physioblocks 1.1.1__py3-none-any.whl → 1.1.3__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- physioblocks/__init__.py +1 -1
- physioblocks/io/aliases.py +25 -4
- physioblocks/references/full_configurations/circulation_alone_sim.jsonc +146 -0
- physioblocks/references/full_configurations/spherical_heart_respiration_sim.jsonc +387 -0
- physioblocks/references/full_configurations/spherical_heart_sim.jsonc +343 -0
- {physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/METADATA +1 -1
- {physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/RECORD +10 -7
- {physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/WHEEL +0 -0
- {physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/licenses/licenses/GPL-3.0-only.txt +0 -0
- {physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/licenses/licenses/LGPL-3.0-only.txt +0 -0
physioblocks/__init__.py
CHANGED
physioblocks/io/aliases.py
CHANGED
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@@ -26,10 +26,16 @@
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"""Defines methods to load aliases folders."""
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import logging
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from pathlib import Path
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from physioblocks.configuration.aliases import add_alias
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from physioblocks.io.configuration import read_json
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from physioblocks.utils.exceptions_utils import log_exception
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_logger = logging.getLogger(__name__)
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_JSON_EXTENSIONS = [".json", ".jsonc"]
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def load_aliases(path: str) -> None:
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@@ -67,7 +73,22 @@ def load_aliases(path: str) -> None:
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# recursivly load child directories
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load_aliases(str(child))
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else:
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-
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if child.suffix not in _JSON_EXTENSIONS:
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continue
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try:
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config_alias = read_json(str(child))
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# get file name without extension as alias id
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alias_id = child.name.removesuffix(child.suffix)
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add_alias(alias_id, config_alias)
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except Exception as error:
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_logger.warning(
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str.format(
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"Error while loading alias from: {0}. File skipped.",
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str(child.absolute()),
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)
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)
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log_exception(
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_logger, type(error), error, error.__traceback__, logging.WARNING
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)
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@@ -0,0 +1,146 @@
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{
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"type": "forward_simulation",
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"time": {
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"type": "time",
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"step_size": 0.001,
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"min_step": 6.25e-05,
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"start": 0.0,
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"duration": 25.0
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},
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"solver": {
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"type": "linear_solver"
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},
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"net": {
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"type": "net",
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"flux_dof_definitions": {
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"blood_flow": "blood_pressure"
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},
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"nodes": [
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"aorta_proximal",
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"aorta_distal",
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"venous"
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],
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"blocks": {
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"circulation_aorta_proximal": {
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"type": "block_description",
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"model_type": "rc_block",
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"time": "time",
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"flux_type": "blood_flow",
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"resistance": "aorta_proximal.resistance",
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"capacitance": "aorta_proximal.capacitance",
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"nodes": {
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"1": "aorta_distal",
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"2": "aorta_proximal"
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}
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},
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"circulation_aorta_distal": {
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"type": "block_description",
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"model_type": "rc_block",
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"time": "time",
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"flux_type": "blood_flow",
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"resistance": "aorta_distal.resistance",
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"capacitance": "aorta_distal.capacitance",
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"nodes": {
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"1": "venous",
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"2": "aorta_distal"
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}
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}
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},
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"boundaries_conditions": {
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"aorta_proximal": [
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{
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"type": "condition",
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"condition_type": "blood_flow",
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"condition_id": "aorta_proximal.blood_flow"
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}
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],
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"venous": [
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{
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"type": "condition",
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"condition_type": "blood_pressure",
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"condition_id": "venous.blood_pressure"
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}
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]
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}
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},
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"variables_magnitudes": {
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"aorta_proximal.blood_pressure": 100000.0,
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"aorta_distal.blood_pressure": 100000.0
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},
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"parameters": {
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"heartbeat_duration": {
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"type": "product",
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"factors": [
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60.0
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],
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"inverses": [
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"heart_rate"
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]
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},
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"aorta_proximal.capacitance": 2e-10,
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"aorta_proximal.blood_flow": {
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"type": "rescale_two_phases_function",
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"rescaled_period": "heartbeat_duration",
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"alpha": 0.8,
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"reference_function": [
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[
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0.0,
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"aorta_proximal.blood_flow.min"
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],
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[
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0.075,
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"aorta_proximal.blood_flow.min"
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],
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[
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0.134,
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"aorta_proximal.blood_flow.max"
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],
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[
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0.142,
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"aorta_proximal.blood_flow.max"
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],
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[
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0.281,
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"aorta_proximal.blood_flow.min"
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],
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[
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"aorta_proximal.blood_flow.min"
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]
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],
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"phases": [
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0,
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0,
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1,
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1,
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0
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]
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},
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"aorta_distal.capacitance": {
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"type": "product",
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"factors": [
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"aorta_distal.time_constant"
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],
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"inverses": [
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"aorta_distal.resistance"
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]
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},
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"heart_rate": 60.0,
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"aorta_proximal.resistance": 7000000.0,
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"aorta_distal.resistance": 110000000.0,
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"aorta_distal.time_constant": 2.0,
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"venous.blood_pressure": 1600.0,
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"aorta_proximal.blood_flow.min": 0.0,
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"aorta_proximal.blood_flow.max": 0.0005
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},
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"variables_initialization": {
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"aorta_proximal.blood_pressure": 10760.0,
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"aorta_distal.blood_pressure": 10760.0
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},
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"output_functions": {
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"aorta_proximal.blood_flow": {
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"type": "watch_quantity",
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"quantity": "aorta_proximal.blood_flow"
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}
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}
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}
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{
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"type": "forward_simulation",
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"time": {
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"type": "time",
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"step_size": 0.001,
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"min_step": 6.25e-05,
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"start": 0.0,
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"duration": 25.0
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},
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"solver": {
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"type": "newton_solver",
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"tolerance": 1e-09,
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"iteration_max": 10
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},
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"net": {
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"type": "net",
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"flux_dof_definitions": {
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"blood_flow": "blood_pressure"
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},
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"nodes": [
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"cavity",
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"atrial",
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"aorta_proximal",
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"aorta_distal",
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"venous"
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],
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"blocks": {
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"cavity": {
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"type": "block_description",
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"model_type": "spherical_cavity_block",
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"time": "time",
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"flux_type": "blood_flow",
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"disp": "cavity.dynamics.disp",
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"radius": "heart_radius",
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"thickness": "heart_thickness",
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"submodels": {
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"dynamics": {
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"type": "model_description",
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"model_type": "spherical_dynamics",
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"time": "time",
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"fib_deform": "cavity.rheology.fib_deform",
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"pressure": "cavity.blood_pressure",
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"pressure_external": "pleural.pressure",
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"vel": "cavity.velocity_law.vel",
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"radius": "heart_radius",
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"thickness": "heart_thickness",
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"series_stiffness": "cavity.rheology.series_stiffness"
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},
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"velocity_law": {
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"type": "model_description",
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"model_type": "velocity_law_hht",
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"time": "time",
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"disp": "cavity.dynamics.disp"
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},
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"rheology": {
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"type": "model_description",
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"model_type": "rheology_fiber_additive",
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"time": "time",
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"disp": "cavity.dynamics.disp",
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"active_tension_discr": "cavity.rheology.active_law.active_tension_discr",
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"radius": "heart_radius",
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"submodels": {
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"active_law": {
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"type": "model_description",
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"model_type": "active_law_macro_huxley_two_moments",
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"time": "time",
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"fib_deform": "cavity.rheology.fib_deform",
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"contractility": "heart_contractility"
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}
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}
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}
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},
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"nodes": {
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"1": "cavity"
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}
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},
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"valve_atrium": {
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"type": "block_description",
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"model_type": "valve_rl_block",
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"time": "time",
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"flux_type": "blood_flow",
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"backward_conductance": "conductance_iso",
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"nodes": {
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"1": "atrial",
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"2": "cavity"
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}
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},
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"valve_arterial": {
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"type": "block_description",
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"model_type": "valve_rl_block",
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"time": "time",
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"flux_type": "blood_flow",
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"backward_conductance": "conductance_iso",
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"nodes": {
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"1": "cavity",
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"2": "aorta_proximal"
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}
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},
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"capacitance_valve": {
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"type": "block_description",
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"model_type": "c_block",
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"time": "time",
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"flux_type": "blood_flow",
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"nodes": {
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"1": "cavity"
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}
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},
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"circulation_aorta_proximal": {
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"type": "block_description",
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"model_type": "rc_block",
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"time": "time",
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"flux_type": "blood_flow",
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"nodes": {
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"1": "aorta_distal",
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"2": "aorta_proximal"
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}
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},
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"circulation_aorta_distal": {
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"type": "block_description",
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"model_type": "rc_block",
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"time": "time",
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"flux_type": "blood_flow",
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"nodes": {
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"1": "venous",
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"2": "aorta_distal"
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}
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}
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},
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"boundaries_conditions": {
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"atrial": [
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{
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"type": "condition",
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"condition_type": "blood_pressure",
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"condition_id": "atrial.blood_pressure"
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}
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+
],
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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"type": "sinus_offset",
|
|
186
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
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|
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|
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|
|
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|
|
225
|
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|
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
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|
|
262
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
|
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|
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|
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275
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|
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|
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|
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|
293
|
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|
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|
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304
|
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|
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|
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|
|
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|
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|
|
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|
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|
|
308
|
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|
|
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|
|
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|
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|
|
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|
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|
|
312
|
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|
|
313
|
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|
|
314
|
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|
|
315
|
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|
|
316
|
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|
|
317
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|
|
318
|
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|
|
319
|
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|
|
320
|
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|
|
321
|
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|
|
322
|
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|
|
323
|
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|
|
324
|
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|
|
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{
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|
326
|
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|
329
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|
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|
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|
331
|
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|
|
332
|
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|
|
333
|
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|
|
334
|
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|
|
335
|
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|
|
336
|
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|
|
337
|
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|
|
338
|
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|
|
339
|
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],
|
|
340
|
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|
|
341
|
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|
|
342
|
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|
|
343
|
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},
|
|
344
|
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|
|
345
|
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|
|
346
|
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|
|
347
|
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|
|
348
|
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|
|
349
|
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|
|
350
|
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|
|
351
|
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]
|
|
352
|
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|
|
353
|
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|
|
354
|
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|
|
355
|
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|
|
356
|
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|
|
357
|
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|
|
358
|
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|
|
359
|
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|
|
360
|
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|
|
361
|
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|
|
362
|
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|
|
363
|
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|
|
364
|
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|
|
365
|
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|
|
366
|
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|
|
367
|
+
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|
|
368
|
+
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|
|
369
|
+
69.0,
|
|
370
|
+
6.5
|
|
371
|
+
]
|
|
372
|
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},
|
|
373
|
+
"output_functions": {
|
|
374
|
+
"atrial.blood_pressure": {
|
|
375
|
+
"type": "watch_quantity",
|
|
376
|
+
"quantity": "atrial.blood_pressure"
|
|
377
|
+
},
|
|
378
|
+
"active_law.activation": {
|
|
379
|
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"type": "watch_quantity",
|
|
380
|
+
"quantity": "cavity.rheology.active_law.activation"
|
|
381
|
+
},
|
|
382
|
+
"pleural.pressure": {
|
|
383
|
+
"type": "watch_quantity",
|
|
384
|
+
"quantity": "pleural.pressure"
|
|
385
|
+
}
|
|
386
|
+
}
|
|
387
|
+
}
|
|
@@ -0,0 +1,343 @@
|
|
|
1
|
+
{
|
|
2
|
+
"type": "forward_simulation",
|
|
3
|
+
"time": {
|
|
4
|
+
"type": "time",
|
|
5
|
+
"step_size": 0.001,
|
|
6
|
+
"min_step": 6.25e-05,
|
|
7
|
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"start": 0.0,
|
|
8
|
+
"duration": 25.0
|
|
9
|
+
},
|
|
10
|
+
"solver": {
|
|
11
|
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"type": "newton_solver",
|
|
12
|
+
"tolerance": 1e-09,
|
|
13
|
+
"iteration_max": 10
|
|
14
|
+
},
|
|
15
|
+
"net": {
|
|
16
|
+
"type": "net",
|
|
17
|
+
"flux_dof_definitions": {
|
|
18
|
+
"blood_flow": "blood_pressure"
|
|
19
|
+
},
|
|
20
|
+
"nodes": [
|
|
21
|
+
"cavity",
|
|
22
|
+
"atrial",
|
|
23
|
+
"aorta_proximal",
|
|
24
|
+
"aorta_distal",
|
|
25
|
+
"venous"
|
|
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|
+
],
|
|
27
|
+
"blocks": {
|
|
28
|
+
"cavity": {
|
|
29
|
+
"type": "block_description",
|
|
30
|
+
"model_type": "spherical_cavity_block",
|
|
31
|
+
"time": "time",
|
|
32
|
+
"flux_type": "blood_flow",
|
|
33
|
+
"disp": "cavity.dynamics.disp",
|
|
34
|
+
"radius": "heart_radius",
|
|
35
|
+
"thickness": "heart_thickness",
|
|
36
|
+
"submodels": {
|
|
37
|
+
"dynamics": {
|
|
38
|
+
"type": "model_description",
|
|
39
|
+
"model_type": "spherical_dynamics",
|
|
40
|
+
"time": "time",
|
|
41
|
+
"fib_deform": "cavity.rheology.fib_deform",
|
|
42
|
+
"pressure": "cavity.blood_pressure",
|
|
43
|
+
"pressure_external": "pleural.pressure",
|
|
44
|
+
"vel": "cavity.velocity_law.vel",
|
|
45
|
+
"radius": "heart_radius",
|
|
46
|
+
"thickness": "heart_thickness",
|
|
47
|
+
"series_stiffness": "cavity.rheology.series_stiffness"
|
|
48
|
+
},
|
|
49
|
+
"velocity_law": {
|
|
50
|
+
"type": "model_description",
|
|
51
|
+
"model_type": "velocity_law_hht",
|
|
52
|
+
"time": "time",
|
|
53
|
+
"disp": "cavity.dynamics.disp"
|
|
54
|
+
},
|
|
55
|
+
"rheology": {
|
|
56
|
+
"type": "model_description",
|
|
57
|
+
"model_type": "rheology_fiber_additive",
|
|
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|
+
"time": "time",
|
|
59
|
+
"disp": "cavity.dynamics.disp",
|
|
60
|
+
"active_tension_discr": "cavity.rheology.active_law.active_tension_discr",
|
|
61
|
+
"radius": "heart_radius",
|
|
62
|
+
"submodels": {
|
|
63
|
+
"active_law": {
|
|
64
|
+
"type": "model_description",
|
|
65
|
+
"model_type": "active_law_macro_huxley_two_moments",
|
|
66
|
+
"time": "time",
|
|
67
|
+
"fib_deform": "cavity.rheology.fib_deform",
|
|
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|
+
"contractility": "heart_contractility"
|
|
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|
+
}
|
|
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|
+
}
|
|
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|
+
}
|
|
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|
+
},
|
|
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|
+
"nodes": {
|
|
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|
+
"1": "cavity"
|
|
75
|
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}
|
|
76
|
+
},
|
|
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|
+
"valve_atrium": {
|
|
78
|
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"type": "block_description",
|
|
79
|
+
"model_type": "valve_rl_block",
|
|
80
|
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"time": "time",
|
|
81
|
+
"flux_type": "blood_flow",
|
|
82
|
+
"backward_conductance": "conductance_iso",
|
|
83
|
+
"nodes": {
|
|
84
|
+
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|
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|
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|
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|
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|
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|
319
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|
320
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|
321
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|
|
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327
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330
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|
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"output_functions": {
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"atrial.blood_pressure": {
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"type": "watch_quantity",
|
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"quantity": "atrial.blood_pressure"
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"quantity": "cavity.rheology.active_law.activation"
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}
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physioblocks/description/nets.py,sha256=pKG2uB-4dABc-lvGswkybiho18bOkUwsVJYBdlX7p5s,23604
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physioblocks/references/spherical_heart_respiration_sim.jsonc,sha256=kKq5xf94r90O1KpkCHk1qwgy6DJ37ePo3-8buEtcu5Y,1397
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physioblocks/references/full_configurations/spherical_heart_respiration_sim.jsonc,sha256=su6ExBBx6yZmoTRzBrTSA18QMFDB2f_S_vBGBmYeA1E,12703
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physioblocks/references/full_configurations/spherical_heart_sim.jsonc,sha256=hQYj-TPEJx3DVqkGKYYOiPRfUBGCE6gWPmbcylbaG9g,11420
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physioblocks-1.1.3.dist-info/RECORD,,
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File without changes
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{physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/licenses/licenses/GPL-3.0-only.txt
RENAMED
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File without changes
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{physioblocks-1.1.1.dist-info → physioblocks-1.1.3.dist-info}/licenses/licenses/LGPL-3.0-only.txt
RENAMED
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File without changes
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