From: Adam Liwo Date: Wed, 18 Jul 2012 10:34:03 +0000 (-0400) Subject: Merge branch 'devel' into adam X-Git-Tag: v.3.2~72 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=commitdiff_plain;h=cadbe84a76bf962574ad446b66153c74c7e69dd0;hp=b64f5db586b97d6f52b422a0edbcbcdadb0400fe;p=unres.git 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 --- 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 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 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 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 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 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 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 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 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 --- 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 --- 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 --- 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 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 --- 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 --- 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 --- 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 --- 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)