Running the program¶
Running with default configurations can be achieved by running the below in a terminal:
mango
This will run the program with the default values shown in the input file. See further examples in Examples. If not specified, the positions of the molecules will be the stable Leonard Jones configuration downloaded from http://doye.chem.ox.ac.uk/jon/structures/LJ/
Other commandline functions include:
MPI calculation command:
mango_mpi
Running the mango test suite:
mango_test
Restart and input file regenerators:
mango_inputregen
mango_restartregen
The rest have their own help with -h:
mango_plotsuscep
mango_strings
mango_vars
mango_vis
Jupyter Notebook or Module use¶
There are currently two functions designed for use as a module import or as part of a jupyter notebook and they are:
mango.run()
mango.help()
Run takes a dictionary as input with the keys and values the same as the input file. To run a simple simulation a python script would be;
import mango
mango.run({'SusceptibilityCalc': True, 'Iterations': 100000,
'Repetitions': 1, 'NumberParticles': 5,
'PositionFile': './Position_file'})
Help prints the help shown below.
Running with an Input or Restarting¶
To use an input file:
-I Inputfile
To restart a run, specify the restart file as shown:
-R Run1restart
Saving Mechanism¶
Saving happens in two stages when running the main calculation as shown below. This reduces the amount of I/O to disk.
There are a two commands to deal with the saving. These are SkipSave (–skip) and SaveChunk (–savechunk). SkipSave deals with the number of iterations that are saved to memory and SaveChunk is the number of saved iterations to be collected before writing to disk.
Errors¶
Errors are split into 2 categories, warning and critical. The program will still run under warnings but it will kill itself under critical errors.
Warning messages will be written like so:
Warning: maximum number of iterations exceeded! [MD step 1] x10
The above message tells us that the error has happened 10 times on the first MD step.
Internal Help¶
To print the help from the commandline use the command mango -h, to print the input file help from the commandline use mango -ifh or call mango.help() from an interactive prompt. For the full input file see Full Input File. The commandline help is shown below.
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Version: 0.8.0-g_616c94e
usage: mango [-h] [-I INPUTFILE] [-R RESTART] [-P LOCATION] [-nu NU] [-f H_0]
[-e ETA] [-Mdens MDENS] [-dn DENS [DENS ...]]
[-rad RADIUS [RADIUS ...]] [-T TEMP] [--no-noise]
[-bx BOXSIZE [BOXSIZE ...]] [--epsilon EPSILON] [-n NMAX]
[--no-labview] [--no-mag] [-np NO_MOLECULES] [--opt] [--no-pbc]
[--potential POTENTIAL] [-st STATS] [-sk SKIP]
[--suscep [{mag,vel,angular,inertia,rotation,} [{mag,vel,angular,inertia,rotation,} ...]]]
[--op_thermal] [-dt DT] [--align] [--bl BLOCK [BLOCK ...]]
[--cfile {xyz,energy,momenta,lf} [{xyz,energy,momenta,lf} ...]]
[-eq EQ] [--column COLUMN [COLUMN ...]] [--run RUN] [--kinetic]
[--lengthcheck] [--showg] [--saveg] [--ufile UFILE] [--logs LOGS]
[--no-parallel] [-sv SAVECHUNK] [--save_type {hdf5,pkl,txt}]
[--scfiter SCFITER] [--walltime WALLTIME] [-v] [--neel] [-k KEFF]
[--tauN_0 TAUN_0] [--temp0 TEMP0]
Mango: magnetic nanoparticle simulator CLI Help
optional arguments:
-h, --help show this help message and exit
-I INPUTFILE Input file location
-R RESTART Restart file location
-P LOCATION Positions file location
-nu NU External Field Frequency
(default: 1.00e-06[Hz])
-f, --field H_0 External Field Strength
(default: 167.0[1e-6 Gauss])
-e, --eta ETA Solvent Viscosity
(default: 0.01002 [g/(cm *s)])
-Mdens MDENS Magnetic Density of particles
(default 85 [emu/g])
-dn, --dens [DENS ...]
Density of each particle
(default: 6.99[g /cm^3])
-rad, --radius [RADIUS ...]
Radius of each particle
(default: 5.0[1e-6cm])
-T, --temp TEMP Temperature
(default: 298.0[K])
--no-noise Background Noise switch
(default: True)
-bx, --boxsize [BOXSIZE ...]
Periodic boundary box size
(default: max of (1.1 * Number of Molecules * Radius) or 50[1e-6cm])
--epsilon EPSILON Set depth of Potential Well
(default: Scales wrt Ar (isothermal compresibility))
-n, --nmax NMAX Number of Iterations
(default: 400.0)
--no-labview Remove initial cluster momentum
(default: True)
--no-mag Magnetisation calculation switch
(default: True)
-np, --no_particles NO_MOLECULES
Number of Particles
(default: 5)
--opt Auto-minimise energy of the system
(default: False)
--no-pbc Periodic Boundary Conditions
(default: True)
--potential POTENTIAL
Change potential used
-st, --stats STATS Number of statistical repetitions
(default: 10)
-sk, --skip SKIP Save every # iterations
(default: 1)
--suscep [{mag,vel,angular,inertia,rotation,} ...]
Zero field Calculation
(default: False)
--op_thermal Add thermal noise to the momentum after the optimisation
(default: False)
-dt DT Timestep
(default: 20[ps])
--align Align with Kabsch algorithm
(default: False)
--bl [BLOCK ...] Block averaging bins
(default: [5, 10, 20, 50, 100])
--cfile [{xyz,energy,momenta,lf} ...]
Create output files
(default: False)
-eq EQ Strip fraction of trajectory for equilibration
(default: 0.1)
--column [COLUMN ...]
Plot simple datasets
--run RUN Select run number
(default: False)
--kinetic Calculate kinetic temperature
(default: False)
--lengthcheck Calculate average particle separation
(default: False)
--showg Show graphs during run
(default: False)
--saveg Save graphs
WARNING: slow for large datasets
(default: False)
--ufile UFILE Post process from a specific file
--logs LOGS Log save directory
(default:./Mango_0.8.0-g_616c94e_Logs)
--no-parallel Parallel Computation
(default: True)
-sv, --savechunk SAVECHUNK
Save to file every # iterations
(default: Smallest of 1e+04 and Nmax)
--save_type {hdf5,pkl,txt}
Save filetype (hdf5, pkl, txt)
(default: hdf5)
--scfiter SCFITER Magnetic self consistancy loop before warning
(default: 20)
--walltime WALLTIME Run time
(default: 1e+07[s])
-v, --verbosity Verbosity level
(default: 2, Max implemented: 5)
--neel Enable Neel relaxations
(default: False)
-k, --keff KEFF Set anisotropic factor
(default: 2.25e-08[erg*cm3])
--tauN_0 TAUN_0 Zero value for τn
(default: 1.70e+00[1.e-12 s])
--temp0 TEMP0 Neel zero temperature
(default: 2.62e+02[K])