89 lines
3.9 KiB
Python
89 lines
3.9 KiB
Python
#!/usr/bin/env python
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################################################################################
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### parse script parameters ###
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################################################################################
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from optparse import OptionParser
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usage = "usage: %prog [options] [<INPUT>] [<STEP_SIZE>] [<ITERATIONS>]"
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arg_parser = OptionParser(usage = usage)
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arg_parser.add_option("-i", "--input", action = "store", type = str,
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dest = "input", default = None,
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help = "input file path (required!)")
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arg_parser.add_option("-t", "--step_size", action = "store", type = float,
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dest = "step_size", default = -1.0,
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help = "time step size (Delta t) for integration (required!)")
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arg_parser.add_option("-N", "--iterations", action = "store", type = int,
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dest = "iterations", default = -1,
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help = "Number of time steps used for Newton's equation integration (required!)")
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arg_parser.add_option("-o", "--output", action = "store", type = str,
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dest = "output", default = "task03.xyz",
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help = "output file path (default: 'task03.xyz')")
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arg_parser.add_option("-s", "--subset", action = "store", type = int,
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dest = "subset", default = 100,
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help = "only stores every subset state to output file (default: 100)")
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arg_parser.add_option("-v", action = "store_true",
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dest = "verbose", default = False,
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help = "turn verbosity mode on (default: off a.k.a. silent)")
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# Parse command line arguments (as def. above) or store defaults to `config`
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config, args = arg_parser.parse_args()
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# overwrite options with positional arguments if supplied
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try:
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if len(args) > 0:
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config.input = args[0]
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if len(args) > 1:
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config.step_size = float(args[1])
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if len(args) > 2:
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config.iterations = int(args[2])
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except ValueError as expression:
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arg_parser.print_help()
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print(f"Error: {expression}")
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exit(-1)
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else:
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# quick and dirty validation
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if not config.step_size > 0.0 \
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or not config.iterations > 0 \
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or config.input is None:
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arg_parser.print_help()
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print("Error: missing or illegal argument")
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exit(-1)
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################################################################################
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### task 3 / trajectory generation ###
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################################################################################
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# note, load module _after_ processing script parameters (no need to load all
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# of the heavy numeric modules if only usage or alike is needed)
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from molecular_dynamics import load, dump, force, mass, step, print_prog_bar
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# load initial state from file
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(position, velocity), box_size = load(config.input)
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# compute initial acceleration using Newton’s second law of motion
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acceleration = force(position, box_size) / mass
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# iterate time steps for system time evolution
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with open(config.output, "w") as output:
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# store initial state to file
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dump(output, position, velocity, box_size,
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comment = f"Initial State with step size {config.step_size}")
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# perform iterations many time steps
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for iteration in range(1, config.iterations):
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# perform a single time step
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position, velocity, acceleration = step(position, velocity, acceleration,
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box_size, config.step_size)
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# dump current state to file
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if (iteration % config.subset) == 0:
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dump(output, position, velocity, box_size,
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comment = f"Iteration: {iteration}")
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# if verbosity turned on, print a progress bar
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if config.verbose:
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print_prog_bar(iteration, config.iterations)
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# In case of final iteration NOT writen to file yet, write also final state
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if (iteration % config.subset) != 0:
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dump(output, position, velocity, box_size,
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comment = f"Iteration: {iteration}")
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# report output file path
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print(f"Done: trajectories saved to '{config.output}'")
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