import argparse
import logging
from schnetpack.md.parsers.md_setup import MDSimulation
try:
import oyaml as yaml
except ImportError:
import yaml
def read_options(yamlpath):
with open(yamlpath, "r") as tf:
tradoffs = yaml.load(tf)
logging.info("Read options from {:s}.".format(yamlpath))
return tradoffs
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("md_input")
args = parser.parse_args()
config = read_options(args.md_input)
md = MDSimulation(config)
md.save_config()
md.run()
def test_run_md(
self,
md_config,
sim_dir,
molecule_path,
md_model_path,
md_thermostats,
md_integrator,
):
md_config = setup_basic_md(md_config, sim_dir, molecule_path,
md_model_path)
md_config = setup_md(md_config, md_integrator, md_thermostats)
md = MDSimulation(md_config)
md.save_config()
md.run()
# Test loading of system state
md_config["dynamics"]["load_system_state"] = os.path.join(
sim_dir, "checkpoint.chk")
md = MDSimulation(md_config)
md.save_config()
md.run()
# Test restart
md_config["overwrite"] = False
md_config["dynamics"]["restart"] = os.path.join(
sim_dir, "checkpoint.chk")
md = MDSimulation(md_config)
md.save_config()
md.run()