File size: 4,141 Bytes
a65f762 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 | #!/usr/bin/env python
"""
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)
# Ensure SIESTA aobasis is available
print("Checking aobasis...")
ensure_aobasis(aobasis_dir, params)
# Displaced configs
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)
# Band structure folders
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()
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