time_Bcastw=time_Bcastw+MPI_Wtime()-time00
c call chainbuild_cart
endif
-c print *,'Processor',myrank,' calling etotal ipot=',ipot
+c write(iout,*) 'Processor',myrank,' calling etotal ipot=',ipot
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
#else
c if (modecalc.eq.12.or.modecalc.eq.14) then
C If performing constraint dynamics, call the constraint energy
C after the equilibration time
if(usampl.and.totT.gt.eq_time) then
+c write (iout,*) "CALL TO ECONSTR_BACK"
call EconstrQ
call Econstr_back
else
common /sccalc/ time11,time12,time112,theti,it,nlobit
delta=0.02d0*pi
escloc=0.0D0
+c write(iout,*) "ESC: loc_start",loc_start," loc_end",loc_end
do i=loc_start,loc_end
costtab(i+1) =dcos(theta(i+1))
sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
integer nnn, i, j, k, ki, irec, l
integer katy, odleglosci, test7
real*8 odleg, odleg2, odleg3, kat, kat2, kat3, gdih(max_template)
+ real*8 Eval,Erot
real*8 distance(max_template),distancek(max_template),
& min_odl,godl(max_template),dih_diff(max_template)
+c
+c FP - 30/10/2014 Temporary specifications for homology restraints
+c
+ double precision utheta_i,gutheta_i,sum_gtheta,sum_sgtheta,
+ & sgtheta
+ double precision, dimension (maxres) :: guscdiff,usc_diff
+ double precision, dimension (max_template) ::
+ & gtheta,dscdiff,uscdiffk,guscdiff2,guscdiff3,
+ & theta_diff
+c
+
include 'COMMON.SBRIDGE'
include 'COMMON.CHAIN'
include 'COMMON.GEO'
include 'COMMON.IOUNITS'
include 'COMMON.MD'
include 'COMMON.CONTROL'
+c
+c From subroutine Econstr_back
+c
+ include 'COMMON.NAMES'
+ include 'COMMON.TIME1'
+c
do i=1,19
c Pseudo-energy and gradient from homology restraints (MODELLER-like
c function)
C AL 5/2/14 - Introduce list of restraints
+c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
+#ifdef DEBUG
+ write(iout,*) "------- dist restrs start -------"
+#endif
do ii = link_start_homo,link_end_homo
i = ires_homo(ii)
j = jres_homo(ii)
dij=dist(i,j)
+c write (iout,*) "dij(",i,j,") =",dij
do k=1,constr_homology
distance(k)=odl(k,ii)-dij
- distancek(k)=0.5d0*waga_dist*distance(k)**2*sigma_odl(k,ii)
+c write (iout,*) "distance(",k,") =",distance(k)
+ distancek(k)=0.5d0*distance(k)**2*sigma_odl(k,ii) ! waga_dist rmvd from Gaussian argument
+c write (iout,*) "sigma_odl(",k,ii,") =",sigma_odl(k,ii)
+c write (iout,*) "distancek(",k,") =",distancek(k)
+c distancek(k)=0.5d0*waga_dist*distance(k)**2*sigma_odl(k,ii)
enddo
min_odl=minval(distancek)
+c write (iout,* )"min_odl",min_odl
#ifdef DEBUG
write (iout,*) "ij dij",i,j,dij
write (iout,*) "distance",(distance(k),k=1,constr_homology)
ccc & "sigma_odl(i,j,k)=", sigma_odl(i,j,k)
enddo
+c write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
+c write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
#ifdef DEBUG
- write (iout,*) "godl",(godl(k),k=1,constr_homology)
- write (iout,*) "ii i j",ii,i,j," odleg2",odleg2
+ write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
+ write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
#endif
odleg=odleg-dLOG(odleg2/constr_homology)+min_odl
+c write (iout,*) "odleg",odleg ! sum of -ln-s
c Gradient
sum_godl=odleg2
- sum_sgodl=0.0
+ sum_sgodl=0.0d0
do k=1,constr_homology
c godl=dexp(((-(distance(i,j,k)**2)/(2*(sigma_odl(i,j,k))**2))
c & *waga_dist)+min_odl
- sgodl=-godl(k)*distance(k)*sigma_odl(k,ii)*waga_dist
+c sgodl=-godl(k)*distance(k)*sigma_odl(k,ii)*waga_dist
+ sgodl=-godl(k)*distance(k)*sigma_odl(k,ii) ! waga_dist rmvd
sum_sgodl=sum_sgodl+sgodl
c sgodl2=sgodl2+sgodl
c write(iout,*) i, j, k, "TEST K"
enddo
- grad_odl3=sum_sgodl/(sum_godl*dij)
+ grad_odl3=waga_dist*sum_sgodl/(sum_godl*dij)
+c grad_odl3=sum_sgodl/(sum_godl*dij)
c write(iout,*) i, j, k, distance(i,j,k), "W GRADIENCIE2"
ghpbc(jik,j)=ghpbc(jik,j)-ggodl
ccc write(iout,746) "GRAD_ODL_2", i, j, jik, ggodl,
ccc & ghpbc(jik,i+1), ghpbc(jik,j+1)
-
+c if (i.eq.25.and.j.eq.27) then
+c write(iout,*) "jik",jik,"i",i,"j",j
+c write(iout,*) "sum_sgodl",sum_sgodl,"sgodl",sgodl
+c write(iout,*) "grad_odl3",grad_odl3
+c write(iout,*) "c(",jik,i,")",c(jik,i),"c(",jik,j,")",c(jik,j)
+c write(iout,*) "ggodl",ggodl
+c write(iout,*) "ghpbc(",jik,i,")",
+c & ghpbc(jik,i),"ghpbc(",jik,j,")",
+c & ghpbc(jik,j)
+c endif
enddo
ccc write(iout,778)"TEST: odleg2=", odleg2, "DLOG(odleg2)=",
ccc & dLOG(odleg2),"-odleg=", -odleg
- enddo ! ii
+ enddo ! ii-loop for dist
+#ifdef DEBUG
+ write(iout,*) "------- dist restrs end -------"
+c if (waga_angle.eq.1.0d0 .or. waga_theta.eq.1.0d0 .or.
+c & waga_d.eq.1.0d0) call sum_gradient
+#endif
c Pseudo-energy and gradient from dihedral-angle restraints from
c homology templates
c write (iout,*) "End of distance loop"
c call flush(iout)
kat=0.0d0
c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
+#ifdef DEBUG
+ write(iout,*) "------- dih restrs start -------"
+ do i=idihconstr_start_homo,idihconstr_end_homo
+ write (iout,*) "gloc_init(",i,icg,")",gloc(i,icg)
+ enddo
+#endif
do i=idihconstr_start_homo,idihconstr_end_homo
kat2=0.0d0
c betai=beta(i,i+1,i+2,i+3)
betai = phi(i+3)
+c write (iout,*) "betai =",betai
do k=1,constr_homology
dih_diff(k)=pinorm(dih(k,i)-betai)
+c write (iout,*) "dih_diff(",k,") =",dih_diff(k)
c if (dih_diff(i,k).gt.3.14159) dih_diff(i,k)=
c & -(6.28318-dih_diff(i,k))
c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
c & 6.28318+dih_diff(i,k)
- kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
+ kat3=-0.5d0*dih_diff(k)**2*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
+c kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
gdih(k)=dexp(kat3)
kat2=kat2+gdih(k)
c write(iout,*) "kat2=", kat2, "exp(kat3)=", exp(kat3)
c write(*,*)""
enddo
+c write (iout,*) "gdih",(gdih(k),k=1,constr_homology) ! exps
+c write (iout,*) "i",i," betai",betai," kat2",kat2 ! sum of exps
#ifdef DEBUG
write (iout,*) "i",i," betai",betai," kat2",kat2
write (iout,*) "gdih",(gdih(k),k=1,constr_homology)
#endif
if (kat2.le.1.0d-14) cycle
kat=kat-dLOG(kat2/constr_homology)
+c write (iout,*) "kat",kat ! sum of -ln-s
ccc write(iout,778)"TEST: kat2=", kat2, "DLOG(kat2)=",
ccc & dLOG(kat2), "-kat=", -kat
c ----------------------------------------------------------------------
sum_gdih=kat2
- sum_sgdih=0.0
+ sum_sgdih=0.0d0
do k=1,constr_homology
- sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
+ sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i) ! waga_angle rmvd
+c sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
sum_sgdih=sum_sgdih+sgdih
enddo
- grad_dih3=sum_sgdih/sum_gdih
+c grad_dih3=sum_sgdih/sum_gdih
+ grad_dih3=waga_angle*sum_sgdih/sum_gdih
c write(iout,*)i,k,gdih,sgdih,beta(i+1,i+2,i+3,i+4),grad_dih3
ccc write(iout,747) "GRAD_KAT_1", i, nphi, icg, grad_dih3,
ccc & gloc(nphi+i-3,icg)
gloc(i,icg)=gloc(i,icg)+grad_dih3
+c if (i.eq.25) then
+c write(iout,*) "i",i,"icg",icg,"gloc(",i,icg,")",gloc(i,icg)
+c endif
ccc write(iout,747) "GRAD_KAT_2", i, nphi, icg, grad_dih3,
ccc & gloc(nphi+i-3,icg)
+ enddo ! i-loop for dih
+#ifdef DEBUG
+ write(iout,*) "------- dih restrs end -------"
+#endif
+
+c Pseudo-energy and gradient for theta angle restraints from
+c homology templates
+c FP 01/15 - inserted from econstr_local_test.F, loop structure
+c adapted
+
+c
+c For constr_homology reference structures (FP)
+c
+c Uconst_back_tot=0.0d0
+ Eval=0.0d0
+ Erot=0.0d0
+c Econstr_back legacy
+ do i=1,nres
+c do i=ithet_start,ithet_end
+ dutheta(i)=0.0d0
+c enddo
+c do i=loc_start,loc_end
+ do j=1,3
+ duscdiff(j,i)=0.0d0
+ duscdiffx(j,i)=0.0d0
+ enddo
+ enddo
+c
+c do iref=1,nref
+c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
+c write (iout,*) "waga_theta",waga_theta
+ if (waga_theta.gt.0.0d0) then
+#ifdef DEBUG
+ write (iout,*) "usampl",usampl
+ write(iout,*) "------- theta restrs start -------"
+c do i=ithet_start,ithet_end
+c write (iout,*) "gloc_init(",nphi+i,icg,")",gloc(nphi+i,icg)
+c enddo
+#endif
+c write (iout,*) "maxres",maxres,"nres",nres
+
+ do i=ithet_start,ithet_end
+c
+c do i=1,nfrag_back
+c ii = ifrag_back(2,i,iset)-ifrag_back(1,i,iset)
+c
+c Deviation of theta angles wrt constr_homology ref structures
+c
+ utheta_i=0.0d0 ! argument of Gaussian for single k
+ gutheta_i=0.0d0 ! Sum of Gaussians over constr_homology ref structures
+c do j=ifrag_back(1,i,iset)+2,ifrag_back(2,i,iset) ! original loop
+c over residues in a fragment
+c write (iout,*) "theta(",i,")=",theta(i)
+ do k=1,constr_homology
+c
+c dtheta_i=theta(j)-thetaref(j,iref)
+c dtheta_i=thetaref(k,i)-theta(i) ! original form without indexing
+ theta_diff(k)=thetatpl(k,i)-theta(i)
+c
+ utheta_i=-0.5d0*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta rmvd from Gaussian argument
+c utheta_i=-0.5d0*waga_theta*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta?
+ gtheta(k)=dexp(utheta_i) ! + min_utheta_i?
+ gutheta_i=gutheta_i+dexp(utheta_i) ! Sum of Gaussians (pk)
+c Gradient for single Gaussian restraint in subr Econstr_back
+c dutheta(j-2)=dutheta(j-2)+wfrag_back(1,i,iset)*dtheta_i/(ii-1)
+c
+ enddo
+c write (iout,*) "gtheta",(gtheta(k),k=1,constr_homology) ! exps
+c write (iout,*) "i",i," gutheta_i",gutheta_i ! sum of exps
+
+c
+c Gradient for multiple Gaussian restraint
+ sum_gtheta=gutheta_i
+ sum_sgtheta=0.0d0
+ do k=1,constr_homology
+c New generalized expr for multiple Gaussian from Econstr_back
+ sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i) ! waga_theta rmvd
+c
+c sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i)*waga_theta ! right functional form?
+ sum_sgtheta=sum_sgtheta+sgtheta ! cum variable
+ enddo
+c grad_theta3=sum_sgtheta/sum_gtheta 1/*theta(i)? s. line below
+c grad_theta3=sum_sgtheta/sum_gtheta
+c
+c Final value of gradient using same var as in Econstr_back
+ dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
+c dutheta(i)=sum_sgtheta/sum_gtheta
+c
+c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
+ Eval=Eval-dLOG(gutheta_i/constr_homology)
+c write (iout,*) "utheta(",i,")=",utheta(i) ! -ln of sum of exps
+c write (iout,*) "Uconst_back",Uconst_back ! sum of -ln-s
+c Uconst_back=Uconst_back+utheta(i)
+ enddo ! (i-loop for theta)
+#ifdef DEBUG
+ write(iout,*) "------- theta restrs end -------"
+#endif
+ endif
+c
+c Deviation of local SC geometry
+c
+c Separation of two i-loops (instructed by AL - 11/3/2014)
+c
+c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
+c write (iout,*) "waga_d",waga_d
+
+#ifdef DEBUG
+ write(iout,*) "------- SC restrs start -------"
+ write (iout,*) "Initial duscdiff,duscdiffx"
+ do i=loc_start,loc_end
+ write (iout,*) i,(duscdiff(jik,i),jik=1,3),
+ & (duscdiffx(jik,i),jik=1,3)
enddo
+#endif
+ do i=loc_start,loc_end
+ usc_diff_i=0.0d0 ! argument of Gaussian for single k
+ guscdiff(i)=0.0d0 ! Sum of Gaussians over constr_homology ref structures
+c do j=ifrag_back(1,i,iset)+1,ifrag_back(2,i,iset)-1 ! Econstr_back legacy
+c write(iout,*) "xxtab, yytab, zztab"
+c write(iout,'(i5,3f8.2)') i,xxtab(i),yytab(i),zztab(i)
+ do k=1,constr_homology
+c
+ dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
+c Original sign inverted for calc of gradients (s. Econstr_back)
+ dyy=-yytpl(k,i)+yytab(i) ! ibid y
+ dzz=-zztpl(k,i)+zztab(i) ! ibid z
+c write(iout,*) "dxx, dyy, dzz"
+c write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
+c
+ usc_diff_i=-0.5d0*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d rmvd from Gaussian argument
+c usc_diff(i)=-0.5d0*waga_d*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d?
+c uscdiffk(k)=usc_diff(i)
+ guscdiff2(k)=dexp(usc_diff_i) ! without min_scdiff
+ guscdiff(i)=guscdiff(i)+dexp(usc_diff_i) !Sum of Gaussians (pk)
+c write (iout,'(i5,6f10.5)') j,xxtab(j),yytab(j),zztab(j),
+c & xxref(j),yyref(j),zzref(j)
+ enddo
+c
+c Gradient
+c
+c Generalized expression for multiple Gaussian acc to that for a single
+c Gaussian in Econstr_back as instructed by AL (FP - 03/11/2014)
+c
+c Original implementation
+c sum_guscdiff=guscdiff(i)
+c
+c sum_sguscdiff=0.0d0
+c do k=1,constr_homology
+c sguscdiff=-guscdiff2(k)*dscdiff(k)*sigma_d(k,i)*waga_d !waga_d?
+c sguscdiff=-guscdiff3(k)*dscdiff(k)*sigma_d(k,i)*waga_d ! w min_uscdiff
+c sum_sguscdiff=sum_sguscdiff+sguscdiff
+c enddo
+c
+c Implementation of new expressions for gradient (Jan. 2015)
+c
+c grad_uscdiff=sum_sguscdiff/(sum_guscdiff*dtab) !?
+ do k=1,constr_homology
+c
+c New calculation of dxx, dyy, and dzz corrected by AL (07/11), was missing and wrong
+c before. Now the drivatives should be correct
+c
+ dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
+c Original sign inverted for calc of gradients (s. Econstr_back)
+ dyy=-yytpl(k,i)+yytab(i) ! ibid y
+ dzz=-zztpl(k,i)+zztab(i) ! ibid z
+c
+c New implementation
+c
+ sum_guscdiff=guscdiff2(k)*!(dsqrt(dxx*dxx+dyy*dyy+dzz*dzz))* -> wrong!
+ & sigma_d(k,i) ! for the grad wrt r'
+c sum_sguscdiff=sum_sguscdiff+sum_guscdiff
+c
+c
+c New implementation
+ sum_guscdiff = waga_d*sum_guscdiff
+ do jik=1,3
+ duscdiff(jik,i-1)=duscdiff(jik,i-1)+
+ & sum_guscdiff*(dXX_C1tab(jik,i)*dxx+
+ & dYY_C1tab(jik,i)*dyy+dZZ_C1tab(jik,i)*dzz)/guscdiff(i)
+ duscdiff(jik,i)=duscdiff(jik,i)+
+ & sum_guscdiff*(dXX_Ctab(jik,i)*dxx+
+ & dYY_Ctab(jik,i)*dyy+dZZ_Ctab(jik,i)*dzz)/guscdiff(i)
+ duscdiffx(jik,i)=duscdiffx(jik,i)+
+ & sum_guscdiff*(dXX_XYZtab(jik,i)*dxx+
+ & dYY_XYZtab(jik,i)*dyy+dZZ_XYZtab(jik,i)*dzz)/guscdiff(i)
+c
+#ifdef DEBUG
+ write(iout,*) "jik",jik,"i",i
+ write(iout,*) "dxx, dyy, dzz"
+ write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
+ write(iout,*) "guscdiff2(",k,")",guscdiff2(k)
+c write(iout,*) "sum_sguscdiff",sum_sguscdiff
+cc write(iout,*) "dXX_Ctab(",jik,i,")",dXX_Ctab(jik,i)
+c write(iout,*) "dYY_Ctab(",jik,i,")",dYY_Ctab(jik,i)
+c write(iout,*) "dZZ_Ctab(",jik,i,")",dZZ_Ctab(jik,i)
+c write(iout,*) "dXX_C1tab(",jik,i,")",dXX_C1tab(jik,i)
+c write(iout,*) "dYY_C1tab(",jik,i,")",dYY_C1tab(jik,i)
+c write(iout,*) "dZZ_C1tab(",jik,i,")",dZZ_C1tab(jik,i)
+c write(iout,*) "dXX_XYZtab(",jik,i,")",dXX_XYZtab(jik,i)
+c write(iout,*) "dYY_XYZtab(",jik,i,")",dYY_XYZtab(jik,i)
+c write(iout,*) "dZZ_XYZtab(",jik,i,")",dZZ_XYZtab(jik,i)
+c write(iout,*) "duscdiff(",jik,i-1,")",duscdiff(jik,i-1)
+c write(iout,*) "duscdiff(",jik,i,")",duscdiff(jik,i)
+c write(iout,*) "duscdiffx(",jik,i,")",duscdiffx(jik,i)
+c endif
+#endif
+ enddo
+ enddo
+c
+c uscdiff(i)=-dLOG(guscdiff(i)/(ii-1)) ! Weighting by (ii-1) required?
+c usc_diff(i)=-dLOG(guscdiff(i)/constr_homology) ! + min_uscdiff ?
+c
+c write (iout,*) i," uscdiff",uscdiff(i)
+c
+c Put together deviations from local geometry
+c Uconst_back=Uconst_back+wfrag_back(1,i,iset)*utheta(i)+
+c & wfrag_back(3,i,iset)*uscdiff(i)
+ Erot=Erot-dLOG(guscdiff(i)/constr_homology)
+c write (iout,*) "usc_diff(",i,")=",usc_diff(i) ! -ln of sum of exps
+c write (iout,*) "Uconst_back",Uconst_back ! cum sum of -ln-s
+c Uconst_back=Uconst_back+usc_diff(i)
+c
+c Gradient of multiple Gaussian restraint (FP - 04/11/2014 - right?)
+c
+c New implment: multiplied by sum_sguscdiff
+c
+
+ enddo ! (i-loop for dscdiff)
+
+c endif
+
+#ifdef DEBUG
+ write(iout,*) "------- SC restrs end -------"
+ write (iout,*) "------ After SC loop in e_modeller ------"
+ do i=loc_start,loc_end
+ write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
+ write (iout,*) "i",i," gradx",(gradx(j,i,icg),j=1,3)
+ enddo
+ if (waga_theta.eq.1.0d0) then
+ write (iout,*) "in e_modeller after SC restr end: dutheta"
+ do i=ithet_start,ithet_end
+ write (iout,*) i,dutheta(i)
+ enddo
+ endif
+ if (waga_d.eq.1.0d0) then
+ write (iout,*) "e_modeller after SC loop: duscdiff/x"
+ do i=1,nres
+ write (iout,*) i,(duscdiff(j,i),j=1,3)
+ write (iout,*) i,(duscdiffx(j,i),j=1,3)
+ enddo
+ endif
+#endif
c Total energy from homology restraints
#ifdef DEBUG
write (iout,*) "odleg",odleg," kat",kat
#endif
- ehomology_constr=odleg+kat
+c
+c Addition of energy of theta angle and SC local geom over constr_homologs ref strs
+c
+c ehomology_constr=odleg+kat
+ ehomology_constr=waga_dist*odleg+waga_angle*kat+waga_theta*Eval
+ & +waga_d*Erot
+c write (iout,*) "odleg",odleg," kat",kat," Uconst_back",Uconst_back
+c write (iout,*) "ehomology_constr",ehomology_constr
+c ehomology_constr=odleg+kat+Uconst_back
return
-
+c
+c FP 01/15 end
+c
748 format(a8,f12.3,a6,f12.3,a7,f12.3)
747 format(a12,i4,i4,i4,f8.3,f8.3)
746 format(a12,i4,i4,i4,f8.3,f8.3,f8.3)
projects / unres.git / blobdiff