Source code for pysisyphus.calculators.Remote

from pathlib import Path
import tarfile

from fabric import Connection
import yaml

from pysisyphus.calculators.Calculator import Calculator
from pysisyphus.helpers_pure import json_to_results

[docs] class Remote(Calculator): def __init__(self, remote_calc, host, prefix="", **kwargs): super().__init__(**kwargs) self.remote_calc = remote_calc = host self.prefix = prefix self.calc_inp = yaml.dump(self.remote_calc) self.tar_fn = "pysis.tar.gz" self.yaml_fn = "inp.yaml" self.run_dict = { "geom": { "fn": None, }, "calc": { "run_func": None, }, } self.run_dict["calc"].update(remote_calc)
[docs] def run_calculation(self, atoms, coords, run_func="get_energy"): con = Connection( res ="mktemp -d", hide=True) tmp_dir = res.stdout.strip() xyz_str = self.prepare_xyz_string(atoms, coords) run_dict = self.run_dict.copy() run_dict["geom"]["fn"] = xyz_str # Inline xyz coordinates run_dict["calc"]["run_func"] = run_func # Create YAML input for remote calculation with open(self.yaml_fn, "w") as handle: yaml.dump(run_dict, handle) with tmp_parent = Path(tmp_dir).parent tar_target = tmp_parent / self.tar_fn con.put(self.yaml_fn, tmp_dir) # yaml_str = yaml.dump(run_dict) #"cat > {self.yaml_fn} <<EOL\n{yaml_str}\nEOL") # Execute pysis with prefix, e.g. activation of conda env or venv with con.prefix(self.prefix):"pysis {self.yaml_fn}", hide=True) # Pack the whole directory"tar -czf {tar_target} .") # and download it. con.get(tar_target, self.tar_fn)"rm -r {tmp_dir}") return self.parse_results()
[docs] def parse_results(self): with, "r:gz") as tfile: as_json = tfile.extractfile("./calculator_000.000.results").read() results = json_to_results(as_json) return results
[docs] def get_energy(self, atoms, coords, **prepare_kwargs): return self.run_calculation(atoms, coords, run_func="get_energy")
[docs] def get_forces(self, atoms, coords, **prepare_kwargs): return self.run_calculation(atoms, coords, run_func="get_forces")
[docs] def get_hessian(self, atoms, coords, **prepare_kwargs): return self.run_calculation(atoms, coords, run_func="get_hessian")