Add the validation for YALES2BIO

YALES2BIO/machines/occigen-bdw/occigen_testcase_big.batch

@@ -5,7 +5,7 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --time=02:00:00
 #SBATCH --exclusive
-#SBATCH --output yales2bio_testcase_big.out
+#SBATCH --output yales2bio_testcase_big.log
 #SBATCH --error yales2bio_testcase_big.err
 
 source $YALES2_HOME/../machines/occigen-bdw/env_bench

YALES2BIO/machines/occigen-bdw/occigen_testcase_small.batch

@@ -5,8 +5,8 @@
 #SBATCH --cpus-per-task=1
 #SBATCH --time=00:30:00
 #SBATCH --exclusive
-#SBATCH --output yales2bio_smalltests.log 
-#SBATCH --error yales2bio_smalltests.err 
+#SBATCH --output yales2bio_testcase_small.log 
+#SBATCH --error yales2bio_testcase_small.err 
 
 source $YALES2_HOME/../machines/occigen-bdw/env_bench
 

YALES2BIO/testcase_big/validate.py

+#!/usr/bin/python
+import argparse
+import os
+import yaml
+import sys
+import csv
+from pprint import pprint
+import re
+import numpy as np
+
+def main():
+    #Reference values
+    time_ref = 0.0019982854160
+    dt_ref = 7.9026791296*10**(-7)
+    dt_force_ref = 7.9026791296*10**(-7)
+
+    #Get the log file
+    log_file = 'yales2bio_testcase_big.log'
+    with open(log_file) as y2b_log:
+        data = y2b_log.read()
+        groups = re.findall(r'(\bBegin\s+[a-z0-9]+.*?)(?=\bBegin|\Z)', data, flags=re.DOTALL|re.MULTILINE)
+
+        #Retrieve the info of the last iteration
+        last_group = groups[len(groups)-1]
+        split = last_group.split('\n')
+        time = float(split[2].split('>')[2].split('time')[1]) 
+        dt = float(split[3].split('>')[2].split('dt')[1])
+        dt_force = float(split[8].split('>')[2].split('dt_force')[1])
+
+        err_time = np.abs(time_ref-time)/time_ref
+        err_dt = np.abs(dt_ref-dt)/dt_ref
+        err_dt_force = np.abs(dt_force_ref-dt_force)/dt_force_ref
+
+        if (err_time*100.0<10.0) and (err_dt*100.0<10.0) and (err_dt_force*100.0<10.0):
+            print("The error values are less than 10%")
+            print("Computation is okay")
+        else:
+            print("One error value is greater than 10%")
+            print("Computation fail")
+            print("time error: ",err_time)
+            print("dt error: ",err_dt)
+            print("dt_force error: ",err_dt_force)
+
+    y2b_log.close()
+
+if __name__ == "__main__":
+    main()
+
+

YALES2BIO/testcase_big/validate.sh

+
+
+if grep -q "Test passed successfully." yales2bio_testcase_big.log; then 
+   echo "TEST HAS PASSED: SUCCESSFUL"
+else
+   echo "TEST HAS NOT PASSED: FAIL" 
+fi
+
+python validate.py

YALES2BIO/testcase_small/validate.py

+#!/usr/bin/python
+import argparse
+import os
+import yaml
+import sys
+import csv
+from pprint import pprint
+import re
+import numpy as np
+
+def main():
+    #Reference values
+    time_ref = 0.00012629592964
+    dt_ref = 5.9664542845*10**(-7)
+    dt_force_ref = 5.9664542845*10**(-7)
+
+    #Get the log file
+    log_file = 'yales2bio_testcase_small.log'
+    with open(log_file) as y2b_log:
+        data = y2b_log.read()
+        groups = re.findall(r'(\bBegin\s+[a-z0-9]+.*?)(?=\bBegin|\Z)', data, flags=re.DOTALL|re.MULTILINE)
+
+        #Retrieve the info of the last iteration
+        last_group = groups[len(groups)-1]
+        split = last_group.split('\n')
+        time = float(split[2].split('>')[2].split('time')[1]) 
+        dt = float(split[3].split('>')[2].split('dt')[1])
+        dt_force = float(split[8].split('>')[2].split('dt_force')[1])
+
+        err_time = np.abs(time_ref-time)/time_ref
+        err_dt = np.abs(dt_ref-dt)/dt_ref
+        err_dt_force = np.abs(dt_force_ref-dt_force)/dt_force_ref
+
+        if (err_time*100.0<10.0) and (err_dt*100.0<10.0) and (err_dt_force*100.0<10.0):
+            print("The error values are less than 10%")
+            print("Computation is okay")
+        else:
+            print("One error value is greater than 10%")
+            print("Computation fail")
+            print("time error: ",err_time)
+            print("dt error: ",err_dt)
+            print("dt_force error: ",err_dt_force)
+
+    y2b_log.close()
+
+if __name__ == "__main__":
+    main()
+
+

YALES2BIO/testcase_small/validate.sh

+#####################################################################
+# VALIDATE THE SIMULATION
+#####################################################################
+if grep -q "Test passed successfully." yales2bio_testcase_small.log; then 
+   echo "TEST HAS PASSED: SUCCESSFUL"
+   python validate.py
+else
+   echo "TEST HAS NOT PASSED: FAIL" 
+fi