+++ /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
- double precision HNose1,HNose,HNose_nh,H,vtnp(maxres6)
- double precision vtnp_(maxres6),vtnp_a(maxres6)
-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 if (tnp1) then
- call tnp1_step1
- else if (tnp) then
- call tnp_step1
- else
- if (tnh) then
-
- call nhcint(EK,scale_nh,wdti,wdti2,wdti4,wdti8)
-
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)*scale_nh
- enddo
- enddo
- endif
- 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
- E_old=potE
- 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 if (tnp1) then
- call tnp1_step2
- else if (tnp) then
- call tnp_step2
- else
- call verlet2
- if (tnh) then
- call kinetic(EK)
- call nhcint(EK,scale_nh,wdti,wdti2,wdti4,wdti8)
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t(j,i)*scale_nh
- enddo
- enddo
- endif
- 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
- if (tnp .or. tnp1) then
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=d_t(j,i)
- d_t(j,i)=d_t(j,i)/s_np
- enddo
- enddo
- endif
- 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)
- if(.not.(tnp .or. tnp1)) d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
- enddo
-c if (mod(itime,ntwe).eq.0 .and. large) then
- if (mod(itime,ntwe).eq.0) then
-
- if(tnp .or. tnp1) then
- HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen)
- H=(HNose1-H0)*s_np
-cd write (iout,'(a,10f)') "hhh",EK,s_np,potE,pi_np,H0
-cd & ,EK+potE+pi_np**2/(2*Q_np)+dimen*0.001986d0*t_bath*log(s_np)
- write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
- endif
-
- if(tnh) then
- HNose1=Hnose_nh(EK,potE)
- H=HNose1-H0
- write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
- endif
-
- if (large) then
- itnp=0
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,0)
- enddo
- do i=nnt,nct-1
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,i)
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,inres)
- enddo
- endif
- enddo
-
-c Transform velocities from UNRES coordinate space to cartesian and Gvec
-c eigenvector space
-
- do i=1,dimen
- vtnp_(i)=0.0d0
- vtnp_a(i)=0.0d0
- do j=1,dimen
- vtnp_(i)=vtnp_(i)+Gvec(j,i)*vtnp(j)
- vtnp_a(i)=vtnp_a(i)+A(i,j)*vtnp(j)
- enddo
- vtnp_(i)=vtnp_(i)*dsqrt(geigen(i))
- enddo
-
- do i=1,dimen
- write (iout,'("WWW",i3,3f10.5)') i,vtnp(i),vtnp_(i),vtnp_a(i)
- enddo
-
- endif
- 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)
- double precision grad_tmp(3,0:maxres2)
- common /stochcalc/ stochforcvec
- integer itime
- logical scale
- double precision vtnp(maxres6), vtnp_(maxres6), vtnp_a(maxres6)
- 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"
-
- if (tnp1) then
-creview call tnp1_respa_step1
- call tnp_respa_step1
- else if (tnp) then
- call tnp_respa_step1
- else
- if (tnh.and..not.xiresp) then
- call nhcint(EK,scale_nh,wdti,wdti2,wdti4,wdti8)
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t(j,i)*scale_nh
- enddo
- enddo
- endif
- call RESPA_vel
- endif
-
-cd if(tnp .or. tnp1) then
-cd write (iout,'(a,3f)') "EE1 NP S, pi",totT, s_np, pi_np
-cd endif
-
- 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
-cr if (tnp) then
-cr do i=0,nres
-cr do j=1,3
-cr grad_tmp(j,i)=gcart(j,i)
-cr grad_tmp(j,i+nres)=gxcart(j,i)
-cr enddo
-cr enddo
-cr endif
-c
-c Compute the short-range forces
- call zerograd
- call etotal_short(energia_short)
- if (tnp.or.tnp1) potE=energia_short(0)
- call cartgrad
- call lagrangian
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- if(.not.(tnp .or. tnp1)) 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
-ctest E_long2=E_long
-c Perform the short-range RESPSA steps (velocity Verlet increments of
-c positions and velocities using short-range forces)
-c write (iout,*) "*********************** RESPA split"
-creview E_old=potE
- 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 if (tnp1) then
- call tnp1_respa_i_step1
-cr if(itsplit.eq.1)then
-cr d_time_s12=d_time0*0.5*s12_np
-cr do j=1,3
-cr d_t_half(j,0)=d_t_old(j,0)+d_a_old(j,0)*d_time_s12
-cr enddo
-cr do i=nnt,nct-1
-cr do j=1,3
-cr d_t_half(j,i)=d_t_old(j,i)+d_a_old(j,i)*d_time_s12
-cr enddo
-cr enddo
-cr do i=nnt,nct
-cr if (itype(i).ne.10) then
-cr inres=i+nres
-cr do j=1,3
-cr d_t_half(j,inres)=d_t_old(j,inres)
-cr & +d_a_old(j,inres)*d_time_s12
-cr enddo
-cr endif
-cr enddo
-cr endif
- else if (tnp) then
- call tnp_respa_i_step1
- else
- if (tnh.and.xiresp) then
- call kinetic(EK)
- call nhcint(EK,scale_nh,wdtii,wdtii2,wdtii4,wdtii8)
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)*scale_nh
- enddo
- enddo
-cd write(iout,*) "SSS1",itsplit,EK,scale_nh
- endif
- 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
-c
-c E_long aproximation
-cr if (tnp .or. tnp1) then
-cr dtmp=0.5*d_time*(1.0/s12_np+1.0/s_np)
-cr do i=0,2*nres
-cr do j=1,3
-cr E_long=E_long+d_t_new(j,i)*dtmp*grad_tmp(j,i)
-cr enddo
-cr enddo
-cr endif
-c-------------------------------------
-c test of reviewer's comment
-cr E_long=0
-c-------------------------------------
-
-
-c
-ctest call etotal_long(energia_long)
-ctest E_long=energia_long(0)
-ctest
- call zerograd
-
- call etotal_short(energia_short)
- E_old=potE
- potE=energia_short(0)
-
-c if(tnp .or. tnp1) then
-c write (iout,*) "kkk",E_long2,E_long
-c endif
-
-
- 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 if (tnp1) then
- call tnp1_respa_i_step2
- else if (tnp) then
- call tnp_respa_i_step2
- else
- call verlet2
- if (tnh.and.xiresp) then
- call kinetic(EK)
- call nhcint(EK,scale_nh,wdtii,wdtii2,wdtii4,wdtii8)
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t(j,i)*scale_nh
- enddo
- enddo
-cd write(iout,*) "SSS2",itsplit,EK,scale_nh
- endif
-
- endif
- if (rattle) call rattle2
-c Backup the coordinates, velocities, and accelerations
- if (tnp .or. tnp1) then
- do i=0,2*nres
- do j=1,3
- d_t_old(j,i)=d_t(j,i)
- if (tnp) d_t(j,i)=d_t(j,i)/s_np
- if (tnp1) d_t(j,i)=d_t(j,i)/s_np
- enddo
- enddo
-
- endif
- do i=0,2*nres
- do j=1,3
- dc_old(j,i)=dc(j,i)
- if(.not.(tnp .or. tnp1)) d_t_old(j,i)=d_t(j,i)
- d_a_old(j,i)=d_a(j,i)
- enddo
- enddo
-
-cd if(tnp .or. tnp1) then
-cd call kinetic(EK)
-cd HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen)
-cd H=(HNose1-H0)*s_np
-cd write (iout,*) "jjj",EK,potE
-cd write (iout,*) "iii H=",H,abs(HNose1-H0)/H0
-cd write (iout,'(a,3f)')
-cd & "III NP S, pi",totT+itsplit*d_time, s_np, pi_np
-cd endif
-
-
- enddo
-c Restore the time step
- d_time=d_time0
-c Compute long-range forces
- call zerograd
- call etotal_long(energia_long)
- E_long=energia_long(0)
- potE=energia_short(0)+energia_long(0)
- 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"
- if (tnp1) then
-creview call tnp1_respa_step2
- call tnp_respa_step2
- else if (tnp) then
- call tnp_respa_step2
- else
- call RESPA_vel
- if (tnh.and..not.xiresp) then
- call kinetic(EK)
- call nhcint(EK,scale_nh,wdti,wdti2,wdti4,wdti8)
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t(j,i)*scale_nh
- enddo
- enddo
- endif
- endif
-
- if (tnp .or. tnp1) then
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_old(j,i)/s_np
- enddo
- enddo
- endif
-
-c Compute the complete potential energy
-cc 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
-
-c-----review
-c if(tnp .or. tnp1) then
-c HNose1=Hnose(EK,s_np,energia_short(0),pi_np,Q_np,t_bath,dimen)
-c_new_var_csplit Csplit=H0-E_long
-c Csplit=H0-energia_short(0)
-c endif
-c----------
-
-
- if (mod(itime,ntwe).eq.0) then
-
- if(tnp .or. tnp1) then
- write (iout,'(a3,7f)') "TTT",EK,s_np,potE,pi_np,Csplit,
- & E_long,energia_short(0)
- HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen)
- H=(HNose1-H0)*s_np
-cd write (iout,'(a,10f)') "hhh",EK,s_np,potE,pi_np,H0
-cd & ,EK+potE+pi_np**2/(2*Q_np)+dimen*0.001986d0*t_bath*log(s_np)
- write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
-cd write (iout,'(a,3f)') "EE2 NP S, pi",totT, s_np, pi_np
- endif
-
- if(tnh) then
- HNose1=Hnose_nh(EK,potE)
- H=HNose1-H0
- write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
- endif
-
-
- if (large) then
- itnp=0
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,0)
- enddo
- do i=nnt,nct-1
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,i)
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- itnp=itnp+1
- vtnp(itnp)=d_t(j,inres)
- enddo
- endif
- enddo
-
-c Transform velocities from UNRES coordinate space to cartesian and Gvec
-c eigenvector space
-
- do i=1,dimen
- vtnp_(i)=0.0d0
- vtnp_a(i)=0.0d0
- do j=1,dimen
- vtnp_(i)=vtnp_(i)+Gvec(j,i)*vtnp(j)
- vtnp_a(i)=vtnp_a(i)+A(i,j)*vtnp(j)
- enddo
- vtnp_(i)=vtnp_(i)*dsqrt(geigen(i))
- enddo
-
- do i=1,dimen
- write (iout,'("WWW",i3,3f10.5)') i,vtnp(i),vtnp_(i),vtnp_a(i)
- enddo
-
- endif
- 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
-
- 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),E_short
- 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)
-
- if(tnp .or. tnp1) then
- s_np=1.0
- pi_np=0.0
- HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen)
- H0=Hnose1
- write(iout,*) 'H0= ',H0
- endif
-
- if(tnh) then
- HNose1=Hnose_nh(EK,potE)
- H0=HNose1
- write (iout,*) 'H0= ',H0
- endif
-
-
- 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
- itime=0
- 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)
- E_long=energia_long(0)
- if(tnp .or. tnp1) then
- call etotal_short(energia_short)
- E_short=energia_short(0)
- HNose1=Hnose(EK,s_np,E_short,pi_np,Q_np,t_bath,dimen)
- Csplit=Hnose1
-c Csplit =110
-c_new_var_csplit Csplit=H0-E_long
-c Csplit = H0-energia_short(0)
- write(iout,*) 'Csplit= ',Csplit
- endif
- 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
-c------------------------------------------------------
- double precision function HNose(ek,s,e,pi,Q,t_bath,dimen)
- implicit none
- double precision ek,s,e,pi,Q,t_bath,Rb
- integer dimen
- Rb=0.001986d0
- HNose=ek+e+pi**2/(2*Q)+dimen*Rb*t_bath*log(s)
-c print '(6f15.5,i5,a2,2f15.5)',ek,s,e,pi,Q,t_bath,dimen,"--",
-c & pi**2/(2*Q),dimen*Rb*t_bath*log(s)
- return
- end
-c-----------------------------------------------------------------
- double precision function HNose_nh(eki,e)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.MD'
- HNose_nh=eki+e+dimen*Rb*t_bath*xlogs(1)+qmass(1)*vlogs(1)**2/2
- do i=2,nnos
- HNose_nh=HNose_nh+qmass(i)*vlogs(i)**2/2+Rb*t_bath*xlogs(i)
- enddo
-c write(4,'(5e15.5)')
-c & vlogs(1),xlogs(1),HNose,eki,e
- return
- end
-c-------------------------------------------------------
-
- subroutine tnp1_step1
-c Applying Nose-Poincare algorithm - step 1 to coordinates
-c JPSJ 70 75 (2001) S. Nose
-c
-c d_t is not updated here
-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 adt,adt2,tmp
-
- tmp=1+pi_np/(2*Q_np)*0.5*d_time
- s12_np=s_np*tmp**2
- pistar=pi_np/tmp
- s12_dt=d_time/s12_np
- d_time_s12=d_time*0.5*s12_np
-
- do j=1,3
- d_t_new(j,0)=d_t_old(j,0)+d_a_old(j,0)*d_time_s12
- dc(j,0)=dc_old(j,0)+d_t_new(j,0)*s12_dt
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_new(j,i)=d_t_old(j,i)+d_a_old(j,i)*d_time_s12
- dc(j,i)=dc_old(j,i)+d_t_new(j,i)*s12_dt
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_new(j,inres)=d_t_old(j,inres)+d_a_old(j,inres)*d_time_s12
- dc(j,inres)=dc_old(j,inres)+d_t_new(j,inres)*s12_dt
- enddo
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine tnp1_step2
-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'
-
- double precision d_time_s12
-
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_new(j,i)
- enddo
- enddo
-
- call kinetic(EK)
- EK=EK/s12_np**2
-
- d_time_s12=0.5d0*s12_np*d_time
-
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+d_a(j,0)*d_time_s12
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+d_a(j,i)*d_time_s12
- 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)+d_a(j,inres)*d_time_s12
- enddo
- endif
- enddo
-
-cd write(iout,*) 'pistar',pistar,EK,E_old,potE,s12_np
- pistar=pistar+(EK-0.5*(E_old+potE)
- & -dimen*Rb*t_bath*log(s12_np)+H0-dimen*Rb*t_bath)*d_time
- tmp=1+pistar/(2*Q_np)*0.5*d_time
- s_np=s12_np*tmp**2
- pi_np=pistar/tmp
-
- return
- end
-c---------------------------------------------------------------------
- subroutine tnp_step1
-c Applying Nose-Poincare algorithm - step 1 to coordinates
-c J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird
-c
-c d_t is not updated here, it is destroyed
-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 C_np,d_time_s,tmp,d_time_ss
-
- d_time_s=d_time*0.5*s_np
-
- do j=1,3
- d_t_new(j,0)=d_t_old(j,0)+d_a_old(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_new(j,i)=d_t_old(j,i)+d_a_old(j,i)*d_time_s
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_new(j,inres)=d_t_old(j,inres)+d_a_old(j,inres)*d_time_s
- enddo
- endif
- enddo
-
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_new(j,i)
- enddo
- enddo
-
- call kinetic(EK)
- EK=EK/s_np**2
-
- C_np=0.5*d_time*(dimen*Rb*t_bath*(1.0+log(s_np))-EK+potE-H0)
- & -pi_np
-
- pistar=-2.0*C_np/(1.0+sqrt(1.0-C_np*d_time/Q_np))
- tmp=0.5*d_time*pistar/Q_np
- s12_np=s_np*(1.0+tmp)/(1.0-tmp)
-c write(iout,*) 'tnp_step1',s_np,s12_np,EK,potE,C_np,pistar,tmp
-
- d_time_ss=0.5*d_time*(1.0/s12_np+1.0/s_np)
-
- do j=1,3
- dc(j,0)=dc_old(j,0)+d_t_new(j,0)*d_time_ss
- enddo
- do i=nnt,nct-1
- do j=1,3
- dc(j,i)=dc_old(j,i)+d_t_new(j,i)*d_time_ss
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- dc(j,inres)=dc_old(j,inres)+d_t_new(j,inres)*d_time_ss
- enddo
- endif
- enddo
-
- return
- end
-c-----------------------------------------------------------------
- subroutine tnp_step2
-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'
-
- double precision d_time_s
-
- EK=EK*(s_np/s12_np)**2
- HNose1=Hnose(EK,s12_np,potE,pistar,Q_np,t_bath,dimen)
- pi_np=pistar+0.5*d_time*(2*EK-dimen*Rb*t_bath)
- & -0.5*d_time*(HNose1-H0)
-
-cd write(iout,'(a,4f)') 'mmm',EK,potE,HNose1,pi_np
- d_time_s=d_time*0.5*s12_np
-
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+d_a(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+d_a(j,i)*d_time_s
- 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)+d_a(j,inres)*d_time_s
- enddo
- endif
- enddo
-
- s_np=s12_np
-
- return
- end
-c-----------------------------------------------------------------
- subroutine tnp1_respa_i_step1
-c Applying Nose-Poincare algorithm - step 1 to coordinates
-c JPSJ 70 75 (2001) S. Nose
-c
-c d_t is not updated here
-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 adt,adt2,tmp
-
- tmp=1+pi_np/(2*Q_np)*0.5*d_time
- s12_np=s_np*tmp**2
- pistar=pi_np/tmp
- s12_dt=d_time/s12_np
- d_time_s12=d_time*0.5*s12_np
-
- do j=1,3
- d_t_new(j,0)=d_t_old(j,0)+d_a_old(j,0)*d_time_s12
- dc(j,0)=dc_old(j,0)+d_t_new(j,0)*s12_dt
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_new(j,i)=d_t_old(j,i)+d_a_old(j,i)*d_time_s12
- dc(j,i)=dc_old(j,i)+d_t_new(j,i)*s12_dt
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_new(j,inres)=d_t_old(j,inres)+d_a_old(j,inres)*d_time_s12
- dc(j,inres)=dc_old(j,inres)+d_t_new(j,inres)*s12_dt
- enddo
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
-c-----------------------------------------------------------------
- subroutine tnp1_respa_step1_
-c Applying Nose-Poincare algorithm - step 1 to vel for RESPA
-c JPSJ 70 75 (2001) S. Nose
-c
-c d_t is not updated here
-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 adt,adt2,tmp
-
- tmp=1+pi_np/(2*Q_np)*0.5*d_time
- s12_np=s_np*tmp**2
- pistar=pi_np/tmp
- s12_dt=d_time/s12_np
- d_time_s12=d_time*0.5*s12_np
-
- do j=1,3
- d_t_old(j,0)=d_t_old(j,0)+d_a(j,0)*d_time_s12
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)+d_a(j,i)*d_time_s12
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_old(j,inres)=d_t_old(j,inres)+d_a(j,inres)*d_time_s12
- enddo
- endif
- enddo
- return
- end
-c---------------------------------------------------------------------
- subroutine tnp1_respa_i_step2
-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'
-
- double precision d_time_s12
-
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_new(j,i)
- enddo
- enddo
-
- call kinetic(EK)
- EK=EK/s12_np**2
-
- d_time_s12=0.5d0*s12_np*d_time
-
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+d_a(j,0)*d_time_s12
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+d_a(j,i)*d_time_s12
- 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)+d_a(j,inres)*d_time_s12
- enddo
- endif
- enddo
-
- pistar=pistar+(EK-0.5*(E_old+potE)
- & -dimen*Rb*t_bath*log(s12_np)+Csplit-dimen*Rb*t_bath)*d_time
- tmp=1+pistar/(2*Q_np)*0.5*d_time
- s_np=s12_np*tmp**2
- pi_np=pistar/tmp
-
- return
- end
-c---------------------------------------------------------------------
- subroutine tnp1_respa_step2_
-c Step 2 of the velocity Verlet algorithm: update velocities for RESPA
- 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 d_time_s12
-
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_half(j,i)
- enddo
- enddo
-
- call kinetic(EK)
- EK=EK/s12_np**2
-
- d_time_s12=0.5d0*s12_np*d_time
-
- do j=1,3
- d_t_old(j,0)=d_t_old(j,0)+d_a(j,0)*d_time_s12
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)+d_a(j,i)*d_time_s12
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_old(j,inres)=d_t_old(j,inres)+d_a(j,inres)*d_time_s12
- enddo
- endif
- enddo
-
-cd write(iout,*) 'pistar',pistar,EK,E_old,potE,s12_np
- pistar=pistar+(EK-0.5*(E_old+potE)
- & -dimen*Rb*t_bath*log(s12_np)+H0-dimen*Rb*t_bath)*d_time
- tmp=1+pistar/(2*Q_np)*0.5*d_time
- s_np=s12_np*tmp**2
- pi_np=pistar/tmp
-
- return
- end
-
-c-----------------------------------------------------------------
- subroutine tnp_respa_i_step1
-c Applying Nose-Poincare algorithm - step 1 to coordinates
-c J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird
-c
-c d_t is not updated here, it is destroyed
-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 C_np,d_time_s,tmp,d_time_ss
-
- d_time_s=d_time*0.5*s_np
-ct2 d_time_s=d_time*0.5*s12_np
-
- do j=1,3
- d_t_new(j,0)=d_t_old(j,0)+d_a_old(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_new(j,i)=d_t_old(j,i)+d_a_old(j,i)*d_time_s
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_new(j,inres)=d_t_old(j,inres)+d_a_old(j,inres)*d_time_s
- enddo
- endif
- enddo
-
- do i=0,2*nres
- do j=1,3
- d_t(j,i)=d_t_new(j,i)
- enddo
- enddo
-
- call kinetic(EK)
- EK=EK/s_np**2
-
- C_np=0.5*d_time*(dimen*Rb*t_bath*(1.0+log(s_np))-EK+potE-Csplit)
- & -pi_np
-
- pistar=-2.0*C_np/(1.0+sqrt(1.0-C_np*d_time/Q_np))
- tmp=0.5*d_time*pistar/Q_np
- s12_np=s_np*(1.0+tmp)/(1.0-tmp)
-
- d_time_ss=0.5*d_time*(1.0/s12_np+1.0/s_np)
-ct2 d_time_ss=d_time/s12_np
-c d_time_ss=0.5*d_time*(1.0/sold_np+1.0/s_np)
-
- do j=1,3
- dc(j,0)=dc_old(j,0)+d_t_new(j,0)*d_time_ss
- enddo
- do i=nnt,nct-1
- do j=1,3
- dc(j,i)=dc_old(j,i)+d_t_new(j,i)*d_time_ss
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- dc(j,inres)=dc_old(j,inres)+d_t_new(j,inres)*d_time_ss
- enddo
- endif
- enddo
-
- return
- end
-c-----------------------------------------------------------------
- subroutine tnp_respa_step1
-c Applying Nose-Poincare algorithm - step 1 to vel for RESPA
-c J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird
-c
-c d_t is not updated here, it is destroyed
-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 C_np,d_time_s,tmp,d_time_ss
- double precision energia(0:n_ene)
-
- d_time_s=d_time*0.5*s_np
-
- do j=1,3
- d_t_old(j,0)=d_t_old(j,0)+d_a(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)+d_a(j,i)*d_time_s
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_old(j,inres)=d_t_old(j,inres)+d_a(j,inres)*d_time_s
- enddo
- endif
- enddo
-
-
-c C_np=0.5*d_time*(dimen*Rb*t_bath*(1.0+log(s_np))-EK+potE-H0)
-c & -pi_np
-c
-c pistar=-2.0*C_np/(1.0+sqrt(1.0-C_np*d_time/Q_np))
-c tmp=0.5*d_time*pistar/Q_np
-c s12_np=s_np*(1.0+tmp)/(1.0-tmp)
-c write(iout,*) 'tnp_respa_step1',s_np,s12_np,EK,potE,C_np,pistar,tmp
-
-ct1 pi_np=pistar
-c sold_np=s_np
-c s_np=s12_np
-
-c-------------------------------------
-c test of reviewer's comment
- pi_np=pi_np-0.5*d_time*(E_long+Csplit-H0)
-cr print '(a,3f)','1 pi_np,s_np',pi_np,s_np,E_long
-c-------------------------------------
-
- return
- end
-c---------------------------------------------------------------------
-
- subroutine tnp_respa_i_step2
-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'
-
- double precision d_time_s
-
- EK=EK*(s_np/s12_np)**2
- HNose1=Hnose(EK,s12_np,potE,pistar,Q_np,t_bath,dimen)
- pi_np=pistar+0.5*d_time*(2*EK-dimen*Rb*t_bath
- & -HNose1+Csplit)
-
-cr print '(a,5f)','i_step2',EK,potE,HNose1,pi_np,E_long
- d_time_s=d_time*0.5*s12_np
-c d_time_s=d_time*0.5*s_np
-
- do j=1,3
- d_t(j,0)=d_t_new(j,0)+d_a(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t(j,i)=d_t_new(j,i)+d_a(j,i)*d_time_s
- 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)+d_a(j,inres)*d_time_s
- enddo
- endif
- enddo
-
- s_np=s12_np
-
- return
- end
-c---------------------------------------------------------------------
- subroutine tnp_respa_step2
-c Step 2 of the velocity Verlet algorithm: update velocities for RESPA
- 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 d_time_s
-
-ct1 s12_np=s_np
-ct2 pistar=pi_np
-
-ct call kinetic(EK)
-ct HNose1=Hnose(EK,s12_np,potE,pistar,Q_np,t_bath,dimen)
-ct pi_np=pistar+0.5*d_time*(2*EK-dimen*Rb*t_bath)
-ct & -0.5*d_time*(HNose1-H0)
-
-c-------------------------------------
-c test of reviewer's comment
- pi_np=pi_np-0.5*d_time*(E_long+Csplit-H0)
-cr print '(a,3f)','2 pi_np,s_np',pi_np,s_np,E_long
-c-------------------------------------
- d_time_s=d_time*0.5*s_np
-
- do j=1,3
- d_t_old(j,0)=d_t_old(j,0)+d_a(j,0)*d_time_s
- enddo
- do i=nnt,nct-1
- do j=1,3
- d_t_old(j,i)=d_t_old(j,i)+d_a(j,i)*d_time_s
- enddo
- enddo
- do i=nnt,nct
- if (itype(i).ne.10) then
- inres=i+nres
- do j=1,3
- d_t_old(j,inres)=d_t_old(j,inres)+d_a(j,inres)*d_time_s
- enddo
- endif
- enddo
-
-cd s_np=s12_np
-
- return
- end
-c-----------------------------------------------------------------
- SUBROUTINE NHCINT(akin,scale,wdti,wdti2,wdti4,wdti8)
- implicit real*8 (a-h,o-z)
- include 'DIMENSIONS'
- include 'COMMON.MD'
- double precision akin,gnkt,dt,aa,gkt,scale
- double precision wdti(maxyosh),wdti2(maxyosh),
- & wdti4(maxyosh),wdti8(maxyosh)
- integer i,iresn,iyosh,inos,nnos1
-
- dt=d_time
- nnos1=nnos+1
- GKT = Rb*t_bath
- GNKT = dimen*GKT
- akin=akin*2
-
-
-C THIS ROUTINE DOES THE NOSE-HOOVER PART OF THE
-C INTEGRATION FROM t=0 TO t=DT/2
-C GET THE TOTAL KINETIC ENERGY
- SCALE = 1.D0
-c CALL GETKINP(MASS,VX,VY,VZ,AKIN)
-C UPDATE THE FORCES
- GLOGS(1) = (AKIN - GNKT)/QMASS(1)
-C START THE MULTIPLE TIME STEP PROCEDURE
- DO IRESN = 1,NRESN
- DO IYOSH = 1,NYOSH
-C UPDATE THE THERMOSTAT VELOCITIES
- VLOGS(NNOS) = VLOGS(NNOS) + GLOGS(NNOS)*WDTI4(IYOSH)
- DO INOS = 1,NNOS-1
- AA = EXP(-WDTI8(IYOSH)*VLOGS(NNOS1-INOS) )
- VLOGS(NNOS-INOS) = VLOGS(NNOS-INOS)*AA*AA
- & + WDTI4(IYOSH)*GLOGS(NNOS-INOS)*AA
- ENDDO
-C UPDATE THE PARTICLE VELOCITIES
- AA = EXP(-WDTI2(IYOSH)*VLOGS(1) )
- SCALE = SCALE*AA
-C UPDATE THE FORCES
- GLOGS(1) = (SCALE*SCALE*AKIN - GNKT)/QMASS(1)
-C UPDATE THE THERMOSTAT POSITIONS
- DO INOS = 1,NNOS
- XLOGS(INOS) = XLOGS(INOS) + VLOGS(INOS)*WDTI2(IYOSH)
- ENDDO
-C UPDATE THE THERMOSTAT VELOCITIES
- DO INOS = 1,NNOS-1
- AA = EXP(-WDTI8(IYOSH)*VLOGS(INOS+1) )
- VLOGS(INOS) = VLOGS(INOS)*AA*AA
- & + WDTI4(IYOSH)*GLOGS(INOS)*AA
- GLOGS(INOS+1) = (QMASS(INOS)*VLOGS(INOS)*VLOGS(INOS)
- & -GKT)/QMASS(INOS+1)
- ENDDO
- VLOGS(NNOS) = VLOGS(NNOS) + GLOGS(NNOS)*WDTI4(IYOSH)
- ENDDO
- ENDDO
-C UPDATE THE PARTICLE VELOCITIES
-c outside of this subroutine
-c DO I = 1,N
-c VX(I) = VX(I)*SCALE
-c VY(I) = VY(I)*SCALE
-c VZ(I) = VZ(I)*SCALE
-c ENDDO
- RETURN
- END
projects / unres.git / blobdiff