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Merged
amcadmus merged 2 commits into from
Nov 28, 2020
Merged

add the replace method to system #120

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5e6da87
add the replace method to system, using for randomly substitute atom …
felix5572 Nov 27, 2020
b293324
add documents for replace() method
felix5572 Nov 27, 2020
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10 changes: 10 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -197,3 +197,13 @@ perturbed_system = dpdata.System('./POSCAR').perturb(pert_num=3,
atom_pert_style='normal')
print(perturbed_system.data)
```

## replace
By the following example, Random 8 Hf atoms in the system will be replaced by Zr atoms with the atom postion unchanged.
```python
s=dpdata.System('tests/poscars/POSCAR.P42nmc',fmt='vasp/poscar')
s.replace('Hf', 'Zr', 8)
s.to_vasp_poscar('POSCAR.P42nmc.replace')
```


34 changes: 34 additions & 0 deletions dpdata/system.py
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Expand Up @@ -799,6 +799,40 @@ def replicate(self, ncopy):
tmp.data['coords'] = np.reshape(np.transpose(tmp.data['coords'], [3,4,0,1,2,5]), (nframes, -1 , 3))
return tmp

def replace(self, initial_atom_type, end_atom_type, replace_num):
if type(self) is not dpdata.System:
raise RuntimeError('Must use method replace() of the instance of class dpdata.System')
if type(replace_num) is not int:
raise ValueError("replace_num must be a integer. Now is {replace_num}".format(replace_num=replace_num))
if replace_num <= 0:
raise ValueError("replace_num must be larger than 0.Now is {replace_num}".format(replace_num=replace_num))

try:
initial_atom_index = self.data['atom_names'].index(initial_atom_type)
except ValueError as e:
raise ValueError("atom_type {initial_atom_type} not in {atom_names}"
.format(initial_atom_type=initial_atom_type, atom_names=self.data['atom_names']))
max_replace_num = self.data['atom_numbs'][initial_atom_index]

if replace_num > max_replace_num:
raise RuntimeError("not enough {initial_atom_type} atom, only {max_replace_num} available, less than {replace_num}.Please check."
.format(initial_atom_type=initial_atom_type,max_replace_num=max_replace_num, replace_num=replace_num))

may_replace_indices = [i for i, x in enumerate(self.data['atom_types']) if x == initial_atom_index]
to_replace_indices = np.random.choice(may_replace_indices, size=replace_num, replace=False)

if end_atom_type not in self.data['atom_names']:
self.data['atom_names'].append(end_atom_type)
self.data['atom_numbs'].append(0)

end_atom_index = self.data['atom_names'].index(end_atom_type)
for ii in to_replace_indices:
self.data['atom_types'][ii] = end_atom_index
self.data['atom_numbs'][initial_atom_index] -= replace_num
self.data['atom_numbs'][end_atom_index] += replace_num
self.sort_atom_types()


def perturb(self,
pert_num,
cell_pert_fraction,
Expand Down
104 changes: 104 additions & 0 deletions tests/poscars/POSCAR.P42nmc
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104 changes: 104 additions & 0 deletions tests/poscars/POSCAR.P42nmc.replace
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Hf24 O64 Zr8
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40 changes: 40 additions & 0 deletions tests/test_replace.py
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import os
import numpy as np
import unittest
from context import dpdata
from comp_sys import CompSys, IsPBC

from unittest.mock import Mock
from unittest.mock import patch, MagicMock


class ConstGenerator(object):
def __init__(self):
self.choice_generator = self.get_choice_generator()
def choice(self, a, size=None, replace=True, p=None):
return next(self.choice_generator)

@staticmethod
def get_choice_generator():
yield np.asarray([20, 6, 7, 22, 29, 2, 23, 10])

class TestReplace(unittest.TestCase, CompSys, IsPBC):
@patch('numpy.random')
def setUp(self, random_mock):
random_mock.choice = ConstGenerator().choice
self.system_1 = dpdata.System('poscars/POSCAR.P42nmc',fmt='vasp/poscar')
self.system_1.replace('Hf', 'Zr', 8)
# print(self.system_1.data)
self.system_2 = dpdata.System('poscars/POSCAR.P42nmc.replace',fmt='vasp/poscar')
# print(self.system_2.data)
self.places = 6

# class TestReplicate123_not_change_origin(unittest.TestCase, CompSys, IsPBC):
# def setUp (self) :
# self.system_1 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar')
# self.system_1.replicate((1,2,3,))
# self.system_2 = dpdata.System('poscars/POSCAR.SiC',fmt='vasp/poscar')
# self.places = 6

if __name__ == '__main__':
unittest.main()