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Commit 149d6417 authored by Germain Clavier's avatar Germain Clavier :smiley_cat:
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Corrected bugs, refactored part of the code

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with 41 additions and 28 deletions
lammps/plot_forces.py
+ 41
− 28
View file @ 149d6417
...@@ -12,6 +12,8 @@ import logging ...@@ -12,6 +12,8 @@ import logging
import sys import sys
from matplotlib import pyplot as plt from matplotlib import pyplot as plt
logger = logging.getLogger(__name__)
def compute_energy(tp): def compute_energy(tp):
r = tp[0] r = tp[0]
...@@ -26,14 +28,14 @@ def compute_energy(tp): ...@@ -26,14 +28,14 @@ def compute_energy(tp):
return e return e
units = { units = {
"lj": {"Energy": "Reduced units", "Force": "Reduced units", "kb": 1}, "lj": {"Distance": "Reduced units","Energy": "Reduced units", "Force": "Reduced units", "kb": 1},
"real": {"Energy": "kcal/mol", "Force": "kcal/mol/A", "kb": 0.001985875}, "real": {"Distance": "[A]","Energy": "[kcal/mol]", "Force": "[kcal/mol/A]", "kb": 0.001985875},
"metal": {"Energy": "eV", "Force": "eV/A", "kb": 8.6173332e-5}, "metal": {"Distance": "[A]","Energy": "[eV]", "Force": "[eV/A]", "kb": 8.6173332e-5},
"si": {"Energy": "J", "Force": "N", "kb": 1.380649e-23}, "si": {"Distance": "[m]","Energy": "[J]", "Force": "[N]", "kb": 1.380649e-23},
"cgs": {"Energy": "ergs", "Force": "dynes", "kb": 1.3806504e-16}, "cgs": {"Distance": "[cm]","Energy": "[ergs]", "Force": "[dynes]", "kb": 1.3806504e-16},
"electron": {"Energy": "Hartrees", "Force": "Hartree/Bohr", "kb": 3.16681534e-6}, "electron": {"Distance": "[Bohr]","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}, "micro": {"Distance": "[um]","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}, "nano": {"Distance": "[nm]","Energy": "[ag·nm^2/ns^2]", "Force": "[ag·nm/ns^2]", "kb": 0.013806504},
} }
def main(): def main():
...@@ -43,9 +45,9 @@ def main(): ...@@ -43,9 +45,9 @@ def main():
) )
parser.add_argument( parser.add_argument(
"-u", "-u",
"--units" "--units",
dest="units" dest="units",
default="real" default="real",
help="Units of the file (LAMMPS units system)", help="Units of the file (LAMMPS units system)",
) )
parser.add_argument( parser.add_argument(
...@@ -86,17 +88,26 @@ def main(): ...@@ -86,17 +88,26 @@ def main():
help="Extract the forces in separate files", help="Extract the forces in separate files",
) )
args = parser.parse_args() args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
########## ##########
# Manage arguments # Manage arguments
uenergy = units(args.units)["Energy"] udistance = units[args.units]["Distance"]
uforce = units(args.units)["Force"] uenergy = units[args.units]["Energy"]
kb = units(args.units)["kb"] uforce = units[args.units]["Force"]
kb = units[args.units]["kb"]
rlabel = ' '.join(["Rij", udistance])
elabel = ' '.join(["E", uenergy])
flabel = ' '.join(["F", uforce])
etitle = "Energy"
ftitle = "Force"
font = "DejaVu Sans"
fontsize = 30
infile = args.infile infile = args.infile
if not os.path.isfile(infile): if not os.path.isfile(infile):
logging.error("Input file not found") logger.error("Input file not found")
sys.exit(1) sys.exit(1)
toplot = [] toplot = []
...@@ -110,7 +121,7 @@ def main(): ...@@ -110,7 +121,7 @@ def main():
tok = [] tok = []
while not tok: while not tok:
tok = next(lines).partition('#')[0].rstrip() tok = next(lines).partition('#')[0].rstrip()
logging.info("Found {} token".format(tok)) logger.info("Found {} token".format(tok))
infos = next(lines).split() infos = next(lines).split()
npoints = int(infos[1]) npoints = int(infos[1])
next(lines) next(lines)
...@@ -128,6 +139,7 @@ def main(): ...@@ -128,6 +139,7 @@ def main():
except StopIteration: except StopIteration:
break break
if args.recompute: if args.recompute:
etitle = "Estimated energy"
for tp in toplot: for tp in toplot:
tp[1] = compute_energy(tp) tp[1] = compute_energy(tp)
...@@ -143,9 +155,10 @@ def main(): ...@@ -143,9 +155,10 @@ def main():
if args.temp > 0: if args.temp > 0:
hmin, hmax = axes[0].get_xlim() hmin, hmax = axes[0].get_xlim()
axes[0].hlines(kb*args.temp, hmin, hmax, color="orange", label=r'$k_BT$', linewidth=3, linestyles="dashdot") 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)) axes[0].text(hmax/2., kb*args.temp, 'KbT', fontsize=0.7*fontsize)
logger.info("KbT value= {:e} {:s}".format(kb*args.temp, uenergy))
else: else:
logging.info("Invalid temperature value: {:e}".format(args.temp)) logger.info("Invalid temperature value: {:e}".format(args.temp))
if args.xrange: if args.xrange:
xmin, xmax = list(map(float, args.xrange.split(":"))) xmin, xmax = list(map(float, args.xrange.split(":")))
...@@ -156,30 +169,30 @@ def main(): ...@@ -156,30 +169,30 @@ def main():
axes[0].set_ylim(ymin, ymax) axes[0].set_ylim(ymin, ymax)
axes[1].set_ylim(ymin, ymax) axes[1].set_ylim(ymin, ymax)
font = "DejaVu Sans"
fontsize = 30
# Setting axes 0 # Setting axes 0
axes[0].set_title("Estimated energy", fontsize=fontsize) axes[0].set_title(etitle, fontsize=fontsize)
# axes[0].legend(frameon=False, fontsize=fontsize) # Fat font, no frame # axes[0].legend(frameon=False, fontsize=fontsize) # Fat font, no frame
axes[0].set_xlabel("r [A]", fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts axes[0].set_xlabel(rlabel, fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts
axes[0].set_ylabel("E [kcal/mol]", fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts axes[0].set_ylabel(elabel, fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts
axes[0].tick_params(axis='both', which='major', labelsize=fontsize) # Biggers ticks, bigger ticks label! axes[0].tick_params(axis='both', which='major', labelsize=fontsize) # Biggers ticks, bigger ticks label!
# Setting axes 1 # Setting axes 1
axes[1].set_title("Tabulated force", fontsize=fontsize) axes[1].set_title(ftitle, fontsize=fontsize)
axes[1].legend(frameon=False, fontsize=fontsize) # Fat font, no frame axes[1].legend(frameon=False, fontsize=fontsize) # Fat font, no frame
axes[1].set_xlabel("r [A]", fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts axes[1].set_xlabel(rlabel, fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts
axes[1].set_ylabel("F [kcal/mol/A]", fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts axes[1].set_ylabel(flabel, fontname=font, fontsize=fontsize) # ylabel name, font is Hack, size 30pts
axes[1].tick_params(axis='both', which='major', labelsize=fontsize) # Biggers ticks, bigger ticks label! axes[1].tick_params(axis='both', which='major', labelsize=fontsize) # Biggers ticks, bigger ticks label!
plt.subplots_adjust(wspace=0.3) plt.subplots_adjust(wspace=0.3)
figManager = plt.get_current_fig_manager()
figManager.window.showMaximized()
plt.show() plt.show()
if args.extract: if args.extract:
for tp in toplot: for tp in toplot:
outfile = "".join([tp[3], '.plot']) outfile = "".join([tp[3], '.plot'])
logging.info("Writing file {}".format(outfile)) logger.info("Writing file {}".format(outfile))
with open(outfile, 'w') as f: with open(outfile, 'w') as f:
f.write("# {} force extracted from {}\n".format(tp[3], infile)) f.write("# {} force extracted from {}\n".format(tp[3], infile))
f.write("# {:^20} {:^20} {:^20}\n".format('r', 'energy', 'force')) f.write("# {:^20} {:^20} {:^20}\n".format('r', 'energy', 'force'))
......
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