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
#endif
else if (lang.eq.1) then
call sddir_verlet1
+C else if (tnp1) then
+C call tnp1_step1
+C else if (tnp) then
+C 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
t_etotal=t_etotal+tcpu()-tt0
#endif
#endif
+ E_old=potE
potE=potEcomp(0)-potEcomp(20)
call cartgrad
c Get the new accelerations
#endif
else if (lang.eq.1) then
call sddir_verlet2
+C> else if (tnp1) then
+C> call tnp1_step2
+C> else if (tnp) then
+C> 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
scale=.false.
endif
enddo
+ 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
+
c Calculate the kinetic and the total energy and the kinetic temperature
call kinetic(EK)
totE=EK+potE
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)
+ 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
if (ntwe.ne.0) then
if (mod(itime,ntwe).eq.0 .and. large) then
+ if(tnp .or. tnp1) then
+ HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen3)
+ 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)+dimen3*0.001986d0*t_bath*log(s_np)
+cd write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
+ hhh=h
+ endif
+
+ if(tnh) then
+ HNose1=Hnose_nh(EK,potE)
+ H=HNose1-H0
+ hhh=h
+cd 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,dimen3
+ vtnp_(i)=0.0d0
+ vtnp_a(i)=0.0d0
+ do j=1,dimen3
+ 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,dimen3
+ write (iout,'("WWW",i3,3f10.5)') i,vtnp(i),vtnp_(i),vtnp_a(i)
+ 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),
enddo
endif
endif
+ endif
return
end
c-------------------------------------------------------------------------------
double precision stochforcvec(MAXRES6)
common /stochcalc/ stochforcvec
integer itime
+ double precision vtnp(maxres6), vtnp_(maxres6), vtnp_a(maxres6)
logical scale
common /cipiszcze/ itt
itt=itime
c
c Perform the initial RESPA step (increment velocities)
c write (iout,*) "*********************** RESPA ini"
- call RESPA_vel
+ if (tnp1) then
+ 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 (ntwe.ne.0) then
if (mod(itime,ntwe).eq.0 .and. large) then
write (iout,*) "Velocities, end"
tt0 = tcpu()
#endif
C 7/2/2009 commented out
+ if (tnp.or.tnp1) potE=energia_short(0)
c call zerograd
c call etotal_short(energia_short)
c call cartgrad
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)
+C d_t_old(j,i)=d_t(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
#endif
else if (lang.eq.1) then
call sddir_verlet1
+ else if (tnp1) then
+ call tnp1_respa_i_step1
+ 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 etotal_short(energia_short)
if (large.and. mod(itime,ntwe).eq.0)
& call enerprint(energia_short)
+ E_old=potE
+ potE=energia_short(0)
+
#ifdef TIMING_ENE
#ifdef MPI
t_eshort=t_eshort+MPI_Wtime()-tt0
#endif
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
+ 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
+
+
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)
+ 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
call etotal_long(energia_long)
if (large.and. mod(itime,ntwe).eq.0)
& call enerprint(energia_long)
+ E_long=energia_long(0)
+ potE=energia_short(0)+energia_long(0)
#ifdef TIMING_ENE
#ifdef MPI
t_elong=t_elong+MPI_Wtime()-tt0
endif
c Compute the final RESPA step (increment velocities)
c write (iout,*) "*********************** RESPA fin"
- call RESPA_vel
+C call RESPA_vel
+ if (tnp1) then
+ 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
do i=0,n_ene
potEcomp(i)=energia_short(i)+energia_long(i)
& (d_t(j,i+nres),j=1,3)
enddo
endif
+ if (mod(itime,ntwe).eq.0) then
+
+ if(tnp .or. tnp1) then
+#ifndef G77
+ write (iout,'(a3,7f20.10)') "TTT",EK,s_np,potE,pi_np,Csplit,
+ & E_long,energia_short(0)
+#else
+ write (iout,'(a3,7f20.10)') "TTT",EK,s_np,potE,pi_np,Csplit,
+ & E_long,energia_short(0)
+#endif
+ HNose1=Hnose(EK,s_np,potE,pi_np,Q_np,t_bath,dimen3)
+ 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)+dimen3*0.001986d0*t_bath*log(s_np)
+cd write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
+ hhh=h
+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
+cd write (iout,*) "HHH H=",H,abs(HNose1-H0)/H0
+ hhh=h
+ 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,dimen3
+ vtnp_(i)=0.0d0
+ vtnp_a(i)=0.0d0
+ do j=1,dimen3
+ 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,dimen3
+ write (iout,'("WWW",i3,3f10.5)') i,vtnp(i),vtnp_(i),vtnp_a(i)
+ enddo
+
+ endif
+ endif
endif
return
end
#endif
#endif
potE=potEcomp(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,dimen3)
+ 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
t_eshort=t_eshort+tcpu()-tt0
#endif
#endif
+ if(tnp .or. tnp1) then
+ E_short=energia_short(0)
+ HNose1=Hnose(EK,s_np,E_short,pi_np,Q_np,t_bath,dimen3)
+ 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
if(.not.out1file .and. large) then
return
end
#endif
+ double precision function HNose(ek,s,e,pi,Q,t_bath,dimenl)
+ implicit none
+ double precision ek,s,e,pi,Q,t_bath,Rb
+ integer dimenl
+ Rb=0.001986d0
+ HNose=ek+e+pi**2/(2*Q)+dimenl*Rb*t_bath*log(s)
+c print '(6f15.5,i5,a2,2f15.5)',ek,s,e,pi,Q,t_bath,dimenl,"--",
+c & pi**2/(2*Q),dimenl*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+dimen3*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 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 = dimen3*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
+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---------------------------------------------------------------------
+ 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)
+ & -dimen3*Rb*t_bath*log(s12_np)+Csplit-dimen3*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_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)
+ & -dimen3*Rb*t_bath*log(s12_np)+H0-dimen3*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*(dimen3*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_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,dimen3)
+ pi_np=pistar+0.5*d_time*(2*EK-dimen3*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_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*(dimen3*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_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,dimen3)
+ct pi_np=pistar+0.5*d_time*(2*EK-dimen3*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 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*(dimen3*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,dimen3)
+ pi_np=pistar+0.5*d_time*(2*EK-dimen3*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
+
projects / unres.git / blobdiff