diff --git a/README.md b/README.md index 109789768..d3ffcc335 100644 --- a/README.md +++ b/README.md @@ -145,7 +145,7 @@ sim.get_parameter(**kwargs) # View the defa sim.set_parameter(**kwargs) # Set any desired simulation parameters sim.write_param(**kwargs) # Write simulation parameters to the param.in sim.save(**kwargs) # Save the simulation initial conditions to init_cond.nc -sim.run(**kwargs) # Run the simulation (leave off if running from the terminal) +sim.run(**kwargs) # Run the simulation (leave off if running from the executable) ``` To read in a set of Swiftest output files using the Swiftest Python package, follow the general script below. For more details on the output files and user options, continue reading this section. @@ -199,7 +199,7 @@ After all desired parameters have been set, the parameters can be saved to the * The state of the system can be saved to the initial conditions NetCDF file, **init_cond.nc**, using the ```save``` method. The key word arguments available to the user for the ```save``` method are described in [save_kwargs](README_tables/save_kwargs.md). -Finally, a simulation can be run from the same script in which it is created (or a separate Python script) using the ```run``` method. This is optional as the simulation can also be run from the terminal. More details on running a Swiftest simulation can be found in the section **Running a Swiftest Simulation**. The key word arguments available to the user for the ```run``` method are the same as those described in [simulation_kwargs](README_tables/simulation_kwargs.md). +Finally, a simulation can be run from the same script in which it is created (or a separate Python script) using the ```run``` method. This is optional as the simulation can also be run from an executable. More details on running a Swiftest simulation can be found in the section **Running a Swiftest Simulation**. The key word arguments available to the user for the ```run``` method are the same as those described in [simulation_kwargs](README_tables/simulation_kwargs.md). **ASCII Input Files** Swiftest accepts 4 ASCII input files. All four input files are necessary, however the structure of each input file varies slightly depending on the features and capabilities of the integrator selected. The four input files are as follows: @@ -257,7 +257,7 @@ Note that the ID numbers of the test particles are a continuation of the ID numb **Running a Swiftest Simulation** -The input files necessary to successfully run Swiftest should now be generated in the simulation directory. The user is now faced with a second choice: to run a Swiftest simulation from a Python environment or to run it directly from the terminal. Either option is possible with NetCDF format input files, however ASCII input files must be run directly from the terminal. +The input files necessary to successfully run Swiftest should now be generated in the simulation directory. The user is now faced with a second choice: to run a Swiftest simulation from a Python environment or to run it directly from an executable. Either option is possible with NetCDF format input files, however ASCII input files must be run directly from an executable. **Running via Python** @@ -274,9 +274,9 @@ sim = swiftest.Simulation(simdir = "directory_name", read_param=True) sim.run() ``` -**Running via a Terminal** +**Running via an Executable** -To run a Swiftest simulation through the terminal, create a symbolic link to the Swiftest driver from your current directory. +To run a Swiftest simulation through an executable, create a symbolic link to the Swiftest driver from your current directory. ``` $ ln -s ~/PATH/TO/swiftest/bin/swiftest_driver . @@ -295,7 +295,7 @@ Where ```INTEGRATOR``` is your integrator of choice, either ```whm```, ```rmvs`` 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: - **data.nc** - 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```). - **collisions.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 update on the status of the run. Only generated if Swiftest is run through the Python package or through a shell script. If Swiftest is run directly through the terminal, these updates are output directly to the terminal. +- **swiftest.log** - A log containing a brief update on the status of the run. Only generated if Swiftest is run through the Python package or through a shell script. If Swiftest is run through an executable, these updates are output directly to the terminal. - **collisions.nc** - The details of each collision that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.collisions```). - **encounters.nc** - The details of each close encounter that occurs in a simulation are recorded in a NetCDF file. Only if ```CHK_CLOSE```/```close_encounter_check``` is ```YES```/```True```. This file can be analyzed using the Swiftest Python package (```sim.encounters```). - **init_cond.nc** - The initial conditions used to run the simulation. This file can be analyzed using the Swiftest Python package (```sim.init_cond```). @@ -324,7 +324,7 @@ The first line includes the simulation time, the fraction of the simulation that **Restarting a Simulation From t $\neq$ 0** -Just like Swiftest allows the user to run a simulation through the terminal or through Python, Swiftest also allows the user to restart a simulation from t $\neq$ 0 in the same two manners. This can be useful in the case of an accidental termination of a simulation, such as through a power outage or computer failure. In many cases, it is also necessary to run a simulation to a new end point, past the original ```TSTOP```. +Just like Swiftest allows the user to run a simulation through an executable or through Python, Swiftest also allows the user to restart a simulation from t $\neq$ 0 in the same two manners. This can be useful in the case of an accidental termination of a simulation, such as through a power outage or computer failure. In many cases, it is also necessary to run a simulation to a new end point, past the original ```TSTOP```. **Restarting via Python** @@ -340,9 +340,9 @@ sim.run() Note that Swiftest will look in the ```/simdata``` subdirectory for the initial conditions by default. You may set a new path to the initial conditions using the ```param_file``` keyword argument. -**Restarting via a Terminal** +**Restarting via an Executable** -Every ```DUMP_CADENCE``` X ```ISTEP_OUT``` timesteps, Swiftest writes all simulation information from memory to the output files. At the same time, Swiftest also writes all simulation information to a new parameter file, titled **param.XXXXXXXXXXXXXXXXXX.in**. To restart a run from a previous parameter file, simply follow the instructions detailed in the **Running via a Terminal** section, replacing ```param.in``` with the name of the parameter file from which you wish to restart. +Every ```DUMP_CADENCE``` X ```ISTEP_OUT``` timesteps, Swiftest writes all simulation information from memory to the output files. At the same time, Swiftest also writes all simulation information to a new parameter file, titled **param.XXXXXXXXXXXXXXXXXX.in**. To restart a run from a previous parameter file, simply follow the instructions detailed in the **Running via an Executable** section, replacing ```param.in``` with the name of the parameter file from which you wish to restart. ---