+++ /dev/null
-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 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
-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)
- & -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_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_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_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_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_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 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
projects / unres.git / blobdiff