From a6e268ec198c7b3d253e59065a20f17a2db6b87b Mon Sep 17 00:00:00 2001
From: Adam Fekete <adam.fekete@kcl.ac.uk>
Date: Mon, 22 Oct 2018 15:06:53 +0100
Subject: [PATCH] adding helper functions to quip tutorial
---
quip-gap/scripts/Preprocess.py | 130 +++++++++++++++++++
quip-gap/scripts/Reader.py | 197 +++++++++++++++++++++++++++++
quip-gap/scripts/Visualise.py | 154 ++++++++++++++++++++++
quip-gap/scripts/Visualise_quip.py | 154 ++++++++++++++++++++++
quip-gap/scripts/__init__.py | 0
5 files changed, 635 insertions(+)
create mode 100644 quip-gap/scripts/Preprocess.py
create mode 100644 quip-gap/scripts/Reader.py
create mode 100644 quip-gap/scripts/Visualise.py
create mode 100644 quip-gap/scripts/Visualise_quip.py
create mode 100644 quip-gap/scripts/__init__.py
diff --git a/quip-gap/scripts/Preprocess.py b/quip-gap/scripts/Preprocess.py
new file mode 100644
index 0000000..6b29c47
--- /dev/null
+++ b/quip-gap/scripts/Preprocess.py
@@ -0,0 +1,130 @@
+from pathlib import Path
+from pprint import pprint
+import json
+from ase.io import read, write
+from ase.geometry import crystal_structure_from_cell
+import numpy as np
+# import numpy.linalg as la
+
+import matplotlib.pyplot as plt
+from scipy.interpolate import interp1d
+
+
+class Calculation(object):
+ def __init__(self, *args, **kwargs):
+ self.filepath = kwargs.pop('filepath', None)
+ self.parameters = kwargs
+
+ def get_data(self, index=-1):
+ return read(str(self.filepath))
+
+ @classmethod
+ def from_path(cls, path: Path):
+ with (path / 'gb.json').open() as data_file:
+ gb_data = json.load(data_file)
+
+ with (path / 'subgb.json').open() as data_file:
+ subgb_data = json.load(data_file)
+
+ # print(gb_data['angle'])
+
+ filename = subgb_data['name'] + "_traj.xyz"
+ filepath = (path / filename).resolve()
+ # configuration = read(str((path / filename).resolve()), index=index)
+ # # gb = read(str((path / filename).resolve()), index=-1)
+
+
+ # print('{:=^60}'.format(' '+str(path)+' '))
+ #
+ # print('{:-^40}'.format(' gb.json '))
+ # pprint(gb_data)
+ #
+ # print('{:-^40}'.format(' subgb.json '))
+ # pprint(subgb_data)
+
+ # print('{:-^40}'.format(' initial '))
+ #
+ # force_norm = np.linalg.norm(gb_initial.arrays['force'], axis=1)
+ # force_mean = np.mean(force_norm)
+ # force_std = np.std(force_norm)
+ #
+ # print('Force mean: {:f}, std: {:f}'.format(force_mean, force_std))
+ # pprint(gb_initial.calc.results)
+ #
+ # print('{:-^40}'.format(' final '))
+ #
+ # force_norm = np.linalg.norm(gb_final.arrays['force'], axis=1)
+ # force_mean = np.mean(force_norm)
+ # force_std = np.std(force_norm)
+ #
+ # print('Force mean: {:f}, std: {:f}'.format(force_mean, force_std))
+ # pprint(gb_final.calc.results)
+
+
+ return cls(**{**gb_data, **subgb_data}, filepath=filepath)
+
+
+if __name__ == '__main__':
+
+ # Read grain boundary database
+ dirpath = Path('../GB_alphaFe_001')
+
+ calculations = {
+ 'tilt': [Calculation.from_path(calc_dir) for calc_dir in (dirpath / 'tilt').iterdir() if calc_dir.is_dir()],
+ 'twist': [Calculation.from_path(calc_dir) for calc_dir in (dirpath / 'twist').iterdir() if calc_dir.is_dir()]
+ }
+
+ # potential energy of the perfect crystal according to a specific potential
+ potential_energy_per_atom = -4.01298214176 # alpha-Fe PotBH
+ eV = 1.6021766208e-19
+ Angstrom = 1.e-10
+
+ angles, energies = [], []
+ for calc in sorted(calculations['tilt'], key=lambda item: item.parameters['angle']):
+
+ # E_gb = calc.parameters.get('E_gb', None)
+ #
+ # if E_gb is None:
+ # print(calc.filepath)
+ # print(calc.parameters['converged'])
+ # else:
+
+ # energy = 16.02 / (2 * calc.parameters['A'] ) * \
+ # (E_gb - potential_energy_per_atom * calc.parameters['n_at'])
+
+ if calc.parameters.get('converged', None):
+ # energy = 16.02 / (2 * calc.parameters['A'] ) * \
+ # (calc.parameters.get('E_gb') - potential_energy_per_atom * calc.parameters['n_at'])
+ #
+ atoms = calc.get_data()
+ cell = atoms.get_cell()
+ A = cell[0, 0] * cell[1, 1]
+
+ energy = (
+ eV / Angstrom**2 /
+ (2 * A) *
+ (atoms.get_potential_energy() - potential_energy_per_atom * len(atoms))
+ )
+
+ write(calc.filepath.name, atoms)
+
+
+ # print(energy)
+ # print(calc.parameters['converged'])
+ # print(data.get_potential_energy()) # data.get_total_energy() == data.get_potential_energy()
+ # energies.append(calc.parameters['E_gb'] - data.get_total_energy())
+ energies.append(energy)
+ angles.append(calc.parameters['angle'] * 180.0 / np.pi)
+ else:
+ print("not converged: ", calc.filepath)
+
+
+ plt.bar(angles, energies)
+
+ # x_smooth = np.linspace(min(angles), max(angles), 1000, endpoint=True)
+ # f = interp1d(angles, energies, kind='cubic')
+ # plt.plot(x_smooth, f(x_smooth), '-')
+
+ plt.show()
+
+
diff --git a/quip-gap/scripts/Reader.py b/quip-gap/scripts/Reader.py
new file mode 100644
index 0000000..cf9a1ab
--- /dev/null
+++ b/quip-gap/scripts/Reader.py
@@ -0,0 +1,197 @@
+from pathlib import Path
+from pprint import pprint
+import json
+from ase.io import read, write
+from ase.geometry import crystal_structure_from_cell
+import numpy as np
+# import numpy.linalg as la
+
+import matplotlib.pyplot as plt
+from scipy.interpolate import interp1d
+
+
+class Calculation(object):
+ def __init__(self, *args, **kwargs):
+ self.filepath = kwargs.pop('filepath', None)
+ self.parameters = kwargs
+
+ def get_data(self, index=-1):
+ return read(str(self.filepath), index=index)
+
+ @classmethod
+ def from_path(cls, path: Path, index=-1):
+ with (path / 'gb.json').open() as data_file:
+ gb_data = json.load(data_file)
+
+ with (path / 'subgb.json').open() as data_file:
+ subgb_data = json.load(data_file)
+
+ # print(gb_data['angle'])
+
+ filename = subgb_data['name'] + "_traj.xyz"
+ filepath = (path / filename).resolve()
+ # configuration = read(str((path / filename).resolve()), index=index)
+ # # gb = read(str((path / filename).resolve()), index=-1)
+
+
+ # print('{:=^60}'.format(' '+str(path)+' '))
+ #
+ # print('{:-^40}'.format(' gb.json '))
+ # pprint(gb_data)
+ #
+ # print('{:-^40}'.format(' subgb.json '))
+ # pprint(subgb_data)
+
+ # print('{:-^40}'.format(' initial '))
+ #
+ # force_norm = np.linalg.norm(gb_initial.arrays['force'], axis=1)
+ # force_mean = np.mean(force_norm)
+ # force_std = np.std(force_norm)
+ #
+ # print('Force mean: {:f}, std: {:f}'.format(force_mean, force_std))
+ # pprint(gb_initial.calc.results)
+ #
+ # print('{:-^40}'.format(' final '))
+ #
+ # force_norm = np.linalg.norm(gb_final.arrays['force'], axis=1)
+ # force_mean = np.mean(force_norm)
+ # force_std = np.std(force_norm)
+ #
+ # print('Force mean: {:f}, std: {:f}'.format(force_mean, force_std))
+ # pprint(gb_final.calc.results)
+
+
+ return cls(**{**gb_data, **subgb_data}, filepath=filepath)
+
+
+if __name__ == '__main__':
+
+ # Read grain boundary database
+ dirpath = Path('../GB_alphaFe_001')
+
+ calculations = {
+ 'tilt': [Calculation.from_path(calc_dir) for calc_dir in (dirpath / 'tilt').iterdir() if calc_dir.is_dir()],
+ 'twist': [Calculation.from_path(calc_dir) for calc_dir in (dirpath / 'twist').iterdir() if calc_dir.is_dir()]
+ }
+
+ # potential energy of the perfect crystal according to a specific potential
+ potential_energy_per_atom = -4.01298214176 # alpha-Fe PotBH
+ eV = 1.6021766208e-19
+ Angstrom = 1.e-10
+
+ angles, energies = [], []
+ for calc in sorted(calculations['tilt'], key=lambda item: item.parameters['angle']):
+ angles.append(calc.parameters['angle'] * 180.0 / np.pi)
+
+
+ energy = 16.02 / (2 * calc.parameters['A'] ) * \
+ (calc.parameters['E_gb'] - potential_energy_per_atom * calc.parameters['n_at'])
+
+ atoms = calc.get_data()
+ cell = atoms.get_cell()
+ A = cell[0, 0] * cell[1, 1]
+
+ energy = (
+ eV / Angstrom**2 /
+ (2 * A) *
+ (atoms.get_total_energy() - potential_energy_per_atom * len(atoms))
+ )
+
+ print(energy)
+ # print(data.get_potential_energy()) # data.get_total_energy() == data.get_potential_energy()
+ # energies.append(calc.parameters['E_gb'] - data.get_total_energy())
+ energies.append(energy)
+
+
+ plt.bar(angles, energies)
+
+ # x_smooth = np.linspace(min(angles), max(angles), 1000, endpoint=True)
+ # f = interp1d(angles, energies, kind='cubic')
+ # plt.plot(x_smooth, f(x_smooth), '-')
+
+ plt.show()
+
+
+# 00171501160
+# {
+# "A": 128.39243418897394,
+# "gbid": "00171501160",
+# "sigma_csl": 0,
+# "H": 181.47714791126677,
+# "n_at": 514,
+# "orientation_axis": [
+# 0,
+# 0,
+# 1
+# ],
+# "boundary_plane": [
+# 1.0,
+# 16.0,
+# 0.0
+# ],
+# "coincident_sites": 2,
+# "angle": 0.12479104151759456,
+# "type": "symmetric tilt boundary",
+# "zplanes": [
+# 45.2801,
+# 136.0193
+# ]
+# }
+# {
+# "A": 1540.7092103178,
+# "E_gb": -98740.56229920377,
+# "gbid": "00171501160_v6bxv2_tv0.4bxv0.1_d1.4z",
+# "name": "00171501160_v6bxv2_tv0.4bxv0.1_d1.4z",
+# "area": 1540.7092103178,
+# "H": 181.47714791,
+# "n_at": 24636,
+# "rbt": [
+# 0.4,
+# 0.1
+# ],
+# "rcut": 1.4,
+# "converged": true,
+# "param_file": "PotBH.xml",
+# "E_gb_init": -97920.0696568818
+# }
+
+# PotBH
+#
+# Min. Energy: 0.6408 J/m^{2}
+# Min. Energy Structure
+# Microscopic Degrees of Freedom (x,y, Cutoff Criterion)
+# (0.4, 0.1, 1.4)
+# (0.4, 0.1, 1.5)
+# Max. Energy:1.5965 J/m^{2}
+# Max. Energy Structure
+# Microscopic Degrees of Freedom (x,y, Cutoff Criterion)
+# (0.0, 0.1, 2.1)
+
+#
+#
+# models.py
+# gb_ener = 16.02*((sub_dict['E_gb']-(-4.2731*sub_dict['n_at']))/(2*sub_dict['A']))
+#
+# gb_ener = 16.02*((gb_dict['E_gb']-(ener_per_atom[param_file]*float(gb_dict['n_at'])))/(2*gb_dict['A']))
+#
+# calc_gap.py
+# subgbs = [(16.02*(subgb['E_gb']-float(subgb['n_at']*ener_per_atom['PotBH.xml']))/(2.0*subgb['area']), subgb) for subgb in subgbs]
+#
+# calc_energy.py
+# def calc_e_gb(at, E_bulk):
+# cell = at.get_cell()
+# A = cell[0,0]*cell[1,1]
+# E_gb = (at.get_potential_energy()-(at.n*(E_bulk)))/(2.*A)
+# print A
+# print at.get_potential_energy()
+# print E_gb, 'eV/A^2'
+# E_gb = 16.02*(at.get_potential_energy()-(at.n*(E_bulk)))/(2.*A)
+ # print E_gb, 'J/m^2'
+# return E_gb
+#
+# relax.py
+# E_gb_init = grain.get_potential_energy()
+# E_gb = grain.get_potential_energy()
+#
+#
+# ener_per_atom = -4.01298214176
\ No newline at end of file
diff --git a/quip-gap/scripts/Visualise.py b/quip-gap/scripts/Visualise.py
new file mode 100644
index 0000000..1ed65c2
--- /dev/null
+++ b/quip-gap/scripts/Visualise.py
@@ -0,0 +1,154 @@
+import io
+import uuid
+
+from nglview import register_backend, Structure
+from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox, Output
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+
+@register_backend('ase')
+class MyASEStructure(Structure):
+ def __init__(self, atoms, bfactor=[], occupancy=[]):
+ # super(MyASEStructure, self).__init__()
+ self.ext = 'pdb'
+ self.params = {}
+ self._atoms = atoms
+ self.bfactor = bfactor # [min, max]
+ self.occupancy = occupancy # [0, 1]
+ self.id = str(uuid.uuid4())
+
+ def get_structure_string(self):
+ """ PDB file format:
+ CRYST1 16.980 62.517 124.864 90.00 90.00 90.00 P 1
+ MODEL 1
+ ATOM 0 Fe MOL 1 15.431 60.277 6.801 1.00 0.00 FE
+ ATOM 1 Fe MOL 1 1.273 3.392 93.940 1.00 0.00 FE
+ """
+ # with io.StringIO() as stream:
+ # self.structure.write(stream, format='proteindatabank')
+ # data = stream.getvalue()
+
+ data = ""
+
+ if self._atoms.get_pbc().any():
+ cellpar = self._atoms.get_cell_lengths_and_angles()
+
+ str_format = 'CRYST1' + '{:9.3f}' * 3 + '{:7.2f}' * 3 + ' P 1\n'
+ data += str_format.format(*cellpar.tolist())
+
+ data += 'MODEL 1\n'
+
+ str_format = 'ATOM {:5d} {:>4s} MOL 1 {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f} {:2s}\n'
+ for index, atom in enumerate(self._atoms):
+ data += str_format.format(
+ index,
+ atom.symbol,
+ atom.position[0].tolist(),
+ atom.position[1].tolist(),
+ atom.position[2].tolist(),
+ self.occupancy[index] if index <= len(self.occupancy) - 1 else 1.0,
+ self.bfactor[index] if index <= len(self.bfactor) - 1 else 1.0,
+ atom.symbol.upper()
+ )
+
+ data += 'ENDMDL\n'
+
+ return data
+
+
+def ViewStructure(atoms):
+ import nglview
+
+ view = nglview.NGLWidget()
+
+ structure = MyASEStructure(atoms)
+ view.add_structure(structure)
+
+ return view
+
+
+
+class AtomViewer(object):
+ def __init__(self, atoms, data=[], xsize=1000, ysize=500):
+ self.view = self._init_nglview(atoms, data, xsize, ysize)
+
+ self.widgets = {
+ 'radius': FloatSlider(
+ value=0.8, min=0.0, max=1.5, step=0.01,
+ description='Ball size'
+ ),
+ 'color_scheme': Dropdown(description='Solor scheme:'),
+ 'colorbar': Output()
+ }
+ self.show_colorbar(data)
+
+ self.widgets['radius'].observe(self._update_repr)
+
+ self.gui = VBox([
+ self.view,
+ self.widgets['colorbar'],
+ self.widgets['radius']])
+
+ def _update_repr(self, chg=None):
+ self.view.update_spacefill(
+ radiusType='radius',
+ radius=self.widgets['radius'].value
+ )
+
+ def show_colorbar(self, data):
+ with self.widgets['colorbar']:
+ # Have colormaps separated into categories:
+ # http://matplotlib.org/examples/color/colormaps_reference.html
+ cmap = 'rainbow'
+
+ fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(16, 2))
+ img = ax1.imshow([[min(data), max(data)]], aspect='auto', cmap=plt.get_cmap(cmap))
+ ax1.remove()
+ cbar = fig.colorbar(img, cax=ax2, orientation='horizontal')
+
+ plt.show()
+
+ @staticmethod
+ def _init_nglview(atoms, data, xsize, ysize):
+ import nglview
+
+ view = nglview.NGLWidget(gui=False)
+ view._remote_call(
+ 'setSize',
+ target='Widget',
+ args=[
+ '{:d}px'.format(xsize),
+ '{:d}px'.format(ysize)
+ ]
+ )
+
+ data = np.max(data)-data
+
+ structure = MyASEStructure(atoms, bfactor=data)
+ view.add_structure(structure)
+
+ view.clear_representations()
+ view.add_unitcell()
+
+ view.add_spacefill(
+ # radiusType='radius',
+ # radius=1.0,
+ color_scheme='bfactor',
+ color_scale='rainbow'
+ )
+ view.update_spacefill(
+ radiusType='radius',
+ radius=1.0
+ )
+
+
+ # update camera type
+ view.control.spin([1, 0, 0], np.pi / 2)
+ view.control.spin([0, 0, 1], np.pi / 2)
+ view.camera = 'orthographic'
+ view.center()
+
+ return view
diff --git a/quip-gap/scripts/Visualise_quip.py b/quip-gap/scripts/Visualise_quip.py
new file mode 100644
index 0000000..1ed65c2
--- /dev/null
+++ b/quip-gap/scripts/Visualise_quip.py
@@ -0,0 +1,154 @@
+import io
+import uuid
+
+from nglview import register_backend, Structure
+from ipywidgets import Dropdown, FloatSlider, IntSlider, HBox, VBox, Output
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+
+
+@register_backend('ase')
+class MyASEStructure(Structure):
+ def __init__(self, atoms, bfactor=[], occupancy=[]):
+ # super(MyASEStructure, self).__init__()
+ self.ext = 'pdb'
+ self.params = {}
+ self._atoms = atoms
+ self.bfactor = bfactor # [min, max]
+ self.occupancy = occupancy # [0, 1]
+ self.id = str(uuid.uuid4())
+
+ def get_structure_string(self):
+ """ PDB file format:
+ CRYST1 16.980 62.517 124.864 90.00 90.00 90.00 P 1
+ MODEL 1
+ ATOM 0 Fe MOL 1 15.431 60.277 6.801 1.00 0.00 FE
+ ATOM 1 Fe MOL 1 1.273 3.392 93.940 1.00 0.00 FE
+ """
+ # with io.StringIO() as stream:
+ # self.structure.write(stream, format='proteindatabank')
+ # data = stream.getvalue()
+
+ data = ""
+
+ if self._atoms.get_pbc().any():
+ cellpar = self._atoms.get_cell_lengths_and_angles()
+
+ str_format = 'CRYST1' + '{:9.3f}' * 3 + '{:7.2f}' * 3 + ' P 1\n'
+ data += str_format.format(*cellpar.tolist())
+
+ data += 'MODEL 1\n'
+
+ str_format = 'ATOM {:5d} {:>4s} MOL 1 {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f} {:2s}\n'
+ for index, atom in enumerate(self._atoms):
+ data += str_format.format(
+ index,
+ atom.symbol,
+ atom.position[0].tolist(),
+ atom.position[1].tolist(),
+ atom.position[2].tolist(),
+ self.occupancy[index] if index <= len(self.occupancy) - 1 else 1.0,
+ self.bfactor[index] if index <= len(self.bfactor) - 1 else 1.0,
+ atom.symbol.upper()
+ )
+
+ data += 'ENDMDL\n'
+
+ return data
+
+
+def ViewStructure(atoms):
+ import nglview
+
+ view = nglview.NGLWidget()
+
+ structure = MyASEStructure(atoms)
+ view.add_structure(structure)
+
+ return view
+
+
+
+class AtomViewer(object):
+ def __init__(self, atoms, data=[], xsize=1000, ysize=500):
+ self.view = self._init_nglview(atoms, data, xsize, ysize)
+
+ self.widgets = {
+ 'radius': FloatSlider(
+ value=0.8, min=0.0, max=1.5, step=0.01,
+ description='Ball size'
+ ),
+ 'color_scheme': Dropdown(description='Solor scheme:'),
+ 'colorbar': Output()
+ }
+ self.show_colorbar(data)
+
+ self.widgets['radius'].observe(self._update_repr)
+
+ self.gui = VBox([
+ self.view,
+ self.widgets['colorbar'],
+ self.widgets['radius']])
+
+ def _update_repr(self, chg=None):
+ self.view.update_spacefill(
+ radiusType='radius',
+ radius=self.widgets['radius'].value
+ )
+
+ def show_colorbar(self, data):
+ with self.widgets['colorbar']:
+ # Have colormaps separated into categories:
+ # http://matplotlib.org/examples/color/colormaps_reference.html
+ cmap = 'rainbow'
+
+ fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(16, 2))
+ img = ax1.imshow([[min(data), max(data)]], aspect='auto', cmap=plt.get_cmap(cmap))
+ ax1.remove()
+ cbar = fig.colorbar(img, cax=ax2, orientation='horizontal')
+
+ plt.show()
+
+ @staticmethod
+ def _init_nglview(atoms, data, xsize, ysize):
+ import nglview
+
+ view = nglview.NGLWidget(gui=False)
+ view._remote_call(
+ 'setSize',
+ target='Widget',
+ args=[
+ '{:d}px'.format(xsize),
+ '{:d}px'.format(ysize)
+ ]
+ )
+
+ data = np.max(data)-data
+
+ structure = MyASEStructure(atoms, bfactor=data)
+ view.add_structure(structure)
+
+ view.clear_representations()
+ view.add_unitcell()
+
+ view.add_spacefill(
+ # radiusType='radius',
+ # radius=1.0,
+ color_scheme='bfactor',
+ color_scale='rainbow'
+ )
+ view.update_spacefill(
+ radiusType='radius',
+ radius=1.0
+ )
+
+
+ # update camera type
+ view.control.spin([1, 0, 0], np.pi / 2)
+ view.control.spin([0, 0, 1], np.pi / 2)
+ view.camera = 'orthographic'
+ view.center()
+
+ return view
diff --git a/quip-gap/scripts/__init__.py b/quip-gap/scripts/__init__.py
new file mode 100644
index 0000000..e69de29
--
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