Merge branch 'debug'

README_tables/param_options.md

@@ -34,7 +34,7 @@
 | ```GR```                | General relativity.                                                                                                          | ```YES```, ```NO```                                                                                     | all
 | ```RHILL_PRESENT```     | Hill Radius present in massive body input file.                                                                              | ```YES```, ```NO```                                                                                     | SyMBA
 | ```ENERGY```            | Track and report the total energy, angular momentum, and mass of the system.                                                 | ```YES```, ```NO```                                                                                     | SyMBA
-| ```FRAGMENTATION```     | Resolve collisions with fragmentation.                                                                                       | ```YES```, ```NO```                                                                                     | SyMBA
+| ```COLLISION_MODEL```   | Resolve collisions.                                                                                                          | ```MERGE```, ```BOUNCE```, ```FRAGGLE```                                                                | SyMBA
 | ```ROTATION```          | Rotation of massive bodies. Requires rotation vectors, radii, and moments of inertia to be provided in initial conditions.   | ```YES```, ```NO```                                                                                     | SyMBA
 | ```GMTINY```            | Mass cutoff between fully and semi-interacting massive bodies in gravitational mass units.                                   | floating point (ex. ```4e-06```)                                                                        | SyMBA
 | ```MIN_GMFRAG```        | Minimum fragment mass in gravitational mass units.                                                                           | floating point (ex. ```1e-09```)                                                                        | SyMBA
@@ -50,5 +50,8 @@ In the above list, the following are defined as:
 - ```XVEL``` - Heliocentric position and velocity components and osculating orbital elements for ```OUT_FORM```
 - ```NETCDF_FLOAT``` - Single precision NetCDF format for ```OUT_TYPE```
 - ```NETCDF_DOUBLE``` - Double precision NetCDF format for ```OUT_TYPE```
+- ```MERGE``` - Perfectly conserve the mass of all colliding bodies into a single resultant body
+- ```BOUNCE``` - Perfectly-elastic collision in which all bodies reverse trajectory after the collision
+- ```FRAGGLE``` - Collisional fragments are generated as a result of a collision
 
 For more details on the ```INTERACTION_LOOPS``` and ```ENCOUNTER_CHECK``` options, see the **Updates to Swifter SyMBA** section below.

README_tables/save_kwargs.md

@@ -0,0 +1,7 @@
+# swiftest.save(**kwargs)
+| Key Word Name   | Key Word Description                                                                                  | Options                                    |
+|-----------------|-------------------------------------------------------------------------------------------------------|--------------------------------------------|
+|```codename```   | Name of the N-body code to use. Default is ```Swiftest```.                                            | ```Swiftest```, ```Swifter```, ```Swift```  
+|```param_file``` | Alternative name of the parameter input file.                                                         | string (ex. ```myparam.in```)  
+|```param```      | Alternative parameter dictionary.                                                                     | dictionary  
+|```framenum```   | Time frame from which to generate initial conditions. Default is -1 or the last frame in the dataset. | integer (ex. ```10```)  

README_tables/simulation_kwargs.md

@@ -4,7 +4,7 @@
 |```simdir```                     | Path to subdirectory in which to store data. Default is ```/simdir```.                             | pathlike string (ex. ```path/to/directory```)                                                      | all
 |```read_param```                 | Read in a pre-existing parameter input file. Default is ```False```.                               | ```True```, ```False```                                                                            | all
 |```param_file```                 | Name of the pre-existing parameter input file. Only used if ```read_param``` is set to ```True```. | string (ex. ```param.in```)                                                                        | all
-|```read_old_output```       | Read in a pre-existing simulation output file. Default is ```False```.                             | ```True```, ```False```                                                                            | all
+|```read_data```       | Read in a pre-existing simulation output file. Default is ```False```.                             | ```True```, ```False```                                                                            | all
 |```codename```                   | Name of the N-body code to use. Default is ```Swiftest```.                                         | ```Swiftest```, ```Swifter```, ```Swift```                                                         | all
 |```integrator```                 | Name of the N-body integrator to use. Default is ```symba```.                                      | ```symba```, ```helio```, ```rmvs```, ```whm```                                                    | all
 |```t0```                         | The reference time for the start of the simulation in time units. Default is ```0.0```.            | floating point (ex. ```0.0```)                                                                     | all
@@ -23,6 +23,9 @@
 |```MU```                         | Mass unit system to use in the simulation. Default is ```Msun```.                                  | ```Msun```, ```Mearth```, ```kg```, ```g``` (case-insensitive)                                     | all                           
 |```DU```                         | Distance unit system to use in the simulation. Default is ```AU```.                                | ```AU```, ```Rearth```, ```m```, ```cm``` (case-insensitive)                                       | all
 |```TU```                         | Time unit system to use in the simulation. Default is ```Y```.                                     | ```Y```, ```YR```, ```DAY``` (Julian day), ```d``` (Julian day), ```JD``` (Julian day), ```s``` (case-insensitive) | all
+|```MU_name```                    | The name of the mass unit. Overrides ```MU```.                                                     | string (ex. ```kilograms```)                                                                       | all
+|```DU_name```                    | The name of the distance unit. Overrides ```DU```.                                                 | string (ex. ```meters```)                                                                          | all
+|```TU_name```                    | The name of the time unit. Overrides ```TU```.                                                     | string (ex. ```seconds```)                                                                         | all
 |```MU2KG```                      | Mass units to kilogram conversion factor. Overrides ```MU```.                                      | floating point (ex. ```1.988409870698051e+30```)                                                   | all
 |```DU2M```                       | Distance units to meters conversion factor. Overrides ```DU```.                                    | floating point (ex. ```31557600.0```)                                                              | all
 |```TU2S```                       | Time units to seconds conversion factor. Overrides ```TU```.                                       | floating point (ex. ```149597870700.0```)                                                          | all
@@ -32,8 +35,9 @@
 |```mtiny```                      | Mass cutoff between fully and semi-interacting massive bodies in mass units. Either ```mtiny``` **OR** ```gmtiny``` may be set. | floating point (ex. ```1e23```)                                       | all
 |```gmtiny```                     | Mass cutoff between fully and semi-interacting massive bodies in gravitational mass units. Default is ```0.0```. Either ```mtiny``` **OR** ```gmtiny``` may be set. | floating point (ex. ```4e-6```)   | all
 |```close_encounter_check```      | Check for close encounters. Default is ```True```. Requires radius of massive bodies to be provided in initial conditions. | ```True```, ```False```                                                    | all
+|```encounter_save```             | Save data for each close encounter to a file. Warning! This can generate very large files!         | ```TRAJECTORY```, ```CLOSEST```, ```BOTH```                                                        | SyMBA
 |```general_relativity```         | General relativity. Default is ```True```.                                                         | ```True```, ```False```                                                                            | all
-|```fragmentation```              | Resolve collisions with fragmentation. Default is ```False```.                                     | ```True```, ```False```                                                                            | SyMBA
+|```collision_model```            | Resolve collisions. Default is ```MERGE```.                                                        | ```MERGE```, ```BOUNCE```, ```FRAGGLE```                                                           | SyMBA
 |```minimum_fragment_gmass```     | Minimum fragment mass in gravitational mass units. Default is ```0.0```. Either ```minimum_fragment_gmass``` **OR** ```minimum_fragment_mass``` may be set. | floating point (ex. ```1e-9```)           | SyMBA
 |```minimum_fragment_mass```      | Minimum fragment mass in mass units. Either ```minimum_fragment_gmass``` **OR** ```minimum_fragment_mass``` may be set. | floating point (ex. ```1e20```)                                               | SyMBA
 |```rotation```                   | Rotation of massive bodies. Requires rotation vectors, radii, and moments of inertia to be provided in initial conditions. Default is ```False```. | ```True```, ```False```                            | SyMBA
@@ -56,4 +60,9 @@ In the above list, the following are defined as:
 - ```REAL4``` - Single precision 4-byte native Fortran binary format (Swifter/Swift only)
 - ```REAL8``` - Double precision 8-byte native Fortran binary format (Swifter/Swift only)
 - ```XDR4``` - Single precision 4-byte XDR format (Swifter/Swift only)
-- ```XDR8``` - Double precision 8-byte XDR format (Swifter/Swift only)
+- ```XDR8``` - Double precision 8-byte XDR format (Swifter/Swift only)
+- ```TRAJECTORY``` - Save the position and velocity vectors of all bodies involved in the close encounter at each intermediary step of the encounter
+- ```CLOSEST``` - Save the position and velocity vectors of all bodies involved in the close encounter at the point of closest approach 
+- ```MERGE``` - Perfectly conserve the mass of all colliding bodies into a single resultant body
+- ```BOUNCE``` - Perfectly-elastic collision in which all bodies reverse trajectory after the collision
+- ```FRAGGLE``` - Collisional fragments are generated as a result of a collision

README_tables/write_param_kwargs.md

@@ -0,0 +1,6 @@
+# swiftest.write_param(**kwargs)
+| Key Word Name   | Key Word Description                                                                               | Options                                    |
+|-----------------|----------------------------------------------------------------------------------------------------|--------------------------------------------|
+|```codename```   | Name of the N-body code to use. Default is ```Swiftest```.                                         | ```Swiftest```, ```Swifter```, ```Swift```  
+|```param_file``` | Alternative name of the parameter input file.                                                      | string (ex. ```myparam.in```)  
+|```param```      | Alternative parameter dictionary.                                                                  | dictionary  

paper/paper.md

@@ -26,7 +26,7 @@ affiliations:
    index: 1
  - name: Independent Researcher, USA
    index: 2
-date: 31 October 2022
+date: 03 February 2023
 bibliography: paper.bib
 ---
 

src/fraggle/fraggle_module.f90

@@ -44,7 +44,7 @@ end subroutine fraggle_generate_disrupt
 
       module subroutine fraggle_generate_hitandrun(self, nbody_system, param, t) 
          implicit none
-         class(collision_fraggle),   intent(inout) :: self         !! Collision system object
+         class(collision_fraggle), intent(inout) :: self         !! Collision system object
          class(base_nbody_system), intent(inout) :: nbody_system !! Swiftest nbody system object
          class(base_parameters),   intent(inout) :: param        !! Current run configuration parameters with SyMBA additions
          real(DP),                 intent(in)    :: t            !! Time of collision

src/swiftest/swiftest_io.f90

@@ -579,7 +579,7 @@ module subroutine swiftest_io_netcdf_get_t0_values_system(self, param)
       integer(I4B)                              :: itmax, idmax, tslot
       real(DP), dimension(:), allocatable       :: vals
       real(DP), dimension(1)                    :: rtemp
-      real(DP), dimension(NDIM)                 :: rot0, Ip0
+      real(DP), dimension(NDIM)                 :: rot0, Ip0, L
       real(DP) :: mass0
 
       associate (nc => self%system_history%nc, cb => self%cb)
@@ -628,6 +628,8 @@ module subroutine swiftest_io_netcdf_get_t0_values_system(self, param)
                rot0(:) = rot0(:) * DEG2RAD
                call netcdf_io_check( nf90_get_var(nc%id, nc%Ip_varid, Ip0, start=[1,1,tslot], count=[NDIM,1,1]), "netcdf_io_get_t0_values_system Ip_varid" )
                cb%L0(:) = Ip0(3) * mass0 * cb%R0**2 * rot0(:)
+               L(:) = cb%Ip(3) * cb%mass * cb%radius**2 * cb%rot(:)
+               cb%dL(:) = L(:) - cb%L0
             end if
 
             ! Retrieve the current bookkeeping variables
@@ -2400,8 +2402,8 @@ module subroutine swiftest_io_param_writer(self, unit, iotype, v_list, iostat, i
          end if
          call io_param_writer_one("FIRSTKICK",param%lfirstkick, unit)
 
-         if (param%GMTINY > 0.0_DP) call io_param_writer_one("GMTINY",param%GMTINY, unit)
-         if (param%min_GMfrag > 0.0_DP) call io_param_writer_one("MIN_GMFRAG",param%min_GMfrag, unit)
+         if (param%GMTINY >= 0.0_DP) call io_param_writer_one("GMTINY",param%GMTINY, unit)
+         if (param%min_GMfrag >= 0.0_DP) call io_param_writer_one("MIN_GMFRAG",param%min_GMfrag, unit)
          call io_param_writer_one("COLLISION_MODEL",param%collision_model, unit)
          if (param%collision_model == "FRAGGLE" ) then
             nseeds = size(param%seed)