source/unres/REMD.f90

   1       module REMD
   2 !-----------------------------------------------------------------------------
   3       use io_units
   4       use MD_data
   5       use REMD_data
   6       use muca_md
   7
   8       implicit none
   9 !-----------------------------------------------------------------------------
  10 !
  11 !
  12 !-----------------------------------------------------------------------------
  13       contains
  14 !-----------------------------------------------------------------------------
  15 ! lagrangian_lesyng.F
  16 !-----------------------------------------------------------------------------
  17       subroutine lagrangian
  18 !-------------------------------------------------------------------------
  19 !  This subroutine contains the total lagrangain from which the accelerations
  20 !  are obtained.  For numerical gradient checking, the derivetive of the
  21 !  lagrangian in the velocities and coordinates are calculated seperately
  22 !-------------------------------------------------------------------------
  23 !       implicit real*8 (a-h,o-z)
  24 !       include 'DIMENSIONS'
  25       use comm_cipiszcze
  26       use energy_data
  27       use geometry_data, only: nres
  28       use control_data    !el, only: mucadyn,lmuca
  29 #ifdef MPI
  30        include 'mpif.h'
  31       real(kind=8) :: time00
  32 #endif
  33 !       include 'COMMON.VAR'
  34 !       include 'COMMON.CHAIN'
  35 !       include 'COMMON.DERIV'
  36 !       include 'COMMON.GEO'
  37 !       include 'COMMON.LOCAL'
  38 !       include 'COMMON.INTERACT'
  39 !       include 'COMMON.MD'
  40 !       include 'COMMON.IOUNITS'
  41 !       include 'COMMON.CONTROL'
  42 !       include 'COMMON.MUCA'
  43 !      include 'COMMON.TIME1'
  44        integer ::i,j,ind,itime,mnum
  45        real(kind=8) :: zapas(6*nres) !,muca_factor      !maxres6=6*maxres
  46        real(kind=8) :: rs(dimen),xsolv(dimen)
  47 #ifdef CHECK5DSOL
  48        real(kind=8) :: rscheck(dimen),rsold(dimen)
  49 #endif
  50        logical :: lprn = .false.
  51 !el       common /cipiszcze/ itime
  52        itime = itt_comm
  53
  54 #ifdef TIMING
  55        time00=MPI_Wtime()
  56 #endif
  57 #ifdef FIVEDIAG
  58       if (lprn) then
  59         write (iout,*) "Potential forces backbone"
  60         do i=nnt,nct
  61           write (iout,'(i5,3e15.5,5x,3e15.5)')i,(-gcart(j,i),j=1,3)
  62         enddo
  63         write (iout,*) "Potential forces sidechain"
  64         do i=nnt,nct
  65           mnum=molnum(i)
  66           if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1.and.mnum.eq.5)&
  67             write (iout,'(i5,3e15.5,5x,3e15.5)') i,(-gxcart(j,i),j=1,3)
  68         enddo
  69       endif
  70        do j=1,3
  71          ind=1
  72          do i=nnt,nct
  73            mnum=molnum(i)
  74            if (itype(i,1).eq.10 .or. itype(i,1).eq.ntyp1 .or. mnum.eq.5)then
  75             rs(ind)=-gcart(j,i)-gxcart(j,i)
  76             ind=ind+1
  77            else
  78             rs(ind)=-gcart(j,i)
  79             rs(ind+1)=-gxcart(j,i)
  80             ind=ind+2
  81            end if
  82          enddo
  83 #ifdef CHECK5DSOL
  84          rsold=rs
  85 #endif
  86          if (lprn) then
  87            write(iout,*) "RHS of the 5-diag equations system"
  88            do i=1,dimen
  89              write(iout,*) i,rs(i)
  90            enddo
  91          endif
  92
  93          call FDISYS (dimen,DM,DU1,DU2,rs,xsolv)
  94          if (lprn) then
  95            write (iout,*) "Solution of the 5-diagonal equations system"
  96            do i=1,dimen
  97              write (iout,'(i5,f10.5)') i,xsolv(i)
  98            enddo
  99          endif
 100 #ifdef CHECK5DSOL
 101 ! Check the solution
 102          rscheck(1)=DMorig(1)*xsolv(1)+DU1orig(1)*xsolv(2)+&
 103            DU2orig(1)*xsolv(3)
 104          rscheck(2)=DU1orig(1)*xsolv(1)+DMorig(2)*xsolv(2)+&
 105            DU1orig(2)*xsolv(3)+DU2orig(2)*xsolv(4)
 106
 107          do i=3,dimen-2
 108           rscheck(i)=DU2orig(i-2)*xsolv(i-2)+DU1orig(i-1)*&
 109             xsolv(i-1)+DMorig(i)*xsolv(i)+DU1orig(i)*&
 110              xsolv(i+1)+DU2orig(i)*xsolv(i+2)
 111          enddo
 112        rscheck(dimen-1)=DU2orig(dimen-3)*xsolv(dimen-3)+&
 113          DU1orig(dimen-2)*xsolv(dimen-2)+DMorig(dimen-1)*&
 114           xsolv(dimen-1)+DU1orig(dimen-1)*&
 115            xsolv(dimen)
 116        rscheck(dimen)=DU2orig(dimen-2)*xsolv(dimen-2)+DU1orig(dimen-1)*&
 117           xsolv(dimen-1)+DMorig(dimen)*xsolv(dimen)
 118
 119          do i=1,dimen
 120             write(iout,*) "i",i,"rsold",rsold(i),"rscheck",rscheck(i),&
 121             "ratio",rscheck(i)/rsold(i)
 122            enddo
 123 ! end check
 124 #endif
 125          ind=1
 126          do i=nnt,nct
 127           mnum=molnum(i)
 128           if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum))then
 129            d_a(j,i)=xsolv(ind)
 130            ind=ind+1
 131           else
 132            d_a(j,i)=xsolv(ind)
 133            d_a(j,i+nres)=xsolv(ind+1)
 134           ind=ind+2
 135           end if
 136          enddo
 137        enddo
 138        if (lprn) then
 139        do i=nnt,nct
 140         write (iout,'(i3,3f10.5)') i,(d_a(j,i),j=1,3)
 141        enddo
 142        do i=nnt,nct
 143         write (iout,'(i3,3f10.5)') i,(d_a(j,i+nres),j=1,3)
 144        enddo
 145        endif
 146        do j=1,3
 147          d_a(j,0)=d_a(j,nnt)
 148        enddo
 149        do i=nnt,nct
 150           mnum=molnum(i)
 151 !         if (itype(i,1).eq.10 .or. itype(i,1).eq.ntyp1) then
 152           if (itype(i,1).eq.10 .or. itype(i,mnum).eq.ntyp1_molec(mnum))then
 153            do j=1,3
 154              d_a(j,i)=d_a(j,i+1)-d_a(j,i)
 155            enddo
 156          else
 157            do j=1,3
 158              d_a(j,i+nres)=d_a(j,i+nres)-d_a(j,i)
 159              d_a(j,i)=d_a(j,i+1)-d_a(j,i)
 160            enddo
 161
 162
 163          end if
 164        enddo
 165
 166       if (lprn) then
 167         write(iout,*) 'acceleration 3D FIVEDIAG'
 168         write (iout,'(i3,3f10.5,3x,3f10.5)') 0,(d_a(j,0),j=1,3)
 169         do i=nnt,nct-1
 170          write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3)
 171         enddo
 172         do i=nnt,nct
 173          write (iout,'(i3,3f10.5,3x,3f10.5)') &
 174            i+nres,(d_a(j,i+nres),j=1,3)
 175         enddo
 176       endif
 177 #else
 178 ! Old procedure
 179        do j=1,3
 180          zapas(j)=-gcart(j,0)
 181        enddo
 182       ind=3
 183       if (lprn) then
 184         write (iout,*) "Potential forces backbone"
 185       endif
 186       do i=nnt,nct-1
 187         if (lprn) write (iout,'(i5,3e15.5,5x,3e15.5)') &
 188           i,(-gcart(j,i),j=1,3)
 189         do j=1,3
 190           ind=ind+1
 191           zapas(ind)=-gcart(j,i)
 192         enddo
 193       enddo
 194       if (lprn) write (iout,*) "Potential forces sidechain"
 195       do i=nnt,nct
 196           mnum=molnum(i)
 197         if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
 198           .and.mnum.ne.5) then
 199           if (lprn) write (iout,'(i5,3e15.5,5x,3e15.5)') &
 200              i,(-gxcart(j,i),j=1,3)
 201           do j=1,3
 202             ind=ind+1
 203             zapas(ind)=-gxcart(j,i)
 204           enddo
 205         endif
 206       enddo
 207
 208       call ginv_mult(zapas,d_a_work)
 209
 210       do j=1,3
 211         d_a(j,0)=d_a_work(j)
 212       enddo
 213       ind=3
 214       do i=nnt,nct-1
 215         do j=1,3
 216           ind=ind+1
 217           d_a(j,i)=d_a_work(ind)
 218         enddo
 219       enddo
 220       do i=nnt,nct
 221        mnum=molnum(i)
 222 !        if (itype(i,1).ne.10 .and. itype(i,1).ne.ntyp1) then
 223          if (itype(i,1).ne.10 .and. itype(i,mnum).ne.ntyp1_molec(mnum)&
 224           .and.mnum.ne.5) then
 225           do j=1,3
 226             ind=ind+1
 227             d_a(j,i+nres)=d_a_work(ind)
 228           enddo
 229         endif
 230       enddo
 231
 232 #endif
 233       if(lmuca) then
 234        imtime=imtime+1
 235        if(mucadyn.gt.0) call muca_update(potE)
 236        factor=muca_factor(potE)*t_bath*Rb
 237
 238 !d       print *,'lmuca ',factor,potE
 239        do j=1,3
 240           d_a(j,0)=d_a(j,0)*factor
 241        enddo
 242        do i=nnt,nct-1
 243          do j=1,3
 244           d_a(j,i)=d_a(j,i)*factor
 245          enddo
 246        enddo
 247        do i=nnt,nct
 248          do j=1,3
 249           d_a(j,i+nres)=d_a(j,i+nres)*factor
 250          enddo
 251        enddo
 252
 253       endif
 254
 255       if (lprn) then
 256         write(iout,*) 'acceleration 3D'
 257         write (iout,'(i3,3f10.5,3x,3f10.5)') 0,(d_a(j,0),j=1,3)
 258         do i=nnt,nct-1
 259          write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3)
 260         enddo
 261         do i=nnt,nct
 262          write (iout,'(i3,3f10.5,3x,3f10.5)') &
 263            i+nres,(d_a(j,i+nres),j=1,3)
 264         enddo
 265       endif
 266 #ifdef TIMING
 267       time_lagrangian=time_lagrangian+MPI_Wtime()-time00
 268 #endif
 269       return
 270       end subroutine lagrangian
 271 !-----------------------------------------------------------------------------
 272       subroutine setup_MD_matrices
 273
 274       use geometry_data, only: nres,nside
 275       use control_data
 276       use MPI_data
 277       use energy_data
 278       use geometry, only:int_bounds
 279       use md_calc
 280 !      implicit real*8 (a-h,o-z)
 281 !      include 'DIMENSIONS'
 282 #ifdef MPI
 283       include 'mpif.h'
 284       integer :: ierror
 285       real(kind=8) :: time00
 286       real(kind=8) ,allocatable, dimension(:)  :: DDM,DDU1,DDU2
 287 #endif
 288 !      include 'COMMON.SETUP'
 289 !      include 'COMMON.VAR'
 290 !      include 'COMMON.CHAIN'
 291 !      include 'COMMON.DERIV'
 292 !      include 'COMMON.GEO'
 293 !      include 'COMMON.LOCAL'
 294 !      include 'COMMON.INTERACT'
 295 !      include 'COMMON.MD'
 296 !#ifndef LANG0
 297 !      include 'COMMON.LANGEVIN'
 298 !#else
 299 !      include 'COMMON.LANGEVIN.lang0'
 300 !#endif
 301 !      include 'COMMON.IOUNITS'
 302 !      include 'COMMON.TIME1'
 303       logical :: lprn = .false.
 304       logical :: osob
 305 #ifndef FIVEDIAG
 306       real(kind=8),allocatable,dimension(:,:) :: Bmat,matmult
 307 #endif
 308       real(kind=8) :: dtdi
 309       real(kind=8),dimension(2*nres) :: massvec,sqreig  !(maxres2) maxres2=2*maxres
 310       real(kind=8) :: relfeh,eps1,eps2
 311 !el      real(kind=8),dimension(:),allocatable :: Ghalf
 312 !el      real(kind=8),dimension(2*nres*(2*nres+1)/2) :: Ghalf   !(mmaxres2) (mmaxres2=(maxres2*(maxres2+1)/2))
 313 !el      real(kind=8),dimension(2*nres,2*nres) :: Gcopy !(maxres2,maxres2)
 314 !el      real(kind=8),dimension(:,:),allocatable :: Gcopy
 315       real(kind=8),dimension(8*6*nres) :: work  !(8*maxres6)
 316       integer,dimension(6*nres) :: iwork        !(maxres6) maxres6=6*maxres
 317 !el      common /przechowalnia/ Gcopy,Ghalf
 318       real(kind=8) :: coeff,mscab
 319       integer :: i,j,ind,ind1,k,l,ii,jj,m,m1,ii1,iti,nres2,ierr,nind,mark
 320       real(kind=8) :: ip4
 321       integer :: iz,mnum
 322       print *,"just entered"
 323       relfeh=1.0d-14
 324       nres2=2*nres
 325       print *,"FIVEDIAG"
 326       write (iout,*) "before FIVEDIAG"
 327 #ifndef FIVEDIAG
 328       write (iout,*) "ALLOCATE"
 329       print *,"ALLOCATE"
 330       if(.not.allocated(Gcopy)) allocate(Gcopy(nres2,nres2)) !(maxres2,maxres2)
 331       if(.not.allocated(Ghalf)) allocate(Ghalf(nres2*(nres2+1)/2)) !mmaxres2=(maxres2*(maxres+1)/2)
 332       if(.not.allocated(Bmat))  allocate(Bmat(nres2,nres2))
 333       if(.not.allocated(matmult)) allocate(matmult(nres2,nres2))
 334 #endif
 335 !
 336 ! Set up the matrix of the (dC,dX)-->(C,X) transformation (A), the
 337 ! inertia matrix (Gmat) and the inverse of the inertia matrix (Ginv)
 338 !
 339 ! Determine the number of degrees of freedom (dimen) and the number of
 340 ! sites (dimen1)
 341       dimen=(nct-nnt+1)+nside
 342       dimen1=(nct-nnt)+(nct-nnt+1)
 343       dimen3=dimen*3
 344       write (iout,*) "nnt",nnt," nct",nct," nside",nside
 345 #ifdef FIVEDIAG
 346        ip4=ip/4
 347        DM(1)=mp/4+ip4
 348        if (iabs(itype(nnt)).eq.10) then
 349          DM(1)=DM(1)+msc(10)
 350          ind=2
 351          nind=1
 352        else
 353          DM(1)=DM(1)+isc(iabs(itype(nnt)))
 354          DM(2)=msc(iabs(itype(nnt)))+isc(iabs(itype(nnt)))
 355          ind=3
 356          nind=2
 357        endif
 358        do i=nnt+1,nct-1
 359 !         if (iabs(itype(i,1)).eq.ntyp1) cycle
 360          DM(ind)=2*ip4+mp/2
 361          if (iabs(itype(i,1)).eq.10 .or. iabs(itype(i,1)).eq.ntyp1) then
 362            if (iabs(itype(i,1)).eq.10) DM(ind)=DM(ind)+msc(10)
 363            ind=ind+1
 364          else
 365            DM(ind)=DM(ind)+isc(iabs(itype(i,1)))
 366            DM(ind+1)=msc(iabs(itype(i,1)))+isc(iabs(itype(i,1)))
 367            ind=ind+2
 368          endif
 369        enddo
 370        if (nct.gt.nnt) then
 371        DM(ind)=ip4+mp/4
 372        if (iabs(itype(nct)).eq.10) then
 373          DM(ind)=DM(ind)+msc(10)
 374          nind=ind
 375        else
 376          DM(ind)=DM(ind)+isc(iabs(itype(nct)))
 377          DM(ind+1)=msc(iabs(itype(nct)))+isc(iabs(itype(nct)))
 378          nind=ind+1
 379         endif
 380         endif
 381
 382
 383         ind=1
 384         do i=nnt,nct
 385         mnum=molnum(i)
 386         if (iabs(itype(i,1)).ne.10 .and.iabs(itype((i))).ne.ntyp1 &
 387           .and.mnum.eq.5) then
 388           DU1(ind)=-isc(iabs(itype(i,1)))
 389           DU1(ind+1)=0.0d0
 390           ind=ind+2
 391         else
 392           DU1(ind)=mp/4-ip4
 393           ind=ind+1
 394         endif
 395         enddo
 396
 397        ind=1
 398        do i=nnt,nct-1
 399        mnum=molnum(i)
 400 !        if (iabs(itype(i,1)).eq.ntyp1) cycle
 401         write (iout,*) "i",i," itype",itype(i,1),ntyp1
 402         if (iabs(itype(i,1)).ne.10 .and. &
 403           iabs(itype(i,mnum)).ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
 404          DU2(ind)=mp/4-ip4
 405          DU2(ind+1)=0.0d0
 406          ind=ind+2
 407         else
 408          DU2(ind)=0.0d0
 409          DU2(ind+1)=0.0d0
 410          ind=ind+1
 411         endif
 412        enddo
 413        DMorig=DM
 414        DU1orig=DU1
 415        DU2orig=DU2
 416        write (iout,*) "nind",nind," dimen",dimen
 417        if (nind.ne.dimen) then
 418          write (iout,*) "ERROR, dimensions differ"
 419 #ifdef MPI
 420          call MPI_Finalize(ierr)
 421 #endif
 422          stop
 423        endif
 424      write (iout,*) "The upper part of the five-diagonal inertia matrix"
 425        do i=1,dimen
 426          if (i.lt.dimen-1) then
 427            write (iout,'(i3,3f10.5)') i,DM(i),DU1(i),DU2(i)
 428          else if (i.eq.dimen-1) then
 429            write (iout,'(i3,3f10.5)') i,DM(i),DU1(i)
 430          else
 431            write (iout,'(i3,3f10.5)') i,DM(i)
 432          endif
 433        enddo
 434
 435         call FDISYP (dimen, DM, DU1, DU2, MARK)
 436
 437         if (mark.eq.-1) then
 438      write (iout,*) "ERROR: the inertia matrix is not positive definite"
 439 #ifdef MPI
 440          call MPI_Finalize(ierr)
 441 #endif
 442          stop
 443         else if (mark.eq.0) then
 444      write (iout,*) "ERROR: the inertia matrix is singular"
 445 #ifdef MPI
 446          call MPI_Finalize(ierr)
 447 #endif
 448         else if (mark.eq.1) then
 449           write (iout,*) "The transformed inertia matrix"
 450           do i=1,dimen
 451             if (i.lt.dimen-1) then
 452               write (iout,'(i3,3f10.5)') i,DM(i),DU1(i),DU2(i)
 453             else if (i.eq.dimen-1) then
 454               write (iout,'(i3,3f10.5)') i,DM(i),DU1(i)
 455             else
 456               write (iout,'(i3,3f10.5)') i,DM(i)
 457             endif
 458           enddo
 459         endif
 460 ! Diagonalization of the pentadiagonal matrix
 461         allocate(DDU1(2*nres))
 462         allocate(DDU2(2*nres))
 463         allocate(DDM(2*nres))
 464         do i=1,dimen-1
 465           DDU1(i+1)=DU1orig(i)
 466         enddo
 467         do i=1,dimen-2
 468           DDU2(i+2)=DU2orig(i)
 469         enddo
 470         DDM=DMorig
 471         call quindibisect2(DDM,DDU1,DDU2,dimen,1,dimen,eps1,relfeh,eps2,iz,geigen)
 472         if (lprn) then
 473           write (iout,*) &
 474            "Eigenvalues of the five-diagonal inertia matrix"
 475           do i=1,dimen
 476             write (iout,'(i5,f10.5)') i,geigen(i)
 477           enddo
 478         endif
 479         deallocate(DDU1)
 480         deallocate(DDU2)
 481         deallocate(DDM)
 482 #else
 483 ! Old Gmatrix
 484 #ifdef MPI
 485       if (nfgtasks.gt.1) then
 486       time00=MPI_Wtime()
 487       call MPI_Bcast(5,1,MPI_INTEGER,king,FG_COMM,IERROR)
 488       time_Bcast=time_Bcast+MPI_Wtime()-time00
 489       call int_bounds(dimen,igmult_start,igmult_end)
 490       igmult_start=igmult_start-1
 491       call MPI_Allgather(3*igmult_start,1,MPI_INTEGER,&
 492           ng_start(0),1,MPI_INTEGER,FG_COMM,IERROR)
 493       my_ng_count=igmult_end-igmult_start
 494       call MPI_Allgather(3*my_ng_count,1,MPI_INTEGER,ng_counts(0),1,&
 495           MPI_INTEGER,FG_COMM,IERROR)
 496       write (iout,*) 'Processor:',fg_rank,' CG group',kolor,&
 497        ' absolute rank',myrank,' igmult_start',igmult_start,&
 498        ' igmult_end',igmult_end,' count',my_ng_count
 499       write (iout,*) "ng_start",(ng_start(i),i=0,nfgtasks-1)
 500       write (iout,*) "ng_counts",(ng_counts(i),i=0,nfgtasks-1)
 501       call flush(iout)
 502       else
 503 #endif
 504       igmult_start=1
 505       igmult_end=dimen
 506       my_ng_count=dimen
 507 #ifdef MPI
 508       endif
 509 #endif
 510 !      write (iout,*) "dimen",dimen," dimen1",dimen1," dimen3",dimen3
 511 !  Zeroing out A and fricmat
 512       do i=1,dimen
 513         do j=1,dimen
 514           A(i,j)=0.0D0
 515         enddo
 516       enddo
 517 !  Diagonal elements of the dC part of A and the respective friction coefficients
 518       ind=1
 519       ind1=0
 520       print *,"TUTUTUT?!",nnt,nct-1
 521       do i=nnt,nct-1
 522         mnum=molnum(i)
 523         ind=ind+1
 524         ind1=ind1+1
 525         coeff=0.25d0*IP(mnum)
 526         if (mnum.eq.5) mp(mnum)=msc(itype(i,mnum),mnum)
 527         print *,i,coeff,mp(mnum)
 528         massvec(ind1)=mp(mnum)
 529         Gmat(ind,ind)=coeff
 530         print *,"i",mp(mnum)
 531         A(ind1,ind)=0.5d0
 532       enddo
 533
 534 !  Off-diagonal elements of the dC part of A
 535       k=3
 536       do i=1,nct-nnt
 537         do j=1,i
 538           A(i,j)=1.0d0
 539         enddo
 540       enddo
 541 !  Diagonal elements of the dX part of A and the respective friction coefficients
 542       m=nct-nnt
 543       m1=nct-nnt+1
 544       ind=0
 545       ind1=0
 546       do i=1,2
 547       msc(ntyp1_molec(i),i)=1.0d0
 548       enddo
 549       do i=nnt,nct
 550         ind=ind+1
 551         ii = ind+m
 552         mnum=molnum(i)
 553         iti=itype(i,mnum)
 554         if (mnum.eq.5) then
 555         mscab=0.0
 556         else
 557         mscab=msc(iabs(iti),mnum)
 558         endif
 559         massvec(ii)=mscab
 560
 561         if (iti.ne.10 .and. iti.ne.ntyp1_molec(mnum) .and. mnum.ne.5) then
 562           ind1=ind1+1
 563           ii1= ind1+m1
 564           A(ii,ii1)=1.0d0
 565           Gmat(ii1,ii1)=ISC(iabs(iti),mnum)
 566         endif
 567       enddo
 568 !  Off-diagonal elements of the dX part of A
 569       ind=0
 570       k=nct-nnt
 571       do i=nnt,nct
 572         iti=itype(i,1)
 573         ind=ind+1
 574         do j=nnt,i
 575           ii = ind
 576           jj = j-nnt+1
 577           A(k+ii,jj)=1.0d0
 578         enddo
 579       enddo
 580       if (lprn) then
 581         write (iout,*)
 582         write (iout,*) "Vector massvec"
 583         do i=1,dimen1
 584           write (iout,*) i,massvec(i)
 585         enddo
 586         write (iout,'(//a)') "A"
 587         call matout(dimen,dimen1,nres2,nres2,A)
 588       endif
 589
 590 ! Calculate the G matrix (store in Gmat)
 591       do k=1,dimen
 592        do i=1,dimen
 593          dtdi=0.0d0
 594          do j=1,dimen1
 595            dtdi=dtdi+A(j,k)*A(j,i)*massvec(j)
 596          enddo
 597          Gmat(k,i)=Gmat(k,i)+dtdi
 598        enddo
 599       enddo
 600
 601       if (lprn) then
 602         write (iout,'(//a)') "Gmat"
 603         call matout(dimen,dimen,nres2,nres2,Gmat)
 604       endif
 605       do i=1,dimen
 606         do j=1,dimen
 607           Ginv(i,j)=0.0d0
 608           Gcopy(i,j)=Gmat(i,j)
 609         enddo
 610         Ginv(i,i)=1.0d0
 611       enddo
 612 ! Invert the G matrix
 613       call MATINVERT(dimen,nres2,Gcopy,Ginv,osob)
 614       if (lprn) then
 615         write (iout,'(//a)') "Ginv"
 616         call matout(dimen,dimen,nres2,nres2,Ginv)
 617       endif
 618
 619       Bmat=0.0d0
 620       Bmat(1,1)=1.0d0
 621       j=2
 622       do i=nnt,nct
 623         mnum=molnum(i)
 624         if ((itype(i,1).eq.10).or.(itype(i,mnum).eq.ntyp1_molec(mnum))&
 625           .or.(mnum.eq.5)) then
 626           Bmat(i-nnt+2,j-1)=-1
 627           Bmat(i-nnt+2,j)=1
 628           j=j+1
 629         else
 630           if (i.lt.nct) then
 631             Bmat(i-nnt+2,j-1)=-1
 632             Bmat(i-nnt+2,j+1)=1
 633             Bmat(i-nnt+1+(nct-nnt)+1,j-1)=-1
 634             Bmat(i-nnt+1+(nct-nnt)+1,j)=1
 635             j=j+2
 636           else
 637             Bmat(i-nnt+1+(nct-nnt)+1,j-1)=-1
 638             Bmat(i-nnt+1+(nct-nnt)+1,j)=1
 639           endif
 640         endif
 641       enddo
 642       write (iout,*) "j",j," dimen",dimen
 643       if (lprn) then
 644         write (iout,'(//a)') "Bmat"
 645         call matout(dimen,dimen,nres2,nres2,Bmat)
 646       endif
 647       Gcopy=0.0d0
 648       write(iout,*) "before Gcopy",dimen,nres*2
 649 #ifdef TESTFIVEDIAG
 650       do i=1,dimen
 651         do j=1,dimen
 652 !            write (iout,*) "myij",i,j
 653             do k=1,dimen
 654                do l=1,dimen
 655 !                 write(iout,*) "i,j,k,l",i,j,k,l
 656                  Gcopy(i,j)=Gcopy(i,j)+Bmat(k,i)*Gmat(k,l)*Bmat(l,j)
 657                enddo
 658             enddo
 659         enddo
 660       enddo
 661 #endif
 662       if (lprn) then
 663         write (iout,'(//a)') "Gmat-transformed"
 664         call matout(dimen,dimen,nres2,nres2,Gcopy)
 665       endif
 666 #ifdef MPI
 667       if (nfgtasks.gt.1) then
 668         myginv_ng_count=nres2*my_ng_count
 669         call MPI_Allgather(nres2*igmult_start,1,MPI_INTEGER,&
 670           nginv_start(0),1,MPI_INTEGER,FG_COMM,IERROR)
 671         call MPI_Allgather(myginv_ng_count,1,MPI_INTEGER,&
 672           nginv_counts(0),1,MPI_INTEGER,FG_COMM,IERROR)
 673         write (iout,*) "nginv_start",(nginv_start(i),i=0,nfgtasks-1)
 674         write (iout,*) "nginv_counts",(nginv_counts(i),i=0,nfgtasks-1)
 675         call flush(iout)
 676 !        call MPI_Scatterv(ginv(1,1),nginv_counts(0),
 677 !     &    nginv_start(0),MPI_DOUBLE_PRECISION,ginv,
 678 !     &    myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
 679 !        call MPI_Barrier(FG_COMM,IERR)
 680         time00=MPI_Wtime()
 681         call MPI_Scatterv(ginv(1,1),nginv_counts(0),&
 682           nginv_start(0),MPI_DOUBLE_PRECISION,gcopy(1,1),&
 683           myginv_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
 684 #ifdef TIMING
 685         time_scatter_ginv=time_scatter_ginv+MPI_Wtime()-time00
 686 #endif
 687         do i=1,dimen
 688           do j=1,2*my_ng_count
 689             ginv(j,i)=gcopy(i,j)
 690           enddo
 691         enddo
 692 !        write (iout,*) "Master's chunk of ginv"
 693 !        call MATOUT2(my_ng_count,dimen,maxres2,maxres2,ginv)
 694       endif
 695 #endif
 696       if (osob) then
 697         write (iout,*) "The G matrix is singular."
 698         stop
 699       endif
 700 ! Compute G**(-1/2) and G**(1/2)
 701       ind=0
 702       do i=1,dimen
 703         do j=1,i
 704           ind=ind+1
 705           Ghalf(ind)=Gmat(i,j)
 706         enddo
 707       enddo
 708       call gldiag(nres2,dimen,dimen,Ghalf,work,Geigen,Gvec,&
 709         ierr,iwork)
 710       if (lprn) then
 711         write (iout,'(//a)') &
 712          "Eigenvectors and eigenvalues of the G matrix"
 713         call eigout(dimen,dimen,nres2,nres2,Gvec,Geigen)
 714       endif
 715       do i=1,dimen
 716         sqreig(i)=dsqrt(Geigen(i))
 717       enddo
 718       do i=1,dimen
 719         do j=1,dimen
 720           Gsqrp(i,j)=0.0d0
 721           Gsqrm(i,j)=0.0d0
 722           Gcopy(i,j)=0.0d0
 723           do k=1,dimen
 724             Gsqrp(i,j)=Gsqrp(i,j)+Gvec(i,k)*Gvec(j,k)*sqreig(k)
 725             Gsqrm(i,j)=Gsqrm(i,j)+Gvec(i,k)*Gvec(j,k)/sqreig(k)
 726             Gcopy(i,j)=Gcopy(i,j)+Gvec(i,k)*Gvec(j,k)*Geigen(k)
 727           enddo
 728         enddo
 729       enddo
 730       if (lprn) then
 731         write (iout,*) "Comparison of original and restored G"
 732         do i=1,dimen
 733           do j=1,dimen
 734             write (iout,'(2i5,5f10.5)') i,j,Gmat(i,j),Gcopy(i,j),&
 735               Gmat(i,j)-Gcopy(i,j),Gsqrp(i,j),Gsqrm(i,j)
 736           enddo
 737         enddo
 738       endif
 739       deallocate(Gcopy)
 740 #endif
 741       return
 742       end subroutine setup_MD_matrices
 743 !-----------------------------------------------------------------------------
 744       subroutine EIGOUT(NC,NR,LM2,LM3,A,B)
 745
 746 !      implicit real*8 (a-h,o-z)
 747 !      include 'DIMENSIONS'
 748 !      include 'COMMON.IOUNITS'
 749       integer :: LM2,LM3,NC,NR,KA,KC,KB,I,J,N
 750       real(kind=8) :: A(LM2,LM3),B(LM2)
 751       KA=1
 752       KC=6
 753     1 KB=MIN0(KC,NC)
 754       WRITE(IOUT,600) (I,I=KA,KB)
 755       WRITE(IOUT,601) (B(I),I=KA,KB)
 756       WRITE(IOUT,602)
 757     2 N=0
 758       DO 3  I=1,NR
 759       WRITE(IOUT,603) I,(A(I,J),J=KA,KB)
 760       N=N+1
 761       IF(N.LT.10) GO TO 3
 762       WRITE(IOUT,602)
 763       N=0
 764     3 CONTINUE
 765     4 IF (KB.EQ.NC) RETURN
 766       KA=KC+1
 767       KC=KC+6
 768       GO TO 1
 769   600 FORMAT (// 9H ROOT NO.,I4,9I11)
 770   601 FORMAT (/5X,10(1PE11.4))
 771   602 FORMAT (2H  )
 772   603 FORMAT (I5,10F11.5)
 773   604 FORMAT (1H1)
 774       end subroutine EIGOUT
 775 !-----------------------------------------------------------------------------
 776       subroutine MATOUT(NC,NR,LM2,LM3,A)
 777
 778 !      implicit real*8 (a-h,o-z)
 779 !      include 'DIMENSIONS'
 780 !      include 'COMMON.IOUNITS'
 781       integer :: LM2,LM3,NC,NR,KA,KC,KB,I,J,N
 782       real(kind=8) :: A(LM2,LM3)
 783       KA=1
 784       KC=6
 785     1 KB=MIN0(KC,NC)
 786       WRITE(IOUT,600) (I,I=KA,KB)
 787       WRITE(IOUT,602)
 788     2 N=0
 789       DO 3  I=1,NR
 790       WRITE(IOUT,603) I,(A(I,J),J=KA,KB)
 791       N=N+1
 792       IF(N.LT.10) GO TO 3
 793       WRITE(IOUT,602)
 794       N=0
 795     3 CONTINUE
 796     4 IF (KB.EQ.NC) RETURN
 797       KA=KC+1
 798       KC=KC+6
 799       GO TO 1
 800   600 FORMAT (//5x,9I11)
 801   602 FORMAT (2H  )
 802   603 FORMAT (I5,10F11.3)
 803   604 FORMAT (1H1)
 804       end subroutine MATOUT
 805 !-----------------------------------------------------------------------------
 806       subroutine MATOUT1(NC,NR,LM2,LM3,A)
 807
 808 !      implicit real*8 (a-h,o-z)
 809 !      include 'DIMENSIONS'
 810 !      include 'COMMON.IOUNITS'
 811       integer :: LM2,LM3,NC,NR,KA,KC,KB,I,J,N
 812       real(kind=8) :: A(LM2,LM3)
 813       KA=1
 814       KC=21
 815     1 KB=MIN0(KC,NC)
 816       WRITE(IOUT,600) (I,I=KA,KB)
 817       WRITE(IOUT,602)
 818     2 N=0
 819       DO 3  I=1,NR
 820       WRITE(IOUT,603) I,(A(I,J),J=KA,KB)
 821       N=N+1
 822       IF(N.LT.3) GO TO 3
 823       WRITE(IOUT,602)
 824       N=0
 825     3 CONTINUE
 826     4 IF (KB.EQ.NC) RETURN
 827       KA=KC+1
 828       KC=KC+21
 829       GO TO 1
 830   600 FORMAT (//5x,7(3I5,2x))
 831   602 FORMAT (2H  )
 832   603 FORMAT (I5,7(3F5.1,2x))
 833   604 FORMAT (1H1)
 834       end subroutine MATOUT1
 835 !-----------------------------------------------------------------------------
 836       subroutine MATOUT2(NC,NR,LM2,LM3,A)
 837
 838 !      implicit real*8 (a-h,o-z)
 839 !      include 'DIMENSIONS'
 840 !      include 'COMMON.IOUNITS'
 841       integer :: I,J,KA,KC,KB,N
 842       integer :: LM2,LM3,NC,NR
 843       real(kind=8) :: A(LM2,LM3)
 844       KA=1
 845       KC=12
 846     1 KB=MIN0(KC,NC)
 847       WRITE(IOUT,600) (I,I=KA,KB)
 848       WRITE(IOUT,602)
 849     2 N=0
 850       DO 3  I=1,NR
 851       WRITE(IOUT,603) I,(A(I,J),J=KA,KB)
 852       N=N+1
 853       IF(N.LT.3) GO TO 3
 854       WRITE(IOUT,602)
 855       N=0
 856     3 CONTINUE
 857     4 IF (KB.EQ.NC) RETURN
 858       KA=KC+1
 859       KC=KC+12
 860       GO TO 1
 861   600 FORMAT (//5x,4(3I9,2x))
 862   602 FORMAT (2H  )
 863   603 FORMAT (I5,4(3F9.3,2x))
 864   604 FORMAT (1H1)
 865       end subroutine MATOUT2
 866 !-----------------------------------------------------------------------------
 867       subroutine ginv_mult(z,d_a_tmp)
 868
 869       use geometry_data, only: nres
 870       use control_data
 871       use MPI_data
 872 !      implicit real*8 (a-h,o-z)
 873 !      include 'DIMENSIONS'
 874 #ifdef MPI
 875       include 'mpif.h'
 876       integer :: ierr,ierror
 877 #endif
 878 !      include 'COMMON.SETUP'
 879 !      include 'COMMON.TIME1'
 880 !      include 'COMMON.MD'
 881       real(kind=8),dimension(dimen3) :: z,z1,d_a_tmp
 882       real(kind=8),dimension(6*nres) :: temp    !(maxres6) maxres6=6*maxres
 883       real(kind=8) :: time00,time01
 884       integer :: i,j,k,ind
 885 #ifdef MPI
 886       if (nfgtasks.gt.1) then
 887         if (fg_rank.eq.0) then
 888 ! The matching BROADCAST for fg processors is called in ERGASTULUM
 889           time00=MPI_Wtime()
 890           call MPI_Bcast(4,1,MPI_INTEGER,king,FG_COMM,IERROR)
 891           time_Bcast=time_Bcast+MPI_Wtime()-time00
 892 !          print *,"Processor",myrank," BROADCAST iorder in GINV_MULT"
 893         endif
 894 !        write (2,*) "time00",time00
 895 !        write (2,*) "Before Scatterv"
 896 !        call flush(2)
 897 !        write (2,*) "Whole z (for FG master)"
 898 !        do i=1,dimen
 899 !          write (2,*) i,z(i)
 900 !        enddo
 901 !        call MPI_Barrier(FG_COMM,IERROR)
 902         time00=MPI_Wtime()
 903 !elwrite(iout,*) "do tej pory jest OK, MPI_Scatterv w ginv_mult"
 904         call MPI_Scatterv(z,ng_counts(0),ng_start(0),&
 905           MPI_DOUBLE_PRECISION,&
 906           z1,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
 907 !        write (2,*) "My chunk of z"
 908 !        do i=1,3*my_ng_count
 909 !          write (2,*) i,z(i)
 910 !        enddo
 911 !        write (2,*) "After SCATTERV"
 912 !        call flush(2)
 913 !        write (2,*) "MPI_Wtime",MPI_Wtime()
 914         time_scatter=time_scatter+MPI_Wtime()-time00
 915 #ifdef TIMING
 916         time_scatter_ginvmult=time_scatter_ginvmult+MPI_Wtime()-time00
 917 #endif
 918 !        write (2,*) "time_scatter",time_scatter
 919 !        write (2,*) "dimen",dimen," dimen3",dimen3," my_ng_count",
 920 !     &    my_ng_count
 921 !        call flush(2)
 922         time01=MPI_Wtime()
 923         do k=0,2
 924           do i=1,dimen
 925             ind=(i-1)*3+k+1
 926             temp(ind)=0.0d0
 927             do j=1,my_ng_count
 928 !              write (2,*) "k,i,j,ind",k,i,j,ind,(j-1)*3+k+1,
 929 !     &         Ginv(i,j),z((j-1)*3+k+1),
 930 !     &          Ginv(i,j)*z((j-1)*3+k+1)
 931 !              temp(ind)=temp(ind)+Ginv(i,j)*z((j-1)*3+k+1)
 932               temp(ind)=temp(ind)+Ginv(j,i)*z1((j-1)*3+k+1)
 933             enddo
 934           enddo
 935         enddo
 936         time_ginvmult=time_ginvmult+MPI_Wtime()-time01
 937 !        write (2,*) "Before REDUCE"
 938 !        call flush(2)
 939 !        write (2,*) "z before reduce"
 940 !        do i=1,dimen
 941 !          write (2,*) i,temp(i)
 942 !        enddo
 943         time00=MPI_Wtime()
 944         call MPI_Reduce(temp(1),d_a_tmp(1),dimen3,MPI_DOUBLE_PRECISION,&
 945             MPI_SUM,king,FG_COMM,IERR)
 946         time_reduce=time_reduce+MPI_Wtime()-time00
 947 !        write (2,*) "After REDUCE"
 948 !        call flush(2)
 949       else
 950 #endif
 951 #ifdef TIMING
 952         time01=MPI_Wtime()
 953 #endif
 954         do k=0,2
 955           do i=1,dimen
 956             ind=(i-1)*3+k+1
 957             d_a_tmp(ind)=0.0d0
 958             do j=1,dimen
 959 !              write (2,*) "k,i,j,ind",k,i,j,ind,(j-1)*3+k+1
 960 !              call flush(2)
 961 !     &         Ginv(i,j),z((j-1)*3+k+1),
 962 !     &          Ginv(i,j)*z((j-1)*3+k+1)
 963               d_a_tmp(ind)=d_a_tmp(ind) &
 964                                +Ginv(j,i)*z((j-1)*3+k+1)
 965 !              d_a_tmp(ind)=d_a_tmp(ind)
 966 !     &                         +Ginv(i,j)*z((j-1)*3+k+1)
 967             enddo
 968           enddo
 969         enddo
 970 #ifdef TIMING
 971         time_ginvmult=time_ginvmult+MPI_Wtime()-time01
 972 #endif
 973 #ifdef MPI
 974       endif
 975 #endif
 976       return
 977       end subroutine ginv_mult
 978 !-----------------------------------------------------------------------------
 979 #ifdef GINV_MULT
 980       subroutine ginv_mult_test(z,d_a_tmp)
 981
 982 !      include 'DIMENSIONS'
 983 !el      integer :: dimen
 984 !      include 'COMMON.MD'
 985       real(kind=8),dimension(dimen) :: z,d_a_tmp
 986       real(kind=8),dimension(dimen/3) :: ztmp,dtmp
 987       integer :: i,j,k,ind
 988 !      do i=1,dimen
 989 !        d_a_tmp(i)=0.0d0
 990 !        do j=1,dimen
 991 !          d_a_tmp(i)=d_a_tmp(i)+Ginv(i,j)*z(j)
 992 !        enddo
 993 !      enddo
 994 !
 995 !      return
 996
 997 !ibm* unroll(3)
 998       do k=0,2
 999        do j=1,dimen/3
1000         ztmp(j)=z((j-1)*3+k+1)
1001        enddo
1002
1003        call alignx(16,ztmp(1))
1004        call alignx(16,dtmp(1))
1005        call alignx(16,Ginv(1,1))
1006
1007        do i=1,dimen/3
1008         dtmp(i)=0.0d0
1009         do j=1,dimen/3
1010            dtmp(i)=dtmp(i)+Ginv(i,j)*ztmp(j)
1011         enddo
1012        enddo
1013        do i=1,dimen/3
1014         ind=(i-1)*3+k+1
1015         d_a_tmp(ind)=dtmp(i)
1016        enddo
1017       enddo
1018       return
1019       end subroutine ginv_mult_test
1020 #endif
1021 !-----------------------------------------------------------------------------
1022       subroutine fricmat_mult(z,d_a_tmp)
1023
1024       use geometry_data, only: nres
1025       use control_data
1026       use MPI_data
1027 !      include 'DIMENSIONS'
1028 #ifdef MPI
1029       include 'mpif.h'
1030       integer :: IERROR,ierr
1031 #endif
1032 !      include 'COMMON.MD'
1033 !      include 'COMMON.IOUNITS'
1034 !      include 'COMMON.SETUP'
1035 !      include 'COMMON.TIME1'
1036 !#ifndef LANG0
1037 !      include 'COMMON.LANGEVIN'
1038 !#else
1039 !      include 'COMMON.LANGEVIN.lang0'
1040 !#endif
1041       real(kind=8),dimension(dimen3) :: z,z1,d_a_tmp
1042       real(kind=8),dimension(6*nres) :: temp    !(maxres6) maxres6=6*maxres
1043       real(kind=8) :: time00,time01
1044       integer :: i,j,k,ind,nres2
1045       nres2=2*nres
1046 !el      if(.not.allocated(fricmat)) allocate(fricmat(nres2,nres2))
1047
1048 #ifdef MPI
1049       if (nfgtasks.gt.1) then
1050         if (fg_rank.eq.0) then
1051 ! The matching BROADCAST for fg processors is called in ERGASTULUM
1052           time00=MPI_Wtime()
1053           call MPI_Bcast(9,1,MPI_INTEGER,king,FG_COMM,IERROR)
1054           time_Bcast=time_Bcast+MPI_Wtime()-time00
1055 !          print *,"Processor",myrank," BROADCAST iorder in FRICMAT_MULT"
1056         endif
1057 !        call MPI_Barrier(FG_COMM,IERROR)
1058         time00=MPI_Wtime()
1059         call MPI_Scatterv(z,ng_counts(0),ng_start(0),&
1060           MPI_DOUBLE_PRECISION,&
1061           z1,3*my_ng_count,MPI_DOUBLE_PRECISION,king,FG_COMM,IERR)
1062 !        write (2,*) "My chunk of z"
1063 !        do i=1,3*my_ng_count
1064 !          write (2,*) i,z(i)
1065 !        enddo
1066         time_scatter=time_scatter+MPI_Wtime()-time00
1067 #ifdef TIMING
1068         time_scatter_fmatmult=time_scatter_fmatmult+MPI_Wtime()-time00
1069 #endif
1070         time01=MPI_Wtime()
1071         do k=0,2
1072           do i=1,dimen
1073             ind=(i-1)*3+k+1
1074             temp(ind)=0.0d0
1075             do j=1,my_ng_count
1076               temp(ind)=temp(ind)-fricmat(j,i)*z1((j-1)*3+k+1)
1077             enddo
1078           enddo
1079         enddo
1080         time_fricmatmult=time_fricmatmult+MPI_Wtime()-time01
1081 !        write (2,*) "Before REDUCE"
1082 !        write (2,*) "d_a_tmp before reduce"
1083 !        do i=1,dimen3
1084 !          write (2,*) i,temp(i)
1085 !        enddo
1086 !        call flush(2)
1087         time00=MPI_Wtime()
1088         call MPI_Reduce(temp(1),d_a_tmp(1),dimen3,MPI_DOUBLE_PRECISION,&
1089             MPI_SUM,king,FG_COMM,IERR)
1090         time_reduce=time_reduce+MPI_Wtime()-time00
1091 !        write (2,*) "After REDUCE"
1092 !        call flush(2)
1093       else
1094 #endif
1095 #ifdef TIMING
1096         time01=MPI_Wtime()
1097 #endif
1098         do k=0,2
1099          do i=1,dimen
1100           ind=(i-1)*3+k+1
1101           d_a_tmp(ind)=0.0d0
1102           do j=1,dimen
1103              d_a_tmp(ind)=d_a_tmp(ind) &
1104                                  -fricmat(j,i)*z((j-1)*3+k+1)
1105           enddo
1106          enddo
1107         enddo
1108 #ifdef TIMING
1109         time_fricmatmult=time_fricmatmult+MPI_Wtime()-time01
1110 #endif
1111 #ifdef MPI
1112       endif
1113 #endif
1114 !      write (iout,*) "Vector d_a"
1115 !      do i=1,dimen3
1116 !        write (2,*) i,d_a_tmp(i)
1117 !      enddo
1118       return
1119       end subroutine fricmat_mult
1120 !-----------------------------------------------------------------------------
1121 !-----------------------------------------------------------------------------
1122       end module REMD