| |
| """ |
| Run HPRO real-space reconstruction for all displaced configs and bands folders. |
| |
| Steps for each directory: |
| 1. Ensures the aobasis exists (runs SIESTA in example/diamond/aobasis/ if needed) |
| 2. Runs HPRO calc.py in reconstruction/ using the hpro conda environment |
| |
| Usage: python reconstruct.py [params.json] |
| """ |
| import glob |
| import json |
| import os |
| import subprocess |
| import sys |
|
|
| SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__)) |
|
|
|
|
| def load_params(path=None): |
| if path is None: |
| path = os.path.join(SCRIPT_DIR, 'params.json') |
| with open(path) as f: |
| return json.load(f) |
|
|
|
|
| def conda_run(env, cmd, cwd, conda_base, log_file=None): |
| """Run a command in a conda environment.""" |
| activate = f"source {conda_base}/etc/profile.d/conda.sh && conda activate {env}" |
| full_cmd = f"{activate} && {cmd}" |
| if log_file: |
| full_cmd += f" > {log_file} 2>&1" |
| subprocess.run(['bash', '-c', full_cmd], cwd=cwd, check=True) |
|
|
|
|
| def ensure_aobasis(aobasis_dir, params): |
| """Run SIESTA in aobasis/ if the HSX file is not present.""" |
| hsx = os.path.join(aobasis_dir, 'siesta.HSX') |
| if os.path.exists(hsx): |
| print(f" aobasis already computed: {aobasis_dir}") |
| return |
|
|
| fdf = os.path.join(aobasis_dir, 'siesta.fdf') |
| if not os.path.exists(fdf): |
| print(f" ERROR: {fdf} not found. Cannot run SIESTA.") |
| print(" Provide siesta.fdf and required pseudopotentials in aobasis/") |
| sys.exit(1) |
|
|
| siesta_exe = params['paths']['siesta'] |
| np_mpi = params['execution']['mpi_np'] |
| print(f" Running SIESTA for aobasis in {aobasis_dir}") |
| bash_cmd = f"mpirun -np {np_mpi} {siesta_exe} < siesta.fdf > siesta.out 2>&1" |
| subprocess.run(['bash', '-c', bash_cmd], cwd=aobasis_dir, check=True) |
|
|
|
|
| def run_hpro(recon_dir, params): |
| """Run HPRO calc.py in reconstruction/ if not already done.""" |
| out_h5 = os.path.join(recon_dir, 'aohamiltonian', 'hamiltonians.h5') |
| if os.path.exists(out_h5): |
| print(f" HPRO already done: {recon_dir}") |
| return |
|
|
| calc_py = os.path.join(recon_dir, 'calc.py') |
| if not os.path.exists(calc_py): |
| print(f" WARNING: {calc_py} not found, skipping") |
| return |
|
|
| print(f" Running HPRO in {recon_dir}") |
| hpro_env = params['hpro']['conda_env'] |
| conda_base = params['paths']['conda_base'] |
| conda_run(hpro_env, 'python calc.py', recon_dir, conda_base, 'hpro.log') |
|
|
|
|
| def main(): |
| params_path = sys.argv[1] if len(sys.argv) > 1 else \ |
| os.path.join(SCRIPT_DIR, 'params.json') |
| params = load_params(params_path) |
|
|
| diamond_dir = os.path.dirname(SCRIPT_DIR) |
| aobasis_dir = os.path.join(diamond_dir, 'aobasis') |
| data_dir = os.path.join(SCRIPT_DIR, 'data') |
|
|
| if not os.path.isdir(data_dir): |
| print("data/ not found – run prepare.py first") |
| sys.exit(1) |
|
|
| |
| print("Checking aobasis...") |
| ensure_aobasis(aobasis_dir, params) |
|
|
| |
| disp_dirs = sorted(glob.glob(os.path.join(data_dir, 'disp-*'))) |
| print(f"\nReconstructing {len(disp_dirs)} displaced configurations...") |
| for disp_dir in disp_dirs: |
| label = os.path.basename(disp_dir) |
| print(f" [{label}]") |
| recon_dir = os.path.join(disp_dir, 'reconstruction') |
| if not os.path.exists(os.path.join(disp_dir, 'scf', 'VSC')): |
| print(f" WARNING: VSC not found, run run.py first") |
| continue |
| run_hpro(recon_dir, params) |
|
|
| |
| for cell_label in ('uc', 'sc'): |
| bands_dir = os.path.join(data_dir, 'bands', cell_label) |
| if not os.path.isdir(bands_dir): |
| continue |
| print(f"\nReconstructing bands/{cell_label}...") |
| recon_dir = os.path.join(bands_dir, 'reconstruction') |
| if not os.path.exists(os.path.join(bands_dir, 'scf', 'VSC')): |
| print(f" WARNING: VSC not found for bands/{cell_label}, run run.py first") |
| continue |
| run_hpro(recon_dir, params) |
|
|
| print("\nreconstruct.py done. Run compare_bands.py to plot results.") |
|
|
|
|
| if __name__ == '__main__': |
| main() |
|
|
