Added automated test based on LPI example

Even though the laser ion test is named as a dependency it is running this
test again. That should ideally be avoided. It would be good to just run
the analysis script as test.

Examples/Physics_applications/laser_ion/CMakeLists.txt

@@ -11,6 +11,16 @@ add_warpx_test(
     OFF  # dependency
 )
 
+add_warpx_test(
+    test_2d_laser_ion_acc_time_avg  # name
+    2  # dims
+    2  # nprocs
+    inputs_test_2d_laser_ion_acc  # inputs; will not be used b/c dependent test
+    analysis_time_avg_diags.py  # analysis
+    diags/diagTimeAvg/  # output
+    test_2d_laser_ion_acc  # dependency
+)
+
 add_warpx_test(
     test_2d_laser_ion_acc_picmi  # name
     2  # dims
@@ -20,3 +30,14 @@ add_warpx_test(
     diags/diagInst/  # output
     OFF  # dependency
 )
+
+# We do not have an intervals parser for PICMI yet which would accept more than a single integer for the output period
+#add_warpx_test(
+#    test_2d_laser_ion_acc_time_avg_picmi  # name
+#    2  # dims
+#    2  # nprocs
+#    inputs_test_2d_laser_ion_acc_picmi.py  # inputs
+#    analysis_time_avg_diags.py  # analysis
+#    diags/diagTimeAvg/  # output
+#    test_2d_laser_ion_acc_picmi  # dependency
+#)

Examples/Physics_applications/laser_ion/analysis_time_avg_diags.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+import sys
+import numpy as np
+import openpmd_api as io
+
+
+def load_field_from_iteration(series, iteration : int, field : str, coord : str = None) -> np.ndarray:
+    """Load iteration of field data from file."""
+
+    it = series.iterations[iteration]
+    field_obj = it.meshes[f"{field}"]
+
+    if field_obj.scalar:
+        field_data = field_obj[io.Mesh_Record_Component.SCALAR].load_chunk()
+    elif coord in [item[0] for item in list(field_obj.items())]:
+        field_data = field_obj[coord].load_chunk()
+    else:
+        raise Exception(f"Specified coordinate: f{coord} is not available for field: f{field}.")
+    series.flush()
+
+    return field_data
+
+
+def main():
+
+    field = "E"
+    coord = "z"
+    avg_period_steps = 5
+    avg_output_step = 100
+
+    path_tpl_inst = "diags/diagInst/openpmd_%T.h5"
+
+    dir_avg = sys.argv[1]
+    path_tpl_avg = f"{dir_avg}/openpmd_%T.h5"
+
+    si = io.Series(path_tpl_inst, io.Access.read_only)
+    sa = io.Series(path_tpl_avg, io.Access.read_only)
+
+    ii0 = si.iterations[0]
+    fi0 = ii0.meshes[field][coord]
+    shape = fi0.shape
+
+    data_inst = np.zeros(shape)
+
+    for i in np.arange(avg_output_step-avg_period_steps+1,avg_output_step+1):
+        data_inst += load_field_from_iteration(si, i, field, coord)
+
+    data_inst = data_inst / avg_period_steps
+
+    data_avg = load_field_from_iteration(sa, avg_output_step, field, coord)
+
+    # Compare the data
+    if np.allclose(data_inst, data_avg):
+        print("Test passed: actual data is close to expected data.")
+    else:
+        print("Test failed: actual data is not close to expected data.")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc

@@ -202,7 +202,8 @@ laser1.profile_focal_distance = 4.0e-6  # focal distance from the antenna [m]
 #
 diagnostics.diags_names = diagInst diagTimeAvg openPMDfw openPMDbw
 
-diagInst.intervals = 100
+# instantaneous field and particle diagnostic
+diagInst.intervals = 100,96:100  # second interval only for CI testing the time-averaged diags
 diagInst.diag_type = Full
 diagInst.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho rho_electrons rho_hydrogen
 # reduce resolution of output fields
@@ -213,10 +214,12 @@ diagInst.hydrogen.plot_filter_function(t,x,y,z,ux,uy,uz) = (uz>=0) * (x<1.0e-6)
 diagInst.format = openpmd
 diagInst.openpmd_backend = h5
 
+# time-averaged particle and field diagnostic
 diagTimeAvg.intervals = 100
 diagTimeAvg.diag_type = TimeAveraged
 diagTimeAvg.time_average_mode = dynamic_start
-diagTimeAvg.average_period_time = 2.67e-15  # period of 800 nm light waves
+#diagTimeAvg.average_period_time = 2.67e-15  # period of 800 nm light waves
+diagTimeAvg.average_period_steps = 5  # use only either `time` or `steps`
 diagTimeAvg.write_species = 0
 diagTimeAvg.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz rho rho_electrons rho_hydrogen
 # reduce resolution of output fields