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Merge pull request #67 from felix5572/devel
replicate and disturb and its document,unittest
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‎README.md

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@@ -152,3 +152,20 @@ Frame selection can be implemented by
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dpdata.LabeledSystem('OUTCAR').sub_system([0,-1]).to_deepmd_raw('dpmd_raw')
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```
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by which only the first and last frames are dumped to `dpmd_raw`.
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## replicate
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dpdata will create a super cell of the current atom configuration.
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```python
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dpdata.System('./POSCAR').replicate((1,2,3,) )
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```
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tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.
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## perturb
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By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
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```python
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perturbed_system = dpdata.System('./POSCAR').perturb(pert_num=3,
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cell_pert_fraction=0.05,
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atom_pert_distance=0.6,
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atom_pert_style='normal')
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print(perturbed_system.data)
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```

‎dpdata/system.py

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@@ -579,6 +579,142 @@ def add_atom_names(self, atom_names):
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self.data['atom_names'].extend(atom_names)
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self.data['atom_numbs'].extend([0 for _ in atom_names])
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def replicate(self, ncopy):
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"""
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Replicate the each frame in the system in 3 dimensions.
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Each frame in the system will become a supercell.
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Parameters
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----------
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ncopy :
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list: [4,2,3]
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or tuple: (4,2,3,)
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make `ncopy[0]` copys in x dimensions,
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make `ncopy[1]` copys in y dimensions,
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make `ncopy[2]` copys in z dimensions.
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Returns
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-------
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tmp : System
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The system after replication.
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"""
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if len(ncopy) !=3:
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raise RuntimeError('ncopy must be a list or tuple with 3 int')
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for ii in ncopy:
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if type(ii) is not int:
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raise RuntimeError('ncopy must be a list or tuple must with 3 int')
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tmp = System()
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nframes = self.get_nframes()
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data = self.data
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tmp.data['atom_names'] = list(np.copy(data['atom_names']))
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tmp.data['atom_numbs'] = list(np.array(np.copy(data['atom_numbs'])) * np.prod(ncopy))
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tmp.data['atom_types'] = np.sort(np.tile(np.copy(data['atom_types']),np.prod(ncopy)))
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tmp.data['cells'] = np.copy(data['cells'])
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for ii in range(3):
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tmp.data['cells'][:,ii,:] *= ncopy[ii]
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tmp.data['coords'] = np.tile(np.copy(data['coords']),tuple(ncopy)+(1,1,1))
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for xx in range(ncopy[0]):
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for yy in range(ncopy[1]):
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for zz in range(ncopy[2]):
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tmp.data['coords'][xx,yy,zz,:,:,:] += xx * np.reshape(data['cells'][:,0,:], [-1,1,3])\
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+ yy * np.reshape(data['cells'][:,1,:], [-1,1,3])\
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+ zz * np.reshape(data['cells'][:,2,:], [-1,1,3])
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tmp.data['coords'] = np.reshape(np.transpose(tmp.data['coords'], [3,4,0,1,2,5]), (nframes, -1 , 3))
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return tmp
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def perturb(self,
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pert_num,
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cell_pert_fraction,
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atom_pert_distance,
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atom_pert_style='normal'):
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"""
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Perturb each frame in the system randomly.
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The cell will be deformed randomly, and atoms will be displaced by a random distance in random direction.
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Parameters
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----------
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pert_num : int
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Each frame in the system will make `pert_num` copies,
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and all the copies will be perturbed.
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That means the system to be returned will contain `pert_num` * frame_num of the input system.
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cell_pert_fraction : float
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A fraction determines how much (relatively) will cell deform.
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The cell of each frame is deformed by a symmetric matrix perturbed from identity.
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The perturbation to the diagonal part is subject to a uniform distribution in [-cell_pert_fraction, cell_pert_fraction),
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and the perturbation to the off-diagonal part is subject to a uniform distribution in [-0.5*cell_pert_fraction, 0.5*cell_pert_fraction).
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atom_pert_distance: float
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unit: Angstrom. A distance determines how far atoms will move.
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Atoms will move about `atom_pert_distance` in random direction.
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The distribution of the distance atoms move is determined by atom_pert_style
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atom_pert_style : str
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Determines the distribution of the distance atoms move is subject to.
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Avaliable options are
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- `'normal'`: the `distance` will be object to `chi-square distribution with 3 degrees of freedom` after normalization.
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The mean value of the distance is `atom_pert_fraction*side_length`
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- `'uniform'`: will generate uniformly random points in a 3D-balls with radius as `atom_pert_distance`.
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These points are treated as vector used by atoms to move.
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Obviously, the max length of the distance atoms move is `atom_pert_distance`.
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- `'const'`: The distance atoms move will be a constant `atom_pert_distance`.
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Returns
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-------
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perturbed_system : System
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The perturbed_system. It contains `pert_num` * frame_num of the input system frames.
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"""
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perturbed_system = System()
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nframes = self.get_nframes()
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for ii in range(nframes):
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for jj in range(pert_num):
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tmp_system = self[ii].copy()
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cell_perturb_matrix = get_cell_perturb_matrix(cell_pert_fraction)
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tmp_system.data['cells'][0] = np.matmul(tmp_system.data['cells'][0],cell_perturb_matrix)
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tmp_system.data['coords'][0] = np.matmul(tmp_system.data['coords'][0],cell_perturb_matrix)
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for kk in range(len(tmp_system.data['coords'][0])):
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atom_perturb_vector = get_atom_perturb_vector(atom_pert_distance, atom_pert_style)
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tmp_system.data['coords'][0][kk] += atom_perturb_vector
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tmp_system.rot_lower_triangular()
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perturbed_system.append(tmp_system)
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return perturbed_system
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def get_cell_perturb_matrix(cell_pert_fraction):
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if cell_pert_fraction<0:
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raise RuntimeError('cell_pert_fraction can not be negative')
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e0 = np.random.rand(6)
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e = e0 * 2 *cell_pert_fraction - cell_pert_fraction
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cell_pert_matrix = np.array(
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[[1+e[0], 0.5 * e[5], 0.5 * e[4]],
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[0.5 * e[5], 1+e[1], 0.5 * e[3]],
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[0.5 * e[4], 0.5 * e[3], 1+e[2]]]
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)
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return cell_pert_matrix
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def get_atom_perturb_vector(atom_pert_distance, atom_pert_style='normal'):
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random_vector = None
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if atom_pert_distance < 0:
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raise RuntimeError('atom_pert_distance can not be negative')
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if atom_pert_style == 'normal':
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e = np.random.randn(3)
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random_vector=(atom_pert_distance/np.sqrt(3))*e
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elif atom_pert_style == 'uniform':
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e = np.random.randn(3)
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while np.linalg.norm(e) < 0.1:
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e = np.random.randn(3)
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random_unit_vector = e/np.linalg.norm(e)
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v0 = np.random.rand(1)
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v = np.power(v0,1/3)
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random_vector = atom_pert_distance*v*random_unit_vector
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elif atom_pert_style == 'const' :
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e = np.random.randn(3)
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while np.linalg.norm(e) < 0.1:
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e = np.random.randn(3)
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random_unit_vector = e/np.linalg.norm(e)
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random_vector = atom_pert_distance*random_unit_vector
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else:
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raise RuntimeError('unsupported options atom_pert_style={}'.format(atom_pert_style))
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return random_vector
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class LabeledSystem (System):
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'''

‎tests/poscars/POSCAR.SiC

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C4 Si4
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1.0
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4.1454462863815970e+00 0.0000000000000000e+00 0.0000000000000000e+00
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1.3000000000000000e-01 3.9594462863815970e+00 0.0000000000000000e+00
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2.5000000000000000e-01 3.7000000000000000e-01 4.0400062863815970e+00
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C Si
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4 4
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cartesian
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-0.0666948568 0.0604660432 2.1539831432
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1.9907431432 -0.0864349568 0.0663397432
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0.0885598432 2.0783031432 0.0622547432
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2.0324731432 2.0217031432 2.0253831432
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-0.0448649568 0.1153571432 0.0540263432
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1.9664731432 1.9313831432 -0.1405848568
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2.0807731432 0.0065058032 1.9956031432
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0.0632185432 1.9999431432 2.0438931432

‎tests/poscars/POSCAR.SiC.const

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C4 Si4
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1.0
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3.9448633066729739e+00 -3.6344794672422329e-18 1.1581293029516294e-17
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1.6817409381958889e-01 4.0320777239133783e+00 -8.7954588948930866e-19
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1.4551929935812052e-01 3.9989012843738053e-01 3.9977352939318109e+00
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C Si
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4 4
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Cartesian
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0.0946327782 -0.2781320996 1.6927633385
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2.1395921916 -0.5505295607 0.3561009428
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-0.2623111485 2.0403483142 0.5289485573
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2.0291102621 2.0166734366 1.4189102698
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-0.4274609464 0.4275845699 -0.2870878166
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1.8398859643 1.9175800522 -0.7344827910
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1.5794721062 0.2698516856 1.5600233361
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0.2272461445 2.4170250626 2.4545090907

‎tests/poscars/POSCAR.SiC.normal

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C4 Si4
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1.0
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4.0354487481064565e+00 1.1027270790560616e-17 2.5642993008475204e-17
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2.0693526054669642e-01 4.1066892997402196e+00 -8.6715682899078028e-18
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4.2891472979598610e-01 5.5796885749827474e-01 4.1100061517204542e+00
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C Si
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4 4
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Cartesian
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0.2840021179 -0.6003817253 2.7192043932
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1.7870636884 0.4043686026 -0.3468222936
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-0.4647946470 2.0243215781 -0.0624256251
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2.1747504767 2.0704389063 2.4228997681
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-0.3817468326 0.0611851697 0.1116535817
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2.1483270977 2.3528212071 -0.3719335435
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2.4540854549 0.7297685673 1.8434611305
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0.1075358778 2.0300985762 2.0687710181

‎tests/poscars/POSCAR.SiC.replicate123

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C24 Si24
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1.000000
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4.14544629 0.00000000 0.00000000
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0.26000000 7.91889257 0.00000000
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0.75000000 1.11000000 12.12001886
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C Si
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24 24
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Cartesian
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-0.06669486 0.06046604 2.15398314
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0.18330514 0.43046604 6.19398943
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0.43330514 0.80046604 10.23399572
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0.06330514 4.01991233 2.15398314
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0.31330514 4.38991233 6.19398943
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0.56330514 4.75991233 10.23399572
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1.99074314 -0.08643496 0.06633974
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2.24074314 0.28356504 4.10634603
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2.49074314 0.65356504 8.14635232
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2.12074314 3.87301133 0.06633974
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2.37074314 4.24301133 4.10634603
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2.62074314 4.61301133 8.14635232
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0.08855984 2.07830314 0.06225474
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0.33855984 2.44830314 4.10226103
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0.58855984 2.81830314 8.14226732
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0.21855984 6.03774943 0.06225474
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0.46855984 6.40774943 4.10226103
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0.71855984 6.77774943 8.14226732
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2.03247314 2.02170314 2.02538314
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2.28247314 2.39170314 6.06538943
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2.53247314 2.76170314 10.10539572
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2.16247314 5.98114943 2.02538314
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2.41247314 6.35114943 6.06538943
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2.66247314 6.72114943 10.10539572
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-0.04486496 0.11535714 0.05402634
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0.20513504 0.48535714 4.09403263
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0.45513504 0.85535714 8.13403892
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0.08513504 4.07480343 0.05402634
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0.33513504 4.44480343 4.09403263
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0.58513504 4.81480343 8.13403892
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1.96647314 1.93138314 -0.14058486
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2.21647314 2.30138314 3.89942143
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2.46647314 2.67138314 7.93942772
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2.09647314 5.89082943 -0.14058486
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2.34647314 6.26082943 3.89942143
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2.59647314 6.63082943 7.93942772
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2.08077314 0.00650580 1.99560314
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2.33077314 0.37650580 6.03560943
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2.58077314 0.74650580 10.07561572
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2.21077314 3.96595209 1.99560314
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2.46077314 4.33595209 6.03560943
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2.71077314 4.70595209 10.07561572
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0.06321854 1.99994314 2.04389314
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0.31321854 2.36994314 6.08389943
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0.56321854 2.73994314 10.12390572
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0.19321854 5.95938943 2.04389314
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0.44321854 6.32938943 6.08389943
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0.69321854 6.69938943 10.12390572

‎tests/poscars/POSCAR.SiC.uniform

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C4 Si4
2+
1.0
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4.0817852422279959e+00 -8.0334347485565818e-20 1.4195449766884313e-17
4+
1.2315711101650186e-01 3.7860044730134366e+00 -1.7522489439993958e-18
5+
4.0639226354941010e-01 3.2444019947671882e-01 4.2124083393682454e+00
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C Si
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4 4
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Cartesian
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-0.1022885809 0.5553879154 2.3401729917
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1.4574918226 -0.0391762715 0.0190932943
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-0.0904993945 1.7684440711 -0.1710987880
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2.0638159391 2.1681985074 2.4580083474
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-0.3261354126 0.1759255681 0.2236316249
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2.0738703301 2.3024191125 -0.5031567813
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2.3488610334 0.3825072268 1.7330866249
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-0.0534780340 1.5938442575 1.8486892947

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