diff --git a/.github/workflows/add-to-project.yml b/.github/workflows/add-to-project.yaml similarity index 100% rename from .github/workflows/add-to-project.yml rename to .github/workflows/add-to-project.yaml diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml new file mode 100644 index 00000000..988d928b --- /dev/null +++ b/.github/workflows/coverage.yaml @@ -0,0 +1,42 @@ +name: Coverage + +on: push +jobs: + run-radicalpy-coverage: + name: Run coverage on RadicalPy + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@master + - name: Set up Python "3.11" 🐍 + uses: actions/setup-python@v4 + with: + python-version: "3.11" + cache: 'pip' + - name: Install packages 📦 + run: >- + python -m + pip install -r requirements.txt + - name: Install coverage + run: >- + python -m + pip install coverage + - name: Reset coverage + run: >- + coverage erase + - name: Run coverage + run: >- + coverage run -a -m + unittest + discover -v + - name: Run examples + run: >- + for file in $(ls examples/aniso*.py); do + PYTHONPATH=. coverage run -a $file --fast + done + - name: Create report + run: >- + coverage report && coverage xml && ls -lrt + - name: Code Coverage Report + uses: irongut/CodeCoverageSummary@v1.3.0 + with: + filename: coverage.xml diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 619b89cb..a12a58cd 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -1,6 +1,6 @@ name: Lint -on: [push, pull_request] +on: [push] jobs: lint: diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yaml similarity index 100% rename from .github/workflows/publish-to-pypi.yml rename to .github/workflows/publish-to-pypi.yaml diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yaml similarity index 64% rename from .github/workflows/run-tests.yml rename to .github/workflows/run-tests.yaml index be813339..d51a4df1 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yaml @@ -12,7 +12,7 @@ jobs: steps: - uses: actions/checkout@master - name: Set up Python ${{ matrix.python }} 🐍 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python }} cache: 'pip' @@ -25,3 +25,12 @@ jobs: python -m unittest discover -v + - name: Run examples + if: runner.os == 'Linux' + # This is bash. + # Need a separate branch to iterate over files on Windows. + run: >- + for file in $(ls examples/*.py); do + echo "Running example: $file" + PYTHONPATH=. python $file --fast + done diff --git a/examples/T1_T2_relaxation_rate.py b/examples/T1_T2_relaxation_rate.py index 091bbc31..0b1c1b94 100644 --- a/examples/T1_T2_relaxation_rate.py +++ b/examples/T1_T2_relaxation_rate.py @@ -10,6 +10,7 @@ aqueous_glycerol_viscosity, rotational_correlation_time_for_protein, ) +from radicalpy.utils import is_fast_run def main(): @@ -26,9 +27,9 @@ def main(): plt.axis("on") plt.rc("axes", edgecolor="k") for t in temperatures: - plt.plot(ratio, eta[t] * f, label=f"{t}$^\circ$C") + plt.plot(ratio, eta[t] * f, label=f"{t}$^\\circ$C") plt.xlabel("Glycerol fraction", size=14) - plt.ylabel("Viscosity ($mN \, s \, m^{-2}$)", size=14) + plt.ylabel(r"Viscosity ($mN \, s \, m^{-2}$)", size=14) plt.legend() plt.tick_params(labelsize=14) path = __file__[:-3] + f"_{0}.png" @@ -47,7 +48,7 @@ def main(): plt.axis("on") plt.rc("axes", edgecolor="k") for t in temperatures: - plt.plot(ratio, tau_c[t] * f2, label=f"{t}$^\circ$C") + plt.plot(ratio, tau_c[t] * f2, label=f"{t}$^\\circ$C") plt.xlabel("Glycerol fraction", size=14) plt.ylabel(r"$\tau _C$ ($\mu s$)", size=14) plt.legend() @@ -73,7 +74,7 @@ def main(): plt.axis("on") plt.rc("axes", edgecolor="k") for t in temperatures: - plt.plot(ratio, 1 / t1[t], label=f"{t}$^\circ$C") + plt.plot(ratio, 1 / t1[t], label=f"{t}$^\\circ$C") plt.xlabel("Glycerol fraction", size=14) plt.ylabel(r"1 / T1 ($s$)", size=14) plt.legend() @@ -86,7 +87,7 @@ def main(): plt.axis("on") plt.rc("axes", edgecolor="k") for t in temperatures: - plt.plot(ratio, 1 / t2[t], label=f"{t}$^\circ$C") + plt.plot(ratio, 1 / t2[t], label=f"{t}$^\\circ$C") plt.xlabel("Glycerol fraction", size=14) plt.ylabel(r"1 / T2 ($s$)", size=14) plt.legend() @@ -96,4 +97,7 @@ def main(): if __name__ == "__main__": - main() + if is_fast_run(): + main() # quick enough + else: + main() diff --git a/examples/anisotropy_3d_polar.py b/examples/anisotropy_3d_polar.py index c3706781..d420f92f 100644 --- a/examples/anisotropy_3d_polar.py +++ b/examples/anisotropy_3d_polar.py @@ -4,22 +4,26 @@ import numpy as np import radicalpy as rp +from radicalpy.experiments import anisotropy from radicalpy.simulation import State +from radicalpy.utils import is_fast_run -def main(): - theta = np.linspace(0, np.pi, 17) - phi = np.linspace(0, 2 * np.pi, 32) +# def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9): +def main(theta_steps=17, phi_steps=32, tmax=5e-6, dt=5e-9): + theta = np.linspace(0, np.pi, theta_steps) + phi = np.linspace(0, 2 * np.pi, phi_steps) flavin = rp.simulation.Molecule.fromdb("flavin_anion", ["N5", "N10"]) Z = rp.simulation.Molecule("zorro", []) sim = rp.simulation.HilbertSimulation([flavin, Z]) - time = np.arange(0, 5e-6, 5e-9) + time = np.arange(0, tmax, dt) B0 = 0.05 k = 1e6 - results = sim.anisotropy( + results = anisotropy( + sim, init_state=State.SINGLET, obs_state=State.SINGLET, time=time, @@ -41,10 +45,15 @@ def main(): print(f"{Y_av=}") print(f"{delta_phi_s=}") print(f"{gamma_s=}") - plt.show() + # plt.show() + path = __file__[:-3] + f"_{3}.png" + plt.savefig(path) return 0 if __name__ == "__main__": - main() + if is_fast_run(): + main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6) + else: + main() diff --git a/examples/anisotropy_3d_polar_paper.py b/examples/anisotropy_3d_polar_paper.py index 1d3ba277..2ae3866c 100644 --- a/examples/anisotropy_3d_polar_paper.py +++ b/examples/anisotropy_3d_polar_paper.py @@ -7,10 +7,10 @@ from radicalpy import kinetics, relaxation from radicalpy.experiments import anisotropy from radicalpy.simulation import State +from radicalpy.utils import is_fast_run -def main(): - +def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9): fad_n5_hfc = np.array( [ [0.280, -0.138, 0.678], @@ -21,14 +21,14 @@ def main(): dipolar = rp.estimations.dipolar_interaction_anisotropic(r=22e-10) - theta = np.linspace(0, np.pi, 35) - phi = np.linspace(0, 2 * np.pi, 58) + theta = np.linspace(0, np.pi, theta_steps) + phi = np.linspace(0, 2 * np.pi, phi_steps) flavin = rp.simulation.Molecule.fromisotopes(isotopes=["14N"], hfcs=[fad_n5_hfc]) Z = rp.simulation.Molecule("zorro", []) sim = rp.simulation.HilbertSimulation([flavin, Z]) - time = np.arange(0, 15e-6, 5e-9) + time = np.arange(0, tmax, dt) B0 = 0.05 k = 1e6 @@ -58,10 +58,15 @@ def main(): print(f"{Y_av=}") print(f"{delta_phi_s=}") print(f"{gamma_s=}") - plt.show() + # plt.show() + path = __file__[:-3] + f"_{3}.png" + plt.savefig(path) return 0 if __name__ == "__main__": - main() + if is_fast_run(): + main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6) + else: + main() diff --git a/examples/anisotropy_3d_polar_paper_2.py b/examples/anisotropy_3d_polar_paper_2.py index 5e6da8c6..ae70b132 100644 --- a/examples/anisotropy_3d_polar_paper_2.py +++ b/examples/anisotropy_3d_polar_paper_2.py @@ -7,10 +7,10 @@ from radicalpy import kinetics, relaxation from radicalpy.experiments import anisotropy from radicalpy.simulation import State +from radicalpy.utils import is_fast_run -def main(): - +def main(theta_steps=35, phi_steps=58, tmax=15e-6, dt=5e-9): fad_n5_hfc = np.array( [ [0.280, -0.138, 0.678], @@ -38,14 +38,14 @@ def main(): * rp.data.Isotope("E").gamma_mT ) - theta = np.linspace(0, np.pi, 35) - phi = np.linspace(0, 2 * np.pi, 58) + theta = np.linspace(0, np.pi, theta_steps) + phi = np.linspace(0, 2 * np.pi, phi_steps) flavin = rp.simulation.Molecule.fromisotopes(isotopes=["14N"], hfcs=[fad_n5_hfc]) trp = rp.simulation.Molecule.fromisotopes(isotopes=["1H"], hfcs=[trp_hbeta_hfc]) sim = rp.simulation.HilbertSimulation([flavin, trp]) - time = np.arange(0, 15e-6, 5e-9) + time = np.arange(0, tmax, dt) B0 = 0.05 k = 1e6 @@ -75,10 +75,15 @@ def main(): print(f"{Y_av=}") print(f"{delta_phi_s=}") print(f"{gamma_s=}") - plt.show() + # plt.show() + path = __file__[:-3] + f"_{3}.png" + plt.savefig(path) return 0 if __name__ == "__main__": - main() + if is_fast_run(): + main(theta_steps=7, phi_steps=6, tmax=10e-6, dt=1e-6) + else: + main() diff --git a/examples/bhalf_data_comparison.py b/examples/bhalf_data_comparison.py deleted file mode 100644 index e43132b4..00000000 --- a/examples/bhalf_data_comparison.py +++ /dev/null @@ -1,87 +0,0 @@ -#! /usr/bin/env python - -from pathlib import Path - -import matplotlib.pyplot as plt -import numpy as np - - -def main(): - - # Load B1/2 spectra, kd = 3e5 - path = "./examples/data/bhalf_analysis/fad_kd3e5" - time_3e5 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("time.txt")] - ) - bhalf_3e5 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf.txt")] - ) - error_3e5 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf_error.txt")] - ) - - # Load B1/2 spectra, kd = 3e6 - path = "./examples/data/bhalf_analysis/fad_kd3e6" - time_3e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("time.txt")] - ) - bhalf_3e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf.txt")] - ) - error_3e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf_error.txt")] - ) - - # Load B1/2 spectra, kd = 7e6 - path = "./examples/data/bhalf_analysis/fad_kd7e6" - time_7e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("time.txt")] - ) - bhalf_7e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf.txt")] - ) - error_7e6 = np.array( - [np.genfromtxt(file_path) for file_path in Path(path).glob("bhalf_error.txt")] - ) - - time_3e5 = time_3e5[0, :] - time_3e6 = time_3e6[0, :] - time_7e6 = time_7e6[0, :] - - bhalf_3e5 = bhalf_3e5[0, :] / bhalf_3e5[0, :].max() - bhalf_3e6 = bhalf_3e6[0, :] / bhalf_3e6[0, :].max() - bhalf_7e6 = bhalf_7e6[0, :] / bhalf_7e6[0, :].max() - - num_samples = 200 - - error_3e5 = error_3e5[0, :] / np.sqrt(num_samples) - error_3e6 = error_3e6[0, :] / np.sqrt(num_samples) - error_7e6 = error_7e6[0, :] / np.sqrt(num_samples) - - factor = 1e6 - cutoff = 5 - - plt.figure(1) - for i in range(2, len(time_3e5), 50): - plt.plot(time_3e5[cutoff:i] * factor, bhalf_3e5[cutoff:i], "r", linewidth=3) - plt.plot(time_3e6[cutoff:i] * factor, bhalf_3e6[cutoff:i], "b", linewidth=3) - plt.plot(time_7e6[cutoff:i] * factor, bhalf_7e6[cutoff:i], "g", linewidth=3) - plt.xlabel("Time / $\mu s$", size=24) - plt.ylabel("Normalised $B_{1/2}$ / a.u.", size=24) - plt.legend( - [ - r"$k_d = 3 \times 10^5 s^{-1}$", - r"$k_d = 3 \times 10^6 s^{-1}$", - r"$k_d = 7 \times 10^6 s^{-1}$", - ], - fontsize=16, - ) - plt.tick_params(labelsize=18) - plt.gcf().set_size_inches(10, 5) - path = __file__[:-3] + f"_{0}.png" - plt.savefig(path, dpi=300, bbox_inches="tight") - plt.close() - - -if __name__ == "__main__": - main() diff --git a/examples/cidnp.py b/examples/cidnp.py index 36a0eb49..2ac1caeb 100644 --- a/examples/cidnp.py +++ b/examples/cidnp.py @@ -8,12 +8,14 @@ import radicalpy as rp from radicalpy import kinetics, relaxation +from radicalpy.experiments import mary_lfe_hfe, mary_loop from radicalpy.shared import constants as C from radicalpy.simulation import LiouvilleSimulation as Liouv from radicalpy.simulation import State +from radicalpy.utils import is_fast_run -def main(): +def main(tmax=5e-6, dt=5e-9, Bmax=20000, dB=100): # Create a radical pair with a 13C nucleus coupled to radical 1 r1 = rp.simulation.Molecule.fromisotopes(isotopes=["13C"], hfcs=[0.0]) r2 = rp.simulation.Molecule("radical 2") @@ -36,8 +38,8 @@ def main(): xi = 0.98 init_state = State.SINGLET - time = np.arange(0, 5e-6, 5e-9) - B = np.arange(0, 20000, 100) + time = np.arange(0, tmax, dt) + B = np.arange(0, Bmax, dB) kinetic = [ kinetics.Haberkorn(ks, State.SINGLET), kinetics.Haberkorn(kt, State.TRIPLET), @@ -71,7 +73,7 @@ def main(): # Run the magnetic field loop sim.apply_liouville_hamiltonian_modifiers(HL, kinetic + relaxations) - rhos = sim.mary_loop(init_state, time, B, HL, theta=None, phi=None) + rhos = mary_loop(sim, init_state, time, B, HL, theta=None, phi=None) # Calculate CIDNP of both singlet and triplet yields --> see Eqs. 6 and 7 product_probabilities1 = np.real(np.trace(obs_state1 @ rhos, axis1=-2, axis2=-1)) @@ -85,7 +87,7 @@ def main(): ) dt = time[1] - time[0] - CIDNP, LFE, HFE = sim.mary_lfe_hfe(init_state, B, product_probabilities, dt, k) + CIDNP, LFE, HFE = mary_lfe_hfe(init_state, B, product_probabilities, dt, k) # Normalise the CIDNP intensity and plot and save figure norm_CIDNP = (CIDNP - CIDNP.max()) / (CIDNP.max() - CIDNP.min()) @@ -99,4 +101,7 @@ def main(): if __name__ == "__main__": - main() + if is_fast_run(): + main(tmax=5e-6, dt=5e-7, Bmax=20000, dB=1000) + else: + main() diff --git a/examples/data/bhalf_analysis/fad_kd3e5/bhalf.txt b/examples/data/bhalf_analysis/fad_kd3e5/bhalf.txt new file mode 100644 index 00000000..940356cf --- /dev/null +++ b/examples/data/bhalf_analysis/fad_kd3e5/bhalf.txt @@ -0,0 +1,1001 @@ +0.000000000000000000e+00 +0.000000000000000000e+00 +3.389469387582897397e+00 +3.499361022813723743e+00 +3.623972873585272314e+00 +3.720661285353069392e+00 +3.790000018732156750e+00 +3.838604765260783758e+00 +3.872626758107115208e+00 +3.896718189982417258e+00 +3.914131550572156559e+00 +3.927071080093008426e+00 +3.937009529600660862e+00 +3.944924548184754798e+00 +3.951463949615636739e+00 +3.957056499158599028e+00 +3.961986791553757659e+00 +3.966443612231399740e+00 +3.970553012673867066e+00 +3.974399579976989116e+00 +3.978040386233322678e+00 +3.981514572136286123e+00 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+9.769999999999999632e-06 +9.779999999999999536e-06 +9.789999999999999441e-06 +9.800000000000001039e-06 +9.810000000000000943e-06 +9.820000000000000847e-06 +9.830000000000000752e-06 +9.840000000000000656e-06 +9.850000000000000560e-06 +9.860000000000000464e-06 +9.870000000000000369e-06 +9.880000000000000273e-06 +9.890000000000000177e-06 +9.900000000000000081e-06 +9.909999999999999986e-06 +9.919999999999999890e-06 +9.929999999999999794e-06 +9.939999999999999698e-06 +9.949999999999999603e-06 +9.959999999999999507e-06 +9.969999999999999411e-06 +9.980000000000001010e-06 +9.990000000000000914e-06 +1.000000000000000082e-05 diff --git a/examples/data/bhalf_data_comparison.py b/examples/data/bhalf_data_comparison.py new file mode 100644 index 00000000..e6734f54 --- /dev/null +++ b/examples/data/bhalf_data_comparison.py @@ -0,0 +1,66 @@ +#! /usr/bin/env python + +from pathlib import Path + +import matplotlib.pyplot as plt +import numpy as np + + +def main(): + + # Load B1/2 spectra, kd = 3e5 + path = Path("./examples/data/bhalf_analysis/fad_kd3e5") + time_3e5 = np.genfromtxt(path / "time.txt") + + bhalf_3e5 = np.genfromtxt(path / "bhalf.txt") + error_3e5 = np.genfromtxt(path / "bhalf_error.txt") + + # Load B1/2 spectra, kd = 3e6 + path = Path("./examples/data/bhalf_analysis/fad_kd3e6") + time_3e6 = np.genfromtxt(path / "time.txt") + bhalf_3e6 = np.genfromtxt(path / "bhalf.txt") + error_3e6 = np.genfromtxt(path / "bhalf_error.txt") + + # Load B1/2 spectra, kd = 7e6 + path = Path("./examples/data/bhalf_analysis/fad_kd7e6") + time_7e6 = np.genfromtxt(path / "time.txt") + bhalf_7e6 = np.genfromtxt(path / "bhalf.txt") + error_7e6 = np.genfromtxt(path / "bhalf_error.txt") + + bhalf_3e5 = bhalf_3e5 / bhalf_3e5.max() + bhalf_3e6 = bhalf_3e6 / bhalf_3e6.max() + bhalf_7e6 = bhalf_7e6 / bhalf_7e6.max() + + num_samples = 200 + + error_3e5 = error_3e5 / np.sqrt(num_samples) + error_3e6 = error_3e6 / np.sqrt(num_samples) + error_7e6 = error_7e6 / np.sqrt(num_samples) + + factor = 1e6 + cutoff = 5 + + plt.figure(1) + for i in range(2, len(time_3e5), 50): + plt.plot(time_3e5[cutoff:i] * factor, bhalf_3e5[cutoff:i], "r", linewidth=3) + plt.plot(time_3e6[cutoff:i] * factor, bhalf_3e6[cutoff:i], "b", linewidth=3) + plt.plot(time_7e6[cutoff:i] * factor, bhalf_7e6[cutoff:i], "g", linewidth=3) + plt.xlabel(r"Time / $\mu s$", size=24) + plt.ylabel("Normalised $B_{1/2}$ / a.u.", size=24) + plt.legend( + [ + r"$k_d = 3 \times 10^5 s^{-1}$", + r"$k_d = 3 \times 10^6 s^{-1}$", + r"$k_d = 7 \times 10^6 s^{-1}$", + ], + fontsize=16, + ) + plt.tick_params(labelsize=18) + plt.gcf().set_size_inches(10, 5) + path = __file__[:-3] + f"_{0}.png" + plt.savefig(path, dpi=300, bbox_inches="tight") + plt.close() + + +if __name__ == "__main__": + main() diff --git a/examples/bhalf_data_saver.py b/examples/data/bhalf_data_saver.py similarity index 63% rename from examples/bhalf_data_saver.py rename to examples/data/bhalf_data_saver.py index fc3b0a17..8bd8b925 100644 --- a/examples/bhalf_data_saver.py +++ b/examples/data/bhalf_data_saver.py @@ -15,32 +15,19 @@ def main(): scale_factor = 2.5e-2 # 4e-1 # Load reference spectra - path = "./examples/data/fad_kinetics" - radical_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_spectrum.txt") - ] - ) - triplet_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_triplet_spectrum.txt") - ] - ) - wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_wavelength.txt") - ] - ) + path = Path("./examples/data/fad_kinetics") + radical_spectrum = np.genfromtxt(path / "fad_radical_spectrum.txt") + triplet_spectrum = np.genfromtxt(path / "fad_triplet_spectrum.txt") + wavelength = np.genfromtxt(path / "fad_radical_wavelength.txt") - radical_spectrum = radical_spectrum[0, :] * 1e3 - triplet_spectrum = triplet_spectrum[0, :] * 1e3 - wavelength = wavelength[0, :] + radical_spectrum = radical_spectrum * 1e3 + triplet_spectrum = triplet_spectrum * 1e3 + wavelength = wavelength result = np.load( - "./examples/data/fad_06_kd7e6/results.npy", allow_pickle=True + # "./examples/data/fad_06_kd7e6/results.npy", + "./examples/data/bhalf_analysis/fad_kd3e6/results.npy", + allow_pickle=True, ).item() time = result["ts"] @@ -83,9 +70,11 @@ def main(): R2_time[i], ) = Bhalf_fit(Bs, mary[i, :, wl]) - np.savetxt("./examples/data/fad_06_kd7e6/time.txt", time) - np.savetxt("./examples/data/fad_06_kd7e6/bhalf.txt", bhalf_time) - np.savetxt("./examples/data/fad_06_kd7e6/bhalf_error.txt", fit_error_time) + np.savetxt("./examples/data/bhalf_analysis/fad_06_kd7e6/time.txt", time) + np.savetxt("./examples/data/bhalf_analysis/fad_06_kd7e6/bhalf.txt", bhalf_time) + np.savetxt( + "./examples/data/bhalf_analysis/fad_06_kd7e6/bhalf_error.txt", fit_error_time + ) if __name__ == "__main__": diff --git a/examples/data_plotter_kinetics_fad_semiclassical_wavelength.py b/examples/data/data_plotter_kinetics_fad_semiclassical_wavelength.py similarity index 80% rename from examples/data_plotter_kinetics_fad_semiclassical_wavelength.py rename to examples/data/data_plotter_kinetics_fad_semiclassical_wavelength.py index f3249a8d..ff9091fe 100644 --- a/examples/data_plotter_kinetics_fad_semiclassical_wavelength.py +++ b/examples/data/data_plotter_kinetics_fad_semiclassical_wavelength.py @@ -21,59 +21,27 @@ def main(): elev = 35 # Load reference spectra - path = "./examples/data/fad_kinetics" - radical_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_spectrum.txt") - ] + path = Path("./examples/data/fad_kinetics") + radical_spectrum = np.genfromtxt(path / "fad_radical_spectrum.txt") + triplet_spectrum = np.genfromtxt(path / "fad_triplet_spectrum.txt") + wavelength = np.genfromtxt(path / "fad_radical_wavelength.txt") + groundstate_spectrum = np.genfromtxt(path / "fad_groundstate_spectrum.txt") + groundstate_wavelength = np.genfromtxt( + path / "fad_groundstate_spectrum_wavelength.txt" ) - triplet_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_triplet_spectrum.txt") - ] - ) - wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_wavelength.txt") - ] - ) - groundstate_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_groundstate_spectrum.txt") - ] - ) - groundstate_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_groundstate_spectrum_wavelength.txt") - ] - ) - emission_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_emission_spectrum.txt") - ] - ) - emission_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_emission_spectrum_wavelength.txt") - ] - ) - radical_spectrum = radical_spectrum[0, :] * 1e3 - triplet_spectrum = triplet_spectrum[0, :] * 1e3 - wavelength = wavelength[0, :] - groundstate_spectrum = groundstate_spectrum[0, :] - groundstate_wavelength = groundstate_wavelength[0, :] - emission_spectrum = emission_spectrum[0, :] - emission_wavelength = emission_wavelength[0, :] + emission_spectrum = np.genfromtxt(path / "fad_emission_spectrum.txt") + emission_wavelength = np.genfromtxt(path / "fad_emission_spectrum_wavelength.txt") + radical_spectrum = radical_spectrum * 1e3 + triplet_spectrum = triplet_spectrum * 1e3 + wavelength = wavelength + groundstate_spectrum = groundstate_spectrum + groundstate_wavelength = groundstate_wavelength + emission_spectrum = emission_spectrum + emission_wavelength = emission_wavelength result = np.load( - "./examples/data/fad_kinetics/results.npy", allow_pickle=True + "./examples/data/fad_kinetics/results_new.npy", + allow_pickle=True, ).item() time = result["ts"] @@ -168,8 +136,8 @@ def main(): for i in range(1, len(emission_wavelength)): mfe_emission_max[i] = mary_emission[:, -1, i].min() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" plot_general( groundstate_wavelength[1:], np.real(mfe_groundstate_max)[1:], @@ -182,8 +150,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta I_F$" plot_general( emission_wavelength[1:], np.real(mfe_emission_max)[1:], @@ -196,8 +164,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" plot_general( wavelength, np.real(mfe_max), @@ -217,8 +185,8 @@ def main(): colors_time = plt.colormaps.get_cmap("viridis").resampled(len(time)).colors colors_field = plt.colormaps.get_cmap("viridis").resampled(len(Bs)).colors - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( groundstate_wavelength, @@ -226,15 +194,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{3}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -242,15 +210,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{4}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -266,8 +234,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( emission_wavelength, @@ -275,15 +243,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{6}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta I_F$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( Bs, @@ -291,15 +259,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{7}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta I_F$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta I_F$" for i in range(0, len(Bs), f): plot_general( time, @@ -315,8 +283,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( wavelength, @@ -324,15 +292,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{9}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -340,15 +308,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{10}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -479,9 +447,9 @@ def main(): plt.close() # 3D plots - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta \Delta A$" plot_3d_results( groundstate_wavelength, time, @@ -497,9 +465,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta \Delta A$" plot_3d_results( groundstate_wavelength, Bs, @@ -516,9 +484,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta I_F$" plot_3d_results( emission_wavelength, time, @@ -534,9 +502,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta I_F$" plot_3d_results( emission_wavelength, Bs, @@ -553,9 +521,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta \Delta A$" plot_3d_results( wavelength, time, @@ -571,9 +539,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta \Delta A$" plot_3d_results( wavelength, Bs, diff --git a/examples/data/fad_kinetics/fad_emission_spectrum.txt b/examples/data/fad_kinetics/fad_emission_spectrum.txt new file mode 100644 index 00000000..ca8e4e3c --- /dev/null +++ b/examples/data/fad_kinetics/fad_emission_spectrum.txt @@ -0,0 +1,27 @@ +0.02830285072034311 +0.09236742617758242 +0.2039780661421613 +0.4108170702632741 +0.5857770511903544 +0.7924798201696133 +0.935765130615442 +0.9998297060726813 +0.9844691938285486 +0.9533054051292531 +0.8744933755662272 +0.7956813460032022 +0.7010319811995505 +0.6063826163958996 +0.4958618575661591 +0.417117945574061 +0.338305916011036 +0.2911685569292608 +0.22822792139232373 +0.18126085623786636 +0.15019924389496264 +0.1031300023841153 +0.08780354892544473 +0.07261333060863073 +0.07322638874697684 +0.0419944824767553 +0.05837675828479938 diff --git a/examples/data/fad_kinetics/fad_emission_spectrum_wavelength.txt b/examples/data/fad_kinetics/fad_emission_spectrum_wavelength.txt new file mode 100644 index 00000000..1ac6b5e0 --- /dev/null +++ b/examples/data/fad_kinetics/fad_emission_spectrum_wavelength.txt @@ -0,0 +1,27 @@ +465.5308061714519 +474.5478696229693 +482.41544906508636 +490.12976397261673 +495.74946357412887 +501.3180749974456 +508.06171451926025 +517.0787779707775 +525.1507101256769 +534.3210381117809 +543.0315724941248 +551.7421068764688 +561.0146112189639 +570.2871155614591 +579.585163993052 +589.3685501175028 +598.0790844998468 +605.6656789618883 +614.3506692551343 +624.619393072443 +635.3989986717074 +644.0584448758557 +652.6668029018085 +663.420864411975 +673.0765300909369 +681.1740063349341 +689.1948503116379 diff --git a/examples/data/fad_kinetics/fad_groundstate_spectrum_wavelength.txt b/examples/data/fad_kinetics/fad_groundstate_spectrum_wavelength.txt new file mode 100644 index 00000000..b4c41acd --- /dev/null +++ b/examples/data/fad_kinetics/fad_groundstate_spectrum_wavelength.txt @@ -0,0 +1,58 @@ +250.07610299931474 +252.2178588371725 +253.94104817879924 +256.0846159928311 +258.6467503030942 +261.19982473248643 +266.25705023456857 +270.40647567339624 +272.0390662063149 +273.258526171525 +274.05398371198146 +275.268007748669 +276.4820317853566 +278.11099836592695 +279.73996494649725 +281.36711955089345 +282.99427415528965 +284.20829819197724 +285.42051025249066 +287.4716672816404 +288.68206736597966 +290.3146578988983 +292.36581492804805 +295.25772890200835 +300.25697116651736 +308.20792261873385 +316.16974592799534 +323.72025064572244 +331.2725673396236 +337.15605397712295 +343.4544831585051 +348.91759132359914 +355.6327750250382 +361.092259237784 +368.6445759316852 +377.43809630488636 +384.9596094038269 +391.2217990617258 +396.2282892309314 +401.66059380106475 +410.03735965420907 +416.3357888355912 +423.0491605608561 +429.76615623846925 +437.73885140477574 +446.1283010911392 +456.1702730483369 +464.10854066733435 +471.62461783775234 +477.8813715671288 +482.8769898792894 +487.8726081914501 +492.4442240788572 +497.023087870961 +502.44270860787515 +508.70308628959987 +516.2245993885404 +524.592305360814 diff --git a/examples/data/fad_ref_spectra.py b/examples/data/fad_ref_spectra.py new file mode 100644 index 00000000..efdb57da --- /dev/null +++ b/examples/data/fad_ref_spectra.py @@ -0,0 +1,42 @@ +#! /usr/bin/env python + +from pathlib import Path + +import matplotlib.pyplot as plt +import numpy as np + + +def main(): + + path = Path("./examples/data/fad_kinetics") + radical_spectrum = np.genfromtxt(path / "fad_radical_spectrum.txt") + radical_wavelength = np.genfromtxt(path / "fad_radical_wavelength.txt") + triplet_spectrum = np.genfromtxt(path / "fad_triplet_spectrum.txt") + triplet_wavelength = np.genfromtxt(path / "fad_triplet_wavelength.txt") + + plt.figure(1) + plt.plot( + radical_wavelength, + radical_spectrum * 1e3, + "ro", + linewidth=3, + ) + plt.plot( + triplet_wavelength, + triplet_spectrum * 1e3, + "bo", + linewidth=3, + ) + plt.xlabel(r"Wavelength / nm", size=24) + plt.ylabel(r"$\epsilon$ / $M^{-1} cm^{-1}$", size=24) + plt.legend(["Radical", "Triplet"], fontsize=16) + plt.tick_params(labelsize=18) + plt.gcf().set_size_inches(10, 5) + # plt.show() + + path = __file__[:-3] + f"_{0}.png" + plt.savefig(path, dpi=300, bbox_inches="tight") + + +if __name__ == "__main__": + main() diff --git a/examples/density_matrix_2d.py b/examples/density_matrix_2d.py index 3db015b1..e7f02532 100644 --- a/examples/density_matrix_2d.py +++ b/examples/density_matrix_2d.py @@ -4,6 +4,7 @@ import numpy as np import radicalpy as rp +from radicalpy.experiments import mary from radicalpy.simulation import State @@ -16,7 +17,8 @@ def main(): Bs = np.arange(0, 10, 1) k = 1e6 - MARY = sim.MARY( + MARY = mary( + sim, init_state=State.SINGLET, obs_state=State.TRIPLET, time=time, @@ -43,7 +45,9 @@ def main(): labels = rp.plot.spin_state_labels(sim) ax.set_xticklabels(labels, rotation=90) ax.set_yticklabels(labels, rotation=0) - plt.show() + # plt.show() + path = __file__[:-3] + f"_{0}.png" + plt.savefig(path) if __name__ == "__main__": diff --git a/examples/density_matrix_3d.py b/examples/density_matrix_3d.py index c81ad8ee..09e61ab7 100644 --- a/examples/density_matrix_3d.py +++ b/examples/density_matrix_3d.py @@ -4,6 +4,7 @@ import numpy as np import radicalpy as rp +from radicalpy.experiments import mary from radicalpy.simulation import State @@ -16,7 +17,8 @@ def main(): Bs = np.arange(0, 3, 1) k = 1e6 - MARY = sim.MARY( + MARY = mary( + sim, init_state=State.SINGLET, obs_state=State.TRIPLET, time=time, diff --git a/examples/energy_level.py b/examples/energy_level.py index 7585190c..bea33287 100644 --- a/examples/energy_level.py +++ b/examples/energy_level.py @@ -17,7 +17,9 @@ def main(): E = np.real(eigval[0]) # 0 = eigenvalues, 1 = eigenvectors rp.plot.energy_levels(sim, B=np.arange(0.01, 1, 0.01), J=0, D=0) - plt.show() + # plt.show() + path = __file__[:-3] + f"_{0}.png" + plt.savefig(path) if __name__ == "__main__": diff --git a/examples/fad_ref_spectra.py b/examples/fad_ref_spectra.py deleted file mode 100644 index 8fecbbe4..00000000 --- a/examples/fad_ref_spectra.py +++ /dev/null @@ -1,62 +0,0 @@ -#! /usr/bin/env python - -from pathlib import Path - -import matplotlib.pyplot as plt -import numpy as np - - -def main(): - - path = "./examples/data/fad_kinetics" - radical_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_spectrum.txt") - ] - ) - radical_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_wavelength.txt") - ] - ) - triplet_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_triplet_spectrum.txt") - ] - ) - triplet_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_triplet_wavelength.txt") - ] - ) - - plt.figure(1) - plt.plot( - radical_wavelength[0, :], - radical_spectrum[0, :] * 1e3, - "ro", - linewidth=3, - ) - plt.plot( - triplet_wavelength[0, :], - triplet_spectrum[0, :] * 1e3, - "bo", - linewidth=3, - ) - plt.xlabel("Wavelength / nm", size=24) - plt.ylabel("$\epsilon$ / $M^{-1} cm^{-1}$", size=24) - plt.legend(["Radical", "Triplet"], fontsize=16) - plt.tick_params(labelsize=18) - plt.gcf().set_size_inches(10, 5) - # plt.show() - - path = __file__[:-3] + f"_{0}.png" - plt.savefig(path, dpi=300, bbox_inches="tight") - - -if __name__ == "__main__": - main() diff --git a/examples/kinetics_cryptochrome.py b/examples/kinetics_cryptochrome.py index 89ed080c..6ec92b33 100644 --- a/examples/kinetics_cryptochrome.py +++ b/examples/kinetics_cryptochrome.py @@ -3,7 +3,7 @@ import matplotlib.pyplot as plt import numpy as np -from radicalpy.classical import RateEquations +from radicalpy.classical import Rate, RateEquations def main(): @@ -106,10 +106,10 @@ def main(): "S": 1, } time = np.linspace(0, 100e-6, 500) - - result_off = RateEquations({**base, **off}, time, initial_states) - result_on = RateEquations({**base, **on}, time, initial_states) - + re_off = RateEquations({**base, **off}) + re_on = RateEquations({**base, **on}) + result_off = re_off.time_evolution(time, initial_states) + result_on = re_on.time_evolution(time, initial_states) fluor_field_off = result_off["A-D"] fluor_field_on = result_on["A-D"] fluor_delta_A = fluor_field_on - fluor_field_off @@ -128,9 +128,9 @@ def main(): axs[1].plot(time * scale, rp_delta_delta_A, color="orange", linewidth=2) plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) - axs[0].set_ylabel("$\Delta A$", size=14) - axs[1].set_ylabel("$\Delta \Delta A$", size=14) + axs[1].set_xlabel(r"Time ($\mu s$)", size=14) + axs[0].set_ylabel(r"$\Delta A$", size=14) + axs[1].set_ylabel(r"$\Delta \Delta A$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) @@ -148,9 +148,9 @@ def main(): axs[1].plot(time * scale, fluor_delta_A, color="orange", linewidth=2) plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) + axs[1].set_xlabel(r"Time ($\mu s$)", size=14) axs[0].set_ylabel("$F$", size=14) - axs[1].set_ylabel("$\Delta F$", size=14) + axs[1].set_ylabel(r"$\Delta F$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) diff --git a/examples/kinetics_fad.py b/examples/kinetics_fad.py index c91d1a97..ce13697f 100644 --- a/examples/kinetics_fad.py +++ b/examples/kinetics_fad.py @@ -107,8 +107,10 @@ def main(): } time = np.linspace(0, 6e-6, 200) - result_off = RateEquations({**base, **off}, time, initial_states) - result_on = RateEquations({**base, **on}, time, initial_states) + re_off = RateEquations({**base, **off}) + re_on = RateEquations({**base, **on}) + result_off = re_off.time_evolution(time, initial_states) + result_on = re_on.time_evolution(time, initial_states) fac = 0.07 keys = ["S", "T+/-", "T0", "Quencher"] + 2 * ["T*+/-", "T*0"] @@ -131,9 +133,9 @@ def main(): axs[1].plot(time * scale, delta_delta_A, color="orange", linewidth=2) plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) - axs[0].set_ylabel("$\Delta A$", size=14) - axs[1].set_ylabel("$\Delta \Delta A$", size=14) + axs[1].set_xlabel(r"Time ($\mu s$)", size=14) + axs[0].set_ylabel(r"$\Delta A$", size=14) + axs[1].set_ylabel(r"$\Delta \Delta A$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) @@ -151,9 +153,9 @@ def main(): axs[1].plot(time * scale, fluor_del_A, color="orange", linewidth=2) plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) - axs[0].set_ylabel("$F$", size=14) - axs[1].set_ylabel("$\Delta F$", size=14) + axs[1].set_xlabel(r"Time ($\mu s$)", size=14) + axs[0].set_ylabel(r"$F$", size=14) + axs[1].set_ylabel(r"$\Delta F$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) diff --git a/examples/kinetics_fad_semiclassical.py b/examples/kinetics_fad_semiclassical.py index 56b03168..c24fdac8 100644 --- a/examples/kinetics_fad_semiclassical.py +++ b/examples/kinetics_fad_semiclassical.py @@ -4,18 +4,18 @@ import numpy as np from radicalpy.classical import Rate, RateEquations, latex_eqlist_to_align, latexify -from radicalpy.experiments import semiclassical_kinetics_mary +from radicalpy.experiments import kine_quantum_mary from radicalpy.plot import plot_3d_results, plot_bhalf_time from radicalpy.relaxation import RandomFields from radicalpy.simulation import Molecule, SemiclassicalSimulation -from radicalpy.utils import Bhalf_fit +from radicalpy.utils import Bhalf_fit, is_fast_run -def main(): +def main(Bmax=30, dB=0.5, tmax=20e-6, dt=10e-9): # Parameters - time = np.arange(0, 20e-6, 10e-9) - Bs = np.arange(0, 30, 0.5) + time = np.arange(0, tmax, dt) + Bs = np.arange(0, Bmax, dB) num_samples = 400 scale_factor = 10 kr = 0 # 1.7e6 # radical pair relaxation rate @@ -166,7 +166,7 @@ def main(): adenine = Molecule.all_nuclei("fad") sim = SemiclassicalSimulation([flavin, adenine]) - results = semiclassical_kinetics_mary( + results = kine_quantum_mary( sim, num_samples, rho0, @@ -231,9 +231,9 @@ def main(): rstride=1, cstride=1, ) - ax.set_xlabel("$B_0$ / mT", size=18) - ax.set_ylabel("Time / $\mu s$", size=18) - ax.set_zlabel("$\Delta \Delta A$", size=18) + ax.set_xlabel(r"$B_0$ / mT", size=18) + ax.set_ylabel(r"Time / $\mu s$", size=18) + ax.set_zlabel(r"$\Delta \Delta A$", size=18) plt.tick_params(labelsize=14) fig.set_size_inches(10, 5) # plt.show() @@ -271,8 +271,8 @@ def main(): color="k", linewidth=2, ) - plt.xlabel("Time / $\mu s$", size=18) - plt.ylabel("$B_{1/2}$ / mT", size=18) + plt.xlabel(r"Time / $\mu s$", size=18) + plt.ylabel(r"$B_{1/2}$ / mT", size=18) plt.tick_params(labelsize=14) plt.gcf().set_size_inches(10, 5) path = __file__[:-3] + f"_{1}.png" @@ -293,9 +293,9 @@ def main(): rstride=1, cstride=1, ) - ax.set_xlabel("$B_0$ / mT", size=18) - ax.set_ylabel("Time / $\mu s$", size=18) - ax.set_zlabel("$\Delta \Delta A$", size=18) + ax.set_xlabel(r"$B_0$ / mT", size=18) + ax.set_ylabel(r"Time / $\mu s$", size=18) + ax.set_zlabel(r"$\Delta \Delta A$", size=18) plt.tick_params(labelsize=14) fig.set_size_inches(10, 5) # plt.show() @@ -327,8 +327,8 @@ def main(): color="k", linewidth=2, ) - plt.xlabel("Time / $\mu s$", size=18) - plt.ylabel("$B_{1/2}$ / mT", size=18) + plt.xlabel(r"Time / $\mu s$", size=18) + plt.ylabel(r"$B_{1/2}$ / mT", size=18) plt.tick_params(labelsize=14) plt.gcf().set_size_inches(10, 5) path = __file__[:-3] + f"_{3}.png" @@ -336,4 +336,7 @@ def main(): if __name__ == "__main__": - main() + if is_fast_run(): + main(Bmax=10, dB=2, tmax=10e-6, dt=1e-6) + else: + main() diff --git a/examples/kinetics_fad_semiclassical_wavelength.py b/examples/kinetics_fad_semiclassical_wavelength.py index fd0cc44f..ee40ea2d 100644 --- a/examples/kinetics_fad_semiclassical_wavelength.py +++ b/examples/kinetics_fad_semiclassical_wavelength.py @@ -7,18 +7,18 @@ import radicalpy as rp from radicalpy.classical import Rate, RateEquations, latex_eqlist_to_align, latexify -from radicalpy.experiments import semiclassical_kinetics_mary +from radicalpy.experiments import kine_quantum_mary from radicalpy.plot import plot_3d_results, plot_bhalf_time, plot_general from radicalpy.relaxation import RandomFields, SingletTripletDephasing from radicalpy.simulation import Basis, Molecule, SemiclassicalSimulation -from radicalpy.utils import Bhalf_fit +from radicalpy.utils import Bhalf_fit, is_fast_run -def main(): +def main(Bmax=30, dB=0.5, tmax=10e-6, dt=10e-9): # Parameters - time = np.arange(0, 10e-6, 10e-9) - Bs = np.arange(0, 30, 0.5) + time = np.arange(0, tmax, dt) + Bs = np.arange(0, Bmax, dB) num_samples = 200 scale_factor = 1 # 4e-1 kr = 7e7 # 1.7e6 # radical pair relaxation rate @@ -32,56 +32,16 @@ def main(): # elev = 35 # Load reference spectra - path = "./examples/data/fad_kinetics" - radical_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_spectrum.txt") - ] - ) - triplet_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_triplet_spectrum.txt") - ] - ) - wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_radical_wavelength.txt") - ] - ) - groundstate_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_groundstate_spectrum.txt") - ] - ) - groundstate_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_groundstate_spectrum_wavelength.txt") - ] - ) - emission_spectrum = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_emission_spectrum.txt") - ] - ) - emission_wavelength = np.array( - [ - np.genfromtxt(file_path) - for file_path in Path(path).glob("fad_emission_spectrum_wavelength.txt") - ] + path = Path("./examples/data/fad_kinetics") + radical_spectrum = 1e3 * np.genfromtxt(path / "fad_radical_spectrum.txt") + triplet_spectrum = 1e3 * np.genfromtxt(path / "fad_triplet_spectrum.txt") + wavelength = np.genfromtxt(path / "fad_radical_wavelength.txt") + groundstate_spectrum = np.genfromtxt(path / "fad_groundstate_spectrum.txt") + groundstate_wavelength = np.genfromtxt( + path / "fad_groundstate_spectrum_wavelength.txt" ) - radical_spectrum = radical_spectrum[0, :] * 1e3 - triplet_spectrum = triplet_spectrum[0, :] * 1e3 - wavelength = wavelength[0, :] - groundstate_spectrum = groundstate_spectrum[0, :] - groundstate_wavelength = groundstate_wavelength[0, :] - emission_spectrum = emission_spectrum[0, :] - emission_wavelength = emission_wavelength[0, :] + emission_spectrum = np.genfromtxt(path / "fad_emission_spectrum.txt") + emission_wavelength = np.genfromtxt(path / "fad_emission_spectrum_wavelength.txt") flavin = Molecule.all_nuclei("fad") adenine = Molecule.all_nuclei("fad") @@ -232,7 +192,7 @@ def main(): latex_equations = latex_eqlist_to_align(latexify(base)) # print(latex_equations) - results = semiclassical_kinetics_mary( + results = kine_quantum_mary( sim, num_samples, rho0, @@ -328,8 +288,8 @@ def main(): for i in range(1, len(emission_wavelength)): mfe_emission_max[i] = mary_emission[:, -1, i].min() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" plot_general( groundstate_wavelength[1:], np.real(mfe_groundstate_max)[1:], @@ -342,8 +302,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta I_F$" plot_general( emission_wavelength[1:], np.real(mfe_emission_max)[1:], @@ -356,8 +316,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" plot_general( wavelength, np.real(mfe_max), @@ -377,8 +337,8 @@ def main(): colors_time = plt.colormaps.get_cmap("viridis").resampled(len(time)).colors colors_field = plt.colormaps.get_cmap("viridis").resampled(len(Bs)).colors - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( groundstate_wavelength, @@ -386,15 +346,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{3}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -402,15 +362,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{4}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -426,8 +386,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( emission_wavelength, @@ -435,15 +395,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{6}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta I_F$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( Bs, @@ -451,15 +411,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{7}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta I_F$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta I_F$" for i in range(0, len(Bs), f): plot_general( time, @@ -475,8 +435,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( wavelength, @@ -484,15 +444,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{9}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -500,15 +460,15 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", colors=colors_time[i], ) path = __file__[:-3] + f"_{10}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -523,8 +483,8 @@ def main(): path = __file__[:-3] + f"_{11}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( groundstate_wavelength, @@ -532,14 +492,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{3}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -547,14 +507,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{4}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -569,8 +529,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( emission_wavelength, @@ -578,14 +538,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{6}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta I_F$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta I_F$" for i in range(0, len(time), n): plot_general( Bs, @@ -593,14 +553,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{7}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta I_F$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta I_F$" for i in range(0, len(Bs), f): plot_general( time, @@ -615,8 +575,8 @@ def main(): plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Wavelength / nm" - ylabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( wavelength, @@ -624,14 +584,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{9}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(time), n): plot_general( Bs, @@ -639,14 +599,14 @@ def main(): xlabel, ylabel, style="-", - label=f"{time[i] * factor: .0f} $\mu s$", + label=f"{time[i] * factor: .0f} $\\mu s$", ) path = __file__[:-3] + f"_{10}.png" plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "Time / $\mu s$" - ylabel = "$\Delta \Delta A$" + xlabel = r"Time / $\mu s$" + ylabel = r"$\Delta \Delta A$" for i in range(0, len(Bs), f): plot_general( time, @@ -719,9 +679,9 @@ def main(): plt.close() # 3D plots - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta \Delta A$" plot_3d_results( groundstate_wavelength, results["ts"], @@ -734,13 +694,13 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta \Delta A$" plot_3d_results( groundstate_wavelength, results["Bs"], - mary_groundstate[250, :, :], + mary_groundstate[len(mary_groundstate) // 4, :, :], xlabel, ylabel, zlabel, @@ -750,9 +710,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta I_F$" plot_3d_results( emission_wavelength, results["ts"], @@ -765,13 +725,13 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta I_F$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta I_F$" plot_3d_results( emission_wavelength, results["Bs"], - mary_emission[250, :, :], + mary_emission[len(mary_emission) // 4, :, :], xlabel, ylabel, zlabel, @@ -781,9 +741,9 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta \Delta A$" plot_3d_results( wavelength, results["ts"], @@ -796,13 +756,13 @@ def main(): plt.savefig(path, dpi=300) plt.close() - xlabel = "Wavelength / nm" - ylabel = "$B_0$ / mT" - zlabel = "$\Delta \Delta A$" + xlabel = r"Wavelength / nm" + ylabel = r"$B_0$ / mT" + zlabel = r"$\Delta \Delta A$" plot_3d_results( wavelength, results["Bs"], - mary[250, :, :], + mary[len(mary) // 4, :, :], xlabel, ylabel, zlabel, @@ -814,4 +774,7 @@ def main(): if __name__ == "__main__": - main() + if is_fast_run(): + main(Bmax=10, dB=2, tmax=10e-6, dt=1e-6) + else: + main() diff --git a/examples/kinetics_flavin_quencher.py b/examples/kinetics_flavin_quencher.py index 285a016e..19ee324d 100644 --- a/examples/kinetics_flavin_quencher.py +++ b/examples/kinetics_flavin_quencher.py @@ -161,8 +161,8 @@ def main(): plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) axs[1].set_xlabel("Time ($ns$)", size=14) - axs[0].set_ylabel("$\Delta A$", size=14) - axs[1].set_ylabel("$\Delta \Delta A$", size=14) + axs[0].set_ylabel(r"$\Delta A$", size=14) + axs[1].set_ylabel(r"$\Delta \Delta A$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) @@ -182,7 +182,7 @@ def main(): axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) axs[1].set_xlabel("Time ($ms$)", size=14) axs[0].set_ylabel("$F$", size=14) - axs[1].set_ylabel("$\Delta F$", size=14) + axs[1].set_ylabel(r"$\Delta F$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) diff --git a/examples/kinetics_simple.py b/examples/kinetics_simple.py index 89b17fda..e4c64b21 100644 --- a/examples/kinetics_simple.py +++ b/examples/kinetics_simple.py @@ -2,18 +2,10 @@ from pathlib import Path -import dot2tex -import graphviz import matplotlib.pyplot as plt import numpy as np -from radicalpy.classical import ( - Rate, - RateEquations, - latex_eqlist_to_align, - latexify, - reaction_scheme, -) +from radicalpy.classical import Rate, RateEquations def main(): @@ -46,8 +38,10 @@ def main(): initial_states = {Tp: 1 / 3, T0: 1 / 3, Tm: 1 / 3} time = np.linspace(0, 1e-6, 10000) - result_off = RateEquations(off, time, initial_states) - result_on = RateEquations(on, time, initial_states) + re_off = RateEquations(off) + re_on = RateEquations(on) + result_off = re_off.time_evolution(time, initial_states) + result_on = re_on.time_evolution(time, initial_states) keys = [S, Tp, T0, Tm] rp_field_off = result_off[keys] @@ -65,9 +59,9 @@ def main(): axs[1].plot(time * scale, rp_delta_delta_A, color="orange", linewidth=2) plt.xscale("linear") axs[0].legend([r"$F (B_0 = 0)$", r"$F (B_0 \neq 0)$"]) - axs[1].set_xlabel("Time ($\mu s$)", size=14) - axs[0].set_ylabel("$\Delta A$", size=14) - axs[1].set_ylabel("$\Delta \Delta A$", size=14) + axs[1].set_xlabel(r"Time ($\mu s$)", size=14) + axs[0].set_ylabel(r"$\Delta A$", size=14) + axs[1].set_ylabel(r"$\Delta \Delta A$", size=14) axs[0].tick_params(labelsize=14) axs[1].tick_params(labelsize=14) fig.set_size_inches(10, 5) @@ -77,7 +71,7 @@ def main(): # for eq in latexify(off): # print(eq) # print(latex_eqlist_to_align(latexify(off))) - reaction_scheme(__file__, on) + # reaction_scheme(__file__, on) if __name__ == "__main__": diff --git a/examples/mary.py b/examples/mary.py index fef1c8f5..e7253d73 100644 --- a/examples/mary.py +++ b/examples/mary.py @@ -5,21 +5,24 @@ import radicalpy as rp from radicalpy import relaxation +from radicalpy.experiments import mary from radicalpy.simulation import State +from radicalpy.utils import is_fast_run -def main(): +def main(Bmax=20, dB=0.5, tmax=10e-6, dt=10e-9): flavin = rp.simulation.Molecule.fromdb("flavin_anion", ["H25"]) # , "H27", "H29"]) trp = rp.simulation.Molecule.fromdb("tryptophan_cation", ["H1"]) # , "Hbeta1"]) sim = rp.simulation.LiouvilleSimulation([flavin, trp]) - time = np.arange(0, 10e-6, 10e-9) - Bs = np.arange(0, 20, 0.5) + time = np.arange(0, tmax, dt) + Bs = np.arange(0, Bmax, dB) krec = 1.1e7 kesc = 7e6 kSTD = 1e8 kr = 7e7 - results = sim.MARY( + results = mary( + sim, init_state=State.TRIPLET, obs_state=State.TRIPLET, time=time, @@ -62,4 +65,7 @@ def main(): if __name__ == "__main__": - main() + if is_fast_run(): + main(Bmax=10, dB=2, tmax=1e-6, dt=10e-8) + else: + main() diff --git a/examples/mie.py b/examples/mie.py index 6a74fb48..40e24d3d 100644 --- a/examples/mie.py +++ b/examples/mie.py @@ -4,6 +4,7 @@ import numpy as np import radicalpy as rp +from radicalpy.experiments import mary from radicalpy.simulation import State @@ -21,7 +22,8 @@ def main(): time = np.arange(0, 5e-6, 5e-9) Bs = np.arange(0, 30, 0.1) - results = sim.MARY( + results = mary( + sim, init_state=State.SINGLET, obs_state=State.SINGLET, time=time, @@ -36,7 +38,8 @@ def main(): HFE = results["HFE"] LFE = results["LFE"] - results2 = sim2.MARY( + results2 = mary( + sim2, init_state=State.SINGLET, obs_state=State.SINGLET, time=time, diff --git a/examples/mod_mary.py b/examples/mod_mary.py index 69d476c3..63cefcfa 100644 --- a/examples/mod_mary.py +++ b/examples/mod_mary.py @@ -4,6 +4,7 @@ import numpy as np from radicalpy.experiments import modulated_mary_brute_force +from radicalpy.utils import is_fast_run def main( @@ -100,4 +101,14 @@ def main( if __name__ == "__main__": - main() + if is_fast_run(): + main( + Bs=np.linspace(-5, 5, 100), + modulation_depths=[2, 1, 0.5], + modulation_frequency=3, + time_constant=0.3, + harmonics=[1, 2, 3, 4, 5], + lfe_magnitude=0.02, + ) + else: + main() diff --git a/examples/semiclassical_micelles.py b/examples/semiclassical_micelles.py index 9b816c27..5b733a6c 100644 --- a/examples/semiclassical_micelles.py +++ b/examples/semiclassical_micelles.py @@ -100,9 +100,9 @@ def main( plt.savefig(path, dpi=300, bbox_inches="tight") plt.close() - xlabel = "$B_0$ / mT" - ylabel = "Time / $\mu s$" - zlabel = "$\Delta \Delta A$" + xlabel = r"$B_0$ / mT" + ylabel = r"Time / $\mu s$" + zlabel = r"$\Delta \Delta A$" plot_3d_results( xdata=Bs, ydata=ts, diff --git a/radicalpy/classical.py b/radicalpy/classical.py index fb830a76..bc12f59a 100644 --- a/radicalpy/classical.py +++ b/radicalpy/classical.py @@ -126,7 +126,7 @@ def check_initial_states(self, initial_states: dict): def _construct_matrix(self): tmp = [ - (v.value, self.indices[i], self.indices[j]) + (v.value if isinstance(v, Rate) else v, self.indices[i], self.indices[j]) for i, d in self.rate_equations.items() for j, v in d.items() ] diff --git a/radicalpy/data.py b/radicalpy/data.py index 8fcc7768..42f85978 100644 --- a/radicalpy/data.py +++ b/radicalpy/data.py @@ -4,6 +4,7 @@ from typing import Iterator, Optional, Tuple import numpy as np +import scipy as sp from importlib_resources import files from importlib_resources.abc import Traversable from numpy.typing import NDArray @@ -232,13 +233,13 @@ def anisotropic(self) -> NDArray: return self._anisotropic @property - def isotropic(self) -> NDArray: + def isotropic(self) -> float: """Isotropic value. Returns: float: The isotropic HFC value. """ - return self._isotropic + return float(self._isotropic) class Nucleus: @@ -305,9 +306,57 @@ def fromisotope(cls, isotope: str, hfc: float | list[list[float]]): nucleus.name = isotope return nucleus + @property + def pauli(self): + """Generate Pauli matrices. + + Generates the Pauli matrices corresponding to a given multiplicity. + + Args: + + mult (int): The multiplicity of the element. + + Returns: + dict: + + A dictionary containing 6 `np.array` matrices of + shape `(mult, mult)`: + + - the unit operator `result["u"]`, + - raising operator `result["p"]`, + - lowering operator `result["m"]`, + - Pauli matrix for x axis `result["x"]`, + - Pauli matrix for y axis `result["y"]`, + - Pauli matrix for z axis `result["z"]`. + """ + mult = self.multiplicity + assert mult > 1 + result = {} + if mult == 2: + result["u"] = np.array([[1, 0], [0, 1]]) + result["p"] = np.array([[0, 1], [0, 0]]) + result["m"] = np.array([[0, 0], [1, 0]]) + result["x"] = 0.5 * np.array([[0.0, 1.0], [1.0, 0.0]]) + result["y"] = 0.5 * np.array([[0.0, -1.0j], [1.0j, 0.0]]) + result["z"] = 0.5 * np.array([[1.0, 0.0], [0.0, -1.0]]) + else: + spin = (mult - 1) / 2 + prjs = np.arange(mult - 1, -1, -1) - spin + + p_data = np.sqrt(spin * (spin + 1) - prjs * (prjs + 1)) + m_data = np.sqrt(spin * (spin + 1) - prjs * (prjs - 1)) + + result["u"] = np.eye(mult) + result["p"] = sp.sparse.spdiags(p_data, [1], mult, mult).toarray() + result["m"] = sp.sparse.spdiags(m_data, [-1], mult, mult).toarray() + result["x"] = 0.5 * (result["p"] + result["m"]) + result["y"] = -0.5 * 1j * (result["p"] - result["m"]) + result["z"] = sp.sparse.spdiags(prjs, 0, mult, mult).toarray() + return result + @property def gamma_mT(self): - """Return magnetogyric ratio, :math:`\gamma` (rad/s/mT).""" + r"""Return magnetogyric ratio, :math:`\gamma` (rad/s/mT).""" return self.magnetogyric_ratio * 0.001 @property @@ -605,7 +654,7 @@ def semiclassical_std(self) -> float: n.spin_quantum_number * (n.spin_quantum_number + 1) * n.hfc.isotropic**2 for n in self.nuclei ) - return np.sqrt(2) / tau + return float(np.sqrt(2) / tau) class Triplet(Molecule): diff --git a/radicalpy/estimations.py b/radicalpy/estimations.py index 9754cd01..4a3f7b7b 100644 --- a/radicalpy/estimations.py +++ b/radicalpy/estimations.py @@ -503,7 +503,7 @@ def k_ST_mixing(Bhalf: float) -> float: def k_electron_transfer( separation: float, driving_force: float = -1, reorganisation_energy: float = 1 ) -> float: - """Electron transfer rate. + r"""Electron transfer rate. The default values (when `-driving_force == reorganisation_energy`) return the maximum electron transfer rate. diff --git a/radicalpy/experiments.py b/radicalpy/experiments.py index f51e9d11..cc720edd 100644 --- a/radicalpy/experiments.py +++ b/radicalpy/experiments.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import itertools +from typing import Optional import numpy as np import scipy as sp @@ -17,6 +18,101 @@ from .utils import anisotropy_check, mary_lorentzian, modulated_signal, reference_signal +def mary_lfe_hfe( + init_state: State, + B: np.ndarray, + product_probability_seq: np.ndarray, + dt: float, + k: float, +) -> (np.ndarray, np.ndarray, np.ndarray): + """Calculate MARY, LFE, HFE.""" + MARY = np.sum(product_probability_seq, axis=1) * dt * k + idx = int(len(MARY) / 2) if B[0] != 0 else 0 + minmax = max if init_state == State.SINGLET else min + HFE = (MARY[-1] - MARY[idx]) / MARY[idx] * 100 + LFE = (minmax(MARY) - MARY[idx]) / MARY[idx] * 100 + MARY = (MARY - MARY[idx]) / MARY[idx] * 100 + return MARY, LFE, HFE + + +def mary_loop( + sim: HilbertSimulation, + init_state: State, + time: np.ndarray, + B: np.ndarray, + H_base: np.ndarray, + theta: Optional[float] = None, + phi: Optional[float] = None, + hfc_anisotropy: bool = False, +) -> np.ndarray: + """Generate density matrices (rhos) for MARY. + + Args: + + init_state (State): initial state. + + Returns: + np.ndarray: + + Density matrices. + + .. todo:: Write proper docs. + """ + H_zee = sim.convert(sim.zeeman_hamiltonian(1, theta, phi)) + shape = sim._get_rho_shape(H_zee.shape[0]) + rhos = np.zeros([len(B), len(time), *shape], dtype=complex) + for i, B0 in enumerate(tqdm(B)): + H = H_base + B0 * H_zee + H_sparse = sp.sparse.csc_matrix(H) + rhos[i] = sim.time_evolution(init_state, time, H_sparse) + return rhos + + +def mary( + sim: HilbertSimulation, + init_state: State, + obs_state: State, + time: np.ndarray, + B: np.ndarray, + D: float, + J: float, + kinetics: list[HilbertIncoherentProcessBase] = [], + relaxations: list[HilbertIncoherentProcessBase] = [], + theta: Optional[float] = None, + phi: Optional[float] = None, + hfc_anisotropy: bool = False, +) -> dict: + H = sim.total_hamiltonian(B0=0, D=D, J=J, hfc_anisotropy=hfc_anisotropy) + + sim.apply_liouville_hamiltonian_modifiers(H, kinetics + relaxations) + rhos = mary_loop(sim, init_state, time, B, H, theta=theta, phi=phi) + product_probabilities = sim.product_probability(obs_state, rhos) + + sim.apply_hilbert_kinetics(time, product_probabilities, kinetics) + k = kinetics[0].rate_constant if kinetics else 1.0 + product_yields, product_yield_sums = sim.product_yield( + product_probabilities, time, k + ) + + dt = time[1] - time[0] + MARY, LFE, HFE = mary_lfe_hfe(init_state, B, product_probabilities, dt, k) + rhos = sim._square_liouville_rhos(rhos) + + return dict( + time=time, + B=B, + theta=theta, + phi=phi, + rhos=rhos, + time_evolutions=product_probabilities, + product_yields=product_yields, + product_yield_sums=product_yield_sums, + MARY=MARY, + LFE=LFE, + HFE=HFE, + ) + + def modulated_mary_brute_force( Bs: np.ndarray, modulation_depths: list, @@ -143,7 +239,7 @@ def semiclassical_mary( return {"ts": ts, "Bs": Bs, "MARY": mary} -def semiclassical_kinetics_mary( +def kine_quantum_mary( sim: SemiclassicalSimulation, num_samples: int, init_state: ArrayLike, @@ -166,7 +262,7 @@ def semiclassical_kinetics_mary( for i, B0 in enumerate(tqdm(Bs)): Hz = sim.zeeman_hamiltonian(B0) - for j, HH in enumerate(HHs): + for HH in HHs: Ht = Hz + HH + HJ + HD L = sim.convert(Ht) sim.apply_liouville_hamiltonian_modifiers(L, relaxations) @@ -181,8 +277,8 @@ def semiclassical_kinetics_mary( loop_rho[k, :] = rho0 rho0 = propagator @ rho0 - loop_yield = (loop_yield + loop_rho) / num_samples - total_yield[:, :, i] = loop_yield + loop_yield = loop_yield + loop_rho + total_yield[:, :, i] = loop_yield / num_samples return {"ts": ts, "Bs": Bs, "yield": total_yield} diff --git a/radicalpy/plot.py b/radicalpy/plot.py index 4b82eaea..9922991a 100644 --- a/radicalpy/plot.py +++ b/radicalpy/plot.py @@ -95,7 +95,7 @@ def energy_levels(sim: HilbertSimulation, B: np.ndarray, J=0, D=0): H_base = sim.total_hamiltonian(0, J, D) H_zee = sim.zeeman_hamiltonian(1) - E = np.zeros([len(B), len(H_base)], dtype=np.complex_) + E = np.zeros([len(B), len(H_base)], dtype=np.complex128) for i, B0 in enumerate(B): H = H_base + B0 * H_zee @@ -225,7 +225,7 @@ def plot_bhalf_time(ts, bhalf_time, fit_error_time, style="ro", factor=1e6): color="k", linewidth=2, ) - plt.xlabel("Time / $\mu s$", size=24) + plt.xlabel(r"Time / $\mu s$", size=24) plt.ylabel("$B_{1/2}$ / mT", size=24) plt.tick_params(labelsize=18) plt.gcf().set_size_inches(5, 5) diff --git a/radicalpy/simulation.py b/radicalpy/simulation.py index 58ce49a2..4fc5f081 100644 --- a/radicalpy/simulation.py +++ b/radicalpy/simulation.py @@ -141,53 +141,6 @@ def ST_basis(self, M): C = np.kron(ST, np.eye(prod([n.multiplicity for n in self.nuclei]))) return C @ M @ C.T - @staticmethod - def pauli(mult: int): - """Generate Pauli matrices. - - Generates the Pauli matrices corresponding to a given multiplicity. - - Args: - - mult (int): The multiplicity of the element. - - Returns: - dict: - - A dictionary containing 6 `np.array` matrices of - shape `(mult, mult)`: - - - the unit operator `result["u"]`, - - raising operator `result["p"]`, - - lowering operator `result["m"]`, - - Pauli matrix for x axis `result["x"]`, - - Pauli matrix for y axis `result["y"]`, - - Pauli matrix for z axis `result["z"]`. - """ - assert mult > 1 - result = {} - if mult == 2: - result["u"] = np.array([[1, 0], [0, 1]]) - result["p"] = np.array([[0, 1], [0, 0]]) - result["m"] = np.array([[0, 0], [1, 0]]) - result["x"] = 0.5 * np.array([[0.0, 1.0], [1.0, 0.0]]) - result["y"] = 0.5 * np.array([[0.0, -1.0j], [1.0j, 0.0]]) - result["z"] = 0.5 * np.array([[1.0, 0.0], [0.0, -1.0]]) - else: - spin = (mult - 1) / 2 - prjs = np.arange(mult - 1, -1, -1) - spin - - p_data = np.sqrt(spin * (spin + 1) - prjs * (prjs + 1)) - m_data = np.sqrt(spin * (spin + 1) - prjs * (prjs - 1)) - - result["u"] = np.eye(mult) - result["p"] = sp.sparse.spdiags(p_data, [1], mult, mult).toarray() - result["m"] = sp.sparse.spdiags(m_data, [-1], mult, mult).toarray() - result["x"] = 0.5 * (result["p"] + result["m"]) - result["y"] = -0.5 * 1j * (result["p"] - result["m"]) - result["z"] = sp.sparse.spdiags(prjs, 0, mult, mult).toarray() - return result - def spin_operator(self, idx: int, axis: str) -> np.ndarray: """Construct the spin operator. @@ -211,7 +164,7 @@ def spin_operator(self, idx: int, axis: str) -> np.ndarray: assert 0 <= idx and idx < len(self.particles) assert axis in "xyzpmu" - sigma = self.pauli(self.particles[idx].multiplicity)[axis] + sigma = self.particles[idx].pauli[axis] before_size = prod(p.multiplicity for p in self.particles[:idx]) after_size = prod(p.multiplicity for p in self.particles[idx + 1 :]) spinop = np.kron(np.eye(before_size), sigma) @@ -717,7 +670,7 @@ def product_yield(product_probability, time, k): product_yield = k * sp.integrate.cumulative_trapezoid( product_probability, time, initial=0 ) - product_yield_sum = k * np.trapz(product_probability, dx=time[1]) + product_yield_sum = k * np.trapezoid(product_probability, dx=time[1]) return product_yield, product_yield_sum def apply_liouville_hamiltonian_modifiers(self, H, modifiers): @@ -730,55 +683,6 @@ def apply_hilbert_kinetics(time, product_probabilities, kinetics): for K in kinetics: # skip in liouville K.adjust_product_probabilities(product_probabilities, time) - def mary_loop( - self, - init_state: State, - time: np.ndarray, - B: np.ndarray, - H_base: np.ndarray, - theta: Optional[float] = None, - phi: Optional[float] = None, - hfc_anisotropy: bool = False, - ) -> np.ndarray: - """Generate density matrices (rhos) for MARY. - - Args: - - init_state (State): initial state. - - Returns: - np.ndarray: - - Density matrices. - - .. todo:: Write proper docs. - """ - H_zee = self.convert(self.zeeman_hamiltonian(1, theta, phi)) - shape = self._get_rho_shape(H_zee.shape[0]) - rhos = np.zeros([len(B), len(time), *shape], dtype=complex) - for i, B0 in enumerate(tqdm(B)): - H = H_base + B0 * H_zee - H_sparse = sp.sparse.csc_matrix(H) - rhos[i] = self.time_evolution(init_state, time, H_sparse) - return rhos - - @staticmethod - def mary_lfe_hfe( - init_state: State, - B: np.ndarray, - product_probability_seq: np.ndarray, - dt: float, - k: float, - ) -> (np.ndarray, np.ndarray, np.ndarray): - """Calculate MARY, LFE, HFE.""" - MARY = np.sum(product_probability_seq, axis=1) * dt * k - idx = int(len(MARY) / 2) if B[0] != 0 else 0 - minmax = max if init_state == State.SINGLET else min - HFE = (MARY[-1] - MARY[idx]) / MARY[idx] * 100 - LFE = (minmax(MARY) - MARY[idx]) / MARY[idx] * 100 - MARY = (MARY - MARY[idx]) / MARY[idx] * 100 - return MARY, LFE, HFE - @staticmethod def _square_liouville_rhos(rhos): return rhos @@ -787,50 +691,6 @@ def _square_liouville_rhos(rhos): def _get_rho_shape(dim): return dim, dim - def MARY( - self, - init_state: State, - obs_state: State, - time: np.ndarray, - B: np.ndarray, - D: float, - J: float, - kinetics: list[HilbertIncoherentProcessBase] = [], - relaxations: list[HilbertIncoherentProcessBase] = [], - theta: Optional[float] = None, - phi: Optional[float] = None, - hfc_anisotropy: bool = False, - ) -> dict: - H = self.total_hamiltonian(B0=0, D=D, J=J, hfc_anisotropy=hfc_anisotropy) - - self.apply_liouville_hamiltonian_modifiers(H, kinetics + relaxations) - rhos = self.mary_loop(init_state, time, B, H, theta=theta, phi=phi) - product_probabilities = self.product_probability(obs_state, rhos) - - self.apply_hilbert_kinetics(time, product_probabilities, kinetics) - k = kinetics[0].rate_constant if kinetics else 1.0 - product_yields, product_yield_sums = self.product_yield( - product_probabilities, time, k - ) - - dt = time[1] - time[0] - MARY, LFE, HFE = self.mary_lfe_hfe(init_state, B, product_probabilities, dt, k) - rhos = self._square_liouville_rhos(rhos) - - return dict( - time=time, - B=B, - theta=theta, - phi=phi, - rhos=rhos, - time_evolutions=product_probabilities, - product_yields=product_yields, - product_yield_sums=product_yield_sums, - MARY=MARY, - LFE=LFE, - HFE=HFE, - ) - @staticmethod def convert(H: np.ndarray) -> np.ndarray: return H @@ -867,14 +727,14 @@ def initial_density_matrix(self, state: State, H: np.ndarray) -> np.ndarray: @staticmethod def unitary_propagator(H: np.ndarray, dt: float) -> np.ndarray: - """Create unitary propagator (Hilbert space). + r"""Create unitary propagator (Hilbert space). Create unitary propagator matrices **U** and **U*** for time evolution of the density matrix in Hilbert space (for the spin Hamiltonian `H`). .. math:: - \mathbf{U} =& \exp( -i \hat{H} t ) \\\\ + \mathbf{U} =& \exp( -i \hat{H} t ) \\ \mathbf{U}^* =& \exp( +i \hat{H} t ) See also: `propagate` and `time_evolution`. @@ -996,7 +856,7 @@ def initial_density_matrix(self, state: State, H: np.ndarray) -> np.ndarray: @staticmethod def unitary_propagator(H, dt): - """Create unitary propagator (Liouville space). + r"""Create unitary propagator (Liouville space). Create unitary propagator matrix **U** for the time evolution of the density matrix in Liouville space (for the spin diff --git a/radicalpy/utils.py b/radicalpy/utils.py index e6c75c52..626eb00e 100644 --- a/radicalpy/utils.py +++ b/radicalpy/utils.py @@ -4,6 +4,7 @@ .. todo:: Add module docstring. """ +import argparse import sys from pathlib import Path from typing import Tuple @@ -24,7 +25,15 @@ def is_fast_run(): called (e.g., by setting fewer number of time steps etc.). """ - return len(sys.argv) == 2 and sys.argv[1] == "--fast" + parser = argparse.ArgumentParser() + parser.add_argument( + "--fast", + default=False, + action="store_true", + help="If set, the experiment should perform a reduced number of steps.", + ) + args = parser.parse_args() + return args.fast def Bhalf_fit( diff --git a/tests/radpy.py b/tests/radpy.py index 5b524714..0cb1fe17 100644 --- a/tests/radpy.py +++ b/tests/radpy.py @@ -948,7 +948,7 @@ def SingletYieldTwoSiteTimePropagation( nt = np.round((tmax / tstep + 1)).astype(int) rho0 = 0.5 * (P12SA + P12SB) propagator = expm(-L * tstep) - singletfraction = np.zeros(nt, dtype=np.complex_) + singletfraction = np.zeros(nt, dtype=np.complex128) for i in range(0, nt): t = i * tstep @@ -1007,7 +1007,7 @@ def SingletYieldTwoSiteTimePropagationApprox( rhoA = rhoB = P12S / 4 propagatorA = expm((-1j * HA - 0.5 * K[0]) * tstep) propagatorB = expm((-1j * HB - 0.5 * K[1]) * tstep) - singletfraction = np.zeros(nt, dtype=np.complex_) + singletfraction = np.zeros(nt, dtype=np.complex128) for i in range(0, nt): t = i * tstep @@ -1117,7 +1117,7 @@ def LinearEnergyLevelPlot2D(H, B, linecolour, title): def EnergyLevelPlot2D(spins, HFC, B_max, B_steps, J, D, xlabel, title): H = HamiltonianZeeman_RadicalPair(spins, B_max) B = np.linspace(0, B_max, B_steps) - E = np.zeros([B_steps, len(H)], dtype=np.complex_) + E = np.zeros([B_steps, len(H)], dtype=np.complex128) for i, B0 in enumerate(B): HZ = HamiltonianZeeman_RadicalPair(spins, B0) diff --git a/tests/test_simulation.py b/tests/test_simulation.py index 4ba2eb50..9265ab72 100644 --- a/tests/test_simulation.py +++ b/tests/test_simulation.py @@ -10,6 +10,7 @@ import radicalpy as rp from radicalpy import estimations, kinetics, relaxation +from radicalpy.experiments import mary from radicalpy.simulation import Basis # quick test: @@ -361,7 +362,8 @@ def test_mary(self): for obs_state in rp.simulation.State: if obs_state == rp.simulation.State.EQUILIBRIUM: continue - rslt = self.sim.MARY( + rslt = mary( + self.sim, init_state, obs_state, self.time, @@ -399,8 +401,8 @@ def test_ST_vs_Zeeman_basis(self): J=PARAMS["J"], kinetics=[kinetics.Exponential(k)], ) - rslt = self.sim.MARY(**kwargs) - strs = st_sim.MARY(**kwargs) + rslt = mary(self.sim, **kwargs) + strs = mary(st_sim, **kwargs) key = "time_evolutions" Bi = 1 @@ -421,7 +423,8 @@ def test_ST_vs_Zeeman_basis(self): plt.show() def test_hyperfine_3d(self): - results = self.sim.MARY( + results = mary( + self.sim, rp.simulation.State.SINGLET, rp.simulation.State.TRIPLET, self.time, @@ -532,7 +535,8 @@ def test_kinetics(self): J=0, ) k = 1e6 - results_haberkorn = self.sim.MARY( + results_haberkorn = mary( + self.sim, kinetics=[ kinetics.Haberkorn(k, rp.simulation.State.TRIPLET), kinetics.Haberkorn(k, rp.simulation.State.SINGLET), @@ -540,7 +544,8 @@ def test_kinetics(self): ], **kwargs, ) - results_jones_hore = self.sim.MARY( + results_jones_hore = mary( + self.sim, kinetics=[ kinetics.JonesHore(k, k), kinetics.Exponential(k), @@ -565,7 +570,8 @@ def test_relaxation(self): J=0, ) k = 1e6 - results = self.sim.MARY( + results = mary( + self.sim, kinetics=[], relaxations=[ # relaxation.SingletTripletDephasing( k),