sgio 0.2.13__tar.gz → 0.2.15__tar.gz

{sgio-0.2.13 → sgio-0.2.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sgio
-Version: 0.2.13
+Version: 0.2.15
 Summary: I/O for VABS and SwiftComp
 Project-URL: Homepage, https://github.com/wenbinyugroup/sgio
 Project-URL: Documentation, https://wenbinyugroup.github.io/sgio/
@@ -10,10 +10,14 @@ License-File: LICENSE
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
+Requires-Dist: build>=1.3.0
+Requires-Dist: hatchling>=1.27.0
 Requires-Dist: matplotlib
 Requires-Dist: meshio
+Requires-Dist: pydantic>=2.0
 Requires-Dist: pyyaml
 Requires-Dist: scipy
+Requires-Dist: twine>=6.2.0
 Provides-Extra: all
 Requires-Dist: h5py; extra == 'all'
 Requires-Dist: netcdf4; extra == 'all'

{sgio-0.2.13 → sgio-0.2.15}/pyproject.toml

@@ -18,8 +18,12 @@ dependencies = [
     # "numpy>=2",
     # "rich",
     "matplotlib",
+    "pydantic>=2.0",
     "pyyaml",
     "scipy",
+    "build>=1.3.0",
+    "hatchling>=1.27.0",
+    "twine>=6.2.0",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

{sgio-0.2.13 → sgio-0.2.15}/sgio/__init__.py

@@ -14,6 +14,7 @@ from ._exceptions import (
 
 from .core import (
     StructureGene,
+    SGMesh,
     check_isolated_nodes,
     renumber_elements,
     )
@@ -50,7 +51,11 @@ from .utils import (
 from ._vendors import inprw
 
 __all__ = [
+    # Version
+    "__version__",
+    # Configuration and logging
     "configure_logging",
+    # I/O functions
     "read",
     "readOutput",
     "readOutputModel",
@@ -58,11 +63,26 @@ __all__ = [
     "write",
     "convert",
     "readLoadCsv",
-    'run',
-    'buildSG1D',
-    'combineSG'
+    "addCellDictDataToMesh",
+    "addPointDictDataToMesh",
+    # Execution
+    "run",
+    # Core functions and classes
+    "buildSG1D",
+    "combineSG",
     "SGMesh",
-    'StructureGene',
+    "StructureGene",
+    "check_isolated_nodes",
+    "renumber_elements",
+    # Utility functions
+    "plot_sg_2d",
+    # Model classes from .model import *
+    "CauchyContinuumModel",
+    "KirchhoffLovePlateShellModel",
+    "ReissnerMindlinPlateShellModel",
+    "EulerBernoulliBeamModel",
+    "TimoshenkoBeamModel",
+    # Exception classes
     "SwiftCompLicenseError",
     "VABSLicenseError",
     "SwiftCompIOError",

sgio-0.2.15/sgio/_version.py

@@ -0,0 +1 @@
+__version__ = "0.2.15"

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/_meshio.py

@@ -281,35 +281,35 @@ def _sg_to_meshio_order(cell_type: str, idx: ArrayLike) -> np.ndarray:
 
 
 
-def _meshio_to_sg_order(cell_type:str, idx:ArrayLike):
-    idx_sg = np.asarray(idx) + 1
+# def _meshio_to_sg_order(cell_type:str, idx:ArrayLike):
+#     idx_sg = np.asarray(idx) + 1
 
-    idx_to_insert = None
-    if cell_type == 'triangle6':
-        idx_to_insert = 3
-    elif cell_type == 'tetra10':
-        idx_to_insert = 4
-    elif cell_type == 'wedge15':
-        idx_to_insert = 6
+#     idx_to_insert = None
+#     if cell_type == 'triangle6':
+#         idx_to_insert = 3
+#     elif cell_type == 'tetra10':
+#         idx_to_insert = 4
+#     elif cell_type == 'wedge15':
+#         idx_to_insert = 6
 
-    max_nodes = idx_sg.shape[1]
-    if cell_type.startswith('line'):
-        max_nodes = 5
-    elif cell_type.startswith('triangle') or cell_type.startswith('quad'):
-        max_nodes = 9
-    elif cell_type.startswith('tetra') or cell_type.startswith('wedge') or cell_type.startswith('hexahedron'):
-        max_nodes = 20
+#     max_nodes = idx_sg.shape[1]
+#     if cell_type.startswith('line'):
+#         max_nodes = 5
+#     elif cell_type.startswith('triangle') or cell_type.startswith('quad'):
+#         max_nodes = 9
+#     elif cell_type.startswith('tetra') or cell_type.startswith('wedge') or cell_type.startswith('hexahedron'):
+#         max_nodes = 20
 
-    # Insert 0 for some types of cells
-    if idx_to_insert:
-        idx_sg = np.insert(idx_sg, idx_to_insert, 0, axis=1)
+#     # Insert 0 for some types of cells
+#     if idx_to_insert:
+#         idx_sg = np.insert(idx_sg, idx_to_insert, 0, axis=1)
 
-    # Fill the remaining location with 0s
-    pad_width = max_nodes - idx_sg.shape[1]
-    # logger.debug('pad width = {}'.format(pad_width))
-    idx_sg = np.pad(idx_sg, ((0, 0), (0, pad_width)), 'constant', constant_values=0)
+#     # Fill the remaining location with 0s
+#     pad_width = max_nodes - idx_sg.shape[1]
+#     # logger.debug('pad width = {}'.format(pad_width))
+#     idx_sg = np.pad(idx_sg, ((0, 0), (0, pad_width)), 'constant', constant_values=0)
 
-    return idx_sg
+#     return idx_sg
 
 
 
@@ -398,7 +398,7 @@ def _write_nodes(
 
 def _meshio_to_sg_order(
     cell_type:str, idx:ArrayLike,
-    node_id=[], renumber_nodes:bool=False
+    node_id=[], renumber_nodes:bool=True
     ):
     """Convert meshio cell ordering to SG ordering.
 
@@ -418,11 +418,14 @@ def _meshio_to_sg_order(
     idx_sg: np.ndarray (n_cells, n_elem_nodes_sg)
         Array of cell connectivity in SG ordering.
     """
+    print(f'{renumber_nodes = }')
     idx_sg = np.asarray(idx)
     if renumber_nodes:
-        idx_map = {v:i+1 for i, v in enumerate(node_id)}
-        idx_sg = np.vectorize(idx_map.get)(idx_sg)
-    # idx_sg = np.asarray(idx) + 1
+        if len(node_id) == 0:
+            idx_sg = np.asarray(idx) + 1
+        else:
+            idx_map = {v: i+1 for i, v in enumerate(node_id)}
+            idx_sg = np.vectorize(idx_map.get)(idx_sg)
 
     idx_to_insert = None
     if cell_type == 'triangle6':

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/main.py

@@ -133,7 +133,7 @@ def readOutputModel(
         with open(filename, "r") as file:
             if file_format.lower().startswith("s"):
                 model = _swiftcomp.read_output_buffer(
-                    file, analysis="h", model_type=model_type, **kwargs
+                    file, analysis="h", model_type=model_type, sg=sg, **kwargs
                 )
             elif file_format.lower().startswith("v"):
                 model = _vabs.read_output_buffer(
@@ -680,6 +680,8 @@ def write(
                 analysis=analysis, model=model_type,
                 macro_responses=macro_responses,
                 model_space=model_space, prop_ref_y=prop_ref_y,
+                renumber_nodes=renumber_nodes,
+                renumber_elements=renumber_elements,
                 load_type=load_type,
                 sfi=sfi, sff=sff, version=format_version
             )

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/swiftcomp/_input.py

@@ -248,7 +248,9 @@ def _readThermalProperty(file, isotropy:int):
 
 
 def writeInputBuffer(
-    sg, file, analysis, physics, model_space,
+    sg, file, analysis, physics,
+    model_space, prop_ref_y,
+    renumber_nodes=False, renumber_elements=False,
     sfi:str='8d', sff:str='20.12e', version=None):
     """
     """
@@ -271,6 +273,9 @@ def writeInputBuffer(
         file=file,
         sgdim=sg.sgdim,
         model_space=model_space,
+        prop_ref_y=prop_ref_y,
+        renumber_nodes=renumber_nodes,
+        renumber_elements=renumber_elements,
         int_fmt=sfi, float_fmt=sff
         )
 
@@ -359,13 +364,19 @@ def writeInputBufferGlobal(
 
 
 
-def _writeMesh(mesh, file, sgdim, model_space, int_fmt, float_fmt):
+def _writeMesh(
+    mesh, file, sgdim, model_space, prop_ref_y='x',
+    renumber_nodes=False, renumber_elements=False,
+    int_fmt='8d', float_fmt='20.12e'
+    ):
     """
     """
     logger.debug('writing mesh...')
 
     write_buffer(
-        file, mesh, sgdim=sgdim, model_space=model_space,
+        file, mesh, sgdim=sgdim,
+        model_space=model_space, prop_ref_y=prop_ref_y,
+        renumber_nodes=renumber_nodes, renumber_elements=renumber_elements,
         int_fmt=int_fmt, float_fmt=float_fmt)
 
     return

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/swiftcomp/_mesh.py

@@ -208,30 +208,52 @@ def _read_property_ref_csys(file, nelem, cells, cell_ids):
 # ====================================================================
 
 def write(
-    filename, mesh:SGMesh, sgdim, model_space,
+    filename, mesh:SGMesh, sgdim, model_space, prop_ref_y='x',
+    renumber_nodes=False, renumber_elements=False,
     int_fmt='8d', float_fmt="20.9e"):
     """
     """
     if is_buffer(filename, 'w'):
-        write_buffer(filename, mesh, sgdim, model_space, int_fmt, float_fmt)
+        write_buffer(
+            filename, mesh, sgdim, model_space,
+            renumber_nodes, renumber_elements,
+            int_fmt, float_fmt
+            )
     else:
         with open(filename, 'at') as file:
-            write_buffer(file, mesh, sgdim, model_space, int_fmt, float_fmt)
+            write_buffer(
+                file, mesh, sgdim, model_space,
+                renumber_nodes, renumber_elements,
+                int_fmt, float_fmt
+                )
 
 
 
 def write_buffer(
-    file, mesh:SGMesh, sgdim, model_space,
-    int_fmt='8d', float_fmt="20.9e"):
+    file, mesh:SGMesh, sgdim, model_space, prop_ref_y='x',
+    renumber_nodes=False, renumber_elements=False,
+    int_fmt='8d', float_fmt="20.9e"
+    ):
     """
     """
 
+    _node_id = mesh.point_data.get('node_id', [])
+
     _write_nodes(
-        file, mesh.points, sgdim, model_space=model_space,
+        file, mesh.points, sgdim, node_id=_node_id,
+        model_space=model_space,
+        renumber_nodes=renumber_nodes,
         int_fmt=int_fmt, float_fmt=float_fmt
         )
 
-    cell_id_to_elem_id = _write_elements(file, mesh.cells, mesh.cell_data['property_id'], int_fmt)
+    if not 'element_id' in mesh.cell_data.keys():
+        mesh.cell_data['element_id'] = []
+    cell_id_to_elem_id = _write_elements(
+        file, mesh.cells, mesh.cell_data['property_id'],
+        mesh.cell_data['element_id'], _node_id,
+        renumber_nodes=renumber_nodes,
+        int_fmt=int_fmt
+        )
 
     if 'property_ref_csys' in mesh.cell_data.keys():
         _write_property_ref_csys(
@@ -244,9 +266,18 @@ def write_buffer(
 
 
 
-def _write_elements(f, cells, cell_prop_ids, int_fmt:str='8d'):
+def _write_elements(
+    f, cells, cell_prop_ids, elem_id, node_id, renumber_nodes=False,
+    int_fmt:str='8d'
+    ):
     """
     """
+    if len(elem_id) == 0:
+        generate_eid = True
+    else:
+        generate_eid = False
+    # print(f'{generate_eid = }')
+
     cell_id_to_elem_id = []
 
     sfi = '{:' + int_fmt + '}'
@@ -254,12 +285,25 @@ def _write_elements(f, cells, cell_prop_ids, int_fmt:str='8d'):
     consecutive_index = 0
     for k, cell_block in enumerate(cells):
         cell_type = cell_block.type
-        node_idcs = _meshio_to_sg_order(cell_type, cell_block.data)
+        # print(f'cell_block.data = {cell_block.data}')
+        node_idcs = _meshio_to_sg_order(
+            cell_type, cell_block.data,
+            node_id=node_id, renumber_nodes=renumber_nodes
+            )
+        print(f'{node_idcs = }')
 
         _cid_to_eid = []
+        if generate_eid:
+            elem_id.append([])
 
         for i, c in enumerate(node_idcs):
-            _eid = consecutive_index + i + 1
+            if generate_eid:
+                _eid = consecutive_index + i + 1
+                elem_id[k].append(_eid)
+            else:
+                _eid = elem_id[k][i]
+            # print(f'{_eid = }')
+
             _pid = cell_prop_ids[k][i]
 
             _nums = [_eid, _pid]  # Element id, property id

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/swiftcomp/_swiftcomp.py

@@ -186,6 +186,7 @@ def read_output_buffer(
 def write_buffer(
     sg:StructureGene, file, analysis='h', model='sd1',
     model_space='xy', prop_ref_y='x',
+    renumber_nodes=False, renumber_elements=False,
     macro_responses:list[smdl.StateCase]=[],
     load_type=0,
     sfi:str='8d', sff:str='20.12e', version=None
@@ -211,7 +212,9 @@ def write_buffer(
 
     if analysis == 'h':
         writeInputBuffer(
-            sg, file, analysis, sg.physics, model_space,
+            sg, file, analysis, sg.physics,
+            model_space, prop_ref_y,
+            renumber_nodes, renumber_elements,
             sfi, sff, version)
 
     elif (analysis == 'd') or (analysis == 'l') or (analysis.startswith('f')):

{sgio-0.2.13 → sgio-0.2.15}/sgio/iofunc/vabs/_mesh.py

@@ -236,7 +236,33 @@ def write_buffer(
     renumber_nodes=False, renumber_elements=False,
     int_fmt='8d', float_fmt="20.9e"
     ):
-    """
+    """Write mesh data to VABS format buffer.
+
+    Parameters
+    ----------
+    file : file
+        The file buffer to write to.
+    mesh : SGMesh
+        The mesh object containing points, cells, and associated data.
+    sgdim : int
+        The spatial dimension of the structural gene (2 or 3).
+    model_space : str, optional
+        The model coordinate space ('xy', 'yz', 'zx'), by default ''.
+    prop_ref_y : str, optional
+        Reference axis for property coordinate system ('x', 'y', 'z'), by default 'x'.
+    renumber_nodes : bool, optional
+        Whether to renumber nodes, by default False.
+    renumber_elements : bool, optional
+        Whether to renumber elements, by default False.
+    int_fmt : str, optional
+        Format string for integer output, by default '8d'.
+    float_fmt : str, optional
+        Format string for float output, by default "20.9e".
+
+    Returns
+    -------
+    None
+        Writes mesh data directly to the file buffer.
     """
 
     # _node_id = []
@@ -290,7 +316,27 @@ def _write_elements(
     f, cells, elem_id, node_id, renumber_nodes=False,
     int_fmt:str='8d'
     ):
-    """
+    """Write element connectivity data to VABS format file.
+
+    Parameters
+    ----------
+    f : file
+        The file object to write to.
+    cells : list
+        List of cell blocks containing element connectivity data.
+    elem_id : list
+        List of element IDs for each cell block. If empty, IDs are auto-generated.
+    node_id : list
+        List of node IDs for renumbering (currently unused).
+    renumber_nodes : bool, optional
+        Whether to renumber nodes (currently unused), by default False.
+    int_fmt : str, optional
+        Format string for integer output, by default '8d'.
+
+    Returns
+    -------
+    None
+        Modifies elem_id list in-place if auto-generating element IDs.
     """
     if len(elem_id) == 0:
         generate_eid = True