From 225ad1b2239a64aee5d46570c477e74c19cf6ef7 Mon Sep 17 00:00:00 2001 From: Cezary Czaplewski Date: Fri, 22 May 2020 23:12:14 +0200 Subject: [PATCH] Adam's corrections --- source/cluster/wham/src-HCD/energy_p_new.F | 22 ++++++---- source/unres/src-HCD-5D/MREMD.F | 61 ++++++++++++++-------------- source/unres/src-HCD-5D/readrtns_CSA.F | 51 ++++++++++++----------- source/wham/src-HCD/DIMENSIONS | 2 +- source/wham/src-HCD/energy_p_new.F | 23 +++++++---- source/wham/src-HCD/read_constr_homology.F | 7 +++- source/wham/src-HCD/readpdb.F | 9 ++-- 7 files changed, 96 insertions(+), 79 deletions(-) diff --git a/source/cluster/wham/src-HCD/energy_p_new.F b/source/cluster/wham/src-HCD/energy_p_new.F index 27e944b..95898b4 100644 --- a/source/cluster/wham/src-HCD/energy_p_new.F +++ b/source/cluster/wham/src-HCD/energy_p_new.F @@ -10203,16 +10203,20 @@ c enddo c min_odl=minval(distancek) - do kk=1,constr_homology - if(l_homo(kk,ii)) then - min_odl=distancek(kk) - exit - endif - enddo - do kk=1,constr_homology - if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl) + if (nexl.gt.0) then + min_odl=0.0d0 + else + do kk=1,constr_homology + if(l_homo(kk,ii)) then + min_odl=distancek(kk) + exit + endif + enddo + do kk=1,constr_homology + if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl) & min_odl=distancek(kk) - enddo + enddo + endif c write (iout,* )"min_odl",min_odl #ifdef DEBUG write (iout,*) "ij dij",i,j,dij diff --git a/source/unres/src-HCD-5D/MREMD.F b/source/unres/src-HCD-5D/MREMD.F index 38db8a8..9191402 100644 --- a/source/unres/src-HCD-5D/MREMD.F +++ b/source/unres/src-HCD-5D/MREMD.F @@ -62,6 +62,7 @@ cold integer nup(0:maxprocs),ndown(0:maxprocs) & ene_i_iex,xxx,tmp,econstr_temp_iex,econstr_temp_i integer iran_num double precision ran_number + integer i_econstr/20/ cdeb imin_itime_old=0 ntwx_cache=0 @@ -186,8 +187,9 @@ cd write (*,*) me," After broadcast: file_exist",file_exist do i=nnt,nct if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i))) & *dsqrt(gamsc(iabs(itype(i)))) - enddo + enddo endif + endif if(me.eq.king) then @@ -250,20 +252,20 @@ cd write (*,*) me," After broadcast: file_exist",file_exist write (iout,'(a6,i4,a1,100i4)') "ndowna",il,":", & (ndowna(i,il),i=1,ndowna(0,il)) enddo + stdfp=dsqrt(2*Rb*t_bath/d_time) do i=1,ntyp stdfsc(i)=dsqrt(2*Rb*t_bath/d_time) enddo if (lang.gt.0 .and. .not.surfarea) then - do i=nnt,nct-1 - stdforcp(i)=stdfp*dsqrt(gamp) - enddo + do i=nnt,nct-1 + stdforcp(i)=stdfp*dsqrt(gamp) + enddo do i=nnt,nct if (itype(i).ne.ntyp1) stdforcsc(i)=stdfsc(iabs(itype(i))) & *dsqrt(gamsc(iabs(itype(i)))) - enddo - endif - + enddo + endif ELSE IF (.not.(rest.and.file_exist)) THEN do il=1,remd_m(1) ifirst(il)=il @@ -319,7 +321,7 @@ cd print *,'ttt',me,remd_tlist,(remd_t(i),i=1,nrep) iset=i2set(me) if(me.eq.king.or..not.out1file) & write(iout,*) me,"iset=",iset,"t_bath=",t_bath - call flush(iout) +c call flush(iout) endif c stdfp=dsqrt(2*Rb*t_bath/d_time) @@ -721,7 +723,7 @@ ctime call flush(iout) write(iout,*) "MIN ii_write=",ii_write endif endif - call flush(iout) +c call flush(iout) endif if (synflag) then c Update the time safety limiy @@ -855,7 +857,7 @@ cd end time05=MPI_WTIME() if (me.eq.king .or. .not. out1file) then write(iout,*) 'REMD writing traj time=',time05-time04 - call flush(iout) +c call flush(iout) endif @@ -1089,12 +1091,12 @@ cd write(iout,*) "i_dir=",i_dir iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1) c 9/1/17 AL: Correction; otherwise the restraint energies are mis-assigned c on failed replica exchange attempt - econstr_temp_i=remd_ene(20,i) - econstr_temp_iex=remd_ene(20,iex) + econstr_temp_i=remd_ene(i_econstr,i) + econstr_temp_iex=remd_ene(i_econstr,iex) c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials) if (adaptive) then - remd_ene(20,i)=remd_ene(n_ene+5,i) - remd_ene(20,iex)=remd_ene(n_ene+6,iex) + remd_ene(i_econstr,i)=remd_ene(n_ene+5,i) + remd_ene(i_econstr,iex)=remd_ene(n_ene+6,iex) endif elseif(i_dir.eq.2 .and. mset(i_iset+1).gt.0)then @@ -1103,10 +1105,10 @@ c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials) i_iset1=i_iset+1 i_mset1=iran_num(1,mset(i_iset1)) iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1) - econstr_temp_i=remd_ene(20,i) - econstr_temp_iex=remd_ene(20,iex) - remd_ene(20,i)=remd_ene(n_ene+3,i) - remd_ene(20,iex)=remd_ene(n_ene+4,iex) + econstr_temp_i=remd_ene(i_econstr,i) + econstr_temp_iex=remd_ene(i_econstr,iex) + remd_ene(i_econstr,i)=remd_ene(n_ene+3,i) + remd_ene(i_econstr,iex)=remd_ene(n_ene+4,iex) elseif(remd_m(i_temp+1).gt.0.and.mset(i_iset+1).gt.0)then @@ -1115,14 +1117,14 @@ c 9/11/17 AL: Adaptive sampling (temperature dependent restraints potentials) i_iset1=i_iset+1 i_mset1=iran_num(1,mset(i_iset1)) iex=i_index(i_temp1,i_mult1,i_iset1,i_mset1) - econstr_temp_i=remd_ene(20,i) - econstr_temp_iex=remd_ene(20,iex) + econstr_temp_i=remd_ene(i_econstr,i) + econstr_temp_iex=remd_ene(i_econstr,iex) if (adaptive) then - remd_ene(20,i)=remd_ene(n_ene+7,i) - remd_ene(20,iex)=remd_ene(n_ene+8,iex) + remd_ene(i_econstr,i)=remd_ene(n_ene+7,i) + remd_ene(i_econstr,iex)=remd_ene(n_ene+8,iex) else - remd_ene(20,i)=remd_ene(n_ene+3,i) - remd_ene(20,iex)=remd_ene(n_ene+4,iex) + remd_ene(i_econstr,i)=remd_ene(n_ene+3,i) + remd_ene(i_econstr,iex)=remd_ene(n_ene+4,iex) endif else goto 444 @@ -1222,8 +1224,8 @@ cd write(iout,'(2i4,a6,2f12.5)') i,iex,' delta',delta,xxx else remd_ene(0,iex)=ene_iex_iex remd_ene(0,i)=ene_i_i - remd_ene(20,iex)=econstr_temp_iex - remd_ene(20,i)=econstr_temp_i + remd_ene(i_econstr,iex)=econstr_temp_iex + remd_ene(i_econstr,i)=econstr_temp_i endif cd do il=1,nset @@ -1259,7 +1261,7 @@ c------------------------------------- enddo endif - call flush(iout) +c call flush(iout) cd write (iout,'(a6,100i4)') "ifirst", cd & (ifirst(i),i=1,remd_m(1)) @@ -1305,7 +1307,6 @@ co & " rescaling weights with temperature",t_bath do i=1,ntyp stdfsc(i)=dsqrt(2*Rb*t_bath/d_time) enddo - c Compute the standard deviations of stochastic forces for Langevin dynamics c if the friction coefficients do not depend on surface area if (lang.gt.0 .and. .not.surfarea) then @@ -1317,11 +1318,11 @@ c if the friction coefficients do not depend on surface area & *dsqrt(gamsc(iabs(itype(i)))) enddo endif -cde write(iout,*) 'REMD after',me,t_bath +cde write(iout,*) 'REMD after',me,t_bath time08=MPI_WTIME() if (me.eq.king .or. .not. out1file) then write(iout,*) 'REMD exchange time=',time08-time00 - call flush(iout) +c call flush(iout) endif endif enddo diff --git a/source/unres/src-HCD-5D/readrtns_CSA.F b/source/unres/src-HCD-5D/readrtns_CSA.F index c51e45e..16c0f37 100644 --- a/source/unres/src-HCD-5D/readrtns_CSA.F +++ b/source/unres/src-HCD-5D/readrtns_CSA.F @@ -2979,10 +2979,11 @@ c & sigma_odl_temp(maxres,maxres,max_template) character*24 model_ki_dist, model_ki_angle character*500 controlcard integer ki,i,ii,j,k,l,ii_in_use(maxdim),i_tmp,idomain_tmp,irec, - & ik,iistart,iishift + & ik,iistart integer ilen external ilen - logical liiflag + logical liiflag,lfirst + integer i01,i10 c c FP - Nov. 2014 Temporary specifications for new vars c @@ -3314,6 +3315,7 @@ c write (iout,*) "waga_dist",waga_dist," nnt",nnt," nct",nct if (waga_dist.ne.0.0d0) then ii=0 liiflag=.true. + lfirst=.true. do i=nnt,nct-2 do j=i+2,nct ii=ii+1 @@ -3321,34 +3323,35 @@ c if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0 c & .and. distal.le.dist2_cut ) then c write (iout,*) "i",i," j",j," ii",ii c call flush(iout) - if (ii_in_use(ii).eq.0.and.liiflag) then + if (ii_in_use(ii).eq.0.and.liiflag.or. + & ii_in_use(ii).eq.1.and.liiflag.and.ii.eq.lim_odl) then liiflag=.false. - iistart=ii + i10=ii + if (lfirst) then + lfirst=.false. + iistart=ii + else + if(i10.eq.lim_odl) i10=i10+1 + do ki=0,i10-i01-1 + ires_homo(iistart+ki)=ires_homo(ki+i01) + jres_homo(iistart+ki)=jres_homo(ki+i01) + ii_in_use(iistart+ki)=ii_in_use(ki+i01) + do k=1,constr_homology + odl(k,iistart+ki)=odl(k,ki+i01) + sigma_odl(k,iistart+ki)=sigma_odl(k,ki+i01) + l_homo(k,iistart+ki)=l_homo(k,ki+i01) + enddo + enddo + iistart=iistart+i10-i01 + endif endif - if (ii_in_use(ii).ne.0.and..not.liiflag.or. - & .not.liiflag.and.ii.eq.lim_odl) then - if (ii.eq.lim_odl) then - iishift=ii-iistart+1 - else - iishift=ii-iistart - endif + if (ii_in_use(ii).ne.0.and..not.liiflag) then + i01=ii liiflag=.true. - do ki=iistart,lim_odl-iishift - ires_homo(ki)=ires_homo(ki+iishift) - jres_homo(ki)=jres_homo(ki+iishift) - ii_in_use(ki)=ii_in_use(ki+iishift) - do k=1,constr_homology - odl(k,ki)=odl(k,ki+iishift) - sigma_odl(k,ki)=sigma_odl(k,ki+iishift) - l_homo(k,ki)=l_homo(k,ki+iishift) - enddo - enddo - ii=ii-iishift - lim_odl=lim_odl-iishift -c endif endif enddo enddo + lim_odl=iistart-1 endif c write (iout,*) "Removing distances completed" c call flush(iout) diff --git a/source/wham/src-HCD/DIMENSIONS b/source/wham/src-HCD/DIMENSIONS index 4bc527f..4d690f3 100644 --- a/source/wham/src-HCD/DIMENSIONS +++ b/source/wham/src-HCD/DIMENSIONS @@ -24,7 +24,7 @@ c Max. number of chains parameter (maxchain=6) C Max number of symetries integer maxsym,maxperm - parameter (maxsym=maxchain,maxperm=1200) + parameter (maxsym=maxchain,maxperm=720) C Max. number of variables integer maxvar parameter (maxvar=4*maxres) diff --git a/source/wham/src-HCD/energy_p_new.F b/source/wham/src-HCD/energy_p_new.F index bd69774..efba869 100644 --- a/source/wham/src-HCD/energy_p_new.F +++ b/source/wham/src-HCD/energy_p_new.F @@ -159,6 +159,7 @@ c write (iout,*) "Calling multibody_hbond" call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1) endif #endif +c write (iout,*) "nsaxs",nsaxs c write (iout,*) "From Esaxs: Esaxs_constr",Esaxs_constr if (nsaxs.gt.0 .and. saxs_mode.eq.0) then call e_saxs(Esaxs_constr) @@ -4609,16 +4610,20 @@ c enddo c min_odl=minval(distancek) - do kk=1,constr_homology - if(l_homo(kk,ii)) then - min_odl=distancek(kk) - exit - endif - enddo - do kk=1,constr_homology - if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl) + if (nexl.gt.0) then + min_odl=0.0d0 + else + do kk=1,constr_homology + if(l_homo(kk,ii)) then + min_odl=distancek(kk) + exit + endif + enddo + do kk=1,constr_homology + if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl) & min_odl=distancek(kk) - enddo + enddo + endif c write (iout,* )"min_odl",min_odl #ifdef DEBUG write (iout,*) "ij dij",i,j,dij diff --git a/source/wham/src-HCD/read_constr_homology.F b/source/wham/src-HCD/read_constr_homology.F index dece50f..0af2bdb 100644 --- a/source/wham/src-HCD/read_constr_homology.F +++ b/source/wham/src-HCD/read_constr_homology.F @@ -165,6 +165,7 @@ c call readpdb write (iout,*) "read_constr_homology: after reading pdb file" call flush(iout) #endif + c c Distance restraints c @@ -553,14 +554,18 @@ c Distance restraints c c ... --> odl(k,ii) C Copy the coordinates from reference coordinates (?) +c write (iout,*) "k",k do i=1,2*nres do j=1,3 c(j,i)=chomo(j,i,k) -c write (iout,*) "c(",j,i,") =",c(j,i) +c write (iout,*) "c(",j,i,") =",c(j,i) enddo enddo +c call cartprint +c write (iout,*) "read_klapaucjusz: calling int_from_cart" call int_from_cart(.true.,.false.) call sc_loc_geom(.false.) +c write (iout,*) "en" do i=1,nres thetaref(i)=theta(i) phiref(i)=phi(i) diff --git a/source/wham/src-HCD/readpdb.F b/source/wham/src-HCD/readpdb.F index 83c63ab..55dcc04 100644 --- a/source/wham/src-HCD/readpdb.F +++ b/source/wham/src-HCD/readpdb.F @@ -27,10 +27,9 @@ C geometry. ibeg=1 ishift1=0 sccalc=.false. - ires=0 do read (ipdbin,'(a80)',end=10) card -c write (iout,'(a)') card +! write (iout,'(a)') card if (card(:5).eq.'HELIX') then nhfrag=nhfrag+1 lsecondary=.true. @@ -59,7 +58,7 @@ c write (iout,'(a)') card iterter(ires_old)=1 ishift1=ishift1+1 ibeg=2 - write (iout,*) "Chain ended",ires,ishift,ires_old +! write (iout,*) "Chain ended",ires,ishift,ires_old if (unres_pdb) then do j=1,3 dc(j,ires)=sccor(j,iii) @@ -120,7 +119,7 @@ c write (iout,*) "BEG ires",ires ! Start a new chain ishift=-ires_old+ires-1 !!!!! ishift1=ishift1-1 !!!!! - write (iout,*) "New chain started",ires,ishift,ishift1,"!" +! write (iout,*) "New chain started",ires,ishift,ishift1,"!" ires=ires-ishift+ishift1 ires_old=ires ibeg=0 @@ -326,7 +325,7 @@ c write (iout,*) i,i-1,(c(j,i),j=1,3),(c(j,i-1),j=1,3),dist(i,i-1) if (itype(i-1).ne.ntyp1 .and. itype(i).ne.ntyp1 .and. & (dist(i,i-1).lt.1.0D0 .or. dist(i,i-1).gt.6.0D0)) then write (iout,'(a,i4)') 'Bad Cartesians for residue',i - stop +c stop endif vbld(i)=dist(i-1,i) vbld_inv(i)=1.0d0/vbld(i) -- 1.7.9.5