From: Cezary Czaplewski Date: Tue, 21 Jul 2015 13:37:27 +0000 (+0200) Subject: read2sigma supports separate domain definition in each *sco file X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;ds=sidebyside;h=a991f3a775c471c0c894f78b8b11ee8152553e30;hp=-c;p=unres.git read2sigma supports separate domain definition in each *sco file --- a991f3a775c471c0c894f78b8b11ee8152553e30 diff --git a/source/unres/src_MD/COMMON.MD b/source/unres/src_MD/COMMON.MD index 7f8a20f..cbb474f 100644 --- a/source/unres/src_MD/COMMON.MD +++ b/source/unres/src_MD/COMMON.MD @@ -54,16 +54,18 @@ c integer nresn,nyosh,nnos double precision glogs,qmass,vlogs,xlogs logical large,print_compon,tbf,rest,reset_moment,reset_vel, - & surfarea,rattle,usampl,mdpdb,RESPA,tnp,tnp1,tnh,xiresp,preminim + & surfarea,rattle,usampl,mdpdb,RESPA,tnp,tnp1,tnh,xiresp,preminim, + & l_homo(max_template,maxdim) integer igmult_start,igmult_end,my_ng_count,ng_start,ng_counts, & nginv_start,nginv_counts,myginv_ng_count + common /back_constr/ uconst_back,utheta,ugamma,uscdiff, & dutheta,dugamma,duscdiff,duscdiffx, & wfrag_back,nfrag_back,ifrag_back common /homrestr/ odl,dih,sigma_dih,sigma_odl, & lim_odl,lim_dih,ires_homo,jres_homo,link_start_homo, & link_end_homo,idihconstr_start_homo,idihconstr_end_homo, - & idomain + & idomain,l_homo c c FP (30/10/2014,04/03/2015) c diff --git a/source/unres/src_MD/Makefile_MPICH_ifort b/source/unres/src_MD/Makefile_MPICH_ifort index 298cff3..a3de06b 100644 --- a/source/unres/src_MD/Makefile_MPICH_ifort +++ b/source/unres/src_MD/Makefile_MPICH_ifort @@ -69,7 +69,7 @@ GAB: ${object} xdrf/libxdrf.a E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DAMD64 -DUNRES -DISNAN -DMP -DMPI \ -DSPLITELE -DLANG0 #E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH2_E0LL2Y.exe -E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y-200.exe +E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y-202.exe E0LL2Y: ${object} xdrf/libxdrf.a cc -o compinfo compinfo.c ./compinfo | true diff --git a/source/unres/src_MD/energy_p_new_barrier.F b/source/unres/src_MD/energy_p_new_barrier.F index 5be1ec5..7d54a78 100644 --- a/source/unres/src_MD/energy_p_new_barrier.F +++ b/source/unres/src_MD/energy_p_new_barrier.F @@ -6038,6 +6038,7 @@ c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d dij=dist(i,j) c write (iout,*) "dij(",i,j,") =",dij do k=1,constr_homology + if(.not.l_homo(k,ii)) cycle distance(k)=odl(k,ii)-dij c write (iout,*) "distance(",k,") =",distance(k) c diff --git a/source/unres/src_MD/readrtns.F b/source/unres/src_MD/readrtns.F index 3aa5fd6..4fd5a31 100644 --- a/source/unres/src_MD/readrtns.F +++ b/source/unres/src_MD/readrtns.F @@ -2719,7 +2719,7 @@ c & sigma_odl_temp(maxres,maxres,max_template) character*2 kic2 character*24 model_ki_dist, model_ki_angle character*500 controlcard - integer ki, i, j, k, l + integer ki, i, j, k, l, ii_in_use(maxdim) logical lprn /.true./ c c FP - Nov. 2014 Temporary specifications for new vars @@ -2772,6 +2772,14 @@ c lim_theta=0 lim_xx=0 c + ii=0 + do i = nnt,nct-2 + do j=i+2,nct + ii=ii+1 + ii_in_use(ii)=0 + enddo + enddo + do k=1,constr_homology c @@ -2849,8 +2857,11 @@ c do i = nnt,nct-2 ! alternative for bounds as used to assign dist restr c do j=i+2,nct ! ibid if (idomain(k,i).eq.idomain(k,j).and.idomain(k,i).ne.0) then - + ii=ii+1 + ii_in_use(ii)=1 + l_homo(k,ii)=.true. + c write (iout,*) "k",k c write (iout,*) "i",i," j",j," constr_homology", c & constr_homology @@ -2913,9 +2924,13 @@ c sigma_odl(k,ii)=sigma_odl(k,ii)*sigma_odl(k,ii) c c sigma_odl(k,ii)=sigma_odl_temp(i,j,k)* ! new var read from file (?) c & sigma_odl_temp(i,j,k) ! not inverse because of use of res. similarity + else + ii=ii+1 + l_homo(k,ii)=.false. endif enddo enddo + lim_odl=ii endif c c Theta, dihedral and SC retraints @@ -2956,9 +2971,8 @@ c rescore(k,i-2)*rescore(k,i-3) ! right expression ? c Instead of res sim other local measure of b/b str reliability possible sigma_dih(k,i)=1.0d0/(sigma_dih(k,i)*sigma_dih(k,i)) c sigma_dih(k,i)=sigma_dih(k,i)*sigma_dih(k,i) - if (i-nnt-2.gt.lim_dih) lim_dih=i-nnt-2 ! right? -c if (i+nnt-1.gt.lim_dih) lim_dih=i+nnt-1 ! original when readin i from file enddo + lim_dih=nct-nnt-2 endif if (waga_theta.gt.0.0d0) then @@ -2991,9 +3005,9 @@ c read (ientin,*) sigma_theta(k,i) ! 1st variant c sigma_theta(k,i)=hmscore(k)*rescore(k,i)*rescore(k,i-1)* c rescore(k,i-2) ! right expression ? c sigma_theta(k,i)=sigma_theta(k,i)*sigma_theta(k,i) - if (i-nnt-1.gt.lim_theta) lim_theta=i-nnt-1 ! right? enddo endif + lim_theta=nct-nnt-1 if (waga_d.gt.0.0d0) then c open (ientin,file=tpl_k_sigma_d,status='old') @@ -3026,11 +3040,36 @@ c write(iout,*) "rescore(",k,i,") =",rescore(k,i) c sigma_d(k,i)=hmscore(k)*rescore(k,i) ! right expression ? c sigma_d(k,i)=sigma_d(k,i)*sigma_d(k,i) c read (ientin,*) sigma_d(k,i) ! 1st variant - if (i-nnt+1.gt.lim_xx) lim_xx=i-nnt+1 ! right? enddo + lim_xx=nct-nnt+1 endif enddo - if (waga_dist.ne.0.0d0) lim_odl=ii +c +c remove distance restraints not used in any model from the list +c shift data in all arrays +c + if (waga_dist.ne.0.0d0) then + ii=0 + do i=nnt,nct-2 + do j=i+2,nct + ii=ii+1 + if (ii_in_use(ii).eq.0) then + do ki=ii,lim_odl-1 + ires_homo(ki)=ires_homo(ki+1) + jres_homo(ki)=jres_homo(ki+1) + ii_in_use(ki)=ii_in_use(ki+1) + do k=1,constr_homology + odl(k,ki)=odl(k,ki+1) + sigma_odl(k,ki)=sigma_odl(k,ki+1) + l_homo(k,ki)=l_homo(k,ki+1) + enddo + enddo + ii=ii-1 + lim_odl=lim_odl-1 + endif + enddo + enddo + endif if (constr_homology.gt.0) call homology_partition if (constr_homology.gt.0) call init_int_table cd write (iout,*) "homology_partition: lim_theta= ",lim_theta, @@ -3045,8 +3084,10 @@ cd write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d if(me.eq.king .or. .not. out1file .and. fg_rank.eq.0) then write (iout,*) "Distance restraints from templates" do ii=1,lim_odl - write(iout,'(3i5,10(2f16.2,4x))') ii,ires_homo(ii),jres_homo(ii), - & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),ki=1,constr_homology) + write(iout,'(3i5,10(2f8.2,1x,l1,4x))') + & ii,ires_homo(ii),jres_homo(ii), + & (odl(ki,ii),1.0d0/dsqrt(sigma_odl(ki,ii)),l_homo(ki,ii), + & ki=1,constr_homology) enddo write (iout,*) "Dihedral angle restraints from templates" do i=nnt+3,lim_dih