added collision and encounter files to output list

README.md

@@ -286,13 +286,16 @@ Where ```INTEGRATOR``` is your integrator of choice, either ```whm```, ```rmvs``
 
 **Outputs**
 
-Swiftest generates between 1 and 6 output files, depending on the input parameters selected and the method through which Swiftest was run. The output files are as follows:
-- **<span>bin.nc</span>** - Always generated, the output file containing the information for every body in the system, recorded every ```ISTEP_OUT``` timesteps and written every ```DUMP_CADENCE```.
-- **fraggle.log** - The log containing the record of each fragmentation event, including the properties of the colliding bodies, the collisional regime, and the properties of the fragments created, only if ```FRAGMENTATION``` is ```YES```, Swiftest SyMBA only, ASCII file format only
-- **encounter_check_plpl_timer.log** - The log containing the encounter check timer for each massive body/massive body encounter,  only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```, ASCII file format only
-- **encounter_check_pltp_time.log** - The log containing the encounter check timer for each massive body/test particle encounter, only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```, ASCII file format only
-- **interaction_timer.log** - The log containing the interaction loop timer for each interacting pair of bodies, only if ```INTERACTION_LOOPS``` is ```ADAPTIVE```, ASCII file format only
-- **swiftest.log** - A log containing the input parameters and a brief updated on the status of the run. Only generated if Swiftest is run through the Python package. If Swiftest is run through the terminal, these updates are output directly to the terminal.
+The number and type of output files generated by Swiftest depends on the input parameters selected and the method through which Swiftest was run. The standard output files are as follows:
+- **<span>data.nc</span>** - Always generated, the output file containing the information for every body in the system, recorded every ```ISTEP_OUT``` timesteps and written every ```DUMP_CADENCE```. This file can be analyzed using the Swiftest Python package (```sim.data```).
+- **fraggle.log** - The log containing the record of each fragmentation event, including the collisional regime, and the number of the fragments created, only if ```FRAGMENTATION``` is ```YES```, Swiftest SyMBA only.
+- **swiftest.log** - A log containing a brief updated on the status of the run. Only generated if Swiftest is run through the Python package. If Swiftest is run through the terminal, these updates are output directly to the terminal.
+- **collision_xxxxxx.nc** - The details of each collision that occurs in a simulation are recorded in a NetCDF file. Each collision receives its own file. These files are consolidated and can be analyzed using the Swiftest Python package (```sim.collisions```). Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```.
+- **encounter_xxxxxx.nc** - The details of each close encounter that occurs in a simulation are recorded in a NetCDF file. Each encounter receives its own file. These files are consolidated and can be analyzed using the Swiftest Python package (```sim.encounters```). Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```.
+- **init_cond.nc** - The initial conditions used to run the simulation. This file can be analyzed using the Swiftest Python package (```sim.init_cond```).
+- **encounter_check_plpl_timer.log** - The log containing the encounter check timer for each massive body/massive body encounter,  only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```.
+- **encounter_check_pltp_time.log** - The log containing the encounter check timer for each massive body/test particle encounter, only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True``` and ```ENCOUNTER_CHECK```/```encounter_check_loops``` is ```ADAPTIVE```.
+- **interaction_timer.log** - The log containing the interaction loop timer for each interacting pair of bodies, only if ```INTERACTION_LOOPS``` is ```ADAPTIVE```.
 
 To read in a Swiftest output file, simply create a new Python script in the simulation directory.