source/unres/src_MD-M-newcorr/readrtns_CSA.F

   1       subroutine readrtns
   2       implicit real*8 (a-h,o-z)
   3       include 'DIMENSIONS'
   4 #ifdef MPI
   5       include 'mpif.h'
   6 #endif
   7       include 'COMMON.SETUP'
   8       include 'COMMON.CONTROL'
   9       include 'COMMON.SBRIDGE'
  10       include 'COMMON.IOUNITS'
  11       logical file_exist
  12 C Read force-field parameters except weights
  13       call parmread
  14 C Read job setup parameters
  15       call read_control
  16 C Read control parameters for energy minimzation if required
  17       if (minim) call read_minim
  18 C Read MCM control parameters if required
  19       if (modecalc.eq.3 .or. modecalc.eq.6) call mcmread
  20 C Read MD control parameters if reqjuired
  21       if (modecalc.eq.12) call read_MDpar
  22 C Read MREMD control parameters if required
  23       if (modecalc.eq.14) then
  24          call read_MDpar
  25          call read_REMDpar
  26       endif
  27 C Read MUCA control parameters if required
  28       if (lmuca) call read_muca
  29 C Read CSA control parameters if required (from fort.40 if exists
  30 C otherwise from general input file)
  31       if (modecalc.eq.8) then
  32        inquire (file="fort.40",exist=file_exist)
  33        if (.not.file_exist) call csaread
  34       endif
  35 cfmc      if (modecalc.eq.10) call mcmfread
  36 C Read molecule information, molecule geometry, energy-term weights, and
  37 C restraints if requested
  38       call molread
  39 C Print restraint information
  40 #ifdef MPI
  41       if (.not. out1file .or. me.eq.king) then
  42 #endif
  43       if (nhpb.gt.nss)
  44      &write (iout,'(a,i5,a)') "The following",nhpb-nss,
  45      & " distance constraints have been imposed"
  46       do i=nss+1,nhpb
  47         write (iout,'(3i6,f10.5)') i-nss,ihpb(i),jhpb(i),forcon(i)
  48       enddo
  49 #ifdef MPI
  50       endif
  51 #endif
  52 c      print *,"Processor",myrank," leaves READRTNS"
  53       return
  54       end
  55 C-------------------------------------------------------------------------------
  56       subroutine read_control
  57 C
  58 C Read contorl data
  59 C
  60       implicit real*8 (a-h,o-z)
  61       include 'DIMENSIONS'
  62 #ifdef MP
  63       include 'mpif.h'
  64       logical OKRandom, prng_restart
  65       real*8  r1
  66 #endif
  67       include 'COMMON.IOUNITS'
  68       include 'COMMON.TIME1'
  69       include 'COMMON.THREAD'
  70       include 'COMMON.SBRIDGE'
  71       include 'COMMON.CONTROL'
  72       include 'COMMON.MCM'
  73       include 'COMMON.MAP'
  74       include 'COMMON.HEADER'
  75       include 'COMMON.CSA'
  76       include 'COMMON.CHAIN'
  77       include 'COMMON.MUCA'
  78       include 'COMMON.MD'
  79       include 'COMMON.FFIELD'
  80       include 'COMMON.INTERACT'
  81       include 'COMMON.SETUP'
  82       COMMON /MACHSW/ KDIAG,ICORFL,IXDR
  83       character*8 diagmeth(0:3) /'Library','EVVRSP','Givens','Jacobi'/
  84       character*80 ucase
  85       character*320 controlcard
  86
  87       nglob_csa=0
  88       eglob_csa=1d99
  89       nmin_csa=0
  90       read (INP,'(a)') titel
  91       call card_concat(controlcard)
  92 c      out1file=index(controlcard,'OUT1FILE').gt.0 .or. fg_rank.gt.0
  93 c      print *,"Processor",me," fg_rank",fg_rank," out1file",out1file
  94       call reada(controlcard,'SEED',seed,0.0D0)
  95       call random_init(seed)
  96 C Set up the time limit (caution! The time must be input in minutes!)
  97       read_cart=index(controlcard,'READ_CART').gt.0
  98       call readi(controlcard,'CONSTR_DIST',constr_dist,0)
  99       call readi(controlcard,'SYM',symetr,1)
 100       call reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
 101       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
 102       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
 103       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
 104       call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
 105       call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
 106       call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
 107       call reada(controlcard,'DRMS',drms,0.1D0)
 108       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
 109        write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
 110        write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
 111        write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
 112        write (iout,'(a,f10.1)')'DRMS    = ',drms
 113        write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
 114        write (iout,'(a,f10.1)') 'Time limit (min):',timlim
 115       endif
 116       call readi(controlcard,'NZ_START',nz_start,0)
 117       call readi(controlcard,'NZ_END',nz_end,0)
 118       call readi(controlcard,'IZ_SC',iz_sc,0)
 119       timlim=60.0D0*timlim
 120       safety = 60.0d0*safety
 121       timem=timlim
 122       modecalc=0
 123       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 124       minim=(index(controlcard,'MINIMIZE').gt.0)
 125       dccart=(index(controlcard,'CART').gt.0)
 126       overlapsc=(index(controlcard,'OVERLAP').gt.0)
 127       overlapsc=.not.overlapsc
 128       searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
 129       searchsc=.not.searchsc
 130       sideadd=(index(controlcard,'SIDEADD').gt.0)
 131       energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
 132       outpdb=(index(controlcard,'PDBOUT').gt.0)
 133       outmol2=(index(controlcard,'MOL2OUT').gt.0)
 134       pdbref=(index(controlcard,'PDBREF').gt.0)
 135       refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
 136       indpdb=index(controlcard,'PDBSTART')
 137       extconf=(index(controlcard,'EXTCONF').gt.0)
 138       call readi(controlcard,'IPRINT',iprint,0)
 139       call readi(controlcard,'MAXGEN',maxgen,10000)
 140       call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
 141       call readi(controlcard,"KDIAG",kdiag,0)
 142       call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
 143       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
 144      & write (iout,*) "RESCALE_MODE",rescale_mode
 145       split_ene=index(controlcard,'SPLIT_ENE').gt.0
 146       if (index(controlcard,'REGULAR').gt.0.0D0) then
 147         call reada(controlcard,'WEIDIS',weidis,0.1D0)
 148         modecalc=1
 149         refstr=.true.
 150       endif
 151       if (index(controlcard,'CHECKGRAD').gt.0) then
 152         modecalc=5
 153         if (index(controlcard,'CART').gt.0) then
 154           icheckgrad=1
 155         elseif (index(controlcard,'CARINT').gt.0) then
 156           icheckgrad=2
 157         else
 158           icheckgrad=3
 159         endif
 160       elseif (index(controlcard,'THREAD').gt.0) then
 161         modecalc=2
 162         call readi(controlcard,'THREAD',nthread,0)
 163         if (nthread.gt.0) then
 164           call reada(controlcard,'WEIDIS',weidis,0.1D0)
 165         else
 166           if (fg_rank.eq.0)
 167      &    write (iout,'(a)')'A number has to follow the THREAD keyword.'
 168           stop 'Error termination in Read_Control.'
 169         endif
 170       else if (index(controlcard,'MCMA').gt.0) then
 171         modecalc=3
 172       else if (index(controlcard,'MCEE').gt.0) then
 173         modecalc=6
 174       else if (index(controlcard,'MULTCONF').gt.0) then
 175         modecalc=4
 176       else if (index(controlcard,'MAP').gt.0) then
 177         modecalc=7
 178         call readi(controlcard,'MAP',nmap,0)
 179       else if (index(controlcard,'CSA').gt.0) then
 180         modecalc=8
 181 crc      else if (index(controlcard,'ZSCORE').gt.0) then
 182 crc
 183 crc  ZSCORE is rm from UNRES, modecalc=9 is available
 184 crc
 185 crc        modecalc=9
 186 cfcm      else if (index(controlcard,'MCMF').gt.0) then
 187 cfmc        modecalc=10
 188       else if (index(controlcard,'SOFTREG').gt.0) then
 189         modecalc=11
 190       else if (index(controlcard,'CHECK_BOND').gt.0) then
 191         modecalc=-1
 192       else if (index(controlcard,'TEST').gt.0) then
 193         modecalc=-2
 194       else if (index(controlcard,'MD').gt.0) then
 195         modecalc=12
 196       else if (index(controlcard,'RE ').gt.0) then
 197         modecalc=14
 198       endif
 199
 200       lmuca=index(controlcard,'MUCA').gt.0
 201       call readi(controlcard,'MUCADYN',mucadyn,0)
 202       call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
 203       if (lmuca .and. (me.eq.king .or. .not.out1file ))
 204      & then
 205        write (iout,*) 'MUCADYN=',mucadyn
 206        write (iout,*) 'MUCASMOOTH=',muca_smooth
 207       endif
 208
 209       iscode=index(controlcard,'ONE_LETTER')
 210       indphi=index(controlcard,'PHI')
 211       indback=index(controlcard,'BACK')
 212       iranconf=index(controlcard,'RAND_CONF')
 213       i2ndstr=index(controlcard,'USE_SEC_PRED')
 214       gradout=index(controlcard,'GRADOUT').gt.0
 215       gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
 216       call reada(controlcard,'DISTCHAINMAX',distchainmax,5.0d0)
 217       if (me.eq.king .or. .not.out1file )
 218      &  write (iout,*) "DISTCHAINMAX",distchainmax
 219
 220       if(me.eq.king.or..not.out1file)
 221      & write (iout,'(2a)') diagmeth(kdiag),
 222      &  ' routine used to diagonalize matrices.'
 223       return
 224       end
 225 c--------------------------------------------------------------------------
 226       subroutine read_REMDpar
 227 C
 228 C Read REMD settings
 229 C
 230       implicit real*8 (a-h,o-z)
 231       include 'DIMENSIONS'
 232       include 'COMMON.IOUNITS'
 233       include 'COMMON.TIME1'
 234       include 'COMMON.MD'
 235 #ifndef LANG0
 236       include 'COMMON.LANGEVIN'
 237 #else
 238       include 'COMMON.LANGEVIN.lang0'
 239 #endif
 240       include 'COMMON.INTERACT'
 241       include 'COMMON.NAMES'
 242       include 'COMMON.GEO'
 243       include 'COMMON.REMD'
 244       include 'COMMON.CONTROL'
 245       include 'COMMON.SETUP'
 246       character*80 ucase
 247       character*320 controlcard
 248       character*3200 controlcard1
 249       integer iremd_m_total
 250
 251       if(me.eq.king.or..not.out1file)
 252      & write (iout,*) "REMD setup"
 253
 254       call card_concat(controlcard)
 255       call readi(controlcard,"NREP",nrep,3)
 256       call readi(controlcard,"NSTEX",nstex,1000)
 257       call reada(controlcard,"RETMIN",retmin,10.0d0)
 258       call reada(controlcard,"RETMAX",retmax,1000.0d0)
 259       mremdsync=(index(controlcard,'SYNC').gt.0)
 260       call readi(controlcard,"NSYN",i_sync_step,100)
 261       restart1file=(index(controlcard,'REST1FILE').gt.0)
 262       traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
 263       call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
 264       if(max_cache_traj_use.gt.max_cache_traj)
 265      &           max_cache_traj_use=max_cache_traj
 266       if(me.eq.king.or..not.out1file) then
 267 cd       if (traj1file) then
 268 crc caching is in testing - NTWX is not ignored
 269 cd        write (iout,*) "NTWX value is ignored"
 270 cd        write (iout,*) "  trajectory is stored to one file by master"
 271 cd        write (iout,*) "  before exchange at NSTEX intervals"
 272 cd       endif
 273        write (iout,*) "NREP= ",nrep
 274        write (iout,*) "NSTEX= ",nstex
 275        write (iout,*) "SYNC= ",mremdsync
 276        write (iout,*) "NSYN= ",i_sync_step
 277        write (iout,*) "TRAJCACHE= ",max_cache_traj_use
 278       endif
 279       remd_tlist=.false.
 280       if (index(controlcard,'TLIST').gt.0) then
 281          remd_tlist=.true.
 282          call card_concat(controlcard1)
 283          read(controlcard1,*) (remd_t(i),i=1,nrep)
 284          if(me.eq.king.or..not.out1file)
 285      &    write (iout,*)'tlist',(remd_t(i),i=1,nrep)
 286       endif
 287       remd_mlist=.false.
 288       if (index(controlcard,'MLIST').gt.0) then
 289          remd_mlist=.true.
 290          call card_concat(controlcard1)
 291          read(controlcard1,*) (remd_m(i),i=1,nrep)
 292          if(me.eq.king.or..not.out1file) then
 293           write (iout,*)'mlist',(remd_m(i),i=1,nrep)
 294           iremd_m_total=0
 295           do i=1,nrep
 296            iremd_m_total=iremd_m_total+remd_m(i)
 297           enddo
 298           write (iout,*) 'Total number of replicas ',iremd_m_total
 299          endif
 300       endif
 301       if(me.eq.king.or..not.out1file)
 302      & write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
 303       return
 304       end
 305 c--------------------------------------------------------------------------
 306       subroutine read_MDpar
 307 C
 308 C Read MD settings
 309 C
 310       implicit real*8 (a-h,o-z)
 311       include 'DIMENSIONS'
 312       include 'COMMON.IOUNITS'
 313       include 'COMMON.TIME1'
 314       include 'COMMON.MD'
 315 #ifndef LANG0
 316       include 'COMMON.LANGEVIN'
 317 #else
 318       include 'COMMON.LANGEVIN.lang0'
 319 #endif
 320       include 'COMMON.INTERACT'
 321       include 'COMMON.NAMES'
 322       include 'COMMON.GEO'
 323       include 'COMMON.SETUP'
 324       include 'COMMON.CONTROL'
 325       include 'COMMON.SPLITELE'
 326       character*80 ucase
 327       character*320 controlcard
 328
 329       call card_concat(controlcard)
 330       call readi(controlcard,"NSTEP",n_timestep,1000000)
 331       call readi(controlcard,"NTWE",ntwe,100)
 332       call readi(controlcard,"NTWX",ntwx,1000)
 333       call reada(controlcard,"DT",d_time,1.0d-1)
 334       call reada(controlcard,"DVMAX",dvmax,2.0d1)
 335       call reada(controlcard,"DAMAX",damax,1.0d1)
 336       call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
 337       call readi(controlcard,"LANG",lang,0)
 338       RESPA = index(controlcard,"RESPA") .gt. 0
 339       call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
 340       ntime_split0=ntime_split
 341       call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
 342       ntime_split0=ntime_split
 343       call reada(controlcard,"R_CUT",r_cut,2.0d0)
 344       call reada(controlcard,"LAMBDA",rlamb,0.3d0)
 345       rest = index(controlcard,"REST").gt.0
 346       tbf = index(controlcard,"TBF").gt.0
 347       usampl = index(controlcard,"USAMPL").gt.0
 348       mdpdb = index(controlcard,"MDPDB").gt.0
 349       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 350       call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
 351       call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
 352       call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
 353       if (count_reset_moment.eq.0) count_reset_moment=1000000000
 354       call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
 355       reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
 356       reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
 357       if (count_reset_vel.eq.0) count_reset_vel=1000000000
 358       large = index(controlcard,"LARGE").gt.0
 359       print_compon = index(controlcard,"PRINT_COMPON").gt.0
 360       rattle = index(controlcard,"RATTLE").gt.0
 361 c  if performing umbrella sampling, fragments constrained are read from the fragment file
 362       nset=0
 363       if(usampl) then
 364         call read_fragments
 365       endif
 366
 367       if(me.eq.king.or..not.out1file) then
 368        write (iout,*)
 369        write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
 370        write (iout,*)
 371        write (iout,'(a)') "The units are:"
 372        write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
 373        write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",
 374      &  " acceleration: angstrom/(48.9 fs)**2"
 375        write (iout,'(a)') "energy: kcal/mol, temperature: K"
 376        write (iout,*)
 377        write (iout,'(a60,i10)') "Number of time steps:",n_timestep
 378        write (iout,'(a60,f10.5,a)')
 379      &  "Initial time step of numerical integration:",d_time,
 380      &  " natural units"
 381        write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
 382        if (RESPA) then
 383         write (iout,'(2a,i4,a)')
 384      &    "A-MTS algorithm used; initial time step for fast-varying",
 385      &    " short-range forces split into",ntime_split," steps."
 386         write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
 387      &   r_cut," lambda",rlamb
 388        endif
 389        write (iout,'(2a,f10.5)')
 390      &  "Maximum acceleration threshold to reduce the time step",
 391      &  "/increase split number:",damax
 392        write (iout,'(2a,f10.5)')
 393      &  "Maximum predicted energy drift to reduce the timestep",
 394      &  "/increase split number:",edriftmax
 395        write (iout,'(a60,f10.5)')
 396      & "Maximum velocity threshold to reduce velocities:",dvmax
 397        write (iout,'(a60,i10)') "Frequency of property output:",ntwe
 398        write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
 399        if (rattle) write (iout,'(a60)')
 400      &  "Rattle algorithm used to constrain the virtual bonds"
 401       endif
 402       reset_fricmat=1000
 403       if (lang.gt.0) then
 404         call reada(controlcard,"ETAWAT",etawat,0.8904d0)
 405         call reada(controlcard,"RWAT",rwat,1.4d0)
 406         call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
 407         surfarea=index(controlcard,"SURFAREA").gt.0
 408         call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
 409         if(me.eq.king.or..not.out1file)then
 410          write (iout,'(/a,$)') "Langevin dynamics calculation"
 411          if (lang.eq.1) then
 412           write (iout,'(a/)')
 413      &      " with direct integration of Langevin equations"
 414          else if (lang.eq.2) then
 415           write (iout,'(a/)') " with TINKER stochasic MD integrator"
 416          else if (lang.eq.3) then
 417           write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
 418          else if (lang.eq.4) then
 419           write (iout,'(a/)') " in overdamped mode"
 420          else
 421           write (iout,'(//a,i5)')
 422      &      "=========== ERROR: Unknown Langevin dynamics mode:",lang
 423           stop
 424          endif
 425          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 426          write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
 427          write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
 428          write (iout,'(a60,f10.5)')
 429      &   "Scaling factor of the friction forces:",scal_fric
 430          if (surfarea) write (iout,'(2a,i10,a)')
 431      &     "Friction coefficients will be scaled by solvent-accessible",
 432      &     " surface area every",reset_fricmat," steps."
 433         endif
 434 c Calculate friction coefficients and bounds of stochastic forces
 435         eta=6*pi*cPoise*etawat
 436         if(me.eq.king.or..not.out1file)
 437      &   write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:"
 438      &   ,eta
 439         gamp=scal_fric*(pstok+rwat)*eta
 440         stdfp=dsqrt(2*Rb*t_bath/d_time)
 441         do i=1,ntyp
 442           gamsc(i)=scal_fric*(restok(i)+rwat)*eta
 443           stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
 444         enddo
 445         if(me.eq.king.or..not.out1file)then
 446          write (iout,'(/2a/)')
 447      &   "Radii of site types and friction coefficients and std's of",
 448      &   " stochastic forces of fully exposed sites"
 449          write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
 450          do i=1,ntyp
 451           write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),
 452      &     gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
 453          enddo
 454         endif
 455       else if (tbf) then
 456         if(me.eq.king.or..not.out1file)then
 457          write (iout,'(a)') "Berendsen bath calculation"
 458          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 459          write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
 460          if (reset_moment)
 461      &   write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 462      &   count_reset_moment," steps"
 463          if (reset_vel)
 464      &    write (iout,'(a,i10,a)')
 465      &    "Velocities will be reset at random every",count_reset_vel,
 466      &   " steps"
 467         endif
 468       else
 469         if(me.eq.king.or..not.out1file)
 470      &   write (iout,'(a31)') "Microcanonical mode calculation"
 471       endif
 472       if(me.eq.king.or..not.out1file)then
 473        if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
 474        if (usampl) then
 475           write(iout,*) "MD running with constraints."
 476           write(iout,*) "Equilibration time ", eq_time, " mtus."
 477           write(iout,*) "Constraining ", nfrag," fragments."
 478           write(iout,*) "Length of each fragment, weight and q0:"
 479           do iset=1,nset
 480            write (iout,*) "Set of restraints #",iset
 481            do i=1,nfrag
 482               write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),
 483      &           ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
 484            enddo
 485            write(iout,*) "constraints between ", npair, "fragments."
 486            write(iout,*) "constraint pairs, weights and q0:"
 487            do i=1,npair
 488             write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),
 489      &             ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
 490            enddo
 491            write(iout,*) "angle constraints within ", nfrag_back,
 492      &      "backbone fragments."
 493            write(iout,*) "fragment, weights:"
 494            do i=1,nfrag_back
 495             write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),
 496      &         ifrag_back(2,i,iset),wfrag_back(1,i,iset),
 497      &         wfrag_back(2,i,iset),wfrag_back(3,i,iset)
 498            enddo
 499           enddo
 500         iset=mod(kolor,nset)+1
 501        endif
 502       endif
 503       if(me.eq.king.or..not.out1file)
 504      & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
 505       return
 506       end
 507 c------------------------------------------------------------------------------
 508       subroutine molread
 509 C
 510 C Read molecular data.
 511 C
 512       implicit real*8 (a-h,o-z)
 513       include 'DIMENSIONS'
 514 #ifdef MPI
 515       include 'mpif.h'
 516       integer error_msg
 517 #endif
 518       include 'COMMON.IOUNITS'
 519       include 'COMMON.GEO'
 520       include 'COMMON.VAR'
 521       include 'COMMON.INTERACT'
 522       include 'COMMON.LOCAL'
 523       include 'COMMON.NAMES'
 524       include 'COMMON.CHAIN'
 525       include 'COMMON.FFIELD'
 526       include 'COMMON.SBRIDGE'
 527       include 'COMMON.HEADER'
 528       include 'COMMON.CONTROL'
 529       include 'COMMON.DBASE'
 530       include 'COMMON.THREAD'
 531       include 'COMMON.CONTACTS'
 532       include 'COMMON.TORCNSTR'
 533       include 'COMMON.TIME1'
 534       include 'COMMON.BOUNDS'
 535       include 'COMMON.MD'
 536       include 'COMMON.SETUP'
 537       character*4 sequence(maxres)
 538       integer rescode
 539       double precision x(maxvar)
 540       character*256 pdbfile
 541       character*320 weightcard
 542       character*80 weightcard_t,ucase
 543       dimension itype_pdb(maxres)
 544       common /pizda/ itype_pdb
 545       logical seq_comp,fail
 546       double precision energia(0:n_ene)
 547       integer ilen
 548       external ilen
 549 C
 550 C Body
 551 C
 552 C Read weights of the subsequent energy terms.
 553       call card_concat(weightcard)
 554       call reada(weightcard,'WLONG',wlong,1.0D0)
 555       call reada(weightcard,'WSC',wsc,wlong)
 556       call reada(weightcard,'WSCP',wscp,wlong)
 557       call reada(weightcard,'WELEC',welec,1.0D0)
 558       call reada(weightcard,'WVDWPP',wvdwpp,welec)
 559       call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 560       call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 561       call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 562       call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 563       call reada(weightcard,'WTURN3',wturn3,1.0D0)
 564       call reada(weightcard,'WTURN4',wturn4,1.0D0)
 565       call reada(weightcard,'WTURN6',wturn6,1.0D0)
 566       call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 567       call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 568       call reada(weightcard,'WBOND',wbond,1.0D0)
 569       call reada(weightcard,'WTOR',wtor,1.0D0)
 570       call reada(weightcard,'WTORD',wtor_d,1.0D0)
 571       call reada(weightcard,'WANG',wang,1.0D0)
 572       call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 573       call reada(weightcard,'SCAL14',scal14,0.4D0)
 574       call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 575       call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 576       call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 577       call reada(weightcard,'TEMP0',temp0,300.0d0)
 578       if (index(weightcard,'SOFT').gt.0) ipot=6
 579 C 12/1/95 Added weight for the multi-body term WCORR
 580       call reada(weightcard,'WCORRH',wcorr,1.0D0)
 581       if (wcorr4.gt.0.0d0) wcorr=wcorr4
 582       weights(1)=wsc
 583       weights(2)=wscp
 584       weights(3)=welec
 585       weights(4)=wcorr
 586       weights(5)=wcorr5
 587       weights(6)=wcorr6
 588       weights(7)=wel_loc
 589       weights(8)=wturn3
 590       weights(9)=wturn4
 591       weights(10)=wturn6
 592       weights(11)=wang
 593       weights(12)=wscloc
 594       weights(13)=wtor
 595       weights(14)=wtor_d
 596       weights(15)=wstrain
 597       weights(16)=wvdwpp
 598       weights(17)=wbond
 599       weights(18)=scal14
 600       weights(21)=wsccor
 601       if(me.eq.king.or..not.out1file)
 602      & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 603      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 604      &  wturn4,wturn6
 605    10 format (/'Energy-term weights (unscaled):'//
 606      & 'WSCC=   ',f10.6,' (SC-SC)'/
 607      & 'WSCP=   ',f10.6,' (SC-p)'/
 608      & 'WELEC=  ',f10.6,' (p-p electr)'/
 609      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 610      & 'WBOND=  ',f10.6,' (stretching)'/
 611      & 'WANG=   ',f10.6,' (bending)'/
 612      & 'WSCLOC= ',f10.6,' (SC local)'/
 613      & 'WTOR=   ',f10.6,' (torsional)'/
 614      & 'WTORD=  ',f10.6,' (double torsional)'/
 615      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 616      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 617      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 618      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 619      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 620      & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
 621      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 622      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 623      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 624       if(me.eq.king.or..not.out1file)then
 625        if (wcorr4.gt.0.0d0) then
 626         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
 627      &   'between contact pairs of peptide groups'
 628         write (iout,'(2(a,f5.3/))')
 629      &  'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
 630      &  'Range of quenching the correlation terms:',2*delt_corr
 631        else if (wcorr.gt.0.0d0) then
 632         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
 633      &   'between contact pairs of peptide groups'
 634        endif
 635        write (iout,'(a,f8.3)')
 636      &  'Scaling factor of 1,4 SC-p interactions:',scal14
 637        write (iout,'(a,f8.3)')
 638      &  'General scaling factor of SC-p interactions:',scalscp
 639       endif
 640       r0_corr=cutoff_corr-delt_corr
 641       do i=1,ntyp
 642         aad(i,1)=scalscp*aad(i,1)
 643         aad(i,2)=scalscp*aad(i,2)
 644         bad(i,1)=scalscp*bad(i,1)
 645         bad(i,2)=scalscp*bad(i,2)
 646       enddo
 647       call rescale_weights(t_bath)
 648       if(me.eq.king.or..not.out1file)
 649      & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 650      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 651      &  wturn4,wturn6
 652    22 format (/'Energy-term weights (scaled):'//
 653      & 'WSCC=   ',f10.6,' (SC-SC)'/
 654      & 'WSCP=   ',f10.6,' (SC-p)'/
 655      & 'WELEC=  ',f10.6,' (p-p electr)'/
 656      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 657      & 'WBOND=  ',f10.6,' (stretching)'/
 658      & 'WANG=   ',f10.6,' (bending)'/
 659      & 'WSCLOC= ',f10.6,' (SC local)'/
 660      & 'WTOR=   ',f10.6,' (torsional)'/
 661      & 'WTORD=  ',f10.6,' (double torsional)'/
 662      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 663      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 664      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 665      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 666      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 667      & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
 668      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 669      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 670      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 671       if(me.eq.king.or..not.out1file)
 672      & write (iout,*) "Reference temperature for weights calculation:",
 673      &  temp0
 674       call reada(weightcard,"D0CM",d0cm,3.78d0)
 675       call reada(weightcard,"AKCM",akcm,15.1d0)
 676       call reada(weightcard,"AKTH",akth,11.0d0)
 677       call reada(weightcard,"AKCT",akct,12.0d0)
 678       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 679       call reada(weightcard,"V2SS",v2ss,7.61d0)
 680       call reada(weightcard,"V3SS",v3ss,13.7d0)
 681       call reada(weightcard,"EBR",ebr,-5.50D0)
 682       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 683       do i=1,maxres
 684         dyn_ss_mask(i)=.false.
 685       enddo
 686       do i=1,maxres-1
 687         do j=i+1,maxres
 688           dyn_ssbond_ij(i,j)=1.0d300
 689         enddo
 690       enddo
 691       call reada(weightcard,"HT",Ht,0.0D0)
 692       if (dyn_ss) then
 693         ss_depth=ebr/wsc-0.25*eps(1,1)
 694         Ht=Ht/wsc-0.25*eps(1,1)
 695         akcm=akcm*wstrain/wsc
 696         akth=akth*wstrain/wsc
 697         akct=akct*wstrain/wsc
 698         v1ss=v1ss*wstrain/wsc
 699         v2ss=v2ss*wstrain/wsc
 700         v3ss=v3ss*wstrain/wsc
 701       else
 702         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 703       endif
 704
 705       if(me.eq.king.or..not.out1file) then
 706        write (iout,*) "Parameters of the SS-bond potential:"
 707        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
 708      & " AKCT",akct
 709        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 710        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 711        write (iout,*)" HT",Ht
 712 c       print *,'indpdb=',indpdb,' pdbref=',pdbref
 713       endif
 714       if (indpdb.gt.0 .or. pdbref) then
 715         read(inp,'(a)') pdbfile
 716         if(me.eq.king.or..not.out1file)
 717      &   write (iout,'(2a)') 'PDB data will be read from file ',
 718      &   pdbfile(:ilen(pdbfile))
 719         open(ipdbin,file=pdbfile,status='old',err=33)
 720         goto 34
 721   33    write (iout,'(a)') 'Error opening PDB file.'
 722         stop
 723   34    continue
 724 c        print *,'Begin reading pdb data'
 725         call readpdb
 726 c        print *,'Finished reading pdb data'
 727         if(me.eq.king.or..not.out1file)
 728      &   write (iout,'(a,i3,a,i3)')'nsup=',nsup,
 729      &   ' nstart_sup=',nstart_sup
 730         do i=1,nres
 731           itype_pdb(i)=itype(i)
 732         enddo
 733         close (ipdbin)
 734         nnt=nstart_sup
 735         nct=nstart_sup+nsup-1
 736         call contact(.false.,ncont_ref,icont_ref,co)
 737
 738         if (sideadd) then
 739          if(me.eq.king.or..not.out1file)
 740      &    write(iout,*)'Adding sidechains'
 741          maxsi=1000
 742          do i=2,nres-1
 743           iti=itype(i)
 744           if (iti.ne.10 .and. itype(i).ne.ntyp1) then
 745             nsi=0
 746             fail=.true.
 747             do while (fail.and.nsi.le.maxsi)
 748               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 749               nsi=nsi+1
 750             enddo
 751             if(fail) write(iout,*)'Adding sidechain failed for res ',
 752      &              i,' after ',nsi,' trials'
 753           endif
 754          enddo
 755         endif
 756       endif
 757       if (indpdb.eq.0) then
 758 C Read sequence if not taken from the pdb file.
 759         read (inp,*) nres
 760 c        print *,'nres=',nres
 761         if (iscode.gt.0) then
 762           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 763         else
 764           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 765         endif
 766 C Convert sequence to numeric code
 767         do i=1,nres
 768           itype(i)=rescode(i,sequence(i),iscode)
 769         enddo
 770 C Assign initial virtual bond lengths
 771         do i=2,nres
 772           vbld(i)=vbl
 773           vbld_inv(i)=vblinv
 774         enddo
 775         do i=2,nres-1
 776           vbld(i+nres)=dsc(iabs(itype(i)))
 777           vbld_inv(i+nres)=dsc_inv(iabs(itype(i)))
 778 c          write (iout,*) "i",i," itype",itype(i),
 779 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 780         enddo
 781       endif
 782 c      print *,nres
 783 c      print '(20i4)',(itype(i),i=1,nres)
 784       do i=1,nres
 785 #ifdef PROCOR
 786         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
 787 #else
 788         if (itype(i).eq.ntyp1) then
 789 #endif
 790           itel(i)=0
 791 #ifdef PROCOR
 792         else if (iabs(itype(i+1)).ne.20) then
 793 #else
 794         else if (iabs(itype(i)).ne.20) then
 795 #endif
 796           itel(i)=1
 797         else
 798           itel(i)=2
 799         endif
 800       enddo
 801       if(me.eq.king.or..not.out1file)then
 802        write (iout,*) "ITEL"
 803        do i=1,nres-1
 804          write (iout,*) i,itype(i),itel(i)
 805        enddo
 806        print *,'Call Read_Bridge.'
 807       endif
 808       call read_bridge
 809 C 8/13/98 Set limits to generating the dihedral angles
 810       do i=1,nres
 811         phibound(1,i)=-pi
 812         phibound(2,i)=pi
 813       enddo
 814       read (inp,*) ndih_constr
 815       if (ndih_constr.gt.0) then
 816         read (inp,*) ftors
 817         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
 818         if(me.eq.king.or..not.out1file)then
 819          write (iout,*)
 820      &   'There are',ndih_constr,' constraints on phi angles.'
 821          do i=1,ndih_constr
 822           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
 823          enddo
 824         endif
 825         do i=1,ndih_constr
 826           phi0(i)=deg2rad*phi0(i)
 827           drange(i)=deg2rad*drange(i)
 828         enddo
 829         if(me.eq.king.or..not.out1file)
 830      &   write (iout,*) 'FTORS',ftors
 831         do i=1,ndih_constr
 832           ii = idih_constr(i)
 833           phibound(1,ii) = phi0(i)-drange(i)
 834           phibound(2,ii) = phi0(i)+drange(i)
 835         enddo
 836       endif
 837       nnt=1
 838 #ifdef MPI
 839       if (me.eq.king) then
 840 #endif
 841        write (iout,'(a)') 'Boundaries in phi angle sampling:'
 842        do i=1,nres
 843          write (iout,'(a3,i5,2f10.1)')
 844      &   restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
 845        enddo
 846 #ifdef MP
 847       endif
 848 #endif
 849       nct=nres
 850 cd      print *,'NNT=',NNT,' NCT=',NCT
 851       if (itype(1).eq.ntyp1) nnt=2
 852       if (itype(nres).eq.ntyp1) nct=nct-1
 853       if (pdbref) then
 854         if(me.eq.king.or..not.out1file)
 855      &   write (iout,'(a,i3)') 'nsup=',nsup
 856         nstart_seq=nnt
 857         if (nsup.le.(nct-nnt+1)) then
 858           do i=0,nct-nnt+1-nsup
 859             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
 860               nstart_seq=nnt+i
 861               goto 111
 862             endif
 863           enddo
 864           write (iout,'(a)')
 865      &            'Error - sequences to be superposed do not match.'
 866           stop
 867         else
 868           do i=0,nsup-(nct-nnt+1)
 869             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
 870      &      then
 871               nstart_sup=nstart_sup+i
 872               nsup=nct-nnt+1
 873               goto 111
 874             endif
 875           enddo
 876           write (iout,'(a)')
 877      &            'Error - sequences to be superposed do not match.'
 878         endif
 879   111   continue
 880         if (nsup.eq.0) nsup=nct-nnt
 881         if (nstart_sup.eq.0) nstart_sup=nnt
 882         if (nstart_seq.eq.0) nstart_seq=nnt
 883         if(me.eq.king.or..not.out1file)
 884      &   write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
 885      &                 ' nstart_seq=',nstart_seq
 886       endif
 887 c--- Zscore rms -------
 888       if (nz_start.eq.0) nz_start=nnt
 889       if (nz_end.eq.0 .and. nsup.gt.0) then
 890         nz_end=nnt+nsup-1
 891       else if (nz_end.eq.0) then
 892         nz_end=nct
 893       endif
 894       if(me.eq.king.or..not.out1file)then
 895        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
 896        write (iout,*) 'IZ_SC=',iz_sc
 897       endif
 898 c----------------------
 899       call init_int_table
 900       if (refstr) then
 901         if (.not.pdbref) then
 902           call read_angles(inp,*38)
 903           goto 39
 904    38     write (iout,'(a)') 'Error reading reference structure.'
 905 #ifdef MPI
 906           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
 907           stop 'Error reading reference structure'
 908 #endif
 909    39     call chainbuild
 910           call setup_var
 911 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
 912           nstart_sup=nnt
 913           nstart_seq=nnt
 914           nsup=nct-nnt+1
 915           kkk=1
 916           do i=1,2*nres
 917             do j=1,3
 918               cref(j,i,kkk)=c(j,i)
 919             enddo
 920           enddo
 921           call contact(.true.,ncont_ref,icont_ref,co)
 922         endif
 923 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
 924         call flush(iout)
 925         if (constr_dist.gt.0) call read_dist_constr
 926         write (iout,*) "After read_dist_constr nhpb",nhpb
 927         call hpb_partition
 928         if(me.eq.king.or..not.out1file)
 929      &   write (iout,*) 'Contact order:',co
 930         if (pdbref) then
 931         if(me.eq.king.or..not.out1file)
 932      &   write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
 933         do i=1,ncont_ref
 934           do j=1,2
 935             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
 936           enddo
 937           if(me.eq.king.or..not.out1file)
 938      &     write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',
 939      &     icont_ref(1,i),' ',
 940      &     restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
 941         enddo
 942         endif
 943       endif
 944       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
 945      &    .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
 946      &    modecalc.ne.10) then
 947 C If input structure hasn't been supplied from the PDB file read or generate
 948 C initial geometry.
 949         if (iranconf.eq.0 .and. .not. extconf) then
 950           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
 951      &     write (iout,'(a)') 'Initial geometry will be read in.'
 952           if (read_cart) then
 953             read(inp,'(8f10.5)',end=36,err=36)
 954      &       ((c(l,k),l=1,3),k=1,nres),
 955      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
 956             write (iout,*) "Exit READ_CART"
 957             write (iout,'(8f10.5)')
 958      &       ((c(l,k),l=1,3),k=1,nres),
 959      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
 960             call int_from_cart1(.true.)
 961             write (iout,*) "Finish INT_TO_CART"
 962             do i=1,nres-1
 963               do j=1,3
 964                 dc(j,i)=c(j,i+1)-c(j,i)
 965                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
 966               enddo
 967             enddo
 968             do i=nnt,nct
 969               if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
 970                 do j=1,3
 971                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
 972                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
 973                 enddo
 974               endif
 975             enddo
 976             return
 977           else
 978             call read_angles(inp,*36)
 979           endif
 980           goto 37
 981    36     write (iout,'(a)') 'Error reading angle file.'
 982 #ifdef MPI
 983           call mpi_finalize( MPI_COMM_WORLD,IERR )
 984 #endif
 985           stop 'Error reading angle file.'
 986    37     continue
 987         else if (extconf) then
 988          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0)
 989      &    write (iout,'(a)') 'Extended chain initial geometry.'
 990          do i=3,nres
 991           theta(i)=90d0*deg2rad
 992          enddo
 993          do i=4,nres
 994           phi(i)=180d0*deg2rad
 995          enddo
 996          do i=2,nres-1
 997           alph(i)=110d0*deg2rad
 998          enddo
 999          do i=2,nres-1
1000           omeg(i)=-120d0*deg2rad
1001           if (itype(i).le.0) omeg(i)=-omeg(i)
1002          enddo
1003         else
1004           if(me.eq.king.or..not.out1file)
1005      &     write (iout,'(a)') 'Random-generated initial geometry.'
1006
1007
1008 #ifdef MPI
1009           if (me.eq.king  .or. fg_rank.eq.0 .and. (
1010      &           modecalc.eq.12 .or. modecalc.eq.14) ) then
1011 #endif
1012             do itrial=1,100
1013               itmp=1
1014               call gen_rand_conf(itmp,*30)
1015               goto 40
1016    30         write (iout,*) 'Failed to generate random conformation',
1017      &          ', itrial=',itrial
1018               write (*,*) 'Processor:',me,
1019      &          ' Failed to generate random conformation',
1020      &          ' itrial=',itrial
1021               call intout
1022
1023 #ifdef AIX
1024               call flush_(iout)
1025 #else
1026               call flush(iout)
1027 #endif
1028             enddo
1029             write (iout,'(a,i3,a)') 'Processor:',me,
1030      &        ' error in generating random conformation.'
1031             write (*,'(a,i3,a)') 'Processor:',me,
1032      &        ' error in generating random conformation.'
1033             call flush(iout)
1034 #ifdef MPI
1035             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1036    40       continue
1037           endif
1038 #else
1039           do itrial=1,100
1040             itmp=1
1041             call gen_rand_conf(itmp,*30)
1042             goto 40
1043    30       write (iout,*) 'Failed to generate random conformation',
1044      &        ', itrial=',itrial
1045             write (*,*) 'Failed to generate random conformation',
1046      &        ', itrial=',itrial
1047           enddo
1048           write (iout,'(a,i3,a)') 'Processor:',me,
1049      &      ' error in generating random conformation.'
1050           write (*,'(a,i3,a)') 'Processor:',me,
1051      &      ' error in generating random conformation.'
1052           stop
1053    40     continue
1054 #endif
1055         endif
1056       elseif (modecalc.eq.4) then
1057         read (inp,'(a)') intinname
1058         open (intin,file=intinname,status='old',err=333)
1059         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0)
1060      &  write (iout,'(a)') 'intinname',intinname
1061         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1062         goto 334
1063   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1064 #ifdef MPI
1065         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1066 #endif
1067         stop 'Error opening angle file.'
1068   334   continue
1069
1070       endif
1071 C Generate distance constraints, if the PDB structure is to be regularized.
1072       if (nthread.gt.0) then
1073         call read_threadbase
1074       endif
1075       call setup_var
1076       if (me.eq.king .or. .not. out1file)
1077      & call intout
1078       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1079         write (iout,'(/a,i3,a)')
1080      &  'The chain contains',ns,' disulfide-bridging cysteines.'
1081         write (iout,'(20i4)') (iss(i),i=1,ns)
1082        if (dyn_ss) then
1083           write(iout,*)"Running with dynamic disulfide-bond formation"
1084        else
1085         write (iout,'(/a/)') 'Pre-formed links are:'
1086         do i=1,nss
1087           i1=ihpb(i)-nres
1088           i2=jhpb(i)-nres
1089           it1=itype(i1)
1090           it2=itype(i2)
1091          write (iout,'(2a,i3,3a,i3,a,3f10.3)')
1092      &    restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
1093      &    ebr,forcon(i)
1094         enddo
1095         write (iout,'(a)')
1096       endif
1097       endif
1098       if (ns.gt.0.and.dyn_ss) then
1099           do i=nss+1,nhpb
1100             ihpb(i-nss)=ihpb(i)
1101             jhpb(i-nss)=jhpb(i)
1102             forcon(i-nss)=forcon(i)
1103             dhpb(i-nss)=dhpb(i)
1104           enddo
1105           nhpb=nhpb-nss
1106           nss=0
1107           call hpb_partition
1108           do i=1,ns
1109             dyn_ss_mask(iss(i))=.true.
1110           enddo
1111       endif
1112       if (i2ndstr.gt.0) call secstrp2dihc
1113 c      call geom_to_var(nvar,x)
1114 c      call etotal(energia(0))
1115 c      call enerprint(energia(0))
1116 c      call briefout(0,etot)
1117 c      stop
1118 cd    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1119 cd    write (iout,'(a)') 'Variable list:'
1120 cd    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1121 #ifdef MPI
1122       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file))
1123      &  write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
1124      &  'Processor',myrank,': end reading molecular data.'
1125 #endif
1126       return
1127       end
1128 c--------------------------------------------------------------------------
1129       logical function seq_comp(itypea,itypeb,length)
1130       implicit none
1131       integer length,itypea(length),itypeb(length)
1132       integer i
1133       do i=1,length
1134         if (itypea(i).ne.itypeb(i)) then
1135           seq_comp=.false.
1136           return
1137         endif
1138       enddo
1139       seq_comp=.true.
1140       return
1141       end
1142 c-----------------------------------------------------------------------------
1143       subroutine read_bridge
1144 C Read information about disulfide bridges.
1145       implicit real*8 (a-h,o-z)
1146       include 'DIMENSIONS'
1147 #ifdef MPI
1148       include 'mpif.h'
1149 #endif
1150       include 'COMMON.IOUNITS'
1151       include 'COMMON.GEO'
1152       include 'COMMON.VAR'
1153       include 'COMMON.INTERACT'
1154       include 'COMMON.LOCAL'
1155       include 'COMMON.NAMES'
1156       include 'COMMON.CHAIN'
1157       include 'COMMON.FFIELD'
1158       include 'COMMON.SBRIDGE'
1159       include 'COMMON.HEADER'
1160       include 'COMMON.CONTROL'
1161       include 'COMMON.DBASE'
1162       include 'COMMON.THREAD'
1163       include 'COMMON.TIME1'
1164       include 'COMMON.SETUP'
1165 C Read bridging residues.
1166       read (inp,*) ns,(iss(i),i=1,ns)
1167 c      print *,'ns=',ns
1168       if(me.eq.king.or..not.out1file)
1169      &  write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
1170 C Check whether the specified bridging residues are cystines.
1171       do i=1,ns
1172         if (itype(iss(i)).ne.1) then
1173           if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
1174      &   'Do you REALLY think that the residue ',
1175      &    restyp(itype(iss(i))),i,
1176      &   ' can form a disulfide bridge?!!!'
1177           write (*,'(2a,i3,a)')
1178      &   'Do you REALLY think that the residue ',
1179      &     restyp(itype(iss(i))),i,
1180      &   ' can form a disulfide bridge?!!!'
1181 #ifdef MPI
1182          call MPI_Finalize(MPI_COMM_WORLD,ierror)
1183          stop
1184 #endif
1185         endif
1186       enddo
1187 C Read preformed bridges.
1188       if (ns.gt.0) then
1189       read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
1190       if(fg_rank.eq.0)
1191      &write (iout,*) 'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
1192       if (nss.gt.0) then
1193         nhpb=nss
1194 C Check if the residues involved in bridges are in the specified list of
1195 C bridging residues.
1196         do i=1,nss
1197           do j=1,i-1
1198             if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
1199      &      .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
1200               write (iout,'(a,i3,a)') 'Disulfide pair',i,
1201      &      ' contains residues present in other pairs.'
1202               write (*,'(a,i3,a)') 'Disulfide pair',i,
1203      &      ' contains residues present in other pairs.'
1204 #ifdef MPI
1205               call MPI_Finalize(MPI_COMM_WORLD,ierror)
1206               stop
1207 #endif
1208             endif
1209           enddo
1210           do j=1,ns
1211             if (ihpb(i).eq.iss(j)) goto 10
1212           enddo
1213           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1214    10     continue
1215           do j=1,ns
1216             if (jhpb(i).eq.iss(j)) goto 20
1217           enddo
1218           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1219    20     continue
1220           dhpb(i)=dbr
1221           forcon(i)=fbr
1222         enddo
1223         do i=1,nss
1224           ihpb(i)=ihpb(i)+nres
1225           jhpb(i)=jhpb(i)+nres
1226         enddo
1227       endif
1228       endif
1229       return
1230       end
1231 c----------------------------------------------------------------------------
1232       subroutine read_x(kanal,*)
1233       implicit real*8 (a-h,o-z)
1234       include 'DIMENSIONS'
1235       include 'COMMON.GEO'
1236       include 'COMMON.VAR'
1237       include 'COMMON.CHAIN'
1238       include 'COMMON.IOUNITS'
1239       include 'COMMON.CONTROL'
1240       include 'COMMON.LOCAL'
1241       include 'COMMON.INTERACT'
1242 c Read coordinates from input
1243 c
1244       read(kanal,'(8f10.5)',end=10,err=10)
1245      &  ((c(l,k),l=1,3),k=1,nres),
1246      &  ((c(l,k+nres),l=1,3),k=nnt,nct)
1247       do j=1,3
1248         c(j,nres+1)=c(j,1)
1249         c(j,2*nres)=c(j,nres)
1250       enddo
1251       call int_from_cart1(.false.)
1252       do i=1,nres-1
1253         do j=1,3
1254           dc(j,i)=c(j,i+1)-c(j,i)
1255           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
1256         enddo
1257       enddo
1258       do i=nnt,nct
1259         if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1260           do j=1,3
1261             dc(j,i+nres)=c(j,i+nres)-c(j,i)
1262             dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
1263           enddo
1264         endif
1265       enddo
1266
1267       return
1268    10 return1
1269       end
1270 c----------------------------------------------------------------------------
1271       subroutine read_threadbase
1272       implicit real*8 (a-h,o-z)
1273       include 'DIMENSIONS'
1274       include 'COMMON.IOUNITS'
1275       include 'COMMON.GEO'
1276       include 'COMMON.VAR'
1277       include 'COMMON.INTERACT'
1278       include 'COMMON.LOCAL'
1279       include 'COMMON.NAMES'
1280       include 'COMMON.CHAIN'
1281       include 'COMMON.FFIELD'
1282       include 'COMMON.SBRIDGE'
1283       include 'COMMON.HEADER'
1284       include 'COMMON.CONTROL'
1285       include 'COMMON.DBASE'
1286       include 'COMMON.THREAD'
1287       include 'COMMON.TIME1'
1288 C Read pattern database for threading.
1289       read (icbase,*) nseq
1290       do i=1,nseq
1291         read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1292      &   nres_base(2,i),nres_base(3,i)
1293         read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1294      &   nres_base(1,i))
1295 c       write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1296 c    &   nres_base(2,i),nres_base(3,i)
1297 c       write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1298 c    &   nres_base(1,i))
1299       enddo
1300       close (icbase)
1301       if (weidis.eq.0.0D0) weidis=0.1D0
1302       do i=nnt,nct
1303         do j=i+2,nct
1304           nhpb=nhpb+1
1305           ihpb(nhpb)=i
1306           jhpb(nhpb)=j
1307           forcon(nhpb)=weidis
1308         enddo
1309       enddo
1310       read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl)
1311       write (iout,'(a,i5)') 'nexcl: ',nexcl
1312       write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl)
1313       return
1314       end
1315 c------------------------------------------------------------------------------
1316       subroutine setup_var
1317       implicit real*8 (a-h,o-z)
1318       include 'DIMENSIONS'
1319       include 'COMMON.IOUNITS'
1320       include 'COMMON.GEO'
1321       include 'COMMON.VAR'
1322       include 'COMMON.INTERACT'
1323       include 'COMMON.LOCAL'
1324       include 'COMMON.NAMES'
1325       include 'COMMON.CHAIN'
1326       include 'COMMON.FFIELD'
1327       include 'COMMON.SBRIDGE'
1328       include 'COMMON.HEADER'
1329       include 'COMMON.CONTROL'
1330       include 'COMMON.DBASE'
1331       include 'COMMON.THREAD'
1332       include 'COMMON.TIME1'
1333 C Set up variable list.
1334       ntheta=nres-2
1335       nphi=nres-3
1336       nvar=ntheta+nphi
1337       nside=0
1338       do i=2,nres-1
1339         if (itype(i).ne.10 .and. itype(i).ne.ntyp1) then
1340           nside=nside+1
1341           ialph(i,1)=nvar+nside
1342           ialph(nside,2)=i
1343         endif
1344       enddo
1345       if (indphi.gt.0) then
1346         nvar=nphi
1347       else if (indback.gt.0) then
1348         nvar=nphi+ntheta
1349       else
1350         nvar=nvar+2*nside
1351       endif
1352 cd    write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
1353       return
1354       end
1355 c----------------------------------------------------------------------------
1356       subroutine gen_dist_constr
1357 C Generate CA distance constraints.
1358       implicit real*8 (a-h,o-z)
1359       include 'DIMENSIONS'
1360       include 'COMMON.IOUNITS'
1361       include 'COMMON.GEO'
1362       include 'COMMON.VAR'
1363       include 'COMMON.INTERACT'
1364       include 'COMMON.LOCAL'
1365       include 'COMMON.NAMES'
1366       include 'COMMON.CHAIN'
1367       include 'COMMON.FFIELD'
1368       include 'COMMON.SBRIDGE'
1369       include 'COMMON.HEADER'
1370       include 'COMMON.CONTROL'
1371       include 'COMMON.DBASE'
1372       include 'COMMON.THREAD'
1373       include 'COMMON.TIME1'
1374       dimension itype_pdb(maxres)
1375       common /pizda/ itype_pdb
1376       character*2 iden
1377 cd      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
1378 cd      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
1379 cd     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
1380 cd     & ' nsup',nsup
1381       do i=nstart_sup,nstart_sup+nsup-1
1382 cd      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
1383 cd     &    ' seq_pdb', restyp(itype_pdb(i))
1384         do j=i+2,nstart_sup+nsup-1
1385           nhpb=nhpb+1
1386           ihpb(nhpb)=i+nstart_seq-nstart_sup
1387           jhpb(nhpb)=j+nstart_seq-nstart_sup
1388           forcon(nhpb)=weidis
1389           dhpb(nhpb)=dist(i,j)
1390         enddo
1391       enddo
1392 cd      write (iout,'(a)') 'Distance constraints:'
1393 cd      do i=nss+1,nhpb
1394 cd        ii=ihpb(i)
1395 cd        jj=jhpb(i)
1396 cd        iden='CA'
1397 cd        if (ii.gt.nres) then
1398 cd          iden='SC'
1399 cd          ii=ii-nres
1400 cd          jj=jj-nres
1401 cd        endif
1402 cd        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
1403 cd     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
1404 cd     &  dhpb(i),forcon(i)
1405 cd      enddo
1406       return
1407       end
1408 c----------------------------------------------------------------------------
1409       subroutine map_read
1410       implicit real*8 (a-h,o-z)
1411       include 'DIMENSIONS'
1412       include 'COMMON.MAP'
1413       include 'COMMON.IOUNITS'
1414       character*3 angid(4) /'THE','PHI','ALP','OME'/
1415       character*80 mapcard,ucase
1416       do imap=1,nmap
1417         read (inp,'(a)') mapcard
1418         mapcard=ucase(mapcard)
1419         if (index(mapcard,'PHI').gt.0) then
1420           kang(imap)=1
1421         else if (index(mapcard,'THE').gt.0) then
1422           kang(imap)=2
1423         else if (index(mapcard,'ALP').gt.0) then
1424           kang(imap)=3
1425         else if (index(mapcard,'OME').gt.0) then
1426           kang(imap)=4
1427         else
1428           write(iout,'(a)')'Error - illegal variable spec in MAP card.'
1429           stop 'Error - illegal variable spec in MAP card.'
1430         endif
1431         call readi (mapcard,'RES1',res1(imap),0)
1432         call readi (mapcard,'RES2',res2(imap),0)
1433         if (res1(imap).eq.0) then
1434           res1(imap)=res2(imap)
1435         else if (res2(imap).eq.0) then
1436           res2(imap)=res1(imap)
1437         endif
1438         if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
1439           write (iout,'(a)')
1440      &    'Error - illegal definition of variable group in MAP.'
1441           stop 'Error - illegal definition of variable group in MAP.'
1442         endif
1443         call reada(mapcard,'FROM',ang_from(imap),0.0D0)
1444         call reada(mapcard,'TO',ang_to(imap),0.0D0)
1445         call readi(mapcard,'NSTEP',nstep(imap),0)
1446         if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
1447           write (iout,'(a)')
1448      &     'Illegal boundary and/or step size specification in MAP.'
1449           stop 'Illegal boundary and/or step size specification in MAP.'
1450         endif
1451       enddo ! imap
1452       return
1453       end
1454 c----------------------------------------------------------------------------
1455       subroutine csaread
1456       implicit real*8 (a-h,o-z)
1457       include 'DIMENSIONS'
1458       include 'COMMON.IOUNITS'
1459       include 'COMMON.GEO'
1460       include 'COMMON.CSA'
1461       include 'COMMON.BANK'
1462       include 'COMMON.CONTROL'
1463       character*80 ucase
1464       character*620 mcmcard
1465       call card_concat(mcmcard)
1466
1467       call readi(mcmcard,'NCONF',nconf,50)
1468       call readi(mcmcard,'NADD',nadd,0)
1469       call readi(mcmcard,'JSTART',jstart,1)
1470       call readi(mcmcard,'JEND',jend,1)
1471       call readi(mcmcard,'NSTMAX',nstmax,500000)
1472       call readi(mcmcard,'N0',n0,1)
1473       call readi(mcmcard,'N1',n1,6)
1474       call readi(mcmcard,'N2',n2,4)
1475       call readi(mcmcard,'N3',n3,0)
1476       call readi(mcmcard,'N4',n4,0)
1477       call readi(mcmcard,'N5',n5,0)
1478       call readi(mcmcard,'N6',n6,10)
1479       call readi(mcmcard,'N7',n7,0)
1480       call readi(mcmcard,'N8',n8,0)
1481       call readi(mcmcard,'N9',n9,0)
1482       call readi(mcmcard,'N14',n14,0)
1483       call readi(mcmcard,'N15',n15,0)
1484       call readi(mcmcard,'N16',n16,0)
1485       call readi(mcmcard,'N17',n17,0)
1486       call readi(mcmcard,'N18',n18,0)
1487
1488       vdisulf=(index(mcmcard,'DYNSS').gt.0)
1489
1490       call readi(mcmcard,'NDIFF',ndiff,2)
1491       call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
1492       call readi(mcmcard,'IS1',is1,1)
1493       call readi(mcmcard,'IS2',is2,8)
1494       call readi(mcmcard,'NRAN0',nran0,4)
1495       call readi(mcmcard,'NRAN1',nran1,2)
1496       call readi(mcmcard,'IRR',irr,1)
1497       call readi(mcmcard,'NSEED',nseed,20)
1498       call readi(mcmcard,'NTOTAL',ntotal,10000)
1499       call reada(mcmcard,'CUT1',cut1,2.0d0)
1500       call reada(mcmcard,'CUT2',cut2,5.0d0)
1501       call reada(mcmcard,'ESTOP',estop,-3000.0d0)
1502       call readi(mcmcard,'ICMAX',icmax,3)
1503       call readi(mcmcard,'IRESTART',irestart,0)
1504 c!bankt      call readi(mcmcard,'NBANKTM',ntbankm,0)
1505       ntbankm=0
1506 c!bankt
1507       call reada(mcmcard,'DELE',dele,20.0d0)
1508       call reada(mcmcard,'DIFCUT',difcut,720.0d0)
1509       call readi(mcmcard,'IREF',iref,0)
1510       call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
1511       call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
1512       call readi(mcmcard,'NCONF_IN',nconf_in,0)
1513       call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
1514       write (iout,*) "NCONF_IN",nconf_in
1515       return
1516       end
1517 c----------------------------------------------------------------------------
1518 cfmc      subroutine mcmfread
1519 cfmc      implicit real*8 (a-h,o-z)
1520 cfmc      include 'DIMENSIONS'
1521 cfmc      include 'COMMON.MCMF'
1522 cfmc      include 'COMMON.IOUNITS'
1523 cfmc      include 'COMMON.GEO'
1524 cfmc      character*80 ucase
1525 cfmc      character*620 mcmcard
1526 cfmc      call card_concat(mcmcard)
1527 cfmc
1528 cfmc      call readi(mcmcard,'MAXRANT',maxrant,1000)
1529 cfmc      write(iout,*)'MAXRANT=',maxrant
1530 cfmc      call readi(mcmcard,'MAXFAM',maxfam,maxfam_p)
1531 cfmc      write(iout,*)'MAXFAM=',maxfam
1532 cfmc      call readi(mcmcard,'NNET1',nnet1,5)
1533 cfmc      write(iout,*)'NNET1=',nnet1
1534 cfmc      call readi(mcmcard,'NNET2',nnet2,4)
1535 cfmc      write(iout,*)'NNET2=',nnet2
1536 cfmc      call readi(mcmcard,'NNET3',nnet3,4)
1537 cfmc      write(iout,*)'NNET3=',nnet3
1538 cfmc      call readi(mcmcard,'ILASTT',ilastt,0)
1539 cfmc      write(iout,*)'ILASTT=',ilastt
1540 cfmc      call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf)
1541 cfmc      write(iout,*)'MAXSTR=',maxstr
1542 cfmc      maxstr_f=maxstr/maxfam
1543 cfmc      write(iout,*)'MAXSTR_F=',maxstr_f
1544 cfmc      call readi(mcmcard,'NMCMF',nmcmf,10)
1545 cfmc      write(iout,*)'NMCMF=',nmcmf
1546 cfmc      call readi(mcmcard,'IFOCUS',ifocus,nmcmf)
1547 cfmc      write(iout,*)'IFOCUS=',ifocus
1548 cfmc      call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000)
1549 cfmc      write(iout,*)'NLOCMCMF=',nlocmcmf
1550 cfmc      call readi(mcmcard,'INTPRT',intprt,1000)
1551 cfmc      write(iout,*)'INTPRT=',intprt
1552 cfmc      call readi(mcmcard,'IPRT',iprt,100)
1553 cfmc      write(iout,*)'IPRT=',iprt
1554 cfmc      call readi(mcmcard,'IMAXTR',imaxtr,100)
1555 cfmc      write(iout,*)'IMAXTR=',imaxtr
1556 cfmc      call readi(mcmcard,'MAXEVEN',maxeven,1000)
1557 cfmc      write(iout,*)'MAXEVEN=',maxeven
1558 cfmc      call readi(mcmcard,'MAXEVEN1',maxeven1,3)
1559 cfmc      write(iout,*)'MAXEVEN1=',maxeven1
1560 cfmc      call readi(mcmcard,'INIMIN',inimin,200)
1561 cfmc      write(iout,*)'INIMIN=',inimin
1562 cfmc      call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10)
1563 cfmc      write(iout,*)'NSTEPMCMF=',nstepmcmf
1564 cfmc      call readi(mcmcard,'NTHREAD',nthread,5)
1565 cfmc      write(iout,*)'NTHREAD=',nthread
1566 cfmc      call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500)
1567 cfmc      write(iout,*)'MAXSTEPMCMF=',maxstepmcmf
1568 cfmc      call readi(mcmcard,'MAXPERT',maxpert,9)
1569 cfmc      write(iout,*)'MAXPERT=',maxpert
1570 cfmc      call readi(mcmcard,'IRMSD',irmsd,1)
1571 cfmc      write(iout,*)'IRMSD=',irmsd
1572 cfmc      call reada(mcmcard,'DENEMIN',denemin,0.01D0)
1573 cfmc      write(iout,*)'DENEMIN=',denemin
1574 cfmc      call reada(mcmcard,'RCUT1S',rcut1s,3.5D0)
1575 cfmc      write(iout,*)'RCUT1S=',rcut1s
1576 cfmc      call reada(mcmcard,'RCUT1E',rcut1e,2.0D0)
1577 cfmc      write(iout,*)'RCUT1E=',rcut1e
1578 cfmc      call reada(mcmcard,'RCUT2S',rcut2s,0.5D0)
1579 cfmc      write(iout,*)'RCUT2S=',rcut2s
1580 cfmc      call reada(mcmcard,'RCUT2E',rcut2e,0.1D0)
1581 cfmc      write(iout,*)'RCUT2E=',rcut2e
1582 cfmc      call reada(mcmcard,'DPERT1',d_pert1,180.0D0)
1583 cfmc      write(iout,*)'DPERT1=',d_pert1
1584 cfmc      call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0)
1585 cfmc      write(iout,*)'DPERT1A=',d_pert1a
1586 cfmc      call reada(mcmcard,'DPERT2',d_pert2,90.0D0)
1587 cfmc      write(iout,*)'DPERT2=',d_pert2
1588 cfmc      call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0)
1589 cfmc      write(iout,*)'DPERT2A=',d_pert2a
1590 cfmc      call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0)
1591 cfmc      write(iout,*)'DPERT2B=',d_pert2b
1592 cfmc      call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0)
1593 cfmc      write(iout,*)'DPERT2C=',d_pert2c
1594 cfmc      d_pert1=deg2rad*d_pert1
1595 cfmc      d_pert1a=deg2rad*d_pert1a
1596 cfmc      d_pert2=deg2rad*d_pert2
1597 cfmc      d_pert2a=deg2rad*d_pert2a
1598 cfmc      d_pert2b=deg2rad*d_pert2b
1599 cfmc      d_pert2c=deg2rad*d_pert2c
1600 cfmc      call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0)
1601 cfmc      write(iout,*)'KT_MCMF1=',kt_mcmf1
1602 cfmc      call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0)
1603 cfmc      write(iout,*)'KT_MCMF2=',kt_mcmf2
1604 cfmc      call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0)
1605 cfmc      write(iout,*)'DKT_MCMF1=',dkt_mcmf1
1606 cfmc      call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0)
1607 cfmc      write(iout,*)'DKT_MCMF2=',dkt_mcmf2
1608 cfmc      call reada(mcmcard,'RCUTINI',rcutini,3.5D0)
1609 cfmc      write(iout,*)'RCUTINI=',rcutini
1610 cfmc      call reada(mcmcard,'GRAT',grat,0.5D0)
1611 cfmc      write(iout,*)'GRAT=',grat
1612 cfmc      call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0)
1613 cfmc      write(iout,*)'BIAS_MCMF=',bias_mcmf
1614 cfmc
1615 cfmc      return
1616 cfmc      end
1617 c----------------------------------------------------------------------------
1618       subroutine mcmread
1619       implicit real*8 (a-h,o-z)
1620       include 'DIMENSIONS'
1621       include 'COMMON.MCM'
1622       include 'COMMON.MCE'
1623       include 'COMMON.IOUNITS'
1624       character*80 ucase
1625       character*320 mcmcard
1626       call card_concat(mcmcard)
1627       call readi(mcmcard,'MAXACC',maxacc,100)
1628       call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
1629       call readi(mcmcard,'MAXTRIAL',maxtrial,100)
1630       call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
1631       call readi(mcmcard,'MAXREPM',maxrepm,200)
1632       call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
1633       call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
1634       call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
1635       call reada(mcmcard,'E_UP',e_up,5.0D0)
1636       call reada(mcmcard,'DELTE',delte,0.1D0)
1637       call readi(mcmcard,'NSWEEP',nsweep,5)
1638       call readi(mcmcard,'NSTEPH',nsteph,0)
1639       call readi(mcmcard,'NSTEPC',nstepc,0)
1640       call reada(mcmcard,'TMIN',tmin,298.0D0)
1641       call reada(mcmcard,'TMAX',tmax,298.0D0)
1642       call readi(mcmcard,'NWINDOW',nwindow,0)
1643       call readi(mcmcard,'PRINT_MC',print_mc,0)
1644       print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
1645       print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
1646       ent_read=(index(mcmcard,'ENT_READ').gt.0)
1647       call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
1648       call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
1649       call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
1650       call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
1651       call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
1652       if (nwindow.gt.0) then
1653         read (inp,*) (winstart(i),winend(i),i=1,nwindow)
1654         do i=1,nwindow
1655           winlen(i)=winend(i)-winstart(i)+1
1656         enddo
1657       endif
1658       if (tmax.lt.tmin) tmax=tmin
1659       if (tmax.eq.tmin) then
1660         nstepc=0
1661         nsteph=0
1662       endif
1663       if (nstepc.gt.0 .and. nsteph.gt.0) then
1664         tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
1665         tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
1666       endif
1667 C Probabilities of different move types
1668       sumpro_type(0)=0.0D0
1669       call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
1670       call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
1671       sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
1672       call reada(mcmcard,'THETA'     ,sumpro_type(3),0.0d0)
1673       sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
1674       call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
1675       sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
1676       do i=1,MaxMoveType
1677         print *,'i',i,' sumprotype',sumpro_type(i)
1678         sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
1679         print *,'i',i,' sumprotype',sumpro_type(i)
1680       enddo
1681       return
1682       end
1683 c----------------------------------------------------------------------------
1684       subroutine read_minim
1685       implicit real*8 (a-h,o-z)
1686       include 'DIMENSIONS'
1687       include 'COMMON.MINIM'
1688       include 'COMMON.IOUNITS'
1689       character*80 ucase
1690       character*320 minimcard
1691       call card_concat(minimcard)
1692       call readi(minimcard,'MAXMIN',maxmin,2000)
1693       call readi(minimcard,'MAXFUN',maxfun,5000)
1694       call readi(minimcard,'MINMIN',minmin,maxmin)
1695       call readi(minimcard,'MINFUN',minfun,maxmin)
1696       call reada(minimcard,'TOLF',tolf,1.0D-2)
1697       call reada(minimcard,'RTOLF',rtolf,1.0D-4)
1698       print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
1699       print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
1700       print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
1701       write (iout,'(/80(1h*)/20x,a/80(1h*))')
1702      &         'Options in energy minimization:'
1703       write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
1704      & 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
1705      & 'MinMin:',MinMin,' MinFun:',MinFun,
1706      & ' TolF:',TolF,' RTolF:',RTolF
1707       return
1708       end
1709 c----------------------------------------------------------------------------
1710       subroutine read_angles(kanal,*)
1711       implicit real*8 (a-h,o-z)
1712       include 'DIMENSIONS'
1713       include 'COMMON.GEO'
1714       include 'COMMON.VAR'
1715       include 'COMMON.CHAIN'
1716       include 'COMMON.IOUNITS'
1717       include 'COMMON.CONTROL'
1718 c Read angles from input
1719 c
1720        read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
1721        read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
1722        read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
1723        read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
1724
1725        do i=1,nres
1726 c 9/7/01 avoid 180 deg valence angle
1727         if (theta(i).gt.179.99d0) theta(i)=179.99d0
1728 c
1729         theta(i)=deg2rad*theta(i)
1730         phi(i)=deg2rad*phi(i)
1731         alph(i)=deg2rad*alph(i)
1732         omeg(i)=deg2rad*omeg(i)
1733        enddo
1734       return
1735    10 return1
1736       end
1737 c----------------------------------------------------------------------------
1738       subroutine reada(rekord,lancuch,wartosc,default)
1739       implicit none
1740       character*(*) rekord,lancuch
1741       double precision wartosc,default
1742       integer ilen,iread
1743       external ilen
1744       iread=index(rekord,lancuch)
1745       if (iread.eq.0) then
1746         wartosc=default
1747         return
1748       endif
1749       iread=iread+ilen(lancuch)+1
1750       read (rekord(iread:),*,err=10,end=10) wartosc
1751       return
1752   10  wartosc=default
1753       return
1754       end
1755 c----------------------------------------------------------------------------
1756       subroutine readi(rekord,lancuch,wartosc,default)
1757       implicit none
1758       character*(*) rekord,lancuch
1759       integer wartosc,default
1760       integer ilen,iread
1761       external ilen
1762       iread=index(rekord,lancuch)
1763       if (iread.eq.0) then
1764         wartosc=default
1765         return
1766       endif
1767       iread=iread+ilen(lancuch)+1
1768       read (rekord(iread:),*,err=10,end=10) wartosc
1769       return
1770   10  wartosc=default
1771       return
1772       end
1773 c----------------------------------------------------------------------------
1774       subroutine multreadi(rekord,lancuch,tablica,dim,default)
1775       implicit none
1776       integer dim,i
1777       integer tablica(dim),default
1778       character*(*) rekord,lancuch
1779       character*80 aux
1780       integer ilen,iread
1781       external ilen
1782       do i=1,dim
1783         tablica(i)=default
1784       enddo
1785       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1786       if (iread.eq.0) return
1787       iread=iread+ilen(lancuch)+1
1788       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1789    10 return
1790       end
1791 c----------------------------------------------------------------------------
1792       subroutine multreada(rekord,lancuch,tablica,dim,default)
1793       implicit none
1794       integer dim,i
1795       double precision tablica(dim),default
1796       character*(*) rekord,lancuch
1797       character*80 aux
1798       integer ilen,iread
1799       external ilen
1800       do i=1,dim
1801         tablica(i)=default
1802       enddo
1803       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1804       if (iread.eq.0) return
1805       iread=iread+ilen(lancuch)+1
1806       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1807    10 return
1808       end
1809 c----------------------------------------------------------------------------
1810       subroutine openunits
1811       implicit real*8 (a-h,o-z)
1812       include 'DIMENSIONS'
1813 #ifdef MPI
1814       include 'mpif.h'
1815       character*16 form,nodename
1816       integer nodelen
1817 #endif
1818       include 'COMMON.SETUP'
1819       include 'COMMON.IOUNITS'
1820       include 'COMMON.MD'
1821       include 'COMMON.CONTROL'
1822       integer lenpre,lenpot,ilen,lentmp
1823       external ilen
1824       character*3 out1file_text,ucase
1825       character*3 ll
1826       external ucase
1827 c      print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
1828       call getenv_loc("PREFIX",prefix)
1829       pref_orig = prefix
1830       call getenv_loc("POT",pot)
1831       call getenv_loc("DIRTMP",tmpdir)
1832       call getenv_loc("CURDIR",curdir)
1833       call getenv_loc("OUT1FILE",out1file_text)
1834 c      print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
1835       out1file_text=ucase(out1file_text)
1836       if (out1file_text(1:1).eq."Y") then
1837         out1file=.true.
1838       else
1839         out1file=fg_rank.gt.0
1840       endif
1841       lenpre=ilen(prefix)
1842       lenpot=ilen(pot)
1843       lentmp=ilen(tmpdir)
1844       if (lentmp.gt.0) then
1845           write (*,'(80(1h!))')
1846           write (*,'(a,19x,a,19x,a)') "!","  A T T E N T I O N  ","!"
1847           write (*,'(80(1h!))')
1848           write (*,*)"All output files will be on node /tmp directory."
1849 #ifdef MPI
1850         call  MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
1851         if (me.eq.king) then
1852           write (*,*) "The master node is ",nodename
1853         else if (fg_rank.eq.0) then
1854           write (*,*) "I am the CG slave node ",nodename
1855         else
1856           write (*,*) "I am the FG slave node ",nodename
1857         endif
1858 #endif
1859         PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
1860         lenpre = lentmp+lenpre+1
1861       endif
1862       entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
1863 C Get the names and open the input files
1864 #if defined(WINIFL) || defined(WINPGI)
1865       open(1,file=pref_orig(:ilen(pref_orig))//
1866      &  '.inp',status='old',readonly,shared)
1867        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1868 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1869 C Get parameter filenames and open the parameter files.
1870       call getenv_loc('BONDPAR',bondname)
1871       open (ibond,file=bondname,status='old',readonly,shared)
1872       call getenv_loc('THETPAR',thetname)
1873       open (ithep,file=thetname,status='old',readonly,shared)
1874       call getenv_loc('ROTPAR',rotname)
1875       open (irotam,file=rotname,status='old',readonly,shared)
1876       call getenv_loc('TORPAR',torname)
1877       open (itorp,file=torname,status='old',readonly,shared)
1878       call getenv_loc('TORDPAR',tordname)
1879       open (itordp,file=tordname,status='old',readonly,shared)
1880       call getenv_loc('FOURIER',fouriername)
1881       open (ifourier,file=fouriername,status='old',readonly,shared)
1882       call getenv_loc('ELEPAR',elename)
1883       open (ielep,file=elename,status='old',readonly,shared)
1884       call getenv_loc('SIDEPAR',sidename)
1885       open (isidep,file=sidename,status='old',readonly,shared)
1886 #elif (defined CRAY) || (defined AIX)
1887       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1888      &  action='read')
1889 c      print *,"Processor",myrank," opened file 1"
1890       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1891 c      print *,"Processor",myrank," opened file 9"
1892 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1893 C Get parameter filenames and open the parameter files.
1894       call getenv_loc('BONDPAR',bondname)
1895       open (ibond,file=bondname,status='old',action='read')
1896 c      print *,"Processor",myrank," opened file IBOND"
1897       call getenv_loc('THETPAR',thetname)
1898       open (ithep,file=thetname,status='old',action='read')
1899 c      print *,"Processor",myrank," opened file ITHEP"
1900       call getenv_loc('ROTPAR',rotname)
1901       open (irotam,file=rotname,status='old',action='read')
1902 c      print *,"Processor",myrank," opened file IROTAM"
1903       call getenv_loc('TORPAR',torname)
1904       open (itorp,file=torname,status='old',action='read')
1905 c      print *,"Processor",myrank," opened file ITORP"
1906       call getenv_loc('TORDPAR',tordname)
1907       open (itordp,file=tordname,status='old',action='read')
1908 c      print *,"Processor",myrank," opened file ITORDP"
1909       call getenv_loc('SCCORPAR',sccorname)
1910       open (isccor,file=sccorname,status='old',action='read')
1911 c      print *,"Processor",myrank," opened file ISCCOR"
1912       call getenv_loc('FOURIER',fouriername)
1913       open (ifourier,file=fouriername,status='old',action='read')
1914 c      print *,"Processor",myrank," opened file IFOURIER"
1915       call getenv_loc('ELEPAR',elename)
1916       open (ielep,file=elename,status='old',action='read')
1917 c      print *,"Processor",myrank," opened file IELEP"
1918       call getenv_loc('SIDEPAR',sidename)
1919       open (isidep,file=sidename,status='old',action='read')
1920 c      print *,"Processor",myrank," opened file ISIDEP"
1921 c      print *,"Processor",myrank," opened parameter files"
1922 #elif (defined G77)
1923       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
1924       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1925 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1926 C Get parameter filenames and open the parameter files.
1927       call getenv_loc('BONDPAR',bondname)
1928       open (ibond,file=bondname,status='old')
1929       call getenv_loc('THETPAR',thetname)
1930       open (ithep,file=thetname,status='old')
1931       call getenv_loc('ROTPAR',rotname)
1932       open (irotam,file=rotname,status='old')
1933       call getenv_loc('TORPAR',torname)
1934       open (itorp,file=torname,status='old')
1935       call getenv_loc('TORDPAR',tordname)
1936       open (itordp,file=tordname,status='old')
1937       call getenv_loc('SCCORPAR',sccorname)
1938       open (isccor,file=sccorname,status='old')
1939       call getenv_loc('FOURIER',fouriername)
1940       open (ifourier,file=fouriername,status='old')
1941       call getenv_loc('ELEPAR',elename)
1942       open (ielep,file=elename,status='old')
1943       call getenv_loc('SIDEPAR',sidename)
1944       open (isidep,file=sidename,status='old')
1945 #else
1946       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
1947      &  readonly)
1948        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
1949 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
1950 C Get parameter filenames and open the parameter files.
1951       call getenv_loc('BONDPAR',bondname)
1952       open (ibond,file=bondname,status='old',readonly)
1953       call getenv_loc('THETPAR',thetname)
1954       open (ithep,file=thetname,status='old',readonly)
1955       call getenv_loc('ROTPAR',rotname)
1956       open (irotam,file=rotname,status='old',readonly)
1957       call getenv_loc('TORPAR',torname)
1958       open (itorp,file=torname,status='old',readonly)
1959       call getenv_loc('TORDPAR',tordname)
1960       open (itordp,file=tordname,status='old',readonly)
1961       call getenv_loc('SCCORPAR',sccorname)
1962       open (isccor,file=sccorname,status='old',readonly)
1963 #ifndef CRYST_THETA
1964       call getenv_loc('THETPARPDB',thetname_pdb)
1965       print *,"thetname_pdb ",thetname_pdb
1966       open (ithep_pdb,file=thetname_pdb,status='old',action='read')
1967       print *,ithep_pdb," opened"
1968 #endif
1969       call getenv_loc('FOURIER',fouriername)
1970       open (ifourier,file=fouriername,status='old',readonly)
1971       call getenv_loc('ELEPAR',elename)
1972       open (ielep,file=elename,status='old',readonly)
1973       call getenv_loc('SIDEPAR',sidename)
1974       open (isidep,file=sidename,status='old',readonly)
1975 #ifndef CRYST_SC
1976       call getenv_loc('ROTPARPDB',rotname_pdb)
1977       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
1978 #endif
1979 #endif
1980 #ifndef OLDSCP
1981 C
1982 C 8/9/01 In the newest version SCp interaction constants are read from a file
1983 C Use -DOLDSCP to use hard-coded constants instead.
1984 C
1985       call getenv_loc('SCPPAR',scpname)
1986 #if defined(WINIFL) || defined(WINPGI)
1987       open (iscpp,file=scpname,status='old',readonly,shared)
1988 #elif (defined CRAY)  || (defined AIX)
1989       open (iscpp,file=scpname,status='old',action='read')
1990 #elif (defined G77)
1991       open (iscpp,file=scpname,status='old')
1992 #else
1993       open (iscpp,file=scpname,status='old',readonly)
1994 #endif
1995 #endif
1996       call getenv_loc('PATTERN',patname)
1997 #if defined(WINIFL) || defined(WINPGI)
1998       open (icbase,file=patname,status='old',readonly,shared)
1999 #elif (defined CRAY)  || (defined AIX)
2000       open (icbase,file=patname,status='old',action='read')
2001 #elif (defined G77)
2002       open (icbase,file=patname,status='old')
2003 #else
2004       open (icbase,file=patname,status='old',readonly)
2005 #endif
2006 #ifdef MPI
2007 C Open output file only for CG processes
2008 c      print *,"Processor",myrank," fg_rank",fg_rank
2009       if (fg_rank.eq.0) then
2010
2011       if (nodes.eq.1) then
2012         npos=3
2013       else
2014         npos = dlog10(dfloat(nodes-1))+1
2015       endif
2016       if (npos.lt.3) npos=3
2017       write (liczba,'(i1)') npos
2018       form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
2019      &  //')'
2020       write (liczba,form) me
2021       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//
2022      &  liczba(:ilen(liczba))
2023       intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2024      &  //'.int'
2025       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2026      &  //'.pdb'
2027       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
2028      &  liczba(:ilen(liczba))//'.mol2'
2029       statname=prefix(:lenpre)//'_'//pot(:lenpot)//
2030      &  liczba(:ilen(liczba))//'.stat'
2031       if (lentmp.gt.0)
2032      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2033      &      //liczba(:ilen(liczba))//'.stat')
2034       rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba))
2035      &  //'.rst'
2036       if(usampl) then
2037           qname=prefix(:lenpre)//'_'//pot(:lenpot)//
2038      & liczba(:ilen(liczba))//'.const'
2039       endif
2040
2041       endif
2042 #else
2043       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
2044       intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
2045       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
2046       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
2047       statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
2048       if (lentmp.gt.0)
2049      &  call copy_to_tmp(pref_orig(:ile(pref_orig))//'_'//pot(:lenpot)//
2050      &    //'.stat')
2051       rest2name=prefix(:ilen(prefix))//'.rst'
2052       if(usampl) then
2053          qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
2054       endif
2055 #endif
2056 #if defined(AIX) || defined(PGI)
2057       if (me.eq.king .or. .not. out1file)
2058      &   open(iout,file=outname,status='unknown')
2059 #ifdef DEBUG
2060       if (fg_rank.gt.0) then
2061         write (liczba,'(i3.3)') myrank/nfgtasks
2062         write (ll,'(bz,i3.3)') fg_rank
2063         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2064      &   status='unknown')
2065       endif
2066 #endif
2067       if(me.eq.king) then
2068        open(igeom,file=intname,status='unknown',position='append')
2069        open(ipdb,file=pdbname,status='unknown')
2070        open(imol2,file=mol2name,status='unknown')
2071        open(istat,file=statname,status='unknown',position='append')
2072       else
2073 c1out       open(iout,file=outname,status='unknown')
2074       endif
2075 #else
2076       if (me.eq.king .or. .not.out1file)
2077      &    open(iout,file=outname,status='unknown')
2078 #ifdef DEBUG
2079       if (fg_rank.gt.0) then
2080         write (liczba,'(i3.3)') myrank/nfgtasks
2081         write (ll,'(bz,i3.3)') fg_rank
2082         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2083      &   status='unknown')
2084       endif
2085 #endif
2086       if(me.eq.king) then
2087        open(igeom,file=intname,status='unknown',access='append')
2088        open(ipdb,file=pdbname,status='unknown')
2089        open(imol2,file=mol2name,status='unknown')
2090        open(istat,file=statname,status='unknown',access='append')
2091       else
2092 c1out       open(iout,file=outname,status='unknown')
2093       endif
2094 #endif
2095       csa_rbank=prefix(:lenpre)//'.CSA.rbank'
2096       csa_seed=prefix(:lenpre)//'.CSA.seed'
2097       csa_history=prefix(:lenpre)//'.CSA.history'
2098       csa_bank=prefix(:lenpre)//'.CSA.bank'
2099       csa_bank1=prefix(:lenpre)//'.CSA.bank1'
2100       csa_alpha=prefix(:lenpre)//'.CSA.alpha'
2101       csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
2102 c!bankt      csa_bankt=prefix(:lenpre)//'.CSA.bankt'
2103       csa_int=prefix(:lenpre)//'.int'
2104       csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
2105       csa_native_int=prefix(:lenpre)//'.CSA.native.int'
2106       csa_in=prefix(:lenpre)//'.CSA.in'
2107 c      print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
2108 C Write file names
2109       if (me.eq.king)then
2110       write (iout,'(80(1h-))')
2111       write (iout,'(30x,a)') "FILE ASSIGNMENT"
2112       write (iout,'(80(1h-))')
2113       write (iout,*) "Input file                      : ",
2114      &  pref_orig(:ilen(pref_orig))//'.inp'
2115       write (iout,*) "Output file                     : ",
2116      &  outname(:ilen(outname))
2117       write (iout,*)
2118       write (iout,*) "Sidechain potential file        : ",
2119      &  sidename(:ilen(sidename))
2120 #ifndef OLDSCP
2121       write (iout,*) "SCp potential file              : ",
2122      &  scpname(:ilen(scpname))
2123 #endif
2124       write (iout,*) "Electrostatic potential file    : ",
2125      &  elename(:ilen(elename))
2126       write (iout,*) "Cumulant coefficient file       : ",
2127      &  fouriername(:ilen(fouriername))
2128       write (iout,*) "Torsional parameter file        : ",
2129      &  torname(:ilen(torname))
2130       write (iout,*) "Double torsional parameter file : ",
2131      &  tordname(:ilen(tordname))
2132       write (iout,*) "SCCOR parameter file : ",
2133      &  sccorname(:ilen(sccorname))
2134       write (iout,*) "Bond & inertia constant file    : ",
2135      &  bondname(:ilen(bondname))
2136       write (iout,*) "Bending parameter file          : ",
2137      &  thetname(:ilen(thetname))
2138       write (iout,*) "Rotamer parameter file          : ",
2139      &  rotname(:ilen(rotname))
2140       write (iout,*) "Thetpdb parameter file          : ",
2141      &  thetname_pdb(:ilen(thetname_pdb))
2142       write (iout,*) "Threading database              : ",
2143      &  patname(:ilen(patname))
2144       if (lentmp.ne.0)
2145      &write (iout,*)" DIRTMP                          : ",
2146      &  tmpdir(:lentmp)
2147       write (iout,'(80(1h-))')
2148       endif
2149       return
2150       end
2151 c----------------------------------------------------------------------------
2152       subroutine card_concat(card)
2153       implicit real*8 (a-h,o-z)
2154       include 'DIMENSIONS'
2155       include 'COMMON.IOUNITS'
2156       character*(*) card
2157       character*80 karta,ucase
2158       external ilen
2159       read (inp,'(a)') karta
2160       karta=ucase(karta)
2161       card=' '
2162       do while (karta(80:80).eq.'&')
2163         card=card(:ilen(card)+1)//karta(:79)
2164         read (inp,'(a)') karta
2165         karta=ucase(karta)
2166       enddo
2167       card=card(:ilen(card)+1)//karta
2168       return
2169       end
2170 c----------------------------------------------------------------------------------
2171       subroutine readrst
2172       implicit real*8 (a-h,o-z)
2173       include 'DIMENSIONS'
2174       include 'COMMON.CHAIN'
2175       include 'COMMON.IOUNITS'
2176       include 'COMMON.MD'
2177       open(irest2,file=rest2name,status='unknown')
2178       read(irest2,*) totT,EK,potE,totE,t_bath
2179       do i=1,2*nres
2180          read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
2181       enddo
2182       do i=1,2*nres
2183          read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
2184       enddo
2185       if(usampl) then
2186              read (irest2,*) iset
2187       endif
2188       close(irest2)
2189       return
2190       end
2191 c---------------------------------------------------------------------------------
2192       subroutine read_fragments
2193       implicit real*8 (a-h,o-z)
2194       include 'DIMENSIONS'
2195 #ifdef MPI
2196       include 'mpif.h'
2197 #endif
2198       include 'COMMON.SETUP'
2199       include 'COMMON.CHAIN'
2200       include 'COMMON.IOUNITS'
2201       include 'COMMON.MD'
2202       include 'COMMON.CONTROL'
2203       read(inp,*) nset,nfrag,npair,nfrag_back
2204       if(me.eq.king.or..not.out1file)
2205      & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
2206      &  " nfrag_back",nfrag_back
2207       do iset=1,nset
2208          read(inp,*) mset(iset)
2209        do i=1,nfrag
2210          read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
2211      &     qinfrag(i,iset)
2212          if(me.eq.king.or..not.out1file)
2213      &    write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
2214      &     ifrag(2,i,iset), qinfrag(i,iset)
2215        enddo
2216        do i=1,npair
2217         read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
2218      &    qinpair(i,iset)
2219         if(me.eq.king.or..not.out1file)
2220      &   write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
2221      &    ipair(2,i,iset), qinpair(i,iset)
2222        enddo
2223        do i=1,nfrag_back
2224         read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2225      &     wfrag_back(3,i,iset),
2226      &     ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2227         if(me.eq.king.or..not.out1file)
2228      &   write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2229      &   wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2230        enddo
2231       enddo
2232       return
2233       end
2234 c-------------------------------------------------------------------------------
2235       subroutine read_dist_constr
2236       implicit real*8 (a-h,o-z)
2237       include 'DIMENSIONS'
2238 #ifdef MPI
2239       include 'mpif.h'
2240 #endif
2241       include 'COMMON.SETUP'
2242       include 'COMMON.CONTROL'
2243       include 'COMMON.CHAIN'
2244       include 'COMMON.IOUNITS'
2245       include 'COMMON.SBRIDGE'
2246       integer ifrag_(2,100),ipair_(2,100)
2247       double precision wfrag_(100),wpair_(100)
2248       character*500 controlcard
2249 c      write (iout,*) "Calling read_dist_constr"
2250 c      write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
2251 c      call flush(iout)
2252       call card_concat(controlcard)
2253       call readi(controlcard,"NFRAG",nfrag_,0)
2254       call readi(controlcard,"NPAIR",npair_,0)
2255       call readi(controlcard,"NDIST",ndist_,0)
2256       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
2257       call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
2258       call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
2259       call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
2260       call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
2261 c      write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
2262 c      write (iout,*) "IFRAG"
2263 c      do i=1,nfrag_
2264 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2265 c      enddo
2266 c      write (iout,*) "IPAIR"
2267 c      do i=1,npair_
2268 c        write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
2269 c      enddo
2270       call flush(iout)
2271       do i=1,nfrag_
2272         if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
2273         if (ifrag_(2,i).gt.nstart_sup+nsup-1)
2274      &    ifrag_(2,i)=nstart_sup+nsup-1
2275 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2276         call flush(iout)
2277         if (wfrag_(i).gt.0.0d0) then
2278         do j=ifrag_(1,i),ifrag_(2,i)-1
2279           do k=j+1,ifrag_(2,i)
2280 c            write (iout,*) "j",j," k",k
2281             ddjk=dist(j,k)
2282             if (constr_dist.eq.1) then
2283               nhpb=nhpb+1
2284               ihpb(nhpb)=j
2285               jhpb(nhpb)=k
2286               dhpb(nhpb)=ddjk
2287               forcon(nhpb)=wfrag_(i)
2288             else if (constr_dist.eq.2) then
2289               if (ddjk.le.dist_cut) then
2290                 nhpb=nhpb+1
2291                 ihpb(nhpb)=j
2292                 jhpb(nhpb)=k
2293                 dhpb(nhpb)=ddjk
2294                 forcon(nhpb)=wfrag_(i)
2295               endif
2296             else
2297               nhpb=nhpb+1
2298               ihpb(nhpb)=j
2299               jhpb(nhpb)=k
2300               dhpb(nhpb)=ddjk
2301               forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
2302             endif
2303 #ifdef MPI
2304             if (.not.out1file .or. me.eq.king)
2305      &      write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2306      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2307 #else
2308             write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2309      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2310 #endif
2311           enddo
2312         enddo
2313         endif
2314       enddo
2315       do i=1,npair_
2316         if (wpair_(i).gt.0.0d0) then
2317         ii = ipair_(1,i)
2318         jj = ipair_(2,i)
2319         if (ii.gt.jj) then
2320           itemp=ii
2321           ii=jj
2322           jj=itemp
2323         endif
2324         do j=ifrag_(1,ii),ifrag_(2,ii)
2325           do k=ifrag_(1,jj),ifrag_(2,jj)
2326             nhpb=nhpb+1
2327             ihpb(nhpb)=j
2328             jhpb(nhpb)=k
2329             forcon(nhpb)=wpair_(i)
2330             dhpb(nhpb)=dist(j,k)
2331 #ifdef MPI
2332             if (.not.out1file .or. me.eq.king)
2333      &      write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2334      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2335 #else
2336             write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2337      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2338 #endif
2339           enddo
2340         enddo
2341         endif
2342       enddo
2343       do i=1,ndist_
2344         read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
2345         if (forcon(nhpb+1).gt.0.0d0) then
2346           nhpb=nhpb+1
2347           dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
2348 #ifdef MPI
2349           if (.not.out1file .or. me.eq.king)
2350      &    write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2351      &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2352 #else
2353           write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2354      &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2355 #endif
2356         endif
2357       enddo
2358       call flush(iout)
2359       return
2360       end
2361 c-------------------------------------------------------------------------------
2362 #ifdef WINIFL
2363       subroutine flush(iu)
2364       return
2365       end
2366 #endif
2367 #ifdef AIX
2368       subroutine flush(iu)
2369       call flush_(iu)
2370       return
2371       end
2372 #endif
2373 c------------------------------------------------------------------------------
2374       subroutine copy_to_tmp(source)
2375       include "DIMENSIONS"
2376       include "COMMON.IOUNITS"
2377       character*(*) source
2378       character* 256 tmpfile
2379       integer ilen
2380       external ilen
2381       logical ex
2382       tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source))
2383       inquire(file=tmpfile,exist=ex)
2384       if (ex) then
2385         write (*,*) "Copying ",tmpfile(:ilen(tmpfile)),
2386      &   " to temporary directory..."
2387         write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir
2388         call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir)
2389       endif
2390       return
2391       end
2392 c------------------------------------------------------------------------------
2393       subroutine move_from_tmp(source)
2394       include "DIMENSIONS"
2395       include "COMMON.IOUNITS"
2396       character*(*) source
2397       integer ilen
2398       external ilen
2399       write (*,*) "Moving ",source(:ilen(source)),
2400      & " from temporary directory to working directory"
2401       write (*,*) "/bin/mv "//source(:ilen(source))//" "//curdir
2402       call system("/bin/mv "//source(:ilen(source))//" "//curdir)
2403       return
2404       end
2405 c------------------------------------------------------------------------------
2406       subroutine random_init(seed)
2407 C
2408 C Initialize random number generator
2409 C
2410       implicit real*8 (a-h,o-z)
2411       include 'DIMENSIONS'
2412 #ifdef MPI
2413       include 'mpif.h'
2414       logical OKRandom, prng_restart
2415       real*8  r1
2416       integer iseed_array(4)
2417 #endif
2418       include 'COMMON.IOUNITS'
2419       include 'COMMON.TIME1'
2420       include 'COMMON.THREAD'
2421       include 'COMMON.SBRIDGE'
2422       include 'COMMON.CONTROL'
2423       include 'COMMON.MCM'
2424       include 'COMMON.MAP'
2425       include 'COMMON.HEADER'
2426       include 'COMMON.CSA'
2427       include 'COMMON.CHAIN'
2428       include 'COMMON.MUCA'
2429       include 'COMMON.MD'
2430       include 'COMMON.FFIELD'
2431       include 'COMMON.SETUP'
2432       iseed=-dint(dabs(seed))
2433       if (iseed.eq.0) then
2434         write (iout,'(/80(1h*)/20x,a/80(1h*))')
2435      &    'Random seed undefined. The program will stop.'
2436         write (*,'(/80(1h*)/20x,a/80(1h*))')
2437      &    'Random seed undefined. The program will stop.'
2438 #ifdef MPI
2439         call mpi_finalize(mpi_comm_world,ierr)
2440 #endif
2441         stop 'Bad random seed.'
2442       endif
2443 #ifdef MPI
2444       if (fg_rank.eq.0) then
2445       seed=seed*(me+1)+1
2446 #ifdef AMD64
2447       if(me.eq.king)
2448      &  write (iout,*) 'MPI: node= ', me, ' iseed= ',iseed
2449       OKRandom = prng_restart(me,iseed)
2450 #else
2451       do i=1,4
2452        tmp=65536.0d0**(4-i)
2453        iseed_array(i) = dint(seed/tmp)
2454        seed=seed-iseed_array(i)*tmp
2455       enddo
2456       if(me.eq.king)
2457      & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ',
2458      &                 (iseed_array(i),i=1,4)
2459       write (*,*) 'MPI: node= ',me, ' iseed(4)= ',
2460      &                 (iseed_array(i),i=1,4)
2461       OKRandom = prng_restart(me,iseed_array)
2462 #endif
2463       if (OKRandom) then
2464 c        r1 = prng_next(me)
2465          r1=ran_number(0.0D0,1.0D0)
2466         if(me.eq.king)
2467      &   write (iout,*) 'ran_num',r1
2468         if (r1.lt.0.0d0) OKRandom=.false.
2469       endif
2470       if (.not.OKRandom) then
2471         write (iout,*) 'PRNG IS NOT WORKING!!!'
2472         print *,'PRNG IS NOT WORKING!!!'
2473         if (me.eq.0) then
2474          call flush(iout)
2475          call mpi_abort(mpi_comm_world,error_msg,ierr)
2476          stop
2477         else
2478          write (iout,*) 'too many processors for parallel prng'
2479          write (*,*) 'too many processors for parallel prng'
2480          call flush(iout)
2481          stop
2482         endif
2483       endif
2484       endif
2485 #else
2486       call vrndst(iseed)
2487       write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0)
2488 #endif
2489       return
2490       end