include 'COMMON.VAR'
include 'COMMON.IOUNITS'
include 'COMMON.CALC'
-#ifndef CLUST
-#ifndef WHAM
+C#ifndef CLUST
+C#ifndef WHAM
C include 'COMMON.MD'
-#endif
-#endif
+C#endif
+C#endif
c External functions
double precision h_base
dyi=dc_norm(2,nres+i)
dzi=dc_norm(3,nres+i)
dsci_inv=vbld_inv(i+nres)
- 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
- 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
+
itypj=itype(j)
- xj=c(1,nres+j)
- yj=c(2,nres+j)
- zj=c(3,nres+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
- 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=xj-xi
- yj=yj-yi
- zj=zj-zi
+ xj=c(1,nres+j)-c(1,nres+i)
+ yj=c(2,nres+j)-c(2,nres+i)
+ zj=c(3,nres+j)-c(3,nres+i)
dxj=dc_norm(1,nres+j)
dyj=dc_norm(2,nres+j)
dzj=dc_norm(3,nres+j)
ljXs=sig-sig0ij
ljA=eps1*eps2rt**2*eps3rt**2
- ljB=ljA*bb
- ljA=ljA*aa
- ljxm=ljXs+(-2.0D0*aa/bb)**(1.0D0/6.0D0)
+ ljB=ljA*bb_aq(itypi,itypj)
+ ljA=ljA*aa_aq(itypi,itypj)
+ ljxm=ljXs+(-2.0D0*aa_aq(itypi,itypj)/
+ & bb_aq(itypi,itypj))**(1.0D0/6.0D0)
ssXs=d0cm
deltat1=1.0d0-om1
c Stop and plot energy and derivative as a function of distance
if (checkstop) then
ssm=ssC-0.25D0*ssB*ssB/ssA
- ljm=-0.25D0*ljB*bb/aa
+ ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
if (ssm.lt.ljm .and.
& dabs(rij-0.5d0*(ssxm+ljxm)).lt.0.35d0*(ljxm-ssxm)) then
nicheck=1000
havebond=.false.
ljd=rij-ljXs
fac=(1.0D0/ljd)**expon
- e1=fac*fac*aa
- e2=fac*bb
+ e1=fac*fac*aa_aq(itypi,itypj)
+ e2=fac*bb_aq(itypi,itypj)
eij=eps1*eps2rt*eps3rt*(e1+e2)
-C write(iout,*) eij,'TU?1'
eps2der=eij*eps3rt
eps3der=eij*eps2rt
eij=eij*eps2rt*eps3rt
havebond=.true.
ssd=rij-ssXs
eij=ssA*ssd*ssd+ssB*ssd+ssC
-C write(iout,*) 'TU?2',ssc,ssd
+
ed=2*akcm*ssd+akct*deltat12
pom1=akct*ssd
pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=ssm*h1+Ht*h2
-C write(iout,*) eij,'TU?3'
delta_inv=1.0d0/(xm-ssxm)
deltasq_inv=delta_inv*delta_inv
fac=ssm*hd1-Ht*hd2
eom12=fac1*d_ssxm(3)+fac2*d_xm(3)+h1*d_ssm(3)
else
havebond=.false.
- ljm=-0.25D0*ljB*bb/aa
- d_ljm(1)=-0.5D0*bb/aa*ljB
+ ljm=-0.25D0*ljB*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)
+ d_ljm(1)=-0.5D0*bb_aq(itypi,itypj)/aa_aq(itypi,itypj)*ljB
d_ljm(2)=d_ljm(1)*(0.5D0*eps2rt_om2/eps2rt+alf2/eps3rt)
d_ljm(3)=d_ljm(1)*(0.5D0*eps1_om12+0.5D0*eps2rt_om12/eps2rt-
+ alf12/eps3rt)
h1=h_base(f1,hd1)
h2=h_base(f2,hd2)
eij=Ht*h1+ljm*h2
-C write(iout,*) 'TU?4',ssA
delta_inv=1.0d0/(ljxm-xm)
deltasq_inv=delta_inv*delta_inv
fac=Ht*hd1-ljm*hd2
c-------END SECOND METHOD, CONTINUOUS SECOND DERIVATIVE
endif
- write(iout,*) 'havebond',havebond
+
if (havebond) then
#ifndef CLUST
#ifndef WHAM
& allihpb(maxdim),alljhpb(maxdim),
& newnss,newihpb(maxdim),newjhpb(maxdim)
logical found
- integer i_newnss(1024),displ(0:1024)
+ integer i_newnss(256),displ(0:256)
integer g_newihpb(maxdim),g_newjhpb(maxdim),g_newnss
allnss=0
return
end
-c----------------------------------------------------------------------------
-
-#ifdef WHAM
- subroutine read_ssHist
- implicit none
-
-c Includes
- include 'DIMENSIONS'
- include "DIMENSIONS.FREE"
- include 'COMMON.FREE'
-
-c Local variables
- integer i,j
- character*80 controlcard
-
- do i=1,dyn_nssHist
- call card_concat(controlcard,.true.)
- read(controlcard,*)
- & dyn_ssHist(i,0),(dyn_ssHist(i,j),j=1,2*dyn_ssHist(i,0))
- enddo
-
- return
- end
-#endif
-
-c----------------------------------------------------------------------------
-
C-----------------------------------------------------------------------------
C-----------------------------------------------------------------------------
C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
-C-----------------------------------------------------------------------------
c$$$c-----------------------------------------------------------------------------
c$$$
double precision ssA,ssB,ssC,ssXs
double precision ssxm,ljxm,ssm,ljm
double precision d_ssxm(1:3),d_ljxm(1:3),d_ssm(1:3),d_ljm(1:3)
-
+ eij=0.0
+ if (dtriss.eq.0) return
i=resi
j=resj
k=resk
C Energy function is E=d/(a*(x-y)**2+b*(x+y)**2+c) where x is first
C distance y is second distance the a,b,c,d are parameters derived for
C this problem d parameter was set as a penalty currenlty set to 1.
- eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**2+ctriss)
+ if ((iabs(j-i).le.2).or.(iabs(i-k).le.2)) then
+ eij1=0.0d0
+ else
+ eij1=dtriss/(atriss*(rij-rik)**2+btriss*(rij+rik)**6+ctriss)
+ endif
C second case jth atom is center
- eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**2+ctriss)
+ if ((iabs(j-i).le.2).or.(iabs(j-k).le.2)) then
+ eij2=0.0d0
+ else
+ eij2=dtriss/(atriss*(rij-rjk)**2+btriss*(rij+rjk)**6+ctriss)
+ endif
C the third case kth atom is the center
- eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**2+ctriss)
+ if ((iabs(i-k).le.2).or.(iabs(j-k).le.2)) then
+ eij3=0.0d0
+ else
+ eij3=dtriss/(atriss*(rik-rjk)**2+btriss*(rik+rjk)**6+ctriss)
+ endif
C eij2=0.0
C eij3=0.0
C eij1=0.0
C write(iout,*)i,j,k,eij
C The energy penalty calculated now time for the gradient part
C derivative over rij
- fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+2.0*btriss*(rij+rik))
- &-eij2**2/dtriss*(2.0*atriss*(rij-rjk)+2.0*btriss*(rij+rjk))
+ fac=-eij1**2/dtriss*(2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5)
+ &-eij2**2/dtriss*(2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)
gg(1)=xij*fac/rij
gg(2)=yij*fac/rij
gg(3)=zij*fac/rij
gvdwc(l,j)=gvdwc(l,j)+gg(l)
enddo
C now derivative over rik
- fac=-eij1**2/dtriss*(-2.0*atriss*(rij-rik)+2.0*btriss*(rij+rik))
- &-eij3**2/dtriss*(2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+ fac=-eij1**2/dtriss*
+ &(-2.0*atriss*(rij-rik)+6.0*btriss*(rij+rik)**5)
+ &-eij3**2/dtriss*(2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
gg(1)=xik*fac/rik
gg(2)=yik*fac/rik
gg(3)=zik*fac/rik
gvdwc(l,k)=gvdwc(l,k)+gg(l)
enddo
C now derivative over rjk
- fac=-eij2**2/dtriss*(-2.0*atriss*(rij-rjk)+2.0*btriss*(rij+rjk))-
- &eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+2.0*btriss*(rik+rjk))
+ fac=-eij2**2/dtriss*
+ &(-2.0*atriss*(rij-rjk)+6.0*btriss*(rij+rjk)**5)-
+ &eij3**2/dtriss*(-2.0*atriss*(rik-rjk)+6.0*btriss*(rik+rjk)**5)
gg(1)=xjk*fac/rjk
gg(2)=yjk*fac/rjk
gg(3)=zjk*fac/rjk
projects / unres.git / blobdiff