capytaine 2.3.1__cp314-cp314t-macosx_14_0_arm64.whl

capytaine/io/legacy.py

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+"""Import or export Nemoh.cal files for backward compatibility with Nemoh 2."""
+# Copyright (C) 2017-2019 Matthieu Ancellin
+# See LICENSE file at <https://github.com/mancellin/capytaine>
+
+import os
+import logging
+
+import numpy as np
+
+from capytaine.bem.solver import BEMSolver
+from capytaine.io.xarray import assemble_dataset
+from capytaine.io.mesh_writers import write_MAR
+from capytaine.bodies.bodies import FloatingBody
+from capytaine.bem.problems_and_results import DiffractionProblem, RadiationProblem
+from capytaine.meshes.geometry import Axis
+
+LOG = logging.getLogger(__name__)
+
+
+def import_cal_file(filepath):
+    """Read a Nemoh.cal file and return a list of problems."""
+
+    with open(filepath, 'r') as cal_file:
+
+        cal_file.readline()  # Unused line.
+        rho = float(cal_file.readline().split()[0])
+        g = float(cal_file.readline().split()[0])
+        water_depth = float(cal_file.readline().split()[0])
+        if water_depth == 0.0:
+            water_depth = np.inf
+        xeff, yeff = (float(x) for x in cal_file.readline().split()[0:2])
+
+        bodies = []
+
+        cal_file.readline()  # Unused line.
+        nb_bodies = int(cal_file.readline().split()[0])
+        for _ in range(nb_bodies):
+            cal_file.readline()  # Unused line.
+            mesh_file = cal_file.readline().split()[0].strip()
+            mesh_file = os.path.join(os.path.dirname(filepath), mesh_file)  # mesh path are relative to Nemoh.cal
+            cal_file.readline()  # Number of points, number of panels (unused)
+
+            if os.path.splitext(mesh_file)[1] == '.py':
+                from importlib.util import spec_from_file_location, module_from_spec
+                spec = spec_from_file_location("body_initialization_module", mesh_file)
+                body_initialization = module_from_spec(spec)
+                spec.loader.exec_module(body_initialization)
+                body = body_initialization.body
+            else:
+                body = FloatingBody.from_file(mesh_file)
+
+            nb_dofs = int(cal_file.readline().split()[0])
+            for i_dof in range(nb_dofs):
+                dof_data = cal_file.readline().split()
+                if int(dof_data[0]) == 1:
+                    direction = np.array([float(x) for x in dof_data[1:4]])
+                    body.add_translation_dof(direction=direction)
+                elif int(dof_data[0]) == 2:
+                    direction = np.array([float(x) for x in dof_data[1:4]])
+                    center_of_mass = np.array([float(x) for x in dof_data[4:7]])
+                    body.add_rotation_dof(Axis(vector=direction, point=center_of_mass))
+
+            nb_forces = int(cal_file.readline().split()[0])
+            for i_force in range(nb_forces):
+                force_data = cal_file.readline().split()
+                if int(force_data[0]) == 1:
+                    direction = np.array([float(x) for x in force_data[1:4]])
+                elif int(force_data[0]) == 2:
+                    direction = np.array([float(x) for x in force_data[1:4]])
+                    center_of_mass = np.array([float(x) for x in force_data[4:7]])
+            # TODO: use the generalized forces.
+
+            nb_additional_lines = int(cal_file.readline().split()[0])
+            for _ in range(nb_additional_lines):
+                cal_file.readline()  # The additional lines are just ignored.
+
+            bodies.append(body)
+
+        if nb_bodies > 1:
+            bodies = FloatingBody.join_bodies(*bodies)
+        else:
+            bodies = bodies[0]
+
+        cal_file.readline()  # Unused line.
+        frequency_data_string_without_comment = cal_file.readline().split('!')[0]
+        frequency_data = frequency_data_string_without_comment.split()
+        if len(frequency_data) == 3:  # Nemoh v2 format
+            omega_range = np.linspace(float(frequency_data[1]), float(frequency_data[2]), int(frequency_data[0]))
+        else:
+            type_of_frequency_data = int(frequency_data[0])
+            if type_of_frequency_data == 1:  # angular frequency
+                omega_range = np.linspace(float(frequency_data[2]), float(frequency_data[3]), int(frequency_data[1]))
+            elif type_of_frequency_data == 2:  # frequency
+                omega_range = 2*np.pi*np.linspace(float(frequency_data[2]), float(frequency_data[3]), int(frequency_data[1]))
+            elif type_of_frequency_data == 3:  # period
+                omega_range = 2*np.pi/np.linspace(float(frequency_data[2]), float(frequency_data[3]), int(frequency_data[1]))
+            else:
+                raise ValueError(f"Cannot parse the frequency data \"{frequency_data_string_without_comment}\" in {filepath}.")
+
+
+        direction_data = cal_file.readline().split()
+        direction_range = np.linspace(float(direction_data[1]), float(direction_data[2]), int(direction_data[0]))
+        direction_range = np.pi/180*direction_range  # conversion from degrees to radians.
+
+        # The options below are not implemented yet.
+
+        cal_file.readline()  # Unused line.
+        irf_data = cal_file.readline()
+        show_pressure = cal_file.readline().split()[0] == "1"
+        kochin_data = cal_file.readline().split()
+        kochin_range = np.linspace(float(kochin_data[1]), float(kochin_data[2]), int(kochin_data[0]))
+        free_surface_data = cal_file.readline().split()
+
+    # Generate Capytaine's problem objects
+    env_args = dict(body=bodies, rho=rho, water_depth=water_depth, g=g)
+    problems = []
+    for omega in omega_range:
+        for direction in direction_range:
+            problems.append(DiffractionProblem(wave_direction=direction, omega=omega, **env_args))
+        for dof in bodies.dofs:
+            problems.append(RadiationProblem(radiating_dof=dof, omega=omega, **env_args))
+
+    return problems
+
+
+def export_as_Nemoh_directory(problem, directory_name, omega_range=None):
+    """Export radiation problems as Nemoh 2.0 directory (experimental).
+
+    TODO: Diffraction problem.
+
+    Parameters
+    ----------
+    problem : RadiationProblem
+        the problem that should be exported
+    directory_name : string
+        path to the directory
+    omega_range : list of float or array of float, optional
+        the exported problem will be set up with the following linear range:
+        linspace(min(omega_range), max(omega_range), len(omega_range))
+    """
+
+    if os.path.isdir(directory_name):
+        LOG.warning(f"""Exporting problem in already existing directory: {directory_name}
+             You might be overwriting existing files!""")
+    else:
+        os.makedirs(directory_name)
+
+    # Export the mesh
+    write_MAR(
+        os.path.join(directory_name, f'{problem.body.name}.dat'),
+        problem.body.mesh.vertices,
+        problem.body.mesh.faces,
+        # xOz_symmetry=isinstance(problem.body, ReflectionSymmetry)
+    )
+
+    # Set range of frequencies
+    if omega_range is None:
+        omega_nb_steps = 1
+        omega_start = problem.omega
+        omega_stop = problem.omega
+    else:
+        omega_nb_steps = len(omega_range)
+        omega_start = min(omega_range)
+        omega_stop = max(omega_range)
+
+    # Write Nemoh.cal
+    with open(os.path.join(directory_name, "Nemoh.cal"), "w") as nemoh_cal:
+        nemoh_cal.write(
+                DEFAULT_NEMOH_CAL.format(
+                    rho=problem.rho,
+                    g=problem.g,
+                    depth=problem.water_depth if problem.water_depth < np.inf else 0,
+                    mesh_filename=f'{problem.body.name}.dat',
+                    mesh_vertices=problem.body.mesh.nb_vertices,
+                    mesh_faces=problem.body.mesh.nb_faces,
+                    omega_nb_steps=omega_nb_steps,
+                    omega_start=omega_start,
+                    omega_stop=omega_stop,
+                    )
+                )
+
+    # Write input.txt
+    with open(os.path.join(directory_name, "input.txt"), "w") as input_txt:
+        input_txt.write(DEFAULT_INPUT_TXT)
+
+    # Write ID.dat
+    with open(os.path.join(directory_name, "ID.dat"), "w") as id_dat:
+        id_dat.write(f"1\n.")
+
+
+DEFAULT_NEMOH_CAL = """--- Environment ------------------------------------------------------------------------------------------------------------------
+{rho}			! RHO			! KG/M**3	! Fluid specific volume
+{g}				! G			! M/S**2	! Gravity
+{depth}			! DEPTH			! M		! Water depth
+0.	0.			! XEFF YEFF		! M		! Wave measurement point
+--- Description of floating bodies -----------------------------------------------------------------------------------------------
+1				! Number of bodies
+--- Body 1 -----------------------------------------------------------------------------------------------------------------------
+{mesh_filename}
+{mesh_vertices} {mesh_faces}
+1				! Number of degrees of freedom
+1 0. 0. 1. 0. 0. 0.		! Heave
+1				! Number of resulting generalised forces
+1 0. 0. 1. 0. 0. 0.		! Heave
+0				! Number of lines of additional information
+--- Load cases to be solved -------------------------------------------------------------------------------------------------------
+{omega_nb_steps} {omega_start} {omega_stop} ! Frequencies range
+0	0.	0.		! Number of wave directions, Min and Max (degrees)
+--- Post processing ---------------------------------------------------------------------------------------------------------------
+0	0.1	10.		! IRF				! IRF calculation (0 for no calculation), time step and duration
+0				! Show pressure
+0	0.	180.		! Kochin function		! Number of directions of calculation (0 for no calculations), Min and Max (degrees)
+0	0	100.	100.	! Free surface elevation	! Number of points in x direction (0 for no calcutions) and y direction and dimensions of domain in x and y direction
+"""
+
+DEFAULT_INPUT_TXT = """--- Calculation parameters ------------------------------------------------------------------------------------
+1				! Indiq_solver		! -		! Solver (0) Direct Gauss (1) GMRES (2) GMRES with FMM acceleration (2 not implemented yet)
+20				! IRES			! -		! Restart parameter for GMRES
+5.E-07				! TOL_GMRES		! -		! Stopping criterion for GMRES
+100				! MAXIT			! -		! Maximum iterations for GMRES
+1				! Sav_potential		! -		! Save potential for visualization
+"""
+
+
+def write_dataset_as_tecplot_files(results_directory, data):
+    """Write some of the data from a xarray dataset into legacy tecplot file outputs."""
+
+    if 'added_mass' in data:
+        with open(os.path.join(results_directory, 'RadiationCoefficients.tec'), 'w') as fi:
+            for i in range(len(data['radiating_dof'])+1):
+                fi.write(f'...\n')
+            for dof in data.radiating_dof:
+                fi.write(f'{dof.values}\n')
+                for o in data.omega:
+                    fi.write(f'  {o.values:e}  ')
+                    for dof2 in data.influenced_dof:
+                        fi.write(f"{data['added_mass'].sel(omega=o, radiating_dof=dof, influenced_dof=dof2).values:e}")
+                        fi.write('  ')
+                        fi.write(f"{data['radiation_damping'].sel(omega=o, radiating_dof=dof, influenced_dof=dof2).values:e}")
+                        fi.write('  ')
+                    fi.write('\n')
+
+    if 'diffraction_force' in data:
+        data['excitation_force'] = data['Froude_Krylov_force'] + data['diffraction_force']
+        with open(os.path.join(results_directory, 'ExcitationForce.tec'), 'w') as fi:
+            for i in range(len(data.influenced_dof)+1):
+                fi.write(f'...\n')
+            for wave_direction in data.wave_direction.values:
+                fi.write(f'angle={wave_direction}\n')
+                for o in data.omega.values:
+                    fi.write(f'  {o:e}  ')
+                    for dof in data.influenced_dof:
+                        val = data['excitation_force'].sel(omega=o, wave_direction=wave_direction, influenced_dof=dof).values
+                        fi.write(f'{np.abs(val):e}')
+                        fi.write('  ')
+                        fi.write(f'{np.angle(val):e}')
+                        fi.write('  ')
+                    fi.write('\n')
+
+
+def _hydrostatics_writer(hydrostatics_file_path, kh_file_path, body):
+    """Write the Hydrostatics.dat and KH.dat files"""
+    with open(hydrostatics_file_path, 'w') as hf:
+        for j in range(3):
+            line =  f'XF = {body.center_of_buoyancy[j]:7.4f} - XG = {body.center_of_mass[j]:7.4f} \n'
+            hf.write(line)
+        line = f'Displacement = {body.volume:1.6E}'
+        hf.write(line)
+        hf.close()
+    np.savetxt(kh_file_path, body.hydrostatic_stiffness.values, fmt='%1.6E')
+
+
+def export_hydrostatics(hydrostatics_directory, bodies):
+    """Export rigid body hydrostatics in Nemoh's format (KH.dat and Hydrostatics.dat).
+
+    Parameters
+    ----------
+    hydrostatics_directory: string
+        Path to the directory in which the data will be written (two files per body)
+    bodies: FloatingBody or list of FloatingBody
+        The body or the list of bodies. Each body is assumed to be a single
+        rigid body with 6 dofs. Each FloatingBody object is expected to have an
+        `inertia_matrix` and a `hydrostatic_stiffness` parameter.
+
+    Return
+    ------
+    None
+    """
+
+    if os.path.isdir(hydrostatics_directory):
+        LOG.warning(f"""Exporting problem in already existing directory: {hydrostatics_directory}
+             You might be overwriting existing files!""")
+    else:
+        os.makedirs(hydrostatics_directory)
+
+    if isinstance(bodies, FloatingBody):
+        bodies = [bodies]
+
+    hydrostatics_file_name = "Hydrostatics.dat"
+    kh_file_name = "KH.dat"
+
+    body_count = len(bodies)
+    if body_count == 1:
+        body = bodies[0]
+        hydrostatics_file_path = os.path.join(hydrostatics_directory, hydrostatics_file_name)
+        kh_file_path = os.path.join(hydrostatics_directory, kh_file_name)
+        _hydrostatics_writer(hydrostatics_file_path, kh_file_path, body)
+    else:
+        for (i, body) in enumerate(bodies):
+            hydrostatics_file_path = os.path.join(hydrostatics_directory, f"Hydrostatics_{i}.dat")
+            kh_file_path = os.path.join(hydrostatics_directory, f"KH_{i}.dat")
+            _hydrostatics_writer(hydrostatics_file_path, kh_file_path, body)
+
+
+def run_cal_file(paramfile):
+    problems = import_cal_file(paramfile)
+    solver = BEMSolver()
+    results = solver.solve_all(problems)
+    data = assemble_dataset(results)
+
+    results_directory = os.path.join(os.path.dirname(paramfile), 'results')
+    try:
+        os.mkdir(results_directory)
+    except FileExistsError:
+        LOG.warning(f"The output directory ({results_directory}) already exists. You might be overwriting existing data.")
+
+    LOG.info("Write results in legacy tecplot format.")
+    write_dataset_as_tecplot_files(results_directory, data)