Glm config management

GLM Configuration File Management

Configuration File Format

GLM uses Fortran namelist format (.nml files). Structure:

&section_name
  parameter1 = value1
  parameter2 = value2
/

Key rules:

• Sections delimited by &section_name (start) and / (end)
• Each parameter on its own line
• Values must match Fortran types (reals for decimals, integers for ints, strings in quotes, logicals .true./.false.)
• Commas optional but allow consistency
• Comments not allowed in namelist sections

Calibration-Safe Parameter Updates

Parameters You CAN Modify

In &light:

• Kw: Real number, currently ~0.3

In &mixing:

• coef_mix_hyp: Real number, currently ~0.5

In &meteorology:

• wind_factor: Real number, currently ~1.0
• lw_factor: Real number, currently ~1.0
• ch: Real number, currently ~0.0013

Parameters You MUST NOT MODIFY

&meteorology:

• sw_factor (solar shortwave multiplier)
• cd (drag coefficient)
• ce (evaporation coefficient)

&init_profiles:

• the_depths (initial depth levels)
• the_temps (initial temperatures)
• the_sals (initial salinities)

All other sections:

• Time period, morphometry, inflows, outflows, etc.

Safe Update Procedure

Python Method (Recommended)

import re

def update_glm_parameter(nml_file, section, param, value):
    """
    Update a single parameter in GLM config, preserving all else.

    Args:
        nml_file: Path to glm3.nml
        section: Section name (e.g., 'light', 'mixing', 'meteorology')
        param: Parameter name (e.g., 'Kw', 'wind_factor')
        value: New value (will be formatted appropriately)
    """
    with open(nml_file, 'r') as f:
        content = f.read()

    # Build regex pattern for the parameter line
    # Matches: param = value (with possible whitespace, commas)
    pattern = rf'({param}\s*=\s*)[-+]?\d*\.?\d+([eE][-+]?\d+)?'

    # Format value
    if isinstance(value, float):
        replacement = rf'\g<1>{value}'
    else:
        replacement = rf'\g<1>{value}'

    # Replace only first occurrence (assumes one per section)
    content_new = re.sub(pattern, replacement, content, count=1)

    # Verify replacement happened
    if content == content_new:
        raise ValueError(f"Parameter {param} not found in &{section}")

    # Write back
    with open(nml_file, 'w') as f:
        f.write(content_new)

    print(f"Updated {section}.{param} to {value}")

# Usage:
update_glm_parameter('/root/glm3.nml', 'light', 'Kw', 0.35)
update_glm_parameter('/root/glm3.nml', 'mixing', 'coef_mix_hyp', 0.45)

Bash Method (Using sed)

# Update Kw in &light section
sed -i 's/Kw = [0-9.e]*/Kw = 0.35/' /root/glm3.nml

# Verify update
grep -A 5 '&light' /root/glm3.nml | grep Kw

Warning: Bash sed is fragile with Fortran format. Use Python for safety.

Validation Procedures

Syntax Check (Python)

import f90wrap  # or similar parser
# Can validate Fortran namelist format
# OR simply run: glm --help (if supported)

Functional Check

cd /root
glm  # Will fail with clear error if config is invalid
# If GLM runs without error, config is OK

Diff Before/After

diff -u glm3.nml.backup glm3.nml

Parameter Ranges and Defaults

Parameter	Section	Min	Default	Max	Type
Kw	light	0.1	0.3	0.5	real
coef_mix_hyp	mixing	0.3	0.5	0.7	real
wind_factor	meteorology	0.7	1.0	1.3	real
lw_factor	meteorology	0.7	1.0	1.3	real
ch	meteorology	0.0005	0.0013	0.002	real
sw_factor	meteorology	-	0.95	-	(locked)
cd	meteorology	-	0.0013	-	(locked)
ce	meteorology	-	0.0013	-	(locked)

Backup Strategy

Before starting calibration:

cp /root/glm3.nml /root/glm3.nml.backup

If config becomes corrupted, restore:

cp /root/glm3.nml.backup /root/glm3.nml

Multi-Iteration Record

For tracking iterations, use a log:

{
  "iteration": 1,
  "parameters": {
    "Kw": 0.30,
    "coef_mix_hyp": 0.50,
    "wind_factor": 1.0,
    "lw_factor": 1.0,
    "ch": 0.0013
  },
  "rmse": {
    "overall": 1.82,
    "annual_deep": 1.90,
    "summer_deep": 1.95
  },
  "timestamp": "2024-03-23T10:30:00Z"
}

This allows retracing steps if needed.