if (nfgtasks.gt.1) then
call MPI_Bcast(itime_mat,1,MPI_INT,king,FG_COMM,IERROR)
endif
+c write (iout,*) "itime_mat",itime_mat," imatupdate",imatupdate
if (mod(itime_mat,imatupdate).eq.0) then
call make_SCp_inter_list
call make_SCSC_inter_list
& sigij,r0ij,rcut,sqrij,sss1,sssgrad1
double precision fcont,fprimcont
double precision sscale,sscagrad
+ double precision boxshift
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
c do i=iatsc_s,iatsc_e
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
C Change 12/1/95
num_conti=0
C
c do j=istart(i,iint),iend(i,iint)
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
C Change 12/1/95 to calculate four-body interactions
rij=xj*xj+yj*yj+zj*zj
rrij=1.0D0/rij
& fac_augm,e_augm,r_inv_ij,r_shift_inv,sss1,sssgrad1
logical scheck
double precision sscale,sscagrad
+ double precision boxshift
c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
c do i=iatsc_s,iatsc_e
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
C
C Calculate SC interaction energy.
C
c do j=istart(i,iint),iend(i,iint)
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
fac_augm=rrij**expon
e_augm=augm(itypi,itypj)*fac_augm
double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,xi,yi,zi,
& sss1,sssgrad1
double precision sscale,sscagrad
+ double precision boxshift
c double precision rrsave(maxdim)
logical lprn
evdw=0.0D0
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
include 'COMMON.SPLITELE'
include 'COMMON.SBRIDGE'
logical lprn
- integer xshift,yshift,zshift,subchap
double precision evdw
integer itypi,itypj,itypi1,iint,ind,ikont
double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,xi,yi,zi
double precision fracinbuf,sslipi,evdwij_przed_tri,sig0ij,
- & sslipj,ssgradlipj,ssgradlipi,dist_init,xj_safe,yj_safe,zj_safe,
- & xj_temp,yj_temp,zj_temp,dist_temp,sig,rij_shift,faclip
+ & sslipj,ssgradlipj,ssgradlipi,sig,rij_shift,faclip
double precision dist,sscale,sscagrad,sscagradlip,sscalelip
+ double precision boxshift
evdw=0.0D0
ccccc energy_dec=.false.
C print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
-C Return atom into box, boxxsize is size of box in x dimension
-c 134 continue
-c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize
-c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize
-C Condition for being inside the proper box
-c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or.
-c & (xi.lt.((xshift-0.5d0)*boxxsize))) then
-c go to 134
-c endif
-c 135 continue
-c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize
-c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize
-C Condition for being inside the proper box
-c if ((yi.gt.((yshift+0.5d0)*boxysize)).or.
-c & (yi.lt.((yshift-0.5d0)*boxysize))) then
-c go to 135
-c endif
-c 136 continue
-c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize
-c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize
-C Condition for being inside the proper box
-c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or.
-c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
-c go to 136
-c endif
- xi=mod(xi,boxxsize)
- if (xi.lt.0) xi=xi+boxxsize
- yi=mod(yi,boxysize)
- if (yi.lt.0) yi=yi+boxysize
- zi=mod(zi,boxzsize)
- if (zi.lt.0) zi=zi+boxzsize
+ call to_box(xi,yi,zi)
C define scaling factor for lipids
C if (positi.le.0) positi=positi+boxzsize
C print *,i
C first for peptide groups
c for each residue check if it is in lipid or lipid water border area
- if ((zi.gt.bordlipbot)
- &.and.(zi.lt.bordliptop)) then
-C the energy transfer exist
- if (zi.lt.buflipbot) then
-C what fraction I am in
- fracinbuf=1.0d0-
- & ((zi-bordlipbot)/lipbufthick)
-C lipbufthick is thickenes of lipid buffore
- sslipi=sscalelip(fracinbuf)
- ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
- fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
- sslipi=sscalelip(fracinbuf)
- ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
- else
- sslipi=1.0d0
- ssgradlipi=0.0
- endif
- else
- sslipi=0.0d0
- ssgradlipi=0.0
- endif
-
+ call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
C xi=xi+xshift*boxxsize
C yi=yi+yshift*boxysize
C zi=zi+zshift*boxzsize
if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
& 'evdw',i,j,evdwij,' ss'
C triple bond artifac removal
- do k=j+1,iend(i,iint)
+ do k=j+1,iend(i,iint)
C search over all next residues
- if (dyn_ss_mask(k)) then
+ if (dyn_ss_mask(k)) then
C check if they are cysteins
C write(iout,*) 'k=',k
c write(iout,*) "PRZED TRI", evdwij
- evdwij_przed_tri=evdwij
- call triple_ssbond_ene(i,j,k,evdwij)
+ evdwij_przed_tri=evdwij
+ call triple_ssbond_ene(i,j,k,evdwij)
c if(evdwij_przed_tri.ne.evdwij) then
c write (iout,*) "TRI:", evdwij, evdwij_przed_tri
c endif
c write(iout,*) "PO TRI", evdwij
C call the energy function that removes the artifical triple disulfide
C bond the soubroutine is located in ssMD.F
- evdw=evdw+evdwij
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
+ evdw=evdw+evdwij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
& 'evdw',i,j,evdwij,'tss'
- endif!dyn_ss_mask(k)
- enddo! k
+ endif!dyn_ss_mask(k)
+ enddo! k
ELSE
- ind=ind+1
- itypj=iabs(itype(j))
- if (itypj.eq.ntyp1) cycle
+ ind=ind+1
+ itypj=iabs(itype(j))
+ if (itypj.eq.ntyp1) cycle
c dscj_inv=dsc_inv(itypj)
- dscj_inv=vbld_inv(j+nres)
+ dscj_inv=vbld_inv(j+nres)
c write (iout,*) "j",j,dsc_inv(itypj),dscj_inv,
c & 1.0d0/vbld(j+nres)
c write (iout,*) "i",i," j", j," itype",itype(i),itype(j)
- sig0ij=sigma(itypi,itypj)
- chi1=chi(itypi,itypj)
- chi2=chi(itypj,itypi)
- chi12=chi1*chi2
- chip1=chip(itypi)
- chip2=chip(itypj)
- chip12=chip1*chip2
- alf1=alp(itypi)
- alf2=alp(itypj)
- alf12=0.5D0*(alf1+alf2)
+ sig0ij=sigma(itypi,itypj)
+ chi1=chi(itypi,itypj)
+ chi2=chi(itypj,itypi)
+ chi12=chi1*chi2
+ chip1=chip(itypi)
+ chip2=chip(itypj)
+ chip12=chip1*chip2
+ alf1=alp(itypi)
+ alf2=alp(itypj)
+ alf12=0.5D0*(alf1+alf2)
C For diagnostics only!!!
c chi1=0.0D0
c chi2=0.0D0
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
- xj=c(1,nres+j)
- yj=c(2,nres+j)
- zj=c(3,nres+j)
-C Return atom J into box the original box
-c 137 continue
-c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
-c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
-C Condition for being inside the proper box
-c if ((xj.gt.((0.5d0)*boxxsize)).or.
-c & (xj.lt.((-0.5d0)*boxxsize))) then
-c go to 137
-c endif
-c 138 continue
-c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
-c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
-C Condition for being inside the proper box
-c if ((yj.gt.((0.5d0)*boxysize)).or.
-c & (yj.lt.((-0.5d0)*boxysize))) then
-c go to 138
-c endif
-c 139 continue
-c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
-c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
-C Condition for being inside the proper box
-c if ((zj.gt.((0.5d0)*boxzsize)).or.
-c & (zj.lt.((-0.5d0)*boxzsize))) then
-c go to 139
-c endif
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- 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
- aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
- & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
- bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
- & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
C write(iout,*) "tu,", i,j,aa_lip(itypi,itypj),bb_lip(itypi,itypj)
C if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)')
C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
C if (ssgradlipj.gt.0.0d0) print *,"??WTF??"
C print *,sslipi,sslipj,bordlipbot,zi,zj
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- subchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- subchap=1
- endif
- enddo
- enddo
- enddo
- if (subchap.eq.1) then
- xj=xj_temp-xi
- yj=yj_temp-yi
- zj=zj_temp-zi
- else
- xj=xj_safe-xi
- yj=yj_safe-yi
- zj=zj_safe-zi
- endif
- dxj=dc_norm(1,nres+j)
- dyj=dc_norm(2,nres+j)
- dzj=dc_norm(3,nres+j)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
C xj=xj-xi
C yj=yj-yi
C zj=zj-zi
c write (iout,*) "dcnorj",dxi*dxi+dyi*dyi+dzi*dzi
c write (iout,*) "j",j," dc_norm",
c & dc_norm(1,nres+j),dc_norm(2,nres+j),dc_norm(3,nres+j)
- rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
- rij=dsqrt(rrij)
- sss=sscale(1.0d0/rij,r_cut_int)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+ sss=sscale(1.0d0/rij,r_cut_int)
c write (iout,'(a7,4f8.3)')
c & "ssscale",sss,((1.0d0/rij)/sigma(itypi,itypj)),r_cut,rlamb
- if (sss.eq.0.0d0) cycle
- sssgrad=sscagrad(1.0d0/rij,r_cut_int)
+ if (sss.eq.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/rij,r_cut_int)
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
- call sc_angular
- sigsq=1.0D0/sigsq
- sig=sig0ij*dsqrt(sigsq)
- rij_shift=1.0D0/rij-sig+sig0ij
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+sig0ij
c for diagnostics; uncomment
c rij_shift=1.2*sig0ij
C I hate to put IF's in the loops, but here don't have another choice!!!!
- if (rij_shift.le.0.0D0) then
- evdw=1.0D20
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
cd write (iout,'(2(a3,i3,2x),17(0pf7.3))')
cd & restyp(itypi),i,restyp(itypj),j,
cd & rij_shift,1.0D0/rij,sig,sig0ij,sigsq,1-dsqrt(sigsq)
- return
- endif
- sigder=-sig*sigsq
+ return
+ endif
+ sigder=-sig*sigsq
c---------------------------------------------------------------
- rij_shift=1.0D0/rij_shift
- fac=rij_shift**expon
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
C here to start with
C if (c(i,3).gt.
- faclip=fac
- e1=fac*fac*aa
- e2=fac*bb
- evdwij=eps1*eps2rt*eps3rt*(e1+e2)
- eps2der=evdwij*eps3rt
- eps3der=evdwij*eps2rt
+ faclip=fac
+ e1=fac*fac*aa
+ e2=fac*bb
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
C write(63,'(2i3,2e10.3,2f10.5)') i,j,aa,bb, evdwij,
C &((sslipi+sslipj)/2.0d0+
C &(2.0d0-sslipi-sslipj)/2.0d0)
c write (iout,*) "sigsq",sigsq," sig",sig," eps2rt",eps2rt,
c & " eps3rt",eps3rt," eps1",eps1," e1",e1," e2",e2
- evdwij=evdwij*eps2rt*eps3rt
- evdw=evdw+evdwij*sss
- if (lprn) then
- sigm=dabs(aa/bb)**(1.0D0/6.0D0)
- epsi=bb**2/aa
- write (iout,'(2(a3,i3,2x),17(0pf7.3))')
- & restyp(itypi),i,restyp(itypj),j,
- & epsi,sigm,chi1,chi2,chip1,chip2,
- & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
- & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
- & evdwij
- endif
+ evdwij=evdwij*eps2rt*eps3rt
+ evdw=evdw+evdwij*sss
+ if (lprn) then
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
+ write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+ & restyp(itypi),i,restyp(itypj),j,
+ & epsi,sigm,chi1,chi2,chip1,chip2,
+ & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
+ & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
+ & evdwij
+ endif
- if (energy_dec) write (iout,'(a,2i5,3f10.5)')
+ if (energy_dec) write (iout,'(a,2i5,3f10.5)')
& 'r sss evdw',i,j,1.0d0/rij,sss,evdwij
C Calculate gradient components.
- e1=e1*eps1*eps2rt**2*eps3rt**2
- fac=-expon*(e1+evdwij)*rij_shift
- sigder=fac*sigder
- fac=rij*fac
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac
c print '(2i4,6f8.4)',i,j,sss,sssgrad*
c & evdwij,fac,sigma(itypi,itypj),expon
- fac=fac+evdwij*sssgrad/sss*rij
+ fac=fac+evdwij*sssgrad/sss*rij
c fac=0.0d0
C Calculate the radial part of the gradient
- gg_lipi(3)=eps1*(eps2rt*eps2rt)
- & *(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
- & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
- & +faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
- gg_lipj(3)=ssgradlipj*gg_lipi(3)
- gg_lipi(3)=gg_lipi(3)*ssgradlipi
+ gg_lipi(3)=eps1*(eps2rt*eps2rt)
+ & *(eps3rt*eps3rt)*sss/2.0d0*(faclip*faclip*
+ & (aa_lip(itypi,itypj)-aa_aq(itypi,itypj))
+ & +faclip*(bb_lip(itypi,itypj)-bb_aq(itypi,itypj)))
+ gg_lipj(3)=ssgradlipj*gg_lipi(3)
+ gg_lipi(3)=gg_lipi(3)*ssgradlipi
C gg_lipi(3)=0.0d0
C gg_lipj(3)=0.0d0
- gg(1)=xj*fac
- gg(2)=yj*fac
- gg(3)=zj*fac
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
C Calculate angular part of the gradient.
c call sc_grad_scale(sss)
- call sc_grad
+ call sc_grad
ENDIF ! dyn_ss
c enddo ! j
c enddo ! iint
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
include 'COMMON.SPLITELE'
- integer xshift,yshift,zshift,subchap
+ double precision boxshift
integer icall
common /srutu/ icall
logical lprn
double precision eps0ij,epsi,sigm,fac,e1,e2,rrij,r0ij,
& xi,yi,zi,fac_augm,e_augm
double precision fracinbuf,sslipi,evdwij_przed_tri,sig0ij,
- & sslipj,ssgradlipj,ssgradlipi,dist_init,xj_safe,yj_safe,zj_safe,
- & xj_temp,yj_temp,zj_temp,dist_temp,sig,rij_shift,faclip,sssgrad1
+ & sslipj,ssgradlipj,ssgradlipi,sig,rij_shift,faclip,sssgrad1
double precision dist,sscale,sscagrad,sscagradlip,sscalelip
evdw=0.0D0
c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
- xi=mod(xi,boxxsize)
- if (xi.lt.0) xi=xi+boxxsize
- yi=mod(yi,boxysize)
- if (yi.lt.0) yi=yi+boxysize
- zi=mod(zi,boxzsize)
- if (zi.lt.0) zi=zi+boxzsize
+ call to_box(xi,yi,zi)
C define scaling factor for lipids
C if (positi.le.0) positi=positi+boxzsize
C print *,i
C first for peptide groups
c for each residue check if it is in lipid or lipid water border area
- if ((zi.gt.bordlipbot)
- &.and.(zi.lt.bordliptop)) then
-C the energy transfer exist
- if (zi.lt.buflipbot) then
-C what fraction I am in
- fracinbuf=1.0d0-
- & ((zi-bordlipbot)/lipbufthick)
-C lipbufthick is thickenes of lipid buffore
- sslipi=sscalelip(fracinbuf)
- ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
- elseif (zi.gt.bufliptop) then
- fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
- sslipi=sscalelip(fracinbuf)
- ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
- else
- sslipi=1.0d0
- ssgradlipi=0.0
- endif
- else
- sslipi=0.0d0
- ssgradlipi=0.0
- endif
-
+ call lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
dxi=dc_norm(1,nres+i)
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
c alf1=0.0D0
c alf2=0.0D0
c alf12=0.0D0
-C xj=c(1,nres+j)-xi
-C yj=c(2,nres+j)-yi
-C zj=c(3,nres+j)-zi
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- 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
- aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
- & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
- bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
- & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ xj=c(1,nres+j)
+ yj=c(2,nres+j)
+ zj=c(3,nres+j)
+ call to_box(xj,yj,zj)
+ call lipid_layer(xj,yj,zj,sslipj,ssgradlipj)
+ aa=aa_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+ bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
+ & +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5')
C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
C write(iout,*) "tu,", i,j,aa,bb,aa_lip(itypi,itypj),sslipi,sslipj
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- subchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- subchap=1
- endif
- enddo
- enddo
- enddo
- if (subchap.eq.1) then
- xj=xj_temp-xi
- yj=yj_temp-yi
- zj=zj_temp-zi
- else
- xj=xj_safe-xi
- yj=yj_safe-yi
- zj=zj_safe-zi
- endif
- dxj=dc_norm(1,nres+j)
- dyj=dc_norm(2,nres+j)
- dzj=dc_norm(3,nres+j)
- rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
- rij=dsqrt(rrij)
- sss=sscale(1.0d0/rij,r_cut_int)
- if (sss.eq.0.0d0) cycle
- sssgrad=sscagrad(1.0d0/rij,r_cut_int)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
+ dxj=dc_norm(1,nres+j)
+ dyj=dc_norm(2,nres+j)
+ dzj=dc_norm(3,nres+j)
+ rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
+ rij=dsqrt(rrij)
+ sss=sscale(1.0d0/rij,r_cut_int)
+ if (sss.eq.0.0d0) cycle
+ sssgrad=sscagrad(1.0d0/rij,r_cut_int)
C Calculate angle-dependent terms of energy and contributions to their
C derivatives.
- call sc_angular
- sigsq=1.0D0/sigsq
- sig=sig0ij*dsqrt(sigsq)
- rij_shift=1.0D0/rij-sig+r0ij
+ call sc_angular
+ sigsq=1.0D0/sigsq
+ sig=sig0ij*dsqrt(sigsq)
+ rij_shift=1.0D0/rij-sig+r0ij
C I hate to put IF's in the loops, but here don't have another choice!!!!
- if (rij_shift.le.0.0D0) then
- evdw=1.0D20
- return
- endif
- sigder=-sig*sigsq
+ if (rij_shift.le.0.0D0) then
+ evdw=1.0D20
+ return
+ endif
+ sigder=-sig*sigsq
c---------------------------------------------------------------
- rij_shift=1.0D0/rij_shift
- fac=rij_shift**expon
- e1=fac*fac*aa
- e2=fac*bb
- evdwij=eps1*eps2rt*eps3rt*(e1+e2)
- eps2der=evdwij*eps3rt
- eps3der=evdwij*eps2rt
- fac_augm=rrij**expon
- e_augm=augm(itypi,itypj)*fac_augm
- evdwij=evdwij*eps2rt*eps3rt
- evdw=evdw+evdwij+e_augm
- if (lprn) then
- sigm=dabs(aa/bb)**(1.0D0/6.0D0)
- epsi=bb**2/aa
- write (iout,'(2(a3,i3,2x),17(0pf7.3))')
+ rij_shift=1.0D0/rij_shift
+ fac=rij_shift**expon
+ e1=fac*fac*aa
+ e2=fac*bb
+ evdwij=eps1*eps2rt*eps3rt*(e1+e2)
+ eps2der=evdwij*eps3rt
+ eps3der=evdwij*eps2rt
+ fac_augm=rrij**expon
+ e_augm=augm(itypi,itypj)*fac_augm
+ evdwij=evdwij*eps2rt*eps3rt
+ evdw=evdw+evdwij+e_augm
+ if (lprn) then
+ sigm=dabs(aa/bb)**(1.0D0/6.0D0)
+ epsi=bb**2/aa
+ write (iout,'(2(a3,i3,2x),17(0pf7.3))')
& restyp(itypi),i,restyp(itypj),j,
& epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
& chi1,chi2,chip1,chip2,
& eps1,eps2rt**2,eps3rt**2,
& om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
& evdwij+e_augm
- endif
+ endif
C Calculate gradient components.
- e1=e1*eps1*eps2rt**2*eps3rt**2
- fac=-expon*(e1+evdwij)*rij_shift
- sigder=fac*sigder
- fac=rij*fac-2*expon*rrij*e_augm
- fac=fac+(evdwij+e_augm)*sssgrad/sss*rij
+ e1=e1*eps1*eps2rt**2*eps3rt**2
+ fac=-expon*(e1+evdwij)*rij_shift
+ sigder=fac*sigder
+ fac=rij*fac-2*expon*rrij*e_augm
+ fac=fac+(evdwij+e_augm)*sssgrad/sss*rij
C Calculate the radial part of the gradient
- gg(1)=xj*fac
- gg(2)=yj*fac
- gg(3)=zj*fac
+ gg(1)=xj*fac
+ gg(2)=yj*fac
+ gg(3)=zj*fac
C Calculate angular part of the gradient.
c call sc_grad_scale(sss)
- call sc_grad
+ call sc_grad
c enddo ! j
c enddo ! iint
enddo ! i
include 'COMMON.IOUNITS'
c include 'COMMON.CONTACTS'
dimension gg(3)
+ double precision boxshift
cd print *,'Entering Esoft_sphere nnt=',nnt,' nct=',nct
evdw=0.0D0
c do i=iatsc_s,iatsc_e
xi=c(1,nres+i)
yi=c(2,nres+i)
zi=c(3,nres+i)
+ call to_box(xi,yi,zi)
C
C Calculate SC interaction energy.
C
c do j=istart(i,iint),iend(i,iint)
itypj=iabs(itype(j))
if (itypj.eq.ntyp1) cycle
- xj=c(1,nres+j)-xi
- yj=c(2,nres+j)-yi
- zj=c(3,nres+j)-zi
+ xj=boxshift(c(1,nres+j)-xi,boxxsize)
+ yj=boxshift(c(2,nres+j)-yi,boxysize)
+ zj=boxshift(c(3,nres+j)-zi,boxzsize)
rij=xj*xj+yj*yj+zj*zj
c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
r0ij=r0(itypi,itypj)
include 'COMMON.VECTORS'
include 'COMMON.FFIELD'
dimension ggg(3)
- integer xshift,yshift,zshift
+ double precision boxshift
C write(iout,*) 'In EELEC_soft_sphere'
ees=0.0D0
evdw1=0.0D0
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ call to_box(xmedi,ymedi,zmedi)
num_conti=0
c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
xj=c(1,j)+0.5D0*dxj
yj=c(2,j)+0.5D0*dyj
zj=c(3,j)+0.5D0*dzj
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
- dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- isubchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- isubchap=1
- endif
- enddo
- enddo
- enddo
- if (isubchap.eq.1) then
- xj=xj_temp-xmedi
- yj=yj_temp-ymedi
- zj=zj_temp-zmedi
- else
- xj=xj_safe-xmedi
- yj=yj_safe-ymedi
- zj=zj_safe-zmedi
- endif
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xmedi,boxxsize)
+ yj=boxshift(yj-ymedi,boxysize)
+ zj=boxshift(zj-zmedi,boxzsize)
rij=xj*xj+yj*yj+zj*zj
sss=sscale(sqrt(rij),r_cut_int)
sssgrad=sscagrad(sqrt(rij),r_cut_int)
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ call to_box(xmedi,ymedi,zmedi)
num_conti=0
call eelecij(i,i+2,ees,evdw1,eel_loc)
if (wturn3.gt.0.0d0) call eturn3(i,eello_turn3)
c & (zmedi.lt.((-0.5d0)*boxzsize))) then
c go to 196
c endif
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
-
+ call to_box(xmedi,ymedi,zmedi)
#ifdef FOURBODY
num_conti=num_cont_hb(i)
#endif
xmedi=c(1,i)+0.5d0*dxi
ymedi=c(2,i)+0.5d0*dyi
zmedi=c(3,i)+0.5d0*dzi
- xmedi=mod(xmedi,boxxsize)
- if (xmedi.lt.0) xmedi=xmedi+boxxsize
- ymedi=mod(ymedi,boxysize)
- if (ymedi.lt.0) ymedi=ymedi+boxysize
- zmedi=mod(zmedi,boxzsize)
- if (zmedi.lt.0) zmedi=zmedi+boxzsize
+ call to_box(xmedi,ymedi,zmedi)
C xmedi=xmedi+xshift*boxxsize
C ymedi=ymedi+yshift*boxysize
C zmedi=zmedi+zshift*boxzsize
C do j=16,17
C write (iout,*) i,j
C if (j.le.1) cycle
- if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
+ if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
c & .or.((j+2).gt.nres)
c & .or.((j-1).le.0)
c & .or.itype(j+2).eq.ntyp1
c & .or.itype(j-1).eq.ntyp1
&) cycle
- call eelecij(i,j,ees,evdw1,eel_loc)
+ call eelecij(i,j,ees,evdw1,eel_loc)
c enddo ! j
#ifdef FOURBODY
num_cont_hb(i)=num_conti
& ecosa1,ecosb1,ecosg1,ecosa2,ecosb2,ecosg2,ecosap,ecosbp,
& ecosgp,ecosam,ecosbm,ecosgm,ghalf,rlocshield
double precision a22,a23,a32,a33,geel_loc_ij,geel_loc_ji
- double precision dist_init,xj_safe,yj_safe,zj_safe,
- & xj_temp,yj_temp,zj_temp,dist_temp,xmedi,ymedi,zmedi
+ double precision xmedi,ymedi,zmedi
double precision sscale,sscagrad,scalar
-
+ double precision boxshift
c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
#ifdef MOMENT
double precision scal_el /1.0d0/
double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
& 0.0d0,1.0d0,0.0d0,
& 0.0d0,0.0d0,1.0d0/
- integer xshift,yshift,zshift
c time00=MPI_Wtime()
cd write (iout,*) "eelecij",i,j
c ind=ind+1
xj=c(1,j)+0.5D0*dxj
yj=c(2,j)+0.5D0*dyj
zj=c(3,j)+0.5D0*dzj
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
- if ((zj.lt.0).or.(xj.lt.0).or.(yj.lt.0)) write (*,*) "CHUJ"
- dist_init=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- isubchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xmedi)**2+(yj-ymedi)**2+(zj-zmedi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- isubchap=1
- endif
- enddo
- enddo
- enddo
- if (isubchap.eq.1) then
- xj=xj_temp-xmedi
- yj=yj_temp-ymedi
- zj=zj_temp-zmedi
- else
- xj=xj_safe-xmedi
- yj=yj_safe-ymedi
- zj=zj_safe-zmedi
- endif
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xmedi,boxxsize)
+ yj=boxshift(yj-ymedi,boxysize)
+ zj=boxshift(zj-zmedi,boxzsize)
C if ((i+3).lt.j) then !this condition keeps for turn3 and turn4 not subject to PBC
c 174 continue
-c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
-c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
-C Condition for being inside the proper box
-c if ((xj.gt.((0.5d0)*boxxsize)).or.
-c & (xj.lt.((-0.5d0)*boxxsize))) then
-c go to 174
-c endif
-c 175 continue
-c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
-c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
-C Condition for being inside the proper box
-c if ((yj.gt.((0.5d0)*boxysize)).or.
-c & (yj.lt.((-0.5d0)*boxysize))) then
-c go to 175
-c endif
-c 176 continue
-c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
-c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
-C Condition for being inside the proper box
-c if ((zj.gt.((0.5d0)*boxzsize)).or.
-c & (zj.lt.((-0.5d0)*boxzsize))) then
-c go to 176
-c endif
-C endif !endPBC condintion
-C xj=xj-xmedi
-C yj=yj-ymedi
-C zj=zj-zmedi
rij=xj*xj+yj*yj+zj*zj
sss=sscale(dsqrt(rij),r_cut_int)
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
dimension ggg(3)
- integer xshift,yshift,zshift
+ double precision boxshift
evdw2=0.0D0
evdw2_14=0.0d0
r0_scp=4.5d0
c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
c go to 136
c endif
- xi=mod(xi,boxxsize)
- if (xi.lt.0) xi=xi+boxxsize
- yi=mod(yi,boxysize)
- if (yi.lt.0) yi=yi+boxysize
- zi=mod(zi,boxzsize)
- if (zi.lt.0) zi=zi+boxzsize
+ call to_box(xi,yi,zi)
C xi=xi+xshift*boxxsize
C yi=yi+yshift*boxysize
C zi=zi+zshift*boxzsize
xj=c(1,j)
yj=c(2,j)
zj=c(3,j)
-c 174 continue
-c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
-c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
-C Condition for being inside the proper box
-c if ((xj.gt.((0.5d0)*boxxsize)).or.
-c & (xj.lt.((-0.5d0)*boxxsize))) then
-c go to 174
-c endif
-c 175 continue
-c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
-c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
-cC Condition for being inside the proper box
-c if ((yj.gt.((0.5d0)*boxysize)).or.
-c & (yj.lt.((-0.5d0)*boxysize))) then
-c go to 175
-c endif
-c 176 continue
-c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
-c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
-C Condition for being inside the proper box
-c if ((zj.gt.((0.5d0)*boxzsize)).or.
-c & (zj.lt.((-0.5d0)*boxzsize))) then
-c go to 176
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- subchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- subchap=1
- endif
- enddo
- enddo
- enddo
- if (subchap.eq.1) then
- xj=xj_temp-xi
- yj=yj_temp-yi
- zj=zj_temp-zi
- else
- xj=xj_safe-xi
- yj=yj_safe-yi
- zj=zj_safe-zi
- endif
-c c endif
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
C xj=xj-xi
C yj=yj-yi
C zj=zj-zi
ggg(1)=xj*fac
ggg(2)=yj*fac
ggg(3)=zj*fac
-cgrad if (j.lt.i) then
-cd write (iout,*) 'j<i'
-C Uncomment following three lines for SC-p interactions
-c do k=1,3
-c gradx_scp(k,j)=gradx_scp(k,j)+ggg(k)
-c enddo
-cgrad else
-cd write (iout,*) 'j>i'
-cgrad do k=1,3
-cgrad ggg(k)=-ggg(k)
-C Uncomment following line for SC-p interactions
-c gradx_scp(k,j)=gradx_scp(k,j)-ggg(k)
-cgrad enddo
-cgrad endif
-cgrad do k=1,3
-cgrad gvdwc_scp(k,i)=gvdwc_scp(k,i)-0.5D0*ggg(k)
-cgrad enddo
-cgrad kstart=min0(i+1,j)
-cgrad kend=max0(i-1,j-1)
-cd write (iout,*) 'i=',i,' j=',j,' kstart=',kstart,' kend=',kend
-cd write (iout,*) ggg(1),ggg(2),ggg(3)
-cgrad do k=kstart,kend
-cgrad do l=1,3
-cgrad gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l)
-cgrad enddo
-cgrad enddo
do k=1,3
gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.SPLITELE'
- integer xshift,yshift,zshift
double precision ggg(3)
integer i,iint,j,k,iteli,itypj,subchap,ikont
double precision xi,yi,zi,xj,yj,zj,rrij,sss1,sssgrad1,
& fac,e1,e2,rij
double precision evdw2,evdw2_14,evdwij
- double precision xj_safe,yj_safe,zj_safe,xj_temp,yj_temp,zj_temp,
- & dist_temp, dist_init
double precision sscale,sscagrad
+ double precision boxshift
evdw2=0.0D0
evdw2_14=0.0d0
c print *,boxxsize,boxysize,boxzsize,'wymiary pudla'
xi=0.5D0*(c(1,i)+c(1,i+1))
yi=0.5D0*(c(2,i)+c(2,i+1))
zi=0.5D0*(c(3,i)+c(3,i+1))
- xi=mod(xi,boxxsize)
- if (xi.lt.0) xi=xi+boxxsize
- yi=mod(yi,boxysize)
- if (yi.lt.0) yi=yi+boxysize
- zi=mod(zi,boxzsize)
- if (zi.lt.0) zi=zi+boxzsize
-c xi=xi+xshift*boxxsize
-c yi=yi+yshift*boxysize
-c zi=zi+zshift*boxzsize
-c print *,xi,yi,zi,'polozenie i'
-C Return atom into box, boxxsize is size of box in x dimension
-c 134 continue
-c if (xi.gt.((xshift+0.5d0)*boxxsize)) xi=xi-boxxsize
-c if (xi.lt.((xshift-0.5d0)*boxxsize)) xi=xi+boxxsize
-C Condition for being inside the proper box
-c if ((xi.gt.((xshift+0.5d0)*boxxsize)).or.
-c & (xi.lt.((xshift-0.5d0)*boxxsize))) then
-c go to 134
-c endif
-c 135 continue
-c print *,xi,boxxsize,"pierwszy"
-
-c if (yi.gt.((yshift+0.5d0)*boxysize)) yi=yi-boxysize
-c if (yi.lt.((yshift-0.5d0)*boxysize)) yi=yi+boxysize
-C Condition for being inside the proper box
-c if ((yi.gt.((yshift+0.5d0)*boxysize)).or.
-c & (yi.lt.((yshift-0.5d0)*boxysize))) then
-c go to 135
-c endif
-c 136 continue
-c if (zi.gt.((zshift+0.5d0)*boxzsize)) zi=zi-boxzsize
-c if (zi.lt.((zshift-0.5d0)*boxzsize)) zi=zi+boxzsize
-C Condition for being inside the proper box
-c if ((zi.gt.((zshift+0.5d0)*boxzsize)).or.
-c & (zi.lt.((zshift-0.5d0)*boxzsize))) then
-c go to 136
-c endif
+ call to_box(xi,yi,zi)
c do iint=1,nscp_gr(i)
c do j=iscpstart(i,iint),iscpend(i,iint)
xj=c(1,j)
yj=c(2,j)
zj=c(3,j)
- xj=mod(xj,boxxsize)
- if (xj.lt.0) xj=xj+boxxsize
- yj=mod(yj,boxysize)
- if (yj.lt.0) yj=yj+boxysize
- zj=mod(zj,boxzsize)
- if (zj.lt.0) zj=zj+boxzsize
-c 174 continue
-c if (xj.gt.((0.5d0)*boxxsize)) xj=xj-boxxsize
-c if (xj.lt.((-0.5d0)*boxxsize)) xj=xj+boxxsize
-C Condition for being inside the proper box
-c if ((xj.gt.((0.5d0)*boxxsize)).or.
-c & (xj.lt.((-0.5d0)*boxxsize))) then
-c go to 174
-c endif
-c 175 continue
-c if (yj.gt.((0.5d0)*boxysize)) yj=yj-boxysize
-c if (yj.lt.((-0.5d0)*boxysize)) yj=yj+boxysize
-cC Condition for being inside the proper box
-c if ((yj.gt.((0.5d0)*boxysize)).or.
-c & (yj.lt.((-0.5d0)*boxysize))) then
-c go to 175
-c endif
-c 176 continue
-c if (zj.gt.((0.5d0)*boxzsize)) zj=zj-boxzsize
-c if (zj.lt.((-0.5d0)*boxzsize)) zj=zj+boxzsize
-C Condition for being inside the proper box
-c if ((zj.gt.((0.5d0)*boxzsize)).or.
-c & (zj.lt.((-0.5d0)*boxzsize))) then
-c go to 176
-c endif
-CHERE IS THE CALCULATION WHICH MIRROR IMAGE IS THE CLOSEST ONE
- dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- xj_safe=xj
- yj_safe=yj
- zj_safe=zj
- subchap=0
- do xshift=-1,1
- do yshift=-1,1
- do zshift=-1,1
- xj=xj_safe+xshift*boxxsize
- yj=yj_safe+yshift*boxysize
- zj=zj_safe+zshift*boxzsize
- dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
- if(dist_temp.lt.dist_init) then
- dist_init=dist_temp
- xj_temp=xj
- yj_temp=yj
- zj_temp=zj
- subchap=1
- endif
- enddo
- enddo
- enddo
- if (subchap.eq.1) then
- xj=xj_temp-xi
- yj=yj_temp-yi
- zj=zj_temp-zi
- else
- xj=xj_safe-xi
- yj=yj_safe-yi
- zj=zj_safe-zi
- endif
+ call to_box(xj,yj,zj)
+ xj=boxshift(xj-xi,boxxsize)
+ yj=boxshift(yj-yi,boxysize)
+ zj=boxshift(zj-zi,boxzsize)
c print *,xj,yj,zj,'polozenie j'
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
c print *,rrij
endif
return
end
+c------------------------------------------------------------------------
+ double precision function boxshift(x,boxsize)
+ implicit none
+ double precision x,boxsize
+ double precision xtemp
+ xtemp=dmod(x,boxsize)
+ if (dabs(xtemp-boxsize).lt.dabs(xtemp)) then
+ boxshift=xtemp-boxsize
+ else if (dabs(xtemp+boxsize).lt.dabs(xtemp)) then
+ boxshift=xtemp+boxsize
+ else
+ boxshift=xtemp
+ endif
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine closest_img(xi,yi,zi,xj,yj,zj)
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ integer xshift,yshift,zshift,subchap
+ double precision dist_init,xj_safe,yj_safe,zj_safe,
+ & xj_temp,yj_temp,zj_temp,dist_temp
+ xj_safe=xj
+ yj_safe=yj
+ zj_safe=zj
+ dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ subchap=0
+ do xshift=-1,1
+ do yshift=-1,1
+ do zshift=-1,1
+ xj=xj_safe+xshift*boxxsize
+ yj=yj_safe+yshift*boxysize
+ zj=zj_safe+zshift*boxzsize
+ dist_temp=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
+ if(dist_temp.lt.dist_init) then
+ dist_init=dist_temp
+ xj_temp=xj
+ yj_temp=yj
+ zj_temp=zj
+ subchap=1
+ endif
+ enddo
+ enddo
+ enddo
+ if (subchap.eq.1) then
+ xj=xj_temp-xi
+ yj=yj_temp-yi
+ zj=zj_temp-zi
+ else
+ xj=xj_safe-xi
+ yj=yj_safe-yi
+ zj=zj_safe-zi
+ endif
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine to_box(xi,yi,zi)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ double precision xi,yi,zi
+ xi=dmod(xi,boxxsize)
+ if (xi.lt.0.0d0) xi=xi+boxxsize
+ yi=dmod(yi,boxysize)
+ if (yi.lt.0.0d0) yi=yi+boxysize
+ zi=dmod(zi,boxzsize)
+ if (zi.lt.0.0d0) zi=zi+boxzsize
+ return
+ end
+c--------------------------------------------------------------------------
+ subroutine lipid_layer(xi,yi,zi,sslipi,ssgradlipi)
+ implicit none
+ include 'DIMENSIONS'
+ include 'COMMON.CHAIN'
+ double precision xi,yi,zi,sslipi,ssgradlipi
+ double precision fracinbuf
+ double precision sscalelip,sscagradlip
+
+ if ((zi.gt.bordlipbot).and.(zi.lt.bordliptop)) then
+C the energy transfer exist
+ if (zi.lt.buflipbot) then
+C what fraction I am in
+ fracinbuf=1.0d0-((zi-bordlipbot)/lipbufthick)
+C lipbufthick is thickenes of lipid buffore
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=-sscagradlip(fracinbuf)/lipbufthick
+ elseif (zi.gt.bufliptop) then
+ fracinbuf=1.0d0-((bordliptop-zi)/lipbufthick)
+ sslipi=sscalelip(fracinbuf)
+ ssgradlipi=sscagradlip(fracinbuf)/lipbufthick
+ else
+ sslipi=1.0d0
+ ssgradlipi=0.0
+ endif
+ else
+ sslipi=0.0d0
+ ssgradlipi=0.0
+ endif
+ return
+ end
projects / unres.git / blobdiff