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Lines changed: 7755 additions & 640 deletions

‎Examples/ThermodynamicsOfGold/plot_dispersion.py‎

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import cellconstructor as CC, cellconstructor.Phonons, cellconstructor.ForceTensor
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import ase, ase.dft.kpoints
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import numpy as np
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import matplotlib.pyplot as plt
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import matplotlib.cm as cm
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import matplotlib.colors as colors
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import sys, os
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NQIRR = 13
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#CMAP = "Spectral_r"
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PATH = "GXWXKGL"
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N_POINTS = 1000
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SPECIAL_POINTS = {"G": [0,0,0],
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"X": [0, .5, .5],
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"L": [.5, .5, .5],
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"W": [.25, .75, .5],
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"K": [3/8., 3/4., 3/8.]}
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# Load the harmonic and sscha phonons
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harmonic_dyn = CC.Phonons.Phonons('harmonic_dyn', NQIRR)
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sscha_dyn = CC.Phonons.Phonons('sscha_T300_dyn', NQIRR)
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# Get the band path
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qpath, data = CC.Methods.get_bandpath(harmonic_dyn.structure.unit_cell,
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PATH,
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SPECIAL_POINTS,
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N_POINTS)
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xaxis, xticks, xlabels = data # Info to plot correclty the x axis
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# Get the phonon dispersion along the path
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harmonic_dispersion = CC.ForceTensor.get_phonons_in_qpath(harmonic_dyn, qpath)
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sscha_dispersion = CC.ForceTensor.get_phonons_in_qpath(sscha_dyn, qpath)
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nmodes = harmonic_dyn.structure.N_atoms * 3
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# Plot the two dispersions
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plt.figure(dpi = 150)
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ax = plt.gca()
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for i in range(nmodes):
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lbl=None
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lblsscha = None
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if i == 0:
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lbl = 'Harmonic'
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lblsscha = 'SSCHA'
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ax.plot(xaxis, harmonic_dispersion[:,i], color = 'k', ls = 'dashed', label = lbl)
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ax.plot(xaxis, sscha_dispersion[:,i], color = 'r', label = lblsscha)
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# Plot vertical lines for each high symmetry points
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for x in xticks:
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ax.axvline(x, 0, 1, color = "k", lw = 0.4)
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ax.axhline(0, 0, 1, color = 'k', ls = ':', lw = 0.4)
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ax.legend()
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# Set the x labels to the high symmetry points
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ax.set_xticks(xticks)
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ax.set_xticklabels(xlabels)
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ax.set_xlabel("Q path")
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ax.set_ylabel("Phonons [cm-1]")
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plt.tight_layout()
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plt.savefig("dispersion.png")
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plt.show()
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‎Examples/ThermodynamicsOfGold/plot_thermal_expansion.py‎

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# Prepare the figure and plot the V(T) from the sscha data
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plt.figure(dpi = 150)
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plt.scatter(temperatures, volumes, label = "SSCHA data")
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plt.scatter(temperatures, volumes, label = "SSCHA data", color = 'r')
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# Fit the data with a quadratic curve
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def parabola(x, a, b, c):
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# Plot the fit
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_t_ = np.linspace(np.min(temperatures), np.max(temperatures), 1000)
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plt.plot(_t_, parabola(_t_, *popt), label = "Fit")
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plt.plot(_t_, parabola(_t_, *popt), label = "Fit", color = 'k', zorder = 0)
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# Adjust the plot adding labels, legend, and saving in eps
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plt.xlabel("Temperature [K]")
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plt.ylabel(r"Volume [$\AA^3$]")
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plt.legend()
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plt.tight_layout()
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plt.savefig("thermal_expansion.eps")
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plt.savefig("thermal_expansion.png")
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plt.show()

‎Examples/sscha_and_dft/Au_ONCV_PBE-1.0.oncvpsp.upf‎

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‎Examples/sscha_and_dft/nvt_local.py‎

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# Import the sscha code
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import sscha, sscha.Ensemble, sscha.SchaMinimizer, sscha.Relax, sscha.Utilities
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# Import the cellconstructor library to manage phonons
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import cellconstructor as CC, cellconstructor.Phonons
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import cellconstructor.Structure, cellconstructor.calculators
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# Import the DFT calculator
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import cellconstructor.calculators
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# Import numerical and general pourpouse libraries
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import numpy as np, matplotlib.pyplot as plt
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import sys, os
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# Initialize the DFT (Quantum Espresso) calculator for gold
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# The input data is a dictionary that encodes the pw.x input file namelist
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input_data = {
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'control' : {
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# Avoid writing wavefunctions on the disk
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'disk_io' : 'None',
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# Where to find the pseudopotential
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'pseudo_dir' : '.'
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},
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'system' : {
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# Specify the basis set cutoffs
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'ecutwfc' : 45, # Cutoff for wavefunction
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'ecutrho' : 45*4, # Cutoff for the density
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# Information about smearing (it is a metal)
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'occupations' : 'smearing',
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'smearing' : 'mv',
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'degauss' : 0.03
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},
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'electrons' : {
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'conv_thr' : 1e-8
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}
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}
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# the pseudopotential for each chemical element
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# In this case just Gold
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pseudopotentials = {'Au' : 'Au_ONCV_PBE-1.0.oncvpsp.upf'}
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# the kpoints mesh and the offset
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kpts = (1,1,1)
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koffset = (1,1,1)
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command = 'mpirun -np 4 pw.x -npool 1 -i PREFIX.pwi > PREFIX.pwo'
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# Prepare the quantum espresso calculator
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calculator = CC.calculators.Espresso(input_data,
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pseudopotentials,
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command = command,
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kpts = kpts,
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koffset = koffset)
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TEMPERATURE = 300
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N_CONFIGS = 50
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MAX_ITERATIONS = 20
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START_DYN = 'start_dyn'
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NQIRR = 13
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# Let us load the starting dynamical matrix
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gold_dyn = CC.Phonons.Phonons(START_DYN, NQIRR)
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# Initialize the random ionic ensemble
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ensemble = sscha.Ensemble.Ensemble(gold_dyn, TEMPERATURE)
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# Initialize the free energy minimizer
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minim = sscha.SchaMinimizer.SSCHA_Minimizer(ensemble)
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minim.set_minimization_step(0.01)
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# Initialize the NVT simulation
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relax = sscha.Relax.SSCHA(minim, calculator, N_configs = N_CONFIGS,
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max_pop = MAX_ITERATIONS)
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# Define the I/O operations
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# To save info about the free energy minimization after each step
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ioinfo = sscha.Utilities.IOInfo()
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ioinfo.SetupSaving("minim_info")
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relax.setup_custom_functions(custom_function_post = ioinfo.CFP_SaveAll)
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# Run the NVT simulation (save the stress to compute the pressure)
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relax.relax(get_stress = True)
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# If instead you want to run a NPT simulation, use
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# The target pressure is given in GPa.
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#relax.vc_relax(target_press = 0)
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# You can also run a mixed simulation (NVT) but with variable lattice parameters
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#relax.vc_relax(fix_volume = True)
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# Now we can save the final dynamical matrix
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# And print in stdout the info about the minimization
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relax.minim.finalize()
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relax.minim.dyn.save_qe("sscha_T{}_dyn".format(TEMPERATURE))
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‎Examples/sscha_and_dft/start_dyn1‎

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Dynamical matrix file
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File generated with the CellConstructor by Lorenzo Monacelli
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1 1 0 1.8897259890000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Basis vectors
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2.9495460300000000 0.0000000000000000 0.0000000000000000
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1.4747730150000002 2.5543817916115379 0.0000000000000000
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1.4747730150000002 0.8514605972038461 2.4082942487839478
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1 'Au ' 179524.0513667391205672
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1 1 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.000000000000 0.000000000000 0.000000000000 )
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1 1
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0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Diagonalizing the dynamical matrix
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q = ( 0.000000000000 0.000000000000 0.000000000000 )
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***************************************************************************
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freq ( 1) = 0.00000000 [THz] = 0.00000000 [cm-1]
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( 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 )
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freq ( 2) = 0.00000000 [THz] = 0.00000000 [cm-1]
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( 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 )
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freq ( 3) = 0.00000000 [THz] = 0.00000000 [cm-1]
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( 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 )
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***************************************************************************

‎Examples/sscha_and_dft/start_dyn10‎

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Dynamical matrix file
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File generated with the CellConstructor by Lorenzo Monacelli
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1 1 0 1.8897259890000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Basis vectors
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2.9495460300000000 0.0000000000000000 0.0000000000000000
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1.4747730150000002 2.5543817916115379 0.0000000000000000
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1.4747730150000002 0.8514605972038461 2.4082942487839478
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1 'Au ' 179524.0513667391205672
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1 1 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.169517612173 0.097871039020 0.069205275373 )
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1 1
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0.0751622289125264 0.0000000000000000 0.0281657539230274 0.0000000000000000 0.0209028729909581 0.0000000000000000
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0.0281657539230274 0.0000000000000000 0.0426392176937492 0.0000000000000000 0.0120682793481662 0.0000000000000000
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0.0209028729909581 0.0000000000000000 0.0120682793481662 0.0000000000000000 0.0353854466021494 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.169517612173 -0.097871039020 -0.069205275373 )
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1 1
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0.0751622289125264 0.0000000000000000 -0.0281657539230274 0.0000000000000000 -0.0209028729909581 0.0000000000000000
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-0.0281657539230274 0.0000000000000000 0.0426392176937492 0.0000000000000000 0.0120682793481662 0.0000000000000000
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-0.0209028729909581 0.0000000000000000 0.0120682793481662 0.0000000000000000 0.0353854466021494 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.000000000000 -0.195742078041 0.069205275373 )
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1 1
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0.0263777120843606 0.0000000000000000 -0.0000000000000000 0.0000000000000000 -0.0000000000000000 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 0.0914237345219151 0.0000000000000000 -0.0241365586963325 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 -0.0241365586963325 0.0000000000000000 0.0353854466021494 0.0000000000000000
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Diagonalizing the dynamical matrix
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q = ( 0.169517612173 0.097871039020 0.069205275373 )
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***************************************************************************
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freq ( 1) = 1.26105061 [THz] = 42.06411449 [cm-1]
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( -0.500000 0.000000 0.866025 0.000000 0.000000 0.000000 )
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freq ( 2) = 1.26213016 [THz] = 42.10012438 [cm-1]
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( -0.301466 0.000000 -0.174051 0.000000 0.937456 0.000000 )
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freq ( 3) = 2.46009088 [THz] = 82.05978700 [cm-1]
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( -0.811861 0.000000 -0.468728 0.000000 -0.348103 0.000000 )
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***************************************************************************

‎Examples/sscha_and_dft/start_dyn11‎

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Dynamical matrix file
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File generated with the CellConstructor by Lorenzo Monacelli
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1 1 0 1.8897259890000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Basis vectors
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2.9495460300000000 0.0000000000000000 0.0000000000000000
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1.4747730150000002 2.5543817916115379 0.0000000000000000
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1.4747730150000002 0.8514605972038461 2.4082942487839478
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1 'Au ' 179524.0513667391205672
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1 1 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( -0.169517612173 -0.097871039020 0.138410550746 )
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1 1
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0.0817675664305969 0.0000000000000000 0.0142701466013224 0.0000000000000000 -0.0183567296612535 0.0000000000000000
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0.0142701466013224 0.0000000000000000 0.0652898204672991 0.0000000000000000 -0.0105982628113659 0.0000000000000000
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-0.0183567296612535 0.0000000000000000 -0.0105982628113659 0.0000000000000000 0.0755111590679396 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( -0.169517612173 0.097871039020 -0.138410550746 )
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1 1
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0.0817675664305969 0.0000000000000000 -0.0142701466013224 0.0000000000000000 0.0183567296612535 0.0000000000000000
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-0.0142701466013224 0.0000000000000000 0.0652898204672991 0.0000000000000000 -0.0105982628113659 0.0000000000000000
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0.0183567296612535 0.0000000000000000 -0.0105982628113659 0.0000000000000000 0.0755111590679395 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.000000000000 0.195742078041 0.138410550746 )
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1 1
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0.0570509474856502 0.0000000000000000 -0.0000000000000000 0.0000000000000000 -0.0000000000000000 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 0.0900064394122459 0.0000000000000000 0.0211965256227318 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 0.0211965256227317 0.0000000000000000 0.0755111590679396 0.0000000000000000
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Diagonalizing the dynamical matrix
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q = ( -0.169517612173 -0.097871039020 0.138410550746 )
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***************************************************************************
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freq ( 1) = 1.85457920 [THz] = 61.86209446 [cm-1]
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( 0.500000 0.000000 -0.866025 0.000000 0.000000 0.000000 )
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freq ( 2) = 1.90756503 [THz] = 63.62951127 [cm-1]
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( 0.503661 0.000000 0.290789 0.000000 0.813491 0.000000 )
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freq ( 3) = 2.51790636 [THz] = 83.98830356 [cm-1]
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( -0.704504 0.000000 -0.406746 0.000000 0.581577 0.000000 )
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***************************************************************************

‎Examples/sscha_and_dft/start_dyn12‎

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Dynamical matrix file
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File generated with the CellConstructor by Lorenzo Monacelli
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1 1 0 1.8897259890000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Basis vectors
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2.9495460300000000 0.0000000000000000 0.0000000000000000
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1.4747730150000002 2.5543817916115379 0.0000000000000000
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1.4747730150000002 0.8514605972038461 2.4082942487839478
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1 'Au ' 179524.0513667391205672
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1 1 0.0000000000000000 0.0000000000000000 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.000000000000 0.000000000000 0.103807913060 )
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1 1
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0.0137058449993487 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 0.0137058449993487 0.0000000000000000 -0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 -0.0000000000000000 0.0000000000000000 0.0888425361262248 0.0000000000000000
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Dynamical Matrix in cartesian axes
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q = ( 0.000000000000 0.000000000000 -0.103807913060 )
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1 1
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0.0137058449993487 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000
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-0.0000000000000000 0.0000000000000000 0.0137058449993487 0.0000000000000000 -0.0000000000000000 0.0000000000000000
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0.0000000000000000 0.0000000000000000 -0.0000000000000000 0.0000000000000000 0.0888425361262248 0.0000000000000000
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Diagonalizing the dynamical matrix
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q = ( 0.000000000000 0.000000000000 0.103807913060 )
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***************************************************************************
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freq ( 1) = 0.90900624 [THz] = 30.32117990 [cm-1]
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( 0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 )
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freq ( 2) = 0.90900624 [THz] = 30.32117990 [cm-1]
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( 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 )
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freq ( 3) = 2.31432543 [THz] = 77.19757585 [cm-1]
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( 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 )
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***************************************************************************

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