Merge branch 'homology' of mmka.chem.univ.gda.pl:unres into homology

Conflicts:
	bin/unres/MD/unres_ifort_MPICH_E0LL2Y_2.exe
	source/unres/src_MD/cinfo.f

diff --cc source/unres/src_MD/Makefile_MPICH_ifort
index 966466d,ebdb428..fb95aa7
--- 1/source/unres/src_MD/Makefile_MPICH_ifort
--- 2/source/unres/src_MD/Makefile_MPICH_ifort
+++ b/source/unres/src_MD/Makefile_MPICH_ifort
@@@ -10,8 -10,8 +10,8 @@@ FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/inc
  FFLAGS1 = -c  -g -CA -CB -I$(INSTALL_DIR)/include 
  FFLAGS2 = -c  -g -O0 -I$(INSTALL_DIR)/include  
  FFLAGSE = -c  -O3 -ipo  -opt_report -I$(INSTALL_DIR)/include
- FFLAGS = ${FFLAGS1}
- FFLAGSE = ${FFLAGS1}
 -# FFLAGS = ${FFLAGS1}
 -# FFLAGSE = ${FFLAGS1}
++#FFLAGS = ${FFLAGS1}
++#FFLAGSE = ${FFLAGS1}
  
  
  LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a

diff --cc source/unres/src_MD/cinfo.f
index ede7c39,ca61054..e00e4af
--- 1/source/unres/src_MD/cinfo.f
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,11 -1,11 +1,11 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
- C 0 40376 3
 -C 3 2 307
++C 0 40376 2
        subroutine cinfo
        include 'COMMON.IOUNITS'
        write(iout,*)'++++ Compile info ++++'
-       write(iout,*)'Version 0.40376 build 3'
-       write(iout,*)'compiled Wed Feb 25 11:40:13 2015'
 -      write(iout,*)'Version 3.2 build 307'
 -      write(iout,*)'compiled Wed Feb 25 10:53:24 2015'
 -      write(iout,*)'compiled by czarek@piasek4'
++      write(iout,*)'Version 0.40376 build 2'
++      write(iout,*)'compiled Wed Feb 25 14:06:14 2015'
 +      write(iout,*)'compiled by felipe@piasek4'
        write(iout,*)'OS name:    Linux '
        write(iout,*)'OS release: 3.2.0-70-generic '
        write(iout,*)'OS version:',

diff --cc source/unres/src_MD/energy_p_new_barrier.F
index 535e8b2,e893d55..cb97c0a
--- 1/source/unres/src_MD/energy_p_new_barrier.F
--- 2/source/unres/src_MD/energy_p_new_barrier.F
+++ b/source/unres/src_MD/energy_p_new_barrier.F
@@@ -257,9 -257,9 +257,9 @@@ cd    print *,'nterm=',nter
  
        if (constr_homology.ge.1) then
          call e_modeller(ehomology_constr)
--        print *,'iset=',iset,'me=',me,ehomology_constr,
--     &  'Processor',fg_rank,' CG group',kolor,
--     &  ' absolute rank',MyRank
++c        print *,'iset=',iset,'me=',me,ehomology_constr,
++c     &  'Processor',fg_rank,' CG group',kolor,
++c     &  ' absolute rank',MyRank
        else
          ehomology_constr=0.0d0
        endif
@@@ -6454,7 -6451,7 +6454,8 @@@ c Addition of energy of theta angle an
  c
  c     ehomology_constr=odleg+kat
        if (homol_nset.gt.1)then
--       ehomology_constr=waga_dist1(iset)*odleg+waga_angle1(iset)*kat+waga_theta*Eval
++       ehomology_constr=waga_dist1(iset)*odleg+waga_angle1(iset)*kat
++     &              +waga_theta*Eval
       &              +waga_d*Erot     
        else
         ehomology_constr=waga_dist*odleg+waga_angle*kat+waga_theta*Eval

diff --cc source/unres/src_MD/readrtns.F
index 056bfd4,056bfd4..8c3938e
--- 1/source/unres/src_MD/readrtns.F
--- 2/source/unres/src_MD/readrtns.F
+++ b/source/unres/src_MD/readrtns.F
@@@ -627,6 -627,6 +627,7 @@@
        common /pizda/ itype_pdb
        logical seq_comp,fail
        double precision energia(0:n_ene)
++      
        integer ilen
        external ilen
  C
@@@ -922,6 -922,6 +923,11 @@@ C 12/1/95 Added weight for the multi-bo
    34    continue
  c        print *,'Begin reading pdb data'
          call readpdb
++        do i=1,2*nres
++          do j=1,3
++            crefjlee(j,i)=c(j,i)
++          enddo
++        enddo
  c        print *,'Finished reading pdb data'
          if(me.eq.king.or..not.out1file)
       &   write (iout,'(a,i3,a,i3)')'nsup=',nsup,
@@@ -1165,6 -1165,6 +1171,14 @@@ c        write (iout,*) "constr_dist",c
  
        if (constr_homology.gt.0) then
          call read_constr_homology
++        if (indpdb.gt.0 .or. pdbref) then
++          do i=1,2*nres
++            do j=1,3
++              c(j,i)=crefjlee(j,i)
++              cref(j,i)=crefjlee(j,i)
++            enddo
++          enddo
++        endif
        else
          homol_nset=0
        endif
@@@ -2734,6 -2734,6 +2748,7 @@@ c       tpl_k_sigma_dih="template"//kic
  c       tpl_k_sigma_theta="template"//kic2//".sigma_theta"
  c       tpl_k_sigma_d="template"//kic2//".sigma_d"
  
++        unres_pdb=.false.
          call readpdb
  c
  c     Distance restraints