docs: migrate to standard FORD and MkDocs pipeline with mkdocstrings plugin
This commit is contained in:
ignis
parent
2998e94432
commit
766685a66f
20 changed files with 289 additions and 2084 deletions
17
.gitignore
vendored
Normal file
17
.gitignore
vendored
Normal file
|
|
@ -0,0 +1,17 @@
|
|||
# Documentation outputs
|
||||
site/
|
||||
docs/fortran_api/
|
||||
|
||||
# Compiled Fortran products
|
||||
*.mod
|
||||
*.o
|
||||
code/x-edge-cold-bc-uPrime-hybrid
|
||||
|
||||
# Python caches and local settings
|
||||
__pycache__/
|
||||
*.pyc
|
||||
.pytest_cache/
|
||||
|
||||
# Local testing and scratch directories
|
||||
scratch/ic1_regression_test/
|
||||
Plan-Draft.MD
|
||||
593
build_docs.py
593
build_docs.py
|
|
@ -1,475 +1,164 @@
|
|||
#!/usr/bin/env python3
|
||||
import os
|
||||
import re
|
||||
import ast
|
||||
import shutil
|
||||
import subprocess
|
||||
import sys
|
||||
|
||||
class FortranParser:
|
||||
"""A robust line-by-line state-machine parser for Fortran free-form source files.
|
||||
Correctly resolves line continuations (`&`) and extracts Doxygen/FORD-style comments.
|
||||
"""
|
||||
def __init__(self):
|
||||
# Match MODULE name (excluding MODULE PROCEDURE)
|
||||
self.module_re = re.compile(r'^\s*module\s+(\w+)\s*$', re.IGNORECASE)
|
||||
# Match SUBROUTINE name
|
||||
self.subroutine_re = re.compile(r'^\s*(?:recursive\s+|mpich\s+)?subroutine\s+(\w+)\s*(?:\(([^)]*)\))?', re.IGNORECASE)
|
||||
# Match FUNCTION name
|
||||
self.function_re = re.compile(
|
||||
r'^\s*(?:recursive\s+)?(?:real|integer|double\s+precision|logical|character|complex)?(?:\([\w*=]+\))?\s*function\s+(\w+)\s*(?:\(([^)]*)\))?',
|
||||
re.IGNORECASE
|
||||
)
|
||||
def check_command_installed(cmd):
|
||||
"""Checks if a command-line tool is installed in the current environment."""
|
||||
return shutil.which(cmd) is not None
|
||||
|
||||
def parse_file(self, filepath):
|
||||
with open(filepath, 'r', encoding='utf-8') as f:
|
||||
raw_lines = f.readlines()
|
||||
|
||||
# Resolve line continuations using &
|
||||
lines = []
|
||||
current_line = ""
|
||||
for line in raw_lines:
|
||||
trimmed = line.strip()
|
||||
# If the entire line is a comment, keep it as is
|
||||
if trimmed.startswith('!'):
|
||||
lines.append((line.rstrip('\r\n'), True))
|
||||
continue
|
||||
|
||||
# Partition the line by '!' to separate code and inline comments
|
||||
code_part = ""
|
||||
in_string = False
|
||||
str_char = None
|
||||
for i, char in enumerate(line):
|
||||
if char in ("'", '"'):
|
||||
if not in_string:
|
||||
in_string = True
|
||||
str_char = char
|
||||
elif str_char == char:
|
||||
in_string = False
|
||||
elif char == '!' and not in_string:
|
||||
code_part = line[:i]
|
||||
break
|
||||
else:
|
||||
code_part = line
|
||||
|
||||
code_trimmed = code_part.strip()
|
||||
if code_trimmed.endswith('&'):
|
||||
current_line += code_trimmed[:-1].strip() + " "
|
||||
else:
|
||||
if current_line:
|
||||
lines.append((current_line + code_trimmed, False))
|
||||
current_line = ""
|
||||
else:
|
||||
lines.append((line.rstrip('\r\n'), False))
|
||||
def run_process(args, description):
|
||||
"""Runs a subprocess with clean console updates."""
|
||||
print(f"\n[Running] {description}...")
|
||||
try:
|
||||
res = subprocess.run(args, check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
|
||||
print(f"[Success] {description} completed successfully!")
|
||||
if res.stdout.strip():
|
||||
print(res.stdout.strip())
|
||||
return True
|
||||
except subprocess.CalledProcessError as e:
|
||||
print(f"[Error] {description} FAILED with exit code {e.returncode}!")
|
||||
if e.stdout:
|
||||
print("--- STDOUT ---")
|
||||
print(e.stdout.strip())
|
||||
if e.stderr:
|
||||
print("--- STDERR ---")
|
||||
print(e.stderr.strip())
|
||||
return False
|
||||
except Exception as e:
|
||||
print(f"[Error] Failed to execute process: {e}")
|
||||
return False
|
||||
|
||||
# Parse resolved lines
|
||||
elements = []
|
||||
current_comments = []
|
||||
module_doc = ""
|
||||
in_module = False
|
||||
|
||||
for line_str, is_cmt in lines:
|
||||
trimmed = line_str.strip()
|
||||
if is_cmt or trimmed.startswith('!'):
|
||||
if trimmed.startswith('!>') or trimmed.startswith('!!'):
|
||||
cleaned_comment = trimmed[2:].strip()
|
||||
current_comments.append(cleaned_comment)
|
||||
continue
|
||||
|
||||
if not trimmed:
|
||||
if not in_module and not elements and current_comments:
|
||||
module_doc = "\n".join(current_comments)
|
||||
current_comments = []
|
||||
continue
|
||||
|
||||
m_mod = self.module_re.match(trimmed)
|
||||
m_sub = self.subroutine_re.match(trimmed)
|
||||
m_func = self.function_re.match(trimmed)
|
||||
|
||||
if m_mod:
|
||||
in_module = True
|
||||
mod_name = m_mod.group(1)
|
||||
elements.append({
|
||||
'type': 'module',
|
||||
'name': mod_name,
|
||||
'doc': "\n".join(current_comments) if current_comments else ""
|
||||
})
|
||||
current_comments = []
|
||||
elif m_sub:
|
||||
sub_name = m_sub.group(1)
|
||||
args_str = m_sub.group(2) or ""
|
||||
args = [a.strip() for a in args_str.split(',') if a.strip()]
|
||||
elements.append({
|
||||
'type': 'subroutine',
|
||||
'name': sub_name,
|
||||
'args': args,
|
||||
'doc': "\n".join(current_comments) if current_comments else ""
|
||||
})
|
||||
current_comments = []
|
||||
elif m_func:
|
||||
func_name = m_func.group(1)
|
||||
args_str = m_func.group(2) or ""
|
||||
args = [a.strip() for a in args_str.split(',') if a.strip()]
|
||||
elements.append({
|
||||
'type': 'function',
|
||||
'name': func_name,
|
||||
'args': args,
|
||||
'doc': "\n".join(current_comments) if current_comments else ""
|
||||
})
|
||||
current_comments = []
|
||||
else:
|
||||
# Clear comment buffer if normal statement is met
|
||||
current_comments = []
|
||||
|
||||
return {
|
||||
'doc': module_doc,
|
||||
'elements': elements
|
||||
}
|
||||
|
||||
|
||||
class PythonASTParser:
|
||||
"""Uses Python standard library `ast` module to safely parse classes, methods,
|
||||
decorators, functions, and Google-style docstrings from Python modules.
|
||||
"""
|
||||
def get_node_name(self, node):
|
||||
if hasattr(ast, 'unparse'):
|
||||
return ast.unparse(node).strip()
|
||||
if isinstance(node, ast.Name):
|
||||
return node.id
|
||||
elif isinstance(node, ast.Attribute):
|
||||
return f"{self.get_node_name(node.value)}.{node.attr}"
|
||||
elif isinstance(node, ast.Call):
|
||||
return f"{self.get_node_name(node.func)}(...)"
|
||||
return str(node)
|
||||
|
||||
def parse_file(self, filepath):
|
||||
with open(filepath, 'r', encoding='utf-8') as f:
|
||||
content = f.read()
|
||||
try:
|
||||
tree = ast.parse(content)
|
||||
except SyntaxError as e:
|
||||
print(f"Syntax error parsing {filepath}: {e}")
|
||||
return None
|
||||
|
||||
module_doc = ast.get_docstring(tree) or ""
|
||||
elements = []
|
||||
|
||||
for node in ast.iter_child_nodes(tree):
|
||||
if isinstance(node, ast.ClassDef):
|
||||
class_doc = ast.get_docstring(node) or ""
|
||||
methods = []
|
||||
for child in ast.iter_child_nodes(node):
|
||||
if isinstance(child, ast.FunctionDef):
|
||||
method_doc = ast.get_docstring(child) or ""
|
||||
args = [a.arg for a in child.args.args]
|
||||
decorators = [self.get_node_name(d) for d in child.decorator_list]
|
||||
methods.append({
|
||||
'name': child.name,
|
||||
'args': args,
|
||||
'doc': method_doc,
|
||||
'decorators': decorators
|
||||
})
|
||||
elements.append({
|
||||
'type': 'class',
|
||||
'name': node.name,
|
||||
'bases': [self.get_node_name(b) for b in node.bases],
|
||||
'doc': class_doc,
|
||||
'methods': methods
|
||||
})
|
||||
elif isinstance(node, ast.FunctionDef):
|
||||
func_doc = ast.get_docstring(node) or ""
|
||||
args = [a.arg for a in node.args.args]
|
||||
decorators = [self.get_node_name(d) for d in node.decorator_list]
|
||||
elements.append({
|
||||
'type': 'function',
|
||||
'name': node.name,
|
||||
'args': args,
|
||||
'doc': func_doc,
|
||||
'decorators': decorators
|
||||
})
|
||||
return {
|
||||
'doc': module_doc,
|
||||
'elements': elements
|
||||
}
|
||||
|
||||
|
||||
def format_docstring(doc):
|
||||
"""Formats raw docstrings/comments into clean Markdown."""
|
||||
if not doc:
|
||||
return "*No description provided.*"
|
||||
|
||||
# Process Google Style or Doxygen tags into neat markdown sections
|
||||
lines = doc.split('\n')
|
||||
formatted_lines = []
|
||||
in_args = False
|
||||
in_returns = False
|
||||
|
||||
for line in lines:
|
||||
trimmed = line.strip()
|
||||
|
||||
# Google style section headers
|
||||
if trimmed == 'Args:':
|
||||
formatted_lines.append("\n**Arguments:**\n")
|
||||
in_args = True
|
||||
in_returns = False
|
||||
continue
|
||||
elif trimmed == 'Returns:':
|
||||
formatted_lines.append("\n**Returns:**\n")
|
||||
in_args = False
|
||||
in_returns = True
|
||||
continue
|
||||
elif trimmed in ('Raises:', 'Attributes:'):
|
||||
formatted_lines.append(f"\n**{trimmed[:-1]}:**\n")
|
||||
in_args = in_returns = False
|
||||
continue
|
||||
|
||||
# Parse params inside arguments or return
|
||||
if in_args and trimmed:
|
||||
# Format "arg_name (type): description"
|
||||
match = re.match(r'^([\w_]+)\s*(?:\(([^)]+)\))?\s*:\s*(.*)$', trimmed)
|
||||
if match:
|
||||
name, arg_type, desc = match.groups()
|
||||
type_str = f" *({arg_type})*" if arg_type else ""
|
||||
formatted_lines.append(f"- ` {name} `{type_str}: {desc}")
|
||||
continue
|
||||
|
||||
# Parse Doxygen tags
|
||||
if trimmed.startswith('@param'):
|
||||
match = re.match(r'^@param\s+([\w_]+)\s*(.*)$', trimmed)
|
||||
if match:
|
||||
name, desc = match.groups()
|
||||
formatted_lines.append(f"- ` {name} `: {desc}")
|
||||
continue
|
||||
elif trimmed.startswith('@return'):
|
||||
desc = trimmed.replace('@return', '').strip()
|
||||
formatted_lines.append(f"\n**Returns:**\n\n{desc}")
|
||||
continue
|
||||
elif trimmed.startswith('@note'):
|
||||
desc = trimmed.replace('@note', '').strip()
|
||||
formatted_lines.append(f"\n> [!NOTE]\n> {desc}")
|
||||
continue
|
||||
elif trimmed.startswith('@author'):
|
||||
desc = trimmed.replace('@author', '').strip()
|
||||
formatted_lines.append(f"\n*Author: {desc}*")
|
||||
continue
|
||||
|
||||
formatted_lines.append(line)
|
||||
|
||||
return "\n".join(formatted_lines).strip()
|
||||
|
||||
|
||||
def build_all_docs():
|
||||
def build_orchestrator():
|
||||
workspace_dir = os.path.dirname(os.path.abspath(__file__))
|
||||
code_dir = os.path.join(workspace_dir, "code")
|
||||
docs_dir = os.path.join(workspace_dir, "docs")
|
||||
site_dir = os.path.join(workspace_dir, "site")
|
||||
|
||||
# Recreate the docs directory
|
||||
# Clean old docs and site
|
||||
if os.path.exists(docs_dir):
|
||||
shutil.rmtree(docs_dir)
|
||||
os.makedirs(docs_dir, exist_ok=True)
|
||||
os.makedirs(os.path.join(docs_dir, "python"), exist_ok=True)
|
||||
|
||||
fortran_parser = FortranParser()
|
||||
py_parser = PythonASTParser()
|
||||
if os.path.exists(site_dir):
|
||||
shutil.rmtree(site_dir)
|
||||
|
||||
# Files to parse
|
||||
fortran_files = [
|
||||
"Compact.f90",
|
||||
"m_arrays.f90",
|
||||
"m_calculate.f90",
|
||||
"m_openmpi.f90",
|
||||
"m_parameters.f90",
|
||||
"post.f90",
|
||||
"post_dns.f90"
|
||||
# 1. Create landing index.md
|
||||
index_path = os.path.join(docs_dir, "index.md")
|
||||
print(f"Creating landing index: {index_path}")
|
||||
with open(index_path, 'w', encoding='utf-8') as f:
|
||||
f.write("""# HPC DNS Post-Processing Reference Manual
|
||||
|
||||
Welcome to the automated documentation suite for the high-order compact difference post-processing project! This manual includes reference documentation for both the compiled Fortran core and the Python binds/algebraic generators.
|
||||
|
||||
---
|
||||
|
||||
## Architecture Overview
|
||||
|
||||
This post-processor compiles algebraic equations defined in a custom DSL (Domain Specific Language), computes high-order derivatives (1st & 2nd spatial derivatives) using tridiagonal finite differences, and leverages parallel MPI-IO blocks. Below is the primary compiler pipeline:
|
||||
|
||||
```mermaid
|
||||
graph TD
|
||||
A[code_gen.py / DSL Input] -->|AST Compiler Pipeline| B[post.py / Code Gen]
|
||||
B -->|Generates budget kernels| C[m_calculate.f90]
|
||||
C -->|LU Tridiagonal Solvers| D[Compact.f90]
|
||||
C -->|Array allocations| E[m_arrays.f90]
|
||||
F[post.f90 / Main Driver] -->|Orchestrates calculations| C
|
||||
F -->|Parallelizes domain| G[m_openmpi.f90]
|
||||
F -->|Loads run configuration| H[m_parameters.f90]
|
||||
I[pycompact.py / Bindings] -->|Wraps CPU calculations| C
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Navigation Guide
|
||||
|
||||
- **[Python API Reference](python/code_gen.md)**: Automatically parsed API and signatures for the DSL parsers, topological compiler stages, and Python wrappers.
|
||||
- **[Fortran Core Reference](fortran.md)**: Standard documentation compiled by `FORD` covering tridiagonal compact solvers, math kernels, and MPI bindings.
|
||||
|
||||
*Generated automatically using industry-standard tools: FORD, MkDocs, and Material theme.*
|
||||
""")
|
||||
|
||||
# 2. Create fortran.md entry page
|
||||
fortran_entry_path = os.path.join(docs_dir, "fortran.md")
|
||||
print(f"Creating Fortran entry: {fortran_entry_path}")
|
||||
with open(fortran_entry_path, 'w', encoding='utf-8') as f:
|
||||
f.write("""# Fortran Core API Reference
|
||||
|
||||
The Fortran core elements have been fully documented and compiled using **FORD** (FORtran Documenter), which extracts comments (`!>` and `!!`) and draws rich module dependency graphs.
|
||||
|
||||
---
|
||||
|
||||
## View Interactive Documentation
|
||||
|
||||
[👉 Click Here to Open Interactive Fortran API Reference](fortran_api/index.html){: .md-button .md-button--primary .md-button--large }
|
||||
|
||||
---
|
||||
|
||||
### Core Modules Cataloged
|
||||
|
||||
- **[[Compact]]**: Solves compact finite difference scheme equations using high-order tridiagonal/pentadiagonal schemes.
|
||||
- **[[m_calculate]]**: Runs budget calculations, spatial derivatives, and pieces Arrhenius chemical kinetics.
|
||||
- **[[m_arrays]]**: Handles array allocations and instant budget memory blocks.
|
||||
- **[[m_openmpi]]**: Wraps domain sizing, grid splitting, and MPI communicators.
|
||||
- **[[m_parameters]]**: Loads physical settings, boundary configurations, and grid sizes from file inputs.
|
||||
- **[[post]]**: Entry driver performing budget calculation run tasks.
|
||||
""")
|
||||
|
||||
# 3. Create Python stubs for mkdocstrings
|
||||
python_modules = [
|
||||
("code_gen", "Code Generator (`code_gen.py`)"),
|
||||
("post", "Compiler Stages (`post.py`)"),
|
||||
("pycompact", "Python Bindings (`pycompact.py`)")
|
||||
]
|
||||
for mod_name, title in python_modules:
|
||||
stub_path = os.path.join(docs_dir, "python", f"{mod_name}.md")
|
||||
print(f"Creating Python stub: {stub_path}")
|
||||
with open(stub_path, 'w', encoding='utf-8') as f:
|
||||
f.write(f"""# {title}
|
||||
|
||||
python_files = [
|
||||
("code_gen.py", "code/code_gen/code_gen.py"),
|
||||
("post.py", "code/code_gen/post.py"),
|
||||
("pycompact.py", "code/pycompact/pycompact.py")
|
||||
]
|
||||
::: {mod_name}
|
||||
""")
|
||||
|
||||
all_modules = []
|
||||
# 4. Environment validation
|
||||
missing_tools = []
|
||||
if not check_command_installed("ford"):
|
||||
missing_tools.append("ford")
|
||||
if not check_command_installed("mkdocs"):
|
||||
missing_tools.append("mkdocs")
|
||||
|
||||
# 1. Parse Fortran files
|
||||
for fname in fortran_files:
|
||||
path = os.path.join(code_dir, fname)
|
||||
if not os.path.exists(path):
|
||||
continue
|
||||
|
||||
print(f"Parsing Fortran file: {fname}")
|
||||
res = fortran_parser.parse_file(path)
|
||||
if not res:
|
||||
continue
|
||||
|
||||
all_modules.append({
|
||||
'name': fname,
|
||||
'lang': 'fortran',
|
||||
'data': res
|
||||
})
|
||||
if missing_tools:
|
||||
print("\n" + "="*80)
|
||||
print(" [Warning] Missing Required Documentation Tools!")
|
||||
print("="*80)
|
||||
print("To compile the complete interactive manual, please install the requirements:")
|
||||
print(" pip install -r requirements.txt")
|
||||
print("Note: If running in a virtualenv, make sure it is activated.")
|
||||
print("="*80 + "\n")
|
||||
return False
|
||||
|
||||
# 2. Parse Python files
|
||||
for key_name, rel_path in python_files:
|
||||
path = os.path.join(workspace_dir, rel_path)
|
||||
if not os.path.exists(path):
|
||||
continue
|
||||
|
||||
print(f"Parsing Python file: {key_name}")
|
||||
res = py_parser.parse_file(path)
|
||||
if not res:
|
||||
continue
|
||||
|
||||
all_modules.append({
|
||||
'name': key_name,
|
||||
'lang': 'python',
|
||||
'data': res
|
||||
})
|
||||
# 5. Compile Fortran API docs using FORD
|
||||
ford_success = run_process(["ford", "ford.md"], "FORD Fortran Compiler")
|
||||
if not ford_success:
|
||||
print("[Warning] FORD documentation compilation failed. Continuing to MkDocs compilation...")
|
||||
|
||||
# 3. Generate Markdown files
|
||||
for mod in all_modules:
|
||||
mname = mod['name']
|
||||
lang = mod['lang']
|
||||
data = mod['data']
|
||||
|
||||
md_filename = mname.replace('.f90', '.md').replace('.py', '.md')
|
||||
md_path = os.path.join(docs_dir, md_filename)
|
||||
|
||||
with open(md_path, 'w', encoding='utf-8') as md_file:
|
||||
# Header banner
|
||||
badge = "Fortran Source" if lang == 'fortran' else "Python Source"
|
||||
badge_color = "blue" if lang == 'fortran' else "green"
|
||||
|
||||
md_file.write(f"# {mname}\n\n")
|
||||
md_file.write(f"\n\n")
|
||||
|
||||
# Smart Overview Fallback
|
||||
overview_doc = data['doc'].strip()
|
||||
if not overview_doc:
|
||||
for elem in data['elements']:
|
||||
if elem['type'] == 'module' and elem.get('doc'):
|
||||
overview_doc = elem['doc'].strip()
|
||||
break
|
||||
else:
|
||||
for elem in data['elements']:
|
||||
if elem.get('doc'):
|
||||
overview_doc = elem['doc'].strip()
|
||||
break
|
||||
|
||||
md_file.write("## Overview\n\n")
|
||||
md_file.write(format_docstring(overview_doc) + "\n\n")
|
||||
|
||||
# Table of Contents
|
||||
md_file.write("## API Index\n\n")
|
||||
has_elements = False
|
||||
for elem in data['elements']:
|
||||
has_elements = True
|
||||
elem_type = elem['type'].capitalize()
|
||||
md_file.write(f"- [{elem_type}: `{elem['name']}`](#{elem['name'].lower()})\n")
|
||||
if not has_elements:
|
||||
md_file.write("*No direct class or function definitions extracted from this file.*\n")
|
||||
md_file.write("\n---\n\n")
|
||||
|
||||
# API Reference details
|
||||
md_file.write("## API Reference\n\n")
|
||||
for elem in data['elements']:
|
||||
el_name = elem['name']
|
||||
el_type = elem['type']
|
||||
el_doc = format_docstring(elem.get('doc', ''))
|
||||
|
||||
# Format headers depending on type
|
||||
if el_type == 'module':
|
||||
md_file.write(f"### [Module] `{el_name}`\n\n")
|
||||
md_file.write(el_doc + "\n\n")
|
||||
elif el_type == 'class':
|
||||
bases_str = f"({', '.join(elem['bases'])})" if elem['bases'] else ""
|
||||
md_file.write(f"### [Class] `{el_name}{bases_str}`\n\n")
|
||||
md_file.write(el_doc + "\n\n")
|
||||
|
||||
if elem['methods']:
|
||||
md_file.write("#### Methods\n\n")
|
||||
for method in elem['methods']:
|
||||
m_args = ", ".join(method['args'])
|
||||
decs = "".join([f"`@{d}`<br>" for d in method['decorators']])
|
||||
md_file.write(f"##### `{method['name']}({m_args})`\n\n")
|
||||
if decs:
|
||||
md_file.write(f"**Decorators:** {decs}\n\n")
|
||||
md_file.write(format_docstring(method['doc']) + "\n\n")
|
||||
elif el_type in ('subroutine', 'function'):
|
||||
args_str = ", ".join(elem['args'])
|
||||
decs = "".join([f"`@{d}`<br>" for d in elem.get('decorators', [])])
|
||||
elem_badge = "Subroutine" if el_type == 'subroutine' else "Function"
|
||||
|
||||
md_file.write(f"### [{elem_badge}] `{el_name}`\n\n")
|
||||
md_file.write("```fortran\n" if lang == 'fortran' else "```python\n")
|
||||
md_file.write(f"{el_type} {el_name}({args_str})\n")
|
||||
md_file.write("```\n\n")
|
||||
|
||||
if decs:
|
||||
md_file.write(f"**Decorators:** {decs}\n\n")
|
||||
|
||||
md_file.write(el_doc + "\n\n")
|
||||
|
||||
md_file.write("---\n\n")
|
||||
|
||||
# 4. Generate master README.md index
|
||||
readme_path = os.path.join(docs_dir, "README.md")
|
||||
with open(readme_path, 'w', encoding='utf-8') as ri:
|
||||
ri.write("# HPC DNS Post-Processing Reference Manual\n\n")
|
||||
ri.write("> [!NOTE]\n")
|
||||
ri.write("> This reference documentation is automatically generated from codebase comments and AST analysis using the literal programming compiler.\n\n")
|
||||
|
||||
ri.write("## Project Architecture Overview\n\n")
|
||||
ri.write("This suite compiles algebraic DSL budget equations, performs high-order compact finite difference calculus, and exports physical terms via MPI-IO. Below is the primary software module pipeline:\n\n")
|
||||
|
||||
# Include a Mermaid architecture diagram
|
||||
ri.write("```mermaid\n")
|
||||
ri.write("graph TD\n")
|
||||
ri.write(" A[code_gen.py / DSL Input] -->|AST Compiler Pipeline| B[post.py / Code Gen]\n")
|
||||
ri.write(" B -->|Generates budget kernels| C[m_calculate.f90]\n")
|
||||
ri.write(" C -->|LU Tridiagonal Solvers| D[Compact.f90]\n")
|
||||
ri.write(" C -->|Array allocations| E[m_arrays.f90]\n")
|
||||
ri.write(" F[post.f90 / Main Driver] -->|Orchestrates calculations| C\n")
|
||||
ri.write(" F -->|Parallelizes domain| G[m_openmpi.f90]\n")
|
||||
ri.write(" F -->|Loads run configuration| H[m_parameters.f90]\n")
|
||||
ri.write(" I[pycompact.py / Bindings] -->|Wraps CPU calculations| C\n")
|
||||
ri.write("```\n\n")
|
||||
|
||||
ri.write("## Reference Files Index\n\n")
|
||||
ri.write("| Document / Code Module | Language | Description | \n")
|
||||
ri.write("| --- | --- | --- |\n")
|
||||
|
||||
for mod in all_modules:
|
||||
mname = mod['name']
|
||||
lang_label = "Fortran 90" if mod['lang'] == 'fortran' else "Python"
|
||||
doc_link = mname.replace('.f90', '.md').replace('.py', '.md')
|
||||
|
||||
# Smart summary from first line of doc
|
||||
overview_doc = mod['data']['doc'].strip()
|
||||
if not overview_doc:
|
||||
for elem in mod['data']['elements']:
|
||||
if elem['type'] == 'module' and elem.get('doc'):
|
||||
overview_doc = elem['doc'].strip()
|
||||
break
|
||||
else:
|
||||
for elem in mod['data']['elements']:
|
||||
if elem.get('doc'):
|
||||
overview_doc = elem['doc'].strip()
|
||||
break
|
||||
|
||||
doc_lines = overview_doc.split('\n')
|
||||
brief = doc_lines[0] if doc_lines and doc_lines[0] else "*No overview description provided.*"
|
||||
brief = brief.replace('@brief', '').replace('@author', '').strip()
|
||||
if brief.startswith('Google') or brief.startswith('Ignis'):
|
||||
for line in doc_lines:
|
||||
line_clean = line.replace('@brief', '').replace('@author', '').strip()
|
||||
if line_clean and not line.strip().startswith('@'):
|
||||
brief = line_clean
|
||||
break
|
||||
|
||||
ri.write(f"| [{mname}]({doc_link}) | **{lang_label}** | {brief} |\n")
|
||||
|
||||
ri.write("\n---\n")
|
||||
ri.write("*Generated dynamically by `build_docs.py`.*")
|
||||
|
||||
print(f"\nDocumentation built successfully under {docs_dir}!")
|
||||
# 6. Compile Python API and build MkDocs site
|
||||
mkdocs_success = run_process(["mkdocs", "build"], "MkDocs Website Compiler")
|
||||
if mkdocs_success:
|
||||
print("\n" + "="*80)
|
||||
print(" 🎉 Documentation manual built successfully!")
|
||||
print("="*80)
|
||||
print(f"Output directory: {site_dir}")
|
||||
print("To view or serve the website locally, run:")
|
||||
print(" mkdocs serve")
|
||||
print("="*80)
|
||||
else:
|
||||
print("\n[Error] MkDocs website compilation FAILED!")
|
||||
return False
|
||||
|
||||
return True
|
||||
|
||||
if __name__ == "__main__":
|
||||
build_all_docs()
|
||||
success = build_orchestrator()
|
||||
sys.exit(0 if success else 1)
|
||||
|
|
|
|||
261
docs/Compact.md
261
docs/Compact.md
|
|
@ -1,261 +0,0 @@
|
|||
# Compact.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*Author: Ignis*
|
||||
@brief High-order compact finite difference scheme solver.
|
||||
|
||||
This module handles the generation of tridiagonal/pentadiagonal matrices,
|
||||
LU decomposition calculations, and tridiagonal solver operations for periodic
|
||||
and non-periodic boundary conditions.
|
||||
|
||||
## API Index
|
||||
|
||||
- [Module: `Compact`](#compact)
|
||||
- [Subroutine: `ludcmp`](#ludcmp)
|
||||
- [Subroutine: `ludcmp_allocate`](#ludcmp_allocate)
|
||||
- [Subroutine: `ludcmp_deallocate`](#ludcmp_deallocate)
|
||||
- [Subroutine: `ludcmp_testalloc`](#ludcmp_testalloc)
|
||||
- [Subroutine: `ludcmp_calculate`](#ludcmp_calculate)
|
||||
- [Subroutine: `test_nonp_lud1`](#test_nonp_lud1)
|
||||
- [Subroutine: `test_nonp_lud2`](#test_nonp_lud2)
|
||||
- [Subroutine: `test_p_lud1`](#test_p_lud1)
|
||||
- [Subroutine: `test_p_lud2`](#test_p_lud2)
|
||||
- [Subroutine: `nonp_lud`](#nonp_lud)
|
||||
- [Subroutine: `p_lud`](#p_lud)
|
||||
- [Subroutine: `stdlu`](#stdlu)
|
||||
- [Subroutine: `ptdlu`](#ptdlu)
|
||||
- [Subroutine: `rhs1np`](#rhs1np)
|
||||
- [Subroutine: `dfnonp`](#dfnonp)
|
||||
- [Subroutine: `dfp`](#dfp)
|
||||
- [Subroutine: `ptdslv`](#ptdslv)
|
||||
- [Subroutine: `d2fp`](#d2fp)
|
||||
- [Subroutine: `tdslv`](#tdslv)
|
||||
- [Subroutine: `d2fnonp`](#d2fnonp)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Module] `Compact`
|
||||
|
||||
*Author: Ignis*
|
||||
@brief High-order compact finite difference scheme solver.
|
||||
|
||||
This module handles the generation of tridiagonal/pentadiagonal matrices,
|
||||
LU decomposition calculations, and tridiagonal solver operations for periodic
|
||||
and non-periodic boundary conditions.
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ludcmp`
|
||||
|
||||
```fortran
|
||||
subroutine ludcmp(nx, ny, nz, xp, yp, zp)
|
||||
```
|
||||
|
||||
Entry point for LU decomposition calculations.
|
||||
|
||||
Prepares the workspace allocations and runs the decomposition calculation for all three directions.
|
||||
|
||||
- ` nx `: Grid size in x-direction.
|
||||
- ` ny `: Grid size in y-direction.
|
||||
- ` nz `: Grid size in z-direction.
|
||||
- ` xp `: Periodic flag for x-direction (0 = periodic, other = non-periodic).
|
||||
- ` yp `: Periodic flag for y-direction (0 = periodic, other = non-periodic).
|
||||
- ` zp `: Periodic flag for z-direction (0 = periodic, other = non-periodic).
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ludcmp_allocate`
|
||||
|
||||
```fortran
|
||||
subroutine ludcmp_allocate(nx, ny, nz, xp, yp, zp)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ludcmp_deallocate`
|
||||
|
||||
```fortran
|
||||
subroutine ludcmp_deallocate(xp, yp, zp)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ludcmp_testalloc`
|
||||
|
||||
```fortran
|
||||
subroutine ludcmp_testalloc()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ludcmp_calculate`
|
||||
|
||||
```fortran
|
||||
subroutine ludcmp_calculate(nx, ny, nz, xp, yp, zp)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `test_nonp_lud1`
|
||||
|
||||
```fortran
|
||||
subroutine test_nonp_lud1(xx, coef)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `test_nonp_lud2`
|
||||
|
||||
```fortran
|
||||
subroutine test_nonp_lud2(xx, coef)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `test_p_lud1`
|
||||
|
||||
```fortran
|
||||
subroutine test_p_lud1(xx, coef1, coef2)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `test_p_lud2`
|
||||
|
||||
```fortran
|
||||
subroutine test_p_lud2(xx, coef1, coef2)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `nonp_lud`
|
||||
|
||||
```fortran
|
||||
subroutine nonp_lud(xyz, xx)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `p_lud`
|
||||
|
||||
```fortran
|
||||
subroutine p_lud(xyz, xx)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `stdlu`
|
||||
|
||||
```fortran
|
||||
subroutine stdlu(a, n, l)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ptdlu`
|
||||
|
||||
```fortran
|
||||
subroutine ptdlu(a, n, l, w)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `rhs1np`
|
||||
|
||||
```fortran
|
||||
subroutine rhs1np(n, h, x, dx, nd)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `dfnonp`
|
||||
|
||||
```fortran
|
||||
subroutine dfnonp(n, h, x, dx, nd, dir)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `dfp`
|
||||
|
||||
```fortran
|
||||
subroutine dfp(n, h, x, dx, nd, dir)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ptdslv`
|
||||
|
||||
```fortran
|
||||
subroutine ptdslv(r, n, l, w, nd)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2fp`
|
||||
|
||||
```fortran
|
||||
subroutine d2fp(n, h, x, dx, nd, dir)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `tdslv`
|
||||
|
||||
```fortran
|
||||
subroutine tdslv(r, n, l, nd)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2fnonp`
|
||||
|
||||
```fortran
|
||||
subroutine d2fnonp(n, h, x, dx, nd, dir)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,38 +0,0 @@
|
|||
# HPC DNS Post-Processing Reference Manual
|
||||
|
||||
> [!NOTE]
|
||||
> This reference documentation is automatically generated from codebase comments and AST analysis using the literal programming compiler.
|
||||
|
||||
## Project Architecture Overview
|
||||
|
||||
This suite compiles algebraic DSL budget equations, performs high-order compact finite difference calculus, and exports physical terms via MPI-IO. Below is the primary software module pipeline:
|
||||
|
||||
```mermaid
|
||||
graph TD
|
||||
A[code_gen.py / DSL Input] -->|AST Compiler Pipeline| B[post.py / Code Gen]
|
||||
B -->|Generates budget kernels| C[m_calculate.f90]
|
||||
C -->|LU Tridiagonal Solvers| D[Compact.f90]
|
||||
C -->|Array allocations| E[m_arrays.f90]
|
||||
F[post.f90 / Main Driver] -->|Orchestrates calculations| C
|
||||
F -->|Parallelizes domain| G[m_openmpi.f90]
|
||||
F -->|Loads run configuration| H[m_parameters.f90]
|
||||
I[pycompact.py / Bindings] -->|Wraps CPU calculations| C
|
||||
```
|
||||
|
||||
## Reference Files Index
|
||||
|
||||
| Document / Code Module | Language | Description |
|
||||
| --- | --- | --- |
|
||||
| [Compact.f90](Compact.md) | **Fortran 90** | This module handles the generation of tridiagonal/pentadiagonal matrices, |
|
||||
| [m_arrays.f90](m_arrays.md) | **Fortran 90** | *No overview description provided.* |
|
||||
| [m_calculate.f90](m_calculate.md) | **Fortran 90** | This module calculates spatial derivatives (first and second derivatives in X, Y, Z directions) |
|
||||
| [m_openmpi.f90](m_openmpi.md) | **Fortran 90** | *No overview description provided.* |
|
||||
| [m_parameters.f90](m_parameters.md) | **Fortran 90** | *No overview description provided.* |
|
||||
| [post.f90](post.md) | **Fortran 90** | *No overview description provided.* |
|
||||
| [post_dns.f90](post_dns.md) | **Fortran 90** | *No overview description provided.* |
|
||||
| [code_gen.py](code_gen.md) | **Python** | Convert the value of `tok` from string to bool, while maintaining line number & column. |
|
||||
| [post.py](post.md) | **Python** | conversion from tree to python data |
|
||||
| [pycompact.py](pycompact.md) | **Python** | *No overview description provided.* |
|
||||
|
||||
---
|
||||
*Generated dynamically by `build_docs.py`.*
|
||||
103
docs/code_gen.md
103
docs/code_gen.md
|
|
@ -1,103 +0,0 @@
|
|||
# code_gen.py
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
Convert the value of `tok` from string to bool, while maintaining line number & column.
|
||||
|
||||
## API Index
|
||||
|
||||
- [Function: `tok_to_bool`](#tok_to_bool)
|
||||
- [Function: `tok_to_int`](#tok_to_int)
|
||||
- [Function: `tok_to_str`](#tok_to_str)
|
||||
- [Class: `VersionInfo`](#versioninfo)
|
||||
- [Function: `test`](#test)
|
||||
- [Function: `build_info`](#build_info)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Function] `tok_to_bool`
|
||||
|
||||
```python
|
||||
function tok_to_bool(tok)
|
||||
```
|
||||
|
||||
Convert the value of `tok` from string to bool, while maintaining line number & column.
|
||||
|
||||
---
|
||||
|
||||
### [Function] `tok_to_int`
|
||||
|
||||
```python
|
||||
function tok_to_int(tok)
|
||||
```
|
||||
|
||||
Convert the value of `tok` from string to int, while maintaining line number & column.
|
||||
|
||||
---
|
||||
|
||||
### [Function] `tok_to_str`
|
||||
|
||||
```python
|
||||
function tok_to_str(tok)
|
||||
```
|
||||
|
||||
Convert the value of `tok` from string to string, while maintaining line number & column.
|
||||
|
||||
---
|
||||
|
||||
### [Class] `VersionInfo(object)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, input_raw)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fparams(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `test`
|
||||
|
||||
```python
|
||||
function test(terms_raw, report, latex)
|
||||
```
|
||||
|
||||
Compiles the post-processing term specifications from DSL into targets.
|
||||
|
||||
This compiles the Lark AST through all 4 pipeline stages (Stage 1 to 4)
|
||||
and outputs the resulting Fortran source code via Jinja2, a LaTeX equation
|
||||
dictionary, or a code generation IR report.
|
||||
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- ` terms_raw ` *(str)*: The raw string contents of the DSL terms specification input file.
|
||||
- ` report ` *(bool)*: If True, generates and saves the intermediate code generation report.
|
||||
- ` latex ` *(bool)*: If True, prints LaTeX equations of the averaged terms to stdout.
|
||||
|
||||
---
|
||||
|
||||
### [Function] `build_info`
|
||||
|
||||
```python
|
||||
function build_info(terms_raw)
|
||||
```
|
||||
|
||||
Generates and prints build information for the current code generation run.
|
||||
|
||||
|
||||
**Arguments:**
|
||||
|
||||
- ` terms_raw ` *(str)*: The raw string contents of the DSL terms specification input file.
|
||||
|
||||
---
|
||||
|
||||
20
docs/fortran.md
Normal file
20
docs/fortran.md
Normal file
|
|
@ -0,0 +1,20 @@
|
|||
# Fortran Core API Reference
|
||||
|
||||
The Fortran core elements have been fully documented and compiled using **FORD** (FORtran Documenter), which extracts comments (`!>` and `!!`) and draws rich module dependency graphs.
|
||||
|
||||
---
|
||||
|
||||
## View Interactive Documentation
|
||||
|
||||
[👉 Click Here to Open Interactive Fortran API Reference](fortran_api/index.html){: .md-button .md-button--primary .md-button--large }
|
||||
|
||||
---
|
||||
|
||||
### Core Modules Cataloged
|
||||
|
||||
- **[[Compact]]**: Solves compact finite difference scheme equations using high-order tridiagonal/pentadiagonal schemes.
|
||||
- **[[m_calculate]]**: Runs budget calculations, spatial derivatives, and pieces Arrhenius chemical kinetics.
|
||||
- **[[m_arrays]]**: Handles array allocations and instant budget memory blocks.
|
||||
- **[[m_openmpi]]**: Wraps domain sizing, grid splitting, and MPI communicators.
|
||||
- **[[m_parameters]]**: Loads physical settings, boundary configurations, and grid sizes from file inputs.
|
||||
- **[[post]]**: Entry driver performing budget calculation run tasks.
|
||||
30
docs/index.md
Normal file
30
docs/index.md
Normal file
|
|
@ -0,0 +1,30 @@
|
|||
# HPC DNS Post-Processing Reference Manual
|
||||
|
||||
Welcome to the automated documentation suite for the high-order compact difference post-processing project! This manual includes reference documentation for both the compiled Fortran core and the Python binds/algebraic generators.
|
||||
|
||||
---
|
||||
|
||||
## Architecture Overview
|
||||
|
||||
This post-processor compiles algebraic equations defined in a custom DSL (Domain Specific Language), computes high-order derivatives (1st & 2nd spatial derivatives) using tridiagonal finite differences, and leverages parallel MPI-IO blocks. Below is the primary compiler pipeline:
|
||||
|
||||
```mermaid
|
||||
graph TD
|
||||
A[code_gen.py / DSL Input] -->|AST Compiler Pipeline| B[post.py / Code Gen]
|
||||
B -->|Generates budget kernels| C[m_calculate.f90]
|
||||
C -->|LU Tridiagonal Solvers| D[Compact.f90]
|
||||
C -->|Array allocations| E[m_arrays.f90]
|
||||
F[post.f90 / Main Driver] -->|Orchestrates calculations| C
|
||||
F -->|Parallelizes domain| G[m_openmpi.f90]
|
||||
F -->|Loads run configuration| H[m_parameters.f90]
|
||||
I[pycompact.py / Bindings] -->|Wraps CPU calculations| C
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## Navigation Guide
|
||||
|
||||
- **[Python API Reference](python/code_gen.md)**: Automatically parsed API and signatures for the DSL parsers, topological compiler stages, and Python wrappers.
|
||||
- **[Fortran Core Reference](fortran.md)**: Standard documentation compiled by `FORD` covering tridiagonal compact solvers, math kernels, and MPI bindings.
|
||||
|
||||
*Generated automatically using industry-standard tools: FORD, MkDocs, and Material theme.*
|
||||
|
|
@ -1,55 +0,0 @@
|
|||
# m_arrays.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*No description provided.*
|
||||
|
||||
## API Index
|
||||
|
||||
- [Module: `m_arrays`](#m_arrays)
|
||||
- [Subroutine: `m_arrays_init`](#m_arrays_init)
|
||||
- [Subroutine: `m_arrays_finalize`](#m_arrays_finalize)
|
||||
- [Subroutine: `m_arrays_calculate_instant`](#m_arrays_calculate_instant)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Module] `m_arrays`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_arrays_init`
|
||||
|
||||
```fortran
|
||||
subroutine m_arrays_init()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_arrays_finalize`
|
||||
|
||||
```fortran
|
||||
subroutine m_arrays_finalize()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_arrays_calculate_instant`
|
||||
|
||||
```fortran
|
||||
subroutine m_arrays_calculate_instant()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,229 +0,0 @@
|
|||
# m_calculate.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*Author: Google DeepMind Team & Ignis*
|
||||
@brief DNS post-processing mathematical operations and derivatives.
|
||||
|
||||
This module calculates spatial derivatives (first and second derivatives in X, Y, Z directions)
|
||||
using high-order compact finite difference schemes. It also calculates chemical reaction rates,
|
||||
positive/negative component extraction, and threshold operations.
|
||||
|
||||
## API Index
|
||||
|
||||
- [Module: `m_calculate`](#m_calculate)
|
||||
- [Subroutine: `m_calculate_init`](#m_calculate_init)
|
||||
- [Subroutine: `m_calculate_finalize`](#m_calculate_finalize)
|
||||
- [Subroutine: `ddx1d`](#ddx1d)
|
||||
- [Subroutine: `ddx`](#ddx)
|
||||
- [Subroutine: `ddy`](#ddy)
|
||||
- [Subroutine: `ddz`](#ddz)
|
||||
- [Subroutine: `d2dx1d`](#d2dx1d)
|
||||
- [Subroutine: `d2dx`](#d2dx)
|
||||
- [Subroutine: `d2dy`](#d2dy)
|
||||
- [Subroutine: `d2dz`](#d2dz)
|
||||
- [Subroutine: `tp`](#tp)
|
||||
- [Subroutine: `tp2`](#tp2)
|
||||
- [Function: `rxn_rate`](#rxn_rate)
|
||||
- [Function: `threshold_min_max`](#threshold_min_max)
|
||||
- [Function: `positive`](#positive)
|
||||
- [Function: `negative`](#negative)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Module] `m_calculate`
|
||||
|
||||
*Author: Google DeepMind Team & Ignis*
|
||||
@brief DNS post-processing mathematical operations and derivatives.
|
||||
|
||||
This module calculates spatial derivatives (first and second derivatives in X, Y, Z directions)
|
||||
using high-order compact finite difference schemes. It also calculates chemical reaction rates,
|
||||
positive/negative component extraction, and threshold operations.
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_calculate_init`
|
||||
|
||||
```fortran
|
||||
subroutine m_calculate_init()
|
||||
```
|
||||
|
||||
Initializes the workspace arrays and matrices.
|
||||
|
||||
Pre-allocates transposed workspace buffers (`xsrc`, `xdst`, `rsrc`, `rdst`)
|
||||
and performs the LU decomposition setup via `ludcmp` for the tridiagonal compact schemes.
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_calculate_finalize`
|
||||
|
||||
```fortran
|
||||
subroutine m_calculate_finalize()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ddx1d`
|
||||
|
||||
```fortran
|
||||
subroutine ddx1d(dst, src)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ddx`
|
||||
|
||||
```fortran
|
||||
subroutine ddx(dst, src)
|
||||
```
|
||||
|
||||
Computes the first-order derivative in the X-direction.
|
||||
|
||||
- ` src `: 3D input scalar field (nxp, nyp, nzp).
|
||||
- ` dst `: 3D output derivative field (nxp, nyp, nzp).
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ddy`
|
||||
|
||||
```fortran
|
||||
subroutine ddy(dst, src)
|
||||
```
|
||||
|
||||
Computes the first-order derivative in the Y-direction.
|
||||
|
||||
- ` src `: 3D input scalar field (nxp, nyp, nzp).
|
||||
- ` dst `: 3D output derivative field (nxp, nyp, nzp).
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `ddz`
|
||||
|
||||
```fortran
|
||||
subroutine ddz(dst, src)
|
||||
```
|
||||
|
||||
Computes the first-order derivative in the Z-direction.
|
||||
|
||||
- ` src `: 3D input scalar field (nxp, nyp, nzp).
|
||||
- ` dst `: 3D output derivative field (nxp, nyp, nzp).
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2dx1d`
|
||||
|
||||
```fortran
|
||||
subroutine d2dx1d(dst, src)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2dx`
|
||||
|
||||
```fortran
|
||||
subroutine d2dx(dst, src)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2dy`
|
||||
|
||||
```fortran
|
||||
subroutine d2dy(dst, src)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `d2dz`
|
||||
|
||||
```fortran
|
||||
subroutine d2dz(dst, src)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `tp`
|
||||
|
||||
```fortran
|
||||
subroutine tp(a, b, nx)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `tp2`
|
||||
|
||||
```fortran
|
||||
subroutine tp2(a, b, n1, n2)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `rxn_rate`
|
||||
|
||||
```fortran
|
||||
function rxn_rate(c)
|
||||
```
|
||||
|
||||
Computes the chemical reaction rate based on the progress variable c.
|
||||
|
||||
This uses a piecewise exponential/Arrhenius model depending on whether the progress variable
|
||||
is below c_cut, above c_ref, or intermediate.
|
||||
|
||||
- ` c `: The progress variable (0.0 to 1.0).
|
||||
|
||||
**Returns:**
|
||||
|
||||
The computed reaction rate.
|
||||
|
||||
---
|
||||
|
||||
### [Function] `threshold_min_max`
|
||||
|
||||
```fortran
|
||||
function threshold_min_max(c, minc, maxc)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `positive`
|
||||
|
||||
```fortran
|
||||
function positive(c)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `negative`
|
||||
|
||||
```fortran
|
||||
function negative(c)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,55 +0,0 @@
|
|||
# m_openmpi.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*No description provided.*
|
||||
|
||||
## API Index
|
||||
|
||||
- [Module: `m_openmpi`](#m_openmpi)
|
||||
- [Subroutine: `m_openmpi_init`](#m_openmpi_init)
|
||||
- [Subroutine: `m_openmpi_exit`](#m_openmpi_exit)
|
||||
- [Subroutine: `openmpi_get_command_line`](#openmpi_get_command_line)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Module] `m_openmpi`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_openmpi_init`
|
||||
|
||||
```fortran
|
||||
subroutine m_openmpi_init()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `m_openmpi_exit`
|
||||
|
||||
```fortran
|
||||
subroutine m_openmpi_exit()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `openmpi_get_command_line`
|
||||
|
||||
```fortran
|
||||
subroutine openmpi_get_command_line()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,44 +0,0 @@
|
|||
# m_parameters.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*No description provided.*
|
||||
|
||||
## API Index
|
||||
|
||||
- [Module: `m_parameters`](#m_parameters)
|
||||
- [Function: `to_omit`](#to_omit)
|
||||
- [Subroutine: `read_intro`](#read_intro)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Module] `m_parameters`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `to_omit`
|
||||
|
||||
```fortran
|
||||
function to_omit(num)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Subroutine] `read_intro`
|
||||
|
||||
```fortran
|
||||
subroutine read_intro()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
694
docs/post.md
694
docs/post.md
|
|
@ -1,694 +0,0 @@
|
|||
# post.py
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
conversion from tree to python data
|
||||
|
||||
## API Index
|
||||
|
||||
- [Class: `LarkToSympy`](#larktosympy)
|
||||
- [Class: `ArrayFCodePrinter`](#arrayfcodeprinter)
|
||||
- [Class: `SympyOptimizer`](#sympyoptimizer)
|
||||
- [Class: `CollectDefinitions`](#collectdefinitions)
|
||||
- [Class: `ExpInspector`](#expinspector)
|
||||
- [Class: `ExpToLatex`](#exptolatex)
|
||||
- [Class: `ExpToCode`](#exptocode)
|
||||
- [Function: `make_allocate`](#make_allocate)
|
||||
- [Class: `FieldBase`](#fieldbase)
|
||||
- [Class: `FieldExporter`](#fieldexporter)
|
||||
- [Class: `Field`](#field)
|
||||
- [Class: `FluctuationField`](#fluctuationfield)
|
||||
- [Class: `PrimaryField`](#primaryfield)
|
||||
- [Class: `DerivedField`](#derivedfield)
|
||||
- [Class: `AveragedField`](#averagedfield)
|
||||
- [Class: `Stage1`](#stage1)
|
||||
- [Class: `Stage2`](#stage2)
|
||||
- [Class: `Stage3`](#stage3)
|
||||
- [Class: `Stage4`](#stage4)
|
||||
- [Class: `Stage5`](#stage5)
|
||||
- [Class: `Stage6`](#stage6)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Class] `LarkToSympy(Transformer)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `number(self, numeral)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `env(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `paren(self, val)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `var(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fluc(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `dnx(self, partial, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `icall(self, op, val)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fcall(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `neg(self, val)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `add(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `sub(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `mul(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `div(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `udf(self, a)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `ArrayFCodePrinter(FCodePrinter)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, settings, array_symbols, avg_symbols)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `_print_Float(self, expr)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `_print_Symbol(self, expr)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `_print_Function(self, expr)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `SympyOptimizer`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `get_instance(cls, fdict)`
|
||||
|
||||
**Decorators:** `@classmethod`<br>
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__init__(self, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `set_averaged(self, averaged_dict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `get_sympy_expr(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `calculate_flops_and_heavy(self, expr)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `count_3d_loads(self, expr, three_d_arrays)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `optimize_field(self, name, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `CollectDefinitions(Visitor)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, primary, derived, averaged)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `varlist(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `assign_var(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `assign_avg_var(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `ExpInspector(Visitor)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `inspect(cls, tree)`
|
||||
|
||||
**Decorators:** `@classmethod`<br>
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__call__(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fluc(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `var(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `dnx(self, tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `ExpToLatex(Transformer)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `arithmatic_rooted(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `parenthise(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `number(self, numeral)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `env(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `paren(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `var(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fluc(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `dnx(self, partial, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `icall(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fcall(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `neg(self, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `add(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `sub(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `mul(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `div(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `ExpToCode(Transformer)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `number(self, numeral)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `env(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `paren(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `var(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fluc(self, name)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `dnx(self, partial, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `icall(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `fcall(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `neg(self, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `add(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `sub(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `mul(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `div(self, a, b)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `make_allocate`
|
||||
|
||||
```python
|
||||
function make_allocate(name, shape, init_zero)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `FieldBase(object)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, name, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `depends_on(self, a)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `is_primary(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `not_primary(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `is_fluctuation(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `export_on(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__repr__(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `checkFluctuation(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `depClosure(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_decl(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_alloc(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_free(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `FieldExporter(object)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, name, attr, parent)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_decl(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_alloc(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_free(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Field(FieldBase)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, name, attr, exp, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `export_on(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `FluctuationField(FieldBase)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, w, field, fset, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `id(cls, w, field)`
|
||||
|
||||
**Decorators:** `@classmethod`<br>
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `PrimaryField(FieldBase)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, name, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_decl(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_alloc(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_free(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `DerivedField(FieldBase)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, op, v, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `AveragedField(FieldBase)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `id(cls, w, tgt)`
|
||||
|
||||
**Decorators:** `@classmethod`<br>
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__init__(self, w, tgt, fdict)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code(self, alloc)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `code_avg(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `isWeighted(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `pass1(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `pass2(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage1`
|
||||
|
||||
conversion from tree to python data
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, raw_tree)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__repr__(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage2`
|
||||
|
||||
expand derivatives and averages
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__repr__(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `dependency(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage3`
|
||||
|
||||
calculate execution order
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `__repr__(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `sort_vars(self, dependency, group)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `calc_size(self, ordered, remaining)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `sort_vars_new(self, dependency, group)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `print_program(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage4`
|
||||
|
||||
analyze liveness and allocate array
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `liveness(self, l1, g)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `allocate_arr(self, l)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `work_array_codes(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `write_avg_codes(self, avglist)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `print_program(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `save_ir(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage5`
|
||||
|
||||
pass1 and pass2 seperation and calculation ordering
|
||||
|
||||
---
|
||||
|
||||
### [Class] `Stage6`
|
||||
|
||||
generate fortran code
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,37 +0,0 @@
|
|||
# post_dns.f90
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*No description provided.*
|
||||
|
||||
## API Index
|
||||
|
||||
- [Function: `build_info_length`](#build_info_length)
|
||||
- [Function: `latex_length`](#latex_length)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Function] `build_info_length`
|
||||
|
||||
```fortran
|
||||
function build_info_length()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `latex_length`
|
||||
|
||||
```fortran
|
||||
function latex_length()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
|
|
@ -1,116 +0,0 @@
|
|||
# pycompact.py
|
||||
|
||||
|
||||
|
||||
## Overview
|
||||
|
||||
*No description provided.*
|
||||
|
||||
## API Index
|
||||
|
||||
- [Class: `CompactScheme`](#compactscheme)
|
||||
- [Function: `read_old_data`](#read_old_data)
|
||||
- [Function: `read_data`](#read_data)
|
||||
- [Function: `validate_trigonometric`](#validate_trigonometric)
|
||||
- [Function: `test_dns_data`](#test_dns_data)
|
||||
|
||||
---
|
||||
|
||||
## API Reference
|
||||
|
||||
### [Class] `CompactScheme`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
#### Methods
|
||||
|
||||
##### `__init__(self, nx, ny, nz, px, py, pz, lx, ly, lz)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `test_ludcmp(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `py_rhs_1_np(self, x)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `py_tdslv(self, r, l)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `test_dfnonp(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `verify_nonp_lud1(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `verify_nonp_lud2(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `py_stdlu(self, aa)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `ddx(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `ddy(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `ddz(self, src)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
##### `port_nonp_coef(self)`
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `read_old_data`
|
||||
|
||||
```python
|
||||
function read_old_data(fname)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `read_data`
|
||||
|
||||
```python
|
||||
function read_data(fname)
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `validate_trigonometric`
|
||||
|
||||
```python
|
||||
function validate_trigonometric()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
### [Function] `test_dns_data`
|
||||
|
||||
```python
|
||||
function test_dns_data()
|
||||
```
|
||||
|
||||
*No description provided.*
|
||||
|
||||
---
|
||||
|
||||
3
docs/python/code_gen.md
Normal file
3
docs/python/code_gen.md
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
# Code Generator (`code_gen.py`)
|
||||
|
||||
::: code_gen
|
||||
3
docs/python/post.md
Normal file
3
docs/python/post.md
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
# Compiler Stages (`post.py`)
|
||||
|
||||
::: post
|
||||
3
docs/python/pycompact.md
Normal file
3
docs/python/pycompact.md
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
# Python Bindings (`pycompact.py`)
|
||||
|
||||
::: pycompact
|
||||
22
ford.md
Normal file
22
ford.md
Normal file
|
|
@ -0,0 +1,22 @@
|
|||
---
|
||||
project: HPC DNS Post-Processing Fortran Core
|
||||
summary: Tridiagonal compact finite difference solver, mathematical operators, and MPI-IO drivers.
|
||||
author: Google DeepMind Team & Ignis
|
||||
version: 1.0.0
|
||||
src_dir: ./code
|
||||
output_dir: ./docs/fortran_api
|
||||
exclude: **/pycompact/**
|
||||
preprocess: true
|
||||
display: public
|
||||
---
|
||||
|
||||
# Fortran Core Documentation
|
||||
|
||||
Welcome to the Fortran Core Reference. This section contains automatically generated docs from `FORD` for the high-order compact difference solver modules:
|
||||
|
||||
- **[[Compact]]**: Compact finite difference scheme equations.
|
||||
- **[[m_calculate]]**: spatial derivatives and chemical kinetics.
|
||||
- **[[m_arrays]]**: post-processing field allocation.
|
||||
- **[[m_openmpi]]**: MPI parallel domain wrapper.
|
||||
- **[[m_parameters]]**: input loaders and physical values.
|
||||
- **[[post]]**: main driver pipeline.
|
||||
45
mkdocs.yml
Normal file
45
mkdocs.yml
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
site_name: HPC DNS Post-Processing Reference Manual
|
||||
theme:
|
||||
name: material
|
||||
palette:
|
||||
- media: "(prefers-color-scheme: dark)"
|
||||
scheme: slate
|
||||
primary: teal
|
||||
accent: cyan
|
||||
toggle:
|
||||
icon: material/brightness-4
|
||||
name: Switch to light mode
|
||||
- media: "(prefers-color-scheme: light)"
|
||||
scheme: default
|
||||
primary: teal
|
||||
accent: cyan
|
||||
toggle:
|
||||
icon: material/brightness-7
|
||||
name: Switch to dark mode
|
||||
features:
|
||||
- navigation.tabs
|
||||
- navigation.sections
|
||||
- navigation.expand
|
||||
- content.code.copy
|
||||
|
||||
plugins:
|
||||
- search
|
||||
- mkdocstrings:
|
||||
default_handler: python
|
||||
handlers:
|
||||
python:
|
||||
paths: [code, code/code_gen, code/pycompact]
|
||||
options:
|
||||
docstring_style: google
|
||||
show_source: true
|
||||
show_root_heading: true
|
||||
show_bases: true
|
||||
|
||||
nav:
|
||||
- Home: index.md
|
||||
- Python API Reference:
|
||||
- Code Generator: python/code_gen.md
|
||||
- Compiler Stages: python/post.md
|
||||
- Python Bindings: python/pycompact.md
|
||||
- Fortran Core Reference:
|
||||
- Modules & Procedures: fortran.md
|
||||
5
requirements.txt
Normal file
5
requirements.txt
Normal file
|
|
@ -0,0 +1,5 @@
|
|||
mkdocs==1.6.1
|
||||
mkdocs-material==9.7.6
|
||||
mkdocstrings[python]==0.25.2
|
||||
ford==7.0.13
|
||||
mkdocs-autorefs==1.3.1
|
||||
Loading…
Add table
Reference in a new issue