# ignore build dir
build/
+# latex files in documentation
+doc/*/*.aux
+doc/*/*.log
+
+
# ignored dirs form adasko
gradcheck/
mapcheck/
bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
DIL
compinfo
+DIL/
+bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
--- /dev/null
+D ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO
+SER D
--- /dev/null
+D ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO
+SER D
--- /dev/null
+XAAAAAAAAAAX
\ No newline at end of file
--- /dev/null
+D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D
\ No newline at end of file
--- /dev/null
+\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}
+
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)
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),
GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \
-DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC\
-DSCCORPDB
-GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB_czyt.exe
+GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB.exe
GAB: ${object} xdrf/libxdrf.a
cc -o compinfo compinfo.c
./compinfo | true
--- /dev/null
+###################################################################
+INSTALL_DIR = /users/software/mpich-1.2.7p1_intel-10.1_em64_ssh
+
+
+FC= ifort
+
+OPT = -g -ip -w -CB
+
+FFLAGS = -c ${OPT} -I$(INSTALL_DIR)/include
+FFLAGS1 = -c -w -g -d2 -CA -CB -I$(INSTALL_DIR)/include
+FFLAGS2 = -c -w -g -O0 -I$(INSTALL_DIR)/include
+FFLAGSE = -c -w -O3 -ipo -ipo_obj -opt_report -I$(INSTALL_DIR)/include
+
+
+LIBS = -L$(INSTALL_DIR)/lib -lmpich xdrf/libxdrf.a
+
+ARCH = LINUX
+PP = /lib/cpp -P
+
+
+all: unres
+
+.SUFFIXES: .F
+.F.o:
+ ${FC} ${FFLAGS} ${CPPFLAGS} $*.F
+
+
+object = unres.o arcos.o cartprint.o chainbuild.o convert.o initialize_p.o \
+ matmult.o readrtns.o parmread.o gen_rand_conf.o printmat.o map.o \
+ pinorm.o randgens.o rescode.o intcor.o timing.o misc.o intlocal.o \
+ cartder.o checkder_p.o econstr_local.o energy_p_new_barrier.o \
+ energy_p_new-sep_barrier.o gradient_p.o minimize_p.o sumsld.o \
+ cored.o rmdd.o geomout.o readpdb.o regularize.o thread.o fitsq.o mcm.o \
+ mc.o bond_move.o refsys.o check_sc_distr.o check_bond.o contact.o djacob.o \
+ eigen.o blas.o add.o entmcm.o minim_mcmf.o \
+ MP.o compare_s1.o prng.o \
+ banach.o rmsd.o elecont.o dihed_cons.o \
+ sc_move.o local_move.o \
+ intcartderiv.o lagrangian_lesyng.o\
+ stochfric.o kinetic_lesyng.o MD_A-MTS.o moments.o int_to_cart.o \
+ surfatom.o sort.o muca_md.o MREMD.o rattle.o gauss.o energy_split-sep.o \
+ q_measure.o gnmr1.o test.o
+
+GAB: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0 -DCRYST_BOND -DCRYST_THETA -DCRYST_SC
+GAB: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_GAB.exe
+GAB: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+E0LL2Y: CPPFLAGS = -DPROCOR -DLINUX -DPGI -DUNRES -DISNAN -DMP -DMPI \
+ -DSPLITELE -DLANG0
+E0LL2Y: BIN = ../../../bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
+E0LL2Y: ${object} xdrf/libxdrf.a
+ cc -o compinfo compinfo.c
+ ./compinfo | true
+ ${FC} ${FFLAGS} cinfo.f
+ ${FC} ${OPT} ${object} cinfo.o ${LIBS} -o ${BIN}
+
+xdrf/libxdrf.a:
+ cd xdrf && make
+
+
+clean:
+ /bin/rm -f *.o && /bin/rm -f compinfo && cd xdrf && make clean
+
+test.o: test.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} test.F
+
+chainbuild.o: chainbuild.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} chainbuild.F
+
+matmult.o: matmult.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} matmult.f
+
+parmread.o : parmread.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} parmread.F
+
+intcor.o : intcor.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} intcor.f
+
+cartder.o : cartder.F
+ ${FC} ${FFLAGS} ${CPPFLAGS} cartder.F
+
+readpdb.o : readpdb.F
+ ${FC} ${FFLAGS2} ${CPPFLAGS} readpdb.F
+
+sumsld.o : sumsld.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} sumsld.f
+
+cored.o : cored.f
+ ${FC} ${FFLAGS1} ${CPPFLAGS} cored.f
+
+rmdd.o : rmdd.f
+ ${FC} ${FFLAGS} ${CPPFLAGS} rmdd.f
+
+energy_p_new_barrier.o : energy_p_new_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new_barrier.F
+
+gradient_p.o : gradient_p.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} gradient_p.F
+
+energy_p_new-sep_barrier.o : energy_p_new-sep_barrier.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} energy_p_new-sep_barrier.F
+
+lagrangian_lesyng.o : lagrangian_lesyng.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} lagrangian_lesyng.F
+
+MD_A-MTS.o : MD_A-MTS.F
+ ${FC} ${FFLAGSE} ${CPPFLAGS} MD_A-MTS.F
+
+blas.o : blas.f
+ ${FC} ${FFLAGS1} blas.f
+
+add.o : add.f
+ ${FC} ${FFLAGS1} add.f
+
+eigen.o : eigen.f
+ ${FC} ${FFLAGS2} eigen.f
+
+proc_proc.o: proc_proc.c
+ ${CC} ${CFLAGS} proc_proc.c
C DO NOT EDIT THIS FILE - IT HAS BEEN GENERATED BY COMPINFO.C
-C 2 5 358
+C 2 5 360
subroutine cinfo
include 'COMMON.IOUNITS'
write(iout,*)'++++ Compile info ++++'
- write(iout,*)'Version 2.5 build 358'
- write(iout,*)'compiled Wed Jul 11 07:10:02 2012'
+ write(iout,*)'Version 2.5 build 360'
+ write(iout,*)'compiled Tue Jul 17 04:36:51 2012'
write(iout,*)'compiled by aks255@matrix.chem.cornell.edu'
write(iout,*)'OS name: Linux '
write(iout,*)'OS release: 2.6.34.9-69.fc13.x86_64 '
--- /dev/null
+../../lib/xdrf
\ No newline at end of file
do while (iret.gt.0)
#if (defined(AIX) && !defined(JUBL))
+#ifdef DEBUG
+ write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
call xdrffloat_(ixdrf, rtime, iret)
-c print *,"rtime",rtime," iret",iret
call xdrffloat_(ixdrf, rpotE, iret)
-c write (iout,*) "rpotE",rpotE," iret",iret
+#ifdef DEBUG
+ write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
call flush(iout)
call xdrffloat_(ixdrf, ruconst, iret)
call xdrffloat_(ixdrf, rt_bath, iret)
call xdrfint_(ixdrf, nss, iret)
+#ifdef DEBUG
+ write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
do j=1,nss
call xdrfint_(ixdrf, ihpb(j), iret)
call xdrfint_(ixdrf, jhpb(j), iret)
call xdrffloat_(ixdrf, rprop(i), iret)
enddo
#else
+#ifdef DEBUG
+ write (iout,*) "ii",ii," itraj",itraj," it",it
+#endif
call xdrffloat(ixdrf, rtime, iret)
call xdrffloat(ixdrf, rpotE, iret)
-c write (iout,*) "rpotE",rpotE," iret",iret
+#ifdef DEBUG
+ write (iout,*) "rtime",rtime," rpotE",rpotE," iret",iret
+#endif
call flush(iout)
call xdrffloat(ixdrf, ruconst, iret)
call xdrffloat(ixdrf, rt_bath, iret)
call xdrfint(ixdrf, nss, iret)
+#ifdef DEBUG
+ write (iout,*) "ruconst",ruconst," rt_bath",rt_bath," nss",nss
+#endif
do j=1,nss
call xdrfint(ixdrf, ihpb(j), iret)
call xdrfint(ixdrf, jhpb(j), iret)
#endif
if (iret.eq.0) exit
itraj=mod(it,totraj(iR,iparm))
-#ifdef DEBUG
- write (iout,*) "ii",ii," itraj",itraj," it",it
-#endif
if (iset.eq.0) iset = 1
call flush(iout)
it=it+1
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
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),
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)
--- /dev/null
+../../lib/xdrf
\ No newline at end of file
# Create files needed for tests
-
-file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/ala10one.seq
-"XAAAAAAAAAAX"
-)
-file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/ala10three.seq
-"D Ala Ala Ala Ala Ala Ala Ala Ala Ala Ala D "
-)
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10one.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10three.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Yone.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Ythree.seq
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
file( COPY ${CMAKE_SOURCE_DIR}/ctest/ala10MD.cx
DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+file( COPY ${CMAKE_SOURCE_DIR}/ctest/1L2Y_MREMD_MD000.cx
+ DESTINATION ${CMAKE_CURRENT_BINARY_DIR} )
+
# Test xdrf2pdb
add_test(NAME XDRF2PDB-one COMMAND xdrf2pdb one ala10one.seq ala10MD.cx )
add_test(NAME XDRF2PDB-three COMMAND xdrf2pdb three ala10three.seq ala10MD.cx )
+# Test xdrf2pdb-m
+add_test(NAME XDRF2PDB-M-one COMMAND xdrf2pdb-m one 1L2Yone.seq 1L2Y_MREMD_MD000.cx 32 30 )
+add_test(NAME XDRF2PDB-M-three COMMAND xdrf2pdb-m three 1L2Ythree.seq 1L2Y_MREMD_MD000.cx 32 30 )
+
# Test xdrf2ang
add_test(NAME XDRF2ANG-one COMMAND xdrf2ang one ala10one.seq ala10MD.cx )
add_test(NAME XDRF2ANG-three COMMAND xdrf2ang three ala10three.seq ala10MD.cx )
projects / unres.git / commitdiff