Merge branch 'devel' into adam

Conflicts:
	bin/wham/wham_ifort_MPICH_GAB.exe
	source/cluster/wham/src/Makefile
	source/unres/src_MD/cinfo.f
	source/wham/src/cinfo.f

diff --git a/.gitignore b/.gitignore
index 25485f3..8145177 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,6 @@
 # ignore compiled stuff
 *.[oa]
+cinfo.f
 
 # ignore texteditors
 *.swp
@@ -11,9 +12,16 @@
 # ignore build dir
 build/
 
+# latex files in documentation 
+doc/*/*.aux
+doc/*/*.log
+
+
 # ignored dirs form adasko
 gradcheck/
 mapcheck/
 run/
 sympcheck/
 compinfo
+DIL/
+bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe

diff --git a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe b/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
deleted file mode 100755 (executable)
index 1069e64..0000000
Binary files a/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe and /dev/null differ

diff --git a/bin/unres/MD/unres_ifort_MPICH_GAB.exe b/bin/unres/MD/unres_ifort_MPICH_GAB.exe
index 2ffec15..da4efff 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_MPICH_GAB.exe and b/bin/unres/MD/unres_ifort_MPICH_GAB.exe differ

diff --git a/bin/unres/MD/unres_ifort_single_GAB.exe b/bin/unres/MD/unres_ifort_single_GAB.exe
index 66109ea..228bcd7 100755 (executable)
Binary files a/bin/unres/MD/unres_ifort_single_GAB.exe and b/bin/unres/MD/unres_ifort_single_GAB.exe differ

diff --git a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe
index b26354a..c93d86e 100755 (executable)
Binary files a/bin/wham/wham_ifort_MPICH_E0LL2Y.exe and b/bin/wham/wham_ifort_MPICH_E0LL2Y.exe differ

diff --git a/bin/wham/wham_ifort_MPICH_GAB.exe b/bin/wham/wham_ifort_MPICH_GAB.exe
deleted file mode 100755 (executable)
index d83f6f7..0000000
Binary files a/bin/wham/wham_ifort_MPICH_GAB.exe and /dev/null differ

diff --git a/bin/wham/wham_multparm-ham_rep-oldparm b/bin/wham/wham_multparm-ham_rep-oldparm
index 2ddc49d..6f60701 100755 (executable)
Binary files a/bin/wham/wham_multparm-ham_rep-oldparm and b/bin/wham/wham_multparm-ham_rep-oldparm differ

diff --git a/doc/INSTALL/HOWTO_build_unres_with_cmake.pdf b/doc/INSTALL/HOWTO_build_unres_with_cmake.pdf
new file mode 100644 (file)
index 0000000..962c9c2
Binary files /dev/null and b/doc/INSTALL/HOWTO_build_unres_with_cmake.pdf differ

diff --git a/doc/INSTALL/HOWTO_build_unres_with_cmake.tex b/doc/INSTALL/HOWTO_build_unres_with_cmake.tex
new file mode 100644 (file)
index 0000000..dabb02e
--- /dev/null
+++ b/doc/INSTALL/HOWTO_build_unres_with_cmake.tex
@@ -0,0 +1,48 @@
+\documentclass{article}
+
+\newcommand{\shellcmd}[1]{\medskip\texttt{\footnotesize #1}\medskip}
+
+\begin{document}
+
+
+\title{Building UNRESPACK with CMake}
+\author{Dawid Jagiela}
+
+\maketitle
+
+
+\section{Requirements}
+
+Starting with UNRESPACK 3.2, CMake (cross-platform, open-source build system ) can be used to build UNRESPACK. 
+Building requires te folowing: 
+\begin{itemize}  
+  \item CMake 2.8 or later 
+  \item Fortran compiler. Currently \emph{Intel Fortran Compiler} and \emph{GNU Fortran Compiler} are supported. The former one is recomended.  
+  \item ANSI C compiler   
+\end{itemize} 
+
+\section{Building}
+
+\raggedright
+
+Prepare the build directory 
+
+\shellcmd{mkdir unrespack \\tar -xvzf unrespack-v.3.2.tar.gz -C unrespack \\cd unrespack \\mkdir build \&\& cd build}
+
+Configure CMake 
+
+\begin{itemize}
+  \item Using command line, interactive mode(recomended) \shellcmd{ccmake ..}
+  \item Using command line, non-interactive mode. This requires to pass all the variables to CMake
+       \shellcmd{ cmake -DCMAKE\_Fortran\_COMPILER=ifort -DUNRES\_MD\_FF=GAB .. } 
+\end{itemize}
+
+To compile the whole package run:
+
+\shellcmd{make}
+
+
+
+
+\end{document}
+

diff --git a/source/cluster/wham/src/COMMON.SCCOR b/source/cluster/wham/src/COMMON.SCCOR
index ca6210f..0857cd8 100644 (file)
--- a/source/cluster/wham/src/COMMON.SCCOR
+++ b/source/cluster/wham/src/COMMON.SCCOR
@@ -7,10 +7,11 @@ cc Parameters of the SCCOR term
       common/sccor/v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
      &    v0sccor(maxterm_sccor,20),
-     &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
-     &    nlor_sccor(ntyp,ntyp),vlor1sccor(maxterm_sccor,20,20),
+     &    vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),
      &    vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),
      &    dcostau(3,3,3,maxres2),dsintau(3,3,3,maxres2),
      &    dtauangle(3,3,3,maxres2),dcosomicron(3,3,3,maxres2),
-     &    domicron(3,3,3,maxres2)
+     &    domicron(3,3,3,maxres2),
+     &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
+     &    nlor_sccor(ntyp,ntyp)

diff --git a/source/cluster/wham/src/Makefile b/source/cluster/wham/src/Makefile
index 6c9226d..b192a7b 100644 (file)
--- a/source/cluster/wham/src/Makefile
+++ b/source/cluster/wham/src/Makefile
@@ -3,9 +3,15 @@ BIN=../../../../bin
 FC = ifort
 OPT = -O3 -ip -w
 OPT = -CB -g 
+<<<<<<< HEAD
 FFLAGS =  ${OPT} -c -I. -Iinclude_unres -I$(INSTALL_DIR)/include
 CPPFLAGS = -DLINUX -DPGI -DSPLITELE -DPROCOR -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DMP -DMPI
 LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a -g -d2 -CA -CB
+=======
+FFLAGS =  ${OPT} -c -I. -I./include_unres -I../src_MD_T-sccor -I/users/adam/MEY_MD/src_Tc-czarek -I$(INSTALL_DIR)/include
+CPPFLAGS = -DLINUX -DPGI -DSPLITELE -DPROCOR -DCRYST_BOND -DCRYST_THETA -DCRYST_SC -DMP -DMPI
+LIBS = -L$(INSTALL_DIR)/lib -lmpich ./xdrf/libxdrf.a -g -d2 -CA -CB
+>>>>>>> devel
 
 .c.o:
        cc -c -DLINUX -DPGI $*.c

diff --git a/source/unres/src_MD/COMMON.SCCOR b/source/unres/src_MD/COMMON.SCCOR
index ca6210f..ccfe0c4 100644 (file)
--- a/source/unres/src_MD/COMMON.SCCOR
+++ b/source/unres/src_MD/COMMON.SCCOR
@@ -6,7 +6,7 @@ cc Parameters of the SCCOR term
       integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
       common/sccor/v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
-     &    v0sccor(maxterm_sccor,20),
+     &    v0sccor(ntyp,ntyp),
      &    nterm_sccor(ntyp,ntyp),isccortyp(ntyp),nsccortyp,
      &    nlor_sccor(ntyp,ntyp),vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),

diff --git a/source/wham/src/cinfo.f b/source/wham/src/cinfo.f
deleted file mode 100644 (file)
index 641b295..0000000
--- a/source/wham/src/cinfo.f
+++ /dev/null
@@ -1,62 +0,0 @@
-C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 0 0 573
-      subroutine cinfo
-      include 'COMMON.IOUNITS'
-      write(iout,*)'++++ Compile info ++++'
-      write(iout,*)'Version 0.0 build 573'
-      write(iout,*)'compiled Wed Jul 18 03:05:03 2012'
-      write(iout,*)'compiled by jal47@matrix.chem.cornell.edu'
-      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:'
-      write(iout,*)'INSTALL_DIR = /users/software/mpich-1.2.7p1_int...'
-      write(iout,*)'BIN = ../../../bin/wham'
-      write(iout,*)'FC= ifort'
-      write(iout,*)'OPT = -mcmodel=medium -O3 -ip -w'
-      write(iout,*)'FFLAGS = ${OPT} -c -I. -I./include_unres -I$(IN...'
-      write(iout,*)'LIBS = -L$(INSTALL_DIR)/lib -lmpich -lpmpich xd...'
-      write(iout,*)'objects = \\'
-      write(iout,*)'   wham_multparm.o \\'
-      write(iout,*)'   bxread.o \\'
-      write(iout,*)'   xread.o \\'
-      write(iout,*)'   cxread.o \\'
-      write(iout,*)'   enecalc1.o \\'
-      write(iout,*)'   energy_p_new.o \\'
-      write(iout,*)'   gnmr1.o \\'
-      write(iout,*)'   initialize_p.o \\'
-      write(iout,*)'   molread_zs.o \\'
-      write(iout,*)'   openunits.o \\'
-      write(iout,*)'   readrtns.o \\'
-      write(iout,*)'   arcos.o \\'
-      write(iout,*)'   cartder.o \\'
-      write(iout,*)'   cartprint.o \\'
-      write(iout,*)'   chainbuild.o \\'
-      write(iout,*)'   geomout.o \\'
-      write(iout,*)'   icant.o \\'
-      write(iout,*)'   intcor.o \\'
-      write(iout,*)'   int_from_cart.o \\'
-      write(iout,*)'   make_ensemble1.o \\'
-      write(iout,*)'   matmult.o \\'
-      write(iout,*)'   misc.o \\'
-      write(iout,*)'   mygetenv.o \\'
-      write(iout,*)'   parmread.o \\'
-      write(iout,*)'   pinorm.o \\'
-      write(iout,*)'   printmat.o \\'
-      write(iout,*)'   proc_proc.o \\'
-      write(iout,*)'   rescode.o \\'
-      write(iout,*)'   setup_var.o \\'
-      write(iout,*)'   slices.o \\'
-      write(iout,*)'   store_parm.o \\'
-      write(iout,*)'   timing.o \\'
-      write(iout,*)'   wham_calc1.o'
-      write(iout,*)'objects_compar = \\'
-      write(iout,*)'        readrtns_compar.o \\'
-      write(iout,*)'        readpdb.o fitsq.o contact.o \\'
-      write(iout,*)'        elecont.o contfunc.o cont_frag.o conf_c...'
-      write(iout,*)'GAB: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLITEL...'
-      write(iout,*)'E0LL2Y: CPPFLAGS = -DMPI -DLINUX -DUNRES -DSPLI...'
-      write(iout,*)'++++ End of compile info ++++'
-      return
-      end

diff --git a/source/wham/src/energy_p_new.F b/source/wham/src/energy_p_new.F
index 27f9010..cb4b7b0 100644 (file)
--- a/source/wham/src/energy_p_new.F
+++ b/source/wham/src/energy_p_new.F
@@ -4534,7 +4534,7 @@ c        amino-acid residues.
 C Set lprn=.true. for debugging
       lprn=.false.
 c      lprn=.true.
-c      write (iout,*) "EBACK_SC_COR",iphi_start,iphi_end,nterm_sccor
+c      write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor
       esccor=0.0D0
       do i=itau_start,itau_end
         esccor_ii=0.0D0

diff --git a/source/wham/src/include_unres/COMMON.SCCOR b/source/wham/src/include_unres/COMMON.SCCOR
index efab24f..28d748a 100644 (file)
--- a/source/wham/src/include_unres/COMMON.SCCOR
+++ b/source/wham/src/include_unres/COMMON.SCCOR
@@ -6,7 +6,7 @@ cc Parameters of the SCCOR term
       integer nterm_sccor,isccortyp,nsccortyp,nlor_sccor
       common /sccor/ v1sccor(maxterm_sccor,3,20,20),
      &    v2sccor(maxterm_sccor,3,20,20),
-     &    v0sccor(maxterm_sccor,20),
+     &    v0sccor(ntyp,ntyp),
      &    vlor1sccor(maxterm_sccor,20,20),
      &    vlor2sccor(maxterm_sccor,20,20),
      &    vlor3sccor(maxterm_sccor,20,20),gloc_sc(3,0:maxres2,10),

diff --git a/source/wham/src/int_from_cart.f b/source/wham/src/int_from_cart.f
index 12d0c9c..c0cd6e7 100644 (file)
--- a/source/wham/src/int_from_cart.f
+++ b/source/wham/src/int_from_cart.f
@@ -26,6 +26,10 @@
         enddo
         be=0.0D0
         if (i.gt.2) phi(i+1)=beta(i-2,i-1,i,i+1)
+        if (i.gt.2) tauangle(3,i+1)=beta(i+nres-1,i-1,i,i+nres)
+        if (i.gt.2) tauangle(1,i+1)=beta(i-1+nres,i-1,i,i+1)
+        if (i.gt.2) tauangle(2,i+1)=beta(i-2,i-1,i,i+nres)
+
         omeg(i)=beta(nres+i,i,maxres2,i+1)
         theta(i+1)=alpha(i-1,i,i+1)
         alph(i)=alpha(nres+i,i,maxres2)

diff --git a/source/wham/src/parmread.F b/source/wham/src/parmread.F
index 9b5e224..1b66ce0 100644 (file)
--- a/source/wham/src/parmread.F
+++ b/source/wham/src/parmread.F
@@ -75,6 +75,7 @@ c
       wtor=ww(13)
       wtor_d=ww(14)
       wvdwpp=ww(16)
+      wstrain=ww(15)
       wbond=ww(18)
       wsccor=ww(19)