NSSC/Exercise_02/task03.py

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