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unres Adam's changes
[unres.git]
/
source
/
unres
/
src-HCD-5D
/
energy_p_new_barrier.F
diff --git
a/source/unres/src-HCD-5D/energy_p_new_barrier.F
b/source/unres/src-HCD-5D/energy_p_new_barrier.F
index
6d6a817
..
2d94dc0
100644
(file)
--- a/
source/unres/src-HCD-5D/energy_p_new_barrier.F
+++ b/
source/unres/src-HCD-5D/energy_p_new_barrier.F
@@
-37,6
+37,7
@@
c include 'COMMON.MD'
& eliptran,Eafmforce,Etube,
& esaxs_constr,ehomology_constr,edfator,edfanei,edfabet
integer n_corr,n_corr1
& eliptran,Eafmforce,Etube,
& esaxs_constr,ehomology_constr,edfator,edfanei,edfabet
integer n_corr,n_corr1
+ double precision time01
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
#ifdef MPI
c print*,"ETOTAL Processor",fg_rank," absolute rank",myrank,
c & " nfgtasks",nfgtasks
@@
-117,6
+118,9
@@
c call chainbuild_cart
endif
c write (iout,*) "itime_mat",itime_mat," imatupdate",imatupdate
if (mod(itime_mat,imatupdate).eq.0) then
endif
c write (iout,*) "itime_mat",itime_mat," imatupdate",imatupdate
if (mod(itime_mat,imatupdate).eq.0) then
+#ifdef TIMING_ENE
+ time01=MPI_Wtime()
+#endif
call make_SCp_inter_list
c write (iout,*) "Finished make_SCp_inter_list"
c call flush(iout)
call make_SCp_inter_list
c write (iout,*) "Finished make_SCp_inter_list"
c call flush(iout)
@@
-126,9
+130,12
@@
c call flush(iout)
call make_pp_inter_list
c write (iout,*) "Finished make_pp_inter_list"
c call flush(iout)
call make_pp_inter_list
c write (iout,*) "Finished make_pp_inter_list"
c call flush(iout)
- call make_pp_vdw_inter_list
+c call make_pp_vdw_inter_list
c write (iout,*) "Finished make_pp_vdw_inter_list"
c call flush(iout)
c write (iout,*) "Finished make_pp_vdw_inter_list"
c call flush(iout)
+#ifdef TIMING_ENE
+ time_list=time_list+MPI_Wtime()-time01
+#endif
endif
c print *,'Processor',myrank,' calling etotal ipot=',ipot
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
endif
c print *,'Processor',myrank,' calling etotal ipot=',ipot
c print *,'Processor',myrank,' nnt=',nnt,' nct=',nct
@@
-151,6
+158,9
@@
C
C Compute the side-chain and electrostatic interaction energy
C
C print *,ipot
C Compute the side-chain and electrostatic interaction energy
C
C print *,ipot
+#ifdef TIMING_ENE
+ time01=MPI_Wtime()
+#endif
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
goto (101,102,103,104,105,106) ipot
C Lennard-Jones potential.
101 call elj(evdw)
@@
-175,6
+185,9
@@
C
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
C Calculate electrostatic (H-bonding) energy of the main chain.
C
107 continue
+#ifdef TIMING_ENE
+ time_evdw=time_evdw+MPI_Wtime()-time01
+#endif
#ifdef DFA
C BARTEK for dfa test!
c print *,"Processors",MyRank," wdfa",wdfa_dist
#ifdef DFA
C BARTEK for dfa test!
c print *,"Processors",MyRank," wdfa",wdfa_dist
@@
-216,6
+229,9
@@
c print *,"Processor",myrank," computed USCSC"
#ifdef TIMING
time_vec=time_vec+MPI_Wtime()-time01
#endif
#ifdef TIMING
time_vec=time_vec+MPI_Wtime()-time01
#endif
+#ifdef TIMING_ENE
+ time01=MPI_Wtime()
+#endif
C Introduction of shielding effect first for each peptide group
C the shielding factor is set this factor is describing how each
C peptide group is shielded by side-chains
C Introduction of shielding effect first for each peptide group
C the shielding factor is set this factor is describing how each
C peptide group is shielded by side-chains
@@
-252,6
+268,9
@@
c print *,"Processor",myrank," left VEC_AND_DERIV"
c call eelec_soft_sphere(ees,evdw1,eel_loc,eello_turn3,
c & eello_turn4)
endif
c call eelec_soft_sphere(ees,evdw1,eel_loc,eello_turn3,
c & eello_turn4)
endif
+#ifdef TIMING_ENE
+ time_eelec=time_eelec+MPI_Wtime()-time01
+#endif
c#ifdef TIMING
c time_enecalc=time_enecalc+MPI_Wtime()-time00
c#endif
c#ifdef TIMING
c time_enecalc=time_enecalc+MPI_Wtime()-time00
c#endif
@@
-260,6
+279,9
@@
C
C Calculate excluded-volume interaction energy between peptide groups
C and side chains.
C
C Calculate excluded-volume interaction energy between peptide groups
C and side chains.
C
+#ifdef TIMING_ENE
+ time01=MPI_Wtime()
+#endif
if (ipot.lt.6) then
if(wscp.gt.0d0) then
call escp(evdw2,evdw2_14)
if (ipot.lt.6) then
if(wscp.gt.0d0) then
call escp(evdw2,evdw2_14)
@@
-271,6
+293,9
@@
C
c write (iout,*) "Soft-sphere SCP potential"
call escp_soft_sphere(evdw2,evdw2_14)
endif
c write (iout,*) "Soft-sphere SCP potential"
call escp_soft_sphere(evdw2,evdw2_14)
endif
+#ifdef TIMING_ENE
+ time_escp=time_escp+MPI_Wtime()-time01
+#endif
c
c Calculate the bond-stretching energy
c
c
c Calculate the bond-stretching energy
c
@@
-839,12
+864,12
@@
c do i=nnt,nres
gradbufc(k,i)=0.0d0
enddo
enddo
gradbufc(k,i)=0.0d0
enddo
enddo
-#ifdef DEBUG
- write (iout,*) "igrad_start",igrad_start," igrad_end",igrad_end
- write (iout,*) (i," jgrad_start",jgrad_start(i),
- & " jgrad_end ",jgrad_end(i),
- & i=igrad_start,igrad_end)
-#endif
+c#ifdef DEBUG
+c write (iout,*) "igrad_start",igrad_start," igrad_end",igrad_end
+c write (iout,*) (i," jgrad_start",jgrad_start(i),
+c & " jgrad_end ",jgrad_end(i),
+c & i=igrad_start,igrad_end)
+c#endif
c
c Obsolete and inefficient code; we can make the effort O(n) and, therefore,
c do not parallelize this part.
c
c Obsolete and inefficient code; we can make the effort O(n) and, therefore,
c do not parallelize this part.
@@
-1510,6
+1535,7
@@
C
double precision sscale,sscagrad,sscagradlip,sscalelip
double precision gg_lipi(3),gg_lipj(3)
double precision boxshift
double precision sscale,sscagrad,sscagradlip,sscalelip
double precision gg_lipi(3),gg_lipj(3)
double precision boxshift
+ external boxshift
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
gg_lipi=0.0d0
c write(iout,*)'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
evdw=0.0D0
gg_lipi=0.0d0
@@
-2039,6
+2065,7
@@
c do j=istart(i,iint),iend(i,iint)
c write(iout,*) "PRZED ZWYKLE", evdwij
call dyn_ssbond_ene(i,j,evdwij)
c write(iout,*) "PO ZWYKLE", evdwij
c write(iout,*) "PRZED ZWYKLE", evdwij
call dyn_ssbond_ene(i,j,evdwij)
c write(iout,*) "PO ZWYKLE", evdwij
+c call flush(iout)
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)')
@@
-2151,7
+2178,7
@@
C I hate to put IF's in the loops, but here don't have another choice!!!!
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)
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)
-c return
+ return
endif
sigder=-sig*sigsq
c---------------------------------------------------------------
endif
sigder=-sig*sigsq
c---------------------------------------------------------------
@@
-3049,7
+3076,7
@@
c
write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
#endif
enddo
write(iout,*) 'b2=',(b2(k,i-2),k=1,2)
#endif
enddo
- mu=0.0d0
+ mu(:,:nres)=0.0d0
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
#ifdef PARMAT
do i=ivec_start+2,ivec_end+2
#else
@@
-5504,6
+5531,9
@@
C peptide-group centers and side chains and its gradient in virtual-bond and
C side-chain vectors.
C
implicit none
C side-chain vectors.
C
implicit none
+#ifdef MPI
+ include 'mpif.h'
+#endif
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
include 'DIMENSIONS'
include 'COMMON.GEO'
include 'COMMON.VAR'
@@
-5515,6
+5545,7
@@
C
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.SPLITELE'
include 'COMMON.IOUNITS'
include 'COMMON.CONTROL'
include 'COMMON.SPLITELE'
+ include 'COMMON.TIME1'
double precision ggg(3)
integer i,iint,j,k,iteli,itypj,subchap,ikont
double precision xi,yi,zi,xj,yj,zj,rrij,sss1,sssgrad1,
double precision ggg(3)
integer i,iint,j,k,iteli,itypj,subchap,ikont
double precision xi,yi,zi,xj,yj,zj,rrij,sss1,sssgrad1,
@@
-5522,6
+5553,10
@@
C
double precision evdw2,evdw2_14,evdwij
double precision sscale,sscagrad
double precision boxshift
double precision evdw2,evdw2_14,evdwij
double precision sscale,sscagrad
double precision boxshift
+ external boxshift,to_box
+c#ifdef TIMING_ENE
+c double precision time01
+c#endif
evdw2=0.0D0
evdw2_14=0.0d0
c print *,boxxsize,boxysize,boxzsize,'wymiary pudla'
evdw2=0.0D0
evdw2_14=0.0d0
c print *,boxxsize,boxysize,boxzsize,'wymiary pudla'
@@
-5533,6
+5568,9
@@
C do zshift=-1,1
if (energy_dec) write (iout,*) "escp:",r_cut_int,rlamb
c do i=iatscp_s,iatscp_e
do ikont=g_listscp_start,g_listscp_end
if (energy_dec) write (iout,*) "escp:",r_cut_int,rlamb
c do i=iatscp_s,iatscp_e
do ikont=g_listscp_start,g_listscp_end
+c#ifdef TIMING_ENE
+c time01=MPI_Wtime()
+c#endif
i=newcontlistscpi(ikont)
j=newcontlistscpj(ikont)
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
i=newcontlistscpi(ikont)
j=newcontlistscpj(ikont)
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1) cycle
@@
-5540,6
+5578,7
@@
c do i=iatscp_s,iatscp_e
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=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))
+!DIR$ INLINE
call to_box(xi,yi,zi)
c do iint=1,nscp_gr(i)
call to_box(xi,yi,zi)
c do iint=1,nscp_gr(i)
@@
-5554,11
+5593,21
@@
C Uncomment following three lines for Ca-p interactions
xj=c(1,j)
yj=c(2,j)
zj=c(3,j)
xj=c(1,j)
yj=c(2,j)
zj=c(3,j)
+!DIR$ INLINE
call to_box(xj,yj,zj)
call to_box(xj,yj,zj)
+c#ifdef TIMING_ENE
+c time_escpsetup=time_escpsetup+MPI_Wtime()-time01
+c time01=MPI_Wtime()
+c#endif
+!DIR$ INLINE
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
c print *,xj,yj,zj,'polozenie j'
xj=boxshift(xj-xi,boxxsize)
yj=boxshift(yj-yi,boxysize)
zj=boxshift(zj-zi,boxzsize)
c print *,xj,yj,zj,'polozenie j'
+c#ifdef TIMING_ENE
+c time_escpsetup=time_escpsetup+MPI_Wtime()-time01
+c time01=MPI_Wtime()
+c#endif
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
c print *,rrij
sss=sscale(1.0d0/(dsqrt(rrij)),r_cut_int)
rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
c print *,rrij
sss=sscale(1.0d0/(dsqrt(rrij)),r_cut_int)
@@
-5619,6
+5668,9
@@
cgrad enddo
gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
enddo
gvdwc_scpp(k,i)=gvdwc_scpp(k,i)-ggg(k)
gvdwc_scp(k,j)=gvdwc_scp(k,j)+ggg(k)
enddo
+c#ifdef TIMING_ENE
+c time_escpcalc=time_escpcalc+MPI_Wtime()-time01
+c#endif
c endif !endif for sscale cutoff
c enddo ! j
c endif !endif for sscale cutoff
c enddo ! j
@@
-5804,7
+5856,8
@@
C 15/02/13 CC dynamic SSbond - additional check
if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
& iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
if (ii.gt.nres .and. iabs(itype(iii)).eq.1 .and.
& iabs(itype(jjj)).eq.1) then
call ssbond_ene(iii,jjj,eij)
- ehpb=ehpb+2*eij
+c ehpb=ehpb+2*eij
+ ehpb=ehpb+eij
endif
cd write (iout,*) "eij",eij
cd & ' waga=',waga,' fac=',fac
endif
cd write (iout,*) "eij",eij
cd & ' waga=',waga,' fac=',fac