Trajectory modifiers¶
Trajectory modifiers classes change the path of particles, examples from standard trajectory_modifiers classes below.
Particle behaviour¶
Particles with a random fraction temporarily frozen on a polygon shaped reef.
class:
trajectory_modifiers.settlement_in_polygon.SettleInPolygon
json parameters
../../../demos/demo_param_files/demo06_reefstranding.json¶
{
"output_file_base": "demo06_reefstranding",
"add_date_to_run_output_dir": false,
"time_step": 600,
"debug": true,
"reader": {
"class_name": "oceantracker.reader.generic_unstructured_reader.GenericUnstructuredReader",
"input_dir": "E:\\H_Local_drive\\ParticleTracking\\oceantracker\\demos\\demo_hindcast",
"file_mask": "demoHindcast2D*.nc",
"search_sub_dirs": true,
"dimension_map": {
"time": "time",
"node": "nodes"
},
"grid_variables": {
"time": "time_sec",
"x": [
"east",
"north"
],
"triangles": "tri"
},
"field_variables": {
"water_velocity": [
"east_vel",
"north_vel"
],
"water_depth": "depth",
"tide": "tide"
},
"time_buffer_size": 15,
"isodate_of_hindcast_time_zero": "2020-06-01"
},
"user_note": "test of notes",
"dispersion_miss-spelt": {
"A_H": 0.1
},
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"write_dry_cell_index": true,
"convert": true
},
"release_groups": {
"P1": {
"points": [
[
1594500,
5482700
],
[
1598000,
5486100
],
[
1595500,
5489700
]
],
"pulse_size": 10,
"release_interval": 10800
},
"poly1": {
"class_name": "oceantracker.release_groups.polygon_release.PolygonRelease",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
],
"pulse_size": 1,
"release_interval": 0
}
},
"particle_properties ": {
"Oxygen": {
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0,
"initial_value": 20.0
},
"distance_travelled": {
"class_name": "oceantracker.particle_properties.distance_travelled.DistanceTravelled"
}
},
"particle_properties": {
"my_constant_prop": {
"class_name": "oceantracker.particle_properties.load_carrying.ParticleLoad",
"initial_value": 100,
"variance": 10.0
}
},
"block_dry_cells": true,
"trajectory_modifiers": {
"settle_in+polygon": {
"class_name": "oceantracker.trajectory_modifiers.settle_in_polygon.SettleInPolygon",
"polygon": {
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
]
},
"probability_of_settlement": 0.1,
"settlement_duration": 10800.0
}
},
"backtracking": true,
"particle_statistics": {
"polystats1": {
"class_name": "oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased",
"update_interval": 1800,
"particle_property_list": [
"water_depth"
],
"use_release_group_polygons": true,
"polygon_list": [
{
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
},
"root_output_dir": "output"
}
yaml parameters
../../../demos/demo_param_files/demo06_reefstranding.yaml¶
add_date_to_run_output_dir: false
backtracking: true
block_dry_cells: true
debug: true
dispersion:
A_H: 0.1
dispersion_miss-spelt:
A_H: 0.1
output_file_base: demo06_reefstranding
particle_properties:
my_constant_prop:
class_name: oceantracker.particle_properties.load_carrying.ParticleLoad
initial_value: 100
variance: 10.0
'particle_properties ':
Oxygen:
class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
initial_value: 20.0
distance_travelled:
class_name: oceantracker.particle_properties.distance_travelled.DistanceTravelled
particle_statistics:
polystats1:
class_name: oceantracker.particle_statistics.polygon_statistics.PolygonStats2D_timeBased
particle_property_list:
- water_depth
polygon_list:
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
update_interval: 1800
use_release_group_polygons: true
reader:
class_name: oceantracker.reader.generic_unstructured_reader.GenericUnstructuredReader
dimension_map:
node: nodes
time: time
field_variables:
tide: tide
water_depth: depth
water_velocity:
- east_vel
- north_vel
file_mask: demoHindcast2D*.nc
grid_variables:
time: time_sec
triangles: tri
x:
- east
- north
input_dir: E:\H_Local_drive\ParticleTracking\oceantracker\demos\demo_hindcast
isodate_of_hindcast_time_zero: '2020-06-01'
search_sub_dirs: true
time_buffer_size: 15
release_groups:
P1:
points:
- - 1594500
- 5482700
- - 1598000
- 5486100
- - 1595500
- 5489700
pulse_size: 10
release_interval: 10800
poly1:
class_name: oceantracker.release_groups.polygon_release.PolygonRelease
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
pulse_size: 1
release_interval: 0
root_output_dir: output
time_step: 600
tracks_writer:
convert: true
write_dry_cell_index: true
trajectory_modifiers:
settle_in+polygon:
class_name: oceantracker.trajectory_modifiers.settle_in_polygon.SettleInPolygon
polygon:
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
probability_of_settlement: 0.1
settlement_duration: 10800.0
user_note: test of notes
Resuspension¶
Particles with fall velocity and resuspension based on critical friction velocity.
class
trajectory_modifiers.resuspension.BasicResuspension
Vertical slice showing one example of a falling particle and resuspension, with particle on bottom during low flows around low and high tides. Blue line is particle status, 10= moving, 6 = on the bottom.
json parameters
../../../demos/demo_param_files/demo58_bottomBounce.json¶
{
"output_file_base": "demo58_bottomBounce",
"debug": true,
"time_step": 120,
"reader": {
"input_dir": "E:\\H_Local_drive\\ParticleTracking\\oceantracker\\demos\\demo_hindcast",
"file_mask": "demoHindcastSchism3D.nc",
"field_variables": {
"water_temperature": "temp"
},
"depth_average": false,
"field_variables_to_depth_average": [
"water_velocity",
"salt",
"water_temperature"
]
},
"dispersion": {
"A_H": 0.1,
"A_V": 0.005
},
"release_groups": {
"P1": {
"points": [
[
1593000.0,
5486000.0,
-1
]
],
"pulse_size": 10,
"release_interval": 0
},
"poly1": {
"class_name": "oceantracker.release_groups.polygon_release.PolygonRelease",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5489000
],
[
1597300,
5489000
],
[
1597682.1237,
5489972.7479
]
],
"z_range": [
-2,
-4.0
],
"pulse_size": 10,
"release_interval": 3600
},
"P11": {
"points": [
[
1593000.0,
5486000.0,
-1
]
],
"pulse_size": 10,
"release_interval": 0
}
},
"particle_properties": {
"age_decay": {
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
},
"event_loggers": {
"inoutpoly": {
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
},
"velocity_modifiers": {
"terminal_velocity": {
"class_name": "oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity",
"value": -0.002,
"variance": 0.0002
}
},
"particle_statistics": {
"grid1": {
"class_name": "oceantracker.particle_statistics.gridded_statistics.GriddedStats2D_timeBased",
"update_interval": 3600,
"particle_property_list": [
"water_depth"
],
"status_min": "moving",
"z_min": -2,
"grid_size": [
120,
121
]
}
},
"resuspension": {
"critical_friction_velocity": 0.005
},
"backtracking": false,
"root_output_dir": "output"
}
yaml parameters
../../../demos/demo_param_files/demo58_bottomBounce.yaml¶
backtracking: false
debug: true
dispersion:
A_H: 0.1
A_V: 0.005
event_loggers:
inoutpoly:
class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
output_file_base: demo58_bottomBounce
particle_properties:
age_decay:
class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
particle_statistics:
grid1:
class_name: oceantracker.particle_statistics.gridded_statistics.GriddedStats2D_timeBased
grid_size:
- 120
- 121
particle_property_list:
- water_depth
status_min: moving
update_interval: 3600
z_min: -2
reader:
depth_average: false
field_variables:
water_temperature: temp
field_variables_to_depth_average:
- water_velocity
- salt
- water_temperature
file_mask: demoHindcastSchism3D.nc
input_dir: E:\H_Local_drive\ParticleTracking\oceantracker\demos\demo_hindcast
release_groups:
P1: &id001
points:
- - 1593000.0
- 5486000.0
- -1
pulse_size: 10
release_interval: 0
P11: *id001
poly1:
class_name: oceantracker.release_groups.polygon_release.PolygonRelease
points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5489000
- - 1597300
- 5489000
- - 1597682.1237
- 5489972.7479
pulse_size: 10
release_interval: 3600
z_range:
- -2
- -4.0
resuspension:
critical_friction_velocity: 0.005
root_output_dir: output
time_step: 120
velocity_modifiers:
terminal_velocity:
class_name: oceantracker.velocity_modifiers.terminal_velocity.TerminalVelocity
value: -0.002
variance: 0.0002
Splitting particles¶
Particles with splitting in two every 6 hours and a 5% chance of dying every 6 hours.
class:
trajectory_modifiers.split_particles.SplitParticlesclass:
trajectory_modifiers.cull_particles.CullParticles
json parameters
../../../demos/demo_param_files/demo08_particle_splitting.json¶
{
"output_file_base": "demo08_particle_splitting",
"add_date_to_run_output_dir": false,
"time_step": 600,
"debug": true,
"reader": {
"class_name": "oceantracker.reader.generic_unstructured_reader.GenericUnstructuredReader",
"input_dir": "E:\\H_Local_drive\\ParticleTracking\\oceantracker\\demos\\demo_hindcast",
"file_mask": "demoHindcast2D*.nc",
"search_sub_dirs": true,
"dimension_map": {
"time": "time",
"node": "nodes"
},
"grid_variables": {
"time": "time_sec",
"x": [
"east",
"north"
],
"triangles": "tri"
},
"field_variables": {
"water_velocity": [
"east_vel",
"north_vel"
],
"water_depth": "depth",
"tide": "tide"
},
"time_buffer_size": 15,
"isodate_of_hindcast_time_zero": "2020-06-01"
},
"user_note": "test of notes",
"dispersion_miss-spelt": {
"A_H": 0.1
},
"dispersion": {
"A_H": 0.1
},
"tracks_writer": {
"write_dry_cell_index": true,
"convert": true
},
"release_groups": {
"P1": {
"points": [
[
1594500,
5483500
],
[
1594500,
5486500
]
],
"pulse_size": 1,
"release_interval": 0
}
},
"particle_properties ": {
"Oxygen": {
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0,
"initial_value": 20.0
},
"distance_travelled": {
"class_name": "oceantracker.particle_properties.distance_travelled.DistanceTravelled"
}
},
"particle_properties": {
"age_decay": {
"class_name": "oceantracker.particle_properties.age_decay.AgeDecay",
"decay_time_scale": 86400.0
}
},
"block_dry_cells": true,
"event_loggers": {
"in_out_poly": {
"class_name": "oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit",
"particle_prop_to_write_list": [
"ID",
"x",
"IDrelease_group",
"status",
"age"
],
"polygon_list": [
{
"user_polygon_name": "A",
"points": [
[
1592682.1237,
5489972.7479
],
[
1593604.1667,
5490275.5488
],
[
1593886.4247,
5489464.0424
],
[
1592917.3387,
5489000.0
],
[
1592300.0,
5489000.0
],
[
1592682.1237,
5489972.7479
]
]
},
{
"user_polygon_name": "B",
"points": [
[
1597682.1237,
5489972.7479
],
[
1598604.1667,
5490275.5488
],
[
1598886.4247,
5489464.0424
],
[
1597917.3387,
5487000
],
[
1597300,
5487000
],
[
1597682.1237,
5489972.7479
]
]
}
]
}
},
"max_particles": 1000,
"particle_buffer_size": 5000,
"trajectory_modifiers": {
"part_spliting": {
"class_name": "oceantracker.trajectory_modifiers.split_particles.SplitParticles",
"splitting_interval": 21600,
"split_status_greater_than": "frozen"
},
"part_culling": {
"class_name": "oceantracker.trajectory_modifiers.cull_particles.CullParticles",
"cull_interval": 21600,
"cull_status_greater_than": "dead",
"probability_of_culling": 0.05
}
},
"root_output_dir": "output"
}
yaml parameters
../../../demos/demo_param_files/demo08_particle_splitting.yaml¶
add_date_to_run_output_dir: false
block_dry_cells: true
debug: true
dispersion:
A_H: 0.1
dispersion_miss-spelt:
A_H: 0.1
event_loggers:
in_out_poly:
class_name: oceantracker.event_loggers.log_polygon_entry_and_exit.LogPolygonEntryAndExit
particle_prop_to_write_list:
- ID
- x
- IDrelease_group
- status
- age
polygon_list:
- points:
- - 1592682.1237
- 5489972.7479
- - 1593604.1667
- 5490275.5488
- - 1593886.4247
- 5489464.0424
- - 1592917.3387
- 5489000.0
- - 1592300.0
- 5489000.0
- - 1592682.1237
- 5489972.7479
user_polygon_name: A
- points:
- - 1597682.1237
- 5489972.7479
- - 1598604.1667
- 5490275.5488
- - 1598886.4247
- 5489464.0424
- - 1597917.3387
- 5487000
- - 1597300
- 5487000
- - 1597682.1237
- 5489972.7479
user_polygon_name: B
max_particles: 1000
output_file_base: demo08_particle_splitting
particle_buffer_size: 5000
particle_properties:
age_decay:
class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
'particle_properties ':
Oxygen:
class_name: oceantracker.particle_properties.age_decay.AgeDecay
decay_time_scale: 86400.0
initial_value: 20.0
distance_travelled:
class_name: oceantracker.particle_properties.distance_travelled.DistanceTravelled
reader:
class_name: oceantracker.reader.generic_unstructured_reader.GenericUnstructuredReader
dimension_map:
node: nodes
time: time
field_variables:
tide: tide
water_depth: depth
water_velocity:
- east_vel
- north_vel
file_mask: demoHindcast2D*.nc
grid_variables:
time: time_sec
triangles: tri
x:
- east
- north
input_dir: E:\H_Local_drive\ParticleTracking\oceantracker\demos\demo_hindcast
isodate_of_hindcast_time_zero: '2020-06-01'
search_sub_dirs: true
time_buffer_size: 15
release_groups:
P1:
points:
- - 1594500
- 5483500
- - 1594500
- 5486500
pulse_size: 1
release_interval: 0
root_output_dir: output
time_step: 600
tracks_writer:
convert: true
write_dry_cell_index: true
trajectory_modifiers:
part_culling:
class_name: oceantracker.trajectory_modifiers.cull_particles.CullParticles
cull_interval: 21600
cull_status_greater_than: dead
probability_of_culling: 0.05
part_spliting:
class_name: oceantracker.trajectory_modifiers.split_particles.SplitParticles
split_status_greater_than: frozen
splitting_interval: 21600
user_note: test of notes