78 lines
3.3 KiB
Python
78 lines
3.3 KiB
Python
|
#!/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("-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 Newton’s 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)
|
|||
|
|
# 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
|
|||
|
|
dump(output, position, velocity, box_size)
|
|||
|
|
# if verbosity turned on, print a progress bar
|
|||
|
|
if config.verbose:
|
|||
|
|
print_prog_bar(iteration, config.iterations)
|
|||
|
|
|
|||
|
|
# report output file path
|
|||
|
|
print(f"Done: trajectories saved to '{config.output}'")
|