Rewritten plot_forces for more generic case (08a7e92c) · Commits · Germain Clavier / python-tools

lammps/plot_forces.py

+40 −26

Original line number	Diff line number	Diff line
		@@ -25,6 +25,16 @@ def compute_energy(tp):
		e -= e[-1]
		return e

		units = {
		"lj": {"Energy": "Reduced units", "Force": "Reduced units", "kb": 1},
		"real": {"Energy": "kcal/mol", "Force": "kcal/mol/A", "kb": 0.001985875},
		"metal": {"Energy": "eV", "Force": "eV/A", "kb": 8.6173332e-5},
		"si": {"Energy": "J", "Force": "N", "kb": 1.380649e-23},
		"cgs": {"Energy": "ergs", "Force": "dynes", "kb": 1.3806504e-16},
		"electron": {"Energy": "Hartrees", "Force": "Hartree/Bohr", "kb": 3.16681534e-6},
		"micro": {"Energy": "pg·um^2/us^2", "Force": "pg·um/us^2", "kb": 1.3806504e-8},
		"nano": {"Energy": "ag·nm^2/ns^2", "Force": "ag·nm/ns^2", "kb": 0.013806504},
		}

		def main():

		@@ -32,12 +42,11 @@ def main():
		description="Plots Lammps tabulated forces."
		)
		parser.add_argument(
		"-v",
		"--verbose",
		dest="verbosity",
		default=0,
		action="count",
		help="display more information",
		"-u",
		"--units"
		dest="units"
		default="real"
		help="Units of the file (LAMMPS units system)",
		)
		parser.add_argument(
		"-f",
		@@ -50,19 +59,25 @@ def main():
		"-x",
		dest="xrange",
		default="",
		help="xrange : separated (for negative values: -x=-3:10)",
		help="xrange separated by : (for negative values: -x=-3:10)",
		)
		parser.add_argument(
		"-y",
		dest="yrange",
		default="",
		help="yrange : separated",
		help="yrange separated by :",
		)
		parser.add_argument(
		"-t",
		dest="temp",
		default=-1, type=float,
		help="temperature for kbT plot [default none]",
		default=None, type=float,
		help="temperature for KbT plot [default none]",
		)
		parser.add_argument(
		"--recompute-energy",
		dest="recompute",
		action="store_true",
		help="Recompute the energies from forces and distances through finite differences",
		)
		parser.add_argument(
		"-e",
		@@ -75,15 +90,9 @@ def main():
		##########
		# Manage arguments

		# -v/--verbose

		kb = 0.001985875 # kcal/K/mol

		try:
		utilsscript.init_logging(args.verbosity)
		except NameError:
		logging.basicConfig(level=logging.WARNING)
		logging.warning("utilsscript lib not found, using default logging at warning level.")
		uenergy = units(args.units)["Energy"]
		uforce = units(args.units)["Force"]
		kb = units(args.units)["kb"]

		infile = args.infile
		if not os.path.isfile(infile):
		@@ -118,6 +127,7 @@ def main():
		next(lines)
		except StopIteration:
		break
		if args.recompute:
		for tp in toplot:
		tp[1] = compute_energy(tp)

		@@ -129,9 +139,13 @@ def main():
		hmin, hmax = axes[1].get_xlim()
		axes[1].hlines(0, hmin, hmax, color="black", linewidth=3, linestyles="dashdot")

		if args.temp:
		if args.temp > 0:
		hmin, hmax = axes[0].get_xlim()
		axes[0].hlines(kb*args.temp, hmin, hmax, color="orange", label=r'$k_BT$', linewidth=3, linestyles="dashdot")
		logging.info("KbT value= {:e}".format(kb*args.temp))
		else:
		logging.info("Invalid temperature value: {:e}".format(args.temp))

		if args.xrange:
		xmin, xmax = list(map(float, args.xrange.split(":")))
		@@ -142,7 +156,7 @@ def main():
		axes[0].set_ylim(ymin, ymax)
		axes[1].set_ylim(ymin, ymax)

		font = "Hack"
		font = "DejaVu Sans"
		fontsize = 30

		# Setting axes 0