From 73c361f9b6f2b88612675f975588ee88dbba3a9c Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Fri, 19 Dec 2014 13:29:56 +0100 Subject: [PATCH] debug w poszukiwaniu bledu w ostatniej reszcie --- source/unres/src_MD-M/COMMON.TORSION | 2 +- source/unres/src_MD-M/energy_p_new_barrier.F | 18 ++++++++++++------ source/unres/src_MD-M/gradient_p.F | 2 ++ source/unres/src_MD-M/int_to_cart.f | 25 +++++++++++++++---------- source/unres/src_MD-M/parmread.F | 3 ++- source/unres/src_MD-M/stochfric.F | 16 ---------------- 6 files changed, 32 insertions(+), 34 deletions(-) diff --git a/source/unres/src_MD-M/COMMON.TORSION b/source/unres/src_MD-M/COMMON.TORSION index 2a887a6..e0f9c5d 100644 --- a/source/unres/src_MD-M/COMMON.TORSION +++ b/source/unres/src_MD-M/COMMON.TORSION @@ -10,7 +10,7 @@ C Torsional constants of the rotation about virtual-bond dihedral angles & nterm(maxtor,maxtor), & nlor(maxtor,maxtor), & nterm_old, - & itortyp(ntyp), + & itortyp(ntyp1), & ntortyp C 6/23/01 - constants for double torsionals double precision v1c,v1s,v2c,v2s diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F index b9d17fe..0c2f5ed 100644 --- a/source/unres/src_MD-M/energy_p_new_barrier.F +++ b/source/unres/src_MD-M/energy_p_new_barrier.F @@ -85,7 +85,7 @@ C FG slaves receive the WEIGHTS array time_Bcastw=time_Bcastw+MPI_Wtime()-time00 c call chainbuild_cart endif -c print *,'Processor',myrank,' calling etotal ipot=',ipot +C print *,'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 @@ -98,6 +98,7 @@ c endif C C Compute the side-chain and electrostatic interaction energy C +C write(iout,*) "zaczynam liczyc energie" goto (101,102,103,104,105,106) ipot C Lennard-Jones potential. 101 call elj(evdw) @@ -117,10 +118,13 @@ C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence). goto 107 C Soft-sphere potential 106 call e_softsphere(evdw) +C write(iout,*) "skonczylem ipoty" + C C Calculate electrostatic (H-bonding) energy of the main chain. C 107 continue +C write(iout,*) "skonczylem ipoty" cmc cmc Sep-06: egb takes care of dynamic ss bonds too cmc @@ -442,7 +446,6 @@ cMS$ATTRIBUTES C :: proc_proc #endif double precision gradbufc(3,maxres),gradbufx(3,maxres), & glocbuf(4*maxres),gradbufc_sum(3,maxres),gloc_scbuf(3,maxres) -#endif include 'COMMON.SETUP' include 'COMMON.IOUNITS' include 'COMMON.FFIELD' @@ -2338,6 +2341,7 @@ C endif c if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then if (i.gt. nnt+2 .and. i.lt.nct+2) then +c write(iout,*) (itype(i-2)) iti = itortyp(itype(i-2)) else iti=ntortyp+1 @@ -2718,7 +2722,7 @@ C dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), - & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4) + & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),eel_loc_ij common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, & num_conti,j1,j2 @@ -2761,6 +2765,7 @@ c call vec_and_deriv time01=MPI_Wtime() #endif call set_matrices +c write (iout,*) "after set matrices" #ifdef TIMING time_mat=time_mat+MPI_Wtime()-time01 #endif @@ -2797,6 +2802,7 @@ c 9/27/08 AL Split the interaction loop to ensure load balancing of turn terms C C Loop over i,i+2 and i,i+3 pairs of the peptide groups C +c write(iout,*) "przed turnem3 loop" do i=iturn3_start,iturn3_end if (itype(i).eq.21 .or. itype(i+1).eq.21 & .or. itype(i+2).eq.21 .or. itype(i+3).eq.21) cycle @@ -2889,7 +2895,7 @@ C------------------------------------------------------------------------------- dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3), & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3) double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4), - & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4) + & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4),a22,a23,a32,a33 common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,a22,a23,a32,a33, & dxi,dyi,dzi,dx_normi,dy_normi,dz_normi,xmedi,ymedi,zmedi, & num_conti,j1,j2 @@ -3659,7 +3665,7 @@ c write (iout,*) "eturn4 i",i," j",j," j1",j1," j2",j2 iti1=itortyp(itype(i+1)) iti2=itortyp(itype(i+2)) iti3=itortyp(itype(i+3)) -c write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3 + write(iout,*) "iti1",iti1," iti2",iti2," iti3",iti3 call transpose2(EUg(1,1,i+1),e1t(1,1)) call transpose2(Eug(1,1,i+2),e2t(1,1)) call transpose2(Eug(1,1,i+3),e3t(1,1)) @@ -5646,7 +5652,7 @@ C Set lprn=.true. for debugging lprn=.false. c lprn=.true. etors_d=0.0D0 -c write(iout,*) "a tu??" +C write(iout,*) "a tu??" do i=iphid_start,iphid_end if (itype(i-2).eq.21 .or. itype(i-1).eq.21 & .or. itype(i).eq.21 .or. itype(i+1).eq.21) cycle diff --git a/source/unres/src_MD-M/gradient_p.F b/source/unres/src_MD-M/gradient_p.F index 2c670f2..b5ba82a 100644 --- a/source/unres/src_MD-M/gradient_p.F +++ b/source/unres/src_MD-M/gradient_p.F @@ -292,9 +292,11 @@ c If performing constraint dynamics, add the gradients of the constraint energy do i=1,nres-3 gloc(i,icg)=gloc(i,icg)+dugamma(i) enddo + write(iout,*) "TU JESTEM?" do i=1,nres-2 gloc(nphi+i,icg)=gloc(nphi+i,icg)+dutheta(i) enddo + write(iout,*) "TU JESTEM?" endif #ifdef TIMING time01=MPI_Wtime() diff --git a/source/unres/src_MD-M/int_to_cart.f b/source/unres/src_MD-M/int_to_cart.f index 24ce0bc..e178afe 100644 --- a/source/unres/src_MD-M/int_to_cart.f +++ b/source/unres/src_MD-M/int_to_cart.f @@ -24,15 +24,16 @@ c calculating dE/ddc1 & gloc(ialph(2,1)+nside,icg)*domega(j,1,2) endif enddo +C write (iout,*) "????A CO TO??" c Calculating the remainder of dE/ddc2 do j=1,3 gcart(j,2)=gcart(j,2)+gloc(1,icg)*dphi(j,2,4)+ & gloc(nres-2,icg)*dtheta(j,2,3)+gloc(nres-1,icg)*dtheta(j,1,4) - if(itype(2).ne.10) then + if((itype(2).ne.10).and.(itype(2).ne.ntyp1)) then gcart(j,2)=gcart(j,2)+gloc(ialph(2,1),icg)*dalpha(j,2,2)+ & gloc(ialph(2,1)+nside,icg)*domega(j,2,2) endif - if(itype(3).ne.10) then + if((itype(3).ne.10).and.(itype(3).ne.21)) then gcart(j,2)=gcart(j,2)+gloc(ialph(3,1),icg)*dalpha(j,1,3)+ & gloc(ialph(3,1)+nside,icg)*domega(j,1,3) endif @@ -56,6 +57,7 @@ c If there are only five residues endif enddo endif +C write (iout,*) "Poniezej blad??",ialph(3,1),nside,ialph(4,1) c If there are more than five residues if(nres.gt.5) then do i=3,nres-3 @@ -64,30 +66,31 @@ c If there are more than five residues & +gloc(i-1,icg)*dphi(j,2,i+2)+ & gloc(i,icg)*dphi(j,1,i+3)+gloc(nres+i-4,icg)*dtheta(j,2,i+1)+ & gloc(nres+i-3,icg)*dtheta(j,1,i+2) - if(itype(i).ne.10) then + if((itype(i).ne.10).and.(itype(i).ne.ntyp1)) then gcart(j,i)=gcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,2,i)+ & gloc(ialph(i,1)+nside,icg)*domega(j,2,i) endif - if(itype(i+1).ne.10) then + if((itype(i+1).ne.10).and.(itype(i+1).ne.ntyp1)) then gcart(j,i)=gcart(j,i)+gloc(ialph(i+1,1),icg)*dalpha(j,1,i+1) & +gloc(ialph(i+1,1)+nside,icg)*domega(j,1,i+1) endif enddo enddo endif -c Setting dE/ddnres-2 +c Setting dE/ddnres-2 + write(iout,*) "ATUCHUJ?" if(nres.gt.5) then do j=1,3 gcart(j,nres-2)=gcart(j,nres-2)+gloc(nres-4,icg)* & dphi(j,3,nres-1)+gloc(nres-3,icg)*dphi(j,2,nres) & +gloc(2*nres-6,icg)* & dtheta(j,2,nres-1)+gloc(2*nres-5,icg)*dtheta(j,1,nres) - if(itype(nres-2).ne.10) then + if((itype(nres-2).ne.10).and.(itype(nres-2).ne.ntyp1)) then gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-2,1),icg)* & dalpha(j,2,nres-2)+gloc(ialph(nres-2,1)+nside,icg)* & domega(j,2,nres-2) endif - if(itype(nres-1).ne.10) then + if((itype(nres-1).ne.10).and.(itype(nres-1).ne.ntyp1)) then gcart(j,nres-2)=gcart(j,nres-2)+gloc(ialph(nres-1,1),icg)* & dalpha(j,1,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* & domega(j,1,nres-1) @@ -98,7 +101,7 @@ c Settind dE/ddnres-1 do j=1,3 gcart(j,nres-1)=gcart(j,nres-1)+gloc(nres-3,icg)*dphi(j,3,nres)+ & gloc(2*nres-5,icg)*dtheta(j,2,nres) - if(itype(nres-1).ne.10) then + if((itype(nres-1).ne.10).and.(itype(nres-1).ne.ntyp1)) then gcart(j,nres-1)=gcart(j,nres-1)+gloc(ialph(nres-1,1),icg)* & dalpha(j,2,nres-1)+gloc(ialph(nres-1,1)+nside,icg)* & domega(j,2,nres-1) @@ -106,13 +109,15 @@ c Settind dE/ddnres-1 enddo c The side-chain vector derivatives do i=2,nres-1 - if(itype(i).ne.10 .and. itype(i).ne.21) then + if(itype(i).ne.10 .and. itype(i).ne.ntyp1) then do j=1,3 gxcart(j,i)=gxcart(j,i)+gloc(ialph(i,1),icg)*dalpha(j,3,i) & +gloc(ialph(i,1)+nside,icg)*domega(j,3,i) enddo endif - enddo + enddo + write(iout,*) "TU DOCHODZE" + c---------------------------------------------------------------------- C INTERTYP=1 SC...Ca...Ca...Ca C INTERTYP=2 Ca...Ca...Ca...SC diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F index 4dd6b0a..9bc2d20 100644 --- a/source/unres/src_MD-M/parmread.F +++ b/source/unres/src_MD-M/parmread.F @@ -397,6 +397,7 @@ C Read torsional parameters C read (itorp,*,end=113,err=113) ntortyp read (itorp,*,end=113,err=113) (itortyp(i),i=1,ntyp) + itortyp(ntyp1)=ntortyp+1 c write (iout,*) 'ntortyp',ntortyp do i=1,ntortyp do j=1,ntortyp @@ -609,7 +610,7 @@ cc maxinter is maximum interaction sites v0ijsccor=v0ijsccor+vlor1sccor(k,i,j)/ &(1+vlor3sccor(k,i,j)**2) enddo - v0sccor(i,j)=v0ijsccor + v0sccor(l,i,j)=v0ijsccor enddo enddo enddo diff --git a/source/unres/src_MD-M/stochfric.F b/source/unres/src_MD-M/stochfric.F index 8d1cf2c..76aa40a 100644 --- a/source/unres/src_MD-M/stochfric.F +++ b/source/unres/src_MD-M/stochfric.F @@ -39,11 +39,7 @@ ind=ind+3 enddo do i=nnt,nct -<<<<<<< HEAD if (itype(i).ne.10 .and. itype(i).ne.21) then -======= - if (itype(i).ne.10) then ->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla do j=1,3 d_t_work(ind+j)=d_t(j,i+nres) enddo @@ -72,11 +68,7 @@ ind=ind+3 enddo do i=nnt,nct -<<<<<<< HEAD if (itype(i).ne.10 .and. itype(i).ne.21) then -======= - if (itype(i).ne.10) then ->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla do j=1,3 friction(j,i+nres)=fric_work(ind+j) enddo @@ -242,11 +234,7 @@ c Compute the stochastic forces acting on virtual-bond vectors. stochforc(j,0)=ff(j)+force(j,nnt+nres) enddo do i=nnt,nct -<<<<<<< HEAD if (itype(i).ne.10 .and. itype(i).ne.21) then -======= - if (itype(i).ne.10) then ->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla do j=1,3 stochforc(j,i+nres)=force(j,i+nres) enddo @@ -264,11 +252,7 @@ c Compute the stochastic forces acting on virtual-bond vectors. ind=ind+3 enddo do i=nnt,nct -<<<<<<< HEAD if (itype(i).ne.10 .and. itype(i).ne.21) then -======= - if (itype(i).ne.10) then ->>>>>>> 2acc991... Wprowadznie potencjalow SC-COR do multichain oraz ich pseudosymetrii dla do j=1,3 stochforcvec(ind+j)=stochforc(j,i+nres) enddo -- 1.7.9.5