5)') - & "=========== ERROR: Unknown Langevin dynamics mode:",lang - stop - endif - write (iout,'(a60,f10.5)') "Temperature:",t_bath - write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat - write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat - write (iout,'(a60,f10.5)') - & "Scaling factor of the friction forces:",scal_fric - if (surfarea) write (iout,'(2a,i10,a)') - & "Friction coefficients will be scaled by solvent-accessible", - & " surface area every",reset_fricmat," steps." - endif -c Calculate friction coefficients and bounds of stochastic forces - eta=6*pi*cPoise*etawat - if(me.eq.king.or..not.out1file) - & write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:" - & ,eta - gamp=scal_fric*(pstok+rwat)*eta - stdfp=dsqrt(2*Rb*t_bath/d_time) - do i=1,ntyp - gamsc(i)=scal_fric*(restok(i)+rwat)*eta - stdfsc(i)=dsqrt(2*Rb*t_bath/d_time) - enddo - if(me.eq.king.or..not.out1file)then - write (iout,'(/2a/)') - & "Radii of site types and friction coefficients and std's of", - & " stochastic forces of fully exposed sites" - write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp) - do i=1,ntyp - write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i), - & gamsc(i),stdfsc(i)*dsqrt(gamsc(i)) - enddo - endif - else if (tbf) then - if(me.eq.king.or..not.out1file)then - write (iout,'(a)') "Berendsen bath calculation" - write (iout,'(a60,f10.5)') "Temperature:",t_bath - write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath - if (reset_moment) - & write (iout,'(a,i10,a)') "Momenta will be reset at zero every", - & count_reset_moment," steps" - if (reset_vel) - & write (iout,'(a,i10,a)') - & "Velocities will be reset at random every",count_reset_vel, - & " steps" - endif - else if (tnp .or. tnp1 .or. tnh) then - if (tnp .or. tnp1) then - write (iout,'(a)') "Nose-Poincare bath calculation" - if (tnp) write (iout,'(a)') - & "J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird" - if (tnp1) write (iout,'(a)') "JPSJ 70 75 (2001) S. Nose" - else - write (iout,'(a)') "Nose-Hoover bath calculation" - write (iout,'(a)') "Mol.Phys. 87 1117 (1996) Martyna et al." - nresn=1 - nyosh=1 - nnos=1 - do i=1,nnos - qmass(i)=Q_np - xlogs(i)=1.0 - vlogs(i)=0.0 - enddo - do i=1,nyosh - WDTI(i) = 1.0*d_time/nresn - WDTI2(i)=WDTI(i)/2 - WDTI4(i)=WDTI(i)/4 - WDTI8(i)=WDTI(i)/8 - enddo - if (RESPA) then - if(xiresp) then - write (iout,'(a)') "NVT-XI-RESPA algorithm" - else - write (iout,'(a)') "NVT-XO-RESPA algorithm" - endif - do i=1,nyosh - WDTIi(i) = 1.0*d_time/nresn/ntime_split - WDTIi2(i)=WDTIi(i)/2 - WDTIi4(i)=WDTIi(i)/4 - WDTIi8(i)=WDTIi(i)/8 - enddo - endif - endif - - write (iout,'(a60,f10.5)') "Temperature:",t_bath - write (iout,'(a60,f10.5)') "Q =",Q_np - if (reset_moment) - & write (iout,'(a,i10,a)') "Momenta will be reset at zero every", - & count_reset_moment," steps" - if (reset_vel) - & write (iout,'(a,i10,a)') - & "Velocities will be reset at random every",count_reset_vel, - & " steps" - - else - if(me.eq.king.or..not.out1file) - & write (iout,'(a31)') "Microcanonical mode calculation" - endif - if(me.eq.king.or..not.out1file)then - if (rest) write (iout,'(/a/)') "===== Calculation restarted ====" - if (usampl) then - write(iout,*) "MD running with constraints." - write(iout,*) "Equilibration time ", eq_time, " mtus." - write(iout,*) "Constraining ", nfrag," fragments." - write(iout,*) "Length of each fragment, weight and q0:" - do iset=1,nset - write (iout,*) "Set of restraints #",iset - do i=1,nfrag - write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset), - & ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset) - enddo - write(iout,*) "constraints between ", npair, "fragments." - write(iout,*) "constraint pairs, weights and q0:" - do i=1,npair - write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset), - & ipair(2,i,iset),wpair(i,iset),qinpair(i,iset) - enddo - write(iout,*) "angle constraints within ", nfrag_back, - & "backbone fragments." - write(iout,*) "fragment, weights:" - do i=1,nfrag_back - write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset), - & ifrag_back(2,i,iset),wfrag_back(1,i,iset), - & wfrag_back(2,i,iset),wfrag_back(3,i,iset) - enddo - enddo - iset=mod(kolor,nset)+1 - endif - endif - if(me.eq.king.or..not.out1file) - & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup " - return - end -c------------------------------------------------------------------------------ - subroutine molread -C -C Read molecular data. -C - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' - integer error_msg -#endif - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.LOCAL' - include 'COMMON.NAMES' - include 'COMMON.CHAIN' - include 'COMMON.FFIELD' - include 'COMMON.SBRIDGE' - include 'COMMON.HEADER' - include 'COMMON.CONTROL' - include 'COMMON.DBASE' - include 'COMMON.THREAD' - include 'COMMON.CONTACTS' - include 'COMMON.TORCNSTR' - include 'COMMON.TIME1' - include 'COMMON.BOUNDS' - include 'COMMON.MD' - include 'COMMON.REMD' - include 'COMMON.SETUP' - character*4 sequence(maxres) - integer rescode - double precision x(maxvar) - character*256 pdbfile - character*320 weightcard - character*80 weightcard_t,ucase - dimension itype_pdb(maxres) - common /pizda/ itype_pdb - logical seq_comp,fail - double precision energia(0:n_ene) - integer ilen - external ilen -C -C Body -C -C Read weights of the subsequent energy terms. - if(hremd.gt.0) then - - k=0 - do il=1,hremd - do i=1,nrep - do j=1,remd_m(i) - i2set(k)=il - k=k+1 - enddo - enddo - enddo - - if(me.eq.king.or..not.out1file) then - write (iout,*) 'Reading ',hremd,' sets of weights for HREMD' - write (iout,*) 'Current weights for processor ', - & me,' set ',i2set(me) - endif - - do i=1,hremd - call card_concat(weightcard) - call reada(weightcard,'WLONG',wlong,1.0D0) - call reada(weightcard,'WSC',wsc,wlong) - call reada(weightcard,'WSCP',wscp,wlong) - call reada(weightcard,'WELEC',welec,1.0D0) - call reada(weightcard,'WVDWPP',wvdwpp,welec) - call reada(weightcard,'WEL_LOC',wel_loc,1.0D0) - call reada(weightcard,'WCORR4',wcorr4,0.0D0) - call reada(weightcard,'WCORR5',wcorr5,0.0D0) - call reada(weightcard,'WCORR6',wcorr6,0.0D0) - call reada(weightcard,'WTURN3',wturn3,1.0D0) - call reada(weightcard,'WTURN4',wturn4,1.0D0) - call reada(weightcard,'WTURN6',wturn6,1.0D0) - call reada(weightcard,'WSCCOR',wsccor,1.0D0) - call reada(weightcard,'WSTRAIN',wstrain,1.0D0) - call reada(weightcard,'WBOND',wbond,1.0D0) - call reada(weightcard,'WTOR',wtor,1.0D0) - call reada(weightcard,'WTORD',wtor_d,1.0D0) - call reada(weightcard,'WANG',wang,1.0D0) - call reada(weightcard,'WSCLOC',wscloc,1.0D0) - call reada(weightcard,'SCAL14',scal14,0.4D0) - call reada(weightcard,'SCALSCP',scalscp,1.0d0) - call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0) - call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) - call reada(weightcard,'TEMP0',temp0,300.0d0) - if (index(weightcard,'SOFT').gt.0) ipot=6 -C 12/1/95 Added weight for the multi-body term WCORR - call reada(weightcard,'WCORRH',wcorr,1.0D0) - if (wcorr4.gt.0.0d0) wcorr=wcorr4 - - hweights(i,1)=wsc - hweights(i,2)=wscp - hweights(i,3)=welec - hweights(i,4)=wcorr - hweights(i,5)=wcorr5 - hweights(i,6)=wcorr6 - hweights(i,7)=wel_loc - hweights(i,8)=wturn3 - hweights(i,9)=wturn4 - hweights(i,10)=wturn6 - hweights(i,11)=wang - hweights(i,12)=wscloc - hweights(i,13)=wtor - hweights(i,14)=wtor_d - hweights(i,15)=wstrain - hweights(i,16)=wvdwpp - hweights(i,17)=wbond - hweights(i,18)=scal14 - hweights(i,21)=wsccor - - enddo - - do i=1,n_ene - weights(i)=hweights(i2set(me),i) - enddo - wsc =weights(1) - wscp =weights(2) - welec =weights(3) - wcorr =weights(4) - wcorr5 =weights(5) - wcorr6 =weights(6) - wel_loc=weights(7) - wturn3 =weights(8) - wturn4 =weights(9) - wturn6 =weights(10) - wang =weights(11) - wscloc =weights(12) - wtor =weights(13) - wtor_d =weights(14) - wstrain=weights(15) - wvdwpp =weights(16) - wbond =weights(17) - scal14 =weights(18) - wsccor =weights(21) - - - else - call card_concat(weightcard) - call reada(weightcard,'WLONG',wlong,1.0D0) - call reada(weightcard,'WSC',wsc,wlong) - call reada(weightcard,'WSCP',wscp,wlong) - call reada(weightcard,'WELEC',welec,1.0D0) - call reada(weightcard,'WVDWPP',wvdwpp,welec) - call reada(weightcard,'WEL_LOC',wel_loc,1.0D0) - call reada(weightcard,'WCORR4',wcorr4,0.0D0) - call reada(weightcard,'WCORR5',wcorr5,0.0D0) - call reada(weightcard,'WCORR6',wcorr6,0.0D0) - call reada(weightcard,'WTURN3',wturn3,1.0D0) - call reada(weightcard,'WTURN4',wturn4,1.0D0) - call reada(weightcard,'WTURN6',wturn6,1.0D0) - call reada(weightcard,'WSCCOR',wsccor,1.0D0) - call reada(weightcard,'WSTRAIN',wstrain,1.0D0) - call reada(weightcard,'WBOND',wbond,1.0D0) - call reada(weightcard,'WTOR',wtor,1.0D0) - call reada(weightcard,'WTORD',wtor_d,1.0D0) - call reada(weightcard,'WANG',wang,1.0D0) - call reada(weightcard,'WSCLOC',wscloc,1.0D0) - call reada(weightcard,'SCAL14',scal14,0.4D0) - call reada(weightcard,'SCALSCP',scalscp,1.0d0) - call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0) - call reada(weightcard,'DELT_CORR',delt_corr,0.5d0) - call reada(weightcard,'TEMP0',temp0,300.0d0) - if (index(weightcard,'SOFT').gt.0) ipot=6 -C 12/1/95 Added weight for the multi-body term WCORR - call reada(weightcard,'WCORRH',wcorr,1.0D0) - if (wcorr4.gt.0.0d0) wcorr=wcorr4 - weights(1)=wsc - weights(2)=wscp - weights(3)=welec - weights(4)=wcorr - weights(5)=wcorr5 - weights(6)=wcorr6 - weights(7)=wel_loc - weights(8)=wturn3 - weights(9)=wturn4 - weights(10)=wturn6 - weights(11)=wang - weights(12)=wscloc - weights(13)=wtor - weights(14)=wtor_d - weights(15)=wstrain - weights(16)=wvdwpp - weights(17)=wbond - weights(18)=scal14 - weights(21)=wsccor - endif - - if(me.eq.king.or..not.out1file) - & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor, - & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3, - & wturn4,wturn6 - 10 format (/'Energy-term weights (unscaled):'// - & 'WSCC= ',f10.6,' (SC-SC)'/ - & 'WSCP= ',f10.6,' (SC-p)'/ - & 'WELEC= ',f10.6,' (p-p electr)'/ - & 'WVDWPP= ',f10.6,' (p-p VDW)'/ - & 'WBOND= ',f10.6,' (stretching)'/ - & 'WANG= ',f10.6,' (bending)'/ - & 'WSCLOC= ',f10.6,' (SC local)'/ - & 'WTOR= ',f10.6,' (torsional)'/ - & 'WTORD= ',f10.6,' (double torsional)'/ - & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ - & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ - & 'WCORR4= ',f10.6,' (multi-body 4th order)'/ - & 'WCORR5= ',f10.6,' (multi-body 5th order)'/ - & 'WCORR6= ',f10.6,' (multi-body 6th order)'/ - & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/ - & 'WTURN3= ',f10.6,' (turns, 3rd order)'/ - & 'WTURN4= ',f10.6,' (turns, 4th order)'/ - & 'WTURN6= ',f10.6,' (turns, 6th order)') - if(me.eq.king.or..not.out1file)then - if (wcorr4.gt.0.0d0) then - write (iout,'(/2a/)') 'Local-electrostatic type correlation ', - & 'between contact pairs of peptide groups' - write (iout,'(2(a,f5.3/))') - & 'Cutoff on 4-6th order correlation terms: ',cutoff_corr, - & 'Range of quenching the correlation terms:',2*delt_corr - else if (wcorr.gt.0.0d0) then - write (iout,'(/2a/)') 'Hydrogen-bonding correlation ', - & 'between contact pairs of peptide groups' - endif - write (iout,'(a,f8.3)') - & 'Scaling factor of 1,4 SC-p interactions:',scal14 - write (iout,'(a,f8.3)') - & 'General scaling factor of SC-p interactions:',scalscp - endif - r0_corr=cutoff_corr-delt_corr - do i=1,20 - aad(i,1)=scalscp*aad(i,1) - aad(i,2)=scalscp*aad(i,2) - bad(i,1)=scalscp*bad(i,1) - bad(i,2)=scalscp*bad(i,2) - enddo - call rescale_weights(t_bath) - if(me.eq.king.or..not.out1file) - & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor, - & wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3, - & wturn4,wturn6 - 22 format (/'Energy-term weights (scaled):'// - & 'WSCC= ',f10.6,' (SC-SC)'/ - & 'WSCP= ',f10.6,' (SC-p)'/ - & 'WELEC= ',f10.6,' (p-p electr)'/ - & 'WVDWPP= ',f10.6,' (p-p VDW)'/ - & 'WBOND= ',f10.6,' (stretching)'/ - & 'WANG= ',f10.6,' (bending)'/ - & 'WSCLOC= ',f10.6,' (SC local)'/ - & 'WTOR= ',f10.6,' (torsional)'/ - & 'WTORD= ',f10.6,' (double torsional)'/ - & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/ - & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/ - & 'WCORR4= ',f10.6,' (multi-body 4th order)'/ - & 'WCORR5= ',f10.6,' (multi-body 5th order)'/ - & 'WCORR6= ',f10.6,' (multi-body 6th order)'/ - & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/ - & 'WTURN3= ',f10.6,' (turns, 3rd order)'/ - & 'WTURN4= ',f10.6,' (turns, 4th order)'/ - & 'WTURN6= ',f10.6,' (turns, 6th order)') - if(me.eq.king.or..not.out1file) - & write (iout,*) "Reference temperature for weights calculation:", - & temp0 - call reada(weightcard,"D0CM",d0cm,3.78d0) - call reada(weightcard,"AKCM",akcm,15.1d0) - call reada(weightcard,"AKTH",akth,11.0d0) - call reada(weightcard,"AKCT",akct,12.0d0) - call reada(weightcard,"V1SS",v1ss,-1.08d0) - call reada(weightcard,"V2SS",v2ss,7.61d0) - call reada(weightcard,"V3SS",v3ss,13.7d0) - call reada(weightcard,"EBR",ebr,-5.50D0) - if(me.eq.king.or..not.out1file) then - write (iout,*) "Parameters of the SS-bond potential:" - write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth, - & " AKCT",akct - write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss - write (iout,*) "EBR",ebr - print *,'indpdb=',indpdb,' pdbref=',pdbref - endif - if (indpdb.gt.0 .or. pdbref) then - read(inp,'(a)') pdbfile - if(me.eq.king.or..not.out1file) - & write (iout,'(2a)') 'PDB data will be read from file ', - & pdbfile(:ilen(pdbfile)) - open(ipdbin,file=pdbfile,status='old',err=33) - goto 34 - 33 write (iout,'(a)') 'Error opening PDB file.' - stop - 34 continue -c print *,'Begin reading pdb data' - call readpdb -c print *,'Finished reading pdb data' - if(me.eq.king.or..not.out1file) - & write (iout,'(a,i3,a,i3)')'nsup=',nsup, - & ' nstart_sup=',nstart_sup - do i=1,nres - itype_pdb(i)=itype(i) - enddo - close (ipdbin) - nnt=nstart_sup - nct=nstart_sup+nsup-1 - call contact(.false.,ncont_ref,icont_ref,co) - - if (sideadd) then - if(me.eq.king.or..not.out1file) - & write(iout,*)'Adding sidechains' - maxsi=1000 - do i=2,nres-1 - iti=itype(i) - if (iti.ne.10) then - nsi=0 - fail=.true. - do while (fail.and.nsi.le.maxsi) - call gen_side(iti,theta(i+1),alph(i),omeg(i),fail) - nsi=nsi+1 - enddo - if(fail) write(iout,*)'Adding sidechain failed for res ', - & i,' after ',nsi,' trials' - endif - enddo - endif - endif - if (indpdb.eq.0) then -C Read sequence if not taken from the pdb file. - read (inp,*) nres -c print *,'nres=',nres - if (iscode.gt.0) then - read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres) - else - read (inp,'(20(1x,a3))') (sequence(i),i=1,nres) - endif -C Convert sequence to numeric code - do i=1,nres - itype(i)=rescode(i,sequence(i),iscode) - enddo -C Assign initial virtual bond lengths - do i=2,nres - vbld(i)=vbl - vbld_inv(i)=vblinv - enddo - do i=2,nres-1 - vbld(i+nres)=dsc(itype(i)) - vbld_inv(i+nres)=dsc_inv(itype(i)) -c write (iout,*) "i",i," itype",itype(i), -c & " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres) - enddo - endif -c print *,nres -c print '(20i4)',(itype(i),i=1,nres) - do i=1,nres -#ifdef PROCOR - if (itype(i).eq.21 .or. itype(i+1).eq.21) then -#else - if (itype(i).eq.21) then -#endif - itel(i)=0 -#ifdef PROCOR - else if (itype(i+1).ne.20) then -#else - else if (itype(i).ne.20) then -#endif - itel(i)=1 - else - itel(i)=2 - endif - enddo - if(me.eq.king.or..not.out1file)then - write (iout,*) "ITEL" - do i=1,nres-1 - write (iout,*) i,itype(i),itel(i) - enddo - print *,'Call Read_Bridge.' - endif - call read_bridge -C 8/13/98 Set limits to generating the dihedral angles - do i=1,nres - phibound(1,i)=-pi - phibound(2,i)=pi - enddo - read (inp,*) ndih_constr - if (ndih_constr.gt.0) then - read (inp,*) ftors - read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr) - if(me.eq.king.or..not.out1file)then - write (iout,*) - & 'There are',ndih_constr,' constraints on phi angles.' - do i=1,ndih_constr - write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i) - enddo - endif - do i=1,ndih_constr - phi0(i)=deg2rad*phi0(i) - drange(i)=deg2rad*drange(i) - enddo - if(me.eq.king.or..not.out1file) - & write (iout,*) 'FTORS',ftors - do i=1,ndih_constr - ii = idih_constr(i) - phibound(1,ii) = phi0(i)-drange(i) - phibound(2,ii) = phi0(i)+drange(i) - enddo - endif - nnt=1 -#ifdef MPI - if (me.eq.king) then -#endif - write (iout,'(a)') 'Boundaries in phi angle sampling:' - do i=1,nres - write (iout,'(a3,i5,2f10.1)') - & restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg - enddo -#ifdef MP - endif -#endif - nct=nres -cd print *,'NNT=',NNT,' NCT=',NCT - if (itype(1).eq.21) nnt=2 - if (itype(nres).eq.21) nct=nct-1 - if (pdbref) then - if(me.eq.king.or..not.out1file) - & write (iout,'(a,i3)') 'nsup=',nsup - nstart_seq=nnt - if (nsup.le.(nct-nnt+1)) then - do i=0,nct-nnt+1-nsup - if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then - nstart_seq=nnt+i - goto 111 - endif - enddo - write (iout,'(a)') - & 'Error - sequences to be superposed do not match.' - stop - else - do i=0,nsup-(nct-nnt+1) - if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1)) - & then - nstart_sup=nstart_sup+i - nsup=nct-nnt+1 - goto 111 - endif - enddo - write (iout,'(a)') - & 'Error - sequences to be superposed do not match.' - endif - 111 continue - if (nsup.eq.0) nsup=nct-nnt - if (nstart_sup.eq.0) nstart_sup=nnt - if (nstart_seq.eq.0) nstart_seq=nnt - if(me.eq.king.or..not.out1file) - & write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup, - & ' nstart_seq=',nstart_seq - endif -c--- Zscore rms ------- - if (nz_start.eq.0) nz_start=nnt - if (nz_end.eq.0 .and. nsup.gt.0) then - nz_end=nnt+nsup-1 - else if (nz_end.eq.0) then - nz_end=nct - endif - if(me.eq.king.or..not.out1file)then - write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end - write (iout,*) 'IZ_SC=',iz_sc - endif -c---------------------- - call init_int_table - if (refstr) then - if (.not.pdbref) then - call read_angles(inp,*38) - goto 39 - 38 write (iout,'(a)') 'Error reading reference structure.' -#ifdef MPI - call MPI_Finalize(MPI_COMM_WORLD,IERROR) - stop 'Error reading reference structure' -#endif - 39 call chainbuild - call setup_var -czscore call geom_to_var(nvar,coord_exp_zs(1,1)) - nstart_sup=nnt - nstart_seq=nnt - nsup=nct-nnt+1 - do i=1,2*nres - do j=1,3 - cref(j,i)=c(j,i) - enddo - enddo - call contact(.true.,ncont_ref,icont_ref,co) - endif -c write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup - call flush(iout) - if (constr_dist.gt.0) call read_dist_constr -c write (iout,*) "After read_dist_constr nhpb",nhpb - call hpb_partition - if(me.eq.king.or..not.out1file) - & write (iout,*) 'Contact order:',co - if (pdbref) then - if(me.eq.king.or..not.out1file) - & write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup - do i=1,ncont_ref - do j=1,2 - icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup - enddo - if(me.eq.king.or..not.out1file) - & write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ', - & icont_ref(1,i),' ', - & restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i) - enddo - endif - endif - if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4 - & .and. modecalc.ne.8 .and. modecalc.ne.9 .and. - & modecalc.ne.10) then -C If input structure hasn't been supplied from the PDB file read or generate -C initial geometry. - if (iranconf.eq.0 .and. .not. extconf) then - if(me.eq.king.or..not.out1file .and.fg_rank.eq.0) - & write (iout,'(a)') 'Initial geometry will be read in.' - if (read_cart) then - read(inp,'(8f10.5)',end=36,err=36) - & ((c(l,k),l=1,3),k=1,nres), - & ((c(l,k+nres),l=1,3),k=nnt,nct) - call int_from_cart1(.false.) - do i=1,nres-1 - do j=1,3 - dc(j,i)=c(j,i+1)-c(j,i) - dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1) - enddo - enddo - do i=nnt,nct - if (itype(i).ne.10) then - do j=1,3 - dc(j,i+nres)=c(j,i+nres)-c(j,i) - dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres) - enddo - endif - enddo - return - else - call read_angles(inp,*36) - endif - goto 37 - 36 write (iout,'(a)') 'Error reading angle file.' -#ifdef MPI - call mpi_finalize( MPI_COMM_WORLD,IERR ) -#endif - stop 'Error reading angle file.' - 37 continue - else if (extconf) then - if(me.eq.king.or..not.out1file .and. fg_rank.eq.0) - & write (iout,'(a)') 'Extended chain initial geometry.' - do i=3,nres - theta(i)=90d0*deg2rad - enddo - do i=4,nres - phi(i)=180d0*deg2rad - enddo - do i=2,nres-1 - alph(i)=110d0*deg2rad - enddo - do i=2,nres-1 - omeg(i)=-120d0*deg2rad - enddo - else - if(me.eq.king.or..not.out1file) - & write (iout,'(a)') 'Random-generated initial geometry.' - - -#ifdef MPI - if (me.eq.king .or. fg_rank.eq.0 .and. ( - & modecalc.eq.12 .or. modecalc.eq.14) ) then -#endif - do itrial=1,100 - itmp=1 - call gen_rand_conf(itmp,*30) - goto 40 - 30 write (iout,*) 'Failed to generate random conformation', - & ', itrial=',itrial - write (*,*) 'Processor:',me, - & ' Failed to generate random conformation', - & ' itrial=',itrial - call intout - -#ifdef AIX - call flush_(iout) -#else - call flush(iout) -#endif - enddo - write (iout,'(a,i3,a)') 'Processor:',me, - & ' error in generating random conformation.' - write (*,'(a,i3,a)') 'Processor:',me, - & ' error in generating random conformation.' - call flush(iout) -#ifdef MPI - call MPI_Abort(mpi_comm_world,error_msg,ierrcode) - 40 continue - endif -#else - 40 continue -#endif - endif - elseif (modecalc.eq.4) then - read (inp,'(a)') intinname - open (intin,file=intinname,status='old',err=333) - if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0) - & write (iout,'(a)') 'intinname',intinname - write (*,'(a)') 'Processor',myrank,' intinname',intinname - goto 334 - 333 write (iout,'(2a)') 'Error opening angle file ',intinname -#ifdef MPI - call MPI_Finalize(MPI_COMM_WORLD,IERR) -#endif - stop 'Error opening angle file.' - 334 continue - - endif -C Generate distance constraints, if the PDB structure is to be regularized. - if (nthread.gt.0) then - call read_threadbase - endif - call setup_var - if (me.eq.king .or. .not. out1file) - & call intout - if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then - write (iout,'(/a,i3,a)') - & 'The chain contains',ns,' disulfide-bridging cysteines.' - write (iout,'(20i4)') (iss(i),i=1,ns) - write (iout,'(/a/)') 'Pre-formed links are:' - do i=1,nss - i1=ihpb(i)-nres - i2=jhpb(i)-nres - it1=itype(i1) - it2=itype(i2) - if (me.eq.king.or..not.out1file) - & write (iout,'(2a,i3,3a,i3,a,3f10.3)') - & restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i), - & ebr,forcon(i) - enddo - write (iout,'(a)') - endif - if (i2ndstr.gt.0) call secstrp2dihc -c call geom_to_var(nvar,x) -c call etotal(energia(0)) -c call enerprint(energia(0)) -c call briefout(0,etot) -c stop -cd write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT -cd write (iout,'(a)') 'Variable list:' -cd write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar) -#ifdef MPI - if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file)) - & write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)') - & 'Processor',myrank,': end reading molecular data.' -#endif - return - end -c-------------------------------------------------------------------------- - logical function seq_comp(itypea,itypeb,length) - implicit none - integer length,itypea(length),itypeb(length) - integer i - do i=1,length - if (itypea(i).ne.itypeb(i)) then - seq_comp=.false. - return - endif - enddo - seq_comp=.true. - return - end -c----------------------------------------------------------------------------- - subroutine read_bridge -C Read information about disulfide bridges. - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.LOCAL' - include 'COMMON.NAMES' - include 'COMMON.CHAIN' - include 'COMMON.FFIELD' - include 'COMMON.SBRIDGE' - include 'COMMON.HEADER' - include 'COMMON.CONTROL' - include 'COMMON.DBASE' - include 'COMMON.THREAD' - include 'COMMON.TIME1' - include 'COMMON.SETUP' -C Read bridging residues. - read (inp,*) ns,(iss(i),i=1,ns) - print *,'ns=',ns - if(me.eq.king.or..not.out1file) - & write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns) -C Check whether the specified bridging residues are cystines. - do i=1,ns - if (itype(iss(i)).ne.1) then - if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, - & ' can form a disulfide bridge?!!!' - write (*,'(2a,i3,a)') - & 'Do you REALLY think that the residue ',restyp(iss(i)),i, - & ' can form a disulfide bridge?!!!' -#ifdef MPI - call MPI_Finalize(MPI_COMM_WORLD,ierror) - stop -#endif - endif - enddo -C Read preformed bridges. - if (ns.gt.0) then - read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss) - write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss) - if (nss.gt.0) then - nhpb=nss -C Check if the residues involved in bridges are in the specified list of -C bridging residues. - do i=1,nss - do j=1,i-1 - if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j) - & .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then - write (iout,'(a,i3,a)') 'Disulfide pair',i, - & ' contains residues present in other pairs.' - write (*,'(a,i3,a)') 'Disulfide pair',i, - & ' contains residues present in other pairs.' -#ifdef MPI - call MPI_Finalize(MPI_COMM_WORLD,ierror) - stop -#endif - endif - enddo - do j=1,ns - if (ihpb(i).eq.iss(j)) goto 10 - enddo - write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.' - 10 continue - do j=1,ns - if (jhpb(i).eq.iss(j)) goto 20 - enddo - write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.' - 20 continue - dhpb(i)=dbr - forcon(i)=fbr - enddo - do i=1,nss - ihpb(i)=ihpb(i)+nres - jhpb(i)=jhpb(i)+nres - enddo - endif - endif - return - end -c---------------------------------------------------------------------------- - subroutine read_x(kanal,*) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.CONTROL' - include 'COMMON.LOCAL' - include 'COMMON.INTERACT' -c Read coordinates from input -c - read(kanal,'(8f10.5)',end=10,err=10) - & ((c(l,k),l=1,3),k=1,nres), - & ((c(l,k+nres),l=1,3),k=nnt,nct) - do j=1,3 - c(j,nres+1)=c(j,1) - c(j,2*nres)=c(j,nres) - enddo - call int_from_cart1(.false.) - do i=1,nres-1 - do j=1,3 - dc(j,i)=c(j,i+1)-c(j,i) - dc_norm(j,i)=dc(j,i)*vbld_inv(i+1) - enddo - enddo - do i=nnt,nct - if (itype(i).ne.10) then - do j=1,3 - dc(j,i+nres)=c(j,i+nres)-c(j,i) - dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres) - enddo - endif - enddo - - return - 10 return1 - end -c---------------------------------------------------------------------------- - subroutine read_threadbase - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.LOCAL' - include 'COMMON.NAMES' - include 'COMMON.CHAIN' - include 'COMMON.FFIELD' - include 'COMMON.SBRIDGE' - include 'COMMON.HEADER' - include 'COMMON.CONTROL' - include 'COMMON.DBASE' - include 'COMMON.THREAD' - include 'COMMON.TIME1' -C Read pattern database for threading. - read (icbase,*) nseq - do i=1,nseq - read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i), - & nres_base(2,i),nres_base(3,i) - read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1, - & nres_base(1,i)) -c write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i), -c & nres_base(2,i),nres_base(3,i) -c write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1, -c & nres_base(1,i)) - enddo - close (icbase) - if (weidis.eq.0.0D0) weidis=0.1D0 - do i=nnt,nct - do j=i+2,nct - nhpb=nhpb+1 - ihpb(nhpb)=i - jhpb(nhpb)=j - forcon(nhpb)=weidis - enddo - enddo - read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl) - write (iout,'(a,i5)') 'nexcl: ',nexcl - write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl) - return - end -c------------------------------------------------------------------------------ - subroutine setup_var - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.LOCAL' - include 'COMMON.NAMES' - include 'COMMON.CHAIN' - include 'COMMON.FFIELD' - include 'COMMON.SBRIDGE' - include 'COMMON.HEADER' - include 'COMMON.CONTROL' - include 'COMMON.DBASE' - include 'COMMON.THREAD' - include 'COMMON.TIME1' -C Set up variable list. - ntheta=nres-2 - nphi=nres-3 - nvar=ntheta+nphi - nside=0 - do i=2,nres-1 - if (itype(i).ne.10) then - nside=nside+1 - ialph(i,1)=nvar+nside - ialph(nside,2)=i - endif - enddo - if (indphi.gt.0) then - nvar=nphi - else if (indback.gt.0) then - nvar=nphi+ntheta - else - nvar=nvar+2*nside - endif -cd write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1) - return - end -c---------------------------------------------------------------------------- - subroutine gen_dist_constr -C Generate CA distance constraints. - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.INTERACT' - include 'COMMON.LOCAL' - include 'COMMON.NAMES' - include 'COMMON.CHAIN' - include 'COMMON.FFIELD' - include 'COMMON.SBRIDGE' - include 'COMMON.HEADER' - include 'COMMON.CONTROL' - include 'COMMON.DBASE' - include 'COMMON.THREAD' - include 'COMMON.TIME1' - dimension itype_pdb(maxres) - common /pizda/ itype_pdb - character*2 iden -cd print *,'gen_dist_constr: nnt=',nnt,' nct=',nct -cd write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct, -cd & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq, -cd & ' nsup',nsup - do i=nstart_sup,nstart_sup+nsup-1 -cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)), -cd & ' seq_pdb', restyp(itype_pdb(i)) - do j=i+2,nstart_sup+nsup-1 - nhpb=nhpb+1 - ihpb(nhpb)=i+nstart_seq-nstart_sup - jhpb(nhpb)=j+nstart_seq-nstart_sup - forcon(nhpb)=weidis - dhpb(nhpb)=dist(i,j) - enddo - enddo -cd write (iout,'(a)') 'Distance constraints:' -cd do i=nss+1,nhpb -cd ii=ihpb(i) -cd jj=jhpb(i) -cd iden='CA' -cd if (ii.gt.nres) then -cd iden='SC' -cd ii=ii-nres -cd jj=jj-nres -cd endif -cd write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)') -cd & restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj, -cd & dhpb(i),forcon(i) -cd enddo - return - end -c---------------------------------------------------------------------------- - subroutine map_read - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.MAP' - include 'COMMON.IOUNITS' - character*3 angid(4) /'THE','PHI','ALP','OME'/ - character*80 mapcard,ucase - do imap=1,nmap - read (inp,'(a)') mapcard - mapcard=ucase(mapcard) - if (index(mapcard,'PHI').gt.0) then - kang(imap)=1 - else if (index(mapcard,'THE').gt.0) then - kang(imap)=2 - else if (index(mapcard,'ALP').gt.0) then - kang(imap)=3 - else if (index(mapcard,'OME').gt.0) then - kang(imap)=4 - else - write(iout,'(a)')'Error - illegal variable spec in MAP card.' - stop 'Error - illegal variable spec in MAP card.' - endif - call readi (mapcard,'RES1',res1(imap),0) - call readi (mapcard,'RES2',res2(imap),0) - if (res1(imap).eq.0) then - res1(imap)=res2(imap) - else if (res2(imap).eq.0) then - res2(imap)=res1(imap) - endif - if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then - write (iout,'(a)') - & 'Error - illegal definition of variable group in MAP.' - stop 'Error - illegal definition of variable group in MAP.' - endif - call reada(mapcard,'FROM',ang_from(imap),0.0D0) - call reada(mapcard,'TO',ang_to(imap),0.0D0) - call readi(mapcard,'NSTEP',nstep(imap),0) - if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then - write (iout,'(a)') - & 'Illegal boundary and/or step size specification in MAP.' - stop 'Illegal boundary and/or step size specification in MAP.' - endif - enddo ! imap - return - end -c---------------------------------------------------------------------------- - subroutine csaread - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - include 'COMMON.GEO' - include 'COMMON.CSA' - include 'COMMON.BANK' - include 'COMMON.CONTROL' - character*80 ucase - character*620 mcmcard - call card_concat(mcmcard) - - call readi(mcmcard,'NCONF',nconf,50) - call readi(mcmcard,'NADD',nadd,0) - call readi(mcmcard,'JSTART',jstart,1) - call readi(mcmcard,'JEND',jend,1) - call readi(mcmcard,'NSTMAX',nstmax,500000) - call readi(mcmcard,'N0',n0,1) - call readi(mcmcard,'N1',n1,6) - call readi(mcmcard,'N2',n2,4) - call readi(mcmcard,'N3',n3,0) - call readi(mcmcard,'N4',n4,0) - call readi(mcmcard,'N5',n5,0) - call readi(mcmcard,'N6',n6,10) - call readi(mcmcard,'N7',n7,0) - call readi(mcmcard,'N8',n8,0) - call readi(mcmcard,'N9',n9,0) - call readi(mcmcard,'N14',n14,0) - call readi(mcmcard,'N15',n15,0) - call readi(mcmcard,'N16',n16,0) - call readi(mcmcard,'N17',n17,0) - call readi(mcmcard,'N18',n18,0) - - vdisulf=(index(mcmcard,'DYNSS').gt.0) - - call readi(mcmcard,'NDIFF',ndiff,2) - call reada(mcmcard,'DIFFCUT',diffcut,0.0d0) - call readi(mcmcard,'IS1',is1,1) - call readi(mcmcard,'IS2',is2,8) - call readi(mcmcard,'NRAN0',nran0,4) - call readi(mcmcard,'NRAN1',nran1,2) - call readi(mcmcard,'IRR',irr,1) - call readi(mcmcard,'NSEED',nseed,20) - call readi(mcmcard,'NTOTAL',ntotal,10000) - call reada(mcmcard,'CUT1',cut1,2.0d0) - call reada(mcmcard,'CUT2',cut2,5.0d0) - call reada(mcmcard,'ESTOP',estop,-3000.0d0) - call readi(mcmcard,'ICMAX',icmax,3) - call readi(mcmcard,'IRESTART',irestart,0) -c!bankt call readi(mcmcard,'NBANKTM',ntbankm,0) - ntbankm=0 -c!bankt - call reada(mcmcard,'DELE',dele,20.0d0) - call reada(mcmcard,'DIFCUT',difcut,720.0d0) - call readi(mcmcard,'IREF',iref,0) - call reada(mcmcard,'RMSCUT',rmscut,4.0d0) - call reada(mcmcard,'PNCCUT',pnccut,0.5d0) - call readi(mcmcard,'NCONF_IN',nconf_in,0) - call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0) - write (iout,*) "NCONF_IN",nconf_in - return - end -c---------------------------------------------------------------------------- -cfmc subroutine mcmfread -cfmc implicit real*8 (a-h,o-z) -cfmc include 'DIMENSIONS' -cfmc include 'COMMON.MCMF' -cfmc include 'COMMON.IOUNITS' -cfmc include 'COMMON.GEO' -cfmc character*80 ucase -cfmc character*620 mcmcard -cfmc call card_concat(mcmcard) -cfmc -cfmc call readi(mcmcard,'MAXRANT',maxrant,1000) -cfmc write(iout,*)'MAXRANT=',maxrant -cfmc call readi(mcmcard,'MAXFAM',maxfam,maxfam_p) -cfmc write(iout,*)'MAXFAM=',maxfam -cfmc call readi(mcmcard,'NNET1',nnet1,5) -cfmc write(iout,*)'NNET1=',nnet1 -cfmc call readi(mcmcard,'NNET2',nnet2,4) -cfmc write(iout,*)'NNET2=',nnet2 -cfmc call readi(mcmcard,'NNET3',nnet3,4) -cfmc write(iout,*)'NNET3=',nnet3 -cfmc call readi(mcmcard,'ILASTT',ilastt,0) -cfmc write(iout,*)'ILASTT=',ilastt -cfmc call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf) -cfmc write(iout,*)'MAXSTR=',maxstr -cfmc maxstr_f=maxstr/maxfam -cfmc write(iout,*)'MAXSTR_F=',maxstr_f -cfmc call readi(mcmcard,'NMCMF',nmcmf,10) -cfmc write(iout,*)'NMCMF=',nmcmf -cfmc call readi(mcmcard,'IFOCUS',ifocus,nmcmf) -cfmc write(iout,*)'IFOCUS=',ifocus -cfmc call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000) -cfmc write(iout,*)'NLOCMCMF=',nlocmcmf -cfmc call readi(mcmcard,'INTPRT',intprt,1000) -cfmc write(iout,*)'INTPRT=',intprt -cfmc call readi(mcmcard,'IPRT',iprt,100) -cfmc write(iout,*)'IPRT=',iprt -cfmc call readi(mcmcard,'IMAXTR',imaxtr,100) -cfmc write(iout,*)'IMAXTR=',imaxtr -cfmc call readi(mcmcard,'MAXEVEN',maxeven,1000) -cfmc write(iout,*)'MAXEVEN=',maxeven -cfmc call readi(mcmcard,'MAXEVEN1',maxeven1,3) -cfmc write(iout,*)'MAXEVEN1=',maxeven1 -cfmc call readi(mcmcard,'INIMIN',inimin,200) -cfmc write(iout,*)'INIMIN=',inimin -cfmc call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10) -cfmc write(iout,*)'NSTEPMCMF=',nstepmcmf -cfmc call readi(mcmcard,'NTHREAD',nthread,5) -cfmc write(iout,*)'NTHREAD=',nthread -cfmc call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500) -cfmc write(iout,*)'MAXSTEPMCMF=',maxstepmcmf -cfmc call readi(mcmcard,'MAXPERT',maxpert,9) -cfmc write(iout,*)'MAXPERT=',maxpert -cfmc call readi(mcmcard,'IRMSD',irmsd,1) -cfmc write(iout,*)'IRMSD=',irmsd -cfmc call reada(mcmcard,'DENEMIN',denemin,0.01D0) -cfmc write(iout,*)'DENEMIN=',denemin -cfmc call reada(mcmcard,'RCUT1S',rcut1s,3.5D0) -cfmc write(iout,*)'RCUT1S=',rcut1s -cfmc call reada(mcmcard,'RCUT1E',rcut1e,2.0D0) -cfmc write(iout,*)'RCUT1E=',rcut1e -cfmc call reada(mcmcard,'RCUT2S',rcut2s,0.5D0) -cfmc write(iout,*)'RCUT2S=',rcut2s -cfmc call reada(mcmcard,'RCUT2E',rcut2e,0.1D0) -cfmc write(iout,*)'RCUT2E=',rcut2e -cfmc call reada(mcmcard,'DPERT1',d_pert1,180.0D0) -cfmc write(iout,*)'DPERT1=',d_pert1 -cfmc call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0) -cfmc write(iout,*)'DPERT1A=',d_pert1a -cfmc call reada(mcmcard,'DPERT2',d_pert2,90.0D0) -cfmc write(iout,*)'DPERT2=',d_pert2 -cfmc call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0) -cfmc write(iout,*)'DPERT2A=',d_pert2a -cfmc call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0) -cfmc write(iout,*)'DPERT2B=',d_pert2b -cfmc call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0) -cfmc write(iout,*)'DPERT2C=',d_pert2c -cfmc d_pert1=deg2rad*d_pert1 -cfmc d_pert1a=deg2rad*d_pert1a -cfmc d_pert2=deg2rad*d_pert2 -cfmc d_pert2a=deg2rad*d_pert2a -cfmc d_pert2b=deg2rad*d_pert2b -cfmc d_pert2c=deg2rad*d_pert2c -cfmc call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0) -cfmc write(iout,*)'KT_MCMF1=',kt_mcmf1 -cfmc call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0) -cfmc write(iout,*)'KT_MCMF2=',kt_mcmf2 -cfmc call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0) -cfmc write(iout,*)'DKT_MCMF1=',dkt_mcmf1 -cfmc call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0) -cfmc write(iout,*)'DKT_MCMF2=',dkt_mcmf2 -cfmc call reada(mcmcard,'RCUTINI',rcutini,3.5D0) -cfmc write(iout,*)'RCUTINI=',rcutini -cfmc call reada(mcmcard,'GRAT',grat,0.5D0) -cfmc write(iout,*)'GRAT=',grat -cfmc call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0) -cfmc write(iout,*)'BIAS_MCMF=',bias_mcmf -cfmc -cfmc return -cfmc end -c---------------------------------------------------------------------------- - subroutine mcmread - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.MCM' - include 'COMMON.MCE' - include 'COMMON.IOUNITS' - character*80 ucase - character*320 mcmcard - call card_concat(mcmcard) - call readi(mcmcard,'MAXACC',maxacc,100) - call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000) - call readi(mcmcard,'MAXTRIAL',maxtrial,100) - call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000) - call readi(mcmcard,'MAXREPM',maxrepm,200) - call reada(mcmcard,'RANFRACT',RanFract,0.5D0) - call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0) - call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3) - call reada(mcmcard,'E_UP',e_up,5.0D0) - call reada(mcmcard,'DELTE',delte,0.1D0) - call readi(mcmcard,'NSWEEP',nsweep,5) - call readi(mcmcard,'NSTEPH',nsteph,0) - call readi(mcmcard,'NSTEPC',nstepc,0) - call reada(mcmcard,'TMIN',tmin,298.0D0) - call reada(mcmcard,'TMAX',tmax,298.0D0) - call readi(mcmcard,'NWINDOW',nwindow,0) - call readi(mcmcard,'PRINT_MC',print_mc,0) - print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0) - print_int=(index(mcmcard,'NO_PRINT_INT').le.0) - ent_read=(index(mcmcard,'ENT_READ').gt.0) - call readi(mcmcard,'SAVE_FREQ',save_frequency,1000) - call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000) - call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000) - call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000) - call readi(mcmcard,'PRINT_FREQ',print_freq,1000) - if (nwindow.gt.0) then - read (inp,*) (winstart(i),winend(i),i=1,nwindow) - do i=1,nwindow - winlen(i)=winend(i)-winstart(i)+1 - enddo - endif - if (tmax.lt.tmin) tmax=tmin - if (tmax.eq.tmin) then - nstepc=0 - nsteph=0 - endif - if (nstepc.gt.0 .and. nsteph.gt.0) then - tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0)) - tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0)) - endif -C Probabilities of different move types - sumpro_type(0)=0.0D0 - call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0) - call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0) - sumpro_type(2)=sumpro_type(1)+sumpro_type(2) - call reada(mcmcard,'THETA' ,sumpro_type(3),0.0d0) - sumpro_type(3)=sumpro_type(2)+sumpro_type(3) - call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0) - sumpro_type(4)=sumpro_type(3)+sumpro_type(4) - do i=1,MaxMoveType - print *,'i',i,' sumprotype',sumpro_type(i) - sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType) - print *,'i',i,' sumprotype',sumpro_type(i) - enddo - return - end -c---------------------------------------------------------------------------- - subroutine read_minim - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.MINIM' - include 'COMMON.IOUNITS' - character*80 ucase - character*320 minimcard - call card_concat(minimcard) - call readi(minimcard,'MAXMIN',maxmin,2000) - call readi(minimcard,'MAXFUN',maxfun,5000) - call readi(minimcard,'MINMIN',minmin,maxmin) - call readi(minimcard,'MINFUN',minfun,maxmin) - call reada(minimcard,'TOLF',tolf,1.0D-2) - call reada(minimcard,'RTOLF',rtolf,1.0D-4) - write (iout,'(/80(1h*)/20x,a/80(1h*))') - & 'Options in energy minimization:' - write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)') - & 'MaxMin:',MaxMin,' MaxFun:',MaxFun, - & 'MinMin:',MinMin,' MinFun:',MinFun, - & ' TolF:',TolF,' RTolF:',RTolF - return - end -c---------------------------------------------------------------------------- - subroutine read_angles(kanal,*) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.GEO' - include 'COMMON.VAR' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.CONTROL' -c Read angles from input -c - read (kanal,*,err=10,end=10) (theta(i),i=3,nres) - read (kanal,*,err=10,end=10) (phi(i),i=4,nres) - read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1) - read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1) - - do i=1,nres -c 9/7/01 avoid 180 deg valence angle - if (theta(i).gt.179.99d0) theta(i)=179.99d0 -c - theta(i)=deg2rad*theta(i) - phi(i)=deg2rad*phi(i) - alph(i)=deg2rad*alph(i) - omeg(i)=deg2rad*omeg(i) - enddo - return - 10 return1 - end -c---------------------------------------------------------------------------- - subroutine reada(rekord,lancuch,wartosc,default) - implicit none - character*(*) rekord,lancuch - double precision wartosc,default - integer ilen,iread - external ilen - iread=index(rekord,lancuch) - if (iread.eq.0) then - wartosc=default - return - endif - iread=iread+ilen(lancuch)+1 - read (rekord(iread:),*,err=10,end=10) wartosc - return - 10 wartosc=default - return - end -c---------------------------------------------------------------------------- - subroutine readi(rekord,lancuch,wartosc,default) - implicit none - character*(*) rekord,lancuch - integer wartosc,default - integer ilen,iread - external ilen - iread=index(rekord,lancuch) - if (iread.eq.0) then - wartosc=default - return - endif - iread=iread+ilen(lancuch)+1 - read (rekord(iread:),*,err=10,end=10) wartosc - return - 10 wartosc=default - return - end -c---------------------------------------------------------------------------- - subroutine multreadi(rekord,lancuch,tablica,dim,default) - implicit none - integer dim,i - integer tablica(dim),default - character*(*) rekord,lancuch - character*80 aux - integer ilen,iread - external ilen - do i=1,dim - tablica(i)=default - enddo - iread=index(rekord,lancuch(:ilen(lancuch))//"=") - if (iread.eq.0) return - iread=iread+ilen(lancuch)+1 - read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim) - 10 return - end -c---------------------------------------------------------------------------- - subroutine multreada(rekord,lancuch,tablica,dim,default) - implicit none - integer dim,i - double precision tablica(dim),default - character*(*) rekord,lancuch - character*80 aux - integer ilen,iread - external ilen - do i=1,dim - tablica(i)=default - enddo - iread=index(rekord,lancuch(:ilen(lancuch))//"=") - if (iread.eq.0) return - iread=iread+ilen(lancuch)+1 - read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim) - 10 return - end -c---------------------------------------------------------------------------- - subroutine openunits - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' - character*16 form,nodename - integer nodelen -#endif - include 'COMMON.SETUP' - include 'COMMON.IOUNITS' - include 'COMMON.MD' - include 'COMMON.CONTROL' - integer lenpre,lenpot,ilen,lentmp - external ilen - character*3 out1file_text,ucase - character*3 ll - external ucase -c print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits" - call getenv_loc("PREFIX",prefix) - pref_orig = prefix - call getenv_loc("POT",pot) - call getenv_loc("DIRTMP",tmpdir) - call getenv_loc("CURDIR",curdir) - call getenv_loc("OUT1FILE",out1file_text) -c print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV" - out1file_text=ucase(out1file_text) - if (out1file_text(1:1).eq."Y") then - out1file=.true. - else - out1file=fg_rank.gt.0 - endif - lenpre=ilen(prefix) - lenpot=ilen(pot) - lentmp=ilen(tmpdir) - if (lentmp.gt.0) then - write (*,'(80(1h!))') - write (*,'(a,19x,a,19x,a)') "!"," A T T E N T I O N ","!" - write (*,'(80(1h!))') - write (*,*)"All output files will be on node /tmp directory." -#ifdef MPI - call MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR ) - if (me.eq.king) then - write (*,*) "The master node is ",nodename - else if (fg_rank.eq.0) then - write (*,*) "I am the CG slave node ",nodename - else - write (*,*) "I am the FG slave node ",nodename - endif -#endif - PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre) - lenpre = lentmp+lenpre+1 - endif - entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr' -C Get the names and open the input files -#if defined(WINIFL) || defined(WINPGI) - open(1,file=pref_orig(:ilen(pref_orig))// - & '.inp',status='old',readonly,shared) - open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown') -C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown') -C Get parameter filenames and open the parameter files. - call getenv_loc('BONDPAR',bondname) - open (ibond,file=bondname,status='old',readonly,shared) - call getenv_loc('THETPAR',thetname) - open (ithep,file=thetname,status='old',readonly,shared) - call getenv_loc('ROTPAR',rotname) - open (irotam,file=rotname,status='old',readonly,shared) - call getenv_loc('TORPAR',torname) - open (itorp,file=torname,status='old',readonly,shared) - call getenv_loc('TORDPAR',tordname) - open (itordp,file=tordname,status='old',readonly,shared) - call getenv_loc('FOURIER',fouriername) - open (ifourier,file=fouriername,status='old',readonly,shared) - call getenv_loc('ELEPAR',elename) - open (ielep,file=elename,status='old',readonly,shared) - call getenv_loc('SIDEPAR',sidename) - open (isidep,file=sidename,status='old',readonly,shared) -#elif (defined CRAY) || (defined AIX) - open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old', - & action='read') -c print *,"Processor",myrank," opened file 1" - open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown') -c print *,"Processor",myrank," opened file 9" -C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown') -C Get parameter filenames and open the parameter files. - call getenv_loc('BONDPAR',bondname) - open (ibond,file=bondname,status='old',action='read') -c print *,"Processor",myrank," opened file IBOND" - call getenv_loc('THETPAR',thetname) - open (ithep,file=thetname,status='old',action='read') -c print *,"Processor",myrank," opened file ITHEP" - call getenv_loc('ROTPAR',rotname) - open (irotam,file=rotname,status='old',action='read') -c print *,"Processor",myrank," opened file IROTAM" - call getenv_loc('TORPAR',torname) - open (itorp,file=torname,status='old',action='read') -c print *,"Processor",myrank," opened file ITORP" - call getenv_loc('TORDPAR',tordname) - open (itordp,file=tordname,status='old',action='read') -c print *,"Processor",myrank," opened file ITORDP" - call getenv_loc('SCCORPAR',sccorname) - open (isccor,file=sccorname,status='old',action='read') -c print *,"Processor",myrank," opened file ISCCOR" - call getenv_loc('FOURIER',fouriername) - open (ifourier,file=fouriername,status='old',action='read') -c print *,"Processor",myrank," opened file IFOURIER" - call getenv_loc('ELEPAR',elename) - open (ielep,file=elename,status='old',action='read') -c print *,"Processor",myrank," opened file IELEP" - call getenv_loc('SIDEPAR',sidename) - open (isidep,file=sidename,status='old',action='read') -c print *,"Processor",myrank," opened file ISIDEP" -c print *,"Processor",myrank," opened parameter files" -#elif (defined G77) - open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old') - open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown') -C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown') -C Get parameter filenames and open the parameter files. - call getenv_loc('BONDPAR',bondname) - open (ibond,file=bondname,status='old') - call getenv_loc('THETPAR',thetname) - open (ithep,file=thetname,status='old') - call getenv_loc('ROTPAR',rotname) - open (irotam,file=rotname,status='old') - call getenv_loc('TORPAR',torname) - open (itorp,file=torname,status='old') - call getenv_loc('TORDPAR',tordname) - open (itordp,file=tordname,status='old') - call getenv_loc('SCCORPAR',sccorname) - open (isccor,file=sccorname,status='old') - call getenv_loc('FOURIER',fouriername) - open (ifourier,file=fouriername,status='old') - call getenv_loc('ELEPAR',elename) - open (ielep,file=elename,status='old') - call getenv_loc('SIDEPAR',sidename) - open (isidep,file=sidename,status='old') -#else - open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old', - & readonly) - open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown') -C open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown') -C Get parameter filenames and open the parameter files. - call getenv_loc('BONDPAR',bondname) - open (ibond,file=bondname,status='old',readonly) - call getenv_loc('THETPAR',thetname) - open (ithep,file=thetname,status='old',readonly) - call getenv_loc('ROTPAR',rotname) - open (irotam,file=rotname,status='old',readonly) - call getenv_loc('TORPAR',torname) - open (itorp,file=torname,status='old',readonly) - call getenv_loc('TORDPAR',tordname) - open (itordp,file=tordname,status='old',readonly) - call getenv_loc('SCCORPAR',sccorname) - open (isccor,file=sccorname,status='old',readonly) - call getenv_loc('FOURIER',fouriername) - open (ifourier,file=fouriername,status='old',readonly) - call getenv_loc('ELEPAR',elename) - open (ielep,file=elename,status='old',readonly) - call getenv_loc('SIDEPAR',sidename) - open (isidep,file=sidename,status='old',readonly) -#endif -#ifndef OLDSCP -C -C 8/9/01 In the newest version SCp interaction constants are read from a file -C Use -DOLDSCP to use hard-coded constants instead. -C - call getenv_loc('SCPPAR',scpname) -#if defined(WINIFL) || defined(WINPGI) - open (iscpp,file=scpname,status='old',readonly,shared) -#elif (defined CRAY) || (defined AIX) - open (iscpp,file=scpname,status='old',action='read') -#elif (defined G77) - open (iscpp,file=scpname,status='old') -#else - open (iscpp,file=scpname,status='old',readonly) -#endif -#endif - call getenv_loc('PATTERN',patname) -#if defined(WINIFL) || defined(WINPGI) - open (icbase,file=patname,status='old',readonly,shared) -#elif (defined CRAY) || (defined AIX) - open (icbase,file=patname,status='old',action='read') -#elif (defined G77) - open (icbase,file=patname,status='old') -#else - open (icbase,file=patname,status='old',readonly) -#endif -#ifdef MPI -C Open output file only for CG processes -c print *,"Processor",myrank," fg_rank",fg_rank - if (fg_rank.eq.0) then - - if (nodes.eq.1) then - npos=3 - else - npos = dlog10(dfloat(nodes-1))+1 - endif - if (npos.lt.3) npos=3 - write (liczba,'(i1)') npos - form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba)) - & //')' - write (liczba,form) me - outname=prefix(:lenpre)//'.out_'//pot(:lenpot)// - & liczba(:ilen(liczba)) - intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) - & //'.int' - pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba)) - & //'.pdb' - mol2name=prefix(:lenpre)//'_'//pot(:lenpot)// - & liczba(:ilen(liczba))//'.mol2' - statname=prefix(:lenpre)//'_'//pot(:lenpot)// - & liczba(:ilen(liczba))//'.stat' - if (lentmp.gt.0) - & call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) - & //liczba(:ilen(liczba))//'.stat') - rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba)) - & //'.rst' - if(usampl) then - qname=prefix(:lenpre)//'_'//pot(:lenpot)// - & liczba(:ilen(liczba))//'.const' - endif - - endif -#else - outname=prefix(:lenpre)//'.out_'//pot(:lenpot) - intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int' - pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb' - mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2' - statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat' - if (lentmp.gt.0) - & call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot) - & //'.stat') - rest2name=prefix(:ilen(prefix))//'.rst' - if(usampl) then - qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const' - endif -#endif -#if defined(AIX) || defined(PGI) - if (me.eq.king .or. .not. out1file) - & open(iout,file=outname,status='unknown') -#ifdef DEBUG - if (fg_rank.gt.0) then - write (liczba,'(i3.3)') myrank/nfgtasks - write (ll,'(bz,i3.3)') fg_rank - open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll, - & status='unknown') - endif -#endif - if(me.eq.king) then - open(igeom,file=intname,status='unknown',position='append') - open(ipdb,file=pdbname,status='unknown') - open(imol2,file=mol2name,status='unknown') - open(istat,file=statname,status='unknown',position='append') - else -c1out open(iout,file=outname,status='unknown') - endif -#else - if (me.eq.king .or. .not.out1file) - & open(iout,file=outname,status='unknown') -#ifdef DEBUG - if (fg_rank.gt.0) then - write (liczba,'(i3.3)') myrank/nfgtasks - write (ll,'(bz,i3.3)') fg_rank - open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll, - & status='unknown') - endif -#endif - if(me.eq.king) then - open(igeom,file=intname,status='unknown',access='append') - open(ipdb,file=pdbname,status='unknown') - open(imol2,file=mol2name,status='unknown') - open(istat,file=statname,status='unknown',access='append') - else -c1out open(iout,file=outname,status='unknown') - endif -#endif - csa_rbank=prefix(:lenpre)//'.CSA.rbank' - csa_seed=prefix(:lenpre)//'.CSA.seed' - csa_history=prefix(:lenpre)//'.CSA.history' - csa_bank=prefix(:lenpre)//'.CSA.bank' - csa_bank1=prefix(:lenpre)//'.CSA.bank1' - csa_alpha=prefix(:lenpre)//'.CSA.alpha' - csa_alpha1=prefix(:lenpre)//'.CSA.alpha1' -c!bankt csa_bankt=prefix(:lenpre)//'.CSA.bankt' - csa_int=prefix(:lenpre)//'.int' - csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized' - csa_native_int=prefix(:lenpre)//'.CSA.native.int' - csa_in=prefix(:lenpre)//'.CSA.in' -c print *,"Processor",myrank,"fg_rank",fg_rank," opened files" -C Write file names - if (me.eq.king)then - write (iout,'(80(1h-))') - write (iout,'(30x,a)') "FILE ASSIGNMENT" - write (iout,'(80(1h-))') - write (iout,*) "Input file : ", - & pref_orig(:ilen(pref_orig))//'.inp' - write (iout,*) "Output file : ", - & outname(:ilen(outname)) - write (iout,*) - write (iout,*) "Sidechain potential file : ", - & sidename(:ilen(sidename)) -#ifndef OLDSCP - write (iout,*) "SCp potential file : ", - & scpname(:ilen(scpname)) -#endif - write (iout,*) "Electrostatic potential file : ", - & elename(:ilen(elename)) - write (iout,*) "Cumulant coefficient file : ", - & fouriername(:ilen(fouriername)) - write (iout,*) "Torsional parameter file : ", - & torname(:ilen(torname)) - write (iout,*) "Double torsional parameter file : ", - & tordname(:ilen(tordname)) - write (iout,*) "SCCOR parameter file : ", - & sccorname(:ilen(sccorname)) - write (iout,*) "Bond & inertia constant file : ", - & bondname(:ilen(bondname)) - write (iout,*) "Bending parameter file : ", - & thetname(:ilen(thetname)) - write (iout,*) "Rotamer parameter file : ", - & rotname(:ilen(rotname)) - write (iout,*) "Threading database : ", - & patname(:ilen(patname)) - if (lentmp.ne.0) - &write (iout,*)" DIRTMP : ", - & tmpdir(:lentmp) - write (iout,'(80(1h-))') - endif - return - end -c---------------------------------------------------------------------------- - subroutine card_concat(card) - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.IOUNITS' - character*(*) card - character*80 karta,ucase - external ilen - read (inp,'(a)') karta - karta=ucase(karta) - card=' ' - do while (karta(80:80).eq.'&') - card=card(:ilen(card)+1)//karta(:79) - read (inp,'(a)') karta - karta=ucase(karta) - enddo - card=card(:ilen(card)+1)//karta - return - end -c---------------------------------------------------------------------------------- - subroutine readrst - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.MD' - open(irest2,file=rest2name,status='unknown') - read(irest2,*) totT,EK,potE,totE,t_bath - do i=1,2*nres - read(irest2,'(3e15.5)') (d_t(j,i),j=1,3) - enddo - do i=1,2*nres - read(irest2,'(3e15.5)') (dc(j,i),j=1,3) - enddo - if(usampl) then - read (irest2,*) iset - endif - close(irest2) - return - end -c--------------------------------------------------------------------------------- - subroutine read_fragments - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SETUP' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.MD' - include 'COMMON.CONTROL' - read(inp,*) nset,nfrag,npair,nfrag_back - if(me.eq.king.or..not.out1file) - & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair, - & " nfrag_back",nfrag_back - do iset=1,nset - read(inp,*) mset(iset) - do i=1,nfrag - read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset), - & qinfrag(i,iset) - if(me.eq.king.or..not.out1file) - & write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset), - & ifrag(2,i,iset), qinfrag(i,iset) - enddo - do i=1,npair - read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset), - & qinpair(i,iset) - if(me.eq.king.or..not.out1file) - & write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset), - & ipair(2,i,iset), qinpair(i,iset) - enddo - do i=1,nfrag_back - read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset), - & wfrag_back(3,i,iset), - & ifrag_back(1,i,iset),ifrag_back(2,i,iset) - if(me.eq.king.or..not.out1file) - & write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset), - & wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset) - enddo - enddo - return - end -c------------------------------------------------------------------------------- - subroutine read_dist_constr - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef MPI - include 'mpif.h' -#endif - include 'COMMON.SETUP' - include 'COMMON.CONTROL' - include 'COMMON.CHAIN' - include 'COMMON.IOUNITS' - include 'COMMON.SBRIDGE' - integer ifrag_(2,100),ipair_(2,100) - double precision wfrag_(100),wpair_(100) - character*500 controlcard -c write (iout,*) "Calling read_dist_constr" -c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup -c call flush(iout) - call card_concat(controlcard) - call readi(controlcard,"NFRAG",nfrag_,0) - call readi(controlcard,"NPAIR",npair_,0) - call readi(controlcard,"NDIST",ndist_,0) - call reada(controlcard,'DIST_CUT',dist_cut,5.0d0) - call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0) - call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0) - call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0) - call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0) -c write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_ -c write (iout,*) "IFRAG" -c do i=1,nfrag_ -c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) -c enddo -c write (iout,*) "IPAIR" -c do i=1,npair_ -c write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i) -c enddo - call flush(iout) - do i=1,nfrag_ - if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup - if (ifrag_(2,i).gt.nstart_sup+nsup-1) - & ifrag_(2,i)=nstart_sup+nsup-1 -c write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i) - call flush(iout) - if (wfrag_(i).gt.0.0d0) then - do j=ifrag_(1,i),ifrag_(2,i)-1 - do k=j+1,ifrag_(2,i) - write (iout,*) "j",j," k",k - ddjk=dist(j,k) - if (constr_dist.eq.1) then - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k - dhpb(nhpb)=ddjk - forcon(nhpb)=wfrag_(i) - else if (constr_dist.eq.2) then - if (ddjk.le.dist_cut) then - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k - dhpb(nhpb)=ddjk - forcon(nhpb)=wfrag_(i) - endif - else - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k - dhpb(nhpb)=ddjk - forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2) - endif -#ifdef MPI - if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#else - write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#endif - enddo - enddo - endif - enddo - do i=1,npair_ - if (wpair_(i).gt.0.0d0) then - ii = ipair_(1,i) - jj = ipair_(2,i) - if (ii.gt.jj) then - itemp=ii - ii=jj - jj=itemp - endif - do j=ifrag_(1,ii),ifrag_(2,ii) - do k=ifrag_(1,jj),ifrag_(2,jj) - nhpb=nhpb+1 - ihpb(nhpb)=j - jhpb(nhpb)=k - forcon(nhpb)=wpair_(i) - dhpb(nhpb)=dist(j,k) -#ifdef MPI - if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#else - write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#endif - enddo - enddo - endif - enddo - do i=1,ndist_ - read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1) - if (forcon(nhpb+1).gt.0.0d0) then - nhpb=nhpb+1 - dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) -#ifdef MPI - if (.not.out1file .or. me.eq.king) - & write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#else - write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ", - & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) -#endif - endif - enddo - call flush(iout) - return - end -c------------------------------------------------------------------------------- -#ifdef WINIFL - subroutine flush(iu) - return - end -#endif -#ifdef AIX - subroutine flush(iu) - call flush_(iu) - return - end -#endif -c------------------------------------------------------------------------------ - subroutine copy_to_tmp(source) - include "DIMENSIONS" - include "COMMON.IOUNITS" - character*(*) source - character* 256 tmpfile - integer ilen - external ilen - logical ex - tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source)) - inquire(file=tmpfile,exist=ex) - if (ex) then - write (*,*) "Copying ",tmpfile(:ilen(tmpfile)), - & " to temporary directory..." - write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir - call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir) - endif - return - end -c------------------------------------------------------------------------------ - subroutine move_from_tmp(source) - include "DIMENSIONS" - include "COMMON.IOUNITS" - character*(*) source - integer ilen - external ilen - write (*,*) "Moving ",source(:ilen(source)), - & " from temporary directory to working directory" - write (*,*) "/bin/mv "//source(:ilen(source))//" "//curdir - call system("/bin/mv "//source(:ilen(source))//" "//curdir) - return - end -c------------------------------------------------------------------------------ - subroutine random_init(seed) -C -C Initialize random number generator -C - implicit real*8 (a-h,o-z) - include 'DIMENSIONS' -#ifdef AMD64 - integer*8 iseedi8 -#endif -#ifdef MPI - include 'mpif.h' - logical OKRandom, prng_restart - real*8 r1 - integer iseed_array(4) -#endif - include 'COMMON.IOUNITS' - include 'COMMON.TIME1' - include 'COMMON.THREAD' - include 'COMMON.SBRIDGE' - include 'COMMON.CONTROL' - include 'COMMON.MCM' - include 'COMMON.MAP' - include 'COMMON.HEADER' - include 'COMMON.CSA' - include 'COMMON.CHAIN' - include 'COMMON.MUCA' - include 'COMMON.MD' - include 'COMMON.FFIELD' - include 'COMMON.SETUP' - iseed=-dint(dabs(seed)) - if (iseed.eq.0) then - write (iout,'(/80(1h*)/20x,a/80(1h*))') - & 'Random seed undefined. The program will stop.' - write (*,'(/80(1h*)/20x,a/80(1h*))') - & 'Random seed undefined. The program will stop.' -#ifdef MPI - call mpi_finalize(mpi_comm_world,ierr) -#endif - stop 'Bad random seed.' - endif -#ifdef MPI - if (fg_rank.eq.0) then - seed=seed*(me+1)+1 -#ifdef AMD64 - iseedi8=dint(seed) - if(me.eq.king .or. .not. out1file) - & write (iout,*) 'MPI: node= ', me, ' iseed= ',iseedi8 - write (*,*) 'MPI: node= ', me, ' iseed= ',iseedi8 - OKRandom = prng_restart(me,iseedi8) -#else - do i=1,4 - tmp=65536.0d0**(4-i) - iseed_array(i) = dint(seed/tmp) - seed=seed-iseed_array(i)*tmp - enddo - if(me.eq.king .or. .not. out1file) - & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ', - & (iseed_array(i),i=1,4) - write (*,*) 'MPI: node= ',me, ' iseed(4)= ', - & (iseed_array(i),i=1,4) - OKRandom = prng_restart(me,iseed_array) -#endif - if (OKRandom) then - r1=ran_number(0.0D0,1.0D0) - if(me.eq.king .or. .not. out1file) - & write (iout,*) 'ran_num',r1 - if (r1.lt.0.0d0) OKRandom=.false. - endif - if (.not.OKRandom) then - write (iout,*) 'PRNG IS NOT WORKING!!!' - print *,'PRNG IS NOT WORKING!!!' - if (me.eq.0) then - call flush(iout) - call mpi_abort(mpi_comm_world,error_msg,ierr) - stop - else - write (iout,*) 'too many processors for parallel prng' - write (*,*) 'too many processors for parallel prng' - call flush(iout) - stop - endif - endif - endif -#else - call vrndst(iseed) - write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0) -#endif - return - end