Add hmc model sampler and fix initial As set to zero

scripts/build_borg.sh

@@ -0,0 +1,29 @@
+#!/bin/sh
+
+# Modules
+module purge
+module restore myborg
+module load cuda/12.3
+
+# Environment
+source /home/bartlett/.bashrc
+source /home/bartlett/anaconda3/etc/profile.d/conda.sh
+conda deactivate
+conda activate borg_env
+
+# Kill job if there are any errors
+set -e
+
+# Path variables
+BORG_DIR=/home/bartlett/borg
+BUILD_DIR=/data101/bartlett/build_borg/
+
+cd $BORG_DIR
+# git pull
+# rm -rf $BUILD_DIR
+bash build.sh --c-compiler $(which x86_64-conda_cos6-linux-gnu-gcc) --cxx-compiler $(which x86_64-conda_cos6-linux-gnu-g++) --python --hades-python --build-dir $BUILD_DIR
+cd $BUILD_DIR
+make -j
+
+
+exit 0

scripts/run_borg.sh

@@ -15,7 +15,7 @@ conda activate borg_env
 set -e
 
 # Path variables
-BORG=/home/bartlett/anaconda3/envs/borg_env/bin/hades_python
+BORG=/data101/bartlett/build_borg/tools/hades_python/hades_python
 RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/basic_run
 
 mkdir -p $RUN_DIR

scripts/submit_borg.sh

@@ -0,0 +1,47 @@
+#!/bin/sh
+#PBS -S /bin/sh
+#PBS -N model_hmc_test
+#PBS -j oe
+#PBS -m ae
+#PBS -l nodes=h13:has1gpu:ppn=40,walltime=24:00:00
+
+# Modules
+module purge
+module restore myborg
+module load cuda/12.3
+
+# Environment
+source /home/bartlett/.bashrc
+source /home/bartlett/anaconda3/etc/profile.d/conda.sh
+conda deactivate
+conda activate borg_env
+
+# Kill job if there are any errors
+set -e
+
+# Path variables
+BORG=/data101/bartlett/build_borg/tools/hades_python/hades_python
+RUN_DIR=/data101/bartlett/fsigma8/borg_velocity/basic_run
+
+mkdir -p $RUN_DIR
+cd $RUN_DIR
+
+# Create a custom file descriptor (3) for tracing
+exec 3>$RUN_DIR/trace_file.txt
+
+# Redirect trace output to the custom file descriptor
+BASH_XTRACEFD="3"
+set -x
+
+# Run BORG
+INI_FILE=/home/bartlett/fsigma8/borg_velocity/conf/basic_ini.ini
+cp $INI_FILE basic_ini.ini
+$BORG INIT basic_ini.ini
+
+conda deactivate
+
+# Disable tracing and close the custom file descriptor
+set +x
+exec 3>&-
+
+exit 0