File size: 4,425 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 | #!/usr/bin/env python
"""
Run QE calculations for all displaced configs and band structure folders.
Runs:
- SCF + pw2bgw for each data/disp-XX/
- SCF + pw2bgw + bands + bands.x for data/bands/uc/ and data/bands/sc/
If params.json has cluster.run_sh set, wraps each job for cluster submission.
Otherwise runs locally with mpirun.
Usage: python run.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 run_qe(cmd_args, cwd, qe_setup, np, log_file, env=None):
"""Run a QE command with mpirun, sourcing qe_setup first."""
mpi = ['mpirun', '-np', str(np)]
bash_cmd = f"source {qe_setup} 2>/dev/null; " + \
' '.join(mpi + cmd_args + [f'> {log_file} 2>&1'])
subprocess.run(['bash', '-c', bash_cmd], cwd=cwd, check=True)
def run_scf(scf_dir, qe_setup, np):
xml = os.path.join(scf_dir, 'diamond.xml')
if os.path.exists(xml):
print(f" SCF already done: {scf_dir}")
return
print(f" Running SCF in {scf_dir}")
run_qe(['pw.x', '<', 'pw.in'], scf_dir, qe_setup, np, 'pw.out')
def run_pw2bgw(scf_dir, qe_setup, np):
vsc = os.path.join(scf_dir, 'VSC')
if os.path.exists(vsc):
print(f" pw2bgw already done: {scf_dir}")
return
print(f" Running pw2bgw in {scf_dir}")
run_qe(['pw2bgw.x', '<', 'pw2bgw.in'], scf_dir, qe_setup, np, 'pw2bgw.out')
def run_bands(scf_dir, qe_setup, np):
gnu = os.path.join(scf_dir, 'bands.dat.gnu')
if os.path.exists(gnu):
print(f" Bands already done: {scf_dir}")
return
print(f" Running bands in {scf_dir}")
run_qe(['pw.x', '<', 'bands.in'], scf_dir, qe_setup, np, 'bands.out')
# bands post-processing
bash_cmd = f"source {qe_setup} 2>/dev/null; bands.x < bands_pp.in > bands_pp.out 2>&1"
subprocess.run(['bash', '-c', bash_cmd], cwd=scf_dir, check=True)
def submit_cluster(script_path, cwd):
"""Submit to cluster using the provided run_sh script."""
subprocess.run(['bash', script_path], cwd=cwd, check=True)
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)
data_dir = os.path.join(SCRIPT_DIR, 'data')
qe_setup = params['paths']['qe_setup']
np_qe = params['execution']['mpi_np']
run_sh = params['execution'].get('run_sh')
if not os.path.isdir(data_dir):
print("data/ not found – run prepare.py first")
sys.exit(1)
# -------------------------------------------------------
# Displaced configurations: SCF + pw2bgw
# -------------------------------------------------------
disp_dirs = sorted(glob.glob(os.path.join(data_dir, 'disp-*')))
print(f"Processing {len(disp_dirs)} displaced configurations...")
for disp_dir in disp_dirs:
label = os.path.basename(disp_dir)
scf_dir = os.path.join(disp_dir, 'scf')
recon_done = os.path.join(disp_dir, 'reconstruction',
'aohamiltonian', 'hamiltonians.h5')
if os.path.exists(recon_done):
print(f" [{label}] Already fully done, skipping")
continue
print(f" [{label}]")
if run_sh:
submit_cluster(run_sh, disp_dir)
else:
run_scf(scf_dir, qe_setup, np_qe)
run_pw2bgw(scf_dir, qe_setup, np_qe)
# -------------------------------------------------------
# Band structure folders: SCF + pw2bgw + bands
# -------------------------------------------------------
for cell_label in ('uc', 'sc'):
bands_dir = os.path.join(data_dir, 'bands', cell_label)
if not os.path.isdir(bands_dir):
continue
scf_dir = os.path.join(bands_dir, 'scf')
print(f"\nProcessing bands/{cell_label}...")
if run_sh:
submit_cluster(run_sh, bands_dir)
else:
run_scf(scf_dir, qe_setup, np_qe)
run_pw2bgw(scf_dir, qe_setup, np_qe)
if os.path.exists(os.path.join(scf_dir, 'bands.in')):
run_bands(scf_dir, qe_setup, np_qe)
print("\nrun.py done. Run reconstruct.py next.")
if __name__ == '__main__':
main()
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