saclay-format 0.2.1__tar.gz

saclay_format-0.2.1/PKG-INFO

@@ -0,0 +1,114 @@
+Metadata-Version: 2.4
+Name: saclay-format
+Version: 0.2.1
+Summary: python parser and usefull script related to the saclay format
+Maintainer-email: Guillaume Scamps <guillaume.scamps@l2it.in2p3.fr>, David Regnier <David.REGNIER@cea.fr>, Wouter Ryssens <Wouter.Ryssens@ulb.be>
+Project-URL: Sources, https://gitlab.com/regnier/Saclay_format
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: h5py
+Requires-Dist: numpy
+Requires-Dist: pyyaml
+Provides-Extra: visu
+Requires-Dist: matplotlib; extra == "visu"
+Requires-Dist: PyQt5; extra == "visu"
+Requires-Dist: scipy; extra == "visu"
+Requires-Dist: scikit-image; extra == "visu"
+
+# Saclay_format (v0.2.1)
+
+This repository contains a proposal format definition to exchange inputs/outputs
+between some mean-field theory codes in the nuclear physics and astrophysics communities.
+This format relies on a series of custom binary files containing the raw data along with
+a YAML header containing metadata. It adheres to the results of the 05/2025 and 10/2025 ESNT 
+workshops entitled *"Simulating dense matter on three-dimensional coordinate space meshes (part I and II)"*.
+
+## Content
+
+* `saclay_format` — Python3 package to parse and visualize this format  
+* `docs` — documentation of the format (not yet up to date)  
+* `examples` — nuclear mean-field outputs in this format  
+* `tests` — unit tests of the package (not yet up to date)
+
+## Requirements
+
+* `pyyaml` — Python3 package for YAML parsing  
+* `h5py` — Python3 package for HDF5 parsing  
+
+## Running the parser
+
+From a Python terminal, import the `parser` module and use its `read()` and `write()` methods.
+To see the expected structure of the data dictionary, check the 
+`create_dummy_data()` function in `tests/test_saclay_format.py`.
+
+Example:
+```bash
+cd tests/
+python3 test_saclay_format.py
+```
+
+## Examples
+
+### Example structure
+
+```
+examples/20Ne_bcs/
+├── 20Ne_rho_n.wdat
+├── 20Ne_state
+├── 20Ne.h5
+├── 20Ne.yaml
+└── README.md
+
+examples/alpha_alpha_3MeV/
+├── reaction_alpha_alpha_3MeV_header.yml
+├── reaction_alpha_alpha_3MeV_rho_n.bin
+├── reaction_alpha_alpha_3MeV_rho_p.bin
+├── README_visualisation_convert.md
+└── script_test.convert.sh
+
+examples/Ca40_ev8/
+├── Ca40_HF_SLy4.yaml
+├── Ca40_HF_SLy4_*.dat
+└── README_test.md
+```
+
+### Conversion test
+
+```bash
+python3 ../../saclay_format/hdf5_yaml_converter.py -h5 Ca40_HF_SLy4.yaml
+python3 ../../saclay_format/ev8_to_ev1.py Ca40_HF_SLy4.h5 -o Ca40_HF_SLy4_ev1.h5
+python3 ../../saclay_format/ev1_to_cr1.py Ca40_HF_SLy4_ev1.h5 -o Ca40_HF_SLy4_cr1.h5
+```
+
+### Visualization test
+
+Static:
+```bash
+python3 ../../saclay_format/visualisation_rho.py reaction_alpha_alpha_3MeV_header.yml
+```
+
+Dynamic:
+```bash
+python3 ../../saclay_format/visualisation_rho_TD.py -H reaction_alpha_alpha_3MeV_header.yml
+```
+
+Conversion and round-trip test:
+```bash
+python3 ../../saclay_format/hdf5_yaml_converter.py -h5 reaction_alpha_alpha_3MeV_header.yml
+mv reaction_alpha_alpha_3MeV_header.h5 reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/visualisation_rho_TD.py reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/hdf5_yaml_converter.py -yaml reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/visualisation_rho_TD.py reaction_alpha_alpha_3MeV_converted.yaml
+rm reaction_alpha_alpha_3MeV_converted*
+```
+
+## Todo
+
+- Test the format  
+- Add documentation  
+- Update unit tests  
+
+## Project layout
+
+This project follows the structure recommended by the Hitchhiker’s Guide to Python:  
+[https://docs.python-guide.org/writing/structure](https://docs.python-guide.org/writing/structure)

saclay_format-0.2.1/README.md

@@ -0,0 +1,97 @@
+# Saclay_format (v0.2.1)
+
+This repository contains a proposal format definition to exchange inputs/outputs
+between some mean-field theory codes in the nuclear physics and astrophysics communities.
+This format relies on a series of custom binary files containing the raw data along with
+a YAML header containing metadata. It adheres to the results of the 05/2025 and 10/2025 ESNT 
+workshops entitled *"Simulating dense matter on three-dimensional coordinate space meshes (part I and II)"*.
+
+## Content
+
+* `saclay_format` — Python3 package to parse and visualize this format  
+* `docs` — documentation of the format (not yet up to date)  
+* `examples` — nuclear mean-field outputs in this format  
+* `tests` — unit tests of the package (not yet up to date)
+
+## Requirements
+
+* `pyyaml` — Python3 package for YAML parsing  
+* `h5py` — Python3 package for HDF5 parsing  
+
+## Running the parser
+
+From a Python terminal, import the `parser` module and use its `read()` and `write()` methods.
+To see the expected structure of the data dictionary, check the 
+`create_dummy_data()` function in `tests/test_saclay_format.py`.
+
+Example:
+```bash
+cd tests/
+python3 test_saclay_format.py
+```
+
+## Examples
+
+### Example structure
+
+```
+examples/20Ne_bcs/
+├── 20Ne_rho_n.wdat
+├── 20Ne_state
+├── 20Ne.h5
+├── 20Ne.yaml
+└── README.md
+
+examples/alpha_alpha_3MeV/
+├── reaction_alpha_alpha_3MeV_header.yml
+├── reaction_alpha_alpha_3MeV_rho_n.bin
+├── reaction_alpha_alpha_3MeV_rho_p.bin
+├── README_visualisation_convert.md
+└── script_test.convert.sh
+
+examples/Ca40_ev8/
+├── Ca40_HF_SLy4.yaml
+├── Ca40_HF_SLy4_*.dat
+└── README_test.md
+```
+
+### Conversion test
+
+```bash
+python3 ../../saclay_format/hdf5_yaml_converter.py -h5 Ca40_HF_SLy4.yaml
+python3 ../../saclay_format/ev8_to_ev1.py Ca40_HF_SLy4.h5 -o Ca40_HF_SLy4_ev1.h5
+python3 ../../saclay_format/ev1_to_cr1.py Ca40_HF_SLy4_ev1.h5 -o Ca40_HF_SLy4_cr1.h5
+```
+
+### Visualization test
+
+Static:
+```bash
+python3 ../../saclay_format/visualisation_rho.py reaction_alpha_alpha_3MeV_header.yml
+```
+
+Dynamic:
+```bash
+python3 ../../saclay_format/visualisation_rho_TD.py -H reaction_alpha_alpha_3MeV_header.yml
+```
+
+Conversion and round-trip test:
+```bash
+python3 ../../saclay_format/hdf5_yaml_converter.py -h5 reaction_alpha_alpha_3MeV_header.yml
+mv reaction_alpha_alpha_3MeV_header.h5 reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/visualisation_rho_TD.py reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/hdf5_yaml_converter.py -yaml reaction_alpha_alpha_3MeV_converted.h5
+python3 ../../saclay_format/visualisation_rho_TD.py reaction_alpha_alpha_3MeV_converted.yaml
+rm reaction_alpha_alpha_3MeV_converted*
+```
+
+## Todo
+
+- Test the format  
+- Add documentation  
+- Update unit tests  
+
+## Project layout
+
+This project follows the structure recommended by the Hitchhiker’s Guide to Python:  
+[https://docs.python-guide.org/writing/structure](https://docs.python-guide.org/writing/structure)

saclay_format-0.2.1/pyproject.toml

@@ -0,0 +1,17 @@
+[project]
+name = "saclay-format"
+version = "0.2.1"
+description = "python parser and usefull script related to the saclay format"
+readme = "README.md"
+requires-python = ">=3.10"
+dependencies = ["h5py","numpy","pyyaml"]
+
+optional-dependencies.visu = ["matplotlib", "PyQt5", "scipy", "scikit-image"]
+
+maintainers = [{ name = "Guillaume Scamps", email = "guillaume.scamps@l2it.in2p3.fr"} ,
+                {name="David Regnier" , email = "David.REGNIER@cea.fr"},
+                {name="Wouter Ryssens" , email = "Wouter.Ryssens@ulb.be"},
+                 ]
+
+urls.Sources="https://gitlab.com/regnier/Saclay_format"
+

saclay_format-0.2.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

saclay_format-0.2.1/src/saclay_format/ev1_to_cr1.py

@@ -0,0 +1,237 @@
+#!/usr/bin/env python3
+import sys, os
+import numpy as np
+
+from saclay_parser import read, write
+
+def kramers_partner(states):
+    """
+    Construct Kramers partners for 2-spinor wavefunctions:
+        psi_T = i sigma_y psi* -> ( psi_down*, -psi_up* )
+    Input shape:  (nx, ny, nz, 2, nw)
+    Output shape: (nx, ny, nz, 2, nw)
+    """
+    conj = np.conjugate(states)
+    up   = conj[..., 0, :]
+    dn   = conj[..., 1, :]
+    partner = np.empty_like(states)
+    partner[..., 0, :] = dn
+    partner[..., 1, :] = -up
+    return partner
+
+def check_orthonormality(states, tol=1e-10):
+    """
+    Check orthonormality of a set of wavefunctions.
+    states: shape (nx, ny, nz, 2, nw)
+    """
+    nx, ny, nz, _, nw = states.shape
+    flat = states.reshape(-1, nw)  # (nx*ny*nz*2, nw)
+    overlaps = flat.conj().T @ flat  # Gram matrix (nw, nw)
+    # Normalize
+    norms = np.sqrt(np.real(np.diag(overlaps)))
+    overlaps = overlaps / (norms[:, None] * norms[None, :])
+    deviation = np.max(np.abs(overlaps - np.eye(nw)))
+    print("Max deviation from orthonormality: {:.2e}".format(deviation))
+    if deviation > tol:
+        print("Warning: orthonormality check FAILED")
+    else:
+        print("Orthonormality OK")
+
+def interleave_with_partners(states, partners):
+    """
+    Interleave original states and their Kramers partners along the last axis:
+    [1,2,...,N] + [1*,2*,...,N*] -> [1,1*,2,2*,...,N,N*]
+    """
+    shape = list(states.shape)
+    shape[-1] *= 2  # double last axis
+    interleaved = np.empty(shape, dtype=states.dtype)
+    interleaved[..., ::2] = states
+    interleaved[..., 1::2] = partners
+    return interleaved
+
+
+def interleave_amplitudes(arr):
+    # arr: shape (N, ...)
+    conj = np.conjugate(arr)
+    shape = list(arr.shape)
+    shape[0] *= 2
+    interleaved = np.empty(shape, dtype=arr.dtype)
+    interleaved[::2] = arr
+    interleaved[1::2] = conj
+    return interleaved
+
+def ev1_to_cr1(data):
+    """
+    Translate EV1 dataset into CR1 by doubling wavefunctions.
+    Only wavefunctions and metadata are modified.
+    """
+    md    = data["metadata"].copy()
+    wf_md = md.get("wavefunction", {}).copy()
+
+    nw_n = wf_md["n_neutron_states"]
+    nw_p = wf_md["n_proton_states"]
+
+    # Build Kramers partners
+    statesn = data["statesn"]
+    statesp = data["statesp"]
+    pn = kramers_partner(statesn)
+    pp = kramers_partner(statesp)
+
+    statesn_cr1 = interleave_with_partners(statesn, pn)
+    statesp_cr1 = interleave_with_partners(statesp, pp)
+
+    # Bogoliubov amplitudes
+    un = data["un"]; vn = data["vn"]
+    up = data["up"]; vp = data["vp"]
+
+    un_cr1 = interleave_amplitudes(un)
+    vn_cr1 = interleave_amplitudes(vn)
+    up_cr1 = interleave_amplitudes(up)
+    vp_cr1 = interleave_amplitudes(vp)
+
+    # Update metadata
+    md["symmetry"] = "cr1"
+    md["prefix"]   = md.get("prefix", "run") + "_cr1"
+    wf_md["n_neutron_states"] = 2 * nw_n
+    wf_md["n_proton_states"]  = 2 * nw_p
+    md["wavefunction"] = wf_md
+
+    cr1_data = data.copy()
+    cr1_data['metadata'] = md
+    cr1_data['statesn']  = statesn_cr1
+    cr1_data['statesp']  = statesp_cr1
+    cr1_data['un']       = un_cr1
+    cr1_data['vn']       = vn_cr1
+    cr1_data['up']       = up_cr1
+    cr1_data['vp']       = vp_cr1
+
+    return cr1_data
+
+def sort_by_occupation(data):
+    """
+    Sort states and Bogoliubov amplitudes by descending occupation number.
+    Occupation is |v|^2 summed over all spatial and spin coordinates.
+    """
+    vn = data["vn"]
+    vp = data["vp"]
+
+    occ_n = np.sum(np.abs(vn)**2, axis=tuple(range(1, vn.ndim)))  # shape (N_n,)
+    occ_p = np.sum(np.abs(vp)**2, axis=tuple(range(1, vp.ndim)))  # shape (N_p,)
+
+    idx_n = np.argsort(-occ_n)  # descending
+    idx_p = np.argsort(-occ_p)
+
+    # Sort all neutron-related arrays
+    data["statesn"] = data["statesn"][..., idx_n]
+    data["un"] = data["un"][idx_n]
+    data["vn"] = data["vn"][idx_n]
+
+    # Sort all proton-related arrays
+    data["statesp"] = data["statesp"][..., idx_p]
+    data["up"] = data["up"][idx_p]
+    data["vp"] = data["vp"][idx_p]
+
+    return data
+    
+    
+#----------------------------------------------------------
+#----------------------------------------------------------
+if __name__ == "__main__":
+    import argparse
+    import os
+    import sys
+
+    description = "Translate EV1 dataset into CR1 (no symmetry)"
+    parser = argparse.ArgumentParser(description=description)
+    parser.add_argument(
+        "input",
+        help="Input file (.yaml/.yml or .h5/.hdf5)"
+    )
+    parser.add_argument(
+        "-o", "--output",
+        type=str,
+        help="Output file name (.yaml/.yml or .h5/.hdf5). Default: overwrite input"
+    )
+    parser.add_argument(
+        "-f", "--format",
+        type=str,
+        choices=["yaml", "yml", "hdf5", "h5"],
+        help="Output format (default: same as input)"
+    )
+
+    args = parser.parse_args()
+
+    input_path = args.input
+    output_path = args.output or input_path
+    output_format = args.format
+
+    if not os.path.exists(input_path):
+        print(f"Input file '{input_path}' not found.")
+        sys.exit(1)
+
+    # --- Determine input format ---
+    ext = os.path.splitext(input_path)[1].lower()
+    if ext in (".yaml", ".yml"):
+        input_format = "yaml"
+    elif ext in (".h5", ".hdf5"):
+        input_format = "hdf5"
+    else:
+        print(f"Unsupported input file extension '{ext}'.")
+        sys.exit(1)
+
+    # --- Default output format same as input ---
+    if output_format is None:
+        output_format = input_format
+
+    # --- Prevent invalid conversion YAML -> HDF5 ---
+    if input_format == "yaml" and output_format in ("hdf5", "h5"):
+        print("ERROR: cannot convert YAML input directly to HDF5. Aborting.")
+        sys.exit(1)
+
+    # --- Read input ---
+    data_all = read(input_path)
+
+    sym = data_all["metadata"].get("symmetry", "").lower()
+    if sym != "ev1":
+        print(f"Symmetry is '{sym}', not 'ev1'. Aborting.")
+        sys.exit(1)
+
+    print("\n--- Input (EV1) ---")
+    wf_meta = data_all["metadata"]["wavefunction"]
+    print(f"Prefix: {data_all['metadata'].get('prefix')}")
+    print(f"Neutron states: {wf_meta['n_neutron_states']}")
+    print(f"Proton states: {wf_meta['n_proton_states']}")
+
+    # --- Translation EV1 -> CR1 ---
+    data_cr1 = ev1_to_cr1(data_all)
+    # data_cr1 = sort_by_occupation(data_cr1)  # optional
+
+    # --- Update prefix to match output ---
+    output_dir = os.path.dirname(output_path) or "."
+    output_base = os.path.basename(output_path)
+    new_prefix = os.path.splitext(output_base)[0]
+    data_cr1["metadata"]["prefix"] = new_prefix
+
+    # --- Ensure file extension matches chosen format ---
+    out_ext = os.path.splitext(output_path)[1].lower()
+    if not out_ext:
+        if output_format in ("yaml", "yml"):
+            output_path += ".yaml"
+        elif output_format in ("hdf5", "h5"):
+            output_path += ".h5"
+
+    # --- Write output ---
+    print(f"\nWriting to '{output_path}' ({output_format} format)")
+    write(data_cr1, output_path)
+
+    print("\n--- Output (CR1) ---")
+    wf_meta = data_cr1["metadata"]["wavefunction"]
+    print(f"Prefix: {data_cr1['metadata'].get('prefix')}")
+    print(f"Neutron states: {wf_meta['n_neutron_states']}")
+    print(f"Proton states: {wf_meta['n_proton_states']}")
+
+    # --- Check orthonormality ---
+    print("\nChecking neutron states:")
+    check_orthonormality(data_cr1["statesn"])
+    print("Checking proton states:")
+    check_orthonormality(data_cr1["statesp"])