Merge branch 'develop' into diel_devel

.gitattributes

@@ -14,4 +14,5 @@ Makefile text eol=lf
 *.jpg binary
 *.gz binary
 *.xz binary
+*.zst binary
 *.zstd binary

.github/workflows/cislowtestmode.yml

@@ -1,5 +1,5 @@
 ---
-name: CI Slow
+name: CI Extensive Test Mode
 
 on:
     push:

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
     - repo: https://github.com/pre-commit/mirrors-clang-format
-      rev: 'v19.1.2'
+      rev: 'v19.1.5'
       hooks:
           - id: clang-format
             files: '\.(c|cc|cpp|h|hpp|cxx|hh|inc)$'

Makefile

@@ -148,28 +148,20 @@ ifeq ($(shell uname -s),Darwin)
 #	CXXFLAGS += -Rpass-missed=loop-vectorize
 #	CXXFLAGS += -Rpass-analysis=loop-vectorize
 
-	# add -lprofiler for gperftools
-	# LDFLAGS += $(LIB)
-	# LDFLAGS += -lprofiler
-
 else
-	# sometimes the login nodes have slightly different CPUs
-	# to the job nodes. Try to find the lowest common denominator here
-	# to enable vector extensions
-	# CXXFLAGS += -march=cascadelake
-	# CXXFLAGS += -march=skylake-avx512
-	# CXXFLAGS += -march=icelake-server
+	# sometimes the login nodes have different CPUs
+	# to the job nodes. march=native assumes that they are the same
+	# (or that the job CPUs support all features of the login CPUs)
 
 	# to get the current CPU architecture, run this:
 	# g++ -march=native -Q --help=target | grep -- '-march=  ' | cut -f3
+
 	ifneq (,$(shell hostname -A | grep gsi.de))
-		# virgo has some AMD nodes and some Intel.
-		# As of 6th July 2024, the login nodes are cascadelake, and we select zen3 nodes to run on.
-		CXXFLAGS += -march=x86-64-v3 -mtune=znver3
+		# virgo has znver4 nodes in the new partition
+		# CXXFLAGS += -march=znver4
+		# and znver3 nodes in the other partitions and login nodes
+		CXXFLAGS += -march=native
 	else
-		# for GitHub actions, checksums must match with different assigned CPUs, so avoid -march=native (use lowest common denominator)
-		# update: all zenver3 now?
-
 		CXXFLAGS += -march=native
 	endif
 

data/alphadecays.txt

@@ -24,115 +24,41 @@
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 213 84 1 0 4.2e-06 8.537 0 8.3759999999999994 3.7382399999999996E-005 0.0000000000000000
-209 81 0 1 132 0 3.977 0.0000000000000000 2.1421209999999999 0.65539999999999998
-209 82 0 1 11710.8 0 0.644 0.0000000000000000 0.0000000000000000 0.19740000000000002
-209 83 0 0 0 0 0 0 0 0
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 214 84 1 0 0.0001643 7.83346 0 7.6870000000000003 8.3017219999999997E-005 0.0000000000000000
-210 81 0 1 78 0 5.482 0.0000000000000000 2.5009739999999998 1.2160000000000000
-210 82 0 0 0 0 0 0 0 0
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 215 83 0 1 462 0 2.189 0.0000000000000000 0.10956380000000000 0.76190000000000002
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 219 86 1 0 3.96 6.9461 0 6.7549999999999999 5.8128189999999996E-002 0.0000000000000000
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-211 83 0.99724 0.00276 128.4 6.7503 0.574 6.5490000000000004 4.7661610000000000E-002 4.7720000000000000E-004
-211 84 1 0 5.160000e-1 7.594500 0 7.4420000000000002 8.0287729999999995E-003 0.0000000000000000
-207 81 0 1 286.2 0 1.418 0.0000000000000000 2.3805810000000001E-003 0.49160000000000004
-207 82 0 0 0 0 0 0 0 0
 220 84 0 1 3e-07 0 1.113 0.0000000000000000 0.37100000000000000 0.0000000000000000
 220 85 0.08 0.92 222.6 6.05 3.74 0.47539999999999999 0.37246040000000002 1.1679999999999999
 220 86 1 0 55.6 6.40467 0 6.2869999999999999 6.2838309999999997E-004 0.0000000000000000
-216 83 0 1 135 0 4.0901 0.0000000000000000 1.3633679999999999 0.0000000000000000
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-212 82 0 1 38304 0 0.5699 0.0000000000000000 0.14333779999999999 0.10020000000000001
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-212 84 1 0 2.99e-07 8.95412 0 8.7850000000000001 0.0000000000000000 0.0000000000000000
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 223 88 1 0 987552 5.9793 0 5.6650000000000000 0.13356070000000000 0.0000000000000000
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-213 83 0.022 0.978 2735.4 5.982 1.423 0.12220000000000000 0.12653610000000001 0.42399999999999999
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decay.cc

@@ -925,20 +925,21 @@ void init_nuclides(const std::vector<int> &custom_zlist, const std::vector<int>
       // columns: # A, Z, Q[MeV], E_gamma[MeV], E_elec[MeV], E_neutrino[MeV], meanlife[s]
       int a = -1;
       int z = -1;
-      double q_mev = 0.;
+      double q_beta_mev = 0.;
       double e_gamma_mev = 0.;
       double e_elec_mev = 0.;
       double e_neutrino = 0.;
       double tau_sec = 0.;
-      std::stringstream(line) >> a >> z >> q_mev >> e_gamma_mev >> e_elec_mev >> e_neutrino >> tau_sec;
-
-      assert_always(!nuc_exists(z, a));
-      nuclides.push_back({.z = z, .a = a, .meanlife = tau_sec});
-      nuclides.back().branchprobs[DECAYTYPE_BETAMINUS] = 1.;
-      nuclides.back().endecay_q[DECAYTYPE_BETAMINUS] = q_mev * MEV;
-      nuclides.back().endecay_electron = e_elec_mev * MEV;
-      nuclides.back().endecay_gamma = e_gamma_mev * MEV;
-      assert_always(e_elec_mev >= 0.);
+      std::stringstream(line) >> a >> z >> q_beta_mev >> e_gamma_mev >> e_elec_mev >> e_neutrino >> tau_sec;
+      if (q_beta_mev > 0.) {
+        assert_always(!nuc_exists(z, a));
+        nuclides.push_back({.z = z, .a = a, .meanlife = tau_sec});
+        nuclides.back().branchprobs[DECAYTYPE_BETAMINUS] = 1.;
+        nuclides.back().endecay_q[DECAYTYPE_BETAMINUS] = q_beta_mev * MEV;
+        nuclides.back().endecay_electron = e_elec_mev * MEV;
+        nuclides.back().endecay_gamma = e_gamma_mev * MEV;
+        assert_always(e_elec_mev >= 0.);
+      }
     }
 
     auto falpha = fstream_required("alphadecays.txt", std::ios::in);

scripts/artis-virgo-submit.sh

@@ -2,3 +2,6 @@
 export APPTAINER_SHARENS=true
 export APPTAINER_CONFIGDIR=/tmp/$USER
 sbatch -J $(basename $(exec pwd)) --ntasks=1920 --ntasks-per-node=128 --mem-per-cpu=2000MB --partition=long --time=24:00:00 --constraint=amd,epyc,7713 --mail-type=ALL --mail-user=${USER}@gsi.de --no-requeue -- artis/scripts/artis-virgo-slurmjob.sh
+
+# AMD EPYC 9654 with 192 real cores per node and 4 GB/core. march=znver4
+#sbatch -J $(basename $(exec pwd)) --ntasks=960 --ntasks-per-node=192 --mem-per-cpu=2000MB --partition=new --time=24:00:00 --mail-type=ALL --mail-user=${USER}@gsi.de --no-requeue -- artis/scripts/artis-virgo-slurmjob.sh

scripts/exspec-after.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # only compress the files if we successfully ran exspec
-if [ -f emission.out* ]; then
+if [[ -f emission.out || -f emission.out.zstd ]]; then
 
   # zstd does decent compression at high speeds
   cmdcompress="zstd -T0 -16 -v --rm -f"

scripts/exspec-before.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # packet output files outside the artis folder, so move them back to run exspec
-if [[ ! -f packets00_0000.out* && -f packets/packets00_0000.out* ]]; then
+if [[ ! -f packets00_0000.out && ! -f packets00_0000.out.zst && (-f packets/packets00_0000.out || -f packets/packets00_0000.out.zst) ]]; then
   mv packets/packets*.out* .
 fi
 

tests/kilonova_1d_1dgrid_inputfiles/results_md5_final.txt

@@ -1,22 +1,22 @@
-a68ab8919d91afb5c3a4b28bb98b75b8  absorption.out
+5e70840457d3ebb1a70aae91797bf12d  absorption.out
 f9bb214eb7f1ac22791a13c8025c4887  bflist.out
-f0db52c346ffcba95d1d8812475f8c34  deposition.out
-065c01cd760d54a888a939dfe00378c4  emission.out
-f345c0a8d5ae60ec17b7bfa78d61abb9  emissiontrue.out
-dd314f8317220adaee8b48aa1b60f2a3  gamma_light_curve.out
-9148bc2382bb01fe9ffa140ff86a5707  gamma_spec.out
-4af36569cc2db94b41cdadbc03354ac4  gammalinelist.out
+57d70ef50670042f0aee39838696b6f4  deposition.out
+bb04fc3f2022fcfe6a6333266b9e5ff2  emission.out
+0d933b1cbf641c1e5662269be44b572d  emissiontrue.out
+abda1035e92b327aa5c331fbf52df955  gamma_light_curve.out
+7dd1e0c57f597e664960f19f50da8ab7  gamma_spec.out
+cfe0877961d7651ddab7826c45ba6770  gammalinelist.out
 7db21c856b5d2784b14eabfd22e5b837  grid.out
-f0b726a4dfbbbe17d71e182cfc251e72  light_curve.out
+bdd30c2ea4f997d076b10a62cee55631  light_curve.out
 3d4b61fa5c0c8987526ebd71787cb8ea  linestat.out
 bc40edd64676f86b6ac2df0934e2ce9a  modelgridrankassignments.out
-8c3d21a3d8646afef626a7adeb0feee8  packets00_0000.out
-67239f5faf43336b8bd4a175553763ee  packets00_0001.out
-b4828c6463ba397ce993bf75488a2a33  packets00_0002.out
-ddfded7dcd44bb1469432977052eca4b  packets00_0003.out
-5bc66d0e2f639e2cd2d2a8d9a6487c3b  spec.out
+f5b542810e6f3fc8a9c2272531c9bc75  packets00_0000.out
+95d2bc8b85d49d64e69d7054efe261dd  packets00_0001.out
+a6b7fc332a6a8c05d77156764d3a7c90  packets00_0002.out
+e6c8d10f260c3007350beeae0d8fc398  packets00_0003.out
+381f8187e7b05d03b62e6d1b38a6b585  spec.out
 a351f1711fecd60c023d0ba7332092db  timesteps.out
-ea174eff24f41e70b1d28e9775e7dfd3  job1/estimators_0000.out
-0690d0264e69496e2a43cfe86bdc9e01  job1/estimators_0001.out
-4c2fa51eabca21c4680661d0db01f811  job1/estimators_0002.out
-fef640281337a9f404fc72a269a20406  job1/estimators_0003.out
+3cab5d3d4e763334d57beaad05cdd867  job1/estimators_0000.out
+db98cbc7fc195bfa9944289927d15c2b  job1/estimators_0001.out
+fedc7856d170715d4e5e3c6037b73521  job1/estimators_0002.out
+e03ce33dc0f2227dbb5cf65ce2dd969c  job1/estimators_0003.out

tests/kilonova_1d_1dgrid_inputfiles/results_md5_job0.txt

@@ -1,21 +1,21 @@
-9b6e08da1a7ff4bb095586408e58c0bc  absorption.out
+2900c3409f983192e778095ee3522780  absorption.out
 f9bb214eb7f1ac22791a13c8025c4887  bflist.out
-a37e9be6c23303199deccfe9a8704b90  deposition.out
-da000c6330f226464a3fc2ba16eb8beb  emission.out
-851560ece3b6630497d362ad8c69a127  emissiontrue.out
-a65c34c5069444d22e04c7efb8bd0d69  gamma_light_curve.out
-4af36569cc2db94b41cdadbc03354ac4  gammalinelist.out
+d78ef9529cf1a41661d26b5a59651659  deposition.out
+2f412c22d3207dc01a4e9c971c61d6e5  emission.out
+ca9e41bb0a16abecf97c2650a59d8cdd  emissiontrue.out
+61619cbe363c8daf005aa8aebfbd0c2a  gamma_light_curve.out
+cfe0877961d7651ddab7826c45ba6770  gammalinelist.out
 7db21c856b5d2784b14eabfd22e5b837  grid.out
-ba3d39bcb52c8f2f4bb30666cec29607  light_curve.out
+e981746ff85b8b009e833d80aef76cc2  light_curve.out
 3d4b61fa5c0c8987526ebd71787cb8ea  linestat.out
 bc40edd64676f86b6ac2df0934e2ce9a  modelgridrankassignments.out
-f267baafef20bacbaf44ac66b4de90d5  packets00_0000.out
-01c4d1d02b822f05d6a0b1a19ae0f6aa  packets00_0001.out
-04fca0a55fde00a2a3b31cf49d611a9b  packets00_0002.out
-54a3b60f3de31e59d9d046f1e133d7ef  packets00_0003.out
-d90011df9b26a1b201891122b690b7e9  spec.out
+57f07070abe7318fbd3add00609d0141  packets00_0000.out
+d57addd2505c8c0a9df15a9f2d43e568  packets00_0001.out
+fe15be88234899aecdad1ae65c8f997a  packets00_0002.out
+14053d099f9bd07041f5c1e5a91da0b3  packets00_0003.out
+5b508166a80f8c15bf7ae775d83d86d0  spec.out
 a351f1711fecd60c023d0ba7332092db  timesteps.out
-59b9ddad12a7142035a8a14a66772533  job0/estimators_0000.out
-914fb771d6a47c19c2902a35f2b31b8a  job0/estimators_0001.out
-2fc6ed25172ee06c660042cc2bd4bb79  job0/estimators_0002.out
-903bf6890de8671b082f96627469ab5e  job0/estimators_0003.out
+485d5556f68c4212629973fcd4c6a988  job0/estimators_0000.out
+ea2e10760b34e985f68aba4bb2a5ec8a  job0/estimators_0001.out
+3ba602640206bbfa1ccecb7a4944e2b1  job0/estimators_0002.out
+95bb5ce9a7be73d10471187f6f60c3e7  job0/estimators_0003.out

tests/kilonova_1d_3dgrid_inputfiles/results_md5_final.txt

@@ -1,22 +1,22 @@
-f06170f48efc0e06240668b75fc209ab  absorption.out
+fb55532ef3cdabf21d284fa99e15faf0  absorption.out
 f9bb214eb7f1ac22791a13c8025c4887  bflist.out
-b0408ab41fc6af31a67b83db2d30995a  deposition.out
-8809f7f9b0de8b9f340bbfcfd74c8971  emission.out
-99b1de21168c8370d1f503eaf46ba252  emissiontrue.out
-7d05408c2969bcf5e2776f3b51716ef1  gamma_light_curve.out
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