enddo
- enddo
+ enddo
+ j=1
+ i=0
+ print *,"KUPA2",gradbufc(j,i),wsc*gvdwc(j,i),
+ & wscp*gvdwc_scp(j,i),gvdwc_scpp(j,i),
+ & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i),
+ & wel_loc*gel_loc_long(j,i),
+ & wcorr*gradcorr_long(j,i),
+ & wcorr5*gradcorr5_long(j,i),
+ & wcorr6*gradcorr6_long(j,i),
+ & wturn6*gcorr6_turn_long(j,i),
+ & wstrain*ghpbc(j,i)
+ & ,wliptran*gliptranc(j,i)
+ & ,gradafm(j,i)
+ & ,welec*gshieldc(j,i)
+ & ,wcorr*gshieldc_ec(j,i)
+ & ,wturn3*gshieldc_t3(j,i)
+ & ,wturn4*gshieldc_t4(j,i)
+ & ,wel_loc*gshieldc_ll(j,i)
+ & ,wtube*gg_tube(j,i)
#else
do i=0,nct
do j=1,3
#ifdef TIMING
c time_allreduce=time_allreduce+MPI_Wtime()-time00
#endif
- do i=nnt,nres
+ do i=0,nres
do k=1,3
gradbufc(k,i)=0.0d0
enddo
enddo
- enddo
+ enddo
+C i=0
+C j=1
+C print *,"KUPA", gradbufc(j,i),welec*gelc(j,i),
+C & wel_loc*gel_loc(j,i),
+C & 0.5d0*wscp*gvdwc_scpp(j,i),
+C & welec*gelc_long(j,i),wvdwpp*gvdwpp(j,i),
+C & wel_loc*gel_loc_long(j,i),
+C & wcorr*gradcorr_long(j,i),
+C & wcorr5*gradcorr5_long(j,i),
+C & wcorr6*gradcorr6_long(j,i),
+C & wturn6*gcorr6_turn_long(j,i),
+C & wbond*gradb(j,i),
+C & wcorr*gradcorr(j,i),
+C & wturn3*gcorr3_turn(j,i),
+C & wturn4*gcorr4_turn(j,i),
+C & wcorr5*gradcorr5(j,i),
+C & wcorr6*gradcorr6(j,i),
+C & wturn6*gcorr6_turn(j,i),
+C & wsccor*gsccorc(j,i)
+C & ,wscloc*gscloc(j,i)
+C & ,wliptran*gliptranc(j,i)
+C & ,gradafm(j,i)
+C & +welec*gshieldc(j,i)
+C & +welec*gshieldc_loc(j,i)
+C & +wcorr*gshieldc_ec(j,i)
+C & +wcorr*gshieldc_loc_ec(j,i)
+C & +wturn3*gshieldc_t3(j,i)
+C & +wturn3*gshieldc_loc_t3(j,i)
+C & +wturn4*gshieldc_t4(j,i)
+C & ,wturn4*gshieldc_loc_t4(j,i)
+C & ,wel_loc*gshieldc_ll(j,i)
+C & ,wel_loc*gshieldc_loc_ll(j,i)
+C & ,wtube*gg_tube(j,i)
+
+C print *,gg_tube(1,0),"TU3"
#ifdef DEBUG
write (iout,*) "gloc before adding corr"
do i=1,4*nres
call MPI_Barrier(FG_COMM,IERR)
time_barrier_g=time_barrier_g+MPI_Wtime()-time00
time00=MPI_Wtime()
- call MPI_Reduce(gradbufc(1,1),gradc(1,1,icg),3*nres,
+ call MPI_Reduce(gradbufc(1,0),gradc(1,0,icg),3*nres+3,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
call MPI_Reduce(gradbufx(1,1),gradx(1,1,icg),3*nres,
& MPI_DOUBLE_PRECISION,MPI_SUM,king,FG_COMM,IERR)
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
include 'COMMON.SBRIDGE'
double precision tub_r,vectube(3),enetube(maxres*2)
Etube=0.0d0
- do i=1,2*nres
+ do i=itube_start,itube_end
enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
enddo
C first we calculate the distance from tube center
C first sugare-phosphate group for NARES this would be peptide group
C for UNRES
- do i=1,nres
+ do i=itube_start,itube_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
enddo
enddo
C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
- do i=1,nres
+C print *,gg_tube(1,0),"TU"
+
+
+ do i=itube_start,itube_end
C Lets not jump over memory as we use many times iti
iti=itype(i)
C lets ommit dummy atoms for now
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
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
enddo
enddo
- do i=1,2*nres
- Etube=Etube+enetube(i)
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
enddo
C print *,"ETUBE", etube
return
include 'COMMON.SBRIDGE'
double precision tub_r,vectube(3),enetube(maxres*2)
Etube=0.0d0
- do i=1,2*nres
+ do i=itube_start,itube_end
enetube(i)=0.0d0
+ enetube(i+nres)=0.0d0
enddo
C first we calculate the distance from tube center
C first sugare-phosphate group for NARES this would be peptide group
C for UNRES
- do i=1,nres
+ do i=itube_start,itube_end
C lets ommit dummy atoms for now
if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
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
enddo
enddo
C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
- do i=1,nres
+C print *,gg_tube(1,0),"TU"
+ do i=itube_start,itube_end
C Lets not jump over memory as we use many times iti
iti=itype(i)
C lets ommit dummy atoms for now
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
&+ssgradtube*enetube(i+nres)/sstube
enddo
- do i=1,2*nres
- Etube=Etube+enetube(i)
+ do i=itube_start,itube_end
+ Etube=Etube+enetube(i)+enetube(i+nres)
enddo
C print *,"ETUBE", etube
return
projects / unres.git / blobdiff