added _irradschedule reading from input file

pypact/input/inputdata.py

@@ -427,8 +427,18 @@ def _deserialize(self, f):
         """
         self.reset()
 
-        lines = f.readlines()
+        lines = iter(f.readlines())  # Convert lines to an iterator
         in_mass_section = False
+        irradiation_active = True  # Flag to track if irradiation schedule is active
+        flux_set = False  # Flag to ensure FLUX is set to a non-zero value before the first irradiation step
+
+        time_unit_to_seconds = {
+            "SECS": 1,
+            "MINS": 60,
+            "HOURS": 3600,
+            "DAYS": 86400,
+            "YEARS": 31536000
+        }
 
         for line in lines:
             line = line.strip()
@@ -451,10 +461,74 @@ def _deserialize(self, f):
                     if num_elements == 0:
                         in_mass_section = False
                 else:
+                    if line.startswith(COMMENT_START) and line.endswith(COMMENT_END):
+                        # Ignore comments
+                        continue
                     raise PypactInvalidOptionException("Invalid element line format in MASS section.")
 
             elif line.startswith("DENSITY"):
                 parts = line.split()
                 if len(parts) != 2:
                     raise PypactInvalidOptionException("Invalid DENSITY line format.")
                 self.setDensity(float(parts[1]))
+
+            elif line.startswith("FLUX") and irradiation_active:
+                # Parse the FLUX line
+                parts = line.split()
+                if len(parts) != 2:
+                    raise PypactInvalidOptionException("Invalid FLUX line format.")
+                fluxAmp = float(parts[1])
+
+                # Ensure FLUX is set to a non-zero value before the first irradiation step
+                if not flux_set and fluxAmp <= 0.0:
+                    raise PypactInvalidOptionException("FLUX must be set to a non-zero positive value before the first irradiation step.")
+                flux_set = True
+
+                # Store the current flux amplitude - we'll use it when we find a TIME command
+                current_flux_amp = fluxAmp
+
+                # If FLUX is 0.0, we're entering the cooling phase
+                if fluxAmp == 0.0:
+                    self.addIrradiation(0.0, fluxAmp)
+                    continue
+
+            # Handle TIME entries - can appear after any number of intermediate commands following FLUX
+            elif line.startswith("TIME") and flux_set:
+                time_parts = line.split()
+
+                # Ensure we have at least the TIME keyword and a value
+                if len(time_parts) < 2:
+                    raise PypactInvalidOptionException(
+                        "Invalid TIME line format: missing time value."
+                    )
+
+                # Get the time value
+                time_value = float(time_parts[1])
+                timeInSecs = time_value  # Default unit is seconds
+
+                # Handle different TIME formats
+                if len(time_parts) >= 3:
+                    # Check if the third part is a time unit
+                    if time_parts[2] in time_unit_to_seconds:
+                        # Format: TIME 10.0 SECS or TIME 0.1 YEARS ATOMS
+                        timeInSecs = time_value * time_unit_to_seconds[time_parts[2]]
+                    # Otherwise, the third part is likely "ATOMS" or something else
+                    # We keep the default assumption of seconds
+
+                # Add the time to the appropriate schedule based on whether we're in irradiation or cooling phase
+                if irradiation_active:
+                    # Still in irradiation phase
+                    self.addIrradiation(timeInSecs, current_flux_amp)
+                else:
+                    # In cooling phase after ZERO
+                    self.addCooling(timeInSecs)
+
+            elif line.startswith("ZERO"):
+                # Ensure FLUX is set to zero before using ZERO
+                if not flux_set:
+                    raise PypactInvalidOptionException(
+                        "FLUX must be set before using the ZERO keyword."
+                    )
+                # Stop processing irradiation schedule
+                irradiation_active = False
+                current_flux_amp = 0.0

reference/test.i

@@ -42,6 +42,8 @@ ATOMS
 << irradiation schedule >>
 FLUX 1100000000000000.0
 TIME 300.0 SECS
+FLUX 42.0
+TIME 200.0 SECS
 ATOMS 
 << end of irradiation >>
 FLUX 0.0

reference/test2.i

@@ -0,0 +1,52 @@
+<< -----set initial switches and get nuclear data----- >>
+CLOBBER
+JSON
+SPEK
+GETXS 1 709
+GETDECAY 1
+FISPACT
+* FNS 5 Minutes Inconel-600
+DENSITY 8.42
+MASS 1.0E-3 4
+NI  75.82
+MN   0.39
+FE   7.82
+CR  15.97
+MIND 1E3
+GRAPH 1 2 1 3
+UNCERTAINTY 2
+HALF
+HAZARDS
+TAB1 1
+<< -----irradiation phase----- >>
+FLUX 1.116E+10
+ATOMS
+TIME 5.0 MINS
+ATOMS
+<< -----cooling phase----- >>
+FLUX 0.
+ZERO
+TIME    36 ATOMS
+TIME    15 ATOMS
+TIME    16 ATOMS
+TIME    15 ATOMS
+TIME    15 ATOMS
+TIME    26 ATOMS
+TIME    33 ATOMS
+TIME    36 ATOMS
+TIME    53 ATOMS
+TIME    66 ATOMS
+TIME    66 ATOMS
+TIME    97 ATOMS
+TIME   127 ATOMS
+TIME   126 ATOMS
+TIME   187 ATOMS
+TIME   246 ATOMS
+TIME   244 ATOMS
+TIME   246 ATOMS
+TIME   428 ATOMS
+TIME   606 ATOMS
+TIME   607 ATOMS
+END
+* END
+/*

reference/test3.i

@@ -0,0 +1,16 @@
+MONITOR 1
+CLOBBER
+JSON
+SPEK
+GETXS 1 709
+GETDECAY 1
+FISPACT
+* irradiation 1
+MASS 1.0 1
+W 100.0
+TAB1 21
+FLUX 1.1e14
+ATOMS
+TIME 5 MINS ATOMS
+END
+* end

reference/test4.i

@@ -0,0 +1,82 @@
+MONITOR 1
+<< Overwrite existing inventory.log and inventory.out files >>
+CLOBBER
+<< Enable JSON file format output for inventory data >>
+JSON
+<< Read ARRAYX and COLLAPX files >>
+GETXS 1 709
+GETDECAY 1
+<< Read gamma bounds from file >>
+READGG
+<< End of control >>
+FISPACT
+* FNS 5 Minutes Inconel-600
+<< Material definition - start of initialisation phase >>
+<< Density is in units of g/cm3 >>
+DENSITY 8.42
+<< Elemental definition of material >>
+<< total mass = 1g, with 4 elements>>
+MASS 1.0E-3 4
+<< Nickel at 75.82%>>
+NI  75.82
+<< Manganese at 0.39%>>
+MN   0.39
+<< Iron at 7.82%>>
+FE   7.82
+<< Chromium at 15.97%>>
+CR  15.97
+<< Set the minimum number of atoms to track - 1000 atom threshold>>
+<< 1e5 atoms is the default >>
+MIND 1E3
+<< Produce some graph files for GNU plot for post processing >>
+<< from left to right: 1 graph, 2= .gra and .plt for gnuplot, 1=use uncertainties, 3=total heat output>>
+GRAPH 1 2 1 3
+<< Output estimates of both uncertainty and pathway analysis >>
+UNCERTAINTY 2
+<< Output half lives to output inventory information >>
+HALF
+<< Output ingestion and inhalation doses to output >>
+HAZARDS
+<< Signify start of inventory phase >>
+<< -----irradiation phase----- >>
+<< Flux amplitude in /cm2 /s >>
+FLUX 1.116E+10
+<< ATOMS= tells F-II to solve rate equations and dump output to file >>
+<< No time is given so it will use 0.0 (initial) >>
+ATOMS
+<< Solve and output at 5 minutes of irradiation>>
+TIME 5.0 MINS
+ATOMS
+<< -----cooling phase----- >>
+<< Set flux to 0 to tell F-II that no irradiation is occuring and it is decay only >>
+FLUX 0.
+<< Whilst it is possible to irradiate again FLUX >0, ZERO tells F-II that no more irradiation can occur >> 
+<< From here on only cooling can happen - this keyword is important for pathways analysis>>
+ZERO
+<< Cooling time - note use of ATOMS to indicate solving and output >>
+<< we could also use STEP or SPECTRUM to reduce output>>
+<< Default time unit is seconds, these are all in seconds >> 
+TIME    36 ATOMS
+TIME    15 ATOMS
+TIME    16 ATOMS
+TIME    15 ATOMS
+TIME    15 ATOMS
+TIME    26 ATOMS
+TIME    33 ATOMS
+TIME    36 ATOMS
+TIME    53 ATOMS
+TIME    66 ATOMS
+TIME    66 ATOMS
+TIME    97 ATOMS
+TIME   127 ATOMS
+TIME   126 ATOMS
+TIME   187 ATOMS
+TIME   246 ATOMS
+TIME   244 ATOMS
+TIME   246 ATOMS
+TIME   428 ATOMS
+TIME   606 ATOMS
+TIME   607 ATOMS
+<< End of file >>
+END
+* END

reference/test5.i

@@ -0,0 +1,28 @@
+MONITOR 1
+CLOBBER
+JSON
+SPEK
+NOERROR
+PROJECTILE 3
+GETXS 1 162
+GETDECAY 1
+FISPACT
+* proton irradiation
+DENSITY 1.0
+MASS 1.0 1
+Y 100.
+FLUX 1e20
+ATOMS
+TIME 1 MINS ATOMS
+TIME 1 MINS ATOMS
+TIME 1 MINS ATOMS
+FLUX 0.0
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+TIME 1 DAYS ATOMS
+END
+* end