Manual
User Manual:
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- I Using the Pencil Code
- System requirements
- Obtaining the code
- Getting started
- Code structure
- Using the code
- Configuring the code to compile and run on your computer
- Adapting Makefile.src [obsolete; see Sect. 5.1]
- Changing the resolution
- Using a non-equidistant grid
- Diagnostic output
- Data files
- Video files and slices
- Averages
- Helper scripts
- RELOAD and STOP files
- RERUN and NEWDIR files
- Start and run parameters
- Physical units
- Minimum amount of viscosity
- The time step
- Boundary conditions
- Restarting a simulation
- One- and two-dimensional runs
- Visualization
- Running on multi-processor computers
- Running in double-precision
- Power spectrum
- Structure functions
- Particles
- Non-cartesian coordinate systems
- The equations
- Continuity equation
- Equation of motion
- Induction equation
- Entropy equation
- Transport equation for a passive scalar
- Bulk viscosity
- Equation of state
- Ionization
- Combustion
- Radiative transfer
- Self-gravity
- Incompressible and anelastic equations
- Dust equations
- Cosmic ray pressure in diffusion approximation
- Chiral MHD
- Particles
- N-body solver
- Test-field equations
- Gravitational wave equations
- Troubleshooting / Frequently Asked Questions
- Download and setup
- Compilation
- Problems compiling syscalls
- Unable to open include file: chemistry.h
- Compiling with ifc under Linux
- Segmentation fault with ifort 8.0 under Linux
- The underscore problem: linking with MPI
- Compilation stops with the cryptic error message:
- The code doesn't compile,
- Some samples don't even compile,
- Internal compiler error with Compaq/Dec F90
- Assertion failure under SunOS
- After some dirty tricks I got pencil code to compile with MPI, ...
- Error: Symbol 'mpi_comm_world' at (1) has no IMPLICIT type
- Error: Can't open included file 'mpif.h'
- Pencil check
- The pencil check complains for no reason.
- The pencil check reports MISSING PENCILS and quits
- The pencil check reports unnecessary pencils
- The pencil check reports that most or all pencils are missing
- Running the pencil check triggers mathematical errors in the code
- The pencil check still complains
- The pencil check is annoying so I turned it off
- Running
- Periodic boundary conditions in start.x
- csh problem?
- run.csh doesn't work:
- Code crashes after restarting
- auto-test gone mad...?
- Can I restart with a different number of cpus?
- Can I restart with a different number of cpus?
- fft_xyz_parallel_3D: nygrid needs to be an integer multiple...
- Unit-agnostic calculations?
- Visualization
- General questions
- II Programming the Pencil Code
- III Appendix
- Timings
- Coding standard
- Some specific initial conditions
- Some specific boundary conditions
- High-frequency filters
- Special techniques
- Runs and reference data
- Numerical methods
- Curvilinear coordinates
- Switchable modules
- Startup and run-time parameters
- Startup parameters for start.in
- Runtime parameters for run.in
- Parameters for print.in
- Parameters for video.in
- Parameters for phiaver.in
- Parameters for xyaver.in
- Parameters for xzaver.in
- Parameters for yzaver.in
- Parameters for yaver.in
- Parameters for zaver.in
- Boundary conditions
- Initial condition parameter dependence
- IV Indexes