From c7410eb935aee0ddbf6ebb863dc74a439b836495 Mon Sep 17 00:00:00 2001
From: Logan Yamamoto Mac <lkyamamo@usc.edu>
Date: Tue, 4 Jun 2024 03:50:00 -1000
Subject: [PATCH] changing paths to use SOURCE_DIR env variable

---
 Examples/01_Optimization/01_Water/run.sh     | 6 +++---
 Examples/02_Adaibatic_MD/01_Water_NVE/run.sh | 4 ++--
 Examples/03_NAQMD/01_Water_NVE/run.sh        | 6 +++---
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/Examples/01_Optimization/01_Water/run.sh b/Examples/01_Optimization/01_Water/run.sh
index 864c20c5..196fb982 100644
--- a/Examples/01_Optimization/01_Water/run.sh
+++ b/Examples/01_Optimization/01_Water/run.sh
@@ -1,7 +1,7 @@
 cp ../../../qxmd .
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/01_Optimization/01_Water/analysis/DOS/.
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/01_Optimization/01_Water/analysis/eng/.
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/01_Optimization/01_Water/analysis/pdb/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/01_Optimization/01_Water/analysis/DOS/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/01_Optimization/01_Water/analysis/eng/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/01_Optimization/01_Water/analysis/pdb/.
 export PYTHONPATH=../../../util/
 export LD_LIBRARY_PATH=../../../fftw-3.3.8/build/lib:${LD_LIBRARY_PATH}
 mkdir data
diff --git a/Examples/02_Adaibatic_MD/01_Water_NVE/run.sh b/Examples/02_Adaibatic_MD/01_Water_NVE/run.sh
index 492d0b25..16b6b4c2 100644
--- a/Examples/02_Adaibatic_MD/01_Water_NVE/run.sh
+++ b/Examples/02_Adaibatic_MD/01_Water_NVE/run.sh
@@ -1,6 +1,6 @@
 cp ../../../qxmd .
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/02_Adaibatic_MD/01_Water_NVE/analysis/bond-angle/.
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/02_Adaibatic_MD/01_Water_NVE/analysis/eng/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/02_Adaibatic_MD/01_Water_NVE/analysis/bond-angle/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/02_Adaibatic_MD/01_Water_NVE/analysis/eng/.
 mkdir data
 export PYTHONPATH=../../../util/
 export LD_LIBRARY_PATH=../../../fftw-3.3.8/build/lib:${LD_LIBRARY_PATH}
diff --git a/Examples/03_NAQMD/01_Water_NVE/run.sh b/Examples/03_NAQMD/01_Water_NVE/run.sh
index 19ec8322..450df11d 100644
--- a/Examples/03_NAQMD/01_Water_NVE/run.sh
+++ b/Examples/03_NAQMD/01_Water_NVE/run.sh
@@ -1,7 +1,7 @@
 cp ../../../qxmd .
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/03_NAQMD/01_Water_NVE/analysis/bond-angle/.
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/03_NAQMD/01_Water_NVE/analysis/eig/.
-cp /content/QXMD/util/qxREAD.py /content/QXMD/Examples/03_NAQMD/01_Water_NVE/analysis/rate/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/03_NAQMD/01_Water_NVE/analysis/bond-angle/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/03_NAQMD/01_Water_NVE/analysis/eig/.
+cp ${SOURCE_DIR}/util/qxREAD.py ${SOURCE_DIR}/Examples/03_NAQMD/01_Water_NVE/analysis/rate/.
 mkdir data
 export PYTHONPATH=../../../util/
 export LD_LIBRARY_PATH=../../../fftw-3.3.8/build/lib:${LD_LIBRARY_PATH}