- 200.00 2.20 3.0
- 1.00 0.50 3.0
- 1.00 0.20 3.0
- 1.00 0.30 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 200.00 2.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
- 1.00 1.00 3.0
-
+ 6.2159898496
+ 6.6717260508
+ 6.6424306340
+ 6.9715947250
+ 6.9241225787
+ 6.5291325353
+ 6.1394821460
+ 5.4415971840
+ 5.2914044780
+ 4.7881880526
+ 4.1302408718
+ 3.9405275117
+ 3.9022731880
+ 3.6078928145
+ 3.0809713206
+ 3.0182595342
+ 4.7935507272
+ 3.8711928134
+ 3.6826168780
+ 4.4872661030
+ 6.6717260508
+ 6.6424306340
+ 5.2914044780
+ 5.2914044780
--- /dev/null
+ 1.1970470 5.3667307 3.0000000
+ 1.5539975 5.6438808 3.0000000
+ 1.6679316 5.6689787 3.0000000
+ 1.6606077 5.9381499 3.0000000
+ 1.7428987 5.8625088 3.0000000
+ 1.7310307 5.9950466 3.0000000
+ 1.6322831 5.8318806 3.0000000
+ 1.5348705 5.4955850 3.0000000
+ 1.3603992 5.3937664 3.0000000
+ 1.3228511 5.4371481 3.0000000
+ 1.1970470 5.3667307 3.0000000
+ 1.0325602 5.5439558 3.0000000
+ 0.98513186 5.3780737 3.0000000
+ 0.97556829 5.3995867 3.0000000
+ 0.90197319 5.4184709 3.0000000
+ 0.77024281 5.4679136 3.0000000
+ 0.75456488 5.4686551 3.0000000
+ 1.1983876 5.3466215 3.0000000
+ 0.96779823 5.2968884 3.0000000
+ 0.92065424 5.3752089 3.0000000
+ 1.1218165 5.6721835 3.0000000
+ 1.6679316 5.7029562 3.0000000
+ 1.6606077 5.9355397 3.0000000
+ 1.3228511 5.4343948 3.0000000
+ 1.3228511 5.4343948 3.0000000
--- /dev/null
+ 2.674806001700000 2.699903447923231 2.969074945285474 2.893433539204819
+ 3.025971784817564 2.862805741160594 2.526510086781303 2.424691603147259
+ 2.468072853823478 2.397655578798363 2.574880627216491 2.408998508198888
+ 2.430511884949466 2.449395893015385 2.498838549850558 2.499580191788341
+ 2.377546242648636 2.327813161765345 2.406133938779852 2.703108539059061
+ 2.7338810145 2.9664647229 2.4653201213 2.4653201213
double precision aa,bb,augm,aad,bad,app,bpp,ale6,ael3,ael6,
&aa_lip,bb_lip,aa_aq,bb_aq,sc_aa_tube_par,sc_bb_tube_par,
& pep_aa_tube,pep_bb_tube
-
+ double precision wdti,wdti2,wdti4,wdti8,
+ & wdtii,wdtii2,wdtii4,wdtii8
+ common /nosehoover_dt/
+ & wdti(maxyosh),wdti2(maxyosh),wdti4(maxyosh),wdti8(maxyosh),
+ & wdtii(maxyosh),wdtii2(maxyosh),wdtii4(maxyosh),wdtii8(maxyosh)
integer expon,expon2
integer nnt,nct,nint_gr,istart,iend,itype,itel,itypro,
& ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr,iscpstart,
& ifrag_back(3,maxfrag_back,maxprocs/20),ntime_split,ntime_split0,
& maxtime_split
logical large,print_compon,tbf,rest,reset_moment,reset_vel,
- & surfarea,rattle,usampl,mdpdb,RESPA
+ & surfarea,rattle,usampl,mdpdb,RESPA,tnp,tnp1,tnh,xiresp
+ integer nresn,nyosh,nnos
+ double precision glogs,qmass,vlogs,xlogs
integer igmult_start,igmult_end,my_ng_count,ng_start,ng_counts,
& nginv_start,nginv_counts,myginv_ng_count
common /back_constr/ uconst_back,utheta,ugamma,uscdiff,
common /mdpar/ v_ini,d_time,d_time0,scal_fric,
& t_bath,tau_bath,dvmax,damax,n_timestep,mdpdb,
& ntime_split,ntime_split0,maxtime_split,
- & ntwx,ntwe,large,print_compon,tbf,rest
+ & ntwx,ntwe,large,print_compon,tbf,rest,tnp,tnp1,tnh
common /MDcalc/ totT,totE,potE,potEcomp,EK,amax,edriftmax,
& kinetic_T
common /lagrange/ d_t,d_t_old,d_t_new,d_t_work,
& myginv_ng_count,
& ng_start(0:MaxProcs-1),ng_counts(0:MaxProcs-1),
& nginv_start(0:MaxProcs),nginv_counts(0:MaxProcs-1)
+ double precision pi_np,pistar,s_np,s12_np,Q_np,E_old,H0,E_long,
+ & sold_np,d_t_half,Csplit,hhh
+ common /nosepoincare/ pi_np,pistar,s_np,s12_np,Q_np,E_old,H0,
+ & E_long,sold_np,d_t_half(3,0:MAXRES2),Csplit,hhh
+ common /nosehoover/ glogs(maxmnh),qmass(maxmnh),
+ & vlogs(maxmnh),xlogs(maxmnh),
+ & nresn,nyosh,nnos,xiresp
+
C to master; depends on nstex / ntwx ratio
integer max_cache_traj
parameter (max_cache_traj=10)
+C NOSE-HOOVER
+ integer maxmnh,maxyosh
+ parameter(maxmnh=10,maxyosh=5)
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
+
C lets ommit dummy atoms for now
if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
C now calculate distance from center of tube and direction vectors
- vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
C and its 6 power
rdiff6=rdiff**6.0d0
C for vectorization reasons we will sumup at the end to avoid depenence of previous
- enetube(i)=pep_aa_tube/rdiff6**2.0d0-pep_bb_tube/rdiff6
+ enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
C write(iout,*) "TU13",i,rdiff6,enetube(i)
C print *,rdiff,rdiff6,pep_aa_tube
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=(-12.0d0*pep_aa_tube/rdiff6+
+ fac=(-12.0d0*pep_aa_tube/rdiff6-
& 6.0d0*pep_bb_tube)/rdiff6/rdiff
C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
C &rdiff,fac
C in UNRES uncomment the line below as GLY has no side-chain...
C .or.(iti.eq.10)
& ) cycle
- vectube(1)=c(1,i+nres)
- vectube(1)=mod(vectube(1),boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=c(2,i+nres)
- vectube(2)=mod(vectube(2),boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
-
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i+nres)),boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i+nres)),boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
+C write(iout,*), "tututu", vectube(1),tubecenter(1),vectube(2),
+C & tubecenter(2)
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
C now normalize vector
vectube(1)=vectube(1)/tub_r
vectube(2)=vectube(2)/tub_r
+
C calculte rdiffrence between r and r0
rdiff=tub_r-tubeR0
C and its 6 power
C for vectorization reasons we will sumup at the end to avoid depenence of previous
sc_aa_tube=sc_aa_tube_par(iti)
sc_bb_tube=sc_bb_tube_par(iti)
- enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0-sc_bb_tube/rdiff6
+ enetube(i+nres)=sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff+
+ fac=-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-
& 6.0d0*sc_bb_tube/rdiff6/rdiff
C now direction of gg_tube vector
do j=1,3
C and its 6 power
rdiff6=rdiff**6.0d0
C for vectorization reasons we will sumup at the end to avoid depenence of previous
- enetube(i)=pep_aa_tube/rdiff6**2.0d0-pep_bb_tube/rdiff6
+ enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
C write(iout,*) "TU13",i,rdiff6,enetube(i)
C print *,rdiff,rdiff6,pep_aa_tube
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=(-12.0d0*pep_aa_tube/rdiff6+
+ fac=(-12.0d0*pep_aa_tube/rdiff6-
& 6.0d0*pep_bb_tube)/rdiff6/rdiff
C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
C &rdiff,fac
C for vectorization reasons we will sumup at the end to avoid depenence of previous
sc_aa_tube=sc_aa_tube_par(iti)
sc_bb_tube=sc_bb_tube_par(iti)
- enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0-sc_bb_tube/rdiff6)
+ enetube(i+nres)=(sc_aa_tube/rdiff6**2.0d0+sc_bb_tube/rdiff6)
& *sstube+enetube(i+nres)
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
- fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff+
+ fac=(-12.0d0*sc_aa_tube/rdiff6**2.0d0/rdiff-
& 6.0d0*sc_bb_tube/rdiff6/rdiff)*sstube
C now direction of gg_tube vector
do j=1,3
c call reada(controlcard,"LAMBDA",rlamb,0.3d0)
rest = index(controlcard,"REST").gt.0
tbf = index(controlcard,"TBF").gt.0
+ tnp = index(controlcard,"NOSEPOINCARE99").gt.0
+ tnp1 = index(controlcard,"NOSEPOINCARE01").gt.0
+ tnh = index(controlcard,"NOSEHOOVER96").gt.0
+ if (RESPA.and.tnh)then
+ xiresp = index(controlcard,"XIRESP").gt.0
+ endif
+ write(iout,*) "tnh",tnh
+ call reada(controlcard,"Q_NP",Q_np,0.1d0)
usampl = index(controlcard,"USAMPL").gt.0
mdpdb = index(controlcard,"MDPDB").gt.0
& "Velocities will be reset at random every",count_reset_vel,
& " steps"
endif
+ else if (tnp .or. tnp1 .or. tnh) then
+ if (tnp .or. tnp1) then
+ write (iout,'(a)') "Nose-Poincare bath calculation"
+ if (tnp) write (iout,'(a)')
+ & "J.Comput.Phys. 151 114 (1999) S.D.Bond B.J.Leimkuhler B.B.Laird"
+ if (tnp1) write (iout,'(a)') "JPSJ 70 75 (2001) S. Nose"
+ else
+ write (iout,'(a)') "Nose-Hoover bath calculation"
+ write (iout,'(a)') "Mol.Phys. 87 1117 (1996) Martyna et al."
+ nresn=1
+ nyosh=1
+ nnos=1
+ do i=1,nnos
+ qmass(i)=Q_np
+ xlogs(i)=1.0
+ vlogs(i)=0.0
+ enddo
+ do i=1,nyosh
+ WDTI(i) = 1.0*d_time/nresn
+ WDTI2(i)=WDTI(i)/2
+ WDTI4(i)=WDTI(i)/4
+ WDTI8(i)=WDTI(i)/8
+ enddo
+ if (RESPA) then
+ if(xiresp) then
+ write (iout,'(a)') "NVT-XI-RESPA algorithm"
+ else
+ write (iout,'(a)') "NVT-XO-RESPA algorithm"
+ endif
+ do i=1,nyosh
+ WDTIi(i) = 1.0*d_time/nresn/ntime_split
+ WDTIi2(i)=WDTIi(i)/2
+ WDTIi4(i)=WDTIi(i)/4
+ WDTIi8(i)=WDTIi(i)/8
+ enddo
+ endif
+ endif
else
if(me.eq.king.or..not.out1file)
& write (iout,'(a31)') "Microcanonical mode calculation"
& wturn6*fact(5)*gcorr6_turn(j,i)+
& wsccor*fact(2)*gsccorc(j,i)
& +wliptran*gliptranc(j,i)
+ & +welec*gshieldc(j,i)
+ & +welec*gshieldc_loc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wcorr*gshieldc_loc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn3*gshieldc_loc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wturn4*gshieldc_loc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+ & +wel_loc*gshieldc_loc_ll(j,i)
+
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& wsccor*fact(2)*gsccorx(j,i)
& +wliptran*gliptranx(j,i)
+ & +welec*gshieldx(j,i)
+ & +wcorr*gshieldx_ec(j,i)
+ & +wturn3*gshieldx_t3(j,i)
+ & +wturn4*gshieldx_t4(j,i)
+ & +wel_loc*gshieldx_ll(j,i)
+
else
gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)
& +fact(1)*wscp*gvdwc_scp(j,i)+
& wturn6*fact(5)*gcorr6_turn(j,i)+
& wsccor*fact(2)*gsccorc(j,i)
& +wliptran*gliptranc(j,i)
+ & +welec*gshieldc(j,i)
+ & +welec*gshieldc_loc(j,i)
+ & +wcorr*gshieldc_ec(j,i)
+ & +wcorr*gshieldc_loc_ec(j,i)
+ & +wturn3*gshieldc_t3(j,i)
+ & +wturn3*gshieldc_loc_t3(j,i)
+ & +wturn4*gshieldc_t4(j,i)
+ & +wturn4*gshieldc_loc_t4(j,i)
+ & +wel_loc*gshieldc_ll(j,i)
+ & +wel_loc*gshieldc_loc_ll(j,i)
+
gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
& wbond*gradbx(j,i)+
& wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
& wsccor*fact(1)*gsccorx(j,i)
& +wliptran*gliptranx(j,i)
+ & +welec*gshieldx(j,i)
+ & +wcorr*gshieldx_ec(j,i)
+ & +wturn3*gshieldx_t3(j,i)
+ & +wturn4*gshieldx_t4(j,i)
+ & +wel_loc*gshieldx_ll(j,i)
+
else
gradc(j,i,icg)=fact(1)*wsc*gvdwc(j,i)+
& fact(1)*wscp*gvdwc_scp(j,i)+
if (ymedi.lt.0) ymedi=ymedi+boxysize
zmedi=mod(zmedi,boxzsize)
if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ zmedi2=mod(zmedi,boxzsize)
+ if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize
+ if ((zmedi2.gt.bordlipbot)
+ &.and.(zmedi2.lt.bordliptop)) then
+C the energy transfer exist
+ if (zmedi2.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zmedi2-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zmedi2.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zmedi2)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0d0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0d0
+ endif
+
num_conti=0
C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
if (yj.lt.0) yj=yj+boxysize
zj=mod(zj,boxzsize)
if (zj.lt.0) zj=zj+boxzsize
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
xj_safe=xj
yj_safe=yj
endif
eel_loc_ij=eel_loc_ij
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
c write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
C write (iout,'(a6,2i5,0pf7.3)')
C & 'eelloc',i,j,eel_loc_ij
& (a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
& +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc_loc(j-1)=gel_loc_loc(j-1)+
& (a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
& +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij)
cd write(iout,*) 'agg ',agg
ggg(l)=(agg(l,1)*muij(1)+
& agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
do k=i+2,j2
gel_loc(l,i)=gel_loc(l,i)+(aggi(l,1)*muij(1)+
& aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,i+1)=gel_loc(l,i+1)+(aggi1(l,1)*muij(1)+
& aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,j)=gel_loc(l,j)+(aggj(l,1)*muij(1)+
& aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
gel_loc(l,j1)=gel_loc(l,j1)+(aggj1(l,1)*muij(1)+
& aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
endif
double precision agg(3,4),aggi(3,4),aggi1(3,4),
& aggj(3,4),aggj1(3,4),a_temp(2,2)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
+ zj=(c(3,j)+c(3,j+1))/2.0d0
+C xj=mod(xj,boxxsize)
+C if (xj.lt.0) xj=xj+boxxsize
+C yj=mod(yj,boxysize)
+C if (yj.lt.0) yj=yj+boxysize
+ zj=mod(zj,boxzsize)
+ if (zj.lt.0) zj=zj+boxzsize
+C if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
+ if ((zj.gt.bordlipbot)
+ &.and.(zj.lt.bordliptop)) then
+C the energy transfer exist
+ if (zj.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-
+ & ((zj-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zj.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zj)/lipbufthick)
+ sslipj=sscalelip(fracinbuf)
+ ssgradlipj=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipj=1.0d0
+ ssgradlipj=0.0
+ endif
+ else
+ sslipj=0.0d0
+ ssgradlipj=0.0
+ endif
+
if (j.eq.i+2) then
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
cd write (2,*) 'i,',i,' j',j,'eello_turn3',
cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
C Derivatives in gamma(i+1)
call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
call transpose2(auxmat2(1,1),pizda(1,1))
gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
C Cartesian derivatives
do l=1,3
gcorr3_turn(l,i)=gcorr3_turn(l,i)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
gcorr3_turn(l,j)=gcorr3_turn(l,j)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
& +0.5d0*(pizda(1,1)+pizda(2,2))
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
endif
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
C Derivatives in gamma(i+1)
call transpose2(EUgder(1,1,i+2),e2tder(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
C Derivatives in gamma(i+2)
call transpose2(EUgder(1,1,i+3),e3tder(1,1))
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
C Cartesian derivatives
ggg(l)=-(s1+s2+s3)
gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
endif
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggi1(l,1)
a_temp(1,2)=aggi1(l,2)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggj(l,1)
a_temp(1,2)=aggj(l,2)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
a_temp(1,1)=aggj1(l,1)
a_temp(1,2)=aggj1(l,2)
s3=0.5d0*(pizda(1,1)+pizda(2,2))
gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
& *fac_shield(i)*fac_shield(j)
+ &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
enddo
+ gshieldc_t4(3,i)=gshieldc_t4(3,i)+
+ & ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j)=gshieldc_t4(3,j)+
+ & ssgradlipj*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,i-1)=gshieldc_t4(3,i-1)+
+ & ssgradlipi*eello_t4/4.0d0*lipscale
+ gshieldc_t4(3,j-1)=gshieldc_t4(3,j-1)+
+ & ssgradlipj*eello_t4/4.0d0*lipscale
endif
178 continue
endif
projects / unres.git / commitdiff