Replacing asap3 potentials with ASE native option (c3da9bfc) · Commits · Leon Pyka / md_practical_nanotech

deform_cnt_nve.py

+4 −3

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ import matplotlib.pyplot as plt
		import json
		from scipy.optimize import curve_fit, root_scalar
		from ase.calculators.emt import EMT
		from asap3 import BrennerPotential
		#from asap3 import BrennerPotential
		from ase.build import nanotube
		from ase.io import Trajectory, read, write, gromacs, extxyz
		from ase.optimize import FIRE
		@@ -20,7 +20,8 @@ plot_dir = 'data_CNT_sim/nve_plots/'
		directory = 'data_CNT_sim/'
		data_directory = 'data_CNT_sim/nve_deform/'
		cnt = nanotube(5, 5, symbol='C', length=3, bond=1.42)
		cnt.calc = BrennerPotential()
		#cnt.calc = BrennerPotential()
		cnt.calc = EMT()
		#adjust cell and pbc (for visualization)
		cnt.cell[:] = cnt.cell[:] + np.array([[10, 0, 0],[0, 10, 0],[0, 0, 0]])
		cnt.set_pbc([0,0,1])
		@@ -108,7 +109,7 @@ if __name__ == '__main__':
		relax_structure(cnt)
		traj_relax_read = Trajectory(f'{directory}relaxed_cell.traj', 'r')
		cnt_rel = traj_relax_read[-1]
		cnt_rel.calc = BrennerPotential()
		cnt_rel.calc = EMT()

		dyn = VelocityVerlet(cnt_rel, timestep=timestep*units.fs)
		data = {'time':[],'temperature':[], 'epot':[],'ekin':[], 'etot': []}

+3 −3

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ import matplotlib.pyplot as plt
		import json
		from scipy.optimize import curve_fit, root_scalar
		from ase.calculators.emt import EMT
		from asap3 import BrennerPotential
		#from asap3 import BrennerPotential
		from ase.build import nanotube
		from ase.io import Trajectory, read, write, gromacs
		from ase.optimize import FIRE
		@@ -20,7 +20,7 @@ plot_dir = 'data_CNT_sim/nvt_plots/'
		directory = 'data_CNT_sim/'
		data_directory = 'data_CNT_sim/nvt_deform/'
		cnt = nanotube(5, 5, symbol='C', length=3, bond=1.42)
		cnt.calc = BrennerPotential()
		cnt.calc = EMT()
		#adjust cell and pbc (for visualization)
		cnt.cell[:] = cnt.cell[:] + np.array([[10, 0, 0],[0, 10, 0],[0, 0, 0]])
		cnt.set_pbc([0,0,1])
		@@ -99,7 +99,7 @@ if __name__ == '__main__':
		# to save time we get the relaxed stucture from the nve sim
		traj_relax_read = Trajectory(f'{directory}relaxed_cell.traj', 'r')
		cnt = traj_relax_read[-1]
		cnt.calc = BrennerPotential() #when reading from trajectory the potential gets lost... why? no idea
		cnt.calc = EMT() #when reading from trajectory the potential gets lost... why? no idea

		dyn = Langevin(cnt, timestep=timestep*units.fs,temperature_K=300, friction=0.01/units.fs)
		data = {'time':[],'temperature':[], 'epot':[],'ekin':[], 'etot': []}

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,8 +2,8 @@ import numpy as np
		import matplotlib.pyplot as plt
		import json
		from scipy.optimize import curve_fit, root_scalar
		#from ase.calculators.emt import EMT
		from asap3 import EMT, EMTRasmussenParameters, EMT2013
		from ase.calculators.emt import EMT
		#from asap3 import EMT, EMTRasmussenParameters, EMT2013
		from ase.lattice.cubic import FaceCenteredCubic, BodyCenteredCubic, SimpleCubic
		from ase.io import Trajectory, read
		from ase.optimize import FIRE

+1 −1