neqsim-notebook-patterns

name	neqsim-notebook-patterns
description	Jupyter notebook patterns for NeqSim. USE WHEN: creating or reviewing Jupyter notebooks that use NeqSim for process simulation, thermodynamics, or PVT analysis. Covers devtools workspace setup, class imports, notebook structure, visualization requirements, and results.json schema.
last_verified	2026-07-09

Jupyter Notebook Patterns for NeqSim

Standard patterns for creating Jupyter notebooks that use workspace NeqSim Java classes via devtools.

Devtools Setup Cell (Use in Every Task Notebook)

Task notebooks under task_solve/ MUST load NeqSim through devtools/neqsim_dev_setup.py. This puts workspace Java classes from target/classes on the JVM classpath, so new or modified Java classes are available without copying a packaged JAR into the neqsim Python package.

import os
import sys
from pathlib import Path


def find_neqsim_project_root():
    env_root = os.environ.get("NEQSIM_PROJECT_ROOT")
    candidates = []
    if env_root:
        candidates.append(Path(env_root).resolve())
    cwd = Path.cwd().resolve()
    candidates.extend([cwd] + list(cwd.parents))
    for candidate in candidates:
        if (candidate / "pom.xml").exists() and (candidate / "devtools" / "neqsim_dev_setup.py").exists():
            return candidate
    raise RuntimeError("Could not find NeqSim project root. Set NEQSIM_PROJECT_ROOT.")


PROJECT_ROOT = find_neqsim_project_root()
sys.path.insert(0, str(PROJECT_ROOT / "devtools"))

from neqsim_dev_setup import neqsim_init, neqsim_classes

ns = neqsim_init(project_root=PROJECT_ROOT, recompile=False, verbose=True)
ns = neqsim_classes(ns)
NEQSIM_MODE = "devtools"
print("NeqSim loaded via devtools workspace classes")

Class Import Cell

# Classes are already available on ns from neqsim_classes(ns):
SystemSrkEos = ns.SystemSrkEos
ProcessSystem = ns.ProcessSystem
Stream = ns.Stream
Separator = ns.Separator
Compressor = ns.Compressor
Cooler = ns.Cooler
Heater = ns.Heater
ThrottlingValve = ns.ThrottlingValve
Mixer = ns.Mixer
Splitter = ns.Splitter

Do not use from neqsim import jneqsim in task notebooks or runner workflows. That imports the installed Python package and can miss workspace Java changes. Only published Colab-style examples outside task_solve/ may use jneqsim as an external-user pattern.

Common Class Paths

# Preloaded aliases from neqsim_classes(ns)
ns.SystemSrkEos
ns.SystemPrEos
ns.SystemSrkCPAstatoil
ns.ThermodynamicOperations
ns.ProcessSystem
ns.Stream
ns.Separator
ns.ThreePhaseSeparator
ns.Compressor
ns.Heater
ns.Cooler
ns.HeatExchanger
ns.ThrottlingValve
ns.Mixer
ns.Splitter
ns.AdiabaticPipe
ns.PipeBeggsAndBrills
ns.DistillationColumn
ns.Expander
ns.Recycle
ns.Adjuster
ns.ProcessModel    # Named collection of ProcessSystems
ns.ProcessModule   # Legacy — prefer ProcessModel

# Load additional classes by fully qualified Java class name
SystemGERG2008Eos = ns.JClass("neqsim.thermo.system.SystemGERG2008Eos")

Loading Custom / NIP Classes via ns.JClass

Some newer classes (CO2 injection well analysis, impurity monitoring, transient wellbore) may not be preloaded by neqsim_classes(ns). Load them with ns.JClass():

# CO2 injection well analysis classes
CO2InjectionWellAnalyzer = ns.JClass("neqsim.process.equipment.pipeline.CO2InjectionWellAnalyzer")
TransientWellbore = ns.JClass("neqsim.process.equipment.pipeline.TransientWellbore")
CO2FlowCorrections = ns.JClass("neqsim.process.equipment.pipeline.CO2FlowCorrections")
ImpurityMonitor = ns.JClass("neqsim.process.measurementdevice.ImpurityMonitor")

Notebook Structure (Follow This Order)

1. Title + Introduction (Markdown) — What the notebook demonstrates. ASCII flow diagram if process simulation. Colab badge.
2. Setup and Imports (Code) — devtools setup cell + class imports
3. Fluid Creation (Code) — Temperature in Kelvin, set mixing rule
4. Process Building (Code + Markdown) — Build flowsheet step by step with explanatory markdown between cells
5. Run Simulation (Code) — Single process.run() call
6. Results Extraction (Code) — Key results in formatted table with units (pandas DataFrame or f-strings)
7. Visualization (Code) — MANDATORY: at least 2-3 matplotlib figures
8. Summary & Next Steps (Markdown) — Key takeaways

Notebook File Safety

• Create notebooks with VS Code notebook tools, nbformat, or valid .ipynb JSON. Do not hand-write partial JSON fragments.
• When generating raw notebook JSON, use nbformat v4, keep cells in the top-level cells array, and include metadata.language on each cell.
• When editing an existing notebook, preserve existing cell metadata, including metadata.id, so notebook diffs and editor state remain stable.
• Avoid interactive prompts, shell-specific commands, and hidden state. Every code cell must run from a fresh kernel in order.
• Results cells must load existing task-level results.json, update only their own keys, and write it back. Runner collection then uses bridge.merge_results_to_task(job_ids) to preserve multi-notebook outputs.

Execution Default for Task Notebooks

For notebooks inside task_solve/, use NeqSim Runner by default instead of manual cell-by-cell execution in a shared VS Code/Jupyter kernel. The runner executes each notebook in an isolated subprocess with its own JVM, records state in runner.db, writes outputs under runner_output/, and retries failed jobs. This avoids kernel-restart loops and RuntimeError: JVM cannot be restarted.

import sys
sys.path.insert(0, str(TASK_DIR.parent.parent / "devtools"))
from neqsim_runner.agent_bridge import AgentBridge

bridge = AgentBridge(task_dir=str(TASK_DIR))
job_ids = []
job_ids.append(bridge.submit_notebook(
    "step2_analysis/01_main_analysis.ipynb",
    mode="execute",
    max_retries=3,
    timeout_seconds=3600,
))
bridge.run_all(max_parallel=1)
summary = bridge.summary()
if summary["failed"] or summary["pending"]:
    raise RuntimeError("NeqSim Runner jobs did not all complete successfully")
bridge.merge_results_to_task(job_ids)

Use interactive notebook cells only for quick debugging or tiny Screening tasks where study_config.yaml explicitly sets notebooks.execution_engine: interactive.

Runner Robustness & Task-Dir Resolution (avoid the common failures)

Three failure modes recur when running task notebooks. Handle all three up front:

1. Resolve the task folder with find_task_dir(), not NOTEBOOK_DIR.parent. The NeqSim Runner runs a notebook from a subprocess whose cwd is the notebook folder (e.g. step2_analysis/) and does not set __vsc_ipynb_file__, so Path.cwd() and NOTEBOOK_DIR.parent frequently overshoot the task root or land in a runner_output/job-*/ scratch folder. Use the canonical walker instead:

from neqsim_dev_setup import find_task_dir   # already on sys.path after setup cell

TASK_DIR = find_task_dir()          # walks up to the real task_solve/<slug>/ root
FIGURES_DIR = TASK_DIR / "figures"
FIGURES_DIR.mkdir(exist_ok=True)

find_task_dir() searches upward for canonical task markers (task_spec.md, study_config.yaml, step1_scope_and_research/, results.json) and honours the NEQSIM_TASK_DIR env var if you need to pin it. This replaces the ad-hoc _find_task_dir() walkers that individual tasks used to re-invent.

2. Delete stale runner outputs before the consistency check. The runner regenerates runner_output/job-*/output/ on every run; leftover copies of a previous run produce duplicate values and false "inconsistency" findings. Clean them before running the checker:

Remove-Item -Recurse -Force task_solve\<slug>\runner_output -ErrorAction SilentlyContinue
python devtools/consistency_checker.py task_solve/<slug>/

The consistency checker is now sweep-aware (it ignores deliberately-varied parametric/sensitivity/Monte-Carlo series and multi-point tables), so genuine parametric studies no longer trip a false CRITICAL. Keep intentionally-varied values inside results.json sweep sections (uncertainty, sensitivity, tornado, scenarios) or label them with a sweep/case/vs context in prose so the checker classifies them correctly. TaskResultValidator remains the authoritative schema gate.

3. Fall back to system Python if the venv is corrupted. A corrupted virtual environment shows up as numpy ... int32 AttributeError or a jpype initialization failure. Run the runner / notebooks with the system interpreter instead:

py -3.12 -m devtools.neqsim_runner go step2_analysis/01_main_analysis.ipynb

Colab Badge

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/equinor/neqsim/blob/master/examples/notebooks/FILENAME.ipynb)

Visualization Requirements (MANDATORY)

Every notebook MUST include at least 2-3 matplotlib figures:

• Axis labels with units — always include (e.g., "Temperature (°C)", "Pressure (bara)")
• Title, legend, grid — for readability
• Save as PNG — plt.savefig("../figures/name.png", dpi=150, bbox_inches="tight")
• Discussion cell after EVERY figure — observation, mechanism, implication, recommendation

Common plot types:

• Process profiles (T, P, flow vs equipment/stage)
• Composition charts (bar/stacked)
• Sensitivity curves (parametric sweeps)
• Phase envelopes (T vs P with boundaries)
• Cost breakdowns (bar charts)
• Tornado diagrams (sensitivity ranking)

Including Extracted PDF Figures in Notebooks

When reference documents (papers, standards, data sheets) are available as PDFs, extract their pages as PNG images for inclusion in the analysis:

# In a notebook cell — extract specific pages from a reference PDF
import subprocess
subprocess.run([
    "python", "../../devtools/pdf_to_figures.py",
    "../step1_scope_and_research/references/compressor_datasheet.pdf",
    "--pages", "3", "5",
    "--outdir", "../figures/"
], check=True)

Or use the Python API directly:

from devtools.pdf_to_figures import pdf_to_pngs
pngs = pdf_to_pngs(
    "../step1_scope_and_research/references/compressor_datasheet.pdf",
    outdir="../figures/", pages=[3, 5]
)

This is useful for:

• Embedding reference diagrams alongside simulation results for comparison
• Digitizing data from charts to validate NeqSim predictions
• Including vendor performance curves in design feasibility notebooks
• Documenting the source drawings/P&IDs that drove the simulation setup

Multi-Area Plant Architecture (ProcessModel)

For large plants (platforms, gas plants, refineries), split into separate ProcessSystem objects per process area and combine with ProcessModel. This is the pattern used in production models for large platforms.

Pattern: Functions Returning ProcessSystem

ProcessModel = ns.ProcessModel

def create_well_feed_model(inp):
    """Each area is a function returning a ProcessSystem."""
    well_process = ns.ProcessSystem()
    feed = Stream("feed", fluid)
    feed.setFlowRate(inp.flow_rate, "kg/hr")
    well_process.add(feed)
    # A manifold is modelled with the Manifold class (not a Splitter): add the
    # routed inlet streams with addStream, then ALWAYS route downstream from a
    # split stream. Single destination -> setSplitFactors([1.0]) + getSplitStream(0);
    # several trains -> setSplitFactors([...]) + getSplitStream(i). getMixedStream()
    # is the internal commingled stream (before the split), for inspection only.
    Manifold = ns.JClass("neqsim.process.equipment.manifold.Manifold")
    manifold = Manifold("well manifold")
    manifold.addStream(feed)
    manifold.setSplitFactors([0.5, 0.5])
    well_process.add(manifold)
    # e.g. train A = manifold.getSplitStream(0), train B = manifold.getSplitStream(1)
    return well_process

def create_separation_process(inp, feed_stream):
    sep_process = ns.ProcessSystem()
    separator = ThreePhaseSeparator("1st stage", feed_stream)
    sep_process.add(separator)
    # ... more equipment
    return sep_process

# Build each area (run individually to populate outlet streams)
well_model = create_well_feed_model(params)
well_model.run()

# Cross-system streams: outlet of one system feeds constructor of next
sep_train_A = create_separation_process(params,
    well_model.getUnit("manifold").getSplitStream(0))
sep_train_A.run()

sep_train_B = create_separation_process(params,
    well_model.getUnit("manifold").getSplitStream(1))
sep_train_B.run()

# Combine all into ProcessModel with named entries
plant = ProcessModel()
plant.add(, well_model)
plant.add(, sep_train_A)
plant.add(, sep_train_B)
plant.run()  


(plant.getConvergenceSummary())
(plant.getMassBalanceReport())
sep_A = plant.get()
(sep_A.getUnit().getGasOutStream().getFlowRate())

Key Rules for Multi-Area Models

• Order matters: add() upstream systems first — they run in insertion order
• Cross-system streams: Pass outlet stream of System A as constructor arg to System B
• Run each area first: Call .run() on each ProcessSystem before combining (populates streams)
• NEVER add ProcessModule/ProcessModel to a ProcessSystem — it will throw TypeError
• Use getUnit("name") to access equipment across systems
• ProcessModel.run() iterates all systems and checks convergence

Getting Results from NeqSim

# Stream properties
stream.getTemperature() - 273.15   # °C (returns Kelvin!)
stream.getPressure()                # bara
stream.getFlowRate("kg/hr")         # mass flow with unit

# Equipment outputs
comp.getPower("kW")                 # compressor power
cooler.getDuty()                    # heat duty in Watts

# Fluid properties (MUST call initProperties() first for standalone flash)
fluid = stream.getFluid()
fluid.initProperties()              # MANDATORY before transport properties
fluid.getDensity("kg/m3")
fluid.getPhase("gas").getViscosity("kg/msec")
fluid.getPhase("gas").getThermalConductivity("W/mK")

Automation API (String-Addressable Variables)

Use ProcessAutomation for agent-friendly access to simulation variables — avoids navigating Java class hierarchies. Preferred when programmatically exploring or modifying process simulations in notebooks.

# Get automation facade
auto = process.getAutomation()

# Discover equipment
units = list(auto.getUnitList())         # ["Feed Gas", "HP Sep", "Compressor", ...]
eq_type = auto.getEquipmentType("HP Sep")  # "Separator"

# List variables for an equipment unit
vars_list = list(auto.getVariableList("HP Sep"))
for v in vars_list:
    print(f"{v.getAddress()} [{v.getType()}] ({v.getDefaultUnit()}) — {v.getDescription()}")

# Read values with unit conversion (dot-notation address)
temp = auto.getVariableValue("HP Sep.gasOutStream.temperature", "C")
flow = auto.getVariableValue("HP Sep.gasOutStream.flowRate", "kg/hr")

# Write INPUT variables and re-run
auto.setVariableValue("Compressor.outletPressure", 150.0, "bara")
process.run()  # propagate changes

# Multi-area plant
plant_auto = plant.getAutomation()
areas = list(plant_auto.getAreaList())  # ["Separation", "Compression"]
t = plant_auto.getVariableValue("Separation::HP Sep.gasOutStream.temperature", "C")

Lifecycle State (Save / Restore / Compare)

JSON snapshots for reproducibility and version comparison in notebooks:

ProcessSystemState = ns.JClass("neqsim.process.processmodel.lifecycle.ProcessSystemState")
ProcessModelState = ns.JClass("neqsim.process.processmodel.lifecycle.ProcessModelState")

# Save state
state = ProcessSystemState.fromProcessSystem(process)
state.setName("Gas Processing")
state.setVersion("1.0.0")
state.saveToFile("model_v1.json")

# Load and validate
loaded = ProcessSystemState.loadFromFile("model_v1.json")
result = loaded.validate()
print(f"Valid: {result.isValid()}")

# Multi-area model state
model_state = ProcessModelState.fromProcessModel(plant)
model_state.setVersion("1.0.0")
model_state.saveToFile("plant_v1.json")

# Compare two versions
v1 = ProcessModelState.fromProcessModel(plant)  # before changes
# ... make changes ...
v2 = ProcessModelState.fromProcessModel(plant)  # after changes
diff = ProcessModelState.compare(v1, v2)
if diff.hasChanges():
    print("Modified parameters:", list(diff.getModifiedParameters()))

results.json Template (for Task-Solving Notebooks)

import json, os, pathlib

NOTEBOOK_DIR = pathlib.Path(globals().get(
    "__vsc_ipynb_file__", os.path.abspath("step2_analysis/notebook.ipynb")
)).resolve().parent
TASK_DIR = NOTEBOOK_DIR.parent
FIGURES_DIR = TASK_DIR / "figures"
FIGURES_DIR.mkdir(exist_ok=True)

results = {
    "key_results": {"outlet_temperature_C": -18.5, "pressure_drop_bar": 3.2},
    "validation": {"mass_balance_error_pct": 0.01, "acceptance_criteria_met": True},
    "approach": "Used SRK EOS with classic mixing rule...",
    "conclusions": "The analysis shows...",
    "figure_captions": {},
    "figure_discussion": [],
    "equations": [],
    "tables": [],
    "references": [],
    "uncertainty": {},
    "risk_evaluation": {}
}
with open(str(TASK_DIR / "results.json"), "w") as f:
    json.dump(results, f, indent=2)

Validate results.json (MANDATORY for Task-Solving Notebooks)

After saving results.json, run the Java TaskResultValidator to catch schema errors before report generation. This is a programmatic quality gate — do NOT proceed to Step 3 if validation fails.

# ── Programmatic quality gate ──
TaskResultValidator = ns.JClass("neqsim.util.agentic.TaskResultValidator")

with open(str(TASK_DIR / "results.json"), "r") as f:
    json_str = f.read()

report = TaskResultValidator.validate(json_str)
print(f"Valid: {report.isValid()}  |  Errors: {report.getErrorCount()}  |  Warnings: {report.getWarningCount()}")

if not report.isValid():
    print("\n❌ ERRORS (must fix before proceeding to report):")
    for err in report.getErrors():
        print(f"  [{err.field}] {err.message}")

if report.getWarningCount() > 0:
    print("\n⚠️ WARNINGS (fix for Standard/Comprehensive tasks):")
    for warn in report.getWarnings():
        print(f"  [{warn.field}] {warn.message}")

assert report.isValid(), "results.json failed validation — fix errors above"

The validator checks:

• Required keys: key_results, validation, approach, conclusions
• Recommended keys: figure_captions, figure_discussion, equations, tables, references, uncertainty, risk_evaluation, standards_applied, benchmark_validation
• Uncertainty section: Monte Carlo N ≥ 200; p10/p50/p90 must be numeric and ordered p10 ≤ p50 ≤ p90 (out-of-order or non-numeric is a hard error)
• Risk evaluation: Risk register with id, description, risk_level
• Standards applied: Array entries with code, scope, status (PASS/FAIL/INFO/N/A)
• Benchmark validation: object/array of entries identifying what was compared, a reference, and a comparison; status (if present) must be PASS/FAIL/WARN/INFO

The same rules run in CI without the JVM via python devtools/validate_task_results.py task_solve/<slug>. See neqsim-professional-reporting for the full results.json master schema and reporting rules.

Type Conversion Tips

# Explicit float for numeric Java parameters
comp.setOutletPressure(float(pressure))

# Python bool works for Java boolean
fluid.setMultiPhaseCheck(True)

# String parameters usually work as-is
stream.setFlowRate(50000.0, "kg/hr")

Performance Estimation and Optimization

Simulation Time Estimates

Use these estimates to warn users about long-running operations and to decide whether Monte Carlo should use full NeqSim simulations or simplified models:

Operation	Typical Time	Notes
Single TPflash (3-5 components)	< 0.01 s	Negligible
Single TPflash (15+ components, CPA)	0.05-0.2 s	CPA adds association iterations
ProcessSystem with 5-10 units	0.5-5 s	Depends on recycles and adjusters
ProcessSystem with 20+ units + recycles	5-30 s	Complex flowsheets need multiple iterations
Phase envelope calculation	2-10 s	Many flash points along the boundary
Hydrate equilibrium temperature	1-3 s	Iterative solid-fluid equilibrium
Distillation column (10 stages)	5-20 s	Inside-out solver faster than standard
Pipeline (PipeBeggsAndBrills, 50 km)	2-10 s	Segmented calculation along length
Monte Carlo N=200 with process sim	5-15 min	200 x 2-5 s per run
Monte Carlo N=1000 with process sim	30-60 min	Consider caching or simplified model
Monte Carlo N=1000 with TPflash only	1-5 min	Fast if no process equipment

When to Warn the User

If estimated total simulation time exceeds 10 minutes, inform the user:

estimated_time_min = N_simulations * time_per_sim_s / 60.0
if estimated_time_min > 10:
    print(f"⚠️ Estimated run time: {estimated_time_min:.0f} minutes ({N_simulations} simulations)")
    print("Consider reducing N or caching intermediate results.")

Optimization Strategies for Monte Carlo

1. Cache expensive NeqSim results that don't change between iterations:

   # Compute base process simulation once
   process.run()
   base_power_kW = comp.getPower("kW")
   base_flow = stream.getFlowRate("kg/hr")
   
   # In Monte Carlo loop, only re-run what changes
   for i in range(N):
       gas_price = np.random.triangular(0.8, 1.5, 2.5)
       npv = calculate_npv(base_flow, gas_price, capex_multiplier)
   

2. Classify parameters for tornado analysis:

   • Economic parameters (gas price, discount rate, CAPEX multiplier): reuse base production profile, recalculate cash flow only — instant
   • Technical parameters (composition, pressure, temperature): require NeqSim re-run — slow

3. Reduce component count for screening-level Monte Carlo:

   # Instead of 15-component fluid, use 5-component lumped version
   fluid = SystemSrkEos(273.15 + 25.0, 60.0)
   fluid.addComponent("methane", 0.85)
   fluid.addComponent("ethane", 0.10)
   fluid.addComponent("propane", 0.05)
   # Skip C4+, N2, CO2 for screening
   

4. Use parallel-safe patterns (when running outside Jupyter): Each NeqSim fluid/process should be independent — clone fluids before branching.

Notebook Placement

• General examples: examples/notebooks/
• Task-solving: task_solve/YYYY-MM-DD_slug/step2_analysis/
• After creating: update docs/examples/index.md if documenting