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

merge adam->devel (2nd attempt)
Conflicts:
	.gitignore
	bin/unres/MD/unres_ifort_MPICH_GAB.exe
	examples/unres/MD/ff_gab/1L2Y_minim.inp
	source/cluster/wham/src/DIMENSIONS.COMPAR
	source/cluster/wham/src/include_unres/COMMON.INTERACT
	source/cluster/wham/src/include_unres/COMMON.SBRIDGE
	source/cluster/wham/src/include_unres/COMMON.TORSION
	source/unres/src_MD/cinfo.f
	source/unres/src_MIN/Makefile
	source/xdrfpdb/src-M/xdrf
	source/xdrfpdb/src/xdrf
	source/xdrfpdb/src/xdrf2ang.f
	source/xdrfpdb/src/xdrf2pdb-m.F

diff --cc .gitignore
index 45bb905,8a8f64c..4c3f4f2
--- 1/.gitignore
--- 2/.gitignore
+++ b/.gitignore
@@@ -1,4 -1,17 +1,24 @@@
++<<<<<<< HEAD
 +*.[oa] 
 +*~
 +*.swp
 +*.[eo][0-9][0-9][0-9][0-9]*
++=======
+ # ignore compiled stuff
+ *.[oa]
+ 
+ # ignore texteditors
+ *.swp
+ *~
+ 
+ 
+ # ignore build dir
+ build/
+ 
+ # ignored dirs form adasko
+ gradcheck/
+ mapcheck/
+ run/
+ sympcheck/
+ 
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1

diff --cc examples/unres/MD/ff_gab/1L2Y_minim.inp
index 2830886,b6e6e25..a770a21
--- 1/examples/unres/MD/ff_gab/1L2Y_minim.inp
--- 2/examples/unres/MD/ff_gab/1L2Y_minim.inp
+++ b/examples/unres/MD/ff_gab/1L2Y_minim.inp
@@@ -1,6 -1,6 +1,11 @@@
  1L2Y
++<<<<<<< HEAD
 +SEED=-3059743 REFSTR PDBREF MINIMIZE
 +
++=======
+ SEED=-3059743 PDBREF ENE
+ maxmin=1000
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
  WLONG=1.35279 WSCP=1.59304 WELEC=0.71534 WBOND=1.00000 WANG=1.13873            &
  WSCLOC=0.16258 WTOR=1.98599 WTORD=1.57069 WCORRH=0.42887 WCORR5=0.00000        &
  WCORR6=0.00000 WEL_LOC=0.16036 WTURN3=1.68722 WTURN4=0.66230 WTURN6=0.00000    &

diff --cc source/cluster/wham/src/DIMENSIONS.COMPAR
index 08e2231,911bd4e..f5d44d1
--- 1/source/cluster/wham/src/DIMENSIONS.COMPAR
--- 2/source/cluster/wham/src/DIMENSIONS.COMPAR
+++ b/source/cluster/wham/src/DIMENSIONS.COMPAR
@@@ -2,6 -2,11 +2,14 @@@
  *
  * Array dimensions for level-based conformation comparison program:
  *
++<<<<<<< HEAD
++=======
+ * Max. number of conformations in the data set.
+ *
+       integer maxconf
+       PARAMETER (MAXCONF=maxstr_proc)
+ *
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
  * Max. number levels of comparison
  *
        integer maxlevel

diff --cc source/cluster/wham/src/energy_p_new.F
Simple merge

diff --cc source/cluster/wham/src/include_unres/COMMON.INTERACT
index 23bfd42,d4a58b5..2545afb
--- 1/source/cluster/wham/src/include_unres/COMMON.INTERACT
--- 2/source/cluster/wham/src/include_unres/COMMON.INTERACT
+++ b/source/cluster/wham/src/include_unres/COMMON.INTERACT
@@@ -19,7 -19,8 +19,15 @@@ C 12/1/95 Array EPS included in the COM
       & r0d(ntyp,2),rpp(2,2),epp(2,2),elpp6(2,2),elpp3(2,2),
       & eps_scp(20,2),rscp(20,2),eps_orig(ntyp,ntyp)
  c 12/5/03 modified 09/18/03 Bond stretching parameters.
++<<<<<<< HEAD
 +      double precision vbldp0,vbldsc0,akp,aksc,abond0
 +      integer nbondterm
 +      common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
 +     & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),nbondterm(ntyp)
++=======
+       double precision vbldp0,vbldsc0,akp,aksc,abond0,distchainmax
+       integer nbondterm
+       common /stretch/ vbldp0,vbldsc0(maxbondterm,ntyp),akp,
+      & aksc(maxbondterm,ntyp),abond0(maxbondterm,ntyp),
+      & distchainmax,nbondterm(ntyp)
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1

diff --cc source/cluster/wham/src/include_unres/COMMON.SBRIDGE
index 7bba010,5c87412..2848b61
--- 1/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
--- 2/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
+++ b/source/cluster/wham/src/include_unres/COMMON.SBRIDGE
@@@ -1,10 -1,9 +1,19 @@@
        double precision ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,dhpb,
++<<<<<<< HEAD
 +     & dhpb1,forcon,weidis
 +      integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end,
 +     & ibecarb
 +      common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
 +     &  nfree,iss(maxss)
 +      common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
 +     & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
++=======
+      & forcon,weidis
+       integer ns,nss,nfree,iss,ihpb,jhpb,nhpb,link_start,link_end
+       common /sbridge/ ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,ns,nss,
+      &  nfree,iss(maxss)
+       common /links/ dhpb(maxdim),forcon(maxdim),ihpb(maxdim),
+      & jhpb(maxdim),nhpb
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
        common /restraints/ weidis
        common /links_split/ link_start,link_end

diff --cc source/cluster/wham/src/include_unres/COMMON.TORSION
index 8a12451,55cc7f4..957dcff
--- 1/source/cluster/wham/src/include_unres/COMMON.TORSION
--- 2/source/cluster/wham/src/include_unres/COMMON.TORSION
+++ b/source/cluster/wham/src/include_unres/COMMON.TORSION
@@@ -4,8 -4,8 +4,13 @@@ C Torsional constants of the rotation a
        common/torsion/v0(maxtor,maxtor),v1(maxterm,maxtor,maxtor),
       &    v2(maxterm,maxtor,maxtor),vlor1(maxlor,maxtor,maxtor),
       &    vlor2(maxlor,maxtor,maxtor),vlor3(maxlor,maxtor,maxtor),
++<<<<<<< HEAD
 +     &    itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),nlor(maxtor,maxtor) 
 +     &    ,nterm_old
++=======
+      &    itortyp(ntyp),ntortyp,nterm(maxtor,maxtor),
+      &    nlor(maxtor,maxtor),nterm_old
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
  C 6/23/01 - constants for double torsionals
        double precision v1c,v1s,v2c,v2s
        integer ntermd_1,ntermd_2

diff --cc source/unres/src_MD-M/unres.F
Simple merge

diff --cc source/unres/src_MD/Makefile_MPICH_ifort
Simple merge

diff --cc source/unres/src_MD/cinfo.f
index 3438039,9b22a2e..b54ec8c
--- 1/source/unres/src_MD/cinfo.f
--- 2/source/unres/src_MD/cinfo.f
+++ b/source/unres/src_MD/cinfo.f
@@@ -1,25 -1,24 +1,42 @@@
  C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
++<<<<<<< HEAD
 +C 2 5 66
 +      subroutine cinfo
 +      include 'COMMON.IOUNITS'
 +      write(iout,*)'++++ Compile info ++++'
 +      write(iout,*)'Version 2.5 build 66'
 +      write(iout,*)'compiled Thu Jun 14 06:40:11 2012'
 +      write(iout,*)'compiled by adam@matrix.chem.cornell.edu'
++=======
+ C 2 5 295
+       subroutine cinfo
+       include 'COMMON.IOUNITS'
+       write(iout,*)'++++ Compile info ++++'
+       write(iout,*)'Version 2.5 build 295'
+       write(iout,*)'compiled Mon Jun 18 05:08:20 2012'
+       write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
        write(iout,*)'OS name:    Linux '
        write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
        write(iout,*)'OS version:',
       & ' #1 SMP Tue May 3 09:23:03 UTC 2011 '
        write(iout,*)'flags:'
++<<<<<<< HEAD
 +      write(iout,*)'FC = ifort'
 +      write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include'
++=======
+       write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
+       write(iout,*)'FC= ifort'
+       write(iout,*)'OPT =  -g -ip -w -CB '
+       write(iout,*)'FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include '
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
        write(iout,*)'FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)...'
 -      write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include  '
 +      write(iout,*)'FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include'
        write(iout,*)'FFLAGSE = -c -w -O3 -ipo -ipo_obj  -opt_report ...'
 -      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdr...'
 +      write(iout,*)'CC = cc'
 +      write(iout,*)'CFLAGS = -DLINUX -DPGI -c'
 +      write(iout,*)'OPT =  -O3 -ip -w'
 +      write(iout,*)'LIBS = -Lxdrf -lxdrf'
        write(iout,*)'ARCH = LINUX'
        write(iout,*)'PP = /lib/cpp -P'
        write(iout,*)'object = unres.o arcos.o cartprint.o chainbuild...'

diff --cc source/unres/src_MD/energy_p_new_barrier.F
Simple merge

diff --cc source/unres/src_MD/readrtns.F
Simple merge

diff --cc source/unres/src_MIN/energy_p_new_barrier.F
Simple merge

diff --cc source/wham/src/energy_p_new.F
Simple merge

diff --cc source/xdrfpdb/src-M/xdrf2pdb-m.F
Simple merge

diff --cc source/xdrfpdb/src/Makefile
Simple merge

diff --cc source/xdrfpdb/src/xdrf2ang.f
index 5714f40,a24d75d..f1c8472
--- 1/source/xdrfpdb/src/xdrf2ang.f
--- 2/source/xdrfpdb/src/xdrf2ang.f
+++ b/source/xdrfpdb/src/xdrf2ang.f
@@@ -14,7 -14,7 +14,11 @@@
        character*8 onethree,cfreq
        character*8 ucase
        external ucase
++<<<<<<< HEAD
 +      logical oneletter,iblnk
++=======
+       logical oneletter, iblnk
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
        integer rescode
        external rescode
        

diff --cc source/xdrfpdb/src/xdrf2pdb-m.F
index edbd0d8,a12edb8..1fbf5af
--- 1/source/xdrfpdb/src/xdrf2pdb-m.F
--- 2/source/xdrfpdb/src/xdrf2pdb-m.F
+++ b/source/xdrfpdb/src/xdrf2pdb-m.F
@@@ -10,10 -10,9 +10,14 @@@
        character*3 sequenc(maxres)
        character*50 tytul
        character*8 onethree,cfreq,cntraj,citraj
 +      character*3 licz
        character*8 ucase
        external ucase
++<<<<<<< HEAD
 +      logical oneletter,iblnk
++=======
+       logical oneletter, iblnk
++>>>>>>> aebadf9023e437f497f92dfcf2303c16f60917c1
        integer rescode
        external rescode