+++ /dev/null
- subroutine MD
-c------------------------------------------------
-c The driver for molecular dynamics subroutines
-c------------------------------------------------
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision cm(3),L(3),vcm(3)
- double precision energia(0:n_ene)
- integer ilen,rstcount
- external ilen
- character*50 tytul
- common /gucio/ cm,energia
- integer itime
-c
- t_MDsetup=0.0d0
- t_langsetup=0.0d0
- t_MD=0.0d0
- t_enegrad=0.0d0
- t_sdsetup=0.0d0
- write (iout,'(20(1h=),a20,20(1h=))') "MD calculation started"
- tt0 = tcpu()
-c Determine the inverse of the inertia matrix.
- call setup_MD_matrices
-c Initialize MD
- call init_MD
- t_MDsetup = tcpu()-tt0
- rstcount=0
-c Entering the MD loop
- tt0 = tcpu()
- if (lang.eq.2 .or. lang.eq.3) then
- call setup_fricmat
- if (lang.eq.2) then
- call sd_verlet_p_setup
- else
- call sd_verlet_ciccotti_setup
- endif
- do i=1,dimen
- do j=1,dimen
- pfric0_mat(i,j,0)=pfric_mat(i,j)
- afric0_mat(i,j,0)=afric_mat(i,j)
- vfric0_mat(i,j,0)=vfric_mat(i,j)
- prand0_mat(i,j,0)=prand_mat(i,j)
- vrand0_mat1(i,j,0)=vrand_mat1(i,j)
- vrand0_mat2(i,j,0)=vrand_mat2(i,j)
- enddo
- enddo
- flag_stoch(0)=.true.
- do i=1,maxflag_stoch
- flag_stoch(i)=.false.
- enddo
- else if (lang.eq.1 .or. lang.eq.4) then
- call setup_fricmat
- endif
- t_langsetup=tcpu()-tt0
- tt0=tcpu()
- do itime=1,n_timestep
- rstcount=rstcount+1
- if (lang.gt.0 .and. surfarea .and.
- & mod(itime,reset_fricmat).eq.0) then
- if (lang.eq.2 .or. lang.eq.3) then
- call setup_fricmat
- if (lang.eq.2) then
- call sd_verlet_p_setup
- else
- call sd_verlet_ciccotti_setup
- endif
- do i=1,dimen
- do j=1,dimen
- pfric0_mat(i,j,0)=pfric_mat(i,j)
- afric0_mat(i,j,0)=afric_mat(i,j)
- vfric0_mat(i,j,0)=vfric_mat(i,j)
- prand0_mat(i,j,0)=prand_mat(i,j)
- vrand0_mat1(i,j,0)=vrand_mat1(i,j)
- vrand0_mat2(i,j,0)=vrand_mat2(i,j)
- enddo
- enddo
- flag_stoch(0)=.true.
- do i=1,maxflag_stoch
- flag_stoch(i)=.false.
- enddo
- else if (lang.eq.1 .or. lang.eq.4) then
- call setup_fricmat
- endif
- write (iout,'(a,i10)')
- & "Friction matrix reset based on surface area, itime",itime
- endif
- if (reset_vel .and. tbf .and. lang.eq.0
- & .and. mod(itime,count_reset_vel).eq.0) then
- call random_vel
- write(iout,'(a,f20.2)')
- & "Velocities reset to random values, time",totT
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=d_t(j,i)
- enddo
- enddo
- endif
- if (reset_moment .and. mod(itime,count_reset_moment).eq.0) then
- call inertia_tensor
- call vcm_vel(vcm)
- do j=1,3
- d_t(j,0)=d_t(j,0)-vcm(j)
- enddo
- call kinetic(EK)
- kinetic_T=2.0d0/(dimen*Rb)*EK
- scalfac=dsqrt(T_bath/kinetic_T)
- write(iout,'(a,f20.2)') "Momenta zeroed out, time",totT
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=scalfac*d_t(j,i)
- enddo
- enddo
- endif
- if (lang.ne.4) then
- if (RESPA) then
-c Time-reversible RESPA algorithm
-c (Tuckerman et al., J. Chem. Phys., 97, 1990, 1992)
- call RESPA_step(itime)
- else
-c Variable time step algorithm.
- call velverlet_step(itime)
- endif
- else
- call brown_step(itime)
- endif
- if (mod(itime,ntwe).eq.0) call statout(itime)
- if (mod(itime,ntwx).eq.0) then
- write (tytul,'("time",f8.2)') totT
- if(mdpdb) then
- call pdbout(potE,tytul,ipdb)
- else
- call cartout(totT)
- endif
- endif
- if (rstcount.eq.1000.or.itime.eq.n_timestep) then
- open(irest2,file=rest2name,status='unknown')
- write(irest2,*) totT,EK,potE,totE
- do i=1,2*nres
- write (irest2,'(3e15.5)') (d_t(j,i),j=1,3)
- enddo
- do i=1,2*nres
- write (irest2,'(3e15.5)') (dc(j,i),j=1,3)
- enddo
- close(irest2)
- rstcount=0
- endif
- enddo
- t_MD=tcpu()-tt0
- write (iout,'(//35(1h=),a10,35(1h=)/10(/a40,1pe15.5))')
- & ' Timing ',
- & 'MD calculations setup:',t_MDsetup,
- & 'Energy & gradient evaluation:',t_enegrad,
- & 'Stochastic MD setup:',t_langsetup,
- & 'Stochastic MD step setup:',t_sdsetup,
- & 'MD steps:',t_MD
- write (iout,'(/28(1h=),a25,27(1h=))')
- & ' End of MD calculation '
- return
- end
-c-------------------------------------------------------------------------------
- subroutine brown_step(itime)
-c------------------------------------------------
-c Perform a single Euler integration step of Brownian dynamics
-c------------------------------------------------
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision energia(0:n_ene),zapas(MAXRES6)
- integer ilen,rstcount
- external ilen
- double precision stochforcvec(MAXRES6)
- double precision Bmat(MAXRES6,MAXRES2),Cmat(maxres2,maxres2),
- & Cinv(maxres2,maxres2),GBmat(MAXRES6,MAXRES2),
- & Tmat(MAXRES6,MAXRES2),Pmat(maxres6,maxres6),Td(maxres6),
- & ppvec(maxres2)
- common /stochcalc/ stochforcvec
- common /gucio/ cm, energia
- integer itime
- logical lprn /.false./,lprn1 /.false./
- integer maxiter /5/
- double precision difftol /1.0d-5/
- nbond=nct-nnt
- do i=nnt,nct
- if (itype(i).ne.10) nbond=nbond+1
- enddo
-c
- if (lprn1) then
- write (iout,*) "Generalized inverse of fricmat"
- call matout(dimen,dimen,MAXRES6,MAXRES6,fricmat)
- endif
- do i=1,dimen
- do j=1,nbond
- Bmat(i,j)=0.0d0
- enddo
- enddo
- ind=3
- ind1=0
- do i=nnt,nct-1
- ind1=ind1+1
- do j=1,3
- Bmat(ind+j,ind1)=dC_norm(j,i)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- ind1=ind1+1
- do j=1,3
- Bmat(ind+j,ind1)=dC_norm(j,i+nres)
- enddo
- ind=ind+3
- endif
- enddo
- if (lprn1) then
- write (iout,*) "Matrix Bmat"
- call MATOUT(nbond,dimen,MAXRES6,MAXRES2,Bmat)
- endif
- do i=1,dimen
- do j=1,nbond
- GBmat(i,j)=0.0d0
- do k=1,dimen
- GBmat(i,j)=GBmat(i,j)+fricmat(i,k)*Bmat(k,j)
- enddo
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Matrix GBmat"
- call MATOUT(nbond,dimen,MAXRES6,MAXRES2,Gbmat)
- endif
- do i=1,nbond
- do j=1,nbond
- Cmat(i,j)=0.0d0
- do k=1,dimen
- Cmat(i,j)=Cmat(i,j)+Bmat(k,i)*GBmat(k,j)
- enddo
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Matrix Cmat"
- call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cmat)
- endif
- call matinvert(nbond,MAXRES2,Cmat,Cinv)
- if (lprn1) then
- write (iout,*) "Matrix Cinv"
- call MATOUT(nbond,nbond,MAXRES2,MAXRES2,Cinv)
- endif
- do i=1,dimen
- do j=1,nbond
- Tmat(i,j)=0.0d0
- do k=1,nbond
- Tmat(i,j)=Tmat(i,j)+GBmat(i,k)*Cinv(k,j)
- enddo
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Matrix Tmat"
- call MATOUT(nbond,dimen,MAXRES6,MAXRES2,Tmat)
- endif
- do i=1,dimen
- do j=1,dimen
- if (i.eq.j) then
- Pmat(i,j)=1.0d0
- else
- Pmat(i,j)=0.0d0
- endif
- do k=1,nbond
- Pmat(i,j)=Pmat(i,j)-Tmat(i,k)*Bmat(j,k)
- enddo
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Matrix Pmat"
- call MATOUT(dimen,dimen,MAXRES6,MAXRES6,Pmat)
- endif
- do i=1,dimen
- Td(i)=0.0d0
- ind=0
- do k=nnt,nct-1
- ind=ind+1
- Td(i)=Td(i)+vbl*Tmat(i,ind)
- enddo
- do k=nnt,nct
- if (itype(k).ne.10) then
- ind=ind+1
- Td(i)=Td(i)+vbldsc0(itype(k))*Tmat(i,ind)
- endif
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Vector Td"
- do i=1,dimen
- write (iout,'(i5,f10.5)') i,Td(i)
- enddo
- endif
- call stochastic_force(stochforcvec)
- if (lprn) then
- write (iout,*) "stochforcvec"
- do i=1,dimen
- write (iout,*) i,stochforcvec(i)
- enddo
- endif
- do j=1,3
- zapas(j)=-gcart(j,0)+stochforcvec(j)
- d_t_work(j)=d_t(j,0)
- dC_work(j)=dC_old(j,0)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- ind=ind+1
- zapas(ind)=-gcart(j,i)+stochforcvec(ind)
- dC_work(ind)=dC_old(j,i)
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- do j=1,3
- ind=ind+1
- zapas(ind)=-gxcart(j,i)+stochforcvec(ind)
- dC_work(ind)=dC_old(j,i+nres)
- enddo
- endif
- enddo
-
- if (lprn) then
- write (iout,*) "Initial d_t_work"
- do i=1,dimen
- write (iout,*) i,d_t_work(i)
- enddo
- endif
-
- do i=1,dimen
- d_t_work(i)=0.0d0
- do j=1,dimen
- d_t_work(i)=d_t_work(i)+fricmat(i,j)*zapas(j)
- enddo
- enddo
-
- do i=1,dimen
- zapas(i)=Td(i)
- do j=1,dimen
- zapas(i)=zapas(i)+Pmat(i,j)*(dC_work(j)+d_t_work(j)*d_time)
- enddo
- enddo
- if (lprn1) then
- write (iout,*) "Final d_t_work and zapas"
- do i=1,dimen
- write (iout,*) i,d_t_work(i),zapas(i)
- enddo
- endif
-
- do j=1,3
- d_t(j,0)=d_t_work(j)
- dc(j,0)=zapas(j)
- dc_work(j)=dc(j,0)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_work(i)
- dc(j,i)=zapas(ind+j)
- dc_work(ind+j)=dc(j,i)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- do j=1,3
- d_t(j,i+nres)=d_t_work(ind+j)
- dc(j,i+nres)=zapas(ind+j)
- dc_work(ind+j)=dc(j,i+nres)
- enddo
- ind=ind+3
- enddo
- if (lprn) then
- call chainbuild_cart
- write (iout,*) "Before correction for rotational lengthening"
- write (iout,*) "New coordinates",
- & " and differences between actual and standard bond lengths"
- ind=0
- do i=nnt,nct-1
- ind=ind+1
- xx=vbld(i+1)-vbl
- write (iout,'(i5,3f10.5,5x,f10.5,e15.5)')
- & i,(dC(j,i),j=1,3),xx
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- ind=ind+1
- xx=vbld(i+nres)-vbldsc0(itype(i))
- write (iout,'(i5,3f10.5,5x,f10.5,e15.5)')
- & i,(dC(j,i+nres),j=1,3),xx
- endif
- enddo
- endif
-c Second correction (rotational lengthening)
-c do iter=1,maxiter
- diffmax=0.0d0
- ind=0
- do i=nnt,nct-1
- ind=ind+1
- blen2 = scalar(dc(1,i),dc(1,i))
- ppvec(ind)=2*vbl**2-blen2
- diffbond=dabs(vbl-dsqrt(blen2))
- if (diffbond.gt.diffmax) diffmax=diffbond
- if (ppvec(ind).gt.0.0d0) then
- ppvec(ind)=dsqrt(ppvec(ind))
- else
- ppvec(ind)=0.0d0
- endif
- if (lprn) then
- write (iout,'(i5,3f10.5)') ind,diffbond,ppvec(ind)
- endif
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- ind=ind+1
- blen2 = scalar(dc(1,i+nres),dc(1,i+nres))
- ppvec(ind)=2*vbldsc0(itype(i))**2-blen2
- diffbond=dabs(vbldsc0(itype(i))-dsqrt(blen2))
- if (diffbond.gt.diffmax) diffmax=diffbond
- if (ppvec(ind).gt.0.0d0) then
- ppvec(ind)=dsqrt(ppvec(ind))
- else
- ppvec(ind)=0.0d0
- endif
- if (lprn) then
- write (iout,'(i5,3f10.5)') ind,diffbond,ppvec(ind)
- endif
- endif
- enddo
- if (lprn) write (iout,*) "iter",iter," diffmax",diffmax
- if (diffmax.lt.difftol) goto 10
- do i=1,dimen
- Td(i)=0.0d0
- do j=1,nbond
- Td(i)=Td(i)+ppvec(j)*Tmat(i,j)
- enddo
- enddo
- do i=1,dimen
- zapas(i)=Td(i)
- do j=1,dimen
- zapas(i)=zapas(i)+Pmat(i,j)*dc_work(j)
- enddo
- enddo
- do j=1,3
- dc(j,0)=zapas(j)
- dc_work(j)=zapas(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- dc(j,i)=zapas(ind+j)
- dc_work(ind+j)=zapas(ind+j)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- do j=1,3
- dc(j,i+nres)=zapas(ind+j)
- dc_work(ind+j)=zapas(ind+j)
- enddo
- ind=ind+3
- endif
- enddo
-c Building the chain from the newly calculated coordinates
- call chainbuild_cart
- if (large.and. mod(itime,ntwe).eq.0) then
- write (iout,*) "Cartesian and internal coordinates: step 1"
- call cartprint
- call intout
- write (iout,'(a)') "Potential forces"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(-gcart(j,i),j=1,3),
- & (-gxcart(j,i),j=1,3)
- enddo
- write (iout,'(a)') "Stochastic forces"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(stochforc(j,i),j=1,3),
- & (stochforc(j,i+nres),j=1,3)
- enddo
- write (iout,'(a)') "Velocities"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
- if (lprn) then
- write (iout,*) "After correction for rotational lengthening"
- write (iout,*) "New coordinates",
- & " and differences between actual and standard bond lengths"
- ind=0
- do i=nnt,nct-1
- ind=ind+1
- xx=vbld(i+1)-vbl
- write (iout,'(i5,3f10.5,5x,f10.5,e15.5)')
- & i,(dC(j,i),j=1,3),xx
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- ind=ind+1
- xx=vbld(i+nres)-vbldsc0(itype(i))
- write (iout,'(i5,3f10.5,5x,f10.5,e15.5)')
- & i,(dC(j,i+nres),j=1,3),xx
- endif
- enddo
- endif
-c ENDDO
-c write (iout,*) "Too many attempts at correcting the bonds"
-c stop
- 10 continue
- tt0 = tcpu()
-c Calculate energy and forces
- call zerograd
- call etotal(energia)
- potE=energia(0)-energia(20)
- call cartgrad
- totT=totT+d_time
-c Calculate the kinetic and total energy and the kinetic temperature
- call kinetic(EK)
- t_enegrad=t_enegrad+tcpu()-tt0
- totE=EK+potE
- kinetic_T=2.0d0/(dimen*Rb)*EK
- return
- end
-c-------------------------------------------------------------------------------
- subroutine velverlet_step(itime)
-c-------------------------------------------------------------------------------
-c Perform a single velocity Verlet step; the time step can be rescaled if
-c increments in accelerations exceed the threshold
-c-------------------------------------------------------------------------------
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- include 'COMMON.MUCA'
- double precision energia(0:n_ene),vcm(3),incr(3)
- double precision cm(3),L(3)
- integer ilen,count,rstcount
- external ilen
- character*50 tytul
- integer maxcount_scale /20/
- common /gucio/ cm, energia
- double precision stochforcvec(MAXRES6)
- common /stochcalc/ stochforcvec
- integer itime
- logical scale
-c
- scale=.true.
- icount_scale=0
- if (lang.eq.1) then
- call sddir_precalc
- else if (lang.eq.2 .or. lang.eq.3) then
- call stochastic_force(stochforcvec)
- endif
- itime_scal=0
- do while (scale)
- icount_scale=icount_scale+1
- if (icount_scale.gt.maxcount_scale) then
- write (iout,*)
- & "ERROR: too many attempts at scaling down the time step. ",
- & "amax=",amax,"epdrift=",epdrift,
- & "damax=",damax,"edriftmax=",edriftmax,
- & "d_time=",d_time
- stop
- endif
-c First step of the velocity Verlet algorithm
- if (lang.eq.2) then
- call sd_verlet1
- else if (lang.eq.3) then
- call sd_verlet1_ciccotti
- else if (lang.eq.1) then
- call sddir_verlet1
- else
- call verlet1
- endif
-c Build the chain from the newly calculated coordinates
- call chainbuild_cart
- if (rattle) call rattle1
- if (large.and. mod(itime,ntwe).eq.0) then
- write (iout,*) "Cartesian and internal coordinates: step 1"
- call cartprint
- call intout
- write (iout,*) "Accelerations"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
- & (d_a(j,i+nres),j=1,3)
- enddo
- write (iout,*) "Velocities, step 1"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
- tt0 = tcpu()
-c Calculate energy and forces
- call zerograd
- call etotal(energia)
- potE=energia(0)-energia(20)
- call cartgrad
-c Get the new accelerations
- call lagrangian
- t_enegrad=t_enegrad+tcpu()-tt0
-c Determine maximum acceleration and scale down the timestep if needed
- call max_accel
- call predict_edrift(epdrift)
- if (amax.gt.damax .or. epdrift.gt.edriftmax) then
-c Maximum acceleration or maximum predicted energy drift exceeded, rescale the time step
- scale=.true.
- ifac_time=dmax1(dlog(amax/damax),dlog(epdrift/edriftmax))
- & /dlog(2.0d0)+1
- itime_scal=itime_scal+ifac_time
-c fac_time=dmin1(damax/amax,0.5d0)
- fac_time=0.5d0**ifac_time
- d_time=d_time*fac_time
- if (lang.eq.2 .or. lang.eq.3) then
-c write (iout,*) "Calling sd_verlet_setup: 1"
-c Rescale the stochastic forces and recalculate or restore
-c the matrices of tinker integrator
- if (itime_scal.gt.maxflag_stoch) then
- if (large) write (iout,'(a,i5,a)')
- & "Calculate matrices for stochastic step;",
- & " itime_scal ",itime_scal
- if (lang.eq.2) then
- call sd_verlet_p_setup
- else
- call sd_verlet_ciccotti_setup
- endif
- write (iout,'(2a,i3,a,i3,1h.)')
- & "Warning: cannot store matrices for stochastic",
- & " integration because the index",itime_scal,
- & " is greater than",maxflag_stoch
- write (iout,'(2a)')"Increase MAXFLAG_STOCH or use direct",
- & " integration Langevin algorithm for better efficiency."
- else if (flag_stoch(itime_scal)) then
- if (large) write (iout,'(a,i5,a,l1)')
- & "Restore matrices for stochastic step; itime_scal ",
- & itime_scal," flag ",flag_stoch(itime_scal)
- do i=1,dimen
- do j=1,dimen
- pfric_mat(i,j)=pfric0_mat(i,j,itime_scal)
- afric_mat(i,j)=afric0_mat(i,j,itime_scal)
- vfric_mat(i,j)=vfric0_mat(i,j,itime_scal)
- prand_mat(i,j)=prand0_mat(i,j,itime_scal)
- vrand_mat1(i,j)=vrand0_mat1(i,j,itime_scal)
- vrand_mat2(i,j)=vrand0_mat2(i,j,itime_scal)
- enddo
- enddo
- else
- if (large) write (iout,'(2a,i5,a,l1)')
- & "Calculate & store matrices for stochastic step;",
- & " itime_scal ",itime_scal," flag ",flag_stoch(itime_scal)
- if (lang.eq.2) then
- call sd_verlet_p_setup
- else
- call sd_verlet_ciccotti_setup
- endif
- flag_stoch(ifac_time)=.true.
- do i=1,dimen
- do j=1,dimen
- pfric0_mat(i,j,itime_scal)=pfric_mat(i,j)
- afric0_mat(i,j,itime_scal)=afric_mat(i,j)
- vfric0_mat(i,j,itime_scal)=vfric_mat(i,j)
- prand0_mat(i,j,itime_scal)=prand_mat(i,j)
- vrand0_mat1(i,j,itime_scal)=vrand_mat1(i,j)
- vrand0_mat2(i,j,itime_scal)=vrand_mat2(i,j)
- enddo
- enddo
- endif
- fac_time=1.0d0/dsqrt(fac_time)
- do i=1,dimen
- stochforcvec(i)=fac_time*stochforcvec(i)
- enddo
- else if (lang.eq.1) then
-c Rescale the accelerations due to stochastic forces
- fac_time=1.0d0/dsqrt(fac_time)
- do i=1,dimen
- d_as_work(i)=d_as_work(i)*fac_time
- enddo
- endif
- if (large) write (iout,'(a,i10,a,f8.6,a,i3,a,i3)')
- & "itime",itime," Timestep scaled down to ",
- & d_time," ifac_time",ifac_time," itime_scal",itime_scal
- else
-c Second step of the velocity Verlet algorithm
- if (lang.eq.2) then
- call sd_verlet2
- else if (lang.eq.3) then
- call sd_verlet2_ciccotti
- else if (lang.eq.1) then
- call sddir_verlet2
- else
- call verlet2
- endif
- if (rattle) call rattle2
- totT=totT+d_time
- if (d_time.ne.d_time0) then
- d_time=d_time0
- if (lang.eq.2 .or. lang.eq.3) then
- if (large) write (iout,'(a)')
- & "Restore original matrices for stochastic step"
-c write (iout,*) "Calling sd_verlet_setup: 2"
-c Restore the matrices of tinker integrator if the time step has been restored
- do i=1,dimen
- do j=1,dimen
- pfric_mat(i,j)=pfric0_mat(i,j,0)
- afric_mat(i,j)=afric0_mat(i,j,0)
- vfric_mat(i,j)=vfric0_mat(i,j,0)
- prand_mat(i,j)=prand0_mat(i,j,0)
- vrand_mat1(i,j)=vrand0_mat1(i,j,0)
- vrand_mat2(i,j)=vrand0_mat2(i,j,0)
- enddo
- enddo
- endif
- endif
- scale=.false.
- endif
- enddo
-c Calculate the kinetic and the total energy and the kinetic temperature
- call kinetic(EK)
- totE=EK+potE
-c diagnostics
-c call kinetic1(EK1)
-c write (iout,*) "step",itime," EK",EK," EK1",EK1
-c end diagnostics
-c Couple the system to Berendsen bath if needed
- if (tbf .and. lang.eq.0) then
- call verlet_bath
- endif
- kinetic_T=2.0d0/(dimen*Rb)*EK
-c Backup the coordinates, velocities, and accelerations
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
- enddo
- if (mod(itime,ntwe).eq.0 .and. large) then
- write (iout,*) "Velocities, step 2"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
- return
- end
-c-------------------------------------------------------------------------------
- subroutine RESPA_step(itime)
-c-------------------------------------------------------------------------------
-c Perform a single RESPA step.
-c-------------------------------------------------------------------------------
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision energia(0:n_ene),energia_short(0:n_ene),
- & energia_long(0:n_ene)
- double precision cm(3),L(3),vcm(3),incr(3)
- integer ilen,count,rstcount
- external ilen
- character*50 tytul
- integer maxcount_scale /10/
- common /gucio/ cm
- double precision stochforcvec(MAXRES6)
- common /stochcalc/ stochforcvec
- integer itime
- logical scale
- if (large.and. mod(itime,ntwe).eq.0) then
- write (iout,*) "***************** RESPA itime",itime
- write (iout,*) "Cartesian and internal coordinates: step 0"
- call cartprint
- call intout
- write (iout,*) "Accelerations"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
- & (d_a(j,i+nres),j=1,3)
- enddo
- write (iout,*) "Velocities, step 0"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
-c
-c Perform the initial RESPA step (increment velocities)
-c write (iout,*) "*********************** RESPA ini"
- call RESPA_vel
- if (mod(itime,ntwe).eq.0 .and. large) then
- write (iout,*) "Velocities, end"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
-c Compute the short-range forces
- call zerograd
- call etotal_short(energia_short)
- call cartgrad
- call lagrangian
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
- enddo
- d_time0=d_time
-c Split the time step
- d_time=d_time/ntime_split
-c Perform the short-range RESPSA steps (velocity Verlet increments of
-c positions and velocities using short-range forces)
-c write (iout,*) "*********************** RESPA split"
- do itsplit=1,ntime_split
- if (lang.eq.1) then
- call sddir_precalc
- else if (lang.eq.2 .or. lang.eq.3) then
- call stochastic_force(stochforcvec)
- endif
-c First step of the velocity Verlet algorithm
- if (lang.eq.2) then
- call sd_verlet1
- else if (lang.eq.3) then
- call sd_verlet1_ciccotti
- else if (lang.eq.1) then
- call sddir_verlet1
- else
- call verlet1
- endif
-c Build the chain from the newly calculated coordinates
- call chainbuild_cart
- if (rattle) call rattle1
- if (large.and. mod(itime,ntwe).eq.0) then
- write (iout,*) "Cartesian and internal coordinates: step 1"
- call cartprint
- call intout
- write (iout,*) "Accelerations"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
- & (d_a(j,i+nres),j=1,3)
- enddo
- write (iout,*) "Velocities, step 1"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
- tt0 = tcpu()
-c Calculate energy and forces
- call zerograd
- call etotal_short(energia_short)
- call cartgrad
-c Get the new accelerations
- call lagrangian
- t_enegrad=t_enegrad+tcpu()-tt0
-c Second step of the velocity Verlet algorithm
- if (lang.eq.2) then
- call sd_verlet2
- else if (lang.eq.3) then
- call sd_verlet2_ciccotti
- else if (lang.eq.1) then
- call sddir_verlet2
- else
- call verlet2
- endif
- if (rattle) call rattle2
-c Backup the coordinates, velocities, and accelerations
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
- enddo
- enddo
-c Restore the time step
- d_time=d_time0
-c Compute long-range forces
- call zerograd
- call etotal_long(energia_long)
- call cartgrad
-c Compute accelerations from long-range forces
- call lagrangian
- if (large.and. mod(itime,ntwe).eq.0) then
- write (iout,*) "Cartesian and internal coordinates: step 2"
- call cartprint
- call intout
- write (iout,*) "Accelerations"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
- & (d_a(j,i+nres),j=1,3)
- enddo
- write (iout,*) "Velocities, step 2"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
-c Compute the final RESPA step (increment velocities)
-c write (iout,*) "*********************** RESPA fin"
- call RESPA_vel
-c Compute the complete potential energy
- potE=energia_short(0)+energia_long(0)
- totT=totT+d_time
-c Calculate the kinetic and the total energy and the kinetic temperature
- call kinetic(EK)
- totE=EK+potE
-c Couple the system to Berendsen bath if needed
- if (tbf .and. lang.eq.0) then
- call verlet_bath
- endif
- kinetic_T=2.0d0/(dimen*Rb)*EK
-c Backup the coordinates, velocities, and accelerations
- if (mod(itime,ntwe).eq.0 .and. large) then
- write (iout,*) "Velocities, end"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- endif
- return
- end
-c---------------------------------------------------------------------
- subroutine RESPA_vel
-c First and last RESPA step (incrementing velocities using long-range
-c forces).
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- do j=1,3
- d_t(j,0)=d_t(j,0)+0.5d0*d_a(j,0)*d_time
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t(j,i)+0.5d0*d_a(j,i)*d_time
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=d_t(j,inres)+0.5d0*d_a(j,inres)*d_time
- enddo
- endif
- enddo
- return
- end
-c-----------------------------------------------------------------
- subroutine verlet1
-c Applying velocity Verlet algorithm - step 1 to coordinates
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision adt,adt2
-
- do j=1,3
- adt=d_a_old(j,0)*d_time
- adt2=0.5d0*adt
- dc(j,0)=dc_old(j,0)+(d_t_old(j,0)+adt2)*d_time
- d_t_new(j,0)=d_t_old(j,0)+adt2
- d_t(j,0)=d_t_old(j,0)+adt
- enddo
- do i=nnt,nct-1
- do j=1,3
- adt=d_a_old(j,i)*d_time
- adt2=0.5d0*adt
- dc(j,i)=dc_old(j,i)+(d_t_old(j,i)+adt2)*d_time
- d_t_new(j,i)=d_t_old(j,i)+adt2
- d_t(j,i)=d_t_old(j,i)+adt
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- adt=d_a_old(j,inres)*d_time
- adt2=0.5d0*adt
- dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
- d_t_new(j,inres)=d_t_old(j,inres)+adt2
- d_t(j,inres)=d_t_old(j,inres)+adt
- enddo
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine verlet2
-c Step 2 of the velocity Verlet algorithm: update velocities
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+0.5d0*d_a(j,0)*d_time
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+0.5d0*d_a(j,i)*d_time
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=d_t_new(j,inres)+0.5d0*d_a(j,inres)*d_time
- enddo
- endif
- enddo
- return
- end
-c-----------------------------------------------------------------
- subroutine sddir_precalc
-c Applying velocity Verlet algorithm - step 1 to coordinates
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6)
- common /stochcalc/ stochforcvec
-c
-c Compute friction and stochastic forces
-c
- call friction_force
- call stochastic_force(stochforcvec)
-c
-c Compute the acceleration due to friction forces (d_af_work) and stochastic
-c forces (d_as_work)
-c
- do i=1,dimen
- d_af_work(i)=0.0d0
- d_as_work(i)=0.0d0
- do j=1,dimen
- d_af_work(i)=d_af_work(i)+Ginv(i,j)*fric_work(j)
- d_as_work(i)=d_as_work(i)+Ginv(i,j)*stochforcvec(j)
- enddo
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine sddir_verlet1
-c Applying velocity Verlet algorithm - step 1 to velocities
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
-c Revised 3/31/05 AL: correlation between random contributions to
-c position and velocity increments included.
- double precision sqrt13 /0.57735026918962576451d0/ ! 1/sqrt(3)
- double precision adt,adt2
-c
-c Add the contribution from BOTH friction and stochastic force to the
-c coordinates, but ONLY the contribution from the friction forces to velocities
-c
- do j=1,3
- adt=(d_a_old(j,0)+d_af_work(j))*d_time
- adt2=0.5d0*adt+sqrt13*d_as_work(j)*d_time
- dc(j,0)=dc_old(j,0)+(d_t_old(j,0)+adt2)*d_time
- d_t_new(j,0)=d_t_old(j,0)+0.5d0*adt
- d_t(j,0)=d_t_old(j,0)+adt
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- adt=(d_a_old(j,i)+d_af_work(ind+j))*d_time
- adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
- dc(j,i)=dc_old(j,i)+(d_t_old(j,i)+adt2)*d_time
- d_t_new(j,i)=d_t_old(j,i)+0.5d0*adt
- d_t(j,i)=d_t_old(j,i)+adt
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- adt=(d_a_old(j,inres)+d_af_work(ind+j))*d_time
- adt2=0.5d0*adt+sqrt13*d_as_work(ind+j)*d_time
- dc(j,inres)=dc_old(j,inres)+(d_t_old(j,inres)+adt2)*d_time
- d_t_new(j,inres)=d_t_old(j,inres)+0.5d0*adt
- d_t(j,inres)=d_t_old(j,inres)+adt
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine sddir_verlet2
-c Calculating the adjusted velocities for accelerations
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6),d_as_work1(MAXRES6)
- double precision cos60 /0.5d0/, sin60 /0.86602540378443864676d0/
-c Revised 3/31/05 AL: correlation between random contributions to
-c position and velocity increments included.
-c The correlation coefficients are calculated at low-friction limit.
-c Also, friction forces are now not calculated with new velocities.
-
-c call friction_force
- call stochastic_force(stochforcvec)
-c
-c Compute the acceleration due to friction forces (d_af_work) and stochastic
-c forces (d_as_work)
-c
- do i=1,dimen
-c d_af_work(i)=0.0d0
- d_as_work1(i)=0.0d0
- do j=1,dimen
-c d_af_work(i)=d_af_work(i)+Ginv(i,j)*fric_work(j)
- d_as_work1(i)=d_as_work1(i)+Ginv(i,j)*stochforcvec(j)
- enddo
- enddo
-c
-c Update velocities
-c
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+(0.5d0*(d_a(j,0)+d_af_work(j))
- & +sin60*d_as_work(j)+cos60*d_as_work1(j))*d_time
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+(0.5d0*(d_a(j,i)+d_af_work(ind+j))
- & +sin60*d_as_work(ind+j)+cos60*d_as_work1(ind+j))*d_time
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=d_t_new(j,inres)+(0.5d0*(d_a(j,inres)
- & +d_af_work(ind+j))+sin60*d_as_work(ind+j)
- & +cos60*d_as_work1(ind+j))*d_time
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine max_accel
-c
-c Find the maximum difference in the accelerations of the the sites
-c at the beginning and the end of the time step.
-c
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- double precision aux(3),accel(3)
- do j=1,3
- aux(j)=d_a(j,0)-d_a_old(j,0)
- enddo
- amax=0.0d0
- do i=nnt,nct
-c Backbone
- if (i.lt.nct) then
- do j=1,3
- accel(j)=aux(j)+0.5d0*(d_a(j,i)-d_a_old(j,i))
- if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
- enddo
- endif
-c Side chains
- do j=1,3
- accel(j)=aux(j)
- enddo
- if (itype(i).ne.10) then
- do j=1,3
- accel(j)=accel(j)+d_a(j,i+nres)-d_a_old(j,i+nres)
- enddo
- endif
- do j=1,3
- if (dabs(accel(j)).gt.amax) amax=dabs(accel(j))
- enddo
- do j=1,3
- aux(j)=aux(j)+d_a(j,i)-d_a_old(j,i)
- enddo
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine predict_edrift(epdrift)
-c
-c Predict the drift of the potential energy
-c
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.MUCA'
- double precision epdrift,epdriftij
-c Drift of the potential energy
- epdrift=0.0d0
- do i=nnt,nct
-c Backbone
- if (i.lt.nct) then
- do j=1,3
- epdriftij=dabs((d_a(j,i)-d_a_old(j,i))*gcart(j,i))
- if (lmuca) epdriftij=epdriftij*factor
-c write (iout,*) "back",i,j,epdriftij
- if (epdriftij.gt.epdrift) epdrift=epdriftij
- enddo
- endif
-c Side chains
- if (itype(i).ne.10) then
- do j=1,3
- epdriftij=
- & dabs((d_a(j,i+nres)-d_a_old(j,i+nres))*gxcart(j,i))
- if (lmuca) epdriftij=epdriftij*factor
-c write (iout,*) "side",i,j,epdriftij
- if (epdriftij.gt.epdrift) epdrift=epdriftij
- enddo
- endif
- enddo
- epdrift=0.5d0*epdrift*d_time*d_time
-c write (iout,*) "epdrift",epdrift
- return
- end
-c-----------------------------------------------------------------------
- subroutine verlet_bath
-c
-c Coupling to the thermostat by using the Berendsen algorithm
-c
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision T_half,fact
-c
- T_half=2.0d0/(dimen*Rb)*EK
- fact=dsqrt(1.0d0+(d_time/tau_bath)*(t_bath/T_half-1.0d0))
-c write(iout,*) "T_half", T_half
-c write(iout,*) "EK", EK
-c write(iout,*) "fact", fact
- do j=1,3
- d_t(j,0)=fact*d_t(j,0)
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=fact*d_t(j,i)
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=fact*d_t(j,inres)
- enddo
- endif
- enddo
- return
- end
-c---------------------------------------------------------
- subroutine init_MD
-c Set up the initial conditions of a MD simulation
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
-#ifdef MP
- include 'mpif.h'
- include 'COMMON.INFO'
- include 'COMMON.SETUP'
- character*4 liczba
- character*16 form
-#endif
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- real*8 energia(0:n_ene),energia_long(0:n_ene),
- & energia_short(0:n_ene),vcm(3),incr(3)
- double precision cm(3),L(3),xv,sigv,lowb,highb
- character*256 qstr
- integer ilen
- external ilen
- character*50 tytul
- common /gucio/ cm
- d_time0=d_time
- write(iout,*) "d_time", d_time
-c Compute the standard deviations of stochastic forces for Langevin dynamics
-c if the friction coefficients do not depend on surface area
- if (lang.gt.0 .and. .not.surfarea) then
- do i=nnt,nct-1
- stdforcp(i)=stdfp*dsqrt(gamp)
- enddo
- do i=nnt,nct
- stdforcsc(i)=stdfsc(itype(i))*dsqrt(gamsc(itype(i)))
- enddo
- endif
-c Open the pdb file for snapshotshots
-#ifdef MPI
- if (nprocs.eq.1) then
- npos=3
- else
- npos = dlog10(dfloat(nprocs-1))+1
- endif
- if (npos.lt.3) npos=3
- write (liczba,'(i1)') npos
- form = '(bz,i'//liczba(:ilen(liczba))//'.'//liczba(:ilen(liczba))
- & //')'
- write (liczba,form) myrank
- if(mdpdb) then
- open(ipdb,
- & file=prefix(:ilen(prefix))//"_MD"//liczba(:ilen(liczba))
- & //".pdb")
- else
- cartname=prefix(:ilen(prefix))//"_MD"//liczba(:ilen(liczba))
- & //".cx"
- endif
-#else
- if(mdpdb) then
- open(ipdb,file=prefix(:ilen(prefix))//"_MD.pdb")
- else
- cartname=prefix(:ilen(prefix))//"_MD.cx"
- endif
-#endif
- if (usampl) then
- write (qstr,'(256(1h ))')
- ipos=1
- do i=1,nfrag
- iq = qinfrag(i)*10
- iw = wfrag(i)/100
- if (iw.gt.0) then
- write (iout,*) "Frag",qinfrag(i),wfrag(i),iq,iw
- write (qstr(ipos:ipos+6),'(2h_f,i1,1h_,i1,1h_,i1)') i,iq,iw
- ipos=ipos+7
- endif
- enddo
- do i=1,npair
- iq = qinpair(i)*10
- iw = wpair(i)/100
- if (iw.gt.0) then
- write (iout,*) "Pair",i,qinpair(i),wpair(i),iq,iw
- write (qstr(ipos:ipos+6),'(2h_p,i1,1h_,i1,1h_,i1)') i,iq,iw
- ipos=ipos+7
- endif
- enddo
- pdbname=pdbname(:ilen(pdbname)-4)//qstr(:ipos-1)//'.pdb'
- cartname=cartname(:ilen(cartname)-2)//qstr(:ipos-1)//'.x'
- statname=statname(:ilen(statname)-5)//qstr(:ipos-1)//'.stat'
- endif
- icg=1
- if (rest) then
- write(iout,*) "Initial state will be read from file ",
- & rest2name(:ilen(rest2name))
- call readrst
- else
-c Generate initial velocities
- write(iout,*) "Initial velocities randomly generated"
- call random_vel
- totT=0.0d0
- endif
-c rest2name = prefix(:ilen(prefix))//'.rst'
- write(iout,*) "Initial backbone velocities"
- do i=nnt,nct-1
- write(iout,*) (d_t(j,i),j=1,3)
- enddo
- write(iout,*) "Initial side-chain velocities"
- do i=nnt,nct
- write(iout,*) (d_t(j,i+nres),j=1,3)
- enddo
-c Zeroing the total angular momentum of the system
- write(iout,*) "Calling the zero-angular
- & momentum subroutine"
- call inertia_tensor
-c Getting the potential energy and forces and velocities and accelerations
- call vcm_vel(vcm)
-c write (iout,*) "velocity of the center of the mass:"
-c write (iout,*) (vcm(j),j=1,3)
- do j=1,3
- d_t(j,0)=d_t(j,0)-vcm(j)
- enddo
-c Removing the velocity of the center of mass
- call vcm_vel(vcm)
- write (iout,*) "vcm right after adjustment:"
- write (iout,*) (vcm(j),j=1,3)
- if (.not.rest) then
- call chainbuild
- endif
- call chainbuild_cart
- call kinetic(EK)
- if (tbf) then
- call verlet_bath(EK)
- endif
- kinetic_T=2.0d0/(dimen*Rb)*EK
- call cartprint
- call intout
- call zerograd
- call etotal(energia)
- potE=energia(0)
- call cartgrad
- call lagrangian
- call max_accel
- if (amax*d_time .gt. dvmax) d_time=d_time*dvmax/amax
- write(iout,*) "Potential energy"
- write(iout,*) (energia(i),i=0,n_ene)
- potE=energia(0)-energia(20)
- totE=EK+potE
- call statout(itime)
- write (iout,*) "Initial:",
- & " Kinetic energy",EK," potential energy",potE,
- & " total energy",totE," maximum acceleration ",
- & amax
- if (large) then
- write (iout,*) "Initial velocities"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_t(j,i),j=1,3),
- & (d_t(j,i+nres),j=1,3)
- enddo
- write (iout,*) "Initial accelerations"
- do i=0,nres
- write (iout,'(i3,3f10.5,3x,3f10.5)') i,(d_a(j,i),j=1,3),
- & (d_a(j,i+nres),j=1,3)
- enddo
- endif
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
-c write (iout,*) "dc_old",i,(dc_old(j,i),j=1,3)
- enddo
- if (RESPA) then
- call zerograd
- call etotal_long(energia_long)
- call cartgrad
- call lagrangian
-c call etotal_short(energia_short)
-c write (iout,*) "energia_long",energia_long(0),
-c & " energia_short",energia_short(0),
-c & " total",energia_long(0)+energia_short(0)
- endif
- return
- end
-c-----------------------------------------------------------
- subroutine random_vel
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision xv,sigv,lowb,highb
-c Generate random velocities from Gaussian distribution of mean 0 and std of KT/m
-c First generate velocities in the eigenspace of the G matrix
-c write (iout,*) "Calling random_vel"
- xv=0.0d0
- do i=1,dimen
- sigv=dsqrt((Rb*t_bath)/geigen(i))
- lowb=-5*sigv
- highb=5*sigv
- d_t_work_new(i)=anorm_distr(xv,sigv,lowb,highb)
- enddo
-c Ek1=0.0d0
-c do i=1,dimen
-c Ek1=Ek1+0.5d0*geigen(i)*d_t_work_new(i)**2
-c enddo
-c Transform velocities to UNRES coordinate space
- do i=1,dimen
- d_t_work(i)=0.0d0
- do j=1,dimen
- d_t_work(i)=d_t_work(i)+Gvec(i,j)*d_t_work_new(j)
- enddo
- enddo
-c Transfer to the d_t vector
- do j=1,3
- d_t(j,0)=d_t_work(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- ind=ind+1
- d_t(j,i)=d_t_work(ind)
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- do j=1,3
- ind=ind+1
- d_t(j,i+nres)=d_t_work(ind)
- enddo
- endif
- enddo
-c call kinetic(EK)
-c write (iout,*) "Kinetic energy",Ek,EK1," kinetic temperature",
-c & 2.0d0/(dimen*Rb)*EK,2.0d0/(dimen*Rb)*EK1
- return
- end
-c-----------------------------------------------------------
- subroutine sd_verlet_p_setup
-c Sets up the parameters of stochastic Verlet algorithm
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision emgdt(MAXRES6),
- & pterm,vterm,rho,rhoc,vsig,
- & pfric_vec(MAXRES6),vfric_vec(MAXRES6),
- & afric_vec(MAXRES6),prand_vec(MAXRES6),
- & vrand_vec1(MAXRES6),vrand_vec2(MAXRES6)
- logical lprn /.false./
- double precision zero /1.0d-8/, gdt_radius /0.05d0/
- double precision ktm
- tt0 = tcpu()
-c
-c AL 8/17/04 Code adapted from tinker
-c
-c Get the frictional and random terms for stochastic dynamics in the
-c eigenspace of mass-scaled UNRES friction matrix
-c
- do i = 1, dimen
- gdt = fricgam(i) * d_time
-c
-c Stochastic dynamics reduces to simple MD for zero friction
-c
- if (gdt .le. zero) then
- pfric_vec(i) = 1.0d0
- vfric_vec(i) = d_time
- afric_vec(i) = 0.5d0 * d_time * d_time
- prand_vec(i) = 0.0d0
- vrand_vec1(i) = 0.0d0
- vrand_vec2(i) = 0.0d0
-c
-c Analytical expressions when friction coefficient is large
-c
- else
- if (gdt .ge. gdt_radius) then
- egdt = dexp(-gdt)
- pfric_vec(i) = egdt
- vfric_vec(i) = (1.0d0-egdt) / fricgam(i)
- afric_vec(i) = (d_time-vfric_vec(i)) / fricgam(i)
- pterm = 2.0d0*gdt - 3.0d0 + (4.0d0-egdt)*egdt
- vterm = 1.0d0 - egdt**2
- rho = (1.0d0-egdt)**2 / sqrt(pterm*vterm)
-c
-c Use series expansions when friction coefficient is small
-c
- else
- gdt2 = gdt * gdt
- gdt3 = gdt * gdt2
- gdt4 = gdt2 * gdt2
- gdt5 = gdt2 * gdt3
- gdt6 = gdt3 * gdt3
- gdt7 = gdt3 * gdt4
- gdt8 = gdt4 * gdt4
- gdt9 = gdt4 * gdt5
- afric_vec(i) = (gdt2/2.0d0 - gdt3/6.0d0 + gdt4/24.0d0
- & - gdt5/120.0d0 + gdt6/720.0d0
- & - gdt7/5040.0d0 + gdt8/40320.0d0
- & - gdt9/362880.0d0) / fricgam(i)**2
- vfric_vec(i) = d_time - fricgam(i)*afric_vec(i)
- pfric_vec(i) = 1.0d0 - fricgam(i)*vfric_vec(i)
- pterm = 2.0d0*gdt3/3.0d0 - gdt4/2.0d0
- & + 7.0d0*gdt5/30.0d0 - gdt6/12.0d0
- & + 31.0d0*gdt7/1260.0d0 - gdt8/160.0d0
- & + 127.0d0*gdt9/90720.0d0
- vterm = 2.0d0*gdt - 2.0d0*gdt2 + 4.0d0*gdt3/3.0d0
- & - 2.0d0*gdt4/3.0d0 + 4.0d0*gdt5/15.0d0
- & - 4.0d0*gdt6/45.0d0 + 8.0d0*gdt7/315.0d0
- & - 2.0d0*gdt8/315.0d0 + 4.0d0*gdt9/2835.0d0
- rho = sqrt(3.0d0) * (0.5d0 - 3.0d0*gdt/16.0d0
- & - 17.0d0*gdt2/1280.0d0
- & + 17.0d0*gdt3/6144.0d0
- & + 40967.0d0*gdt4/34406400.0d0
- & - 57203.0d0*gdt5/275251200.0d0
- & - 1429487.0d0*gdt6/13212057600.0d0)
- end if
-c
-c Compute the scaling factors of random terms for the nonzero friction case
-c
- ktm = 0.5d0*d_time/fricgam(i)
- psig = dsqrt(ktm*pterm) / fricgam(i)
- vsig = dsqrt(ktm*vterm)
- rhoc = dsqrt(1.0d0 - rho*rho)
- prand_vec(i) = psig
- vrand_vec1(i) = vsig * rho
- vrand_vec2(i) = vsig * rhoc
- end if
- end do
- if (lprn) then
- write (iout,*)
- & "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",
- & " vrand_vec2"
- do i=1,dimen
- write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),
- & afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
- enddo
- endif
-c
-c Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
-c
- call eigtransf(dimen,maxres6,mt3,mt2,pfric_vec,pfric_mat)
- call eigtransf(dimen,maxres6,mt3,mt2,vfric_vec,vfric_mat)
- call eigtransf(dimen,maxres6,mt3,mt2,afric_vec,afric_mat)
- call eigtransf(dimen,maxres6,mt3,mt1,prand_vec,prand_mat)
- call eigtransf(dimen,maxres6,mt3,mt1,vrand_vec1,vrand_mat1)
- call eigtransf(dimen,maxres6,mt3,mt1,vrand_vec2,vrand_mat2)
-c call eigtransf1(dimen,maxres6,mt3mt2,pfric_vec,pfric_mat)
-c call eigtransf1(dimen,maxres6,mt3mt2,vfric_vec,vfric_mat)
-c call eigtransf1(dimen,maxres6,mt3mt2,afric_vec,afric_mat)
-c call eigtransf1(dimen,maxres6,mt3mt1,prand_vec,prand_mat)
-c call eigtransf1(dimen,maxres6,mt3mt1,vrand_vec1,vrand_mat1)
-c call eigtransf1(dimen,maxres6,mt3mt1,vrand_vec2,vrand_mat2)
- t_sdsetup=t_sdsetup+tcpu()-tt0
- return
- end
-c-------------------------------------------------------------
- subroutine eigtransf1(n,ndim,ab,d,c)
- implicit none
- integer n,ndim
- double precision ab(ndim,ndim,n),c(ndim,n),d(ndim)
- integer i,j,k
- do i=1,n
- do j=1,n
- c(i,j)=0.0d0
- do k=1,n
- c(i,j)=c(i,j)+ab(k,j,i)*d(k)
- enddo
- enddo
- enddo
- return
- end
-c-------------------------------------------------------------
- subroutine eigtransf(n,ndim,a,b,d,c)
- implicit none
- integer n,ndim
- double precision a(ndim,n),b(ndim,n),c(ndim,n),d(ndim)
- integer i,j,k
- do i=1,n
- do j=1,n
- c(i,j)=0.0d0
- do k=1,n
- c(i,j)=c(i,j)+a(i,k)*b(k,j)*d(k)
- enddo
- enddo
- enddo
- return
- end
-c-------------------------------------------------------------
- subroutine sd_verlet1
-c Applying stochastic velocity Verlet algorithm - step 1 to velocities
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6)
- common /stochcalc/ stochforcvec
- logical lprn /.false./
-
-c write (iout,*) "dc_old"
-c do i=0,nres
-c write (iout,'(i5,3f10.5,5x,3f10.5)')
-c & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
-c enddo
- do j=1,3
- dc_work(j)=dc_old(j,0)
- d_t_work(j)=d_t_old(j,0)
- d_a_work(j)=d_a_old(j,0)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- dc_work(ind+j)=dc_old(j,i)
- d_t_work(ind+j)=d_t_old(j,i)
- d_a_work(ind+j)=d_a_old(j,i)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- do j=1,3
- dc_work(ind+j)=dc_old(j,i+nres)
- d_t_work(ind+j)=d_t_old(j,i+nres)
- d_a_work(ind+j)=d_a_old(j,i+nres)
- enddo
- ind=ind+3
- endif
- enddo
-
- if (lprn) then
- write (iout,*)
- & "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",
- & " vrand_mat2"
- do i=1,dimen
- do j=1,dimen
- write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),
- & vfric_mat(i,j),afric_mat(i,j),
- & prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
- enddo
- enddo
- endif
- do i=1,dimen
- ddt1=0.0d0
- ddt2=0.0d0
- do j=1,dimen
- dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j)
- & +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
- ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
- ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
- enddo
- d_t_work_new(i)=ddt1+0.5d0*ddt2
- d_t_work(i)=ddt1+ddt2
- enddo
- do j=1,3
- dc(j,0)=dc_work(j)
- d_t(j,0)=d_t_work(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- dc(j,i)=dc_work(ind+j)
- d_t(j,i)=d_t_work(ind+j)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- dc(j,inres)=dc_work(ind+j)
- d_t(j,inres)=d_t_work(ind+j)
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
-c--------------------------------------------------------------------------
- subroutine sd_verlet2
-c Calculating the adjusted velocities for accelerations
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6),stochforcvecV(MAXRES6)
- common /stochcalc/ stochforcvec
-c
-c Compute the stochastic forces which contribute to velocity change
-c
- call stochastic_force(stochforcvecV)
-
- do i=1,dimen
- ddt1=0.0d0
- ddt2=0.0d0
- do j=1,dimen
- ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
- ddt2=ddt2+vrand_mat1(i,j)*stochforcvec(j)+
- & vrand_mat2(i,j)*stochforcvecV(j)
- enddo
- d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
- enddo
- do j=1,3
- d_t(j,0)=d_t_work(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_work(ind+j)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=d_t_work(ind+j)
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
-c-----------------------------------------------------------
- subroutine sd_verlet_ciccotti_setup
-c Sets up the parameters of stochastic velocity Verlet algorithmi; Ciccotti's
-c version
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- include 'COMMON.TIME1'
- double precision emgdt(MAXRES6),
- & pterm,vterm,rho,rhoc,vsig,
- & pfric_vec(MAXRES6),vfric_vec(MAXRES6),
- & afric_vec(MAXRES6),prand_vec(MAXRES6),
- & vrand_vec1(MAXRES6),vrand_vec2(MAXRES6)
- logical lprn /.false./
- double precision zero /1.0d-8/, gdt_radius /0.05d0/
- double precision ktm
- tt0 = tcpu()
-c
-c AL 8/17/04 Code adapted from tinker
-c
-c Get the frictional and random terms for stochastic dynamics in the
-c eigenspace of mass-scaled UNRES friction matrix
-c
- do i = 1, dimen
- write (iout,*) "i",i," fricgam",fricgam(i)
- gdt = fricgam(i) * d_time
-c
-c Stochastic dynamics reduces to simple MD for zero friction
-c
- if (gdt .le. zero) then
- pfric_vec(i) = 1.0d0
- vfric_vec(i) = d_time
- afric_vec(i) = 0.5d0*d_time*d_time
- prand_vec(i) = afric_vec(i)
- vrand_vec2(i) = vfric_vec(i)
-c
-c Analytical expressions when friction coefficient is large
-c
- else
- egdt = dexp(-gdt)
- pfric_vec(i) = egdt
- vfric_vec(i) = dexp(-0.5d0*gdt)*d_time
- afric_vec(i) = 0.5d0*dexp(-0.25d0*gdt)*d_time*d_time
- prand_vec(i) = afric_vec(i)
- vrand_vec2(i) = vfric_vec(i)
-c
-c Compute the scaling factors of random terms for the nonzero friction case
-c
-c ktm = 0.5d0*d_time/fricgam(i)
-c psig = dsqrt(ktm*pterm) / fricgam(i)
-c vsig = dsqrt(ktm*vterm)
-c prand_vec(i) = psig*afric_vec(i)
-c vrand_vec2(i) = vsig*vfric_vec(i)
- end if
- end do
- if (lprn) then
- write (iout,*)
- & "pfric_vec, vfric_vec, afric_vec, prand_vec, vrand_vec1,",
- & " vrand_vec2"
- do i=1,dimen
- write (iout,'(i5,6e15.5)') i,pfric_vec(i),vfric_vec(i),
- & afric_vec(i),prand_vec(i),vrand_vec1(i),vrand_vec2(i)
- enddo
- endif
-c
-c Transform from the eigenspace of mass-scaled friction matrix to UNRES variables
-c
- call eigtransf(dimen,maxres6,mt3,mt2,pfric_vec,pfric_mat)
- call eigtransf(dimen,maxres6,mt3,mt2,vfric_vec,vfric_mat)
- call eigtransf(dimen,maxres6,mt3,mt2,afric_vec,afric_mat)
- call eigtransf(dimen,maxres6,mt3,mt1,prand_vec,prand_mat)
- call eigtransf(dimen,maxres6,mt3,mt1,vrand_vec2,vrand_mat2)
- t_sdsetup=t_sdsetup+tcpu()-tt0
- return
- end
-c-------------------------------------------------------------
- subroutine sd_verlet1_ciccotti
-c Applying stochastic velocity Verlet algorithm - step 1 to velocities
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6)
- common /stochcalc/ stochforcvec
- logical lprn /.false./
-
-c write (iout,*) "dc_old"
-c do i=0,nres
-c write (iout,'(i5,3f10.5,5x,3f10.5)')
-c & i,(dc_old(j,i),j=1,3),(dc_old(j,i+nres),j=1,3)
-c enddo
- do j=1,3
- dc_work(j)=dc_old(j,0)
- d_t_work(j)=d_t_old(j,0)
- d_a_work(j)=d_a_old(j,0)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- dc_work(ind+j)=dc_old(j,i)
- d_t_work(ind+j)=d_t_old(j,i)
- d_a_work(ind+j)=d_a_old(j,i)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- do j=1,3
- dc_work(ind+j)=dc_old(j,i+nres)
- d_t_work(ind+j)=d_t_old(j,i+nres)
- d_a_work(ind+j)=d_a_old(j,i+nres)
- enddo
- ind=ind+3
- endif
- enddo
-
- if (lprn) then
- write (iout,*)
- & "pfric_mat, vfric_mat, afric_mat, prand_mat, vrand_mat1,",
- & " vrand_mat2"
- do i=1,dimen
- do j=1,dimen
- write (iout,'(2i5,6e15.5)') i,j,pfric_mat(i,j),
- & vfric_mat(i,j),afric_mat(i,j),
- & prand_mat(i,j),vrand_mat1(i,j),vrand_mat2(i,j)
- enddo
- enddo
- endif
- do i=1,dimen
- ddt1=0.0d0
- ddt2=0.0d0
- do j=1,dimen
- dc_work(i)=dc_work(i)+vfric_mat(i,j)*d_t_work(j)
- & +afric_mat(i,j)*d_a_work(j)+prand_mat(i,j)*stochforcvec(j)
- ddt1=ddt1+pfric_mat(i,j)*d_t_work(j)
- ddt2=ddt2+vfric_mat(i,j)*d_a_work(j)
- enddo
- d_t_work_new(i)=ddt1+0.5d0*ddt2
- d_t_work(i)=ddt1+ddt2
- enddo
- do j=1,3
- dc(j,0)=dc_work(j)
- d_t(j,0)=d_t_work(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- dc(j,i)=dc_work(ind+j)
- d_t(j,i)=d_t_work(ind+j)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- dc(j,inres)=dc_work(ind+j)
- d_t(j,inres)=d_t_work(ind+j)
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
-c--------------------------------------------------------------------------
- subroutine sd_verlet2_ciccotti
-c Calculating the adjusted velocities for accelerations
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.CONTROL'
- include 'COMMON.VAR'
- include 'COMMON.MD'
- include 'COMMON.LANGEVIN'
- include 'COMMON.CHAIN'
- include 'COMMON.DERIV'
- include 'COMMON.GEO'
- include 'COMMON.LOCAL'
- include 'COMMON.INTERACT'
- include 'COMMON.IOUNITS'
- include 'COMMON.NAMES'
- double precision stochforcvec(MAXRES6),stochforcvecV(MAXRES6)
- common /stochcalc/ stochforcvec
-c
-c Compute the stochastic forces which contribute to velocity change
-c
- call stochastic_force(stochforcvecV)
-
- do i=1,dimen
- ddt1=0.0d0
- ddt2=0.0d0
- do j=1,dimen
- ddt1=ddt1+vfric_mat(i,j)*d_a_work(j)
-c ddt2=ddt2+vrand_mat2(i,j)*stochforcvecV(j)
- ddt2=ddt2+vrand_mat2(i,j)*stochforcvec(j)
- enddo
- d_t_work(i)=d_t_work_new(i)+0.5d0*ddt1+ddt2
- enddo
- do j=1,3
- d_t(j,0)=d_t_work(j)
- enddo
- ind=3
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_work(ind+j)
- enddo
- ind=ind+3
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t(j,inres)=d_t_work(ind+j)
- enddo
- ind=ind+3
- endif
- enddo
- return
- end
projects / unres.git / blobdiff