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dimonaks
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dimonaks
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Доработай Тох плиз по комментам моим
| @@ -717,6 +715,11 @@ def actualize_set(self, curset = None, params = None): | |||
| if hasattr(self.init, 'magmom') and hasattr(self.init.magmom, '__iter__') and not None in self.init.magmom and bool(self.init.magmom): | |||
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Тут дичь получилась, два раза один и тот же код вставить предлагает
| plt.show() | ||
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| def plot_energy_total_step(self,): |
| return | ||
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| def plot_energy_total_step2(self,): | ||
| # print(self.maxforce) |
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Добавить описание. Подумать над названием, сейчас непонятно в чем разница между функциями из названия
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| def read_oszicar(path_to_file): | ||
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Добавить описание, перевести комменты
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| return child | ||
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| return st | ||
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| def exchange_axes_with_atoms(self, i1_r, i2_r): | ||
| """ |
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дописать описание, что значит rotate atoms?
| return st | ||
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| def remove_atoms_randomly(self, el, n_at2remove, clear_magmom = 1): | ||
| """ |
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Привести описание в соответствие с нашим форматом. Добавить автора метода
| from pymatgen.analysis.wulff import WulffShape | ||
| WS = WulffShape(lat, miller_list, e_surf_list) | ||
| # print(dir(WS)) | ||
| print(WS.area_fraction_dict) |
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использовать printlog(), добавить вывод что это? Иначе потом не найти этот print
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| if 'iconst_str' in params or ('LBLUEOUT' in cl.set.vasp_params and cl.set.vasp_params['LBLUEOUT'] == 1): #copy iconst file | ||
| if 'iconst_str' in params: | ||
| # with tempfile.NamedTemporaryFile('w', delete=False) as tmp: |
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убрать лишние закомменченные строки
| self.etotal = float(line.split()[4]) # Total energy in MD simulation | ||
| self.list_etotal.append(self.etotal) | ||
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| if "kinetic energy EKIN =" in line: |
| # print(a) | ||
| nebmaker('POSCAR1','POSCAR2', images) | ||
| printlog('Starting nebmaker ...', imp = 'y') | ||
| nebmaker('POSCAR1','POSCAR2', images, idpp = False) |
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Не надо выключять полностью , давай добавим параметр для add_neb
2 participants
Functionality for constrained AIMD calculations:
- set VASP params
- additional file ICONST pushing to server. Constrains should be given as list of strings under parameter 'iconst_str' = ['R 98 172 0\n', 'R 98 202 0\n'] for example
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plot_energy_total_step2() - method for Calculation() allowing to plot E_tot(t) dependence for AIMD calculations
remove_atoms_randomly(self, el, n_at2remove, clear_magmom = 1) - method for Calculation()
Some minor changes