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-rw-r--r--sci-chemistry/ambertools/files/ambertools-12-gentoo.patch1345
1 files changed, 0 insertions, 1345 deletions
diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
deleted file mode 100644
index 110343e22..000000000
--- a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch
+++ /dev/null
@@ -1,1345 +0,0 @@
- AmberTools/src/Makefile | 42 +-
- AmberTools/src/configure2 | 63 +-
- AmberTools/src/cpptraj/src/Makefile_at | 14 +-
- AmberTools/src/mdgx/Makefile | 9 +-
- AmberTools/src/mdgx/Trajectory.c | 2 +-
- .../src/mmpbsa_py/MMPBSA_mods/amber_outputs.py | 4 +-
- AmberTools/src/nab/database.c | 2 +-
- AmberTools/src/nab/nab.c | 4 +-
- AmberTools/src/pbsa/Makefile | 44 +-
- AmberTools/src/ptraj/Makefile | 9 +-
- AmberTools/src/ptraj/trajectory.c | 2 +-
- AmberTools/src/sff/Makefile | 4 +-
- AmberTools/src/sff/dsarpack.f | 654 +++++++++++++++++++++
- AmberTools/src/sqm/Makefile | 7 +-
- AmberTools/test/Makefile | 4 +-
- .../01_Generalized_Born/energies.csv.save | 8 +-
- AmberTools/test/nab/Makefile | 2 +
- AmberTools/test/nab/Run.rism_sp | 2 +-
- AmberTools/test/nab/Run.rism_sp2 | 2 +-
- AmberTools/test/test_at_serial.sh | 6 +
- Makefile | 2 +-
- 21 files changed, 725 insertions(+), 161 deletions(-)
-
-diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile
-index e5c0ded..ce8f883 100644
---- a/AmberTools/src/Makefile
-+++ b/AmberTools/src/Makefile
-@@ -13,12 +13,6 @@ install: $(INSTALLTYPE)
- serial: configured_serial THIRDPARTY $(MTKPP)
- @echo "Starting installation of ${AMBERTOOLS} serial at `date`".
- # utility routines and libraries:
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
-- (cd byacc && $(MAKE) install )
-- (cd arpack && $(MAKE) install );
-- (cd lapack && $(MAKE) $(LAPACK) )
-- (cd blas && $(MAKE) $(BLAS) )
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- (cd etc && $(MAKE) install )
- (cd chamber && $(MAKE) install )
- (cd pbsa && $(MAKE) install )
-@@ -34,13 +28,11 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- (cd cpptraj && $(MAKE) install)
-
- # miscellaneous:
-- (cd reduce && $(MAKE) install )
-
- # leap
- (cd leap && $(MAKE) install )
-
- # nab:
-- (cd cifparse && $(MAKE) install )
- (cd sff && $(MAKE) install )
- (cd pbsa && $(MAKE) libinstall )
- (cd rism && $(MAKE) $(RISM) )
-@@ -77,17 +69,10 @@ serial: configured_serial THIRDPARTY $(MTKPP)
- @echo "Installation of ${AMBERTOOLS} serial is complete at `date`."
- @echo ""
-
--nabonly: $(NETCDF) $(XBLAS)
-+nabonly: $(XBLAS)
- # utility routines and libraries:
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
-- (cd byacc && $(MAKE) install )
-- (cd arpack && $(MAKE) install );
-- (cd lapack && $(MAKE) $(LAPACK) )
-- (cd blas && $(MAKE) $(BLAS) )
-- (cd c9x-complex && $(MAKE) $(C9XCOMPLEX) )
- (cd pbsa && $(MAKE) libinstall )
- (cd rism && $(MAKE) $(RISM) )
-- (cd cifparse && $(MAKE) install )
- (cd sff && $(MAKE) install )
- (cd nab && $(MAKE) install )
- (cd nss && $(MAKE) install )
-@@ -119,8 +104,6 @@ parallel: configured_parallel THIRDPARTY
- (cd sff && $(MAKE) libsff_mpi )
- # (cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
- (cd pbsa && $(MAKE) libinstall )
-- (cd byacc && $(MAKE) install )
-- (cd ucpp-1.3 && $(MAKE) $(UCPP) )
- # (cd mdgx && $(MAKE) parallel )
- (if [ "$(RISM)" = "yes" ]; then \
- cd rism && $(MAKE) install_mpi ; \
-@@ -162,18 +145,11 @@ configured_parallel: configured
- )
-
- clean:: netcdf_clean
-- -(cd ucpp-1.3 && $(MAKE) clean )
-- -(cd byacc && $(MAKE) clean )
-- -(cd cifparse && $(MAKE) clean )
- -(cd nab && $(MAKE) clean )
- -(cd sff && $(MAKE) clean )
- -(cd nss && $(MAKE) clean )
- -(cd leap && $(MAKE) clean )
-- -(cd arpack && $(MAKE) clean )
-- -(cd blas && $(MAKE) clean )
- -(cd xblas && $(MAKE) clean )
-- -(cd lapack && $(MAKE) clean )
-- -(cd c9x-complex && $(MAKE) clean )
- -(cd etc && $(MAKE) clean )
- -(cd chamber && $(MAKE) clean )
- -(cd pbsa && $(MAKE) clean )
-@@ -182,15 +158,12 @@ clean:: netcdf_clean
- -(cd lib && $(MAKE) clean )
- -(cd ptraj && $(MAKE) clean )
- -(cd cpptraj && $(MAKE) clean)
-- -(cd reduce && $(MAKE) clean )
- -(cd mtkpp && $(MAKE) clean )
- -(cd mdgx && $(MAKE) clean )
- -(cd xtalutil/CPrograms && $(MAKE) clean )
- -(cd xray && $(MAKE) clean )
- -(cd paramfit && $(MAKE) clean )
- -(cd rism && $(MAKE) clean )
-- -(cd fftw-3.3 && $(MAKE) clean )
-- -($(RM) -f fftw-3.3/mpi/fftw3-mpi.f03 )
- -(cd mmpbsa_py && $(MAKE) clean )
- -(cd parmed && $(MAKE) clean )
-
-@@ -201,18 +174,11 @@ netcdf_clean:
- -(cd netcdf/bin && rm -f *)
-
- uninstall:
-- -(cd ucpp-1.3 && $(MAKE) uninstall )
-- -(cd byacc && $(MAKE) uninstall )
-- -(cd cifparse && $(MAKE) uninstall )
- -(cd nab && $(MAKE) uninstall )
- -(cd sff && $(MAKE) uninstall )
- -(cd nss && $(MAKE) uninstall )
- -(cd leap && $(MAKE) uninstall )
-- -(cd arpack && $(MAKE) uninstall )
-- -(cd blas && $(MAKE) uninstall )
- -($(RM) -f $(LIBDIR)/libxblas.a )
-- -(cd lapack && $(MAKE) uninstall )
-- -(cd c9x-complex && $(MAKE) uninstall )
- -(cd etc && $(MAKE) uninstall )
- -(cd chamber && $(MAKE) uninstall )
- -(cd pbsa && $(MAKE) uninstall )
-@@ -220,7 +186,6 @@ uninstall:
- -(cd sqm && $(MAKE) uninstall )
- -(cd lib && $(MAKE) uninstall )
- -(cd ptraj && $(MAKE) uninstall )
-- -(cd reduce && $(MAKE) uninstall )
- -(cd mdgx && $(MAKE) uninstall )
- -(cd xtalutil/CPrograms && $(MAKE) uninstall )
- -(cd xray && $(MAKE) uninstall )
-@@ -228,15 +193,12 @@ uninstall:
- -(cd paramfit && $(MAKE) uninstall )
- -(cd rism && $(MAKE) uninstall )
- -(cd netcdf/src && $(MAKE) uninstall)
-- -(cd fftw-3.3 && $(MAKE) uninstall)
- -(cd cpptraj && $(MAKE) uninstall)
- -(cd mmpbsa_py && $(MAKE) uninstall )
- -(cd parmed && $(MAKE) uninstall )
- -(cd amberlite && $(MAKE) uninstall )
- -/bin/rm -f ../test/numprocs
- -/bin/rm -fr $(BINDIR)/ncmpidump $(BINDIR)/ncmpigen $(BINDIR)/ncvalid $(LIBDIR)/libnetcdf.a $(INCDIR)/mtkpp
-- -(cd $(LIBDIR) && /bin/rm -f libxblas-amb.a libfftw3_mpi.a libfftw3_mpi.la)
-- -(cd $(INCDIR) && /bin/rm -f fftw3-mpi.f03 fftw3-mpi.h)
-
- $(INCDIR)/netcdf.mod:
- cd netcdf/src && $(MAKE) && $(MAKE) -j 1 install
-@@ -247,7 +209,7 @@ $(LIBDIR)/libxblas-amb.a:
- $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a:
- cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
-
--THIRDPARTY: $(NETCDF) $(XBLAS) $(FFTW3)
-+THIRDPARTY: $(XBLAS)
-
- cuda:
- @echo "$(AMBERTOOLS) has no CUDA-enabled components"
-diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2
-index 25d3f0a..1ad86e6 100755
---- a/AmberTools/src/configure2
-+++ b/AmberTools/src/configure2
-@@ -387,11 +387,11 @@ omp_flag=
- mpi_flag=
- lex=flex
- flibs_mkl=
--lapack=install
--blas=install
-+lapack=skip
-+blas=skip
- f2c=skip
--ucpp=install
--cpp="ucpp -l"
-+ucpp=skip
-+cpp="\$(EPREFIX)/usr/bin/ucpp -l"
-
- #-----------------------------------
- # skip building of xleap?
-@@ -618,13 +618,14 @@ gnu)
- flibs_arch="-lgfortran -w"
- flibsf_arch=
- cc=gcc
-- cflags=
-+ cflags="GENTOO_CFLAGS"
- ambercflags=""
- cplusplus=g++
-- cxxflags=
-+ cxxflags="GENTOO_CXXFLAGS"
- ambercxxflags=""
- fc=gfortran
-- fflags=
-+ fflags="GENTOO_FFLAGS"
-+ ldflags="GENTOO_LDFLAGS"
- staticflag='-static'
-
- # If -noopt has been requested, force lack of optimisation;
-@@ -645,11 +646,11 @@ gnu)
- foptflags=""
- else
- cnooptflags=
-- coptflags="-O3"
-+ coptflags="GENTOO_CFLAGS"
- cxxnooptflags=
-- cxxoptflags="-O3"
-+ cxxoptflags="GENTOO_CXXFLAGS"
- fnooptflags="-O0"
-- foptflags="-O3"
-+ foptflags="GENTOO_FFLAGS"
- fi
-
- # Debugging options
-@@ -2026,26 +2027,26 @@ EOF
- if [ "$sse" = "yes" ]; then
- enable_sse="--enable-sse2=yes" # --enable-avx=yes"
- fi
-- cd fftw-3.3 && \
-- ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-- --enable-static=yes \
-- $enable_mpi $enable_debug $enable_sse\
-- CC="$cc" CFLAGS="$cflags $coptflags" \
-- F77="$fc" FFLAGS="$fflags $foptflags" \
-- FLIBS="$flibs_arch" \
-- > ../fftw3_config.log 2>&1
-- ncerror=$?
-- if [ $ncerror -gt 0 ]; then
-- echo " Error: FFTW configure returned $ncerror"
-- echo " FFTW configure failed! Check the fftw3_config.log file"
-- echo " in the $AMBERHOME/AmberTools/src diretory."
-- exit 1
-- else
-- echo " fftw-3.3 configure succeeded."
-- fi
-- cd ..
-+# cd fftw-3.3 && \
-+# ./configure --prefix=$AMBERHOME --libdir=$AMBERHOME/lib \
-+# --enable-static=yes \
-+# $enable_mpi $enable_debug $enable_sse\
-+# CC="$cc" CFLAGS="$cflags $coptflags" \
-+# F77="$fc" FFLAGS="$fflags $foptflags" \
-+# FLIBS="$flibs_arch" \
-+# > ../fftw3_config.log 2>&1
-+# ncerror=$?
-+# if [ $ncerror -gt 0 ]; then
-+# echo " Error: FFTW configure returned $ncerror"
-+# echo " FFTW configure failed! Check the fftw3_config.log file"
-+# echo " in the $AMBERHOME/AmberTools/src diretory."
-+# exit 1
-+# else
-+# echo " fftw-3.3 configure succeeded."
-+# fi
-+# cd ..
- fftw3="FFTW3"
-- flibs_fftw3="-lfftw3"
-+ flibs_fftw3="GENTOO_FFTW3_LIBS"
- fftw3="\$(LIBDIR)/libfftw3.a"
- if [ "$mpi" = 'yes' ]; then
- flibs_fftw3="-lfftw3_mpi $flibs_fftw3"
-@@ -2282,7 +2283,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS)
- AMBERLDFLAGS=\$(AMBERBUILDFLAGS)
-
- LEX= $lex
--YACC= \$(BINDIR)/yacc
-+YACC= byacc
- AR= ar rv
- M4= $m4
- RANLIB=$ranlib
-@@ -2319,7 +2320,7 @@ CP=$localcp
- # Information about Fortran compilation:
-
- FC=$fc
--FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -I\$(INCDIR) \$(NETCDFINC) $mklinc
-+FFLAGS= $fflags \$(LOCALFLAGS) \$(CUSTOMBUILDFLAGS) -IGENTOO_INCLUDE \$(NETCDFINC) $mklinc
- FNOOPTFLAGS= $fnooptflags
- FOPTFLAGS= $foptflags
- AMBERFFLAGS=\$(AMBERBUILDFLAGS)
-diff --git a/AmberTools/src/cpptraj/src/Makefile_at b/AmberTools/src/cpptraj/src/Makefile_at
-index 822b451..0684b0c 100644
---- a/AmberTools/src/cpptraj/src/Makefile_at
-+++ b/AmberTools/src/cpptraj/src/Makefile_at
-@@ -29,22 +29,10 @@ dependclean:
- -/bin/rm FindDepend.o
- -/bin/rm findDepend
-
--cpptraj$(SFX): $(NETCDF) $(OBJECTS) $(PTRAJ_OBJECTS) $(EXTERNAL_LIBS)
-+cpptraj$(SFX): $(OBJECTS) $(PTRAJ_OBJECTS)
- $(CXX) $(LDFLAGS) -o cpptraj$(SFX) $(OBJECTS) $(PTRAJ_OBJECTS) \
- -L$(LIBDIR) $(NETCDFLIB) $(ZLIB) $(BZLIB) $(FLIBS_PTRAJ)
-
--$(INCDIR)/netcdf.mod: ../../netcdf_config.log
-- cd ../../netcdf/src && $(MAKE) install
--
--$(LIBDIR)/libarpack.a:
-- cd ../../arpack && $(MAKE) install
--
--$(LIBDIR)/liblapack.a:
-- cd ../../lapack && $(MAKE) $(LAPACK)
--
--$(LIBDIR)/libblas.a:
-- cd ../../blas && $(MAKE) $(BLAS)
--
- thermo.o: ../../ptraj/thermo.F90
- $(FC) $(FPPFLAGS) -c $(FREEFORMAT_FLAG) $(FOPTFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o $@ ../../ptraj/thermo.F90
-
-diff --git a/AmberTools/src/mdgx/Makefile b/AmberTools/src/mdgx/Makefile
-index 7bad950..b7a560b 100644
---- a/AmberTools/src/mdgx/Makefile
-+++ b/AmberTools/src/mdgx/Makefile
-@@ -132,19 +132,16 @@ MDGX_HEADERS = \
- ptrajmask.h \
- ../sff/AmberNetcdf.h
-
--mdgx$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
-+mdgx$(SFX) : $(MDGX_OBJS)
- $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- -o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
-
--mdgx.MPI$(SFX) : $(MDGX_OBJS) $(LIBDIR)/libfftw3.a
-+mdgx.MPI$(SFX) : $(MDGX_OBJS)
- $(CC) $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) \
- -o $@ $(MDGX_OBJS) $(FFTWLIB) -L$(LIBDIR) $(NETCDFLIB) $(LM)
-
--$(LIBDIR)/fftw3.a: ../fftw-3.3/config.log
-- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install;
--
- .c.o:
-- $(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -I../fftw-3.3/api -o $@ $<
-+ $(CC) -c $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) -I$(INCDIR) -o $@ $<
-
- clean:
- /bin/rm -f $(MDGX_OBJS) mdgx$(SFX)
-diff --git a/AmberTools/src/mdgx/Trajectory.c b/AmberTools/src/mdgx/Trajectory.c
-index 524dad8..5df64c6 100644
---- a/AmberTools/src/mdgx/Trajectory.c
-+++ b/AmberTools/src/mdgx/Trajectory.c
-@@ -214,7 +214,7 @@ void ExtendCoordinates(coord *tc, prmtop *tp)
- coord ReadRst(prmtop *tp, char* source)
- {
- int i, rsttype;
-- char line[128];
-+ char line[MAXLINE];
- FILE *inp;
- coord tc;
-
-diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-index b01b891..24ea20f 100644
---- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-+++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py
-@@ -210,7 +210,7 @@ class AmberOutput(object):
-
- # write out each frame
- for i in range(len(self.data[print_keys[0]])):
-- csvwriter.writerow([i] + [self.data[key][i] for key in print_keys])
-+ csvwriter.writerow([i] + ["%.4f" % self.data[key][i] for key in print_keys])
-
- #==================================================
-
-@@ -1003,7 +1003,7 @@ class BindingStatistics(object):
-
- # write out each frame
- for i in range(len(self.data[print_keys[0]])):
-- csvwriter.writerow([i]+[self.data[key][i] for key in print_keys])
-+ csvwriter.writerow([i]+["%.4f" % self.data[key][i] for key in print_keys])
- csvwriter.writerow([])
-
- #==================================================
-diff --git a/AmberTools/src/nab/database.c b/AmberTools/src/nab/database.c
-index 0b98d35..9aad62a 100644
---- a/AmberTools/src/nab/database.c
-+++ b/AmberTools/src/nab/database.c
-@@ -1135,7 +1135,7 @@ int* iPLines;
- char* PBuffer;
- int iBufferInc;
- {
--String sLine;
-+String sLine[MAXDATALINELEN];
-
-
-
-diff --git a/AmberTools/src/nab/nab.c b/AmberTools/src/nab/nab.c
-index 84e03ef..d49b711 100644
---- a/AmberTools/src/nab/nab.c
-+++ b/AmberTools/src/nab/nab.c
-@@ -161,8 +161,8 @@ char *cppstring;
- fprintf( stderr, "AMBERHOME is not set!\n" );
- exit(1);
- }
-- sprintf( cmd, "%s/bin/%s %s -I%s/include %s ",
-- amberhome, CPP, cppstring, amberhome,
-+ sprintf( cmd, "%s %s -I%s/include %s ",
-+ CPP, cppstring, amberhome,
- argv[ ac ] ? argv[ ac ] : "" );
- if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd );
- nfields = split( cmd, fields, " " );
-diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile
-index 0a3f12f..2105b00 100644
---- a/AmberTools/src/pbsa/Makefile
-+++ b/AmberTools/src/pbsa/Makefile
-@@ -144,23 +144,23 @@ configured_parallel: configured
- )
-
- #---------------------------------------------------------------------------
--pbsa$(SFX): FFTW3 $(OBJ) syslib netlib c9x-complex configured_serial
-+pbsa$(SFX): $(OBJ) syslib configured_serial
- $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa$(SFX) $(OBJ) \
- ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
-
--pbsa.MPI$(SFX): FFTW3.MPI $(OBJ) syslib netlib c9x-complex configured_parallel
-+pbsa.MPI$(SFX): $(OBJ) syslib configured_parallel
- $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o pbsa.MPI$(SFX) $(OBJ) \
- ../lib/nxtsec.o ../lib/random.o $(FLIBS_FFTW3) \
- -L$(LIBDIR) $(FLIBSF) $(LDFLAGS) $(AMBERLDFLAGS)
-
--simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib netlib c9x-complex
-+simplepbsa$(SFX): simplepbsa.o gopt.o libpbsa.a sfflib syslib
- $(FC) $(PBSAFLAG) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o simplepbsa$(SFX) simplepbsa.o gopt.o \
- libpbsa.a $(LIBDIR)/libsff.a ../lib/nxtsec.o -L$(LIBDIR) $(FLIBSF) \
- $(LDFLAGS) $(AMBERLDFLAGS)
- /bin/mv simplepbsa$(SFX) $(BINDIR)
-
--libpbsa.a: FFTW3 $(LIBPBSAOBJS) syslib
-+libpbsa.a: $(LIBPBSAOBJS) syslib
- -rm -f libpbsa.a
- $(AR) libpbsa.a $(LIBPBSAOBJS) ../lib/random.o
- $(RANLIB) libpbsa.a
-@@ -188,48 +188,12 @@ libFpbsa.parallel: $(SANDERPBSAOBJS)
- $(RANLIB) libFpbsa.a
- /bin/mv libFpbsa.a $(LIBDIR)
-
--FFTW3:
-- @if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
-- if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
-- cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
-- compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
-- INSTALL_DIR=$(LIBDIR); \
-- else \
-- if [ ! -f $(INCDIR)/fftw3.f03 ]; then\
-- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
-- fi \
-- fi \
-- fi
--
--FFTW3.MPI:
-- @if [ "$(PBSAFLAG)" = "-DFFTW" ]; then \
-- if [ "$(FLIBS_FFTW3)" = '-lfftw3xf_$(COMPILER)' ]; then\
-- cd $(MKL)/interfaces/fftw3xf && $(MAKE) lib$(MKL_PROCESSOR) \
-- compiler=$(COMPILER) PRECISION=MKL_DOUBLE \
-- INSTALL_DIR=$(LIBDIR); \
-- else \
-- if [ ! -f $(INCDIR)/fftw3-mpi.f03 ]; then\
-- cd ../fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; \
-- fi \
-- fi \
-- fi
--
- syslib:
- cd ../lib && $(MAKE) nxtsec.o random.o
-
- sfflib:
- cd ../sff && $(MAKE) install
-
--netlib:
-- cd ../lapack && $(MAKE) $(LAPACK)
-- cd ../blas && $(MAKE) $(BLAS)
-- cd ../arpack && $(MAKE) install
--
--c9x-complex:
-- @if test $(C9XCOMPLEX) != "skip"; then \
-- cd ../c9x-complex && $(MAKE) libmc.a; \
-- fi
--
- pb_init.o: pb_init.F90
- $(FC) $(PBSAFLAG) $(FPPFLAGS) -c -O0 $(FFLAGS) $(AMBERFFLAGS) -o $@ $<
-
-diff --git a/AmberTools/src/ptraj/Makefile b/AmberTools/src/ptraj/Makefile
-index 3e643b9..b3089f1 100644
---- a/AmberTools/src/ptraj/Makefile
-+++ b/AmberTools/src/ptraj/Makefile
-@@ -61,21 +61,16 @@ rdparm$(SFX): libs $(OBJECTS)
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- -o rdparm$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
-
--ptraj$(SFX): libs netlib $(OBJECTS)
-+ptraj$(SFX): libs $(OBJECTS)
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- -o ptraj$(SFX) $(OBJECTS) $(LIBS) $(NETCDFLIB) $(LM)
-
--ptraj.MPI$(SFX): libs netlib $(OBJECTS)
-+ptraj.MPI$(SFX): libs $(OBJECTS)
- $(CC) $(CFLAGS) $(AMBERCFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \
- -o ptraj.MPI$(SFX) $(OBJECTS) $(LIBS) $(PNETCDFLIB) $(LM)
-
- libs:
- cd pdb && $(MAKE)
-- cd ../arpack && $(MAKE)
--
--netlib:
-- cd ../lapack && $(MAKE) $(LAPACK)
-- cd ../blas && $(MAKE) $(BLAS)
-
- clean:
- cd pdb && $(MAKE) clean
-diff --git a/AmberTools/src/ptraj/trajectory.c b/AmberTools/src/ptraj/trajectory.c
-index 110ffce..49bdf1a 100644
---- a/AmberTools/src/ptraj/trajectory.c
-+++ b/AmberTools/src/ptraj/trajectory.c
-@@ -1315,7 +1315,7 @@ readAmberTrajectory_nobuffer(FILE *fpin, int natoms,
- {
- fpos_t fileMarker; /* marker for current file postition */
- char *junk;
-- char buffer[120];
-+ char buffer[BUFFER_SIZE];
- char coords[26]; /* room for 24 characters (3f8.3) + \n + (char) 0 */
- char c;
- int j,ret;
-diff --git a/AmberTools/src/sff/Makefile b/AmberTools/src/sff/Makefile
-index 83f362c..13efc78 100644
---- a/AmberTools/src/sff/Makefile
-+++ b/AmberTools/src/sff/Makefile
-@@ -3,7 +3,7 @@ include ../config.h
- .c.o:
- $(CC) -c -Dflex $(COPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) $(RISMSFF) $(NETCDFINC) -o $@ $<
-
--OBJS = binpos.o conjgrad.o lmodC.o memutil.o nblist.o newton.o nmode.o \
-+OBJS = binpos.o conjgrad.o dsarpack.o lmodC.o memutil.o nblist.o newton.o nmode.o \
- prm.o rand2.o sasad.o sff.o time.o xminC.o AmberNetcdf.o $(SFF_RISM_INTERFACE)
-
-
-@@ -63,7 +63,7 @@ xminC.o: sff.h
- AmberNetcdf.o: AmberNetcdf.h
-
- hcp_getpdb: hcp_getpdb.c
-- $(CC) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
-+ $(CC) $(CFLAGS) $(LDFLAGS) -o $(BINDIR)/hcp_getpdb hcp_getpdb.c
-
- .PHONY: ../rism/amber_rism_interface.NAB.o
- ../rism/amber_rism_interface.NAB.o:
-diff --git a/AmberTools/src/sff/dsarpack.f b/AmberTools/src/sff/dsarpack.f
-new file mode 100644
-index 0000000..5544df9
---- /dev/null
-+++ b/AmberTools/src/sff/dsarpack.f
-@@ -0,0 +1,654 @@
-+ subroutine dsarpack(n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,
-+ & eigval_tol,eigvals,eigvecs,spectrum,
-+ & need_eigvecs,ierr,debug_arpack,
-+ & v,workl,workd,d,resid,ax,select,
-+ & xyz,grad,return_flag,label)
-+c
-+ implicit none
-+c
-+c %-----------------%
-+c | Dummy Arguments |
-+c %-----------------%
-+c
-+ integer n_dim,n_eig_in,n_eig_out,ncv_in,itr_in,spectrum,
-+ & need_eigvecs,ierr,debug_arpack,return_flag,label
-+ Double precision eigval_tol
-+ Double precision eigvals(n_eig_in),eigvecs(n_dim * n_eig_in)
-+ Double precision v(n_dim,ncv_in),
-+ & workl(ncv_in*(ncv_in+8)),workd(3*n_dim),
-+ & d(ncv_in,2),resid(n_dim),ax(n_dim),
-+ & xyz(n_dim),grad(n_dim)
-+ logical select(ncv_in)
-+c
-+ save
-+c
-+c %---------------%
-+c | Include Files |
-+c %---------------%
-+c
-+c include 'debug.h'
-+c
-+c\SCCS Information: @(#)
-+c FILE: debug.h SID: 2.3 DATE OF SID: 11/16/95 RELEASE: 2
-+c
-+c %---------------------------------%
-+c | See debug.doc for documentation |
-+c %---------------------------------%
-+ integer logfil, ndigit, mgetv0,
-+ & msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+ & mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+ & mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+ common /debug/
-+ & logfil, ndigit, mgetv0,
-+ & msaupd, msaup2, msaitr, mseigt, msapps, msgets, mseupd,
-+ & mnaupd, mnaup2, mnaitr, mneigh, mnapps, mngets, mneupd,
-+ & mcaupd, mcaup2, mcaitr, mceigh, mcapps, mcgets, mceupd
-+c
-+c This code shows how to use ARPACK to find a few eigenvalues
-+c (lambda) and corresponding eigenvectors (x) for the standard
-+c eigenvalue problem:
-+c
-+c A*x = lambda*x
-+c
-+c where A is an n by n real symmetric matrix.
-+c
-+c The main points illustrated here are
-+c
-+c 1) How to declare sufficient memory to find NEV
-+c eigenvalues of largest magnitude. Other options
-+c are available.
-+c
-+c 2) Illustration of the reverse communication interface
-+c needed to utilize the top level ARPACK routine DSAUPD
-+c that computes the quantities needed to construct
-+c the desired eigenvalues and eigenvectors(if requested).
-+c
-+c 3) How to extract the desired eigenvalues and eigenvectors
-+c using the ARPACK routine DSEUPD.
-+c
-+c The only thing that must be supplied in order to use this
-+c routine on your problem is to change the array dimensions
-+c appropriately, to specify WHICH eigenvalues you want to compute
-+c and to supply a matrix-vector product
-+c
-+c w <- Av
-+c
-+c in place of the call to AV( ) below.
-+c
-+c Once usage of this routine is understood, you may wish to explore
-+c the other available options to improve convergence, to solve generalized
-+c problems, etc. Look at the file ex-sym.doc in DOCUMENTS directory.
-+c This codes implements
-+c
-+c\Example-1
-+c ... Suppose we want to solve A*x = lambda*x in regular mode,
-+c where A is derived from the central difference discretization
-+c of the 2-dimensional Laplacian on the unit square with
-+c zero Dirichlet boundary condition.
-+c ... OP = A and B = I.
-+c ... Assume "call av (n,x,y)" computes y = A*x
-+c ... Use mode 1 of DSAUPD.
-+c
-+c\BeginLib
-+c
-+c\Routines called:
-+c dsaupd ARPACK reverse communication interface routine.
-+c dseupd ARPACK routine that returns Ritz values and (optionally)
-+c Ritz vectors.
-+c dnrm2 Level 1 BLAS that computes the norm of a vector.
-+c daxpy Level 1 BLAS that computes y <- alpha*x+y.
-+c
-+c\Author
-+c Richard Lehoucq
-+c Danny Sorensen
-+c Chao Yang
-+c Dept. of Computational &
-+c Applied Mathematics
-+c Rice University
-+c Houston, Texas
-+c
-+c\SCCS Information: %Z%
-+c FILE: %M% SID: %I% DATE OF SID: %G% RELEASE: %R%
-+c
-+c\Remarks
-+c 1. None
-+c
-+c\EndLib
-+c
-+c-----------------------------------------------------------------------
-+c
-+c %-------------------------------------------------------%
-+c | Storage Declarations: |
-+c | |
-+c | The maximum dimensions for all arrays are |
-+c | set here to accommodate a problem size of |
-+c | N .le. MAXN |
-+c | |
-+c | NEV is the number of eigenvalues requested. |
-+c | See specifications for ARPACK usage below. |
-+c | |
-+c | NCV is the largest number of basis vectors that will |
-+c | be used in the Implicitly Restarted Arnoldi |
-+c | Process. Work per major iteration is |
-+c | proportional to N*NCV*NCV. |
-+c | |
-+c | You must set: |
-+c | |
-+c | MAXN: Maximum dimension of the A allowed. (dynamic) |
-+c | MAXNEV: Maximum NEV allowed. (dynamic) |
-+c | MAXNCV: Maximum NCV allowed. (dynamic) |
-+c %-------------------------------------------------------%
-+c
-+C %--------------------------------------%
-+C | F90 Allocatable Arrays (on the heap) |
-+C %--------------------------------------%
-+c
-+C Double precision,allocatable,save :: v(:,:)
-+C integer,save :: v_row_allocated = 0, v_col_allocated = 0
-+c
-+c %----------------------------------------------%
-+c | Originally, as F77 parameters, the following |
-+c | integers were used to dimension work arrays. |
-+c | They are replaced by dummy arguments used to |
-+c | dimension the work arrays as F90 automatic |
-+c | arrays, but the integers are still used for |
-+c | passing the dimensions to lower level ARPACK |
-+c | routines dsaupd, dseupd and dmout. |
-+c %----------------------------------------------%
-+c
-+ integer maxn, maxnev, maxncv, ldv
-+c
-+c %-------------------------------------------%
-+c | Local F90 Automatic Arrays (on the stack) |
-+c %-------------------------------------------%
-+c
-+ Double precision
-+C & workl(ncv_in*(ncv_in+8)),
-+C & workd(3*n_dim), d(ncv_in,2), resid(n_dim),
-+C & ax(n_dim),
-+ & cg_dstat(4)
-+C logical select(ncv_in)
-+ integer iparam(11), ipntr(11),
-+ & cg_istat(4)
-+c
-+c %---------------%
-+c | Local Scalars |
-+c %---------------%
-+c
-+ character bmat*1, which*2
-+ integer ido, n, nev, ncv, lworkl, info,
-+ & i, j, nx, ishfts, maxitr, mode1, nconv
-+ integer L12, L18, ARPACK_ERROR, status_flag
-+ data L12, L18, ARPACK_ERROR /1, 2, -2/
-+C integer v_row_needed, v_col_needed
-+ logical rvec
-+ Double precision
-+ & tol, sigma
-+c
-+c %------------%
-+c | Parameters |
-+c %------------%
-+c
-+ Double precision
-+ & zero
-+ parameter (zero = 0.0D+0)
-+c
-+c %-----------------------------%
-+c | BLAS & LAPACK routines used |
-+c %-----------------------------%
-+c
-+ Double precision
-+ & dnrm2
-+ external dnrm2, daxpy, hessvec
-+c
-+c %--------------------%
-+c | Intrinsic function |
-+c %--------------------%
-+c
-+ intrinsic abs
-+c
-+c %-----------------------%
-+c | Executable Statements |
-+c %-----------------------%
-+c
-+ if ( label.eq.0 ) go to 1
-+ go to (12,18) label
-+ 1 continue
-+c
-+c %------------------------------------------------%
-+c | Values used to calculate work array dimensions |
-+c %------------------------------------------------%
-+c
-+ maxn = n_dim
-+ maxnev = n_eig_in
-+ maxncv = ncv_in
-+ ldv = maxn
-+c
-+c %---------------------------------------------------%
-+c | The include debug.h statement above and |
-+c | assignments here initiate trace output from the |
-+c | internal actions of ARPACK. See debug.doc in the |
-+c | DOCUMENTS directory for usage. Initially, the |
-+c | most useful information will be a breakdown of |
-+c | time spent in the various stages of computation |
-+c | given by setting msaupd = 1. |
-+c %---------------------------------------------------%
-+c
-+ ndigit = -5
-+ logfil = 6
-+ msgets = 0
-+ msaitr = 0
-+ msapps = 0
-+ if ( debug_arpack.eq.1 ) then
-+ msaupd = 1
-+ else
-+ msaupd = 0
-+ endif
-+ msaup2 = 0
-+ mseigt = 0
-+ mseupd = 0
-+c
-+c *** Allocatable array v will be allowed to grow to its largest size;
-+c *** it is never deallocated:
-+C v_row_needed = n_dim !!! ldv
-+C v_col_needed = ncv_in !!! maxncv
-+C if( allocated(v) )then
-+C if( (v_row_needed .gt. v_row_allocated)
-+C & .or. (v_col_needed .gt. v_col_allocated) )then
-+C deallocate(v,stat=ierr)
-+C if( ierr .ne. 0 )then
-+C write( logfil, '(a,i16,1x,i8)' )
-+C & 'ARPACK: could not deallocate v'
-+C go to 9000
-+C endif
-+C endif
-+C endif
-+C if( .not. allocated(v) )then
-+C allocate( v(v_row_needed,v_col_needed), stat=ierr )
-+C if( ierr .ne. 0 )then
-+C write( logfil, '(a,2i10)' )
-+C & 'ARPACK: could not allocate v'
-+C go to 9000
-+C endif
-+C v_row_allocated = v_row_needed
-+C v_col_allocated = v_col_needed
-+C endif
-+C v = zero !!! zero out entire v array
-+c
-+c %-------------------------------------------------%
-+c | The following sets dimensions for this problem. |
-+c %-------------------------------------------------%
-+c
-+ n = n_dim
-+c
-+c %----------------------------------------------%
-+c | |
-+c | Specifications for ARPACK usage are set |
-+c | below: |
-+c | |
-+c | 1) NEV = N_EIG_IN asks for N_EIG_IN |
-+c | eigenvalues to be computed. |
-+c | |
-+c | 2) NCV = NCV_IN sets the length of the |
-+c | Arnoldi factorization |
-+c | |
-+c | 3) This is a standard problem |
-+c | (indicated by bmat = 'I') |
-+c | |
-+c | 4) Ask for the NEV eigenvalues of |
-+c | smallest magnitude |
-+c | (indicated by which = 'SM') |
-+c | See documentation in SSAUPD for the |
-+c | other options SA, LA, LM, BE. |
-+c | |
-+c | Note: NEV and NCV must satisfy the following |
-+c | conditions: |
-+c | NEV <= MAXNEV |
-+c | NEV + 1 <= NCV <= MAXNCV |
-+c %----------------------------------------------%
-+c
-+ nev = n_eig_in
-+ ncv = ncv_in
-+ bmat = 'I'
-+ if ( spectrum .eq. 1 ) then
-+ which = 'SM'
-+ else if ( spectrum .eq. 2 ) then
-+ which = 'SA'
-+ else if ( spectrum .eq. 3 ) then
-+ which = 'LM'
-+ else if ( spectrum .eq. 4 ) then
-+ which = 'LA'
-+ else if ( spectrum .eq. 5 ) then
-+ which = 'BE'
-+ else
-+ print *, ' ERROR with _SSIMP: Spectrum .NE. (SM|SA|LA|LM|BE)'
-+ go to 9000
-+ end if
-+c
-+ if ( n .gt. maxn ) then
-+ print *, ' ERROR with _SSIMP: N is greater than MAXN '
-+ go to 9000
-+ else if ( nev .gt. maxnev ) then
-+ print *, ' ERROR with _SSIMP: NEV is greater than MAXNEV '
-+ go to 9000
-+ else if ( ncv .gt. maxncv ) then
-+ print *, ' ERROR with _SSIMP: NCV is greater than MAXNCV '
-+ go to 9000
-+ end if
-+c
-+c %-----------------------------------------------------%
-+c | |
-+c | Specification of stopping rules and initial |
-+c | conditions before calling DSAUPD |
-+c | |
-+c | TOL determines the stopping criterion. |
-+c | |
-+c | Expect |
-+c | abs(lambdaC - lambdaT) < TOL*abs(lambdaC) |
-+c | computed true |
-+c | |
-+c | If TOL .le. 0, then TOL <- macheps |
-+c | (machine precision) is used. |
-+c | |
-+c | IDO is the REVERSE COMMUNICATION parameter |
-+c | used to specify actions to be taken on return |
-+c | from DSAUPD. (See usage below.) |
-+c | |
-+c | It MUST initially be set to 0 before the first |
-+c | call to DSAUPD. |
-+c | |
-+c | INFO on entry specifies starting vector information |
-+c | and on return indicates error codes |
-+c | |
-+c | Initially, setting INFO=0 indicates that a |
-+c | random starting vector is requested to |
-+c | start the ARNOLDI iteration. Setting INFO to |
-+c | a nonzero value on the initial call is used |
-+c | if you want to specify your own starting |
-+c | vector (This vector must be placed in RESID.) |
-+c | |
-+c | The work array WORKL is used in DSAUPD as |
-+c | workspace. Its dimension LWORKL is set as |
-+c | illustrated below. |
-+c | |
-+c %-----------------------------------------------------%
-+c
-+ lworkl = ncv*(ncv+8)
-+ tol = eigval_tol
-+ info = 0
-+ ido = 0
-+c
-+c %---------------------------------------------------%
-+c | Specification of Algorithm Mode: |
-+c | |
-+c | This program uses the exact shift strategy |
-+c | (indicated by setting PARAM(1) = 1). |
-+c | IPARAM(3) specifies the maximum number of Arnoldi |
-+c | iterations allowed. Mode 1 of DSAUPD is used |
-+c | (IPARAM(7) = 1). All these options can be changed |
-+c | by the user. For details see the documentation in |
-+c | DSAUPD. |
-+c %---------------------------------------------------%
-+c
-+ ishfts = 1
-+ maxitr = itr_in
-+ mode1 = 1
-+c
-+ iparam(1) = ishfts
-+c
-+ iparam(3) = maxitr
-+c
-+ iparam(7) = mode1
-+c
-+c %------------------------------------------------%
-+c | M A I N L O O P (Reverse communication loop) |
-+c %------------------------------------------------%
-+c
-+ 10 continue
-+c
-+c %---------------------------------------------%
-+c | Repeatedly call the routine DSAUPD and take |
-+c | actions indicated by parameter IDO until |
-+c | either convergence is indicated or maxitr |
-+c | has been exceeded. |
-+c %---------------------------------------------%
-+c
-+ call dsaupd ( ido, bmat, n, which, nev, tol, resid,
-+ & ncv, v, ldv, iparam, ipntr, workd, workl,
-+ & lworkl, info )
-+c
-+ if (ido .eq. -1 .or. ido .eq. 1) then
-+c
-+c %--------------------------------------%
-+c | Perform matrix vector multiplication |
-+c | y <--- OP*x |
-+c | The user should supply his/her own |
-+c | matrix vector multiplication routine |
-+c | here that takes workd(ipntr(1)) as |
-+c | the input, and return the result to |
-+c | workd(ipntr(2)). |
-+c %--------------------------------------%
-+c
-+ status_flag = 0
-+ 11 continue
-+ call hessvec ( n, workd(ipntr(1)), workd(ipntr(2)),
-+ & xyz, grad, return_flag, status_flag )
-+ if ( status_flag.eq.0 ) go to 13
-+ if ( status_flag.lt.0 ) go to 9000
-+ label = L12
-+ return
-+ 12 go to 11
-+ 13 continue
-+c
-+c %-----------------------------------------%
-+c | L O O P B A C K to call DSAUPD again. |
-+c %-----------------------------------------%
-+c
-+ go to 10
-+c
-+ end if
-+c
-+c %----------------------------------------%
-+c | Either we have convergence or there is |
-+c | an error. |
-+c %----------------------------------------%
-+c
-+ if ( info .lt. 0 ) then
-+c
-+c %--------------------------%
-+c | Error message. Check the |
-+c | documentation in DSAUPD. |
-+c %--------------------------%
-+c
-+ print *, ' '
-+ print *, ' Error with _saupd, info = ', info
-+ print *, ' Check documentation in _saupd '
-+ print *, ' '
-+ go to 9000
-+c
-+ else
-+c
-+c %-------------------------------------------%
-+c | No fatal errors occurred. |
-+c | Post-Process using DSEUPD. |
-+c | |
-+c | Computed eigenvalues may be extracted. |
-+c | |
-+c | Eigenvectors may be also computed now if |
-+c | desired. (indicated by rvec = .true.) |
-+c | |
-+c | The routine DSEUPD now called to do this |
-+c | post processing (Other modes may require |
-+c | more complicated post processing than |
-+c | mode1.) |
-+c | |
-+c %-------------------------------------------%
-+c
-+ if ( need_eigvecs .eq. 1 ) then
-+ rvec = .true.
-+ else
-+ rvec = .false.
-+ end if
-+c
-+ call dseupd ( rvec, 'All', select, d, v, ldv, sigma,
-+ & bmat, n, which, nev, tol, resid, ncv, v, ldv,
-+ & iparam, ipntr, workd, workl, lworkl, ierr )
-+c
-+c %----------------------------------------------%
-+c | Eigenvalues are returned in the first column |
-+c | of the two dimensional array D and the |
-+c | corresponding eigenvectors are returned in |
-+c | the first NCONV (=IPARAM(5)) columns of the |
-+c | two dimensional array V if requested. |
-+c | Otherwise, an orthogonal basis for the |
-+c | invariant subspace corresponding to the |
-+c | eigenvalues in D is returned in V. |
-+c %----------------------------------------------%
-+c
-+ if ( ierr .ne. 0) then
-+c
-+c %------------------------------------%
-+c | Error condition: |
-+c | Check the documentation of DSEUPD. |
-+c %------------------------------------%
-+c
-+ print *, ' '
-+ print *, ' Error with _seupd, info = ', ierr
-+ print *, ' Check the documentation of _seupd. '
-+ print *, ' '
-+ go to 9000
-+c
-+ else if ( debug_arpack.eq.1 ) then
-+c
-+ nconv = iparam(5)
-+ n_eig_out = nconv
-+ if ( nconv .le. 0 ) then
-+ print *, ' '
-+ print *, ' ARPACK: Not a single mode converged.'
-+ print *, ' '
-+ go to 9000
-+ endif
-+c
-+C %--------------------------------------------%
-+C | "UnDO" DO 20 j=1,nconv loop, because it is |
-+C | illegal to jump in and out from a DO loop. |
-+C %--------------------------------------------%
-+c
-+ j = 1
-+ 16 continue
-+c
-+c %---------------------------%
-+c | Compute the residual norm |
-+c | |
-+c | || A*x - lambda*x || |
-+c | |
-+c | for the NCONV accurately |
-+c | computed eigenvalues and |
-+c | eigenvectors. (iparam(5) |
-+c | indicates how many are |
-+c | accurate to the requested |
-+c | tolerance) |
-+c %---------------------------%
-+c
-+ status_flag = 0
-+ 17 continue
-+ call hessvec ( n, v(1,j), ax, xyz, grad,
-+ & return_flag, status_flag )
-+ if ( status_flag.eq.0 ) go to 19
-+ if ( status_flag.lt.0 ) go to 9000
-+ label = L18
-+ return
-+ 18 go to 17
-+ 19 continue
-+c
-+ call daxpy(n, -d(j,1), v(1,j), 1, ax, 1)
-+ d(j,2) = dnrm2(n, ax, 1)
-+ d(j,2) = d(j,2) / abs(d(j,1))
-+c
-+ j = j + 1
-+ if ( j .gt. nconv ) go to 20
-+c
-+ go to 16
-+c
-+ 20 continue
-+c
-+c %-----------------------------%
-+c | Display computed residuals. |
-+c %-----------------------------%
-+c
-+ call dmout(6, nconv, 2, d, maxncv, -6,
-+ & 'Ritz values and relative residuals')
-+c
-+c %-------------------------------------------%
-+c | Print additional convergence information. |
-+c %-------------------------------------------%
-+c
-+ if ( info .eq. 1) then
-+ print *, ' '
-+ print *, ' Maximum number of iterations reached.'
-+ print *, ' '
-+ else if ( info .eq. 3) then
-+ print *, ' '
-+ print *, ' No shifts could be applied during implicit',
-+ & ' Arnoldi update, try increasing NCV.'
-+ print *, ' '
-+ end if
-+c
-+ print *, ' '
-+ print *, ' _SSIMP '
-+ print *, ' ====== '
-+ print *, ' '
-+ print *, ' Size of the matrix is ', n
-+ print *, ' The number of Ritz values requested is ', nev
-+ print *, ' The number of Arnoldi vectors generated',
-+ & ' (NCV) is ', ncv
-+ print *, ' What portion of the spectrum: ', which
-+ print *, ' The number of converged Ritz values is ',
-+ & nconv
-+ print *, ' The number of Implicit Arnoldi update',
-+ & ' iterations taken is ', iparam(3)
-+ print *, ' The number of OP*x is ', iparam(9)
-+ print *, ' The convergence criterion is ', tol
-+ print *, ' '
-+ end if
-+c
-+c %----------------------------%
-+c | Return eigvals and eigvecs |
-+c %----------------------------%
-+c
-+ nconv = iparam(5)
-+ n_eig_out = nconv
-+ if ( nconv .le. 0 ) then
-+ print *, ' '
-+ print *, ' ARPACK: Not a single mode converged.'
-+ print *, ' '
-+ go to 9000
-+ endif
-+c
-+ do 40 j=1, nconv
-+ eigvals(j) = d(j,1)
-+c
-+ do 30 i=1, n
-+ eigvecs((j-1)*n+i) = v(i,j)
-+ 30 continue
-+ 40 continue
-+c
-+ end if
-+c
-+c %--------------------------------%
-+c | Done with subroutine dsarpack. |
-+c %--------------------------------%
-+c
-+ label = 0
-+ return
-+c
-+ 9000 continue !!! Error
-+c
-+ if( status_flag.eq.0 ) status_flag = ARPACK_ERROR
-+c
-+ label = status_flag
-+ return
-+c
-+ end
-+c
-+c ------------------------------------------------------------------
-diff --git a/AmberTools/src/sqm/Makefile b/AmberTools/src/sqm/Makefile
-index 3b49c55..61d0dc3 100644
---- a/AmberTools/src/sqm/Makefile
-+++ b/AmberTools/src/sqm/Makefile
-@@ -82,7 +82,7 @@ QMOBJ = qm2_allocate_e_repul.o qm2_calc_charges.o qm2_calc_dipole.o \
- install: sqm$(SFX)
- mv sqm$(SFX) $(BINDIR)
-
--sqm$(SFX): $(SQMOBJ) $(QMOBJ) netlib sys
-+sqm$(SFX): $(SQMOBJ) $(QMOBJ) sys
- $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o sqm$(SFX) $(SQMOBJ) $(QMOBJ) \
- -L$(LIBDIR) $(FLIBSF) ../lib/sys.a $(LDFLAGS) $(AMBERLDFLAGS)
-
-@@ -101,11 +101,6 @@ $(LIBDIR)/libsqm.a: $(QMOBJ) $(LIBQMOBJ)
- sys:
- cd ../lib; $(MAKE) sys.a
-
--netlib:
-- cd ../lapack; $(MAKE) $(LAPACK)
-- cd ../blas; $(MAKE) $(BLAS)
-- cd ../arpack && $(MAKE) install
--
- clean:
- /bin/rm -f *.o *.mod *.d sqm$(SFX)
-
-diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile
-index 27afe24..4796250 100644
---- a/AmberTools/test/Makefile
-+++ b/AmberTools/test/Makefile
-@@ -3,14 +3,14 @@ include ../src/config.h
- ###### Top-level targets, for general use: ############################
-
- test:
-- ./test_at_serial.sh
-+ +./test_at_serial.sh
-
- test.parallel:
- ./test_at_parallel.sh
-
- ###### Intermediate-level targets: ############################
-
--test.serial: clean is_amberhome_defined \
-+test.serial: is_amberhome_defined \
- test.nab test.ptraj test.cpptraj test.antechamber \
- test.leap test.resp test.pbsa test.mmpbsa test.parmed \
- test.ambpdb test.elsize test.chamber test.sqm test.rism1d \
-diff --git a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-index 3595375..1a0be46 100644
---- a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-+++ b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save
-@@ -7,16 +7,16 @@ Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
- Receptor Energy Terms
- Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
- 0,-1969.4265,-17103.7958,-3027.0953,101.7772,-19073.2223,-2925.3181,-21998.5404
--1,-1956.6674,-17020.9923,-3062.954,102.3918,-18977.6597,-2960.5622,-21938.2219
-+1,-1956.6674,-17020.9923,-3062.9540,102.3918,-18977.6597,-2960.5622,-21938.2219
-
- Ligand Energy Terms
- Frame #,VDWAALS,EEL,EGB,ESURF,G gas,G solv,TOTAL
--0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.014
-+0,-1.2566,-5.6263,-28.5797,4.4486,-6.8829,-24.1311,-31.0140
- 1,-3.1118,-6.1548,-29.3738,4.4016,-9.2666,-24.9722,-34.2388
-
- DELTA Energy Terms
- Frame #,VDWAALS,EEL,EGB,ESURF,DELTA G gas,DELTA G solv,DELTA TOTAL
--0,-63.4582,-32.3518,35.2679,-8.3751,-95.81,26.8928,-68.9172
--1,-60.9966,-35.1045,41.6205,-8.465,-96.1011,33.1555,-62.9456
-+0,-63.4582,-32.3518,35.2679,-8.3751,-95.8100,26.8928,-68.9172
-+1,-60.9966,-35.1045,41.6205,-8.4650,-96.1011,33.1555,-62.9456
-
-
-diff --git a/AmberTools/test/nab/Makefile b/AmberTools/test/nab/Makefile
-index 1bb2505..7459a15 100644
---- a/AmberTools/test/nab/Makefile
-+++ b/AmberTools/test/nab/Makefile
-@@ -12,6 +12,8 @@ testrism: \
- rism_ion-noasymp rism_ion_pse1 rism_ion_pse3 rism_mdiis0 rism_mdiis1 \
- rism_sp rism_sp2
-
-+.NOTPARALLEL:
-+
- duplex_test::
- @./Run.duplex
-
-diff --git a/AmberTools/test/nab/Run.rism_sp b/AmberTools/test/nab/Run.rism_sp
-index bd8471d..a88bf58 100755
---- a/AmberTools/test/nab/Run.rism_sp
-+++ b/AmberTools/test/nab/Run.rism_sp
-@@ -47,7 +47,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.nc \
- --polarDecomp\
- --noprogress > rism3d.snglpnt.out || error
-
--checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
-+./checkrism3d -err 1e-6 rism3d.snglpnt.out.check rism3d.snglpnt.out
-
- awk '{if (NR % 10 == 0) print $0}' quv.1.xyzv > quv.1.xyzv.trunc
- ../dacdif -r 1e-6 quv.1.xyzv.trunc.check quv.1.xyzv.trunc
-diff --git a/AmberTools/test/nab/Run.rism_sp2 b/AmberTools/test/nab/Run.rism_sp2
-index a2b9521..11da8de 100755
---- a/AmberTools/test/nab/Run.rism_sp2
-+++ b/AmberTools/test/nab/Run.rism_sp2
-@@ -38,7 +38,7 @@ $DO_PARALLEL $cmd --pdb ala.pdb --prmtop ala.parm7 --traj ala.crd \
- --buffer 10 --guv guv.2\
- --noprogress > rism3d.snglpnt.2.out || error
-
--checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
-+./checkrism3d -err 1e-6 rism3d.snglpnt.2.out.check rism3d.snglpnt.2.out
- ../dacdif -a 1e-6 guv.2.O.1.dx.check guv.2.O.1.dx
- ../dacdif -a 1e-6 guv.2.H1.2.dx.check guv.2.H1.2.dx
- ../dacdif -a 1e-6 guv.2.O.3.dx.check guv.2.O.3.dx
-diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh
-index 15bb590..8fa52e3 100755
---- a/AmberTools/test/test_at_serial.sh
-+++ b/AmberTools/test/test_at_serial.sh
-@@ -39,3 +39,9 @@ fi
-
- # save summary for later reporting:
- tail -5 ${logfile} > ${logdir}/at_summary
-+
-+if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ]
-+then
-+ # Tests failed
-+ exit 1
-+fi
-diff --git a/Makefile b/Makefile
-index 54ddfcb..643ba15 100644
---- a/Makefile
-+++ b/Makefile
-@@ -30,7 +30,7 @@ clean.test:
- test:: test.$(INSTALLTYPE)
-
- test.serial:
-- -(cd AmberTools/test && $(MAKE) test)
-+ (cd AmberTools/test && $(MAKE) test)
- -@(if [ -n "$(BUILDAMBER)" ] ; then \
- cd test && $(MAKE) test; \
- echo "" ; \