git: db8a20e23f08 - main - science/bagel: update 1.2.2-132 → 1.2.2.147
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Date: Thu, 08 Oct 2026 21:54:15 UTC
The branch main has been updated by yuri:
URL: https://cgit.FreeBSD.org/ports/commit/?id=db8a20e23f08d409c4a30b00b1176fcf4286cf6a
commit db8a20e23f08d409c4a30b00b1176fcf4286cf6a
Author: Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-10-08 21:53:37 +0000
Commit: Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-10-08 21:54:13 +0000
science/bagel: update 1.2.2-132 → 1.2.2.147
---
science/bagel/Makefile | 19 +++++++--
science/bagel/distinfo | 6 +--
science/bagel/files/menthol.json | 50 +++++++++++++++++++++++
science/bagel/files/patch-src_util_input_input.cc | 18 ++++++++
4 files changed, 86 insertions(+), 7 deletions(-)
diff --git a/science/bagel/Makefile b/science/bagel/Makefile
index b2f03de56ea7..e0cd13ca14fa 100644
--- a/science/bagel/Makefile
+++ b/science/bagel/Makefile
@@ -1,8 +1,7 @@
PORTNAME= bagel
DISTVERSIONPREFIX= v
-DISTVERSION= 1.2.2-132
-DISTVERSIONSUFFIX= -g2955e4d1a
-PORTREVISION= 21
+DISTVERSION= 1.2.2-147
+DISTVERSIONSUFFIX= -gad8c7c89e
CATEGORIES= science
MAINTAINER= yuri@FreeBSD.org
@@ -29,6 +28,9 @@ GH_ACCOUNT= qsimulate-open
GNU_CONFIGURE= yes
CONFIGURE_ARGS= --datarootdir=${DATADIR}
+CXXFLAGS+= -Wno-invalid-specialization # fix build on 16
+LDFLAGS+= -Wl,--allow-shlib-undefined # fix build on 16
+
INSTALL_TARGET= install-strip
OPTIONS_DEFINE= MPI LIBXC SCALAPACK SMITH # SLATER (needs a separate lib)
@@ -56,7 +58,16 @@ SMITH_IMPLIES= MPI
TEST_TARGET= check
TEST_ARGS= LDFLAGS+="-lcblas -lblas" ${TEST_TARGET}
+test-quick: stage # smoke test
+ @${ECHO_CMD} "==> Running BAGEL smoke test..."
+ @cd ${TEST_WRKSRC} && \
+ ${SETENV} LD_LIBRARY_PATH=${STAGEDIR}${PREFIX}/lib BAGEL_BASIS_DIR=${STAGEDIR}${DATADIR} \
+ ${STAGEDIR}${PREFIX}/bin/BAGEL ${FILESDIR}/menthol.json > menthol.out
+ @${ECHO_CMD} "==> BAGEL smoke test succeeded"
+
post-test: # tests fail, see https://github.com/qsimulate-open/bagel/issues/248
- @cd ${WRKSRC}/src && ./TestSuite --log_level=all
+ @cd ${WRKSRC}/src && \
+ ${SETENV} LD_LIBRARY_PATH=${STAGEDIR}${PREFIX}/lib BAGEL_BASIS_DIR=${STAGEDIR}${DATADIR} \
+ ./TestSuite --log_level=all
.include <bsd.port.mk>
diff --git a/science/bagel/distinfo b/science/bagel/distinfo
index 7566be8b899d..5520c44bf969 100644
--- a/science/bagel/distinfo
+++ b/science/bagel/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1655961216
-SHA256 (qsimulate-open-bagel-v1.2.2-132-g2955e4d1a_GH0.tar.gz) = 15789ea304d28cd62203973772e198b80846bb1fa8d6c148289d6471abb26fcf
-SIZE (qsimulate-open-bagel-v1.2.2-132-g2955e4d1a_GH0.tar.gz) = 35668444
+TIMESTAMP = 1791495870
+SHA256 (qsimulate-open-bagel-v1.2.2-147-gad8c7c89e_GH0.tar.gz) = 2842995488f32c72815d1ac981d0e491e9bd1f568d5eebd0aa663184a75ea6aa
+SIZE (qsimulate-open-bagel-v1.2.2-147-gad8c7c89e_GH0.tar.gz) = 35670548
diff --git a/science/bagel/files/menthol.json b/science/bagel/files/menthol.json
new file mode 100644
index 000000000000..28e255e4a3df
--- /dev/null
+++ b/science/bagel/files/menthol.json
@@ -0,0 +1,50 @@
+{
+ "bagel" : [
+ {
+ "title" : "molecule",
+ "basis" : "cc-pvdz",
+ "df_basis" : "cc-pvdz-jkfit",
+ "angstrom" : true,
+ "geometry" : [
+ { "atom" : "C", "xyz" : [ -0.760, 1.320, -0.340 ] },
+ { "atom" : "C", "xyz" : [ 0.640, 1.340, 0.280 ] },
+ { "atom" : "C", "xyz" : [ 1.540, 0.200, -0.220 ] },
+ { "atom" : "C", "xyz" : [ 0.960, -1.140, 0.230 ] },
+ { "atom" : "C", "xyz" : [ -0.440, -1.150, -0.400 ] },
+ { "atom" : "C", "xyz" : [ -1.330, -0.010, 0.110 ] },
+ { "atom" : "O", "xyz" : [ 1.210, 2.560, -0.160 ] },
+ { "atom" : "C", "xyz" : [ -1.680, 2.490, 0.070 ] },
+ { "atom" : "C", "xyz" : [ 3.020, 0.230, 0.200 ] },
+ { "atom" : "C", "xyz" : [ -2.760, -0.020, -0.420 ] },
+ { "atom" : "C", "xyz" : [ 3.890, -0.910, -0.350 ] },
+ { "atom" : "C", "xyz" : [ 3.120, 0.270, 1.730 ] },
+ { "atom" : "H", "xyz" : [ -0.660, 1.320, -1.440 ] },
+ { "atom" : "H", "xyz" : [ 0.550, 1.340, 1.380 ] },
+ { "atom" : "H", "xyz" : [ 1.610, 0.210, -1.320 ] },
+ { "atom" : "H", "xyz" : [ 0.880, -1.150, 1.330 ] },
+ { "atom" : "H", "xyz" : [ 1.590, -2.000, -0.050 ] },
+ { "atom" : "H", "xyz" : [ -0.350, -1.130, -1.500 ] },
+ { "atom" : "H", "xyz" : [ -0.920, -2.090, -0.110 ] },
+ { "atom" : "H", "xyz" : [ -1.410, -0.020, 1.210 ] },
+ { "atom" : "H", "xyz" : [ 2.150, 2.490, 0.070 ] },
+ { "atom" : "H", "xyz" : [ -2.700, 2.400, -0.320 ] },
+ { "atom" : "H", "xyz" : [ -1.260, 3.430, -0.310 ] },
+ { "atom" : "H", "xyz" : [ -1.740, 2.560, 1.160 ] },
+ { "atom" : "H", "xyz" : [ 3.420, 1.170, -0.210 ] },
+ { "atom" : "H", "xyz" : [ -3.370, 0.790, -0.010 ] },
+ { "atom" : "H", "xyz" : [ -3.240, -0.960, -0.130 ] },
+ { "atom" : "H", "xyz" : [ -2.760, 0.060, -1.520 ] },
+ { "atom" : "H", "xyz" : [ 4.950, -0.870, -0.060 ] },
+ { "atom" : "H", "xyz" : [ 3.560, -1.890, -0.000 ] },
+ { "atom" : "H", "xyz" : [ 4.850, -0.900, -1.450 ] },
+ { "atom" : "H", "xyz" : [ 4.160, 0.310, 2.070 ] },
+ { "atom" : "H", "xyz" : [ 2.620, 1.160, 2.130 ] },
+ { "atom" : "H", "xyz" : [ 2.650, -0.610, 2.180 ] }
+ ]
+ },
+ {
+ "title" : "hf"
+ }
+ ]
+}
+
diff --git a/science/bagel/files/patch-src_util_input_input.cc b/science/bagel/files/patch-src_util_input_input.cc
new file mode 100644
index 000000000000..59e472c419f5
--- /dev/null
+++ b/science/bagel/files/patch-src_util_input_input.cc
@@ -0,0 +1,18 @@
+-- allow to override the basis directory with an environment variable
+
+--- src/util/input/input.cc.orig 2022-06-03 20:23:32 UTC
++++ src/util/input/input.cc
+@@ -119,7 +119,12 @@ shared_ptr<const PTree> PTree::read_basis(string name)
+ } catch (...) {
+ // next, the standard install location
+ try {
+- const string prefix(BASIS_DIR);
++ string prefix(BASIS_DIR);
++
++ // override with the environment variable if it is set
++ if (auto env_basis_dir = std::getenv("BAGEL_BASIS_DIR"))
++ prefix = env_basis_dir;
++
+ const string filename = prefix + "/" + name + ".json";
+ out = make_shared<const PTree>(filename);
+ } catch (...) {