building docs structure

docs/documentation/api/couplings.md

@@ -0,0 +1 @@
+::: intrinsic.couplings

docs/documentation/api/inputs.md

@@ -0,0 +1,5 @@
+# Input containers
+
+## Intrinsic modal solution
+
+::: preprocessor.containers.intrinsicmodal

docs/documentation/examples.md

@@ -1 +1,2 @@
 # Examples
+

docs/documentation/requirements.txt

@@ -1,5 +1,6 @@
 # Latest versions at time of writing.
 mkdocs           # Main documentation generator.
+mkdocstrings[python]
 mkdocs-material  # Theme
 pymdown-extensions  # Markdown extensions e.g. to handle LaTeX.
 mkdocstrings    # Autogenerate documentation from docstrings.

docs/documentation/theory.md

@@ -0,0 +1,6 @@
+# Theoretical background
+
+## Reduction to Load paths:
+## Intrinsic modes:
+## Nonlinear couplings:
+## Aeroelastic system:

docs/reports/CPC24/main.org

@@ -32,12 +32,12 @@ We propose a non-intrusive framework to enhance complex FE structural and aeroel
         '("latexmk -pdflatex='pdflatex --syntex=1 -shell-escape -interaction nonstopmode' -pdf -bibtex -f %f"
           "latexmk -pdflatex='pdflatex --syntex=1 -shell-escape -interaction nonstopmode' -pdf -bibtex -f %f"))
   ;; (setq org-latex-pdf-process (list "latexmk -f -pdf -interaction=nonstopmode -output-directory=%o %f"))
-  (pyvenv-workon "feniax.ev")
+  (pyvenv-workon "feniax")
   (require 'org-tempo)
   ;; Veval_blocks -> eval blocks of latex
   ;; Veval_blocks_run -> eval blocks to obtain results
   (setq Veval_blocks "yes") ;; yes, no, no-export 
-  (setq Veval_blocks_run "no-export")
+  (setq Veval_blocks_run "yes")
   (setq Vpics "png") ;; yes, no, no-export   
   (setq pythonShell "py2")
   ;; export_blocks: code, results, both, none

examples/ArgyrisBeam/settings.py

@@ -1,13 +1,11 @@
-import pathlib
-import pdb
-import sys
-import numpy as np
 import datetime
+import pathlib
+
+import feniax.feniax_main
 import feniax.preprocessor.configuration as configuration  # import Config, dump_to_yaml
 from feniax.preprocessor.inputs import Inputs
-import feniax.feniax_main
-import jax.numpy as jnp
-import jax
+
+
 #jax.config.update("jax_enable_compilation_cache", False)
 
 

feniax/feniax_main.py

@@ -1,4 +1,4 @@
-"""FEM4INAS main"""
+"""Main FENIAX"""
 
 import feniax.drivers
 import feniax.preprocessor.configuration as configuration  # Config, ValidateConfig

feniax/intrinsic/couplings.py

@@ -36,6 +36,26 @@ def f_gamma1(phi1: jnp.array, psi1: jnp.array) -> jnp.array:
 def f_gamma2(
     phi1m: jnp.array, phi2: jnp.array, psi2: jnp.array, delta_s: jnp.array
 ) -> jnp.array:
+    """Gamma1 tensor calculation.
+
+    Parameters
+    ----------
+    psi1m : jnp.array
+        Velocity modal shapes at mid-points (Nmx6xNn)    
+    phi2 : jnp.array
+        Internal force modal shapes (Nmx6xNn)
+    psi2 : jnp.array
+        Strain modal shapes (Nmx6xNn)
+    delta_s : jnp.array
+        1D differential path increments (Nn)
+    
+    Returns
+    -------
+    jnp.array
+        Gamma2 tensor (NmxNmxNm)
+
+    """
+
     phi1mi = phi1m[:, :, 1:]
     phi2i = phi2[:, :, 1:]
     psi2i = psi2[:, :, 1:]
@@ -55,12 +75,45 @@ def f_gamma2(
 
 @jax.jit
 def f_alpha1(phi1: jnp.array, psi1: jnp.array) -> jnp.array:
+    """Gamma1 tensor calculation.
+
+    Parameters
+    ----------
+    phi1 : jnp.array
+        Velocity modal shapes (Nmx6xNn)
+    psi1 : jnp.array
+        Momentum modal shapes (Nmx6xNn)
+    Returns
+    -------
+    jnp.array
+        alpha1 tensor (NmxNm)
+
+    """
+
     alpha1 = jnp.einsum("isn,jsn->ij", phi1, psi1)
     return alpha1
 
 
 @jax.jit
 def f_alpha2(phi2: jnp.array, psi2: jnp.array, delta_s: jnp.array) -> jnp.array:
+    """Gamma1 tensor calculation.
+
+    Parameters
+    ----------
+    phi2 : jnp.array
+        Internal force modal shapes (Nmx6xNn)
+    psi2 : jnp.array
+        Strain modal shapes (Nmx6xNn)
+    delta_s : jnp.array
+        1D differential path increments (Nn)
+    
+    Returns
+    -------
+    jnp.array
+        Alpha2 tensor (NmxNm)
+
+    """
+
     phi2i = phi2[:, :, 1:]
     psi2i = psi2[:, :, 1:]
     delta_si = delta_s[1:]

feniax/preprocessor/containers/intrinsicmodal.py

@@ -1,5 +1,5 @@
 """
-xxxx
+Containers for the intrinsic modal solution settings
 """
 
 import inspect
@@ -897,7 +897,12 @@ def __post_init__(self):
         if self.components is None:
             object.__setattr__(self, "components", tuple(range(self._numcomponents)))
 
-
+
+class ADinputType(Enum):
+    POINT_FORCES = 1
+    GUST1 = 2
+    FEM = 3
+
 @dataclass(frozen=True, kw_only=True)
 class DtoAD(Dlibrary):
     """Algorithm differentiation settings
@@ -952,61 +957,7 @@ def __post_init__(self):
                 _numcomponents=self._numcomponents,
             ),
         )
-
-@dataclass(frozen=True)
-class Dsystems(DataContainer):
-    """Input setting for the range of systems in the simulation
-
-    Parameters
-    ----------
-    sett : dict
-    mapper : dict
-    borrow : dict
-    _fem : Dfem
-    
-    Attributes
-    ----------
-
-    
-    """
-
-    sett: dict[str:dict] = dfield("Settings ", yaml_save=True)
-    mapper: dict[str:Dsystem] = dfield(
-        "Dictionary with systems in the simulation", init=False
-    )
-    borrow: dict[str:str] = dfield(
-        """Borrow settings from another system:
-    if there is only one system, then inactive; otherwise default to take settings from
-    the first system unless specified.
-    """,
-        default=None,
-    )
-    _fem: Dfem = dfield("", default=None, yaml_save=False)
 
-    def __post_init__(self):
-        mapper = dict()
-        counter = 0
-        for k, v in self.sett.items():
-            if self.borrow is None:
-                # pass self._fem to the system here, the others should already have
-                # a reference
-                mapper[k] = initialise_Dclass(v, Dsystem, name=k, _fem=self._fem)
-            elif isinstance(self.borrow, str):
-                assert self.borrow in self.sett.keys(), "borrow not in system names"
-                if k == self.borrow:
-                    mapper[k] = initialise_Dclass(v, Dsystem, name=k)
-                else:
-                    v0 = self.sett[self.borrow]
-                    mapper[k] = initialise_Dclass(v0, Dsystem, name=k, **v)
-            else:
-                if k in self.borrow.keys():
-                    v0 = self.sett[self.borrow[k]]
-                    mapper[k] = initialise_Dclass(v0, Dsystem, name=k, **v)
-                else:
-                    mapper[k] = initialise_Dclass(v, Dsystem, name=k)
-
-            counter += 1
-        object.__setattr__(self, "mapper", mapper)
 
 @dataclass(frozen=True, kw_only=True)
 class Dsystem(DataContainer):
@@ -1259,11 +1210,61 @@ def build_label(self):
         object.__setattr__(self, "label_map", lmap)
         object.__setattr__(self, "label", label)  # f"dq_{label}")
 
+
+@dataclass(frozen=True)
+class Dsystems(DataContainer):
+    """Input setting for the range of systems in the simulation
 
-class ADinputType(Enum):
-    POINT_FORCES = 1
-    GUST1 = 2
-    FEM = 3
+    Parameters
+    ----------
+    sett : dict
+    mapper : dict
+    borrow : dict
+    _fem : Dfem
+    
+    Attributes
+    ----------
+
+    
+    """
+
+    sett: dict[str:dict] = dfield("Settings ", yaml_save=True)
+    mapper: dict[str:Dsystem] = dfield(
+        "Dictionary with systems in the simulation", init=False
+    )
+    borrow: dict[str:str] = dfield(
+        """Borrow settings from another system:
+    if there is only one system, then inactive; otherwise default to take settings from
+    the first system unless specified.
+    """,
+        default=None,
+    )
+    _fem: Dfem = dfield("", default=None, yaml_save=False)
+
+    def __post_init__(self):
+        mapper = dict()
+        counter = 0
+        for k, v in self.sett.items():
+            if self.borrow is None:
+                # pass self._fem to the system here, the others should already have
+                # a reference
+                mapper[k] = initialise_Dclass(v, Dsystem, name=k, _fem=self._fem)
+            elif isinstance(self.borrow, str):
+                assert self.borrow in self.sett.keys(), "borrow not in system names"
+                if k == self.borrow:
+                    mapper[k] = initialise_Dclass(v, Dsystem, name=k)
+                else:
+                    v0 = self.sett[self.borrow]
+                    mapper[k] = initialise_Dclass(v0, Dsystem, name=k, **v)
+            else:
+                if k in self.borrow.keys():
+                    v0 = self.sett[self.borrow[k]]
+                    mapper[k] = initialise_Dclass(v0, Dsystem, name=k, **v)
+                else:
+                    mapper[k] = initialise_Dclass(v, Dsystem, name=k)
+
+            counter += 1
+        object.__setattr__(self, "mapper", mapper)
 
 
 def generate_docstring(cls: Any) -> Any:

mkdocs.yml

@@ -86,7 +86,7 @@ plugins:
         default_handler: python
         handlers:
             python:
-              paths: [fem4inas]
+              paths: [feniax]
               options:
                 docstring_style: numpy # 'google' 'numpy', 'rst', etc.
                 filters: ["!^_[^_]"]  # Exclude private members
@@ -115,5 +115,8 @@ nav:
   #- Tutorials
   - Examples: examples.md
   #- Postprocessing
+  - Theoretical background: theory.md
   - Codes:
+      - Inputs: api/inputs.md
       - Modes: api/modes.md
+      - Nonlinear couplings: api/couplings.md