science/berkeleygw: Update 2.0.0 -> 3.0.1

science/berkeleygw/Makefile

@@ -1,26 +1,30 @@
 PORTNAME=	BerkeleyGW
-DISTVERSION=	2.0.0
-PORTREVISION=	5
+DISTVERSION=	3.0.1
 CATEGORIES=	science
 MASTER_SITES=	https://berkeley.box.com/shared/static/
-DISTFILES=	wkqu37wu77tll53r8t1soe6ozqja67yy.gz
+DISTFILES=	m1dgnhiemo47lhxczrn6si71bwxoxor8.gz
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Scientific program aimed at the ab initio virtual experimentation
 
 LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/license.txt
 
+BUILD_DEPENDS=	bash:shells/bash
 LIB_DEPENDS=	libfftw3.so:math/fftw3
+RUN_DEPENDS=	bash:shells/bash
 
 USES=		blaslapack:openblas gmake fortran python shebangfix
+
 SHEBANG_GLOB=	*.sh *.py *awk
 
-WRKSRC=		${WRKDIR}/BGW-${DISTVERSION}
 BINARY_ALIAS=	make=${GMAKE} gcc=${CC}
+
 MAKE_ARGS=	FREEBSD_GCC_DEFAULT=${GCC_DEFAULT} FREEBSD_PREFIX=${PREFIX} INSTDIR=${STAGEDIR}${PREFIX}
 
-OPTIONS_DEFINE=	DOCS EXAMPLES
+TEST_TARGET=	check # 2 testcases fail: https://groups.google.com/a/berkeleygw.org/g/help/c/jVdxCAzM7A4
+
+OPTIONS_DEFINE=	EXAMPLES
 
 EXAMPLES_MAKE_ARGS=	INSTALL_EXAMPLES=yes
 
@@ -37,4 +41,7 @@ post-patch:
 	@${LN} -s ${WRKSRC}/flavor_real.mk ${WRKSRC}/flavor.mk
 	@${FIND} ${WRKSRC} -name "script*" -o -name "*.scr" | ${XARGS} ${REINPLACE_CMD} -i '' 's|#! */bin/bash.*|#!/bin/sh|'
 
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.x
+
 .include <bsd.port.post.mk>

science/berkeleygw/distinfo

@@ -1,3 +1,3 @@
-TIMESTAMP = 1535150795
-SHA256 (wkqu37wu77tll53r8t1soe6ozqja67yy.gz) = 887146cc6598a509a6d2a7b5044d12ebc5a4a2c7b028513f247fe62cf0861563
-SIZE (wkqu37wu77tll53r8t1soe6ozqja67yy.gz) = 71864027
+TIMESTAMP = 1653108006
+SHA256 (m1dgnhiemo47lhxczrn6si71bwxoxor8.gz) = 7d8c2cc1ee679afb48efbdd676689d4d537226b50e13a049dbcb052aaaf3654f
+SIZE (m1dgnhiemo47lhxczrn6si71bwxoxor8.gz) = 63370642

science/berkeleygw/files/patch-Makefile

@@ -1,31 +1,28 @@
---- Makefile.orig	2018-06-01 08:57:02 UTC
+--- Makefile.orig	2021-05-25 22:46:17 UTC
 +++ Makefile
-@@ -106,7 +106,7 @@ all-flavors:
- manual: printsvninfo
- 	bin/assemble_manual.sh > documentation/users/manual.html
+@@ -130,7 +130,7 @@ cplx:
+ 	cp flavor_cplx.mk flavor.mk
+ 	$(MAKE) all
 
 -install: all
 +install:
  ifdef INSTDIR
  	mkdir -p $(INSTDIR)/bin
  	install bin/*.x $(INSTDIR)/bin/
-@@ -119,12 +119,16 @@ ifdef INSTDIR
+@@ -143,11 +143,14 @@ ifdef INSTDIR
  	mkdir -p $(INSTDIR)/include
  	install library/*.mod $(INSTDIR)/include/
 
 -	mkdir -p $(INSTDIR)/share
  	mkdir -p $(INSTDIR)/share/BerkeleyGW
-+	mkdir -p $(INSTDIR)/share/doc/BerkeleyGW
  # install cannot work on a whole directory
 -	cp -rf examples  $(INSTDIR)/share/BerkeleyGW/
 +ifdef INSTALL_EXAMPLES
 +	mkdir -p $(INSTDIR)/share/examples/BerkeleyGW
 +	cp -rf examples  $(INSTDIR)/share/examples/BerkeleyGW
 +	find $(INSTDIR)/share/examples/BerkeleyGW -type d -empty -delete
-+endif
  	cp -rf testsuite $(INSTDIR)/share/BerkeleyGW/
--	install manual.html $(INSTDIR)/share/BerkeleyGW/
-+	install documentation/users/manual.html $(INSTDIR)/share/doc/BerkeleyGW/
++endif
  else
  	$(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.)
  endif

science/berkeleygw/pkg-plist

@@ -1,14 +1,15 @@
+bin/EXX.py
 bin/abi2bgw.x
 bin/abi2bgw_nc_h5.py
 bin/absorption.real.x
-bin/assemble_manual.sh
 bin/average.py
-bin/backport.sh
 bin/bgw2para.real.x
+bin/bgw2sgw.x
 bin/bseascbin.real.x
 bin/bsebinasc.real.x
 bin/bsemat_check.real.x
 bin/bsemat_hdf5_upgrade.py
+bin/check_eig.x
 bin/common.py
 bin/compare_wfns.py
 bin/convert.py
@@ -26,51 +27,62 @@ bin/epsmat_hdf5_merge.py
 bin/epsmat_merge.real.x
 bin/epsomega.real.x
 bin/eqp.py
+bin/eqp_convert.x
 bin/fix_occ.x
+bin/getbox.x
 bin/gsphere.py
 bin/icm.x
 bin/inteqp.real.x
 bin/kernel.real.x
 bin/kgrid.x
 bin/kptlist.pl
 bin/link.py
-bin/mako_preprocess.py
 bin/matrix.py
 bin/matter.py
+bin/merge_spin.py
 bin/mf_convert.x
 bin/mf_convert_wrapper.sh
 bin/nonlinearoptics.real.x
 bin/offdiag.real.x
 bin/parabands.real.x
 bin/ploteps.real.x
 bin/plotxct.real.x
+bin/print_version_info.x
 bin/printchi.real.x
-bin/printsvninfo.x
 bin/qp_shifts.py
 bin/qptlist.pl
 bin/rho2cd.x
 bin/sapo.real.x
+bin/scGWtool.py
 bin/scissors2eqp.x
-bin/setup_bse_subsample.x
+bin/setup_subsampling_csi.x
+bin/setup_subsampling_nns.x
 bin/siesta2bgw.real.x
 bin/sig2wan.x
 bin/sigma.real.x
 bin/split_spin.real.x
 bin/split_up_epsilon_pts.py
 bin/split_up_sigma_pts.py
-bin/subsample_plan.x
 bin/sum_degenerate_excitons.py
 bin/summarize_eigenvectors.real.x
 bin/surface.x
+bin/test_evecs.real.x
+bin/update_bse.py
 bin/volume.py
 bin/wfn_dotproduct.x
 bin/wfn_rho_vxc_info.x
 bin/wfn_time_reversal.x
 bin/wfnmerge.x
-include/intrinsics_m.mod
+include/check_inversion_m.mod
+include/global_m.mod
 include/message_m.mod
 include/nrtype_m.mod
+include/os_m.mod
 include/peinfo_m.mod
+include/push_pop_m.mod
+include/scalapack_aux_m.mod
+include/sort_m.mod
+include/timing_m.mod
 include/typedefs_m.mod
 include/wfn_rho_vxc_io_m.mod
 lib/libBGW_wfn.a
@@ -91,7 +103,7 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/AlAs-DFT/sigma_hl.inp
 %%DATADIR%%/testsuite/AlAs-DFT/sigma_ra.inp
 %%DATADIR%%/testsuite/BN/BN.test
-%%DATADIR%%/testsuite/BN/QE_BN.tgz
+%%DATADIR%%/testsuite/BN/QE_BN.tar.xz
 %%DATADIR%%/testsuite/BN/absorption.inp
 %%DATADIR%%/testsuite/BN/epsilon_NNS.inp
 %%DATADIR%%/testsuite/BN/epsilon_co.inp
@@ -101,7 +113,7 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/BN/kernel_csi.inp
 %%DATADIR%%/testsuite/BN/sigma.inp
 %%DATADIR%%/testsuite/Benzene-SAPO/Benzene.test
-%%DATADIR%%/testsuite/Benzene-SAPO/DFT_inputs.tar.gz
+%%DATADIR%%/testsuite/Benzene-SAPO/DFT_inputs.tar.xz
 %%DATADIR%%/testsuite/Benzene-SAPO/epsilon.inp
 %%DATADIR%%/testsuite/Benzene-SAPO/g_eps.in
 %%DATADIR%%/testsuite/Benzene-SAPO/in_denchar
@@ -125,7 +137,11 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/CUBE/pp_out
 %%DATADIR%%/testsuite/CUBE/script
 %%DATADIR%%/testsuite/CUBE/surface.inp
+%%DATADIR%%/testsuite/Common/unit.test
+%%DATADIR%%/testsuite/Common/unit_hdf5.test
 %%DATADIR%%/testsuite/GaAs-EPM/GaAs.test
+%%DATADIR%%/testsuite/GaAs-EPM/GaAs_spinor.test
+%%DATADIR%%/testsuite/GaAs-EPM/GaAs_spinor_hdf5.test
 %%DATADIR%%/testsuite/GaAs-EPM/WFN.in
 %%DATADIR%%/testsuite/GaAs-EPM/WFN_co.in
 %%DATADIR%%/testsuite/GaAs-EPM/WFN_fi.in
@@ -136,19 +152,30 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/GaAs-EPM/WFNq_fi_finiteq.in
 %%DATADIR%%/testsuite/GaAs-EPM/absorption.inp
 %%DATADIR%%/testsuite/GaAs-EPM/absorption_finiteq.inp
+%%DATADIR%%/testsuite/GaAs-EPM/absorption_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/absp_haydock.inp
 %%DATADIR%%/testsuite/GaAs-EPM/absp_mom.inp
 %%DATADIR%%/testsuite/GaAs-EPM/absp_mom_ca.inp
+%%DATADIR%%/testsuite/GaAs-EPM/absp_mom_ca_spinor.inp
+%%DATADIR%%/testsuite/GaAs-EPM/absp_mom_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/eps_ff.inp
 %%DATADIR%%/testsuite/GaAs-EPM/eps_ff1_elements.inp
+%%DATADIR%%/testsuite/GaAs-EPM/eps_ff1_elements_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/eps_ff_elements.inp
+%%DATADIR%%/testsuite/GaAs-EPM/eps_ff_elements_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/eps_ff_parallel_freq.inp
 %%DATADIR%%/testsuite/GaAs-EPM/eps_ff_parallel_freq_elements.inp
+%%DATADIR%%/testsuite/GaAs-EPM/eps_ff_parallel_freq_elements_spinor.inp
+%%DATADIR%%/testsuite/GaAs-EPM/eps_ff_parallel_freq_spinor.inp
+%%DATADIR%%/testsuite/GaAs-EPM/eps_ff_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/epsilon.inp
+%%DATADIR%%/testsuite/GaAs-EPM/epsilon_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/gsphere_input
 %%DATADIR%%/testsuite/GaAs-EPM/inteqp.inp
+%%DATADIR%%/testsuite/GaAs-EPM/inteqp_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/kernel.inp
 %%DATADIR%%/testsuite/GaAs-EPM/kernel_finiteq.inp
+%%DATADIR%%/testsuite/GaAs-EPM/kernel_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/kgrid.in
 %%DATADIR%%/testsuite/GaAs-EPM/kgrid/WFN.in
 %%DATADIR%%/testsuite/GaAs-EPM/kgrid/WFN.log
@@ -167,15 +194,22 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/GaAs-EPM/kgrid/WFNq_fi.out
 %%DATADIR%%/testsuite/GaAs-EPM/kgrid/kgrid.sh
 %%DATADIR%%/testsuite/GaAs-EPM/plotxct.inp
+%%DATADIR%%/testsuite/GaAs-EPM/plotxct_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/sig_COHSEX.inp
+%%DATADIR%%/testsuite/GaAs-EPM/sig_COHSEX_offdiag_spinor.inp
+%%DATADIR%%/testsuite/GaAs-EPM/sig_COHSEX_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/sig_GPP.inp
+%%DATADIR%%/testsuite/GaAs-EPM/sig_GPP_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/sig_HF.inp
+%%DATADIR%%/testsuite/GaAs-EPM/sig_HF_spinor.inp
 %%DATADIR%%/testsuite/GaAs-EPM/sig_ff.inp
+%%DATADIR%%/testsuite/GaAs-EPM/sig_ff_spinor.inp
+%%DATADIR%%/testsuite/GaAs-EPM/vxc_spinor.pl
 %%DATADIR%%/testsuite/Graphene/CD.input
 %%DATADIR%%/testsuite/Graphene/C_POT.DAT.gz
 %%DATADIR%%/testsuite/Graphene/Graphene.test
 %%DATADIR%%/testsuite/Graphene/Graphene_3D.test
-%%DATADIR%%/testsuite/Graphene/PARATEC_graphene.tgz
+%%DATADIR%%/testsuite/Graphene/PARATEC_graphene.tar.xz
 %%DATADIR%%/testsuite/Graphene/WFN_co.input
 %%DATADIR%%/testsuite/Graphene/WFN_fi.input
 %%DATADIR%%/testsuite/Graphene/absorption.inp
@@ -196,6 +230,8 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/Si-EPM/Si.nnkp
 %%DATADIR%%/testsuite/Si-EPM/Si.test
 %%DATADIR%%/testsuite/Si-EPM/Si_cplx_spin.test
+%%DATADIR%%/testsuite/Si-EPM/Si_hdf5.test
+%%DATADIR%%/testsuite/Si-EPM/Si_hdf5_cplx_spin.test
 %%DATADIR%%/testsuite/Si-EPM/WFN.in
 %%DATADIR%%/testsuite/Si-EPM/WFN_co.in
 %%DATADIR%%/testsuite/Si-EPM/WFN_fi.in
@@ -277,6 +313,7 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/Si-Wire-EPM/kgrid_WFN_fi.in
 %%DATADIR%%/testsuite/Si-Wire-EPM/kgrid_WFNq.in
 %%DATADIR%%/testsuite/Si-Wire-EPM/plotxct.inp
+%%DATADIR%%/testsuite/Si-Wire-EPM/sig_COHSEX.inp
 %%DATADIR%%/testsuite/Si-Wire-EPM/sig_GPP.inp
 %%DATADIR%%/testsuite/Si-Wire-EPM/sig_GPP_avg.inp
 %%DATADIR%%/testsuite/Si-Wire-EPM/sig_GPP_ca.inp
@@ -286,7 +323,7 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/Si2-SAPO/sapo.inp
 %%DATADIR%%/testsuite/Si2-SAPO/vkb.complex
 %%DATADIR%%/testsuite/Si2-SAPO/vsc.real
-%%DATADIR%%/testsuite/Si2-SAPO/wfns.tgz
+%%DATADIR%%/testsuite/Si2-SAPO/wfns.tar.xz
 %%DATADIR%%/testsuite/Silane-PARATEC/DFT_inputs.tar.gz
 %%DATADIR%%/testsuite/Silane-PARATEC/OUT_WFNq
 %%DATADIR%%/testsuite/Silane-PARATEC/OUT_paratec
@@ -310,6 +347,8 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/buildbot_query.pl
 %%DATADIR%%/testsuite/comet.scr
 %%DATADIR%%/testsuite/cori1.scr
+%%DATADIR%%/testsuite/cori2.scr
+%%DATADIR%%/testsuite/cori2_haswell.scr
 %%DATADIR%%/testsuite/cruller.scr
 %%DATADIR%%/testsuite/edison.scr
 %%DATADIR%%/testsuite/fix_testsuite.py
@@ -325,15 +364,39 @@ lib/libBGW_wfn.a
 %%DATADIR%%/testsuite/nanaimo.scr
 %%DATADIR%%/testsuite/nano.scr
 %%DATADIR%%/testsuite/no_hires.sh
+%%DATADIR%%/testsuite/parabands/Si-force-spin/Si-force-spin.test
+%%DATADIR%%/testsuite/parabands/Si-force-spin/Si-force-spin.test.mako
+%%DATADIR%%/testsuite/parabands/Si-force-spin/Si-force-spin.tgz
+%%DATADIR%%/testsuite/parabands/Si-force-spin/WFN_ref_no_pseudobands.h5
+%%DATADIR%%/testsuite/parabands/Si-force-spin/WFN_ref_pseudobands.h5
+%%DATADIR%%/testsuite/parabands/Si-force-spin/data.tgz
+%%DATADIR%%/testsuite/parabands/Si-force-spin/parabands.inp
+%%DATADIR%%/testsuite/parabands/Si-force-spin/repack.sh
+%%DATADIR%%/testsuite/parabands/Zn2O2/WFN_ref_no_pseudobands.h5
+%%DATADIR%%/testsuite/parabands/Zn2O2/WFN_ref_pseudobands.h5
+%%DATADIR%%/testsuite/parabands/Zn2O2/Zn2O2.tgz
+%%DATADIR%%/testsuite/parabands/Zn2O2/Zn2O2_pb.test
+%%DATADIR%%/testsuite/parabands/Zn2O2/Zn2O2_pb.test.mako
+%%DATADIR%%/testsuite/parabands/Zn2O2/data.tgz
+%%DATADIR%%/testsuite/parabands/Zn2O2/parabands.inp
+%%DATADIR%%/testsuite/parabands/Zn2O2/repack.sh
+%%DATADIR%%/testsuite/parabands/benzothiazole/WFN_ref.h5
+%%DATADIR%%/testsuite/parabands/benzothiazole/benzothiazole.tgz
+%%DATADIR%%/testsuite/parabands/benzothiazole/benzothiazole_pb.test
+%%DATADIR%%/testsuite/parabands/benzothiazole/benzothiazole_pb.test.mako
+%%DATADIR%%/testsuite/parabands/benzothiazole/data.tgz
+%%DATADIR%%/testsuite/parabands/benzothiazole/parabands.inp
+%%DATADIR%%/testsuite/parabands/benzothiazole/repack.sh
 %%DATADIR%%/testsuite/queenbee.scr
 %%DATADIR%%/testsuite/queue_monitor.pl
 %%DATADIR%%/testsuite/run_regression_test.pl
 %%DATADIR%%/testsuite/run_testsuite.sh
 %%DATADIR%%/testsuite/singularity.scr
 %%DATADIR%%/testsuite/stampede.scr
 %%DATADIR%%/testsuite/stampede2.scr
+%%DATADIR%%/testsuite/stampede2_skylake.scr
+%%DATADIR%%/testsuite/summarize_tests.py
 %%DATADIR%%/testsuite/titan.scr
 %%DATADIR%%/testsuite/toggle_tests.py
 %%DATADIR%%/testsuite/vulcan.scr
 %%DATADIR%%/testsuite/yuva.scr
-%%PORTDOCS%%%%DOCSDIR%%/manual.html