corrected name npt -> nvt, adjusted friction coef (dff2c792) · Commits · Leon Pyka / md_practical_nanotech

README.md

+3 −2

Original line number	Diff line number	Diff line
		@@ -37,6 +37,7 @@ The data is written to `data_elastic_constants`. Plot the data and fit a 2nd ord
		## Running NVE/NPT simulations
		Run using:
		`python3 deform_cnt_nve.py`
		(make sure to run this one first, the second script is relying on the minimized structure generated in the first script)
		and
		`python3 deform_cnt_npt.py`
		the results are written to the folders `data_cnt_sim/nve_deform/cnt_nve_data.csv` and `data_cnt_sim/npt_deform/cnt_npt_data.csv` accordingly.
		`python3 deform_cnt_nvt.py`
		the results are written to the folders `data_cnt_sim/nve_deform/cnt_nve_data.csv` and `data_cnt_sim/nvt_deform/cnt_nvt_data.csv` accordingly.

+3 −3

Original line number	Diff line number	Diff line
		@@ -101,15 +101,15 @@ if __name__ == '__main__':
		cnt = traj_relax_read[-1]
		cnt.calc = BrennerPotential() #when reading from trajectory the potential gets lost... why? no idea

		dyn = Langevin(cnt, timestep=timestep*units.fs,temperature_K=300, friction=0.1/units.fs)
		dyn = Langevin(cnt, timestep=timestep*units.fs,temperature_K=300, friction=0.01/units.fs)
		data = {'time':[],'temperature':[], 'epot':[],'ekin':[], 'etot': []}
		cnt_array_original = cnt.cell[:]
		run_simulation(loop_number, step_number, timestep, eps, start_deform)
		with open(f'{data_directory}data.json', 'r') as fp:
		data = json.load(fp)
		df = pd.DataFrame.from_dict(data)
		df.to_csv(f'{data_directory}cnt_npt_data.csv')
		print(f'Saving data to {data_directory}cnt_npt_data.csv')
		df.to_csv(f'{data_directory}cnt_nvt_data.csv')
		print(f'Saving data to {data_directory}cnt_nvt_data.csv')
		print('done')