diff options
Diffstat (limited to 'science')
46 files changed, 0 insertions, 1359 deletions
diff --git a/science/Makefile b/science/Makefile index 075b75b807b8..a95d819a21d2 100644 --- a/science/Makefile +++ b/science/Makefile @@ -22,13 +22,11 @@ SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 - SUBDIR += abinit SUBDIR += afni SUBDIR += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += apbs - SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro2 SUBDIR += avogadrolibs @@ -55,7 +53,6 @@ SUBDIR += code_saturne SUBDIR += colt SUBDIR += coordgenlibs - SUBDIR += cp2k SUBDIR += cp2k-data SUBDIR += crf++ SUBDIR += dalton @@ -75,7 +72,6 @@ SUBDIR += erd SUBDIR += erkale SUBDIR += erkale-pseudopotentials - SUBDIR += esys-particle SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab @@ -174,7 +170,6 @@ SUBDIR += openbabel SUBDIR += openkim SUBDIR += openkim-models - SUBDIR += openmx SUBDIR += opensim-core SUBDIR += opensph SUBDIR += opsin @@ -204,7 +199,6 @@ SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea - SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol @@ -287,7 +281,6 @@ SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-tensorflow - SUBDIR += py-tensorflow-estimator SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain diff --git a/science/abinit/Makefile b/science/abinit/Makefile deleted file mode 100644 index 6e552ca045d6..000000000000 --- a/science/abinit/Makefile +++ /dev/null @@ -1,48 +0,0 @@ -# Created by: NAKATA Maho <maho@FreeBSD.org> -# $FreeBSD$ - -PORTNAME= abinit -DISTVERSION= 8.10.3 -PORTREVISION= 6 -CATEGORIES= science -MASTER_SITES= https://www.abinit.org/sites/default/files/packages/ - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Full-featured atomic-scale first-principles simulation software - -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/COPYING - -ONLY_FOR_ARCHS= amd64 i386 -BROKEN_i386= Type mismatch in argument 'block_displ', see https://github.com/abinit/abinit/issues/19 - -LIB_DEPENDS= liblapack.so:math/lapack \ - libblas.so:math/blas -RUN_DEPENDS= atompaw:science/atompaw - -USES= fortran gmake localbase:ldflags -GNU_CONFIGURE= yes - -CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}" -CONFIGURE_ARGS= --enable-shared --disable-static -FCFLAGS+= -ffree-line-length-none - -OPTIONS_DEFINE= OPENMP MPI -OPTIONS_DEFAULT= OPENMP MPI - -OPENMP_CONFIGURE_ENABLE= openmp -OPENMP_LDFLAGS= -lomp - -MPI_CONFIGURE_ENABLE= mpi -MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include -MPI_LDFLAGS= ${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpicxx.so ${LOCALBASE}/lib/libmpifort.so -MPI_LIB_DEPENDS= libmpi.so:net/mpich - -do-test: - @cd ${WRKSRC}/tests && ./configure && ${GMAKE} check - -.include <bsd.port.mk> diff --git a/science/abinit/distinfo b/science/abinit/distinfo deleted file mode 100644 index e68949fac546..000000000000 --- a/science/abinit/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1550812825 -SHA256 (abinit-8.10.3.tar.gz) = 922e38edab95e1763c4d504a927f7ea4e19da3143e5b33c5d6e4b41210bf5a9d -SIZE (abinit-8.10.3.tar.gz) = 88310400 diff --git a/science/abinit/files/patch-Makefile.in b/science/abinit/files/patch-Makefile.in deleted file mode 100644 index 05da3e07cc89..000000000000 --- a/science/abinit/files/patch-Makefile.in +++ /dev/null @@ -1,11 +0,0 @@ ---- Makefile.in.orig 2018-06-14 05:16:42 UTC -+++ Makefile.in -@@ -876,7 +876,7 @@ AM_DISTCHECK_CONFIGURE_FLAGS = \ - @abi_ac_distcheck@ \ - PYFLAGS="@PYFLAGS@ -B" - --SUBDIRS = fallbacks src abichecks tests -+SUBDIRS = fallbacks src abichecks - - # Additional files to clean - CLEANFILES = config.optim config.fc_info.tmp diff --git a/science/abinit/files/patch-src_02__clib_md5.c b/science/abinit/files/patch-src_02__clib_md5.c deleted file mode 100644 index f40bca3c14f3..000000000000 --- a/science/abinit/files/patch-src_02__clib_md5.c +++ /dev/null @@ -1,11 +0,0 @@ ---- src/02_clib/md5.c.orig 2017-02-28 12:02:53 UTC -+++ src/02_clib/md5.c -@@ -47,7 +47,7 @@ - #ifdef HAVE_MALLOC_MALLOC_H - # include <malloc/malloc.h> - #else --# include <malloc.h> -+# include <stdlib.h> - #endif - - #include "md5.h" diff --git a/science/abinit/pkg-descr b/science/abinit/pkg-descr deleted file mode 100644 index 2cb92bc2a7c6..000000000000 --- a/science/abinit/pkg-descr +++ /dev/null @@ -1,14 +0,0 @@ -ABINIT is a package whose main program allows one to find the total energy, -charge density and electronic structure of systems made of electrons and nuclei -(molecules and periodic solids) within Density Functional Theory (DFT), using -pseudopotentials and a planewave or wavelet basis. ABINIT also includes options -to optimize the geometry according to the DFT forces and stresses, or to perform -molecular dynamics simulations using these forces, or to generate dynamical -matrices, Born effective charges, and dielectric tensors, based on -Density-Functional Perturbation Theory, and many more properties. Excited states -can be computed within the Many-Body Perturbation Theory (the GW approximation -and the Bethe-Salpeter equation), and Time-Dependent Density Functional Theory -(for molecules). In addition to the main ABINIT code, different utility programs -are provided. - -WWW: https://www.abinit.org diff --git a/science/abinit/pkg-plist b/science/abinit/pkg-plist deleted file mode 100644 index 007b179620fe..000000000000 --- a/science/abinit/pkg-plist +++ /dev/null @@ -1,23 +0,0 @@ -bin/abinit -bin/aim -bin/anaddb -bin/band2eps -bin/bsepostproc -bin/conducti -bin/cut3d -bin/dummy_tests -bin/fftprof -bin/fold2Bloch -bin/ioprof -bin/lapackprof -bin/macroave -bin/mrgddb -bin/mrgdv -bin/mrggkk -bin/mrgscr -bin/multibinit -bin/optic -bin/tdep -bin/ujdet -bin/vdw_kernelgen -libdata/pkgconfig/abinit.pc diff --git a/science/atom/Makefile b/science/atom/Makefile deleted file mode 100644 index 982db8b91e6d..000000000000 --- a/science/atom/Makefile +++ /dev/null @@ -1,44 +0,0 @@ -# $FreeBSD$ - -PORTNAME= atom -DISTVERSION= 4.2.7-100 -PORTREVISION= 5 -CATEGORIES= science -MASTER_SITES= https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/ \ - https://departments.icmab.es/leem/siesta/Pseudopotentials/:lic -PKGNAMESUFFIX= -chemistry -DISTFILES= ${DISTNAME}${EXTRACT_SUFX} atom_licence.html:lic -DIST_SUBDIR= ${PORTNAME}${PKGNAMESUFFIX} -EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Program for DFT calculations in atoms - -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -LICENSE= ATOM_LICENSE -LICENSE_NAME= ATOM ACADEMIC LICENCE -LICENSE_FILE= ${DISTDIR}/${DIST_SUBDIR}/atom_licence.html -LICENSE_PERMS= # none - -LIB_DEPENDS= libGridXC.so:science/libgridxc \ - libxc.so:science/libxc \ - libxmlf90.so:textproc/xmlf90 - -USES= fortran gmake tar:tgz - -MAKE_ENV= XMLF90_ROOT=${LOCALBASE} GRIDXC_ROOT=${LOCALBASE} LIBXC_ROOT=${LOCALBASE} -MAKE_ARGS= FC=gfortran${GCC_DEFAULT} LDFLAGS="${LDFLAGS}" -ALL_TARGET= default - -PLIST_FILES= bin/atm - -post-patch: - @${CP} ${WRKSRC}/arch.make.sample ${WRKSRC}/arch.make - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/atm ${STAGEDIR}${PREFIX}/bin/ - -.include <bsd.port.mk> diff --git a/science/atom/distinfo b/science/atom/distinfo deleted file mode 100644 index 5680866b31e3..000000000000 --- a/science/atom/distinfo +++ /dev/null @@ -1,5 +0,0 @@ -TIMESTAMP = 1536079047 -SHA256 (atom-chemistry/atom-4.2.7-100.tgz) = 266a4119e64ca398444df7bc2f5004513891f2189cba33595a1742c64f8f3edc -SIZE (atom-chemistry/atom-4.2.7-100.tgz) = 260386 -SHA256 (atom-chemistry/atom_licence.html) = 93cc2ed5498d47c5439fcf45ea1501e4e0cadb8197aefc6235ecedd36c849d93 -SIZE (atom-chemistry/atom_licence.html) = 5673 diff --git a/science/atom/files/patch-arch.make.sample b/science/atom/files/patch-arch.make.sample deleted file mode 100644 index fd46b2bdb04b..000000000000 --- a/science/atom/files/patch-arch.make.sample +++ /dev/null @@ -1,11 +0,0 @@ ---- arch.make.sample.orig 2018-09-04 08:05:21 UTC -+++ arch.make.sample -@@ -20,7 +20,7 @@ ARCH=macosx-gfortran - # installation trees and use the appropriate path to the .mk file. - # - include $(XMLF90_ROOT)/share/org.siesta-project/xmlf90.mk --include $(GRIDXC_ROOT)/gridxc.mk -+include $(GRIDXC_ROOT)/share/mk/gridxc.mk - # - # -----Compiler-dependent settings ------------------------------------- - # diff --git a/science/atom/pkg-descr b/science/atom/pkg-descr deleted file mode 100644 index 2673cbd318e8..000000000000 --- a/science/atom/pkg-descr +++ /dev/null @@ -1,4 +0,0 @@ -ATOM, a program for DFT calculations in atoms and pseudopotential -generation, maintained by Alberto Garcia. - -WWW: https://departments.icmab.es/leem/siesta/ diff --git a/science/cp2k/Makefile b/science/cp2k/Makefile deleted file mode 100644 index a346ffbf27e6..000000000000 --- a/science/cp2k/Makefile +++ /dev/null @@ -1,90 +0,0 @@ -# $FreeBSD$ - -PORTNAME= cp2k -DISTVERSIONPREFIX= v -DISTVERSION= 6.1.0 -PORTREVISION= 7 -CATEGORIES= science - -PATCH_SITES= https://github.com/${PORTNAME}/${PORTNAME}/commit/ -PATCHFILES= f03e6277feea9a65d543ca6c1184f58d3e83bc2a.patch:-p2 \ - d00a71c4d0276aab849ac6a6483b9dcdb65613c9.patch:-p2 - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Quantum chemistry and solid state physics software package - -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -LICENSE= GPLv2+ - -LIB_DEPENDS= libblas.so:math/blas \ - libfftw3.so:math/fftw3 \ - liblapack.so:math/lapack -RUN_DEPENDS= cp2k-data>0:science/cp2k-data - -USES= fortran gmake localbase:ldflags python:build tar:bz2 -USE_GITHUB= yes - -MAKEFILE= ${WRKSRC}/makefiles/Makefile -MAKE_ARGS= XARCH=FreeBSD-${NOLIBINT}libint-gfortran VERSION=${VERSION} FC=gfortran${GCC_DEFAULT} CC=${CC} LD=gfortran${GCC_DEFAULT} \ - DATA_DIR=${DATADIR} - -BUILD_WRKSRC= ${WRKSRC}/.build -INSTALL_WRKSRC= ${BUILD_WRKSRC} - -BINARY_ALIAS= python=${PYTHON_CMD} - -OPTIONS_DEFINE= LIBINT -OPTIONS_SINGLE= MULTIPROCESSING -OPTIONS_SINGLE_MULTIPROCESSING= SERIAL OPENMP MPI OPENMP_MPI # for the complete list see "3a. ARCH files" in https://www.cp2k.org/howto:compile -OPTIONS_DEFAULT= LIBINT SERIAL -MULTIPROCESSING_DESC= Multiprocessing - -LIBINT_DESC= Use libint to evaluate integrals -LIBINT_VARS_OFF= NOLIBINT=no -LIBINT_LIB_DEPENDS= libint.so:science/libint - -SERIAL_DESC= Single core (no multiprocessing) -SERIAL_VARS= VERSION=sopt - -OPENMP_VARS= VERSION=ssmp - -MPI_VARS= VERSION=popt -MPI_LIB_DEPENDS= libmpich.so:net/mpich \ - libscalapack.so:math/scalapack -MPI_LDFLAGS= -lmpifort - -OPENMP_MPI_DESC= Enable both OpenMP and MPI -OPENMP_MPI_VARS= VERSION=psmp -OPENMP_MPI_LIB_DEPENDS= ${MPI_LIB_DEPENDS} -OPENMP_MPI_LDFLAGS= ${MPI_LDFLAGS} - -EXECUTABLES= cp2k graph cp2k_shell dbcsr_performance_driver - -PLIST_FILES= ${EXECUTABLES:C/(.*)/bin\/\1.${VERSION}/} - -.include <bsd.port.options.mk> - -.if ${PORT_OPTIONS:MOPENMP} || ${PORT_OPTIONS:MOPENMP_MPI} -pre-configure: - @if [ ! -e ${LOCALBASE}/lib/libfftw3_omp.so ] ; then \ - ${ECHO_MSG} "The OPENMP and OPENMP_MPI options require math/fftw3" ; \ - ${ECHO_MSG} "to be built and installed with the OPENMP option ON" ; \ - exit 1; \ - fi -.endif - -post-patch: - @${REINPLACE_CMD} 's|LIBS.*=.*|& ${LDFLAGS}|; s|^FCFLAGS.*=.*|& -I${LOCALBASE}/include|; s| -march=native||' ${WRKSRC}/arch/FreeBSD-* - -pre-build: - @${MKDIR} ${BUILD_WRKSRC} - -do-install: -.for e in ${EXECUTABLES} - ${INSTALL_PROGRAM} ${WRKSRC}/exe/*/${e}.${VERSION} ${STAGEDIR}${PREFIX}/bin -.endfor - -.include <bsd.port.mk> diff --git a/science/cp2k/distinfo b/science/cp2k/distinfo deleted file mode 100644 index 842610dcc942..000000000000 --- a/science/cp2k/distinfo +++ /dev/null @@ -1,7 +0,0 @@ -TIMESTAMP = 1554565553 -SHA256 (cp2k-cp2k-v6.1.0_GH0.tar.gz) = d7dd5f164e1e51d2dcb8c7d927b99f6ac1d0f8de4a665bd9daee1a14864c30ae -SIZE (cp2k-cp2k-v6.1.0_GH0.tar.gz) = 63576088 -SHA256 (f03e6277feea9a65d543ca6c1184f58d3e83bc2a.patch) = 5c7a010738e52cd9f0c8d8e10e3627dae7e2f05833cce343f87b0dbb7c7e6531 -SIZE (f03e6277feea9a65d543ca6c1184f58d3e83bc2a.patch) = 1418 -SHA256 (d00a71c4d0276aab849ac6a6483b9dcdb65613c9.patch) = 4cf2a15b3b859b07f11e21bd2a928cb2ac78866a2174e06551c861e633eb112d -SIZE (d00a71c4d0276aab849ac6a6483b9dcdb65613c9.patch) = 3823 diff --git a/science/cp2k/files/patch-makefiles_Makefile b/science/cp2k/files/patch-makefiles_Makefile deleted file mode 100644 index 94f4180a7370..000000000000 --- a/science/cp2k/files/patch-makefiles_Makefile +++ /dev/null @@ -1,96 +0,0 @@ ---- makefiles/Makefile.orig 2018-09-04 19:11:12 UTC -+++ makefiles/Makefile -@@ -11,7 +11,7 @@ SHELL = /bin/sh - # also works fine - # - CP2KHOME := $(abspath $(PWD)/..) --ARCH := local -+XARCH := local - export VERSION=sopt - - MAKEFILE := $(CP2KHOME)/makefiles/Makefile -@@ -25,7 +25,7 @@ PRETTYOBJDIR := $(CP2KHOME)/obj/prettifi - DOXIFYOBJDIR := $(CP2KHOME)/obj/doxified - TOOLSRC := $(CP2KHOME)/tools - SRCDIR := $(CP2KHOME)/src --EXEDIR := $(MAINEXEDIR)/$(ARCH) -+EXEDIR := $(MAINEXEDIR)/$(XARCH) - REVISION := $(shell $(CP2KHOME)/tools/build_utils/get_revision_number $(SRCDIR)) - - -@@ -39,10 +39,10 @@ EXE_NAMES := $(basename $(notdir $(ALL_E - # this only happens on stage 3 and 4 - ifneq ($(ONEVERSION),) - MODDEPS = "lower" --include $(CP2KHOME)/arch/$(ARCH).$(ONEVERSION) --LIBDIR := $(MAINLIBDIR)/$(ARCH)/$(ONEVERSION) --OBJDIR := $(MAINOBJDIR)/$(ARCH)/$(ONEVERSION) --TSTDIR := $(MAINTSTDIR)/$(ARCH)/$(ONEVERSION) -+include $(CP2KHOME)/arch/$(XARCH).$(ONEVERSION) -+LIBDIR := $(MAINLIBDIR)/$(XARCH)/$(ONEVERSION) -+OBJDIR := $(MAINOBJDIR)/$(XARCH)/$(ONEVERSION) -+TSTDIR := $(MAINTSTDIR)/$(XARCH)/$(ONEVERSION) - ifeq ($(NVCC),) - EXE_NAMES := $(basename $(notdir $(filter-out %.cu, $(ALL_EXE_FILES)))) - endif -@@ -130,7 +130,7 @@ all: dirs makedep - - # foreground testing, compilation happens in do_regtest - test: dirs -- cd $(TSTDIR); $(TOOLSRC)/regtesting/do_regtest -nosvn -quick -arch $(ARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) -+ cd $(TSTDIR); $(TOOLSRC)/regtesting/do_regtest -nosvn -quick -arch $(XARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) - - # background testing, compilation happens here - testbg: dirs makedep all -@@ -191,7 +191,7 @@ $(LIBDIR)/libcp2k$(ARCHIVE_EXT) : $(ALL_ - - testbg: - @echo "testing: $(ONEVERSION) : full log in $(TSTDIR)/regtest.log " -- @$(TOOLSRC)/regtesting/do_regtest -nobuild -nosvn -arch $(ARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) >& $(TSTDIR)/regtest.log -+ @$(TOOLSRC)/regtesting/do_regtest -nobuild -nosvn -arch $(XARCH) -version $(ONEVERSION) -cp2kdir ../../../ $(TESTOPTS) >& $(TSTDIR)/regtest.log - @cat `grep 'regtesting location error_summary file:' $(TSTDIR)/regtest.log | awk '{print $$NF}'` - @cat `grep 'regtesting location summary file:' $(TSTDIR)/regtest.log | awk '{print $$NF}'` - @grep "Number of FAILED tests 0" $(TSTDIR)/regtest.log >& /dev/null -@@ -244,9 +244,9 @@ define get_extensions - endef - clean: - rm -rf $(LIBCUSMM_ABS_DIR)/libcusmm.cu $(LIBCUSMM_ABS_DIR)/libcusmm_part*.cu -- @echo rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(ARCH)/$(v)) -- @$(foreach v, $(VERSION), $(foreach ext, $(call get_extensions, $(MAINOBJDIR)/$(ARCH)/$(v)/), $(shell rm -rf $(MAINOBJDIR)/$(ARCH)/$(v)/*.$(ext)))) -- rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(ARCH)/$(v)) -+ @echo rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(XARCH)/$(v)) -+ @$(foreach v, $(VERSION), $(foreach ext, $(call get_extensions, $(MAINOBJDIR)/$(XARCH)/$(v)/), $(shell rm -rf $(MAINOBJDIR)/$(XARCH)/$(v)/*.$(ext)))) -+ rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(XARCH)/$(v)) - OTHER_HELP += "clean : Remove intermediate object and mod files, but not the libraries and executables, for given ARCH and VERSION" - - execlean: -@@ -258,16 +258,16 @@ OTHER_HELP += "execlean : Remove the exe - # Use this if you want to fully rebuild an executable (for a given compiler and or VERSION) - # - realclean: clean execlean -- rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(ARCH)/$(v)) -- rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(ARCH)/$(v)) -+ rm -rf $(foreach v, $(VERSION), $(MAINOBJDIR)/$(XARCH)/$(v)) -+ rm -rf $(foreach v, $(VERSION), $(MAINLIBDIR)/$(XARCH)/$(v)) - OTHER_HELP += "realclean : Remove all files for given ARCH and VERSION" - - testclean: -- rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(ARCH)/$(v)/TEST-*) -+ rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(XARCH)/$(v)/TEST-*) - OTHER_HELP += "testclean : Remove all TEST-* files for given ARCH and VERSION" - - testrealclean: testclean -- rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(ARCH)/$(v)/LAST-*) -+ rm -rf $(foreach v, $(VERSION), $(MAINTSTDIR)/$(XARCH)/$(v)/LAST-*) - OTHER_HELP += "testrealclean : Remove all LAST-* and TEST-* files for given ARCH and VERSION" - - # -@@ -426,7 +426,7 @@ endif - - # some practical variables for the build - ifeq ($(CPPSHELL),) --CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ -+CPPSHELL := -D__COMPILE_ARCH="\"$(XARCH)\""\ - -D__COMPILE_DATE="\"$(shell date)\""\ - -D__COMPILE_HOST="\"$(shell hostname)\""\ - -D__COMPILE_REVISION="\"$(strip $(REVISION))\""\ diff --git a/science/cp2k/pkg-descr b/science/cp2k/pkg-descr deleted file mode 100644 index 1fd0f215eaa7..000000000000 --- a/science/cp2k/pkg-descr +++ /dev/null @@ -1,12 +0,0 @@ -CP2K is a quantum chemistry and solid state physics software package that can -perform atomistic simulations of solid state, liquid, molecular, periodic, -material, crystal, and biological systems. CP2K provides a general framework for -different modeling methods such as DFT using the mixed Gaussian and plane waves -approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, -RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, ...), and classical force -fields (AMBER, CHARMM, ...). CP2K can do simulations of molecular dynamics, -metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level -spectroscopy, energy minimization, and transition state optimization using NEB -or dimer method. - -WWW: https://www.cp2k.org/ diff --git a/science/esys-particle/Makefile b/science/esys-particle/Makefile deleted file mode 100644 index b8c8d6799c59..000000000000 --- a/science/esys-particle/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -# $FreeBSD$ - -PORTNAME= esys-particle -DISTVERSION= 2.3.5 -PORTREVISION= 7 -CATEGORIES= science -MASTER_SITES= https://launchpad.net/${PORTNAME}/trunk/${DISTVERSION}/+download/ -DISTNAME= ESyS-Particle-${DISTVERSION} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Particle-based numerical modelling software - -LICENSE= APACHE20 - -BROKEN= The upstream doesn't answer bug reports: https://bugs.launchpad.net/esys-particle/+bug/1808617 -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -LIB_DEPENDS= libboost_system.so:devel/boost-libs \ - libmpi.so:net/mpich - -USES= cmake fortran -USE_LDCONFIG= yes - -LDFLAGS+= ${LOCALBASE}/lib/libboost_filesystem.so - -pre-build: - @${ECHO} "static int s_bzr_revision=-1;" > ${WRKSRC}/bzrversion.h - -.include <bsd.port.mk> diff --git a/science/esys-particle/distinfo b/science/esys-particle/distinfo deleted file mode 100644 index f9d0dc5d5eb9..000000000000 --- a/science/esys-particle/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1541392871 -SHA256 (ESyS-Particle-2.3.5.tar.gz) = 97f53fd0056c8f90771e1e2ff91bcea67a419bc68fcd91c68f7df76339680888 -SIZE (ESyS-Particle-2.3.5.tar.gz) = 8197209 diff --git a/science/esys-particle/files/patch-CMakeLists.txt b/science/esys-particle/files/patch-CMakeLists.txt deleted file mode 100644 index 97f2e0b56b98..000000000000 --- a/science/esys-particle/files/patch-CMakeLists.txt +++ /dev/null @@ -1,22 +0,0 @@ ---- CMakeLists.txt.orig 2017-01-06 06:14:00 UTC -+++ CMakeLists.txt -@@ -2,8 +2,8 @@ PROJECT(Esys C CXX) - CMAKE_MINIMUM_REQUIRED(VERSION 2.8) - - --FIND_PACKAGE(Boost COMPONENTS system filesystem python thread REQUIRED) --INCLUDE(FindPythonLibs) -+FIND_PACKAGE(Boost COMPONENTS system filesystem thread REQUIRED) -+#INCLUDE(FindPythonLibs) - - INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}) - INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/Foundation) -@@ -25,7 +25,7 @@ ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/To - ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/ntable") - ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/tml") - ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/ppa/src") --ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Python") -+#ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Python") - - - ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/Parallel") diff --git a/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp b/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp deleted file mode 100644 index 5206377f0713..000000000000 --- a/science/esys-particle/files/patch-Geometry_SphAggGougeBlock.hpp +++ /dev/null @@ -1,11 +0,0 @@ ---- Geometry/SphAggGougeBlock.hpp.orig 2018-11-05 04:51:07 UTC -+++ Geometry/SphAggGougeBlock.hpp -@@ -36,7 +36,7 @@ namespace esys { - void SphAggGougeBlock::visitParticles(TmplVisitor& visitor) const - { - GougeBlock3D::visitParticles(visitor); -- for(vector<SBG_ptr>::iterator it = m_grainParticleGen.begin(); -+ for(auto it = m_grainParticleGen.begin(); - it != m_grainParticleGen.end(); - it++) - { diff --git a/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp b/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp deleted file mode 100644 index 84fe9a0d33f3..000000000000 --- a/science/esys-particle/files/patch-Tools_StressCalculator_Contact.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- Tools/StressCalculator/Contact.cpp.orig 2018-11-05 04:44:17 UTC -+++ Tools/StressCalculator/Contact.cpp -@@ -18,7 +18,7 @@ namespace esys - namespace lsm - { - bool ParticleData::s_is3d = true; -- const double ParticleData::FOUR_THIRDS_PI = ((4.0/3.0)*M_PIl); -+ const double ParticleData::FOUR_THIRDS_PI = ((4.0/3.0)*M_PI); - } - } - diff --git a/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp b/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp deleted file mode 100644 index 28c517c68025..000000000000 --- a/science/esys-particle/files/patch-Tools_dump2vtk_frame__vtk.cpp +++ /dev/null @@ -1,11 +0,0 @@ ---- Tools/dump2vtk/frame_vtk.cpp.orig 2018-11-05 04:45:11 UTC -+++ Tools/dump2vtk/frame_vtk.cpp -@@ -1276,7 +1276,7 @@ void writeMeshFile(const string& infilen - string header,skip; - int numMeshIG; - -- while (datafile >> header != NULL){ -+ while (datafile >> header){ - if (header == "TMIG"){ - datafile >> numMeshIG; - for(int ni=0;ni<numMeshIG;ni++){ diff --git a/science/esys-particle/pkg-descr b/science/esys-particle/pkg-descr deleted file mode 100644 index abbb8592e1b6..000000000000 --- a/science/esys-particle/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -ESyS-Particle is Open Source Software for particle-based numerical modelling -using the Discrete Element Method (DEM); a widely adapted technique for -modelling processes involving large deformations, granular flow and/or -fragmentation. ESyS-Particle is best suited for execution on parallel -supercomputers, clusters or multi-core PCs running a Linux-based operating -system. The C++ DEM simulation engine implements spatial domain decomposition -via the Message Passing Interface (MPI). - -WWW: http://www.esys-particle.org/wiki/ diff --git a/science/esys-particle/pkg-plist b/science/esys-particle/pkg-plist deleted file mode 100644 index 8da97b057ffe..000000000000 --- a/science/esys-particle/pkg-plist +++ /dev/null @@ -1,19 +0,0 @@ -bin/dump2geo -bin/dump2vtk -bin/fcconv -bin/fracextract -bin/grainextract -bin/raw2tostress -bin/rotextract -bin/strainextract -lib/libFields.so -lib/libFoundation.so -lib/libGeometry.so -lib/libModel.so -lib/libParallel.so -lib/libTmlComm.so -lib/libTmlMessage.so -lib/libTmlType.so -lib/liblibppa.so -lib/libntable.so -lib/libpis.so diff --git a/science/openmx/Makefile b/science/openmx/Makefile deleted file mode 100644 index 3ddb73e7198a..000000000000 --- a/science/openmx/Makefile +++ /dev/null @@ -1,75 +0,0 @@ -# $FreeBSD$ - -PORTNAME= openmx -DISTVERSION= 3.8.5 # the 18June12 patch upgrades 3.8 -> 3.8.5 -PORTREVISION= 7 -CATEGORIES= science -MASTER_SITES= http://www.openmx-square.org/ \ - http://www.openmx-square.org/bugfixed/18June12/:patch -DISTFILES= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} \ - patch${DISTVERSION}${EXTRACT_SUFX}:patch # this patch isn't a patch, but a set of file updates -DIST_SUBDIR= ${PORTNAME} -EXTRACT_ONLY= ${PORTNAME}${DISTVERSION:R}${EXTRACT_SUFX} - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Nanoscale material simulations using density functional theories (DFT) - -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -LICENSE= GPLv2 - -BROKEN_i386= undefined reference to `__atomic_load', see bug#229605 and https://reviews.llvm.org/D42154 - -LIB_DEPENDS= libblas.so:math/blas \ - libfftw3.so:math/fftw3 \ - liblapack.so:math/lapack \ - libmpich.so:net/mpich - -USES= dos2unix fortran gmake localbase:ldflags -DOS2UNIX_FILES= openmx_common.h -USE_CXXSTD= c++11 -MAKEFILE= makefile - -WRKSRC= ${WRKDIR}/${PORTNAME}${DISTVERSION:R} - -CFLAGS+= -Dkcomp -LDFLAGS+= ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so ${LOCALBASE}/lib/libmpifort.so - -WRKSRC_SUBDIR= source - -MAKE_ENV= MPICH_CC=${CC} -MAKE_ARGS+= CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}" LDFLAGS="${LDFLAGS}" GCC_LIB=${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgfortran.so - -BINARY_ALIAS= gcc=${CXX} gcc7=${CXX} - -UTIL_PROGS= DosMain jx analysis_example esp polB bandgnu13 bin2txt cube2xsf intensity_map md2axsf - -PLIST_FILES= bin/${PORTNAME} ${UTIL_PROGS:C/^/bin\//} - -OPTIONS_DEFINE_amd64= SIMD -OPTIONS_DEFINE_i386= SIMD -OPTIONS_DEFAULT_amd64= SIMD -OPTIONS_DEFAULT_i386= SIMD - -SIMD_CFLAGS= -msse -msse2 -mfpmath=sse -SIMD_CFLAGS_OFF= -Dnosse -CFLAGS+= ${ARCH:S/amd64//:S/i386//:S/${ARCH}/-Dnosse/} - -pre-patch: # overlay files before patching - @cd ${WRKSRC} && ${TAR} xzf ${DISTDIR}/${DIST_SUBDIR}/patch${DISTVERSION}${EXTRACT_SUFX} - -post-patch: - @cd ${WRKSRC} && ${REINPLACE_CMD} 's|DFT_DATA_PATH|"${DATADIR}/DFT_DATA13"|' Input_std.c check_lead.c SetPara_DFT.c OutData.c OutData_Binary.c - -post-install: -.for u in ${UTIL_PROGS} - ${INSTALL_PROGRAM} ${WRKSRC}/${u} ${STAGEDIR}${PREFIX}/bin -.endfor - cd ${WRKSRC}/.. && ${COPYTREE_SHARE} DFT_DATA13 ${STAGEDIR}${DATADIR} - # autoplist for potentials: about 500 files in DATADIR - @cd ${STAGEDIR}${PREFIX} && \ - ${FIND} ${DATADIR:S/^${PREFIX}\///} -type f >> ${TMPPLIST} - -.include <bsd.port.mk> diff --git a/science/openmx/distinfo b/science/openmx/distinfo deleted file mode 100644 index 9794f107d104..000000000000 --- a/science/openmx/distinfo +++ /dev/null @@ -1,5 +0,0 @@ -TIMESTAMP = 1536713126 -SHA256 (openmx/openmx3.8.tar.gz) = 36ee10d8b1587b25a2ca1d57f110111be65c4fb4dc820e6d93e1ed2b562634a1 -SIZE (openmx/openmx3.8.tar.gz) = 143086177 -SHA256 (openmx/patch3.8.5.tar.gz) = d0fea2ce956d796a87a4bc9e9d580fb115ff2a22764650fffa78bb79a1b30468 -SIZE (openmx/patch3.8.5.tar.gz) = 316333 diff --git a/science/openmx/files/patch-Band__DFT__Col.c b/science/openmx/files/patch-Band__DFT__Col.c deleted file mode 100644 index a22e95c8e542..000000000000 --- a/science/openmx/files/patch-Band__DFT__Col.c +++ /dev/null @@ -1,15 +0,0 @@ ---- Band_DFT_Col.c.orig 2018-08-29 06:24:38 UTC -+++ Band_DFT_Col.c -@@ -483,9 +483,9 @@ double Band_DFT_Col(int SCF_iter, - - /* allocation */ - -- stat_send = malloc(sizeof(MPI_Status)*numprocs2); -- request_send = malloc(sizeof(MPI_Request)*numprocs2); -- request_recv = malloc(sizeof(MPI_Request)*numprocs2); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs2); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); - - is1 = (int*)malloc(sizeof(int)*numprocs2); - ie1 = (int*)malloc(sizeof(int)*numprocs2); diff --git a/science/openmx/files/patch-Band__DFT__NonCol.c b/science/openmx/files/patch-Band__DFT__NonCol.c deleted file mode 100644 index dfbcc2493215..000000000000 --- a/science/openmx/files/patch-Band__DFT__NonCol.c +++ /dev/null @@ -1,15 +0,0 @@ ---- Band_DFT_NonCol.c.orig 2018-08-29 06:26:10 UTC -+++ Band_DFT_NonCol.c -@@ -554,9 +554,9 @@ double Band_DFT_NonCol(int SCF_iter, - - /* allocation */ - -- stat_send = malloc(sizeof(MPI_Status)*numprocs1); -- request_send = malloc(sizeof(MPI_Request)*numprocs1); -- request_recv = malloc(sizeof(MPI_Request)*numprocs1); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs1); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs1); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs1); - - is1 = (int*)malloc(sizeof(int)*numprocs1); - ie1 = (int*)malloc(sizeof(int)*numprocs1); diff --git a/science/openmx/files/patch-Cluster__DFT.c b/science/openmx/files/patch-Cluster__DFT.c deleted file mode 100644 index cbf76c632080..000000000000 --- a/science/openmx/files/patch-Cluster__DFT.c +++ /dev/null @@ -1,46 +0,0 @@ ---- Cluster_DFT.c.orig 2018-08-29 06:05:22 UTC -+++ Cluster_DFT.c -@@ -194,9 +194,9 @@ static double Cluster_collinear( - - Num_Comm_World1 = SpinP_switch + 1; - -- stat_send = malloc(sizeof(MPI_Status)*numprocs0); -- request_send = malloc(sizeof(MPI_Request)*numprocs0); -- request_recv = malloc(sizeof(MPI_Request)*numprocs0); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs0); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs0); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs0); - - /*********************************************** - allocation of arrays for the first world -@@ -1541,9 +1541,9 @@ static double Cluster_non_collinear( - - /* allocation of arrays */ - -- stat_send = malloc(sizeof(MPI_Status)*numprocs); -- request_send = malloc(sizeof(MPI_Request)*numprocs); -- request_recv = malloc(sizeof(MPI_Request)*numprocs); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); - - /**************************************************** - calculation of the array size -@@ -2649,7 +2649,7 @@ void Save_DOS_Col(int n, int MaxN, int * - MPI_Comm_size(mpi_comm_level1,&numprocs); - MPI_Comm_rank(mpi_comm_level1,&myid); - -- request_recv = malloc(sizeof(MPI_Request)*numprocs); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); - - /* open file pointers */ - -@@ -2901,7 +2901,7 @@ void Save_DOS_NonCol(int n, int MaxN, in - MPI_Comm_size(mpi_comm_level1,&numprocs); - MPI_Comm_rank(mpi_comm_level1,&myid); - -- request_recv = malloc(sizeof(MPI_Request)*numprocs); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs); - - /* open file pointers */ - diff --git a/science/openmx/files/patch-Cluster__DFT__ON2.c b/science/openmx/files/patch-Cluster__DFT__ON2.c deleted file mode 100644 index 8c9a7660b1f4..000000000000 --- a/science/openmx/files/patch-Cluster__DFT__ON2.c +++ /dev/null @@ -1,23 +0,0 @@ ---- Cluster_DFT_ON2.c.orig 2016-03-27 06:53:28 UTC -+++ Cluster_DFT_ON2.c -@@ -10,6 +10,7 @@ - - ***********************************************************************/ - -+#include <complex.h> - #include <stdio.h> - #include <stdlib.h> - #include <string.h> -@@ -1275,9 +1276,9 @@ static void OND_Solver( - MPI_Request *request_send; - MPI_Request *request_recv; - -- stat_send = malloc(sizeof(MPI_Status)*numprocs2); -- request_send = malloc(sizeof(MPI_Request)*numprocs2); -- request_recv = malloc(sizeof(MPI_Request)*numprocs2); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*numprocs2); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*numprocs2); - - al.r = 1.0; - al.i = 0.0; diff --git a/science/openmx/files/patch-Input__std.c b/science/openmx/files/patch-Input__std.c deleted file mode 100644 index d8e1325a911b..000000000000 --- a/science/openmx/files/patch-Input__std.c +++ /dev/null @@ -1,11 +0,0 @@ ---- Input_std.c.orig 2018-09-12 02:18:32 UTC -+++ Input_std.c -@@ -85,7 +85,7 @@ void Input_std(char *file) - - input_string("System.CurrrentDirectory",filepath,"./"); - input_string("System.Name",filename,"default"); -- input_string("DATA.PATH",DFT_DATA_PATH,"../DFT_DATA13"); -+ //input_string("DATA.PATH",DFT_DATA_PATH,"../DFT_DATA13"); - input_int("level.of.stdout", &level_stdout,1); - input_int("level.of.fileout",&level_fileout,1); - input_logical("memory.usage.fileout",&memoryusage_fileout,0); /* default=off */ diff --git a/science/openmx/files/patch-Mixing__H.c b/science/openmx/files/patch-Mixing__H.c deleted file mode 100644 index ff3e86664dae..000000000000 --- a/science/openmx/files/patch-Mixing__H.c +++ /dev/null @@ -1,218 +0,0 @@ ---- Mixing_H.c.orig 2018-08-29 05:53:55 UTC -+++ Mixing_H.c -@@ -74,7 +74,7 @@ void Pulay_Mixing_H_MultiSecant(int MD_i - double sum,my_sum,tmp1,tmp2,alpha; - double r,r10,r11,r12,r13,r20,r21,r22; - double h,h10,h11,h12,h13,h20,h21,h22; -- double my_sy,my_yy,sy,yy,norm,s,y,or,al,be; -+ double my_sy,my_yy,sy,yy,norm,s,y,orx,al,be; - double **A,**IA,*coes,*coes2,*ror; - char nanchar[300]; - -@@ -635,44 +635,44 @@ void Pulay_Mixing_H_MultiSecant(int MD_i - s = HisH1[m][0][Mc_AN][h_AN][i][j] - HisH1[m+1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[m][0][Mc_AN][h_AN][i][j] - ResidualH1[m+1][0][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH1[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH1[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH1[m][1][Mc_AN][h_AN][i][j] - HisH1[m+1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[m][1][Mc_AN][h_AN][i][j] - ResidualH1[m+1][1][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH1[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH1[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH1[m][2][Mc_AN][h_AN][i][j] - HisH1[m+1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[m][2][Mc_AN][h_AN][i][j] - ResidualH1[m+1][2][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH1[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH1[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH1[m][3][Mc_AN][h_AN][i][j] - HisH1[m+1][3][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[m][3][Mc_AN][h_AN][i][j] - ResidualH1[m+1][3][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH1[dim+1][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH1[dim+1][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH2[m][0][Mc_AN][h_AN][i][j] - HisH2[m+1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[m][0][Mc_AN][h_AN][i][j] - ResidualH2[m+1][0][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH2[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH2[dim+1][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH2[m][1][Mc_AN][h_AN][i][j] - HisH2[m+1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[m][1][Mc_AN][h_AN][i][j] - ResidualH2[m+1][1][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH2[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH2[dim+1][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - s = HisH2[m][2][Mc_AN][h_AN][i][j] - HisH2[m+1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[m][2][Mc_AN][h_AN][i][j] - ResidualH2[m+1][2][Mc_AN][h_AN][i][j]; /* y */ - r = s - al*y; /* r */ -- or = ResidualH2[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += r*or; -+ orx = ResidualH2[dim+1][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += r*orx; - - } - } -@@ -696,8 +696,8 @@ void Pulay_Mixing_H_MultiSecant(int MD_i - s = HisH1[m][spin][Mc_AN][h_AN][i][j] - HisH1[m+1][spin][Mc_AN][h_AN][i][j]; - y = ResidualH1[m][spin][Mc_AN][h_AN][i][j] - ResidualH1[m+1][spin][Mc_AN][h_AN][i][j]; - r = s - al*y; -- or = ResidualH1[dim+1][spin][Mc_AN][h_AN][i][j]; -- my_sum += r*or; -+ orx = ResidualH1[dim+1][spin][Mc_AN][h_AN][i][j]; -+ my_sum += r*orx; - } - } - } -@@ -986,7 +986,7 @@ void Pulay_Mixing_H_with_One_Shot_Hessia - double my_sum,tmp1,tmp2,alpha; - double r,r10,r11,r12,r13,r20,r21,r22; - double h,h10,h11,h12,h13,h20,h21,h22; -- double my_sy,my_yy,sy,yy,norm,s,y,or,al,be; -+ double my_sy,my_yy,sy,yy,norm,s,y,orx,al,be; - double **A,**IA,*coes; - char nanchar[300]; - -@@ -1427,38 +1427,38 @@ void Pulay_Mixing_H_with_One_Shot_Hessia - - s = HisH1[0][0][Mc_AN][h_AN][i][j] - HisH1[1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][0][Mc_AN][h_AN][i][j] - ResidualH1[1][0][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH1[0][1][Mc_AN][h_AN][i][j] - HisH1[1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][1][Mc_AN][h_AN][i][j] - ResidualH1[1][1][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH1[0][2][Mc_AN][h_AN][i][j] - HisH1[1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][2][Mc_AN][h_AN][i][j] - ResidualH1[1][2][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH1[0][3][Mc_AN][h_AN][i][j] - HisH1[1][3][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][3][Mc_AN][h_AN][i][j] - ResidualH1[1][3][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH2[0][0][Mc_AN][h_AN][i][j] - HisH2[1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][0][Mc_AN][h_AN][i][j] - ResidualH2[1][0][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH2[0][1][Mc_AN][h_AN][i][j] - HisH2[1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][1][Mc_AN][h_AN][i][j] - ResidualH2[1][1][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - - s = HisH2[0][2][Mc_AN][h_AN][i][j] - HisH2[1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][2][Mc_AN][h_AN][i][j] - ResidualH2[1][2][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - } - } - } -@@ -1479,8 +1479,8 @@ void Pulay_Mixing_H_with_One_Shot_Hessia - for (j=0; j<Spe_Total_NO[Hwan]; j++){ - s = HisH1[0][spin][Mc_AN][h_AN][i][j] - HisH1[1][spin][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][spin][Mc_AN][h_AN][i][j] - ResidualH1[1][spin][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- my_sum += (s-al*y)*or; -+ orx = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ my_sum += (s-al*y)*orx; - } - } - } -@@ -1541,38 +1541,38 @@ void Pulay_Mixing_H_with_One_Shot_Hessia - - s = HisH1[0][0][Mc_AN][h_AN][i][j] - HisH1[1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][0][Mc_AN][h_AN][i][j] - ResidualH1[1][0][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- H[0][Mc_AN][h_AN][i][j] = h10 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH1[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ H[0][Mc_AN][h_AN][i][j] = h10 - alpha*(al*orx + (s-al*y)*be); - - s = HisH1[0][1][Mc_AN][h_AN][i][j] - HisH1[1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][1][Mc_AN][h_AN][i][j] - ResidualH1[1][1][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- H[1][Mc_AN][h_AN][i][j] = h11 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH1[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ H[1][Mc_AN][h_AN][i][j] = h11 - alpha*(al*orx + (s-al*y)*be); - - s = HisH1[0][2][Mc_AN][h_AN][i][j] - HisH1[1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][2][Mc_AN][h_AN][i][j] - ResidualH1[1][2][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- H[2][Mc_AN][h_AN][i][j] = h12 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH1[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ H[2][Mc_AN][h_AN][i][j] = h12 - alpha*(al*orx + (s-al*y)*be); - - s = HisH1[0][3][Mc_AN][h_AN][i][j] - HisH1[1][3][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][3][Mc_AN][h_AN][i][j] - ResidualH1[1][3][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- H[3][Mc_AN][h_AN][i][j] = h13 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH1[dim][3][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ H[3][Mc_AN][h_AN][i][j] = h13 - alpha*(al*orx + (s-al*y)*be); - - s = HisH2[0][0][Mc_AN][h_AN][i][j] - HisH2[1][0][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][0][Mc_AN][h_AN][i][j] - ResidualH2[1][0][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- iHNL[0][Mc_AN][h_AN][i][j] = h20 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH2[dim][0][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ iHNL[0][Mc_AN][h_AN][i][j] = h20 - alpha*(al*orx + (s-al*y)*be); - - s = HisH2[0][1][Mc_AN][h_AN][i][j] - HisH2[1][1][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][1][Mc_AN][h_AN][i][j] - ResidualH2[1][1][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- iHNL[1][Mc_AN][h_AN][i][j] = h21 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH2[dim][1][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ iHNL[1][Mc_AN][h_AN][i][j] = h21 - alpha*(al*orx + (s-al*y)*be); - - s = HisH2[0][2][Mc_AN][h_AN][i][j] - HisH2[1][2][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH2[0][2][Mc_AN][h_AN][i][j] - ResidualH2[1][2][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- iHNL[2][Mc_AN][h_AN][i][j] = h22 - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH2[dim][2][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ iHNL[2][Mc_AN][h_AN][i][j] = h22 - alpha*(al*orx + (s-al*y)*be); - } - } - } -@@ -1599,8 +1599,8 @@ void Pulay_Mixing_H_with_One_Shot_Hessia - - s = HisH1[0][spin][Mc_AN][h_AN][i][j] - HisH1[1][spin][Mc_AN][h_AN][i][j]; /* s */ - y = ResidualH1[0][spin][Mc_AN][h_AN][i][j] - ResidualH1[1][spin][Mc_AN][h_AN][i][j]; /* y */ -- or = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ -- H[spin][Mc_AN][h_AN][i][j] = h - alpha*(al*or + (s-al*y)*be); -+ orx = ResidualH1[dim][spin][Mc_AN][h_AN][i][j]; /* OptResidualH */ -+ H[spin][Mc_AN][h_AN][i][j] = h - alpha*(al*orx + (s-al*y)*be); - - } - } diff --git a/science/openmx/files/patch-Poisson.c b/science/openmx/files/patch-Poisson.c deleted file mode 100644 index 6705c1abff28..000000000000 --- a/science/openmx/files/patch-Poisson.c +++ /dev/null @@ -1,84 +0,0 @@ ---- Poisson.c.orig 2018-08-29 05:58:06 UTC -+++ Poisson.c -@@ -141,8 +141,8 @@ void FFT_Poisson(double *ReRhor, double - allocation of arrays: - ****************************************************/ - -- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); - - /*------------------ FFT along the C-axis in the AB partition ------------------*/ - -@@ -182,10 +182,10 @@ void FFT_Poisson(double *ReRhor, double - array0 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_S[NN_B_AB2CA_S]); - array1 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_R[NN_B_AB2CA_R]); - -- request_send = malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); -- request_recv = malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); -- stat_send = malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); -- stat_recv = malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); -+ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); - - NN_S = 0; - NN_R = 0; -@@ -307,10 +307,10 @@ void FFT_Poisson(double *ReRhor, double - array0 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_S[NN_B_CA2CB_S]); - array1 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_R[NN_B_CA2CB_R]); - -- request_send = malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); -- request_recv = malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); -- stat_send = malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); -- stat_recv = malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); -+ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); - - NN_S = 0; - NN_R = 0; -@@ -503,8 +503,8 @@ void Inverse_FFT_Poisson(double *ReRhor, - fftw_complex out[List_YOUSO[17]]; - ****************************************************/ - -- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); - - /*------------------ Inverse FFT along the A-axis in the CB partition ------------------*/ - -@@ -544,10 +544,10 @@ void Inverse_FFT_Poisson(double *ReRhor, - array0 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_R[NN_B_CA2CB_R]); - array1 = (double*)malloc(sizeof(double)*2*GP_B_CA2CB_S[NN_B_CA2CB_S]); - -- request_send = malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); -- request_recv = malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); -- stat_send = malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); -- stat_recv = malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_R); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_CA2CB_S); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_R); -+ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_CA2CB_S); - - NN_S = 0; - NN_R = 0; -@@ -669,10 +669,10 @@ void Inverse_FFT_Poisson(double *ReRhor, - array0 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_R[NN_B_AB2CA_R]); - array1 = (double*)malloc(sizeof(double)*2*GP_B_AB2CA_S[NN_B_AB2CA_S]); - -- request_send = malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); -- request_recv = malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); -- stat_send = malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); -- stat_recv = malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); -+ request_send = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_R); -+ request_recv = (MPI_Request *)malloc(sizeof(MPI_Request)*NN_B_AB2CA_S); -+ stat_send = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_R); -+ stat_recv = (MPI_Status *)malloc(sizeof(MPI_Status)*NN_B_AB2CA_S); - - NN_S = 0; - NN_R = 0; diff --git a/science/openmx/files/patch-Poisson__ESM.c b/science/openmx/files/patch-Poisson__ESM.c deleted file mode 100644 index 19224a759e79..000000000000 --- a/science/openmx/files/patch-Poisson__ESM.c +++ /dev/null @@ -1,24 +0,0 @@ ---- Poisson_ESM.c.orig 2018-08-29 06:03:16 UTC -+++ Poisson_ESM.c -@@ -71,8 +71,8 @@ double Poisson_ESM(int fft_charge_flag, - fftw_complex out[List_YOUSO[17]]; - ****************************************************/ - -- in0 = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -- out0 = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ in0 = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ out0 = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); - - - if (myid==Host_ID) { -@@ -908,8 +908,8 @@ void One_dim_FFT(FILE *fp, - fftw_complex out[List_YOUSO[17]]; - ****************************************************/ - -- in = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -- out = fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ in = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); -+ out = (fftw_complex *)fftw_malloc(sizeof(fftw_complex)*List_YOUSO[17]); - - p = fftw_plan_dft_1d(Ngrid1, in, out, sgn2, FFTW_ESTIMATE); - diff --git a/science/openmx/files/patch-bandgnu13.c b/science/openmx/files/patch-bandgnu13.c deleted file mode 100644 index 3c6172bc62e6..000000000000 --- a/science/openmx/files/patch-bandgnu13.c +++ /dev/null @@ -1,11 +0,0 @@ ---- bandgnu13.c.orig 2018-09-11 19:33:10 UTC -+++ bandgnu13.c -@@ -75,7 +75,7 @@ void vk_rtv(double vk[4], double rtv[4][ - - #define MUNIT 2 - --main(int argc, char **argv) -+int main(int argc, char **argv) - { - static double Unit0[MUNIT]={27.2,1.0}; /* Hartree-> eV */ - static char *Unitname0[MUNIT]={"eV","Hartree"}; diff --git a/science/openmx/files/patch-makefile b/science/openmx/files/patch-makefile deleted file mode 100644 index 2a21aa3db1fe..000000000000 --- a/science/openmx/files/patch-makefile +++ /dev/null @@ -1,43 +0,0 @@ ---- makefile.orig 2016-04-02 12:43:42 UTC -+++ makefile -@@ -136,15 +136,15 @@ - # - - --CC = mpicc -O3 -xHOST -ip -no-prec-div -openmp -I/opt/intel/mkl/include/fftw --FC = mpif90 -O3 -xHOST -ip -no-prec-div -openmp --LIB= -L/opt/intel/mkl/lib -mkl=parallel -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lifcore -lmpi -lmpi_f90 -lmpi_f77 -+CC = mpicc $(CFLAGS) -fopenmp -+FC = mpif90 $(FFLAGS) -fopenmp -+LIB= $(LDFLAGS) -lpthread -llapack -lblas -lgfortran -lfftw3 -lomp - - - - - --CFLAGS = -g -+#CFLAGS = -g - - OBJS = openmx.o openmx_common.o Input_std.o Inputtools.o \ - init.o LU_inverse.o ReLU_inverse.o \ -@@ -661,7 +661,7 @@ Show_DFT_DATA.o: Show_DFT_DATA.c openmx_ - - install: $(PROG) - strip $(PROG) -- cp $(PROG) $(DESTDIR)/$(PROG) -+ install $(PROG) $(DESTDIR)$(PREFIX)/bin/$(PROG) - - # - # -@@ -889,9 +889,9 @@ TRAN_CDen_Main.o: TRAN_CDen_Main.c openm - - elpa1.o: elpa1.f90 - $(FC) -c elpa1.f90 --solve_evp_real.o: solve_evp_real.f90 -+solve_evp_real.o: solve_evp_real.f90 elpa1.o - $(FC) -c solve_evp_real.f90 --solve_evp_complex.o: solve_evp_complex.f90 -+solve_evp_complex.o: solve_evp_complex.f90 elpa1.o - $(FC) -c solve_evp_complex.f90 - - diff --git a/science/openmx/files/patch-tran__variables.h b/science/openmx/files/patch-tran__variables.h deleted file mode 100644 index 7d7d961603d6..000000000000 --- a/science/openmx/files/patch-tran__variables.h +++ /dev/null @@ -1,10 +0,0 @@ ---- tran_variables.h.orig 2018-08-29 05:50:14 UTC -+++ tran_variables.h -@@ -46,7 +46,6 @@ double TRAN_Poisson_Gpara_Scaling; - double ScaleSize_e[2]; - int SpinP_switch_e[2], atomnum_e[2], SpeciesNum_e[2], Max_FSNAN_e[2]; - int TCpyCell_e[2], Matomnum_e[2], MatomnumF_e[2], MatomnumS_e[2]; --int Latomnum,Ratomnum,Catomnum; - int *WhatSpecies_e[2]; - int *Spe_Total_CNO_e[2]; - int *Spe_Total_NO_e[2]; diff --git a/science/openmx/pkg-descr b/science/openmx/pkg-descr deleted file mode 100644 index edb2f2d3343f..000000000000 --- a/science/openmx/pkg-descr +++ /dev/null @@ -1,24 +0,0 @@ -OpenMX (Open source package for Material eXplorer) is a software package for -nano-scale material simulations based on density functional theories (DFT), -norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. -The methods and algorithms used in OpenMX and their implementation are carefully -designed for the realization of large-scale ab initio electronic structure -calculations on parallel computers based on the MPI or MPI/OpenMP hybrid -parallelism. The efficient implementation of DFT enables us to investigate -electronic, magnetic, and geometrical structures of a wide variety of materials -such as biological molecules, carbon-based materials, magnetic materials, and -nanoscale conductors. Systems consisting of 1000 atoms can be treated using the -conventional diagonalization method if several hundreds cores on a parallel -computer are used. Even ab initio electronic structure calculations for systems -consisting of more than 10000 atoms are possible with the O(N) method -implemented in OpenMX if several thousands cores on a parallel computer are -available. Since optimized pseudopotentials and basis functions, which are well -tested, are provided for many elements, users may be able to quickly start own -calculations without preparing those data by themselves. Considerable -functionalities have been implemented for calculations of physical properties -such as magnetic, dielectric, and electric transport properties. Thus, we expect -that OpenMX can be a useful and powerful theoretical tool for nano-scale -material sciences, leading to better and deeper understanding of complicated and -useful materials based on quantum mechanics. - -WWW: http://www.openmx-square.org/ diff --git a/science/p5-Geo-ReadGRIB/Makefile b/science/p5-Geo-ReadGRIB/Makefile deleted file mode 100644 index cc893e92cd0e..000000000000 --- a/science/p5-Geo-ReadGRIB/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Created by: Wen Heping <wenheping@gmail.com> -# $FreeBSD$ - -PORTNAME= Geo-ReadGRIB -PORTVERSION= 1.21 -PORTREVISION= 1 -CATEGORIES= science perl5 -MASTER_SITES= CPAN -PKGNAMEPREFIX= p5- - -MAINTAINER= wen@FreeBSD.org -COMMENT= Perl module provides read access to GRIB files - -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -USES= perl5 -USE_PERL5= configure - -.include <bsd.port.mk> diff --git a/science/p5-Geo-ReadGRIB/distinfo b/science/p5-Geo-ReadGRIB/distinfo deleted file mode 100644 index e3876cfbfae6..000000000000 --- a/science/p5-Geo-ReadGRIB/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (Geo-ReadGRIB-1.21.tar.gz) = fdcd194790d1813668a18f9ecd787da15d2f1d50ff935c9263d303981acfe10c -SIZE (Geo-ReadGRIB-1.21.tar.gz) = 894058 diff --git a/science/p5-Geo-ReadGRIB/pkg-descr b/science/p5-Geo-ReadGRIB/pkg-descr deleted file mode 100644 index 043b04bbc03e..000000000000 --- a/science/p5-Geo-ReadGRIB/pkg-descr +++ /dev/null @@ -1,6 +0,0 @@ -Geo::ReadGRIB is an object Perl module that provides read -access to data distributed in GRIB files. Specifically, -it is wrote to access NOAA Wavewatch III marine weather -model forecasts which are packaged as GRIB. - -WWW: https://metacpan.org/release/Geo-ReadGRIB diff --git a/science/p5-Geo-ReadGRIB/pkg-plist b/science/p5-Geo-ReadGRIB/pkg-plist deleted file mode 100644 index b82a241b79e4..000000000000 --- a/science/p5-Geo-ReadGRIB/pkg-plist +++ /dev/null @@ -1,9 +0,0 @@ -%%SITE_PERL%%/Geo/wgrib.exe -%%SITE_PERL%%/Geo/ReadGRIB.pm -%%SITE_PERL%%/Geo/Sample-GRIB/akw.HTSGW.grb -%%SITE_PERL%%/Geo/Sample-GRIB/2009100900_P000.grib -%%SITE_PERL%%/Geo/ReadGRIB/PlaceIterator.pm -%%SITE_PERL%%/Geo/ReadGRIB/Place.pm -%%PERL5_MAN3%%/Geo::ReadGRIB.3.gz -%%PERL5_MAN3%%/Geo::ReadGRIB::Place.3.gz -%%PERL5_MAN3%%/Geo::ReadGRIB::PlaceIterator.3.gz diff --git a/science/py-tensorflow-estimator/Makefile b/science/py-tensorflow-estimator/Makefile deleted file mode 100644 index 1d302a3041f4..000000000000 --- a/science/py-tensorflow-estimator/Makefile +++ /dev/null @@ -1,54 +0,0 @@ -# $FreeBSD$ - -PORTNAME= tensorflow-estimator -DISTVERSIONPREFIX= v -DISTVERSION= 1.14.0 -PORTREVISION= 1 -CATEGORIES= science python -PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} - -MAINTAINER= amzo1337@gmail.com -COMMENT= TensorFlow Estimator, an API to simplify machine learning programming - -LICENSE= APACHE20 - -BROKEN= fails to build -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2020-05-05 - -BUILD_DEPENDS= bash:shells/bash \ - bazel:devel/bazel029 \ - ${PYTHON_PKGNAMEPREFIX}tensorflow>=1.14.0:science/py-tensorflow@${PY_FLAVOR} - -USES= python shebangfix -SHEBANG_GLOB= *.py -USE_GITHUB= yes -GH_ACCOUNT= tensorflow -GH_PROJECT= estimator - -NO_ARCH= yes - -BAZEL_BOOT= --output_user_root=${WRKDIR}/bazel_out - -post-patch: - @${REINPLACE_CMD} "s#%%PYTHON%%#${PYTHON_CMD}#" \ - ${WRKSRC}/tensorflow_estimator/tools/pip_package/build_pip_package.sh - -do-build: - @cd ${WRKSRC} && \ - bazel ${BAZEL_BOOT} build -s \ - //tensorflow_estimator/tools/pip_package:build_pip_package - @cd ${WRKSRC} && ${SETENV} TMPDIR=${WRKDIR} && \ - bazel-bin/tensorflow_estimator/tools/pip_package/build_pip_package \ - ${WRKDIR}/whl - -do-install: - @${MKDIR} ${STAGEDIR}/${PYTHON_SITELIBDIR} - @${MKDIR} ${WRKDIR}/tmp - @${UNZIP_NATIVE_CMD} -d ${WRKDIR}/tmp ${WRKDIR}/whl/${PORTNAME:S/-/_/}-${PORTVERSION}-*.whl - cd ${WRKDIR}/tmp && ${COPYTREE_SHARE} ${PORTNAME:S/-/_/} \ - ${STAGEDIR}${PYTHON_SITELIBDIR} - cd ${WRKDIR}/tmp && ${COPYTREE_SHARE} ${PORTNAME:S/-/_/}-${PORTVERSION}.dist-info \ - ${STAGEDIR}${PYTHON_SITELIBDIR} - -.include <bsd.port.mk> diff --git a/science/py-tensorflow-estimator/distinfo b/science/py-tensorflow-estimator/distinfo deleted file mode 100644 index eedb8d467e96..000000000000 --- a/science/py-tensorflow-estimator/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1565118650 -SHA256 (tensorflow-estimator-v1.14.0_GH0.tar.gz) = 1f0b80b8067a52cc33bbe390d34791eb3e12453c506daa1b4c8fc07fbf962d9f -SIZE (tensorflow-estimator-v1.14.0_GH0.tar.gz) = 670750 diff --git a/science/py-tensorflow-estimator/files/patch-tensorflow__estimator_tools_pip__package_build__pip__package.sh b/science/py-tensorflow-estimator/files/patch-tensorflow__estimator_tools_pip__package_build__pip__package.sh deleted file mode 100644 index f7d51529f643..000000000000 --- a/science/py-tensorflow-estimator/files/patch-tensorflow__estimator_tools_pip__package_build__pip__package.sh +++ /dev/null @@ -1,20 +0,0 @@ ---- tensorflow_estimator/tools/pip_package/build_pip_package.sh.orig 2019-06-11 17:18:02 UTC -+++ tensorflow_estimator/tools/pip_package/build_pip_package.sh -@@ -38,7 +38,7 @@ function prepare_src() { - - # Verifies all expected files are in pip. - # Creates init files in all directory in pip. -- python tensorflow_estimator/tools/pip_package/create_pip_helper.py --pip-root "${TMPDIR}/tensorflow_estimator/" --bazel-root "./tensorflow_estimator" -+ %%PYTHON%% tensorflow_estimator/tools/pip_package/create_pip_helper.py --pip-root "${TMPDIR}/tensorflow_estimator/" --bazel-root "./tensorflow_estimator" - } - - function build_wheel() { -@@ -53,7 +53,7 @@ function build_wheel() { - - pushd ${TMPDIR} > /dev/null - echo $(date) : "=== Building wheel" -- "${PYTHON_BIN_PATH:-python}" setup.py bdist_wheel --universal --project_name $PROJECT_NAME -+ %%PYTHON%% setup.py bdist_wheel --universal --project_name $PROJECT_NAME - mkdir -p ${DEST} - cp dist/* ${DEST} - popd > /dev/null diff --git a/science/py-tensorflow-estimator/pkg-descr b/science/py-tensorflow-estimator/pkg-descr deleted file mode 100644 index 7f650a3d96a4..000000000000 --- a/science/py-tensorflow-estimator/pkg-descr +++ /dev/null @@ -1,5 +0,0 @@ -TensorFlow Estimator is a high-level TensorFlow API that greatly -simplifies machine learning programming. Estimators encapsulate -training, evaluation, prediction, and exporting for your model. - -WWW: https://github.com/tensorflow/estimator diff --git a/science/py-tensorflow-estimator/pkg-plist b/science/py-tensorflow-estimator/pkg-plist deleted file mode 100644 index 1dfcd430389f..000000000000 --- a/science/py-tensorflow-estimator/pkg-plist +++ /dev/null @@ -1,133 +0,0 @@ -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/DESCRIPTION.rst -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/METADATA -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/RECORD -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/WHEEL -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/metadata.json -%%PYTHON_SITELIBDIR%%/tensorflow_estimator-1.14.0.dist-info/top_level.txt -%%PYTHON_SITELIBDIR%%/tensorflow_estimator/__init__.py -%%PYTHON_SITELIBDIR%%/tensorflow_estimator/_api/__init__.py -%%PYTHON_SITELIBDIR%%/tensorflow_estimator/_api/v1/__init__.py 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