How to use relax method in fMBT

Best Python code snippet using fMBT_python

relaxation_test.py

Source:relaxation_test.py Github

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...27 msd = 4 * time * known_diffusion + offset28 diff, diff_err = relaxation.diffusion_constant(time, msd)29 assert np.isclose(diff, known_diffusion)30 assert np.isclose(diff_err, 0)31def test_exponential_relax():32 """Ensure the exponential_relaxation function working appropriately."""33 known_decay = 1e434 time = np.arange(100000)35 value = np.exp(-time / known_decay)36 relax, *_ = relaxation.exponential_relaxation(time, value)37 assert np.isclose(relax, known_decay)38@pytest.fixture39def linear_relax():40 num_values = 100041 time = np.arange(num_values)42 values = np.arange(num_values) / num_values43 return time, values44class TestThresholdRelaxation:45 def test_decay(self, linear_relax):46 time, values = linear_relax47 # This is to turn the linear growth into linear decay48 values = 1 - values49 logger.debug("Values: %s", values)50 relax, _ = relaxation.threshold_relaxation(51 time, values, threshold=0.5, decay=True52 )53 assert relax == len(time) / 2 + 1...

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problem_3.py

Source:problem_3.py Github

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1# import the code for the simulation2from simulator import Simulation3import matplotlib.pyplot as plt4import matplotlib5matplotlib.use("TkAgg")6import numpy as np7from time import time8plt.rc('font', family='serif')9plt.rcParams['text.usetex'] = False10fs = 1811# update various fontsizes to match12params = {'figure.figsize': (12, 8),13 'legend.fontsize': fs,14 'axes.labelsize': fs,15 'xtick.labelsize': 0.9 * fs,16 'ytick.labelsize': 0.9 * fs,17 'axes.linewidth': 1.1,18 'xtick.major.size': 7,19 'xtick.minor.size': 4,20 'ytick.major.size': 7,21 'ytick.minor.size': 4}22plt.rcParams.update(params)23def t_relax_analytic(N, size, radius, E, mass):24 n = N / size**225 sigma = radius * 226 v0 = np.sqrt(2 * E / mass)27 return (n * sigma * v0)**(-1)28def get_N_comparison(size=1000, radius=20, E=0.1, mass=1, repeats=10):29 start = time()30 N_range = np.array([25, 50, 75, 100, 125, 150, 175, 200])31 t_relax_list = []32 for N in N_range:33 t_relax = []34 for _ in range(repeats):35 sim = Simulation(N=N, E=E, size=size, radius=radius, masses=mass, visualise=False)36 t_relax.append(sim.run_simulation(run_until_steadystate=True))37 print("N =", N, "done", t_relax)38 t_relax_list.append(t_relax)39 np.save("data/t_relax_N.npy", t_relax_list)40 print("Runtime {:1.2f}s".format(time() - start))41 return N_range, t_relax_list42def get_r_comparison(N=100, size=1000, E=0.1, mass=1, repeats=10):43 start = time()44 r_range = np.array([10, 12.5, 15, 17.5, 20, 22.5, 25, 27.5, 30])45 t_relax_list = []46 for radius in r_range:47 t_relax = []48 for _ in range(repeats):49 sim = Simulation(N=N, E=E, size=size, radius=radius, masses=mass, visualise=False)50 t_relax.append(sim.run_simulation(run_until_steadystate=True))51 print("r =", radius, "done", t_relax)52 t_relax_list.append(t_relax)53 np.save("data/t_relax_r.npy", t_relax_list)54 print("Runtime {:1.2f}s".format(time() - start))55 return r_range, t_relax_list56def main():57 N = 10058 radius = 2059 size = 100060 E = 0.161 mass = 162 fig, axes = plt.subplots(1, 2, figsize=(18, 7))63 N_range, t_relax_N = get_N_comparison(radius=radius, size=size, E=E, mass=mass)64 r_range, t_relax_r = get_r_comparison(N=N, size=size, E=E, mass=mass)65 ax = axes[0]66 t_relax = t_relax_N67 N_range_smooth = np.linspace(N_range.min(), N_range.max(), 1000)68 ax.plot(N_range_smooth, t_relax_analytic(N_range_smooth, size, radius, E, mass) * 1.2,69 linestyle="dotted", lw=3, color=plt.get_cmap("plasma")(0.8),70 label=r"Analytic function, $X = 1.2$")71 ax.set_xlabel(r"Number of Particles")72 ax.set_ylabel(r"Relaxation Time, $\tau_{\rm relax} \, [\rm s]$")73 ax.errorbar(N_range, np.median(t_relax, axis=1), xerr=0.0,74 yerr=[np.median(t_relax, axis=1) - np.min(t_relax, axis=1),75 np.max(t_relax, axis=1) - np.median(t_relax, axis=1)],76 marker="o", color=plt.get_cmap("plasma")(0.2), label="Simulated results")77 ax.legend()78 ax = axes[1]79 t_relax = t_relax_r80 r_range_smooth = np.linspace(r_range.min(), r_range.max(), 1000)81 ax.plot(r_range_smooth, t_relax_analytic(N=N, size=size, radius=r_range_smooth, E=E, mass=mass) * 1.2,82 linestyle="dotted", lw=3, color=plt.get_cmap("plasma")(0.8),83 label=r"Analytic function, $X = 1.2$")84 ax.set_xlabel(r"Radius, $r \, [\rm cm]$")85 ax.set_ylabel(r"Relaxation Time, $\tau_{\rm relax} \, [\rm s]$")86 ax.errorbar(r_range, np.median(t_relax, axis=1), xerr=0.0,87 yerr=[np.median(t_relax, axis=1) - np.min(t_relax, axis=1),88 np.max(t_relax, axis=1) - np.median(t_relax, axis=1)],89 marker="o", color=plt.get_cmap("plasma")(0.2), label="Simulated results")90 ax.legend()91 plt.savefig("figures/3c.pdf", format="pdf", bbox_inches="tight")92 plt.show()93if __name__ == "__main__":...

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relax.py

Source:relax.py Github

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1import os2import yaml3import sys4import logging5def check_package(package_name,import_name):6 from importlib.util import find_spec7 has_lib = find_spec(package_name)8 if not has_lib:9 print("%s is not installed!!"%(import_name))10 return False11 12if __name__ == "__main__":13 package_list = {"biopython":"Bio","pandas":"pandas"}14 config_path = os.path.join(os.path.dirname(sys.argv[0]),"config.yaml")15 with open(config_path,"r") as f:16 config = yaml.load(f,Loader=yaml.FullLoader)17 #relax18 19 #score_jd220 if config["relax"]["need_prepare"]:21 cmd = os.path.join(os.path.dirname(sys.argv[0]),"jd2.run.sh") + " " +\22 config["input"]["path"] +" " +\23 os.path.join(config["input"]["rosetta_bin"],config["relax"]["score_jd2_exec"])24 ex = os.system(cmd)25 if ex:26 logging.error("run score_jd2 failed !")27 sys.exit(1)28 jd2_file = os.path.abspath(config["input"]["path"]) + "/jd2_pdb.list"29 else:30 jd2_file = config["input"]["path"]31 #if mpi_run relax32 if config["relax"]["mpi_run"]["use_mpi"]:33 mpi_cores = str(config["relax"]["mpi_run"]["mpi_cores"])34 else:35 mpi_cores = "0"36 #run relax37 cmd = os.path.join(os.path.dirname(sys.argv[0]),"relax.run.sh") + " " +\38 str(mpi_cores) + " " +\39 str(config["relax"]["relax_threads"])+ " " +\40 os.path.abspath(os.path.join(os.path.dirname(sys.argv[0]),config["relax"]["flag"])) + " " +\41 os.path.join(config["input"]["rosetta_bin"],config["relax"]["relax_exec"]) + " " +\42 jd2_file + " " +\43 config["input"]["path"]44 ex = os.system(cmd)45 if ex:46 logging.error("run relax failed !")47 sys.exit(1)48 relax_file = os.path.abspath(config["input"]["path"]) + "/relax_sc.list"49 could_flex = True50 51 ...

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