source/unres/src_MD/readrtns.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 csa      if (modecalc.eq.8) then
  32 csa       inquire (file="fort.40",exist=file_exist)
  33 csa       if (.not.file_exist) call csaread
  34 csa      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,i2,3f10.5)') i-nss,ihpb(i),jhpb(i),
  48      &     ibecarb(i),dhpb(i),dhpb1(i),forcon(i)
  49       enddo
  50 #ifdef MPI
  51       endif
  52 #endif
  53 c      print *,"Processor",myrank," leaves READRTNS"
  54       return
  55       end
  56 C-------------------------------------------------------------------------------
  57       subroutine read_control
  58 C
  59 C Read contorl data
  60 C
  61       implicit real*8 (a-h,o-z)
  62       include 'DIMENSIONS'
  63 #ifdef MP
  64       include 'mpif.h'
  65       logical OKRandom, prng_restart
  66       real*8  r1
  67 #endif
  68       include 'COMMON.IOUNITS'
  69       include 'COMMON.TIME1'
  70       include 'COMMON.THREAD'
  71       include 'COMMON.SBRIDGE'
  72       include 'COMMON.CONTROL'
  73       include 'COMMON.MCM'
  74       include 'COMMON.MAP'
  75       include 'COMMON.HEADER'
  76 csa      include 'COMMON.CSA'
  77       include 'COMMON.CHAIN'
  78       include 'COMMON.MUCA'
  79       include 'COMMON.MD'
  80       include 'COMMON.FFIELD'
  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 reada(controlcard,'TIMLIM',timlim,960.0D0) ! default 16 hours
 100       unres_pdb = index(controlcard,'UNRES_PDB') .gt. 0
 101       call reada(controlcard,'SAFETY',safety,30.0D0) ! default 30 minutes
 102       call reada(controlcard,'RMSDBC',rmsdbc,3.0D0)
 103       call reada(controlcard,'RMSDBC1',rmsdbc1,0.5D0)
 104       call reada(controlcard,'RMSDBC1MAX',rmsdbc1max,1.5D0)
 105       call reada(controlcard,'RMSDBCM',rmsdbcm,3.0D0)
 106       call reada(controlcard,'DRMS',drms,0.1D0)
 107       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then
 108        write (iout,'(a,f10.1)')'RMSDBC = ',rmsdbc
 109        write (iout,'(a,f10.1)')'RMSDBC1 = ',rmsdbc1
 110        write (iout,'(a,f10.1)')'RMSDBC1MAX = ',rmsdbc1max
 111        write (iout,'(a,f10.1)')'DRMS    = ',drms
 112        write (iout,'(a,f10.1)')'RMSDBCM = ',rmsdbcm
 113        write (iout,'(a,f10.1)') 'Time limit (min):',timlim
 114       endif
 115       call readi(controlcard,'NZ_START',nz_start,0)
 116       call readi(controlcard,'NZ_END',nz_end,0)
 117       call readi(controlcard,'IZ_SC',iz_sc,0)
 118       timlim=60.0D0*timlim
 119       safety = 60.0d0*safety
 120       timem=timlim
 121       modecalc=0
 122       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 123       minim=(index(controlcard,'MINIMIZE').gt.0)
 124       dccart=(index(controlcard,'CART').gt.0)
 125       overlapsc=(index(controlcard,'OVERLAP').gt.0)
 126       overlapsc=.not.overlapsc
 127       searchsc=(index(controlcard,'NOSEARCHSC').gt.0)
 128       searchsc=.not.searchsc
 129       sideadd=(index(controlcard,'SIDEADD').gt.0)
 130       energy_dec=(index(controlcard,'ENERGY_DEC').gt.0)
 131       outpdb=(index(controlcard,'PDBOUT').gt.0)
 132       outmol2=(index(controlcard,'MOL2OUT').gt.0)
 133       pdbref=(index(controlcard,'PDBREF').gt.0)
 134       refstr=pdbref .or. (index(controlcard,'REFSTR').gt.0)
 135       indpdb=index(controlcard,'PDBSTART')
 136       extconf=(index(controlcard,'EXTCONF').gt.0)
 137       call readi(controlcard,'IPRINT',iprint,0)
 138       call readi(controlcard,'MAXGEN',maxgen,10000)
 139       call readi(controlcard,'MAXOVERLAP',maxoverlap,1000)
 140       call readi(controlcard,"KDIAG",kdiag,0)
 141       call readi(controlcard,"RESCALE_MODE",rescale_mode,2)
 142       if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0)
 143      & write (iout,*) "RESCALE_MODE",rescale_mode
 144       split_ene=index(controlcard,'SPLIT_ENE').gt.0
 145       if (index(controlcard,'REGULAR').gt.0.0D0) then
 146         call reada(controlcard,'WEIDIS',weidis,0.1D0)
 147         modecalc=1
 148         refstr=.true.
 149       endif
 150       if (index(controlcard,'CHECKGRAD').gt.0) then
 151         modecalc=5
 152         if (index(controlcard,'CART').gt.0) then
 153           icheckgrad=1
 154         elseif (index(controlcard,'CARINT').gt.0) then
 155           icheckgrad=2
 156         else
 157           icheckgrad=3
 158         endif
 159       elseif (index(controlcard,'THREAD').gt.0) then
 160         modecalc=2
 161         call readi(controlcard,'THREAD',nthread,0)
 162         if (nthread.gt.0) then
 163           call reada(controlcard,'WEIDIS',weidis,0.1D0)
 164         else
 165           if (fg_rank.eq.0)
 166      &    write (iout,'(a)')'A number has to follow the THREAD keyword.'
 167           stop 'Error termination in Read_Control.'
 168         endif
 169       else if (index(controlcard,'MCMA').gt.0) then
 170         modecalc=3
 171       else if (index(controlcard,'MCEE').gt.0) then
 172         modecalc=6
 173       else if (index(controlcard,'MULTCONF').gt.0) then
 174         modecalc=4
 175       else if (index(controlcard,'MAP').gt.0) then
 176         modecalc=7
 177         call readi(controlcard,'MAP',nmap,0)
 178       else if (index(controlcard,'CSA').gt.0) then
 179            write(*,*) "CSA not supported in this version"
 180            stop
 181 csa        modecalc=8
 182 crc      else if (index(controlcard,'ZSCORE').gt.0) then
 183 crc
 184 crc  ZSCORE is rm from UNRES, modecalc=9 is available
 185 crc
 186 crc        modecalc=9
 187 cfcm      else if (index(controlcard,'MCMF').gt.0) then
 188 cfmc        modecalc=10
 189       else if (index(controlcard,'SOFTREG').gt.0) then
 190         modecalc=11
 191       else if (index(controlcard,'CHECK_BOND').gt.0) then
 192         modecalc=-1
 193       else if (index(controlcard,'TEST').gt.0) then
 194         modecalc=-2
 195       else if (index(controlcard,'MD').gt.0) then
 196         modecalc=12
 197       else if (index(controlcard,'RE ').gt.0) then
 198         modecalc=14
 199       endif
 200
 201       lmuca=index(controlcard,'MUCA').gt.0
 202       call readi(controlcard,'MUCADYN',mucadyn,0)
 203       call readi(controlcard,'MUCASMOOTH',muca_smooth,0)
 204       if (lmuca .and. (me.eq.king .or. .not.out1file ))
 205      & then
 206        write (iout,*) 'MUCADYN=',mucadyn
 207        write (iout,*) 'MUCASMOOTH=',muca_smooth
 208       endif
 209
 210       iscode=index(controlcard,'ONE_LETTER')
 211       indphi=index(controlcard,'PHI')
 212       indback=index(controlcard,'BACK')
 213       iranconf=index(controlcard,'RAND_CONF')
 214       i2ndstr=index(controlcard,'USE_SEC_PRED')
 215       gradout=index(controlcard,'GRADOUT').gt.0
 216       gnorm_check=index(controlcard,'GNORM_CHECK').gt.0
 217
 218       if(me.eq.king.or..not.out1file)
 219      & write (iout,'(2a)') diagmeth(kdiag),
 220      &  ' routine used to diagonalize matrices.'
 221       return
 222       end
 223 c--------------------------------------------------------------------------
 224       subroutine read_REMDpar
 225 C
 226 C Read REMD settings
 227 C
 228       implicit real*8 (a-h,o-z)
 229       include 'DIMENSIONS'
 230       include 'COMMON.IOUNITS'
 231       include 'COMMON.TIME1'
 232       include 'COMMON.MD'
 233 #ifndef LANG0
 234       include 'COMMON.LANGEVIN'
 235 #else
 236       include 'COMMON.LANGEVIN.lang0'
 237 #endif
 238       include 'COMMON.INTERACT'
 239       include 'COMMON.NAMES'
 240       include 'COMMON.GEO'
 241       include 'COMMON.REMD'
 242       include 'COMMON.CONTROL'
 243       include 'COMMON.SETUP'
 244       character*80 ucase
 245       character*320 controlcard
 246       character*3200 controlcard1
 247       integer iremd_m_total
 248
 249       if(me.eq.king.or..not.out1file)
 250      & write (iout,*) "REMD setup"
 251
 252       call card_concat(controlcard)
 253       call readi(controlcard,"NREP",nrep,3)
 254       call readi(controlcard,"NSTEX",nstex,1000)
 255       call reada(controlcard,"RETMIN",retmin,10.0d0)
 256       call reada(controlcard,"RETMAX",retmax,1000.0d0)
 257       mremdsync=(index(controlcard,'SYNC').gt.0)
 258       call readi(controlcard,"NSYN",i_sync_step,100)
 259       restart1file=(index(controlcard,'REST1FILE').gt.0)
 260       traj1file=(index(controlcard,'TRAJ1FILE').gt.0)
 261       call readi(controlcard,"TRAJCACHE",max_cache_traj_use,1)
 262       if(max_cache_traj_use.gt.max_cache_traj)
 263      &           max_cache_traj_use=max_cache_traj
 264       if(me.eq.king.or..not.out1file) then
 265 cd       if (traj1file) then
 266 crc caching is in testing - NTWX is not ignored
 267 cd        write (iout,*) "NTWX value is ignored"
 268 cd        write (iout,*) "  trajectory is stored to one file by master"
 269 cd        write (iout,*) "  before exchange at NSTEX intervals"
 270 cd       endif
 271        write (iout,*) "NREP= ",nrep
 272        write (iout,*) "NSTEX= ",nstex
 273        write (iout,*) "SYNC= ",mremdsync
 274        write (iout,*) "NSYN= ",i_sync_step
 275        write (iout,*) "TRAJCACHE= ",max_cache_traj_use
 276       endif
 277
 278       t_exchange_only=(index(controlcard,'TONLY').gt.0)
 279       call readi(controlcard,"HREMD",hremd,0)
 280       if((me.eq.king.or..not.out1file).and.hremd.gt.0) then
 281         write (iout,*) "Hamiltonian REMD with ",hremd," sets of weights"
 282       endif
 283       if(usampl.and.hremd.gt.0) then
 284             write (iout,'(//a)')
 285      &      "========== ERROR: USAMPL and HREMD cannot be used together"
 286 #ifdef MPI
 287             call MPI_Abort(MPI_COMM_WORLD,IERROR,ERRCODE)
 288 #endif
 289             stop
 290       endif
 291
 292
 293       remd_tlist=.false.
 294       if (index(controlcard,'TLIST').gt.0) then
 295          remd_tlist=.true.
 296          call card_concat(controlcard1)
 297          read(controlcard1,*) (remd_t(i),i=1,nrep)
 298          if(me.eq.king.or..not.out1file)
 299      &    write (iout,*)'tlist',(remd_t(i),i=1,nrep)
 300       endif
 301       remd_mlist=.false.
 302       if (index(controlcard,'MLIST').gt.0) then
 303          remd_mlist=.true.
 304          call card_concat(controlcard1)
 305          read(controlcard1,*) (remd_m(i),i=1,nrep)
 306          if(me.eq.king.or..not.out1file) then
 307           write (iout,*)'mlist',(remd_m(i),i=1,nrep)
 308           iremd_m_total=0
 309           do i=1,nrep
 310            iremd_m_total=iremd_m_total+remd_m(i)
 311           enddo
 312           if(hremd.gt.1)then
 313            write (iout,*) 'Total number of replicas ',
 314      &       iremd_m_total*hremd
 315           else
 316            write (iout,*) 'Total number of replicas ',iremd_m_total
 317           endif
 318          endif
 319       endif
 320       if(me.eq.king.or..not.out1file)
 321      &   write (iout,'(/30(1h=),a,29(1h=)/)') " End of REMD run setup "
 322       return
 323       end
 324 c--------------------------------------------------------------------------
 325       subroutine read_MDpar
 326 C
 327 C Read MD settings
 328 C
 329       implicit real*8 (a-h,o-z)
 330       include 'DIMENSIONS'
 331       include 'COMMON.IOUNITS'
 332       include 'COMMON.TIME1'
 333       include 'COMMON.MD'
 334 #ifndef LANG0
 335       include 'COMMON.LANGEVIN'
 336 #else
 337       include 'COMMON.LANGEVIN.lang0'
 338 #endif
 339       include 'COMMON.INTERACT'
 340       include 'COMMON.NAMES'
 341       include 'COMMON.GEO'
 342       include 'COMMON.SETUP'
 343       include 'COMMON.CONTROL'
 344       include 'COMMON.SPLITELE'
 345       character*80 ucase
 346       character*320 controlcard
 347
 348       call card_concat(controlcard)
 349       call readi(controlcard,"NSTEP",n_timestep,1000000)
 350       call readi(controlcard,"NTWE",ntwe,100)
 351       call readi(controlcard,"NTWX",ntwx,1000)
 352       call reada(controlcard,"DT",d_time,1.0d-1)
 353       call reada(controlcard,"DVMAX",dvmax,2.0d1)
 354       call reada(controlcard,"DAMAX",damax,1.0d1)
 355       call reada(controlcard,"EDRIFTMAX",edriftmax,1.0d+1)
 356       call readi(controlcard,"LANG",lang,0)
 357       RESPA = index(controlcard,"RESPA") .gt. 0
 358       call readi(controlcard,"NTIME_SPLIT",ntime_split,1)
 359       ntime_split0=ntime_split
 360       call readi(controlcard,"MAXTIME_SPLIT",maxtime_split,64)
 361       ntime_split0=ntime_split
 362       call reada(controlcard,"R_CUT",r_cut,2.0d0)
 363       call reada(controlcard,"LAMBDA",rlamb,0.3d0)
 364       rest = index(controlcard,"REST").gt.0
 365       tbf = index(controlcard,"TBF").gt.0
 366       call readi(controlcard,"HMC",hmc,0)
 367       tnp = index(controlcard,"NOSEPOINCARE99").gt.0
 368       tnp1 = index(controlcard,"NOSEPOINCARE01").gt.0
 369       tnh = index(controlcard,"NOSEHOOVER96").gt.0
 370       if (RESPA.and.tnh)then
 371         xiresp = index(controlcard,"XIRESP").gt.0
 372       endif
 373       call reada(controlcard,"Q_NP",Q_np,0.1d0)
 374       usampl = index(controlcard,"USAMPL").gt.0
 375
 376       mdpdb = index(controlcard,"MDPDB").gt.0
 377       call reada(controlcard,"T_BATH",t_bath,300.0d0)
 378       call reada(controlcard,"TAU_BATH",tau_bath,1.0d-1)
 379       call reada(controlcard,"EQ_TIME",eq_time,1.0d+4)
 380       call readi(controlcard,"RESET_MOMENT",count_reset_moment,1000)
 381       if (count_reset_moment.eq.0) count_reset_moment=1000000000
 382       call readi(controlcard,"RESET_VEL",count_reset_vel,1000)
 383       reset_moment=lang.eq.0 .and. tbf .and. count_reset_moment.gt.0
 384       reset_vel=lang.eq.0 .and. tbf .and. count_reset_vel.gt.0
 385       if (count_reset_vel.eq.0) count_reset_vel=1000000000
 386       large = index(controlcard,"LARGE").gt.0
 387       print_compon = index(controlcard,"PRINT_COMPON").gt.0
 388       rattle = index(controlcard,"RATTLE").gt.0
 389 c  if performing umbrella sampling, fragments constrained are read from the fragment file
 390       nset=0
 391       if(usampl) then
 392         call read_fragments
 393       endif
 394
 395       if(me.eq.king.or..not.out1file) then
 396        write (iout,*)
 397        write (iout,'(27(1h=),a26,27(1h=))') " Parameters of the MD run "
 398        write (iout,*)
 399        write (iout,'(a)') "The units are:"
 400        write (iout,'(a)') "positions: angstrom, time: 48.9 fs"
 401        write (iout,'(2a)') "velocity: angstrom/(48.9 fs),",
 402      &  " acceleration: angstrom/(48.9 fs)**2"
 403        write (iout,'(a)') "energy: kcal/mol, temperature: K"
 404        write (iout,*)
 405        write (iout,'(a60,i10)') "Number of time steps:",n_timestep
 406        write (iout,'(a60,f10.5,a)')
 407      &  "Initial time step of numerical integration:",d_time,
 408      &  " natural units"
 409        write (iout,'(60x,f10.5,a)') d_time*48.9," fs"
 410        if (RESPA) then
 411         write (iout,'(2a,i4,a)')
 412      &    "A-MTS algorithm used; initial time step for fast-varying",
 413      &    " short-range forces split into",ntime_split," steps."
 414         write (iout,'(a,f5.2,a,f5.2)') "Short-range force cutoff",
 415      &   r_cut," lambda",rlamb
 416        endif
 417        write (iout,'(2a,f10.5)')
 418      &  "Maximum acceleration threshold to reduce the time step",
 419      &  "/increase split number:",damax
 420        write (iout,'(2a,f10.5)')
 421      &  "Maximum predicted energy drift to reduce the timestep",
 422      &  "/increase split number:",edriftmax
 423        write (iout,'(a60,f10.5)')
 424      & "Maximum velocity threshold to reduce velocities:",dvmax
 425        write (iout,'(a60,i10)') "Frequency of property output:",ntwe
 426        write (iout,'(a60,i10)') "Frequency of coordinate output:",ntwx
 427        if (rattle) write (iout,'(a60)')
 428      &  "Rattle algorithm used to constrain the virtual bonds"
 429       endif
 430       reset_fricmat=1000
 431       if (lang.gt.0) then
 432         call reada(controlcard,"ETAWAT",etawat,0.8904d0)
 433         call reada(controlcard,"RWAT",rwat,1.4d0)
 434         call reada(controlcard,"SCAL_FRIC",scal_fric,2.0d-2)
 435         surfarea=index(controlcard,"SURFAREA").gt.0
 436         call readi(controlcard,"RESET_FRICMAT",reset_fricmat,1000)
 437         if(me.eq.king.or..not.out1file)then
 438          write (iout,'(/a,$)') "Langevin dynamics calculation"
 439          if (lang.eq.1) then
 440           write (iout,'(a/)')
 441      &      " with direct integration of Langevin equations"
 442          else if (lang.eq.2) then
 443           write (iout,'(a/)') " with TINKER stochasic MD integrator"
 444          else if (lang.eq.3) then
 445           write (iout,'(a/)') " with Ciccotti's stochasic MD integrator"
 446          else if (lang.eq.4) then
 447           write (iout,'(a/)') " in overdamped mode"
 448          else
 449           write (iout,'(//a,i5)')
 450      &      "=========== ERROR: Unknown Langevin dynamics mode:",lang
 451           stop
 452          endif
 453          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 454          write (iout,'(a60,f10.5)') "Viscosity of the solvent:",etawat
 455          write (iout,'(a60,f10.5)') "Radius of solvent molecule:",rwat
 456          write (iout,'(a60,f10.5)')
 457      &   "Scaling factor of the friction forces:",scal_fric
 458          if (surfarea) write (iout,'(2a,i10,a)')
 459      &     "Friction coefficients will be scaled by solvent-accessible",
 460      &     " surface area every",reset_fricmat," steps."
 461         endif
 462 c Calculate friction coefficients and bounds of stochastic forces
 463         eta=6*pi*cPoise*etawat
 464         if(me.eq.king.or..not.out1file)
 465      &   write(iout,'(a60,f10.5)')"Eta of the solvent in natural units:"
 466      &   ,eta
 467         gamp=scal_fric*(pstok+rwat)*eta
 468         stdfp=dsqrt(2*Rb*t_bath/d_time)
 469         do i=1,ntyp
 470           gamsc(i)=scal_fric*(restok(i)+rwat)*eta
 471           stdfsc(i)=dsqrt(2*Rb*t_bath/d_time)
 472         enddo
 473         if(me.eq.king.or..not.out1file)then
 474          write (iout,'(/2a/)')
 475      &   "Radii of site types and friction coefficients and std's of",
 476      &   " stochastic forces of fully exposed sites"
 477          write (iout,'(a5,f5.2,2f10.5)')'p',pstok,gamp,stdfp*dsqrt(gamp)
 478          do i=1,ntyp
 479           write (iout,'(a5,f5.2,2f10.5)') restyp(i),restok(i),
 480      &     gamsc(i),stdfsc(i)*dsqrt(gamsc(i))
 481          enddo
 482         endif
 483       else if (tbf) then
 484         if(me.eq.king.or..not.out1file)then
 485          write (iout,'(a)') "Berendsen bath calculation"
 486          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 487          write (iout,'(a60,f10.5)') "Coupling constant (tau):",tau_bath
 488          if (reset_moment)
 489      &   write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 490      &   count_reset_moment," steps"
 491          if (reset_vel)
 492      &    write (iout,'(a,i10,a)')
 493      &    "Velocities will be reset at random every",count_reset_vel,
 494      &   " steps"
 495         endif
 496       else if (tnp .or. tnp1 .or. tnh) then
 497         if (tnp .or. tnp1) then
 498            write (iout,'(a)') "Nose-Poincare bath calculation"
 499            if (tnp) write (iout,'(a)')
 500      & "J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird"
 501            if (tnp1) write (iout,'(a)') "JPSJ 70 75 (2001) S. Nose"
 502         else
 503            write (iout,'(a)') "Nose-Hoover bath calculation"
 504            write (iout,'(a)') "Mol.Phys. 87 1117 (1996) Martyna et al."
 505               nresn=1
 506               nyosh=1
 507               nnos=1
 508               do i=1,nnos
 509                qmass(i)=Q_np
 510                xlogs(i)=1.0
 511                vlogs(i)=0.0
 512               enddo
 513               do i=1,nyosh
 514                WDTI(i) = 1.0*d_time/nresn
 515                WDTI2(i)=WDTI(i)/2
 516                WDTI4(i)=WDTI(i)/4
 517                WDTI8(i)=WDTI(i)/8
 518               enddo
 519               if (RESPA) then
 520                if(xiresp) then
 521                  write (iout,'(a)') "NVT-XI-RESPA algorithm"
 522                else
 523                  write (iout,'(a)') "NVT-XO-RESPA algorithm"
 524                endif
 525                do i=1,nyosh
 526                 WDTIi(i) = 1.0*d_time/nresn/ntime_split
 527                 WDTIi2(i)=WDTIi(i)/2
 528                 WDTIi4(i)=WDTIi(i)/4
 529                 WDTIi8(i)=WDTIi(i)/8
 530                enddo
 531               endif
 532         endif
 533
 534         write (iout,'(a60,f10.5)') "Temperature:",t_bath
 535         write (iout,'(a60,f10.5)') "Q =",Q_np
 536         if (reset_moment)
 537      &  write (iout,'(a,i10,a)') "Momenta will be reset at zero every",
 538      &   count_reset_moment," steps"
 539         if (reset_vel)
 540      &    write (iout,'(a,i10,a)')
 541      &    "Velocities will be reset at random every",count_reset_vel,
 542      &   " steps"
 543
 544       else if (hmc.gt.0) then
 545          write (iout,'(a)') "Hybrid Monte Carlo calculation"
 546          write (iout,'(a60,f10.5)') "Temperature:",t_bath
 547          write (iout,'(a60,i10)')
 548      &         "Number of MD steps between Metropolis tests:",hmc
 549
 550       else
 551         if(me.eq.king.or..not.out1file)
 552      &   write (iout,'(a31)') "Microcanonical mode calculation"
 553       endif
 554       if(me.eq.king.or..not.out1file)then
 555        if (rest) write (iout,'(/a/)') "===== Calculation restarted ===="
 556        if (usampl) then
 557           write(iout,*) "MD running with constraints."
 558           write(iout,*) "Equilibration time ", eq_time, " mtus."
 559           write(iout,*) "Constraining ", nfrag," fragments."
 560           write(iout,*) "Length of each fragment, weight and q0:"
 561           do iset=1,nset
 562            write (iout,*) "Set of restraints #",iset
 563            do i=1,nfrag
 564               write(iout,'(2i5,f8.1,f7.4)') ifrag(1,i,iset),
 565      &           ifrag(2,i,iset),wfrag(i,iset),qinfrag(i,iset)
 566            enddo
 567            write(iout,*) "constraints between ", npair, "fragments."
 568            write(iout,*) "constraint pairs, weights and q0:"
 569            do i=1,npair
 570             write(iout,'(2i5,f8.1,f7.4)') ipair(1,i,iset),
 571      &             ipair(2,i,iset),wpair(i,iset),qinpair(i,iset)
 572            enddo
 573            write(iout,*) "angle constraints within ", nfrag_back,
 574      &      "backbone fragments."
 575            write(iout,*) "fragment, weights:"
 576            do i=1,nfrag_back
 577             write(iout,'(2i5,3f8.1)') ifrag_back(1,i,iset),
 578      &         ifrag_back(2,i,iset),wfrag_back(1,i,iset),
 579      &         wfrag_back(2,i,iset),wfrag_back(3,i,iset)
 580            enddo
 581           enddo
 582         iset=mod(kolor,nset)+1
 583        endif
 584       endif
 585       if(me.eq.king.or..not.out1file)
 586      & write (iout,'(/30(1h=),a,29(1h=)/)') " End of MD run setup "
 587       return
 588       end
 589 c------------------------------------------------------------------------------
 590       subroutine molread
 591 C
 592 C Read molecular data.
 593 C
 594       implicit real*8 (a-h,o-z)
 595       include 'DIMENSIONS'
 596 #ifdef MPI
 597       include 'mpif.h'
 598       integer error_msg
 599 #endif
 600       include 'COMMON.IOUNITS'
 601       include 'COMMON.GEO'
 602       include 'COMMON.VAR'
 603       include 'COMMON.INTERACT'
 604       include 'COMMON.LOCAL'
 605       include 'COMMON.NAMES'
 606       include 'COMMON.CHAIN'
 607       include 'COMMON.FFIELD'
 608       include 'COMMON.SBRIDGE'
 609       include 'COMMON.HEADER'
 610       include 'COMMON.CONTROL'
 611       include 'COMMON.DBASE'
 612       include 'COMMON.THREAD'
 613       include 'COMMON.CONTACTS'
 614       include 'COMMON.TORCNSTR'
 615       include 'COMMON.TIME1'
 616       include 'COMMON.BOUNDS'
 617       include 'COMMON.MD'
 618       include 'COMMON.REMD'
 619       include 'COMMON.SETUP'
 620       character*4 sequence(maxres)
 621       integer rescode
 622       double precision x(maxvar)
 623       character*256 pdbfile
 624       character*320 weightcard
 625       character*80 weightcard_t,ucase
 626       dimension itype_pdb(maxres)
 627       common /pizda/ itype_pdb
 628       logical seq_comp,fail
 629       double precision energia(0:n_ene)
 630       integer ilen
 631       external ilen
 632 C
 633 C Body
 634 C
 635 C Read weights of the subsequent energy terms.
 636       if(hremd.gt.0) then
 637
 638        k=0
 639        do il=1,hremd
 640         do i=1,nrep
 641          do j=1,remd_m(i)
 642           i2set(k)=il
 643           k=k+1
 644          enddo
 645         enddo
 646        enddo
 647
 648        if(me.eq.king.or..not.out1file) then
 649         write (iout,*) 'Reading ',hremd,' sets of weights for HREMD'
 650         write (iout,*) 'Current weights for processor ',
 651      &                 me,' set ',i2set(me)
 652        endif
 653
 654        do i=1,hremd
 655          call card_concat(weightcard)
 656          call reada(weightcard,'WLONG',wlong,1.0D0)
 657          call reada(weightcard,'WSC',wsc,wlong)
 658          call reada(weightcard,'WSCP',wscp,wlong)
 659          call reada(weightcard,'WELEC',welec,1.0D0)
 660          call reada(weightcard,'WVDWPP',wvdwpp,welec)
 661          call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 662          call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 663          call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 664          call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 665          call reada(weightcard,'WTURN3',wturn3,1.0D0)
 666          call reada(weightcard,'WTURN4',wturn4,1.0D0)
 667          call reada(weightcard,'WTURN6',wturn6,1.0D0)
 668          call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 669          call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 670          call reada(weightcard,'WBOND',wbond,1.0D0)
 671          call reada(weightcard,'WTOR',wtor,1.0D0)
 672          call reada(weightcard,'WTORD',wtor_d,1.0D0)
 673          call reada(weightcard,'WANG',wang,1.0D0)
 674          call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 675          call reada(weightcard,'SCAL14',scal14,0.4D0)
 676          call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 677          call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 678          call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 679          call reada(weightcard,'TEMP0',temp0,300.0d0)
 680          if (index(weightcard,'SOFT').gt.0) ipot=6
 681 C 12/1/95 Added weight for the multi-body term WCORR
 682          call reada(weightcard,'WCORRH',wcorr,1.0D0)
 683          if (wcorr4.gt.0.0d0) wcorr=wcorr4
 684
 685          hweights(i,1)=wsc
 686          hweights(i,2)=wscp
 687          hweights(i,3)=welec
 688          hweights(i,4)=wcorr
 689          hweights(i,5)=wcorr5
 690          hweights(i,6)=wcorr6
 691          hweights(i,7)=wel_loc
 692          hweights(i,8)=wturn3
 693          hweights(i,9)=wturn4
 694          hweights(i,10)=wturn6
 695          hweights(i,11)=wang
 696          hweights(i,12)=wscloc
 697          hweights(i,13)=wtor
 698          hweights(i,14)=wtor_d
 699          hweights(i,15)=wstrain
 700          hweights(i,16)=wvdwpp
 701          hweights(i,17)=wbond
 702          hweights(i,18)=scal14
 703          hweights(i,21)=wsccor
 704
 705        enddo
 706
 707        do i=1,n_ene
 708          weights(i)=hweights(i2set(me),i)
 709        enddo
 710        wsc    =weights(1)
 711        wscp   =weights(2)
 712        welec  =weights(3)
 713        wcorr  =weights(4)
 714        wcorr5 =weights(5)
 715        wcorr6 =weights(6)
 716        wel_loc=weights(7)
 717        wturn3 =weights(8)
 718        wturn4 =weights(9)
 719        wturn6 =weights(10)
 720        wang   =weights(11)
 721        wscloc =weights(12)
 722        wtor   =weights(13)
 723        wtor_d =weights(14)
 724        wstrain=weights(15)
 725        wvdwpp =weights(16)
 726        wbond  =weights(17)
 727        scal14 =weights(18)
 728        wsccor =weights(21)
 729
 730
 731       else
 732        call card_concat(weightcard)
 733        call reada(weightcard,'WLONG',wlong,1.0D0)
 734        call reada(weightcard,'WSC',wsc,wlong)
 735        call reada(weightcard,'WSCP',wscp,wlong)
 736        call reada(weightcard,'WELEC',welec,1.0D0)
 737        call reada(weightcard,'WVDWPP',wvdwpp,welec)
 738        call reada(weightcard,'WEL_LOC',wel_loc,1.0D0)
 739        call reada(weightcard,'WCORR4',wcorr4,0.0D0)
 740        call reada(weightcard,'WCORR5',wcorr5,0.0D0)
 741        call reada(weightcard,'WCORR6',wcorr6,0.0D0)
 742        call reada(weightcard,'WTURN3',wturn3,1.0D0)
 743        call reada(weightcard,'WTURN4',wturn4,1.0D0)
 744        call reada(weightcard,'WTURN6',wturn6,1.0D0)
 745        call reada(weightcard,'WSCCOR',wsccor,1.0D0)
 746        call reada(weightcard,'WSTRAIN',wstrain,1.0D0)
 747        call reada(weightcard,'WBOND',wbond,1.0D0)
 748        call reada(weightcard,'WTOR',wtor,1.0D0)
 749        call reada(weightcard,'WTORD',wtor_d,1.0D0)
 750        call reada(weightcard,'WANG',wang,1.0D0)
 751        call reada(weightcard,'WSCLOC',wscloc,1.0D0)
 752        call reada(weightcard,'SCAL14',scal14,0.4D0)
 753        call reada(weightcard,'SCALSCP',scalscp,1.0d0)
 754        call reada(weightcard,'CUTOFF',cutoff_corr,7.0d0)
 755        call reada(weightcard,'DELT_CORR',delt_corr,0.5d0)
 756        call reada(weightcard,'TEMP0',temp0,300.0d0)
 757        if (index(weightcard,'SOFT').gt.0) ipot=6
 758 C 12/1/95 Added weight for the multi-body term WCORR
 759        call reada(weightcard,'WCORRH',wcorr,1.0D0)
 760        if (wcorr4.gt.0.0d0) wcorr=wcorr4
 761        weights(1)=wsc
 762        weights(2)=wscp
 763        weights(3)=welec
 764        weights(4)=wcorr
 765        weights(5)=wcorr5
 766        weights(6)=wcorr6
 767        weights(7)=wel_loc
 768        weights(8)=wturn3
 769        weights(9)=wturn4
 770        weights(10)=wturn6
 771        weights(11)=wang
 772        weights(12)=wscloc
 773        weights(13)=wtor
 774        weights(14)=wtor_d
 775        weights(15)=wstrain
 776        weights(16)=wvdwpp
 777        weights(17)=wbond
 778        weights(18)=scal14
 779        weights(21)=wsccor
 780       endif
 781
 782       if(me.eq.king.or..not.out1file)
 783      & write (iout,10) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 784      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 785      &  wturn4,wturn6
 786    10 format (/'Energy-term weights (unscaled):'//
 787      & 'WSCC=   ',f10.6,' (SC-SC)'/
 788      & 'WSCP=   ',f10.6,' (SC-p)'/
 789      & 'WELEC=  ',f10.6,' (p-p electr)'/
 790      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 791      & 'WBOND=  ',f10.6,' (stretching)'/
 792      & 'WANG=   ',f10.6,' (bending)'/
 793      & 'WSCLOC= ',f10.6,' (SC local)'/
 794      & 'WTOR=   ',f10.6,' (torsional)'/
 795      & 'WTORD=  ',f10.6,' (double torsional)'/
 796      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 797      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 798      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 799      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 800      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 801      & 'WSCCOR= ',f10.6,' (back-scloc correlation)'/
 802      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 803      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 804      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 805       if(me.eq.king.or..not.out1file)then
 806        if (wcorr4.gt.0.0d0) then
 807         write (iout,'(/2a/)') 'Local-electrostatic type correlation ',
 808      &   'between contact pairs of peptide groups'
 809         write (iout,'(2(a,f5.3/))')
 810      &  'Cutoff on 4-6th order correlation terms: ',cutoff_corr,
 811      &  'Range of quenching the correlation terms:',2*delt_corr
 812        else if (wcorr.gt.0.0d0) then
 813         write (iout,'(/2a/)') 'Hydrogen-bonding correlation ',
 814      &   'between contact pairs of peptide groups'
 815        endif
 816        write (iout,'(a,f8.3)')
 817      &  'Scaling factor of 1,4 SC-p interactions:',scal14
 818        write (iout,'(a,f8.3)')
 819      &  'General scaling factor of SC-p interactions:',scalscp
 820       endif
 821       r0_corr=cutoff_corr-delt_corr
 822       do i=1,20
 823         aad(i,1)=scalscp*aad(i,1)
 824         aad(i,2)=scalscp*aad(i,2)
 825         bad(i,1)=scalscp*bad(i,1)
 826         bad(i,2)=scalscp*bad(i,2)
 827       enddo
 828       call rescale_weights(t_bath)
 829       if(me.eq.king.or..not.out1file)
 830      & write (iout,22) wsc,wscp,welec,wvdwpp,wbond,wang,wscloc,wtor,
 831      &  wtor_d,wstrain,wel_loc,wcorr,wcorr5,wcorr6,wsccor,wturn3,
 832      &  wturn4,wturn6
 833    22 format (/'Energy-term weights (scaled):'//
 834      & 'WSCC=   ',f10.6,' (SC-SC)'/
 835      & 'WSCP=   ',f10.6,' (SC-p)'/
 836      & 'WELEC=  ',f10.6,' (p-p electr)'/
 837      & 'WVDWPP= ',f10.6,' (p-p VDW)'/
 838      & 'WBOND=  ',f10.6,' (stretching)'/
 839      & 'WANG=   ',f10.6,' (bending)'/
 840      & 'WSCLOC= ',f10.6,' (SC local)'/
 841      & 'WTOR=   ',f10.6,' (torsional)'/
 842      & 'WTORD=  ',f10.6,' (double torsional)'/
 843      & 'WSTRAIN=',f10.6,' (SS bridges & dist. cnstr.)'/
 844      & 'WEL_LOC=',f10.6,' (multi-body 3-rd order)'/
 845      & 'WCORR4= ',f10.6,' (multi-body 4th order)'/
 846      & 'WCORR5= ',f10.6,' (multi-body 5th order)'/
 847      & 'WCORR6= ',f10.6,' (multi-body 6th order)'/
 848      & 'WSCCOR= ',f10.6,' (back-scloc correlatkion)'/
 849      & 'WTURN3= ',f10.6,' (turns, 3rd order)'/
 850      & 'WTURN4= ',f10.6,' (turns, 4th order)'/
 851      & 'WTURN6= ',f10.6,' (turns, 6th order)')
 852       if(me.eq.king.or..not.out1file)
 853      & write (iout,*) "Reference temperature for weights calculation:",
 854      &  temp0
 855       call reada(weightcard,"D0CM",d0cm,3.78d0)
 856       call reada(weightcard,"AKCM",akcm,15.1d0)
 857       call reada(weightcard,"AKTH",akth,11.0d0)
 858       call reada(weightcard,"AKCT",akct,12.0d0)
 859       call reada(weightcard,"V1SS",v1ss,-1.08d0)
 860       call reada(weightcard,"V2SS",v2ss,7.61d0)
 861       call reada(weightcard,"V3SS",v3ss,13.7d0)
 862       call reada(weightcard,"EBR",ebr,-5.50D0)
 863       call reada(weightcard,"DTRISS",dtriss,1.0D0)
 864       call reada(weightcard,"ATRISS",atriss,0.3D0)
 865       call reada(weightcard,"BTRISS",btriss,0.02D0)
 866       call reada(weightcard,"CTRISS",ctriss,1.0D0)
 867       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
 868       do i=1,maxres
 869         dyn_ss_mask(i)=.false.
 870       enddo
 871       do i=1,maxres-1
 872         do j=i+1,maxres
 873           dyn_ssbond_ij(i,j)=1.0d300
 874         enddo
 875       enddo
 876       call reada(weightcard,"HT",Ht,0.0D0)
 877       if (dyn_ss) then
 878         ss_depth=ebr/wsc-0.25*eps(1,1)
 879         Ht=Ht/wsc-0.25*eps(1,1)
 880         akcm=akcm*wstrain/wsc
 881         akth=akth*wstrain/wsc
 882         akct=akct*wstrain/wsc
 883         v1ss=v1ss*wstrain/wsc
 884         v2ss=v2ss*wstrain/wsc
 885         v3ss=v3ss*wstrain/wsc
 886       else
 887         ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain
 888       endif
 889
 890       if(me.eq.king.or..not.out1file) then
 891        write (iout,*) "Parameters of the SS-bond potential:"
 892        write (iout,*) "D0CM",d0cm," AKCM",akcm," AKTH",akth,
 893      & " AKCT",akct
 894        write (iout,*) "V1SS",v1ss," V2SS",v2ss," V3SS",v3ss
 895        write (iout,*) "EBR",ebr," SS_DEPTH",ss_depth
 896        write (iout,*)" HT",Ht
 897        print *,'indpdb=',indpdb,' pdbref=',pdbref
 898       endif
 899       if (indpdb.gt.0 .or. pdbref) then
 900         read(inp,'(a)') pdbfile
 901         if(me.eq.king.or..not.out1file)
 902      &   write (iout,'(2a)') 'PDB data will be read from file ',
 903      &   pdbfile(:ilen(pdbfile))
 904         open(ipdbin,file=pdbfile,status='old',err=33)
 905         goto 34
 906   33    write (iout,'(a)') 'Error opening PDB file.'
 907         stop
 908   34    continue
 909 c        print *,'Begin reading pdb data'
 910         call readpdb
 911 c        print *,'Finished reading pdb data'
 912         if(me.eq.king.or..not.out1file)
 913      &   write (iout,'(a,i3,a,i3)')'nsup=',nsup,
 914      &   ' nstart_sup=',nstart_sup
 915         do i=1,nres
 916           itype_pdb(i)=itype(i)
 917         enddo
 918         close (ipdbin)
 919         nnt=nstart_sup
 920         nct=nstart_sup+nsup-1
 921         call contact(.false.,ncont_ref,icont_ref,co)
 922
 923         if (sideadd) then
 924 C Following 2 lines for diagnostics; comment out if not needed
 925          write (iout,*) "Before sideadd"
 926          call intout
 927          if(me.eq.king.or..not.out1file)
 928      &    write(iout,*)'Adding sidechains'
 929          maxsi=1000
 930          do i=2,nres-1
 931           iti=itype(i)
 932           if (iti.ne.10) then
 933             nsi=0
 934             fail=.true.
 935             do while (fail.and.nsi.le.maxsi)
 936               call gen_side(iti,theta(i+1),alph(i),omeg(i),fail)
 937               nsi=nsi+1
 938             enddo
 939             if(fail) write(iout,*)'Adding sidechain failed for res ',
 940      &              i,' after ',nsi,' trials'
 941           endif
 942          enddo
 943 C 10/03/12 Adam: Recalculate coordinates with new side chain positions
 944          call chainbuild
 945         endif
 946 C Following 2 lines for diagnostics; comment out if not needed
 947 c        write (iout,*) "After sideadd"
 948 c        call intout
 949       endif
 950       if (indpdb.eq.0) then
 951 C Read sequence if not taken from the pdb file.
 952         read (inp,*) nres
 953 c        print *,'nres=',nres
 954         if (iscode.gt.0) then
 955           read (inp,'(80a1)') (sequence(i)(1:1),i=1,nres)
 956         else
 957           read (inp,'(20(1x,a3))') (sequence(i),i=1,nres)
 958         endif
 959 C Convert sequence to numeric code
 960         do i=1,nres
 961           itype(i)=rescode(i,sequence(i),iscode)
 962         enddo
 963 C Assign initial virtual bond lengths
 964         do i=2,nres
 965           vbld(i)=vbl
 966           vbld_inv(i)=vblinv
 967         enddo
 968         do i=2,nres-1
 969           vbld(i+nres)=dsc(itype(i))
 970           vbld_inv(i+nres)=dsc_inv(itype(i))
 971 c          write (iout,*) "i",i," itype",itype(i),
 972 c     &      " dsc",dsc(itype(i))," vbld",vbld(i),vbld(i+nres)
 973         enddo
 974       endif
 975 c      print *,nres
 976 c      print '(20i4)',(itype(i),i=1,nres)
 977       do i=1,nres
 978 #ifdef PROCOR
 979         if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) then
 980 #else
 981         if (itype(i).eq.ntyp1) then
 982 #endif
 983           itel(i)=0
 984 #ifdef PROCOR
 985         else if (itype(i+1).ne.20) then
 986 #else
 987         else if (itype(i).ne.20) then
 988 #endif
 989           itel(i)=1
 990         else
 991           itel(i)=2
 992         endif
 993       enddo
 994       if(me.eq.king.or..not.out1file)then
 995        write (iout,*) "ITEL"
 996        do i=1,nres-1
 997          write (iout,*) i,itype(i),itel(i)
 998        enddo
 999        print *,'Call Read_Bridge.'
1000       endif
1001       call read_bridge
1002 C 8/13/98 Set limits to generating the dihedral angles
1003       do i=1,nres
1004         phibound(1,i)=-pi
1005         phibound(2,i)=pi
1006       enddo
1007       read (inp,*) ndih_constr
1008       if (ndih_constr.gt.0) then
1009         read (inp,*) ftors
1010         read (inp,*) (idih_constr(i),phi0(i),drange(i),i=1,ndih_constr)
1011         if(me.eq.king.or..not.out1file)then
1012          write (iout,*)
1013      &   'There are',ndih_constr,' constraints on phi angles.'
1014          do i=1,ndih_constr
1015           write (iout,'(i5,2f8.3)') idih_constr(i),phi0(i),drange(i)
1016          enddo
1017         endif
1018         do i=1,ndih_constr
1019           phi0(i)=deg2rad*phi0(i)
1020           drange(i)=deg2rad*drange(i)
1021         enddo
1022         if(me.eq.king.or..not.out1file)
1023      &   write (iout,*) 'FTORS',ftors
1024         do i=1,ndih_constr
1025           ii = idih_constr(i)
1026           phibound(1,ii) = phi0(i)-drange(i)
1027           phibound(2,ii) = phi0(i)+drange(i)
1028         enddo
1029       endif
1030       nnt=1
1031 #ifdef MPI
1032       if (me.eq.king) then
1033 #endif
1034        write (iout,'(a)') 'Boundaries in phi angle sampling:'
1035        do i=1,nres
1036          write (iout,'(a3,i5,2f10.1)')
1037      &   restyp(itype(i)),i,phibound(1,i)*rad2deg,phibound(2,i)*rad2deg
1038        enddo
1039 #ifdef MP
1040       endif
1041 #endif
1042       nct=nres
1043 cd      print *,'NNT=',NNT,' NCT=',NCT
1044       if (itype(1).eq.ntyp1) nnt=2
1045       if (itype(nres).eq.ntyp1) nct=nct-1
1046       if (pdbref) then
1047         if(me.eq.king.or..not.out1file)
1048      &   write (iout,'(a,i3)') 'nsup=',nsup
1049         nstart_seq=nnt
1050         if (nsup.le.(nct-nnt+1)) then
1051           do i=0,nct-nnt+1-nsup
1052             if (seq_comp(itype(nnt+i),itype_pdb(nstart_sup),nsup)) then
1053               nstart_seq=nnt+i
1054               goto 111
1055             endif
1056           enddo
1057           write (iout,'(a)')
1058      &            'Error - sequences to be superposed do not match.'
1059           stop
1060         else
1061           do i=0,nsup-(nct-nnt+1)
1062             if (seq_comp(itype(nnt),itype_pdb(nstart_sup+i),nct-nnt+1))
1063      &      then
1064               nstart_sup=nstart_sup+i
1065               nsup=nct-nnt+1
1066               goto 111
1067             endif
1068           enddo
1069           write (iout,'(a)')
1070      &            'Error - sequences to be superposed do not match.'
1071         endif
1072   111   continue
1073         if (nsup.eq.0) nsup=nct-nnt
1074         if (nstart_sup.eq.0) nstart_sup=nnt
1075         if (nstart_seq.eq.0) nstart_seq=nnt
1076         if(me.eq.king.or..not.out1file)
1077      &   write (iout,*) 'nsup=',nsup,' nstart_sup=',nstart_sup,
1078      &                 ' nstart_seq=',nstart_seq
1079       endif
1080 c--- Zscore rms -------
1081       if (nz_start.eq.0) nz_start=nnt
1082       if (nz_end.eq.0 .and. nsup.gt.0) then
1083         nz_end=nnt+nsup-1
1084       else if (nz_end.eq.0) then
1085         nz_end=nct
1086       endif
1087       if(me.eq.king.or..not.out1file)then
1088        write (iout,*) 'NZ_START=',nz_start,' NZ_END=',nz_end
1089        write (iout,*) 'IZ_SC=',iz_sc
1090       endif
1091 c----------------------
1092       call init_int_table
1093       if (refstr) then
1094         if (.not.pdbref) then
1095           call read_angles(inp,*38)
1096           goto 39
1097    38     write (iout,'(a)') 'Error reading reference structure.'
1098 #ifdef MPI
1099           call MPI_Finalize(MPI_COMM_WORLD,IERROR)
1100           stop 'Error reading reference structure'
1101 #endif
1102    39     call chainbuild
1103           call setup_var
1104 czscore          call geom_to_var(nvar,coord_exp_zs(1,1))
1105           nstart_sup=nnt
1106           nstart_seq=nnt
1107           nsup=nct-nnt+1
1108           do i=1,2*nres
1109             do j=1,3
1110               cref(j,i)=c(j,i)
1111             enddo
1112           enddo
1113           call contact(.true.,ncont_ref,icont_ref,co)
1114         endif
1115         if(me.eq.king.or..not.out1file)
1116      &   write (iout,*) 'Contact order:',co
1117         if (pdbref) then
1118         if(me.eq.king.or..not.out1file)
1119      &   write (2,*) 'Shifting contacts:',nstart_seq,nstart_sup
1120         do i=1,ncont_ref
1121           do j=1,2
1122             icont_ref(j,i)=icont_ref(j,i)+nstart_seq-nstart_sup
1123           enddo
1124           if(me.eq.king.or..not.out1file)
1125      &     write (2,*) i,' ',restyp(itype(icont_ref(1,i))),' ',
1126      &     icont_ref(1,i),' ',
1127      &     restyp(itype(icont_ref(2,i))),' ',icont_ref(2,i)
1128         enddo
1129         endif
1130       endif
1131 c        write (iout,*) "constr_dist",constr_dist,nstart_sup,nsup
1132       if (constr_dist.gt.0) then
1133         call read_dist_constr
1134       endif
1135       if (nhpb.gt.0) call hpb_partition
1136 c      write (iout,*) "After read_dist_constr nhpb",nhpb
1137 c      call flush(iout)
1138       if (indpdb.eq.0 .and. modecalc.ne.2 .and. modecalc.ne.4
1139      &    .and. modecalc.ne.8 .and. modecalc.ne.9 .and.
1140      &    modecalc.ne.10) then
1141 C If input structure hasn't been supplied from the PDB file read or generate
1142 C initial geometry.
1143         if (iranconf.eq.0 .and. .not. extconf) then
1144           if(me.eq.king.or..not.out1file .and.fg_rank.eq.0)
1145      &     write (iout,'(a)') 'Initial geometry will be read in.'
1146           if (read_cart) then
1147             read(inp,'(8f10.5)',end=36,err=36)
1148      &       ((c(l,k),l=1,3),k=1,nres),
1149      &       ((c(l,k+nres),l=1,3),k=nnt,nct)
1150             call int_from_cart1(.false.)
1151             do i=1,nres-1
1152               do j=1,3
1153                 dc(j,i)=c(j,i+1)-c(j,i)
1154                 dc_norm(j,i)=dc_norm(j,i)*vbld_inv(i+1)
1155               enddo
1156             enddo
1157             do i=nnt,nct
1158               if (itype(i).ne.10) then
1159                 do j=1,3
1160                   dc(j,i+nres)=c(j,i+nres)-c(j,i)
1161                   dc_norm(j,i+nres)=dc_norm(j,i+nres)*vbld_inv(i+nres)
1162                 enddo
1163               endif
1164             enddo
1165             return
1166           else
1167             call read_angles(inp,*36)
1168           endif
1169           goto 37
1170    36     write (iout,'(a)') 'Error reading angle file.'
1171 #ifdef MPI
1172           call mpi_finalize( MPI_COMM_WORLD,IERR )
1173 #endif
1174           stop 'Error reading angle file.'
1175    37     continue
1176         else if (extconf) then
1177          if(me.eq.king.or..not.out1file .and. fg_rank.eq.0)
1178      &    write (iout,'(a)') 'Extended chain initial geometry.'
1179          do i=3,nres
1180           theta(i)=90d0*deg2rad
1181          enddo
1182          do i=4,nres
1183           phi(i)=180d0*deg2rad
1184          enddo
1185          do i=2,nres-1
1186           alph(i)=110d0*deg2rad
1187          enddo
1188          do i=2,nres-1
1189           omeg(i)=-120d0*deg2rad
1190          enddo
1191         else
1192           if(me.eq.king.or..not.out1file)
1193      &     write (iout,'(a)') 'Random-generated initial geometry.'
1194
1195
1196 #ifdef MPI
1197           if (me.eq.king  .or. fg_rank.eq.0 .and. (
1198      &           modecalc.eq.12 .or. modecalc.eq.14) ) then
1199 #endif
1200             do itrial=1,100
1201               itmp=1
1202               call gen_rand_conf(itmp,*30)
1203               goto 40
1204    30         write (iout,*) 'Failed to generate random conformation',
1205      &          ', itrial=',itrial
1206               write (*,*) 'Processor:',me,
1207      &          ' Failed to generate random conformation',
1208      &          ' itrial=',itrial
1209               call intout
1210
1211 #ifdef AIX
1212               call flush_(iout)
1213 #else
1214               call flush(iout)
1215 #endif
1216             enddo
1217             write (iout,'(a,i3,a)') 'Processor:',me,
1218      &        ' error in generating random conformation.'
1219             write (*,'(a,i3,a)') 'Processor:',me,
1220      &        ' error in generating random conformation.'
1221             call flush(iout)
1222 #ifdef MPI
1223             call MPI_Abort(mpi_comm_world,error_msg,ierrcode)
1224    40       continue
1225           endif
1226 #else
1227    40     continue
1228 #endif
1229         endif
1230       elseif (modecalc.eq.4) then
1231         read (inp,'(a)') intinname
1232         open (intin,file=intinname,status='old',err=333)
1233         if (me.eq.king .or. .not.out1file.and.fg_rank.eq.0)
1234      &  write (iout,'(a)') 'intinname',intinname
1235         write (*,'(a)') 'Processor',myrank,' intinname',intinname
1236         goto 334
1237   333   write (iout,'(2a)') 'Error opening angle file ',intinname
1238 #ifdef MPI
1239         call MPI_Finalize(MPI_COMM_WORLD,IERR)
1240 #endif
1241         stop 'Error opening angle file.'
1242   334   continue
1243
1244       endif
1245 C Generate distance constraints, if the PDB structure is to be regularized.
1246       if (nthread.gt.0) then
1247         call read_threadbase
1248       endif
1249       call setup_var
1250       if (me.eq.king .or. .not. out1file)
1251      & call intout
1252       if (ns.gt.0 .and. (me.eq.king .or. .not.out1file) ) then
1253         write (iout,'(/a,i3,a)')
1254      &  'The chain contains',ns,' disulfide-bridging cysteines.'
1255         write (iout,'(20i4)') (iss(i),i=1,ns)
1256        if (dyn_ss) then
1257           write(iout,*)"Running with dynamic disulfide-bond formation"
1258        else
1259         write (iout,'(/a/)') 'Pre-formed links are:'
1260         do i=1,nss
1261           i1=ihpb(i)-nres
1262           i2=jhpb(i)-nres
1263           it1=itype(i1)
1264           it2=itype(i2)
1265           write (iout,'(2a,i3,3a,i3,a,3f10.3)')
1266      &    restyp(it1),'(',i1,') -- ',restyp(it2),'(',i2,')',dhpb(i),
1267      &    ebr,forcon(i)
1268         enddo
1269         write (iout,'(a)')
1270        endif
1271       endif
1272       if (ns.gt.0.and.dyn_ss) then
1273           do i=nss+1,nhpb
1274             ihpb(i-nss)=ihpb(i)
1275             jhpb(i-nss)=jhpb(i)
1276             forcon(i-nss)=forcon(i)
1277             dhpb(i-nss)=dhpb(i)
1278           enddo
1279           nhpb=nhpb-nss
1280           nss=0
1281           call hpb_partition
1282           do i=1,ns
1283             dyn_ss_mask(iss(i))=.true.
1284           enddo
1285       endif
1286       if (i2ndstr.gt.0) call secstrp2dihc
1287 c      call geom_to_var(nvar,x)
1288 c      call etotal(energia(0))
1289 c      call enerprint(energia(0))
1290 c      call briefout(0,etot)
1291 c      stop
1292 cd    write (iout,'(2(a,i3))') 'NNT',NNT,' NCT',NCT
1293 cd    write (iout,'(a)') 'Variable list:'
1294 cd    write (iout,'(i4,f10.5)') (i,rad2deg*x(i),i=1,nvar)
1295 #ifdef MPI
1296       if (me.eq.king .or. (fg_rank.eq.0 .and. .not.out1file))
1297      &  write (iout,'(//80(1h*)/20x,a,i4,a/80(1h*)//)')
1298      &  'Processor',myrank,': end reading molecular data.'
1299 #endif
1300       return
1301       end
1302 c--------------------------------------------------------------------------
1303       logical function seq_comp(itypea,itypeb,length)
1304       implicit none
1305       integer length,itypea(length),itypeb(length)
1306       integer i
1307       do i=1,length
1308         if (itypea(i).ne.itypeb(i)) then
1309           seq_comp=.false.
1310           return
1311         endif
1312       enddo
1313       seq_comp=.true.
1314       return
1315       end
1316 c-----------------------------------------------------------------------------
1317       subroutine read_bridge
1318 C Read information about disulfide bridges.
1319       implicit real*8 (a-h,o-z)
1320       include 'DIMENSIONS'
1321 #ifdef MPI
1322       include 'mpif.h'
1323 #endif
1324       include 'COMMON.IOUNITS'
1325       include 'COMMON.GEO'
1326       include 'COMMON.VAR'
1327       include 'COMMON.INTERACT'
1328       include 'COMMON.LOCAL'
1329       include 'COMMON.NAMES'
1330       include 'COMMON.CHAIN'
1331       include 'COMMON.FFIELD'
1332       include 'COMMON.SBRIDGE'
1333       include 'COMMON.HEADER'
1334       include 'COMMON.CONTROL'
1335       include 'COMMON.DBASE'
1336       include 'COMMON.THREAD'
1337       include 'COMMON.TIME1'
1338       include 'COMMON.SETUP'
1339 C Read bridging residues.
1340       read (inp,*) ns,(iss(i),i=1,ns)
1341       print *,'ns=',ns
1342       if(me.eq.king.or..not.out1file)
1343      &  write (iout,*) 'ns=',ns,' iss:',(iss(i),i=1,ns)
1344 C Check whether the specified bridging residues are cystines.
1345       do i=1,ns
1346         if (itype(iss(i)).ne.1) then
1347           if (me.eq.king.or..not.out1file) write (iout,'(2a,i3,a)')
1348      &   'Do you REALLY think that the residue ',
1349      &    restyp(itype(iss(i))),i,
1350      &   ' can form a disulfide bridge?!!!'
1351           write (*,'(2a,i3,a)')
1352      &   'Do you REALLY think that the residue ',
1353      &    restyp(itype(iss(i))),i,
1354      &   ' can form a disulfide bridge?!!!'
1355 #ifdef MPI
1356          call MPI_Finalize(MPI_COMM_WORLD,ierror)
1357          stop
1358 #endif
1359         endif
1360       enddo
1361 C Read preformed bridges.
1362       if (ns.gt.0) then
1363       read (inp,*) nss,(ihpb(i),jhpb(i),i=1,nss)
1364       if(fg_rank.eq.0)
1365      & write(iout,*)'nss=',nss,' ihpb,jhpb: ',(ihpb(i),jhpb(i),i=1,nss)
1366       if (nss.gt.0) then
1367         nhpb=nss
1368 C Check if the residues involved in bridges are in the specified list of
1369 C bridging residues.
1370         do i=1,nss
1371           do j=1,i-1
1372             if (ihpb(i).eq.ihpb(j).or.ihpb(i).eq.jhpb(j)
1373      &      .or.jhpb(i).eq.ihpb(j).or.jhpb(i).eq.jhpb(j)) then
1374               write (iout,'(a,i3,a)') 'Disulfide pair',i,
1375      &      ' contains residues present in other pairs.'
1376               write (*,'(a,i3,a)') 'Disulfide pair',i,
1377      &      ' contains residues present in other pairs.'
1378 #ifdef MPI
1379               call MPI_Finalize(MPI_COMM_WORLD,ierror)
1380               stop
1381 #endif
1382             endif
1383           enddo
1384           do j=1,ns
1385             if (ihpb(i).eq.iss(j)) goto 10
1386           enddo
1387           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1388    10     continue
1389           do j=1,ns
1390             if (jhpb(i).eq.iss(j)) goto 20
1391           enddo
1392           write (iout,'(a,i3,a)') 'Pair',i,' contains unknown cystine.'
1393    20     continue
1394           dhpb(i)=dbr
1395           forcon(i)=fbr
1396         enddo
1397         do i=1,nss
1398           ihpb(i)=ihpb(i)+nres
1399           jhpb(i)=jhpb(i)+nres
1400         enddo
1401       endif
1402       endif
1403       return
1404       end
1405 c----------------------------------------------------------------------------
1406       subroutine read_x(kanal,*)
1407       implicit real*8 (a-h,o-z)
1408       include 'DIMENSIONS'
1409       include 'COMMON.GEO'
1410       include 'COMMON.VAR'
1411       include 'COMMON.CHAIN'
1412       include 'COMMON.IOUNITS'
1413       include 'COMMON.CONTROL'
1414       include 'COMMON.LOCAL'
1415       include 'COMMON.INTERACT'
1416 c Read coordinates from input
1417 c
1418       read(kanal,'(8f10.5)',end=10,err=10)
1419      &  ((c(l,k),l=1,3),k=1,nres),
1420      &  ((c(l,k+nres),l=1,3),k=nnt,nct)
1421       do j=1,3
1422         c(j,nres+1)=c(j,1)
1423         c(j,2*nres)=c(j,nres)
1424       enddo
1425       call int_from_cart1(.false.)
1426       do i=1,nres-1
1427         do j=1,3
1428           dc(j,i)=c(j,i+1)-c(j,i)
1429           dc_norm(j,i)=dc(j,i)*vbld_inv(i+1)
1430         enddo
1431       enddo
1432       do i=nnt,nct
1433         if (itype(i).ne.10) then
1434           do j=1,3
1435             dc(j,i+nres)=c(j,i+nres)-c(j,i)
1436             dc_norm(j,i+nres)=dc(j,i+nres)*vbld_inv(i+nres)
1437           enddo
1438         endif
1439       enddo
1440
1441       return
1442    10 return1
1443       end
1444 c----------------------------------------------------------------------------
1445       subroutine read_threadbase
1446       implicit real*8 (a-h,o-z)
1447       include 'DIMENSIONS'
1448       include 'COMMON.IOUNITS'
1449       include 'COMMON.GEO'
1450       include 'COMMON.VAR'
1451       include 'COMMON.INTERACT'
1452       include 'COMMON.LOCAL'
1453       include 'COMMON.NAMES'
1454       include 'COMMON.CHAIN'
1455       include 'COMMON.FFIELD'
1456       include 'COMMON.SBRIDGE'
1457       include 'COMMON.HEADER'
1458       include 'COMMON.CONTROL'
1459       include 'COMMON.DBASE'
1460       include 'COMMON.THREAD'
1461       include 'COMMON.TIME1'
1462 C Read pattern database for threading.
1463       read (icbase,*) nseq
1464       do i=1,nseq
1465         read (icbase,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1466      &   nres_base(2,i),nres_base(3,i)
1467         read (icbase,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1468      &   nres_base(1,i))
1469 c       write (iout,'(i5,2x,a8,2i4)') nres_base(1,i),str_nam(i),
1470 c    &   nres_base(2,i),nres_base(3,i)
1471 c       write (iout,'(9f8.3)') ((cart_base(k,j,i),k=1,3),j=1,
1472 c    &   nres_base(1,i))
1473       enddo
1474       close (icbase)
1475       if (weidis.eq.0.0D0) weidis=0.1D0
1476       do i=nnt,nct
1477         do j=i+2,nct
1478           nhpb=nhpb+1
1479           ihpb(nhpb)=i
1480           jhpb(nhpb)=j
1481           forcon(nhpb)=weidis
1482         enddo
1483       enddo
1484       read (inp,*) nexcl,(iexam(1,i),iexam(2,i),i=1,nexcl)
1485       write (iout,'(a,i5)') 'nexcl: ',nexcl
1486       write (iout,'(2i5)') (iexam(1,i),iexam(2,i),i=1,nexcl)
1487       return
1488       end
1489 c------------------------------------------------------------------------------
1490       subroutine setup_var
1491       implicit real*8 (a-h,o-z)
1492       include 'DIMENSIONS'
1493       include 'COMMON.IOUNITS'
1494       include 'COMMON.GEO'
1495       include 'COMMON.VAR'
1496       include 'COMMON.INTERACT'
1497       include 'COMMON.LOCAL'
1498       include 'COMMON.NAMES'
1499       include 'COMMON.CHAIN'
1500       include 'COMMON.FFIELD'
1501       include 'COMMON.SBRIDGE'
1502       include 'COMMON.HEADER'
1503       include 'COMMON.CONTROL'
1504       include 'COMMON.DBASE'
1505       include 'COMMON.THREAD'
1506       include 'COMMON.TIME1'
1507 C Set up variable list.
1508       ntheta=nres-2
1509       nphi=nres-3
1510       nvar=ntheta+nphi
1511       nside=0
1512       do i=2,nres-1
1513         if (itype(i).ne.10) then
1514           nside=nside+1
1515           ialph(i,1)=nvar+nside
1516           ialph(nside,2)=i
1517         endif
1518       enddo
1519       if (indphi.gt.0) then
1520         nvar=nphi
1521       else if (indback.gt.0) then
1522         nvar=nphi+ntheta
1523       else
1524         nvar=nvar+2*nside
1525       endif
1526 cd    write (iout,'(3i4)') (i,ialph(i,1),ialph(i,2),i=2,nres-1)
1527       return
1528       end
1529 c----------------------------------------------------------------------------
1530       subroutine gen_dist_constr
1531 C Generate CA distance constraints.
1532       implicit real*8 (a-h,o-z)
1533       include 'DIMENSIONS'
1534       include 'COMMON.IOUNITS'
1535       include 'COMMON.GEO'
1536       include 'COMMON.VAR'
1537       include 'COMMON.INTERACT'
1538       include 'COMMON.LOCAL'
1539       include 'COMMON.NAMES'
1540       include 'COMMON.CHAIN'
1541       include 'COMMON.FFIELD'
1542       include 'COMMON.SBRIDGE'
1543       include 'COMMON.HEADER'
1544       include 'COMMON.CONTROL'
1545       include 'COMMON.DBASE'
1546       include 'COMMON.THREAD'
1547       include 'COMMON.TIME1'
1548       dimension itype_pdb(maxres)
1549       common /pizda/ itype_pdb
1550       character*2 iden
1551 cd      print *,'gen_dist_constr: nnt=',nnt,' nct=',nct
1552 cd      write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct,
1553 cd     & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq,
1554 cd     & ' nsup',nsup
1555       do i=nstart_sup,nstart_sup+nsup-1
1556 cd      write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)),
1557 cd     &    ' seq_pdb', restyp(itype_pdb(i))
1558         do j=i+2,nstart_sup+nsup-1
1559           nhpb=nhpb+1
1560           ihpb(nhpb)=i+nstart_seq-nstart_sup
1561           jhpb(nhpb)=j+nstart_seq-nstart_sup
1562           forcon(nhpb)=weidis
1563           dhpb(nhpb)=dist(i,j)
1564         enddo
1565       enddo
1566 cd      write (iout,'(a)') 'Distance constraints:'
1567 cd      do i=nss+1,nhpb
1568 cd        ii=ihpb(i)
1569 cd        jj=jhpb(i)
1570 cd        iden='CA'
1571 cd        if (ii.gt.nres) then
1572 cd          iden='SC'
1573 cd          ii=ii-nres
1574 cd          jj=jj-nres
1575 cd        endif
1576 cd        write (iout,'(a,1x,a,i4,3x,a,1x,a,i4,2f10.3)')
1577 cd     &  restyp(itype(ii)),iden,ii,restyp(itype(jj)),iden,jj,
1578 cd     &  dhpb(i),forcon(i)
1579 cd      enddo
1580       return
1581       end
1582 c----------------------------------------------------------------------------
1583       subroutine map_read
1584       implicit real*8 (a-h,o-z)
1585       include 'DIMENSIONS'
1586       include 'COMMON.MAP'
1587       include 'COMMON.IOUNITS'
1588       character*3 angid(4) /'THE','PHI','ALP','OME'/
1589       character*80 mapcard,ucase
1590       do imap=1,nmap
1591         read (inp,'(a)') mapcard
1592         mapcard=ucase(mapcard)
1593         if (index(mapcard,'PHI').gt.0) then
1594           kang(imap)=1
1595         else if (index(mapcard,'THE').gt.0) then
1596           kang(imap)=2
1597         else if (index(mapcard,'ALP').gt.0) then
1598           kang(imap)=3
1599         else if (index(mapcard,'OME').gt.0) then
1600           kang(imap)=4
1601         else
1602           write(iout,'(a)')'Error - illegal variable spec in MAP card.'
1603           stop 'Error - illegal variable spec in MAP card.'
1604         endif
1605         call readi (mapcard,'RES1',res1(imap),0)
1606         call readi (mapcard,'RES2',res2(imap),0)
1607         if (res1(imap).eq.0) then
1608           res1(imap)=res2(imap)
1609         else if (res2(imap).eq.0) then
1610           res2(imap)=res1(imap)
1611         endif
1612         if(res1(imap)*res2(imap).eq.0 .or. res1(imap).gt.res2(imap))then
1613           write (iout,'(a)')
1614      &    'Error - illegal definition of variable group in MAP.'
1615           stop 'Error - illegal definition of variable group in MAP.'
1616         endif
1617         call reada(mapcard,'FROM',ang_from(imap),0.0D0)
1618         call reada(mapcard,'TO',ang_to(imap),0.0D0)
1619         call readi(mapcard,'NSTEP',nstep(imap),0)
1620         if (ang_from(imap).eq.ang_to(imap) .or. nstep(imap).eq.0) then
1621           write (iout,'(a)')
1622      &     'Illegal boundary and/or step size specification in MAP.'
1623           stop 'Illegal boundary and/or step size specification in MAP.'
1624         endif
1625       enddo ! imap
1626       return
1627       end
1628 c----------------------------------------------------------------------------
1629 csa      subroutine csaread
1630 csa      implicit real*8 (a-h,o-z)
1631 csa      include 'DIMENSIONS'
1632 csa      include 'COMMON.IOUNITS'
1633 csa      include 'COMMON.GEO'
1634 csa      include 'COMMON.CSA'
1635 csa      include 'COMMON.BANK'
1636 csa      include 'COMMON.CONTROL'
1637 csa      character*80 ucase
1638 csa      character*620 mcmcard
1639 csa      call card_concat(mcmcard)
1640 csa
1641 csa      call readi(mcmcard,'NCONF',nconf,50)
1642 csa      call readi(mcmcard,'NADD',nadd,0)
1643 csa      call readi(mcmcard,'JSTART',jstart,1)
1644 csa      call readi(mcmcard,'JEND',jend,1)
1645 csa      call readi(mcmcard,'NSTMAX',nstmax,500000)
1646 csa      call readi(mcmcard,'N0',n0,1)
1647 csa      call readi(mcmcard,'N1',n1,6)
1648 csa      call readi(mcmcard,'N2',n2,4)
1649 csa      call readi(mcmcard,'N3',n3,0)
1650 csa      call readi(mcmcard,'N4',n4,0)
1651 csa      call readi(mcmcard,'N5',n5,0)
1652 csa      call readi(mcmcard,'N6',n6,10)
1653 csa      call readi(mcmcard,'N7',n7,0)
1654 csa      call readi(mcmcard,'N8',n8,0)
1655 csa      call readi(mcmcard,'N9',n9,0)
1656 csa      call readi(mcmcard,'N14',n14,0)
1657 csa      call readi(mcmcard,'N15',n15,0)
1658 csa      call readi(mcmcard,'N16',n16,0)
1659 csa      call readi(mcmcard,'N17',n17,0)
1660 csa      call readi(mcmcard,'N18',n18,0)
1661 csa
1662 csa      vdisulf=(index(mcmcard,'DYNSS').gt.0)
1663 csa
1664 csa      call readi(mcmcard,'NDIFF',ndiff,2)
1665 csa      call reada(mcmcard,'DIFFCUT',diffcut,0.0d0)
1666 csa      call readi(mcmcard,'IS1',is1,1)
1667 csa      call readi(mcmcard,'IS2',is2,8)
1668 csa      call readi(mcmcard,'NRAN0',nran0,4)
1669 csa      call readi(mcmcard,'NRAN1',nran1,2)
1670 csa      call readi(mcmcard,'IRR',irr,1)
1671 csa      call readi(mcmcard,'NSEED',nseed,20)
1672 csa      call readi(mcmcard,'NTOTAL',ntotal,10000)
1673 csa      call reada(mcmcard,'CUT1',cut1,2.0d0)
1674 csa      call reada(mcmcard,'CUT2',cut2,5.0d0)
1675 csa      call reada(mcmcard,'ESTOP',estop,-3000.0d0)
1676 csa      call readi(mcmcard,'ICMAX',icmax,3)
1677 csa      call readi(mcmcard,'IRESTART',irestart,0)
1678 csac!bankt      call readi(mcmcard,'NBANKTM',ntbankm,0)
1679 csa      ntbankm=0
1680 csac!bankt
1681 csa      call reada(mcmcard,'DELE',dele,20.0d0)
1682 csa      call reada(mcmcard,'DIFCUT',difcut,720.0d0)
1683 csa      call readi(mcmcard,'IREF',iref,0)
1684 csa      call reada(mcmcard,'RMSCUT',rmscut,4.0d0)
1685 csa      call reada(mcmcard,'PNCCUT',pnccut,0.5d0)
1686 csa      call readi(mcmcard,'NCONF_IN',nconf_in,0)
1687 csa      call reada(mcmcard,'RDIH_BIAS',rdih_bias,0.5d0)
1688 csa      write (iout,*) "NCONF_IN",nconf_in
1689 csa      return
1690 csa      end
1691 c----------------------------------------------------------------------------
1692 cfmc      subroutine mcmfread
1693 cfmc      implicit real*8 (a-h,o-z)
1694 cfmc      include 'DIMENSIONS'
1695 cfmc      include 'COMMON.MCMF'
1696 cfmc      include 'COMMON.IOUNITS'
1697 cfmc      include 'COMMON.GEO'
1698 cfmc      character*80 ucase
1699 cfmc      character*620 mcmcard
1700 cfmc      call card_concat(mcmcard)
1701 cfmc
1702 cfmc      call readi(mcmcard,'MAXRANT',maxrant,1000)
1703 cfmc      write(iout,*)'MAXRANT=',maxrant
1704 cfmc      call readi(mcmcard,'MAXFAM',maxfam,maxfam_p)
1705 cfmc      write(iout,*)'MAXFAM=',maxfam
1706 cfmc      call readi(mcmcard,'NNET1',nnet1,5)
1707 cfmc      write(iout,*)'NNET1=',nnet1
1708 cfmc      call readi(mcmcard,'NNET2',nnet2,4)
1709 cfmc      write(iout,*)'NNET2=',nnet2
1710 cfmc      call readi(mcmcard,'NNET3',nnet3,4)
1711 cfmc      write(iout,*)'NNET3=',nnet3
1712 cfmc      call readi(mcmcard,'ILASTT',ilastt,0)
1713 cfmc      write(iout,*)'ILASTT=',ilastt
1714 cfmc      call readi(mcmcard,'MAXSTR',maxstr,maxstr_mcmf)
1715 cfmc      write(iout,*)'MAXSTR=',maxstr
1716 cfmc      maxstr_f=maxstr/maxfam
1717 cfmc      write(iout,*)'MAXSTR_F=',maxstr_f
1718 cfmc      call readi(mcmcard,'NMCMF',nmcmf,10)
1719 cfmc      write(iout,*)'NMCMF=',nmcmf
1720 cfmc      call readi(mcmcard,'IFOCUS',ifocus,nmcmf)
1721 cfmc      write(iout,*)'IFOCUS=',ifocus
1722 cfmc      call readi(mcmcard,'NLOCMCMF',nlocmcmf,1000)
1723 cfmc      write(iout,*)'NLOCMCMF=',nlocmcmf
1724 cfmc      call readi(mcmcard,'INTPRT',intprt,1000)
1725 cfmc      write(iout,*)'INTPRT=',intprt
1726 cfmc      call readi(mcmcard,'IPRT',iprt,100)
1727 cfmc      write(iout,*)'IPRT=',iprt
1728 cfmc      call readi(mcmcard,'IMAXTR',imaxtr,100)
1729 cfmc      write(iout,*)'IMAXTR=',imaxtr
1730 cfmc      call readi(mcmcard,'MAXEVEN',maxeven,1000)
1731 cfmc      write(iout,*)'MAXEVEN=',maxeven
1732 cfmc      call readi(mcmcard,'MAXEVEN1',maxeven1,3)
1733 cfmc      write(iout,*)'MAXEVEN1=',maxeven1
1734 cfmc      call readi(mcmcard,'INIMIN',inimin,200)
1735 cfmc      write(iout,*)'INIMIN=',inimin
1736 cfmc      call readi(mcmcard,'NSTEPMCMF',nstepmcmf,10)
1737 cfmc      write(iout,*)'NSTEPMCMF=',nstepmcmf
1738 cfmc      call readi(mcmcard,'NTHREAD',nthread,5)
1739 cfmc      write(iout,*)'NTHREAD=',nthread
1740 cfmc      call readi(mcmcard,'MAXSTEPMCMF',maxstepmcmf,2500)
1741 cfmc      write(iout,*)'MAXSTEPMCMF=',maxstepmcmf
1742 cfmc      call readi(mcmcard,'MAXPERT',maxpert,9)
1743 cfmc      write(iout,*)'MAXPERT=',maxpert
1744 cfmc      call readi(mcmcard,'IRMSD',irmsd,1)
1745 cfmc      write(iout,*)'IRMSD=',irmsd
1746 cfmc      call reada(mcmcard,'DENEMIN',denemin,0.01D0)
1747 cfmc      write(iout,*)'DENEMIN=',denemin
1748 cfmc      call reada(mcmcard,'RCUT1S',rcut1s,3.5D0)
1749 cfmc      write(iout,*)'RCUT1S=',rcut1s
1750 cfmc      call reada(mcmcard,'RCUT1E',rcut1e,2.0D0)
1751 cfmc      write(iout,*)'RCUT1E=',rcut1e
1752 cfmc      call reada(mcmcard,'RCUT2S',rcut2s,0.5D0)
1753 cfmc      write(iout,*)'RCUT2S=',rcut2s
1754 cfmc      call reada(mcmcard,'RCUT2E',rcut2e,0.1D0)
1755 cfmc      write(iout,*)'RCUT2E=',rcut2e
1756 cfmc      call reada(mcmcard,'DPERT1',d_pert1,180.0D0)
1757 cfmc      write(iout,*)'DPERT1=',d_pert1
1758 cfmc      call reada(mcmcard,'DPERT1A',d_pert1a,180.0D0)
1759 cfmc      write(iout,*)'DPERT1A=',d_pert1a
1760 cfmc      call reada(mcmcard,'DPERT2',d_pert2,90.0D0)
1761 cfmc      write(iout,*)'DPERT2=',d_pert2
1762 cfmc      call reada(mcmcard,'DPERT2A',d_pert2a,45.0D0)
1763 cfmc      write(iout,*)'DPERT2A=',d_pert2a
1764 cfmc      call reada(mcmcard,'DPERT2B',d_pert2b,90.0D0)
1765 cfmc      write(iout,*)'DPERT2B=',d_pert2b
1766 cfmc      call reada(mcmcard,'DPERT2C',d_pert2c,60.0D0)
1767 cfmc      write(iout,*)'DPERT2C=',d_pert2c
1768 cfmc      d_pert1=deg2rad*d_pert1
1769 cfmc      d_pert1a=deg2rad*d_pert1a
1770 cfmc      d_pert2=deg2rad*d_pert2
1771 cfmc      d_pert2a=deg2rad*d_pert2a
1772 cfmc      d_pert2b=deg2rad*d_pert2b
1773 cfmc      d_pert2c=deg2rad*d_pert2c
1774 cfmc      call reada(mcmcard,'KT_MCMF1',kt_mcmf1,1.0D0)
1775 cfmc      write(iout,*)'KT_MCMF1=',kt_mcmf1
1776 cfmc      call reada(mcmcard,'KT_MCMF2',kt_mcmf2,1.0D0)
1777 cfmc      write(iout,*)'KT_MCMF2=',kt_mcmf2
1778 cfmc      call reada(mcmcard,'DKT_MCMF1',dkt_mcmf1,10.0D0)
1779 cfmc      write(iout,*)'DKT_MCMF1=',dkt_mcmf1
1780 cfmc      call reada(mcmcard,'DKT_MCMF2',dkt_mcmf2,1.0D0)
1781 cfmc      write(iout,*)'DKT_MCMF2=',dkt_mcmf2
1782 cfmc      call reada(mcmcard,'RCUTINI',rcutini,3.5D0)
1783 cfmc      write(iout,*)'RCUTINI=',rcutini
1784 cfmc      call reada(mcmcard,'GRAT',grat,0.5D0)
1785 cfmc      write(iout,*)'GRAT=',grat
1786 cfmc      call reada(mcmcard,'BIAS_MCMF',bias_mcmf,0.0D0)
1787 cfmc      write(iout,*)'BIAS_MCMF=',bias_mcmf
1788 cfmc
1789 cfmc      return
1790 cfmc      end
1791 c----------------------------------------------------------------------------
1792       subroutine mcmread
1793       implicit real*8 (a-h,o-z)
1794       include 'DIMENSIONS'
1795       include 'COMMON.MCM'
1796       include 'COMMON.MCE'
1797       include 'COMMON.IOUNITS'
1798       character*80 ucase
1799       character*320 mcmcard
1800       call card_concat(mcmcard)
1801       call readi(mcmcard,'MAXACC',maxacc,100)
1802       call readi(mcmcard,'MAX_MCM_IT',max_mcm_it,10000)
1803       call readi(mcmcard,'MAXTRIAL',maxtrial,100)
1804       call readi(mcmcard,'MAXTRIAL_ITER',maxtrial_iter,1000)
1805       call readi(mcmcard,'MAXREPM',maxrepm,200)
1806       call reada(mcmcard,'RANFRACT',RanFract,0.5D0)
1807       call reada(mcmcard,'POOL_FRACT',pool_fraction,0.01D0)
1808       call reada(mcmcard,'OVERLAP',overlap_cut,1.0D3)
1809       call reada(mcmcard,'E_UP',e_up,5.0D0)
1810       call reada(mcmcard,'DELTE',delte,0.1D0)
1811       call readi(mcmcard,'NSWEEP',nsweep,5)
1812       call readi(mcmcard,'NSTEPH',nsteph,0)
1813       call readi(mcmcard,'NSTEPC',nstepc,0)
1814       call reada(mcmcard,'TMIN',tmin,298.0D0)
1815       call reada(mcmcard,'TMAX',tmax,298.0D0)
1816       call readi(mcmcard,'NWINDOW',nwindow,0)
1817       call readi(mcmcard,'PRINT_MC',print_mc,0)
1818       print_stat=(index(mcmcard,'NO_PRINT_STAT').le.0)
1819       print_int=(index(mcmcard,'NO_PRINT_INT').le.0)
1820       ent_read=(index(mcmcard,'ENT_READ').gt.0)
1821       call readi(mcmcard,'SAVE_FREQ',save_frequency,1000)
1822       call readi(mcmcard,'MESSAGE_FREQ',message_frequency,1000)
1823       call readi(mcmcard,'POOL_READ_FREQ',pool_read_freq,5000)
1824       call readi(mcmcard,'POOL_SAVE_FREQ',pool_save_freq,1000)
1825       call readi(mcmcard,'PRINT_FREQ',print_freq,1000)
1826       if (nwindow.gt.0) then
1827         read (inp,*) (winstart(i),winend(i),i=1,nwindow)
1828         do i=1,nwindow
1829           winlen(i)=winend(i)-winstart(i)+1
1830         enddo
1831       endif
1832       if (tmax.lt.tmin) tmax=tmin
1833       if (tmax.eq.tmin) then
1834         nstepc=0
1835         nsteph=0
1836       endif
1837       if (nstepc.gt.0 .and. nsteph.gt.0) then
1838         tsteph=(tmax/tmin)**(1.0D0/(nsteph+0.0D0))
1839         tstepc=(tmax/tmin)**(1.0D0/(nstepc+0.0D0))
1840       endif
1841 C Probabilities of different move types
1842       sumpro_type(0)=0.0D0
1843       call reada(mcmcard,'MULTI_BOND',sumpro_type(1),1.0d0)
1844       call reada(mcmcard,'ONE_ANGLE' ,sumpro_type(2),2.0d0)
1845       sumpro_type(2)=sumpro_type(1)+sumpro_type(2)
1846       call reada(mcmcard,'THETA'     ,sumpro_type(3),0.0d0)
1847       sumpro_type(3)=sumpro_type(2)+sumpro_type(3)
1848       call reada(mcmcard,'SIDE_CHAIN',sumpro_type(4),0.5d0)
1849       sumpro_type(4)=sumpro_type(3)+sumpro_type(4)
1850       do i=1,MaxMoveType
1851         print *,'i',i,' sumprotype',sumpro_type(i)
1852         sumpro_type(i)=sumpro_type(i)/sumpro_type(MaxMoveType)
1853         print *,'i',i,' sumprotype',sumpro_type(i)
1854       enddo
1855       return
1856       end
1857 c----------------------------------------------------------------------------
1858       subroutine read_minim
1859       implicit real*8 (a-h,o-z)
1860       include 'DIMENSIONS'
1861       include 'COMMON.MINIM'
1862       include 'COMMON.IOUNITS'
1863       character*80 ucase
1864       character*320 minimcard
1865       call card_concat(minimcard)
1866       call readi(minimcard,'MAXMIN',maxmin,2000)
1867       call readi(minimcard,'MAXFUN',maxfun,5000)
1868       call readi(minimcard,'MINMIN',minmin,maxmin)
1869       call readi(minimcard,'MINFUN',minfun,maxmin)
1870       call reada(minimcard,'TOLF',tolf,1.0D-2)
1871       call reada(minimcard,'RTOLF',rtolf,1.0D-4)
1872       print_min_stat=min0(index(minimcard,'PRINT_MIN_STAT'),1)
1873       print_min_res=min0(index(minimcard,'PRINT_MIN_RES'),1)
1874       print_min_ini=min0(index(minimcard,'PRINT_MIN_INI'),1)
1875       write (iout,'(/80(1h*)/20x,a/80(1h*))')
1876      &         'Options in energy minimization:'
1877       write (iout,'(4(a,i5),a,1pe14.5,a,1pe14.5)')
1878      & 'MaxMin:',MaxMin,' MaxFun:',MaxFun,
1879      & 'MinMin:',MinMin,' MinFun:',MinFun,
1880      & ' TolF:',TolF,' RTolF:',RTolF
1881       return
1882       end
1883 c----------------------------------------------------------------------------
1884       subroutine read_angles(kanal,*)
1885       implicit real*8 (a-h,o-z)
1886       include 'DIMENSIONS'
1887       include 'COMMON.GEO'
1888       include 'COMMON.VAR'
1889       include 'COMMON.CHAIN'
1890       include 'COMMON.IOUNITS'
1891       include 'COMMON.CONTROL'
1892 c Read angles from input
1893 c
1894        read (kanal,*,err=10,end=10) (theta(i),i=3,nres)
1895        read (kanal,*,err=10,end=10) (phi(i),i=4,nres)
1896        read (kanal,*,err=10,end=10) (alph(i),i=2,nres-1)
1897        read (kanal,*,err=10,end=10) (omeg(i),i=2,nres-1)
1898
1899        do i=1,nres
1900 c 9/7/01 avoid 180 deg valence angle
1901         if (theta(i).gt.179.99d0) theta(i)=179.99d0
1902 c
1903         theta(i)=deg2rad*theta(i)
1904         phi(i)=deg2rad*phi(i)
1905         alph(i)=deg2rad*alph(i)
1906         omeg(i)=deg2rad*omeg(i)
1907        enddo
1908       return
1909    10 return1
1910       end
1911 c----------------------------------------------------------------------------
1912       subroutine reada(rekord,lancuch,wartosc,default)
1913       implicit none
1914       character*(*) rekord,lancuch
1915       double precision wartosc,default
1916       integer ilen,iread
1917       external ilen
1918       iread=index(rekord,lancuch)
1919       if (iread.eq.0) then
1920         wartosc=default
1921         return
1922       endif
1923       iread=iread+ilen(lancuch)+1
1924       read (rekord(iread:),*,err=10,end=10) wartosc
1925       return
1926   10  wartosc=default
1927       return
1928       end
1929 c----------------------------------------------------------------------------
1930       subroutine readi(rekord,lancuch,wartosc,default)
1931       implicit none
1932       character*(*) rekord,lancuch
1933       integer wartosc,default
1934       integer ilen,iread
1935       external ilen
1936       iread=index(rekord,lancuch)
1937       if (iread.eq.0) then
1938         wartosc=default
1939         return
1940       endif
1941       iread=iread+ilen(lancuch)+1
1942       read (rekord(iread:),*,err=10,end=10) wartosc
1943       return
1944   10  wartosc=default
1945       return
1946       end
1947 c----------------------------------------------------------------------------
1948       subroutine multreadi(rekord,lancuch,tablica,dim,default)
1949       implicit none
1950       integer dim,i
1951       integer tablica(dim),default
1952       character*(*) rekord,lancuch
1953       character*80 aux
1954       integer ilen,iread
1955       external ilen
1956       do i=1,dim
1957         tablica(i)=default
1958       enddo
1959 #ifdef G77
1960       aux=lancuch(:ilen(lancuch))//"="
1961       iread=index(rekord,aux)
1962 #else
1963       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1964 #endif
1965       if (iread.eq.0) return
1966       iread=iread+ilen(lancuch)+1
1967       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1968    10 return
1969       end
1970 c----------------------------------------------------------------------------
1971       subroutine multreada(rekord,lancuch,tablica,dim,default)
1972       implicit none
1973       integer dim,i
1974       double precision tablica(dim),default
1975       character*(*) rekord,lancuch
1976       character*80 aux
1977       integer ilen,iread
1978       external ilen
1979       do i=1,dim
1980         tablica(i)=default
1981       enddo
1982 #ifdef G77
1983       aux=lancuch(:ilen(lancuch))//"="
1984       iread=index(rekord,aux)
1985 #else
1986       iread=index(rekord,lancuch(:ilen(lancuch))//"=")
1987 #endif
1988       if (iread.eq.0) return
1989       iread=iread+ilen(lancuch)+1
1990       read (rekord(iread:),*,end=10,err=10) (tablica(i),i=1,dim)
1991    10 return
1992       end
1993 c----------------------------------------------------------------------------
1994       subroutine openunits
1995       implicit real*8 (a-h,o-z)
1996       include 'DIMENSIONS'
1997 #ifdef MPI
1998       include 'mpif.h'
1999       character*16 form,nodename
2000       integer nodelen
2001 #endif
2002       include 'COMMON.SETUP'
2003       include 'COMMON.IOUNITS'
2004       include 'COMMON.MD'
2005       include 'COMMON.CONTROL'
2006       integer lenpre,lenpot,ilen,lentmp
2007       external ilen
2008       character*3 out1file_text,ucase
2009       character*3 ll
2010       external ucase
2011 c      print *,"Processor",myrank,"fg_rank",fg_rank," entered openunits"
2012       call getenv_loc("PREFIX",prefix)
2013       pref_orig = prefix
2014       call getenv_loc("POT",pot)
2015       call getenv_loc("DIRTMP",tmpdir)
2016       call getenv_loc("CURDIR",curdir)
2017       call getenv_loc("OUT1FILE",out1file_text)
2018 c      print *,"Processor",myrank,"fg_rank",fg_rank," did GETENV"
2019       out1file_text=ucase(out1file_text)
2020       if (out1file_text(1:1).eq."Y") then
2021         out1file=.true.
2022       else
2023         out1file=fg_rank.gt.0
2024       endif
2025       lenpre=ilen(prefix)
2026       lenpot=ilen(pot)
2027       lentmp=ilen(tmpdir)
2028       if (lentmp.gt.0) then
2029           write (*,'(80(1h!))')
2030           write (*,'(a,19x,a,19x,a)') "!","  A T T E N T I O N  ","!"
2031           write (*,'(80(1h!))')
2032           write (*,*)"All output files will be on node /tmp directory."
2033 #ifdef MPI
2034         call  MPI_GET_PROCESSOR_NAME( nodename, nodelen, IERROR )
2035         if (me.eq.king) then
2036           write (*,*) "The master node is ",nodename
2037         else if (fg_rank.eq.0) then
2038           write (*,*) "I am the CG slave node ",nodename
2039         else
2040           write (*,*) "I am the FG slave node ",nodename
2041         endif
2042 #endif
2043         PREFIX = tmpdir(:lentmp)//'/'//prefix(:lenpre)
2044         lenpre = lentmp+lenpre+1
2045       endif
2046       entname=prefix(:lenpre)//'_'//pot(:lenpot)//'.entr'
2047 C Get the names and open the input files
2048 #if defined(WINIFL) || defined(WINPGI)
2049       open(1,file=pref_orig(:ilen(pref_orig))//
2050      &  '.inp',status='old',readonly,shared)
2051        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2052 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2053 C Get parameter filenames and open the parameter files.
2054       call getenv_loc('BONDPAR',bondname)
2055       open (ibond,file=bondname,status='old',readonly,shared)
2056       call getenv_loc('THETPAR',thetname)
2057       open (ithep,file=thetname,status='old',readonly,shared)
2058 #ifndef CRYST_THETA
2059       call getenv_loc('THETPARPDB',thetname_pdb)
2060       open (ithep_pdb,file=thetname_pdb,status='old',readonly,shared)
2061 #endif
2062       call getenv_loc('ROTPAR',rotname)
2063       open (irotam,file=rotname,status='old',readonly,shared)
2064 #ifndef CRYST_SC
2065       call getenv_loc('ROTPARPDB',rotname_pdb)
2066       open (irotam_pdb,file=rotname_pdb,status='old',readonly,shared)
2067 #endif
2068       call getenv_loc('TORPAR',torname)
2069       open (itorp,file=torname,status='old',readonly,shared)
2070       call getenv_loc('TORDPAR',tordname)
2071       open (itordp,file=tordname,status='old',readonly,shared)
2072       call getenv_loc('FOURIER',fouriername)
2073       open (ifourier,file=fouriername,status='old',readonly,shared)
2074       call getenv_loc('ELEPAR',elename)
2075       open (ielep,file=elename,status='old',readonly,shared)
2076       call getenv_loc('SIDEPAR',sidename)
2077       open (isidep,file=sidename,status='old',readonly,shared)
2078 #elif (defined CRAY) || (defined AIX)
2079       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
2080      &  action='read')
2081 c      print *,"Processor",myrank," opened file 1"
2082       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2083 c      print *,"Processor",myrank," opened file 9"
2084 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2085 C Get parameter filenames and open the parameter files.
2086       call getenv_loc('BONDPAR',bondname)
2087       open (ibond,file=bondname,status='old',action='read')
2088 c      print *,"Processor",myrank," opened file IBOND"
2089       call getenv_loc('THETPAR',thetname)
2090       open (ithep,file=thetname,status='old',action='read')
2091 c      print *,"Processor",myrank," opened file ITHEP"
2092 #ifndef CRYST_THETA
2093       call getenv_loc('THETPARPDB',thetname_pdb)
2094       open (ithep_pdb,file=thetname_pdb,status='old',action='read')
2095 #endif
2096       call getenv_loc('ROTPAR',rotname)
2097       open (irotam,file=rotname,status='old',action='read')
2098 c      print *,"Processor",myrank," opened file IROTAM"
2099 #ifndef CRYST_SC
2100       call getenv_loc('ROTPARPDB',rotname_pdb)
2101       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
2102 #endif
2103       call getenv_loc('TORPAR',torname)
2104       open (itorp,file=torname,status='old',action='read')
2105 c      print *,"Processor",myrank," opened file ITORP"
2106       call getenv_loc('TORDPAR',tordname)
2107       open (itordp,file=tordname,status='old',action='read')
2108 c      print *,"Processor",myrank," opened file ITORDP"
2109       call getenv_loc('SCCORPAR',sccorname)
2110       open (isccor,file=sccorname,status='old',action='read')
2111 c      print *,"Processor",myrank," opened file ISCCOR"
2112       call getenv_loc('FOURIER',fouriername)
2113       open (ifourier,file=fouriername,status='old',action='read')
2114 c      print *,"Processor",myrank," opened file IFOURIER"
2115       call getenv_loc('ELEPAR',elename)
2116       open (ielep,file=elename,status='old',action='read')
2117 c      print *,"Processor",myrank," opened file IELEP"
2118       call getenv_loc('SIDEPAR',sidename)
2119       open (isidep,file=sidename,status='old',action='read')
2120 c      print *,"Processor",myrank," opened file ISIDEP"
2121 c      print *,"Processor",myrank," opened parameter files"
2122 #elif (defined G77)
2123       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old')
2124       open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2125 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2126 C Get parameter filenames and open the parameter files.
2127       call getenv_loc('BONDPAR',bondname)
2128       open (ibond,file=bondname,status='old')
2129       call getenv_loc('THETPAR',thetname)
2130       open (ithep,file=thetname,status='old')
2131 #ifndef CRYST_THETA
2132       call getenv_loc('THETPARPDB',thetname_pdb)
2133       open (ithep_pdb,file=thetname_pdb,status='old')
2134 #endif
2135       call getenv_loc('ROTPAR',rotname)
2136       open (irotam,file=rotname,status='old')
2137 #ifndef CRYST_SC
2138       call getenv_loc('ROTPARPDB',rotname_pdb)
2139       open (irotam_pdb,file=rotname_pdb,status='old')
2140 #endif
2141       call getenv_loc('TORPAR',torname)
2142       open (itorp,file=torname,status='old')
2143       call getenv_loc('TORDPAR',tordname)
2144       open (itordp,file=tordname,status='old')
2145       call getenv_loc('SCCORPAR',sccorname)
2146       open (isccor,file=sccorname,status='old')
2147       call getenv_loc('FOURIER',fouriername)
2148       open (ifourier,file=fouriername,status='old')
2149       call getenv_loc('ELEPAR',elename)
2150       open (ielep,file=elename,status='old')
2151       call getenv_loc('SIDEPAR',sidename)
2152       open (isidep,file=sidename,status='old')
2153 #else
2154       open(1,file=pref_orig(:ilen(pref_orig))//'.inp',status='old',
2155      &action='read')
2156        open (9,file=prefix(:ilen(prefix))//'.intin',status='unknown')
2157 C      open (18,file=prefix(:ilen(prefix))//'.entin',status='unknown')
2158 C Get parameter filenames and open the parameter files.
2159       call getenv_loc('BONDPAR',bondname)
2160       open (ibond,file=bondname,status='old',action='read')
2161       call getenv_loc('THETPAR',thetname)
2162       open (ithep,file=thetname,status='old',action='read')
2163 #ifndef CRYST_THETA
2164       call getenv_loc('THETPARPDB',thetname_pdb)
2165       print *,"thetname_pdb ",thetname_pdb
2166       open (ithep_pdb,file=thetname_pdb,status='old',action='read')
2167       print *,ithep_pdb," opened"
2168 #endif
2169       call getenv_loc('ROTPAR',rotname)
2170       open (irotam,file=rotname,status='old',action='read')
2171 #ifndef CRYST_SC
2172       call getenv_loc('ROTPARPDB',rotname_pdb)
2173       open (irotam_pdb,file=rotname_pdb,status='old',action='read')
2174 #endif
2175       call getenv_loc('TORPAR',torname)
2176       open (itorp,file=torname,status='old',action='read')
2177       call getenv_loc('TORDPAR',tordname)
2178       open (itordp,file=tordname,status='old',action='read')
2179       call getenv_loc('SCCORPAR',sccorname)
2180       open (isccor,file=sccorname,status='old',action='read')
2181       call getenv_loc('FOURIER',fouriername)
2182       open (ifourier,file=fouriername,status='old',action='read')
2183       call getenv_loc('ELEPAR',elename)
2184       open (ielep,file=elename,status='old',action='read')
2185       call getenv_loc('SIDEPAR',sidename)
2186       open (isidep,file=sidename,status='old',action='read')
2187 #endif
2188 #ifndef OLDSCP
2189 C
2190 C 8/9/01 In the newest version SCp interaction constants are read from a file
2191 C Use -DOLDSCP to use hard-coded constants instead.
2192 C
2193       call getenv_loc('SCPPAR',scpname)
2194 #if defined(WINIFL) || defined(WINPGI)
2195       open (iscpp,file=scpname,status='old',readonly,shared)
2196 #elif (defined CRAY)  || (defined AIX)
2197       open (iscpp,file=scpname,status='old',action='read')
2198 #elif (defined G77)
2199       open (iscpp,file=scpname,status='old')
2200 #else
2201       open (iscpp,file=scpname,status='old',action='read')
2202 #endif
2203 #endif
2204       call getenv_loc('PATTERN',patname)
2205 #if defined(WINIFL) || defined(WINPGI)
2206       open (icbase,file=patname,status='old',readonly,shared)
2207 #elif (defined CRAY)  || (defined AIX)
2208       open (icbase,file=patname,status='old',action='read')
2209 #elif (defined G77)
2210       open (icbase,file=patname,status='old')
2211 #else
2212       open (icbase,file=patname,status='old',action='read')
2213 #endif
2214 #ifdef MPI
2215 C Open output file only for CG processes
2216 c      print *,"Processor",myrank," fg_rank",fg_rank
2217       if (fg_rank.eq.0) then
2218
2219       if (nodes.eq.1) then
2220         npos=3
2221       else
2222         npos = dlog10(dfloat(nodes-1))+1
2223       endif
2224       if (npos.lt.3) npos=3
2225       write (liczba,'(i1)') npos
2226       form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
2227      &  //')'
2228       write (liczba,form) me
2229       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)//
2230      &  liczba(:ilen(liczba))
2231       intname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2232      &  //'.int'
2233       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//liczba(:ilen(liczba))
2234      &  //'.pdb'
2235       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//
2236      &  liczba(:ilen(liczba))//'.mol2'
2237       statname=prefix(:lenpre)//'_'//pot(:lenpot)//
2238      &  liczba(:ilen(liczba))//'.stat'
2239       if (lentmp.gt.0)
2240      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2241      &      //liczba(:ilen(liczba))//'.stat')
2242       rest2name=prefix(:ilen(prefix))//"_"//liczba(:ilen(liczba))
2243      &  //'.rst'
2244       if(usampl) then
2245           qname=prefix(:lenpre)//'_'//pot(:lenpot)//
2246      & liczba(:ilen(liczba))//'.const'
2247       endif
2248
2249       endif
2250 #else
2251       outname=prefix(:lenpre)//'.out_'//pot(:lenpot)
2252       intname=prefix(:lenpre)//'_'//pot(:lenpot)//'.int'
2253       pdbname=prefix(:lenpre)//'_'//pot(:lenpot)//'.pdb'
2254       mol2name=prefix(:lenpre)//'_'//pot(:lenpot)//'.mol2'
2255       statname=prefix(:lenpre)//'_'//pot(:lenpot)//'.stat'
2256       if (lentmp.gt.0)
2257      &  call copy_to_tmp(pref_orig(:ilen(pref_orig))//'_'//pot(:lenpot)
2258      &    //'.stat')
2259       rest2name=prefix(:ilen(prefix))//'.rst'
2260       if(usampl) then
2261          qname=prefix(:lenpre)//'_'//pot(:lenpot)//'.const'
2262       endif
2263 #endif
2264 #if defined(AIX) || defined(PGI)
2265       if (me.eq.king .or. .not. out1file)
2266      &   open(iout,file=outname,status='unknown')
2267 c#define DEBUG
2268 #ifdef DEBUG
2269       if (fg_rank.gt.0) then
2270         write (liczba,'(i3.3)') myrank/nfgtasks
2271         write (ll,'(bz,i3.3)') fg_rank
2272         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2273      &   status='unknown')
2274       endif
2275 #endif
2276 c#undef DEBUG
2277       if(me.eq.king) then
2278        open(igeom,file=intname,status='unknown',position='append')
2279        open(ipdb,file=pdbname,status='unknown')
2280        open(imol2,file=mol2name,status='unknown')
2281        open(istat,file=statname,status='unknown',position='append')
2282       else
2283 c1out       open(iout,file=outname,status='unknown')
2284       endif
2285 #else
2286       if (me.eq.king .or. .not.out1file)
2287      &    open(iout,file=outname,status='unknown')
2288 c#define DEBUG
2289 #ifdef DEBUG
2290       if (fg_rank.gt.0) then
2291         print "Processor",fg_rank," opening output file"
2292         write (liczba,'(i3.3)') myrank/nfgtasks
2293         write (ll,'(bz,i3.3)') fg_rank
2294         open(iout,file="debug"//liczba(:ilen(liczba))//"."//ll,
2295      &   status='unknown')
2296       endif
2297 #endif
2298 c#undef DEBUG
2299       if(me.eq.king) then
2300        open(igeom,file=intname,status='unknown',access='append')
2301        open(ipdb,file=pdbname,status='unknown')
2302        open(imol2,file=mol2name,status='unknown')
2303        open(istat,file=statname,status='unknown',access='append')
2304       else
2305 c1out       open(iout,file=outname,status='unknown')
2306       endif
2307 #endif
2308 csa      csa_rbank=prefix(:lenpre)//'.CSA.rbank'
2309 csa      csa_seed=prefix(:lenpre)//'.CSA.seed'
2310 csa      csa_history=prefix(:lenpre)//'.CSA.history'
2311 csa      csa_bank=prefix(:lenpre)//'.CSA.bank'
2312 csa      csa_bank1=prefix(:lenpre)//'.CSA.bank1'
2313 csa      csa_alpha=prefix(:lenpre)//'.CSA.alpha'
2314 csa      csa_alpha1=prefix(:lenpre)//'.CSA.alpha1'
2315 csac!bankt      csa_bankt=prefix(:lenpre)//'.CSA.bankt'
2316 csa      csa_int=prefix(:lenpre)//'.int'
2317 csa      csa_bank_reminimized=prefix(:lenpre)//'.CSA.bank_reminimized'
2318 csa      csa_native_int=prefix(:lenpre)//'.CSA.native.int'
2319 csa      csa_in=prefix(:lenpre)//'.CSA.in'
2320 c      print *,"Processor",myrank,"fg_rank",fg_rank," opened files"
2321 C Write file names
2322       if (me.eq.king)then
2323       write (iout,'(80(1h-))')
2324       write (iout,'(30x,a)') "FILE ASSIGNMENT"
2325       write (iout,'(80(1h-))')
2326       write (iout,*) "Input file                      : ",
2327      &  pref_orig(:ilen(pref_orig))//'.inp'
2328       write (iout,*) "Output file                     : ",
2329      &  outname(:ilen(outname))
2330       write (iout,*)
2331       write (iout,*) "Sidechain potential file        : ",
2332      &  sidename(:ilen(sidename))
2333 #ifndef OLDSCP
2334       write (iout,*) "SCp potential file              : ",
2335      &  scpname(:ilen(scpname))
2336 #endif
2337       write (iout,*) "Electrostatic potential file    : ",
2338      &  elename(:ilen(elename))
2339       write (iout,*) "Cumulant coefficient file       : ",
2340      &  fouriername(:ilen(fouriername))
2341       write (iout,*) "Torsional parameter file        : ",
2342      &  torname(:ilen(torname))
2343       write (iout,*) "Double torsional parameter file : ",
2344      &  tordname(:ilen(tordname))
2345       write (iout,*) "SCCOR parameter file : ",
2346      &  sccorname(:ilen(sccorname))
2347       write (iout,*) "Bond & inertia constant file    : ",
2348      &  bondname(:ilen(bondname))
2349       write (iout,*) "Bending parameter file          : ",
2350      &  thetname(:ilen(thetname))
2351       write (iout,*) "Rotamer parameter file          : ",
2352      &  rotname(:ilen(rotname))
2353       write (iout,*) "Threading database              : ",
2354      &  patname(:ilen(patname))
2355       if (lentmp.ne.0)
2356      &write (iout,*)" DIRTMP                          : ",
2357      &  tmpdir(:lentmp)
2358       write (iout,'(80(1h-))')
2359       endif
2360       return
2361       end
2362 c----------------------------------------------------------------------------
2363       subroutine card_concat(card)
2364       implicit real*8 (a-h,o-z)
2365       include 'DIMENSIONS'
2366       include 'COMMON.IOUNITS'
2367       character*(*) card
2368       character*80 karta,ucase
2369       external ilen
2370       read (inp,'(a)') karta
2371       karta=ucase(karta)
2372       card=' '
2373       do while (karta(80:80).eq.'&')
2374         card=card(:ilen(card)+1)//karta(:79)
2375         read (inp,'(a)') karta
2376         karta=ucase(karta)
2377       enddo
2378       card=card(:ilen(card)+1)//karta
2379       return
2380       end
2381 c----------------------------------------------------------------------------------
2382       subroutine readrst
2383       implicit real*8 (a-h,o-z)
2384       include 'DIMENSIONS'
2385       include 'COMMON.CHAIN'
2386       include 'COMMON.IOUNITS'
2387       include 'COMMON.MD'
2388       open(irest2,file=rest2name,status='unknown')
2389       read(irest2,*) totT,EK,potE,totE,t_bath
2390       do i=1,2*nres
2391          read(irest2,'(3e15.5)') (d_t(j,i),j=1,3)
2392       enddo
2393       do i=1,2*nres
2394          read(irest2,'(3e15.5)') (dc(j,i),j=1,3)
2395       enddo
2396       if(usampl) then
2397              read (irest2,*) iset
2398       endif
2399       close(irest2)
2400       return
2401       end
2402 c---------------------------------------------------------------------------------
2403       subroutine read_fragments
2404       implicit real*8 (a-h,o-z)
2405       include 'DIMENSIONS'
2406 #ifdef MPI
2407       include 'mpif.h'
2408 #endif
2409       include 'COMMON.SETUP'
2410       include 'COMMON.CHAIN'
2411       include 'COMMON.IOUNITS'
2412       include 'COMMON.MD'
2413       include 'COMMON.CONTROL'
2414       read(inp,*) nset,nfrag,npair,nfrag_back
2415       if(me.eq.king.or..not.out1file)
2416      & write(iout,*) "nset",nset," nfrag",nfrag," npair",npair,
2417      &  " nfrag_back",nfrag_back
2418       do iset=1,nset
2419          read(inp,*) mset(iset)
2420        do i=1,nfrag
2421          read(inp,*) wfrag(i,iset),ifrag(1,i,iset),ifrag(2,i,iset),
2422      &     qinfrag(i,iset)
2423          if(me.eq.king.or..not.out1file)
2424      &    write(iout,*) "R ",i,wfrag(i,iset),ifrag(1,i,iset),
2425      &     ifrag(2,i,iset), qinfrag(i,iset)
2426        enddo
2427        do i=1,npair
2428         read(inp,*) wpair(i,iset),ipair(1,i,iset),ipair(2,i,iset),
2429      &    qinpair(i,iset)
2430         if(me.eq.king.or..not.out1file)
2431      &   write(iout,*) "R ",i,wpair(i,iset),ipair(1,i,iset),
2432      &    ipair(2,i,iset), qinpair(i,iset)
2433        enddo
2434        do i=1,nfrag_back
2435         read(inp,*) wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2436      &     wfrag_back(3,i,iset),
2437      &     ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2438         if(me.eq.king.or..not.out1file)
2439      &   write(iout,*) "A",i,wfrag_back(1,i,iset),wfrag_back(2,i,iset),
2440      &   wfrag_back(3,i,iset),ifrag_back(1,i,iset),ifrag_back(2,i,iset)
2441        enddo
2442       enddo
2443       return
2444       end
2445 c-------------------------------------------------------------------------------
2446       subroutine read_dist_constr
2447       implicit real*8 (a-h,o-z)
2448       include 'DIMENSIONS'
2449 #ifdef MPI
2450       include 'mpif.h'
2451 #endif
2452       include 'COMMON.SETUP'
2453       include 'COMMON.CONTROL'
2454       include 'COMMON.CHAIN'
2455       include 'COMMON.IOUNITS'
2456       include 'COMMON.SBRIDGE'
2457       integer ifrag_(2,100),ipair_(2,100)
2458       double precision wfrag_(100),wpair_(100)
2459       character*500 controlcard
2460 c      write (iout,*) "Calling read_dist_constr"
2461 c      write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup
2462 c      call flush(iout)
2463       call card_concat(controlcard)
2464       call readi(controlcard,"NFRAG",nfrag_,0)
2465       call readi(controlcard,"NPAIR",npair_,0)
2466       call readi(controlcard,"NDIST",ndist_,0)
2467       call reada(controlcard,'DIST_CUT',dist_cut,5.0d0)
2468       call multreadi(controlcard,"IFRAG",ifrag_(1,1),2*nfrag_,0)
2469       call multreadi(controlcard,"IPAIR",ipair_(1,1),2*npair_,0)
2470       call multreada(controlcard,"WFRAG",wfrag_(1),nfrag_,0.0d0)
2471       call multreada(controlcard,"WPAIR",wpair_(1),npair_,0.0d0)
2472 c      write (iout,*) "NFRAG",nfrag_," NPAIR",npair_," NDIST",ndist_
2473 c      write (iout,*) "IFRAG"
2474 c      do i=1,nfrag_
2475 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2476 c      enddo
2477 c      write (iout,*) "IPAIR"
2478 c      do i=1,npair_
2479 c        write (iout,*) i,ipair_(1,i),ipair_(2,i),wpair_(i)
2480 c      enddo
2481       if (.not.refstr .and. nfrag.gt.0) then
2482         write (iout,*)
2483      &  "ERROR: no reference structure to compute distance restraints"
2484         write (iout,*)
2485      &  "Restraints must be specified explicitly (NDIST=number)"
2486         stop
2487       endif
2488       if (nfrag.lt.2 .and. npair.gt.0) then
2489         write (iout,*) "ERROR: Less than 2 fragments specified",
2490      &   " but distance restraints between pairs requested"
2491         stop
2492       endif
2493       call flush(iout)
2494       do i=1,nfrag_
2495         if (ifrag_(1,i).lt.nstart_sup) ifrag_(1,i)=nstart_sup
2496         if (ifrag_(2,i).gt.nstart_sup+nsup-1)
2497      &    ifrag_(2,i)=nstart_sup+nsup-1
2498 c        write (iout,*) i,ifrag_(1,i),ifrag_(2,i),wfrag_(i)
2499         call flush(iout)
2500         if (wfrag_(i).gt.0.0d0) then
2501         do j=ifrag_(1,i),ifrag_(2,i)-1
2502           do k=j+1,ifrag_(2,i)
2503 c            write (iout,*) "j",j," k",k
2504             ddjk=dist(j,k)
2505             if (constr_dist.eq.1) then
2506             nhpb=nhpb+1
2507             ihpb(nhpb)=j
2508             jhpb(nhpb)=k
2509               dhpb(nhpb)=ddjk
2510             forcon(nhpb)=wfrag_(i)
2511             else if (constr_dist.eq.2) then
2512               if (ddjk.le.dist_cut) then
2513                 nhpb=nhpb+1
2514                 ihpb(nhpb)=j
2515                 jhpb(nhpb)=k
2516                 dhpb(nhpb)=ddjk
2517                 forcon(nhpb)=wfrag_(i)
2518               endif
2519             else
2520               nhpb=nhpb+1
2521               ihpb(nhpb)=j
2522               jhpb(nhpb)=k
2523               dhpb(nhpb)=ddjk
2524               forcon(nhpb)=wfrag_(i)*dexp(-0.5d0*(ddjk/dist_cut)**2)
2525             endif
2526 #ifdef MPI
2527             if (.not.out1file .or. me.eq.king)
2528      &      write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2529      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2530 #else
2531             write (iout,'(a,3i5,f8.2,1pe12.2)') "+dist.constr ",
2532      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2533 #endif
2534           enddo
2535         enddo
2536         endif
2537       enddo
2538       do i=1,npair_
2539         if (wpair_(i).gt.0.0d0) then
2540         ii = ipair_(1,i)
2541         jj = ipair_(2,i)
2542         if (ii.gt.jj) then
2543           itemp=ii
2544           ii=jj
2545           jj=itemp
2546         endif
2547         do j=ifrag_(1,ii),ifrag_(2,ii)
2548           do k=ifrag_(1,jj),ifrag_(2,jj)
2549             nhpb=nhpb+1
2550             ihpb(nhpb)=j
2551             jhpb(nhpb)=k
2552             forcon(nhpb)=wpair_(i)
2553             dhpb(nhpb)=dist(j,k)
2554 #ifdef MPI
2555             if (.not.out1file .or. me.eq.king)
2556      &      write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2557      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2558 #else
2559             write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
2560      &       nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
2561 #endif
2562           enddo
2563         enddo
2564         endif
2565       enddo
2566       do i=1,ndist_
2567         read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
2568      &     ibecarb(i),forcon(nhpb+1)
2569         if (forcon(nhpb+1).gt.0.0d0) then
2570           nhpb=nhpb+1
2571           if (ibecarb(i).gt.0) then
2572             ihpb(i)=ihpb(i)+nres
2573             jhpb(i)=jhpb(i)+nres
2574           endif
2575           if (dhpb(nhpb).eq.0.0d0)
2576      &       dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
2577         endif
2578       enddo
2579 #ifdef MPI
2580       if (.not.out1file .or. me.eq.king) then
2581 #endif
2582       do i=1,nhpb
2583           write (iout,'(a,3i5,2f8.2,i2,f10.1)') "+dist.constr ",
2584      &     i,ihpb(i),jhpb(i),dhpb(i),dhpb1(i),ibecarb(i),forcon(i)
2585       enddo
2586       call flush(iout)
2587 #ifdef MPI
2588       endif
2589 #endif
2590       return
2591       end
2592 c-------------------------------------------------------------------------------
2593 #ifdef WINIFL
2594       subroutine flush(iu)
2595       return
2596       end
2597 #endif
2598 #ifdef AIX
2599       subroutine flush(iu)
2600       call flush_(iu)
2601       return
2602       end
2603 #endif
2604 c------------------------------------------------------------------------------
2605       subroutine copy_to_tmp(source)
2606       include "DIMENSIONS"
2607       include "COMMON.IOUNITS"
2608       character*(*) source
2609       character* 256 tmpfile
2610       integer ilen
2611       external ilen
2612       logical ex
2613       tmpfile=curdir(:ilen(curdir))//"/"//source(:ilen(source))
2614       inquire(file=tmpfile,exist=ex)
2615       if (ex) then
2616         write (*,*) "Copying ",tmpfile(:ilen(tmpfile)),
2617      &   " to temporary directory..."
2618         write (*,*) "/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir
2619         call system("/bin/cp "//tmpfile(:ilen(tmpfile))//" "//tmpdir)
2620       endif
2621       return
2622       end
2623 c------------------------------------------------------------------------------
2624       subroutine move_from_tmp(source)
2625       include "DIMENSIONS"
2626       include "COMMON.IOUNITS"
2627       character*(*) source
2628       character* 256 tmpfile
2629       integer ilen
2630       external ilen
2631       tmpfile=source(:ilen(source))
2632       write (*,*) "Moving ",source(:ilen(source)),
2633      & " from temporary directory to working directory"
2634       write (*,*) "/bin/mv "//tmpfile//" "//curdir
2635       call system("/bin/mv "//tmpfile//" "//curdir)
2636       return
2637       end
2638 c------------------------------------------------------------------------------
2639       subroutine random_init(seed)
2640 C
2641 C Initialize random number generator
2642 C
2643       implicit real*8 (a-h,o-z)
2644       include 'DIMENSIONS'
2645 #ifdef AMD64
2646       integer*8 iseedi8
2647 #endif
2648 #ifdef MPI
2649       include 'mpif.h'
2650       logical OKRandom, prng_restart
2651       real*8  r1
2652       integer iseed_array(4)
2653 #endif
2654       include 'COMMON.IOUNITS'
2655       include 'COMMON.TIME1'
2656       include 'COMMON.THREAD'
2657       include 'COMMON.SBRIDGE'
2658       include 'COMMON.CONTROL'
2659       include 'COMMON.MCM'
2660       include 'COMMON.MAP'
2661       include 'COMMON.HEADER'
2662 csa      include 'COMMON.CSA'
2663       include 'COMMON.CHAIN'
2664       include 'COMMON.MUCA'
2665       include 'COMMON.MD'
2666       include 'COMMON.FFIELD'
2667       include 'COMMON.SETUP'
2668       iseed=-dint(dabs(seed))
2669       if (iseed.eq.0) then
2670         write (iout,'(/80(1h*)/20x,a/80(1h*))')
2671      &    'Random seed undefined. The program will stop.'
2672         write (*,'(/80(1h*)/20x,a/80(1h*))')
2673      &    'Random seed undefined. The program will stop.'
2674 #ifdef MPI
2675         call mpi_finalize(mpi_comm_world,ierr)
2676 #endif
2677         stop 'Bad random seed.'
2678       endif
2679 #ifdef MPI
2680       if (fg_rank.eq.0) then
2681       seed=seed*(me+1)+1
2682 #ifdef AMD64
2683       iseedi8=dint(seed)
2684       if(me.eq.king .or. .not. out1file)
2685      &  write (iout,*) 'MPI: node= ', me, ' iseed= ',iseedi8
2686       write (*,*) 'MPI: node= ', me, ' iseed= ',iseedi8
2687       OKRandom = prng_restart(me,iseedi8)
2688 #else
2689       do i=1,4
2690        tmp=65536.0d0**(4-i)
2691        iseed_array(i) = dint(seed/tmp)
2692        seed=seed-iseed_array(i)*tmp
2693       enddo
2694       if(me.eq.king .or. .not. out1file)
2695      & write (iout,*) 'MPI: node= ', me, ' iseed(4)= ',
2696      &                 (iseed_array(i),i=1,4)
2697       write (*,*) 'MPI: node= ',me, ' iseed(4)= ',
2698      &                 (iseed_array(i),i=1,4)
2699       OKRandom = prng_restart(me,iseed_array)
2700 #endif
2701       if (OKRandom) then
2702         r1=ran_number(0.0D0,1.0D0)
2703         if(me.eq.king .or. .not. out1file)
2704      &   write (iout,*) 'ran_num',r1
2705         if (r1.lt.0.0d0) OKRandom=.false.
2706       endif
2707       if (.not.OKRandom) then
2708         write (iout,*) 'PRNG IS NOT WORKING!!!'
2709         print *,'PRNG IS NOT WORKING!!!'
2710         if (me.eq.0) then
2711          call flush(iout)
2712          call mpi_abort(mpi_comm_world,error_msg,ierr)
2713          stop
2714         else
2715          write (iout,*) 'too many processors for parallel prng'
2716          write (*,*) 'too many processors for parallel prng'
2717          call flush(iout)
2718          stop
2719         endif
2720       endif
2721       endif
2722 #else
2723       call vrndst(iseed)
2724       write (iout,*) 'ran_num',ran_number(0.0d0,1.0d0)
2725 #endif
2726       return
2727       end