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()