RWSims

Collection of rw sim scripts

Usage

# the next lines are only necessary if the python script is not in the same folder as rwsims
import sys
sys.path.append('/path/to/RWSims')

from rwsims.sims import run_ste_sim, run_spectrum_sim

run_ste_sim('/path/to/json-file')
run_spectrum_sim('/path/to/json-file')

Parameter file

Parameter for a simulation are given by a JSON file, sections are:

simulation

key	type	description
num	integer	Number of trajectories
seed	integer or null	Seed value for random number generator

molecule

key	type	description
delta	float	Anisotropy (in Hz)
eta	float	Asymmetry

correlation_times

key	type	description
distribution	string	Name of distribution. Possible values: DeltaDistribution, LogGaussian
tau	variable	Characteristic time of distribution (in s)
Other parameter	variable	Additional parameter, e.g., sigma

motion

key	type	description
model	string	Name of motion. Possible values: RandomJump, TetrahedralJump

spectrum

key	type	description
dwell_time	float	Dwell time of acquisition (in s)
num_points	integer	Number of acquisition points
t_echo	variable	One or more echo delays (use zero for FID) (in s)
line_broadening	float	Additional exponential broadening (in Hz)
t_pulse	float	Pulse length used of attenuation (in s)

ste

key	type	description
t_evo	variable	One or more evolution times
t_mix	variable	One or more mixing times
t_echo	float	Optional echo delay for 4-pulse sequence (in s)

variable type

Keys of type variable can be a single value, a list of values, or values between a given start and stop value.

Examples:

• A single value

{
  // Other parameter...
  "tau": 1e-3,
  // More parameter..
}

• A list of predefined values, defined by key list

{
  // Other parameter...
  "tau": {
    "list": [1e-5, 1e-4, 1e-3, 1e-2]
  },
  // More parameter..
}

++ A list of predefined values, based on start and end value

{
  // Other parameter...
  "tau": {
    "start": 1e-6,
    "stop": 1e0,
    "steps": 31,
    "is_log": true  // this parameter is optional, default is false
  },
  // More parameter..
}

Output

Results are written to text files and png images.

• For spectrum simulations:
  1. Each combination of distribution and motion parameter produces files for the dependence of timesignals/spectra on the echo delay.
  2. The reduction factor vs. correlation time is plotted for all variable together in one png plot
• For STE simulation:
  1. Each combination of distribution and motion parameter produces files for the CC/SS decays.
  2. The dependence on the evolution of the fit parameter is saved and plotted for the various variable combinations