Restructuring so that the saving collisions is not a user option (col…

…lision info should always be saved when collisions are turned on)

examples/Basic_Simulation/output_reader.py

@@ -28,7 +28,7 @@
 import matplotlib.pyplot as plt
 
 # Read in the simulation output and store it as an Xarray dataset.
-sim = swiftest.Simulation(read_old_output_file=True)
+sim = swiftest.Simulation(read_old_output=True)
 
 # Plot of the data and save the output plot.
 colors = ['white' if x == 'Massive Body' else 'black' for x in sim.data['particle_type']]

examples/Fragmentation/Fragmentation_Movie.py

@@ -202,7 +202,7 @@ def data_stream(self, frame=0):
         # Set fragmentation parameters
         minimum_fragment_gmass = 0.2 * body_Gmass[style][1] # Make the minimum fragment mass a fraction of the smallest body
         gmtiny = 0.99 * body_Gmass[style][1] # Make GMTINY just smaller than the smallest original body. This will prevent runaway collisional cascades
-        sim.set_parameter(fragmentation=True, collision_save="TRAJECTORY", encounter_save="TRAJECTORY", gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
+        sim.set_parameter(fragmentation=True, encounter_save="TRAJECTORY", gmtiny=gmtiny, minimum_fragment_gmass=minimum_fragment_gmass, verbose=False)
         sim.run(dt=1e-4, tstop=1.0e-3, istep_out=1, dump_cadence=1)
 
         print("Generating animation")

python/swiftest/swiftest/io.py

@@ -32,8 +32,7 @@
                   "ENCOUNTER_CHECK",
                   "TSTART",
                   "DUMP_CADENCE",
-                  "ENCOUNTER_SAVE",
-                  "COLLISION_SAVE")
+                  "ENCOUNTER_SAVE")
 
 
 
@@ -55,7 +54,7 @@
 float_param = ["T0", "TSTART", "TSTOP", "DT", "CHK_RMIN", "CHK_RMAX", "CHK_EJECT", "CHK_QMIN", "DU2M", "MU2KG",
                "TU2S", "MIN_GMFRAG", "GMTINY"]
 
-upper_str_param = ["OUT_TYPE","OUT_FORM","OUT_STAT","IN_TYPE","IN_FORM","ENCOUNTER_SAVE","COLLISION_SAVE", "CHK_QMIN_COORD"]
+upper_str_param = ["OUT_TYPE","OUT_FORM","OUT_STAT","IN_TYPE","IN_FORM","ENCOUNTER_SAVE", "CHK_QMIN_COORD"]
 lower_str_param = ["NC_IN", "PL_IN", "TP_IN", "CB_IN", "CHK_QMIN_RANGE"]
 
 param_keys = ['! VERSION'] + int_param + float_param + upper_str_param + lower_str_param+ bool_param

python/swiftest/swiftest/simulation_class.py

@@ -43,7 +43,7 @@ class Simulation:
     This is a class that defines the basic Swift/Swifter/Swiftest simulation object
     """
 
-    def __init__(self,read_param: bool = False, read_old_output_file: bool = False, simdir: os.PathLike | str = "simdata", **kwargs: Any):
+    def __init__(self,read_param: bool = False, read_old_output: bool = False, simdir: os.PathLike | str = "simdata", **kwargs: Any):
         """
 
         Parameters
@@ -65,7 +65,7 @@ def __init__(self,read_param: bool = False, read_old_output_file: bool = False,
                   inside the current working directory, which can be changed by passing `param_file` as an argument.
                 - The argument has an equivalent parameter or set of parameters in the parameter input file.
             3. Default values (see below)
-        read_old_output_file : bool, default False
+        read_old_output : bool, default False
             If true, read in a pre-existing binary input file given by the argument `output_file_name` if it exists.
             Parameter input file equivalent: None
         simdir : PathLike, default `"simdir"`
@@ -227,12 +227,6 @@ def __init__(self,read_param: bool = False, read_old_output_file: bool = False,
             If set to True, this turns on the Fraggle fragment generation code and `rotation` must also be True.
             This argument only applies to Swiftest-SyMBA simulations. It will be ignored otherwise.
             Parameter input file equivalent: `FRAGMENTATION`
-        collision_save : {"NONE","TRAJECTORY","CLOSEST"}, default "NONE"
-            Indicate if and how fragmentation data should be saved. If set to "TRAJECTORY" the full close encounter
-            trajectories associated with each collision are saved to file. If set to "CLOSEST" only the trajectories
-            at a the time the collision occurs are saved. If set to "NONE" no trajectory information is saved (collision
-            details are still logged fraggle.log).
-            *WARNING*: Enabling this feature could lead to very large files.
         minimum_fragment_gmass : float, optional
             If fragmentation is turned on, this sets the mimimum G*mass of a collisional fragment that can be generated.
             *Note.* Only set one of minimum_fragment_gmass or minimum_fragment_mass
@@ -329,7 +323,7 @@ def __init__(self,read_param: bool = False, read_old_output_file: bool = False,
                 msg += "\nDelete the file or change the location of param_file"
                 raise NotADirectoryError(msg)
         else:
-            if read_old_output_file or read_param:
+            if read_old_output or read_param:
                 raise NotADirectoryError(f"Cannot find directory {self.simdir.resolve()} ")
             else:
                 self.simdir.mkdir(parents=True, exist_ok=False)
@@ -354,8 +348,8 @@ def __init__(self,read_param: bool = False, read_old_output_file: bool = False,
         # If the user asks to read in an old parameter file or output file, override any default parameters with values from the file
         # If the file doesn't exist, flag it for now so we know to create it
         param_file_found = False
-        if read_param or read_old_output_file:
-            if self.read_param(read_init_cond = not read_old_output_file):
+        if read_param or read_old_output:
+            if self.read_param(read_init_cond = not read_old_output):
                 # We will add the parameter file to the kwarg list. This will keep the set_parameter method from
                 # overriding everything with defaults when there are no arguments passed to Simulation()
                 kwargs['param_file'] = self.param_file
@@ -375,7 +369,7 @@ def __init__(self,read_param: bool = False, read_old_output_file: bool = False,
             self.write_param()
 
         # Read in an old simulation file if requested
-        if read_old_output_file:
+        if read_old_output:
             binpath = os.path.join(self.simdir, self.param['BIN_OUT'])
             if os.path.exists(binpath):
                 self.read_output_file()
@@ -762,7 +756,7 @@ def set_parameter(self, verbose: bool = True, **kwargs):
             "init_cond_file_type": "NETCDF_DOUBLE",
             "init_cond_file_name": None,
             "init_cond_format": "EL",
-            "read_old_output_file": False,
+            "read_old_output": False,
             "output_file_type": "NETCDF_DOUBLE",
             "output_file_name": None,
             "output_format": "XVEL",
@@ -794,8 +788,7 @@ def set_parameter(self, verbose: bool = True, **kwargs):
             "encounter_check_loops": "TRIANGULAR",
             "ephemeris_date": "MBCL",
             "restart": False,
-            "encounter_save" : "NONE",
-            "collision_save" : "NONE"
+            "encounter_save" : "NONE"
         }
         param_file = kwargs.pop("param_file",None)
 
@@ -1032,7 +1025,6 @@ def set_feature(self,
                     interaction_loops: Literal["TRIANGULAR", "FLAT", "ADAPTIVE"] | None = None,
                     encounter_check_loops: Literal["TRIANGULAR", "SORTSWEEP", "ADAPTIVE"] | None = None,
                     encounter_save: Literal["NONE", "TRAJECTORY", "CLOSEST"] | None = None,
-                    collision_save: Literal["NONE", "TRAJECTORY", "CLOSEST"] | None = None,
                     verbose: bool | None = None,
                     **kwargs: Any
                     ):
@@ -1054,12 +1046,6 @@ def set_feature(self,
         fragmentation : bool, optional
             If set to True, this turns on the Fraggle fragment generation code and `rotation` must also be True.
             This argument only applies to Swiftest-SyMBA simulations. It will be ignored otherwise.
-        collision_save : {"NONE","TRAJECTORY","CLOSEST"}, default "NONE"
-            Indicate if and how fragmentation data should be saved. If set to "TRAJECTORY" the full close encounter
-            trajectories associated with each collision are saved to file. If set to "CLOSEST" only the trajectories
-            at a the time the collision occurs are saved. If set to "NONE" no trajectory information is saved (collision
-            details are still logged fraggle.log).
-            *WARNING*: Enabling this feature could lead to very large files.
         minimum_fragment_gmass : float, optional
             If fragmentation is turned on, this sets the mimimum G*mass of a collisional fragment that can be generated.
             *Note.* Only set one of minimum_fragment_gmass or minimum_fragment_mass
@@ -1226,20 +1212,6 @@ def set_feature(self,
                 self.param["ENCOUNTER_SAVE"] = encounter_save
                 update_list.append("encounter_save")
 
-
-        if collision_save is not None:
-            collision_save = collision_save.upper()
-            valid_vals = ["NONE", "TRAJECTORY", "CLOSEST"]
-            if collision_save not in valid_vals:
-                msg = f"{collision_save} is not a valid option for collision_save."
-                msg += f"\nMust be one of {valid_vals}"
-                warnings.warn(msg,stacklevel=2)
-                if "COLLISION_SAVE" not in self.param:
-                    self.param["COLLISION_SAVE"] = valid_vals[0]
-            else:
-                self.param["COLLISION_SAVE"] = collision_save
-                update_list.append("collision_save")
-
         self.param["TIDES"] = False
 
         feature_dict = self.get_feature(update_list, verbose)
@@ -1272,7 +1244,6 @@ def get_feature(self, arg_list: str | List[str] | None = None, verbose: bool | N
         valid_var = {"close_encounter_check": "CHK_CLOSE",
                      "fragmentation": "FRAGMENTATION",
                      "encounter_save": "ENCOUNTER_SAVE",
-                     "collision_save": "COLLISION_SAVE",
                      "minimum_fragment_gmass": "MIN_GMFRAG",
                      "rotation": "ROTATION",
                      "general_relativity": "GR",
@@ -2740,11 +2711,6 @@ def read_output_file(self,read_init_cond : bool = True):
         else:
             read_encounters = False
 
-        if "COLLISION_SAVE" in self.param:
-            read_collisions = self.param["COLLISION_SAVE"] != "NONE"
-        else:
-            read_collisions = False
-
         param_tmp = self.param.copy()
         param_tmp['BIN_OUT'] = os.path.join(self.simdir, self.param['BIN_OUT'])
         if self.codename == "Swiftest":

src/io/io.f90

@@ -682,7 +682,7 @@ module subroutine io_param_reader(self, unit, iotype, v_list, iostat, iomsg)
                      param%lrestart = .true.
                   end if 
                ! Ignore SyMBA-specific, not-yet-implemented, or obsolete input parameters
-               case ("NPLMAX", "NTPMAX", "GMTINY", "MIN_GMFRAG", "FRAGMENTATION", "SEED", "YARKOVSKY", "YORP", "ENCOUNTER_SAVE", "COLLISION_SAVE") 
+               case ("NPLMAX", "NTPMAX", "GMTINY", "MIN_GMFRAG", "FRAGMENTATION", "SEED", "YARKOVSKY", "YORP", "ENCOUNTER_SAVE") 
                case default
                   write(*,*) "Ignoring unknown parameter -> ",param_name
                end select

src/modules/symba_classes.f90

@@ -31,8 +31,7 @@ module symba_classes
       integer(I4B), dimension(:), allocatable :: seed                         !! Random seeds
       logical                                 :: lfragmentation     = .false. !! Do fragmentation modeling instead of simple merger.
       character(STRMAX)                       :: encounter_save     = "NONE"  !! Indicate if and how encounter data should be saved
-      character(STRMAX)                       :: collision_save = "NONE"  !! Indicate if and how fragmentation data should be saved
-      logical                                 :: lencounter_save    = .false. !! Turns on encounter saving
+      logical                                 :: lencounter_save   
       type(encounter_storage(nframes=:)), allocatable :: encounter_history  !! Stores encounter history for later retrieval and saving to file
       type(collision_storage(nframes=:)), allocatable :: collision_history  !! Stores encounter history for later retrieval and saving to file
    contains
@@ -175,7 +174,7 @@ module symba_classes
    !> SyMBA class for tracking pl-pl close encounters in a step
    type, extends(symba_encounter) :: symba_plplenc
    contains
-      procedure :: extract_collisions     => symba_collision_encounter_extract_collisions !! Processes the pl-pl encounter list remove only those encounters that led to a collision
+      procedure :: extract_collisions     => symba_collision_extract_collisions_from_encounters !! Processes the pl-pl encounter list remove only those encounters that led to a collision
       procedure :: resolve_fragmentations => symba_resolve_collision_fragmentations       !! Process list of collisions, determine the collisional regime, and then create fragments
       procedure :: resolve_mergers        => symba_resolve_collision_mergers              !! Process list of collisions and merge colliding bodies together
       procedure :: resolve_collision      => symba_resolve_collision_plplenc              !! Process the pl-pl collision list, then modifiy the massive bodies based on the outcome of the c
@@ -207,7 +206,7 @@ module symba_classes
 
    interface
 
-      module subroutine symba_collision_check_encounter(self, system, param, t, dt, irec, lany_collision, lany_closest)
+      module subroutine symba_collision_check_encounter(self, system, param, t, dt, irec, lany_collision)
          use swiftest_classes, only : swiftest_parameters
          implicit none
          class(symba_encounter),     intent(inout) :: self           !! SyMBA pl-tp encounter list object
@@ -217,10 +216,9 @@ module subroutine symba_collision_check_encounter(self, system, param, t, dt, ir
          real(DP),                   intent(in)    :: dt             !! step size
          integer(I4B),               intent(in)    :: irec           !! Current recursion level
          logical,                    intent(out)   :: lany_collision !! Returns true if any pair of encounters resulted in a collision 
-         logical,                    intent(out)   :: lany_closest   !! Returns true if any pair of encounters reached their closest approach without colliding
       end subroutine symba_collision_check_encounter
 
-      module subroutine symba_collision_encounter_extract_collisions(self, system, param)
+      module subroutine symba_collision_extract_collisions_from_encounters(self, system, param)
          implicit none
          class(symba_plplenc),       intent(inout) :: self   !! SyMBA pl-pl encounter list
          class(symba_nbody_system),  intent(inout) :: system !! SyMBA nbody system object

src/symba/symba_collision.f90

@@ -262,7 +262,7 @@ subroutine symba_collision_collider_message(pl, collidx, collider_message)
    end subroutine symba_collision_collider_message
 
 
-   module subroutine symba_collision_check_encounter(self, system, param, t, dt, irec, lany_collision, lany_closest)
+   module subroutine symba_collision_check_encounter(self, system, param, t, dt, irec, lany_collision)
       !! author: David A. Minton
       !!
       !! Check for merger between massive bodies and test particles in SyMBA
@@ -278,7 +278,7 @@ module subroutine symba_collision_check_encounter(self, system, param, t, dt, ir
       real(DP),                   intent(in)    :: t              !! current time
       real(DP),                   intent(in)    :: dt             !! step size
       integer(I4B),               intent(in)    :: irec           !! Current recursion level
-      logical,                    intent(out)   :: lany_collision, lany_closest !! Returns true if cany pair of encounters resulted in a collision 
+      logical,                    intent(out)   :: lany_collision !! Returns true if cany pair of encounters resulted in a collision 
       ! Internals
       logical, dimension(:), allocatable        :: lcollision, lclosest, lmask
       real(DP), dimension(NDIM)                 :: xr, vr
@@ -289,7 +289,6 @@ module subroutine symba_collision_check_encounter(self, system, param, t, dt, ir
       class(symba_encounter), allocatable       :: tmp       
 
       lany_collision = .false.
-      lany_closest = .false.
       if (self%nenc == 0) return
 
       select type(self)
@@ -339,7 +338,6 @@ module subroutine symba_collision_check_encounter(self, system, param, t, dt, ir
             end if
 
             lany_collision = any(lcollision(:))
-            lany_closest = any(lclosest(:))
 
             if (lany_collision) then
                call pl%rh2rb(system%cb) ! Update the central body barycenteric position vector to get us out of DH and into bary
@@ -391,6 +389,11 @@ module subroutine symba_collision_check_encounter(self, system, param, t, dt, ir
                end select
             end if
 
+            ! Take snapshots of pairs of bodies at close approach (but not collision) if requested
+            if (any(lclosest(:))) then
+
+            end if
+
          end select
       end select
 
@@ -580,7 +583,7 @@ function symba_collision_consolidate_colliders(pl, cb, param, idx_parent, collid
    end function symba_collision_consolidate_colliders
 
 
-   module subroutine symba_collision_encounter_extract_collisions(self, system, param)
+   module subroutine symba_collision_extract_collisions_from_encounters(self, system, param)
       !! author: David A. Minton
       !! 
       !! Processes the pl-pl encounter list remove only those encounters that led to a collision
@@ -646,7 +649,7 @@ module subroutine symba_collision_encounter_extract_collisions(self, system, par
       end select
 
       return
-   end subroutine symba_collision_encounter_extract_collisions
+   end subroutine symba_collision_extract_collisions_from_encounters
 
 
    module subroutine symba_collision_make_colliders_pl(self, idx)
@@ -984,7 +987,7 @@ module subroutine symba_resolve_collision_plplenc(self, system, param, t, dt, ir
       integer(I4B),               intent(in)    :: irec   !! Current recursion level
       ! Internals
       real(DP) :: Eorbit_before, Eorbit_after
-      logical :: lplpl_collision, lplpl_closest
+      logical :: lplpl_collision
       character(len=STRMAX) :: timestr
       class(symba_parameters), allocatable :: tmp_param
 
@@ -1037,7 +1040,7 @@ module subroutine symba_resolve_collision_plplenc(self, system, param, t, dt, ir
                   deallocate(tmp_param)
 
                   ! Check whether or not any of the particles that were just added are themselves in a collision state. This will generate a new plplcollision_list 
-                  call plplenc_list%collision_check(system, param, t, dt, irec, lplpl_collision, lplpl_closest)
+                  call plplenc_list%collision_check(system, param, t, dt, irec, lplpl_collision)
 
                   if (.not.lplpl_collision) exit
                end do