Coverage for /builds/kinetik161/ase/ase/gui/view.py: 63.41%

1from math import cos, sin, sqrt 

2from os.path import basename 

3 

4import numpy as np 

5 

6from ase.calculators.calculator import PropertyNotImplementedError 

7from ase.data import atomic_numbers 

8from ase.data.colors import jmol_colors 

9from ase.geometry import complete_cell 

10from ase.gui.colors import ColorWindow 

11from ase.gui.i18n import ngettext 

12from ase.gui.render import Render 

13from ase.gui.repeat import Repeat 

14from ase.gui.rotate import Rotate 

15from ase.gui.utils import get_magmoms 

16from ase.utils import rotate 

17 

18GREEN = '#74DF00' 

19PURPLE = '#AC58FA' 

20BLACKISH = '#151515' 

21 

22 

23def get_cell_coordinates(cell, shifted=False): 

24 """Get start and end points of lines segments used to draw cell.""" 

25 nn = [] 

26 for c in range(3): 

27 v = cell[c] 

28 d = sqrt(np.dot(v, v)) 

29 if d < 1e-12: 

30 n = 0 

31 else: 

32 n = max(2, int(d / 0.3)) 

33 nn.append(n) 

34 B1 = np.zeros((2, 2, sum(nn), 3)) 

35 B2 = np.zeros((2, 2, sum(nn), 3)) 

36 n1 = 0 

37 for c, n in enumerate(nn): 

38 n2 = n1 + n 

39 h = 1.0 / (2 * n - 1) 

40 R = np.arange(n) * (2 * h) 

41 

42 for i, j in [(0, 0), (0, 1), (1, 0), (1, 1)]: 

43 B1[i, j, n1:n2, c] = R 

44 B1[i, j, n1:n2, (c + 1) % 3] = i 

45 B1[i, j, n1:n2, (c + 2) % 3] = j 

46 B2[:, :, n1:n2] = B1[:, :, n1:n2] 

47 B2[:, :, n1:n2, c] += h 

48 n1 = n2 

49 B1.shape = (-1, 3) 

50 B2.shape = (-1, 3) 

51 if shifted: 

52 B1 -= 0.5 

53 B2 -= 0.5 

54 return B1, B2 

55 

56 

57def get_bonds(atoms, covalent_radii): 

58 from ase.neighborlist import NeighborList 

59 nl = NeighborList(covalent_radii * 1.5, 

60 skin=0, self_interaction=False) 

61 nl.update(atoms) 

62 nbonds = nl.nneighbors + nl.npbcneighbors 

63 

64 bonds = np.empty((nbonds, 5), int) 

65 if nbonds == 0: 

66 return bonds 

67 

68 n1 = 0 

69 for a in range(len(atoms)): 

70 indices, offsets = nl.get_neighbors(a) 

71 n2 = n1 + len(indices) 

72 bonds[n1:n2, 0] = a 

73 bonds[n1:n2, 1] = indices 

74 bonds[n1:n2, 2:] = offsets 

75 n1 = n2 

76 

77 i = bonds[:n2, 2:].any(1) 

78 pbcbonds = bonds[:n2][i] 

79 bonds[n2:, 0] = pbcbonds[:, 1] 

80 bonds[n2:, 1] = pbcbonds[:, 0] 

81 bonds[n2:, 2:] = -pbcbonds[:, 2:] 

82 return bonds 

83 

84 

85class View: 

86 def __init__(self, rotations): 

87 self.colormode = 'jmol' # The default colors 

88 self.labels = None 

89 self.axes = rotate(rotations) 

90 self.configured = False 

91 self.frame = None 

92 

93 # XXX 

94 self.colormode = 'jmol' 

95 self.colors = {} 

96 

97 for i, rgb in enumerate(jmol_colors): 

98 self.colors[i] = ('#{:02X}{:02X}{:02X}' 

99 .format(*(int(x * 255) for x in rgb))) 

100 

101 # scaling factors for vectors 

102 self.force_vector_scale = self.config['force_vector_scale'] 

103 self.velocity_vector_scale = self.config['velocity_vector_scale'] 

104 

105 # buttons 

106 self.b1 = 1 # left 

107 self.b3 = 3 # right 

108 if self.config['swap_mouse']: 

109 self.b1 = 3 

110 self.b3 = 1 

111 

112 @property 

113 def atoms(self): 

114 return self.images[self.frame] 

115 

116 def set_frame(self, frame=None, focus=False): 

117 if frame is None: 

118 frame = self.frame 

119 assert frame < len(self.images) 

120 self.frame = frame 

121 self.set_atoms(self.images[frame]) 

122 

123 fname = self.images.filenames[frame] 

124 if fname is None: 

125 header = 'ase.gui' 

126 else: 

127 # fname is actually not necessarily the filename but may 

128 # contain indexing like filename@0 

129 header = basename(fname) 

130 

131 images_loaded_text = ngettext( 

132 'one image loaded', 

133 '{} images loaded', 

134 len(self.images) 

135 ).format(len(self.images)) 

136 

137 self.window.title = f'{header} — {images_loaded_text}' 

138 

139 if focus: 

140 self.focus() 

141 else: 

142 self.draw() 

143 

144 def set_atoms(self, atoms): 

145 natoms = len(atoms) 

146 

147 if self.showing_cell(): 

148 B1, B2 = get_cell_coordinates(atoms.cell, 

149 self.config['shift_cell']) 

150 else: 

151 B1 = B2 = np.zeros((0, 3)) 

152 

153 if self.showing_bonds(): 

154 atomscopy = atoms.copy() 

155 atomscopy.cell *= self.images.repeat[:, np.newaxis] 

156 bonds = get_bonds(atomscopy, self.get_covalent_radii(atoms)) 

157 else: 

158 bonds = np.empty((0, 5), int) 

159 

160 # X is all atomic coordinates, and starting points of vectors 

161 # like bonds and cell segments. 

162 # The reason to have them all in one big list is that we like to 

163 # eventually rotate/sort it by Z-order when rendering. 

164 

165 # Also B are the end points of line segments. 

166 

167 self.X = np.empty((natoms + len(B1) + len(bonds), 3)) 

168 self.X_pos = self.X[:natoms] 

169 self.X_pos[:] = atoms.positions 

170 self.X_cell = self.X[natoms:natoms + len(B1)] 

171 self.X_bonds = self.X[natoms + len(B1):] 

172 

173 if 1: # if init or frame != self.frame: 

174 cell = atoms.cell 

175 ncellparts = len(B1) 

176 nbonds = len(bonds) 

177 

178 if 1: # init or (atoms.cell != self.atoms.cell).any(): 

179 self.X_cell[:] = np.dot(B1, cell) 

180 self.B = np.empty((ncellparts + nbonds, 3)) 

181 self.B[:ncellparts] = np.dot(B2, cell) 

182 

183 if nbonds > 0: 

184 P = atoms.positions 

185 Af = self.images.repeat[:, np.newaxis] * cell 

186 a = P[bonds[:, 0]] 

187 b = P[bonds[:, 1]] + np.dot(bonds[:, 2:], Af) - a 

188 d = (b**2).sum(1)**0.5 

189 r = 0.65 * self.get_covalent_radii() 

190 x0 = (r[bonds[:, 0]] / d).reshape((-1, 1)) 

191 x1 = (r[bonds[:, 1]] / d).reshape((-1, 1)) 

192 self.X_bonds[:] = a + b * x0 

193 b *= 1.0 - x0 - x1 

194 b[bonds[:, 2:].any(1)] *= 0.5 

195 self.B[ncellparts:] = self.X_bonds + b 

196 

197 def showing_bonds(self): 

198 return self.window['toggle-show-bonds'] 

199 

200 def showing_cell(self): 

201 return self.window['toggle-show-unit-cell'] 

202 

203 def toggle_show_unit_cell(self, key=None): 

204 self.set_frame() 

205 

206 def update_labels(self): 

207 index = self.window['show-labels'] 

208 if index == 0: 

209 self.labels = None 

210 elif index == 1: 

211 self.labels = list(range(len(self.atoms))) 

212 elif index == 2: 

213 self.labels = list(get_magmoms(self.atoms)) 

214 elif index == 4: 

215 Q = self.atoms.get_initial_charges() 

216 self.labels = [f'{q:.4g}' for q in Q] 

217 else: 

218 self.labels = self.atoms.get_chemical_symbols() 

219 

220 def show_labels(self): 

221 self.update_labels() 

222 self.draw() 

223 

224 def toggle_show_axes(self, key=None): 

225 self.draw() 

226 

227 def toggle_show_bonds(self, key=None): 

228 self.set_frame() 

229 

230 def toggle_show_velocities(self, key=None): 

231 self.draw() 

232 

233 def get_forces(self): 

234 if self.atoms.calc is not None: 

235 try: 

236 return self.atoms.get_forces() 

237 except PropertyNotImplementedError: 

238 pass 

239 return np.zeros((len(self.atoms), 3)) 

240 

241 def toggle_show_forces(self, key=None): 

242 self.draw() 

243 

244 def hide_selected(self): 

245 self.images.visible[self.images.selected] = False 

246 self.draw() 

247 

248 def show_selected(self): 

249 self.images.visible[self.images.selected] = True 

250 self.draw() 

251 

252 def repeat_window(self, key=None): 

253 return Repeat(self) 

254 

255 def rotate_window(self): 

256 return Rotate(self) 

257 

258 def colors_window(self, key=None): 

259 win = ColorWindow(self) 

260 self.register_vulnerable(win) 

261 return win 

262 

263 def focus(self, x=None): 

264 cell = (self.window['toggle-show-unit-cell'] and 

265 self.images[0].cell.any()) 

266 if (len(self.atoms) == 0 and not cell): 

267 self.scale = 20.0 

268 self.center = np.zeros(3) 

269 self.draw() 

270 return 

271 

272 # Get the min and max point of the projected atom positions 

273 # including the covalent_radii used for drawing the atoms 

274 P = np.dot(self.X, self.axes) 

275 n = len(self.atoms) 

276 covalent_radii = self.get_covalent_radii() 

277 P[:n] -= covalent_radii[:, None] 

278 P1 = P.min(0) 

279 P[:n] += 2 * covalent_radii[:, None] 

280 P2 = P.max(0) 

281 self.center = np.dot(self.axes, (P1 + P2) / 2) 

282 self.center += self.atoms.get_celldisp().reshape((3,)) / 2 

283 # Add 30% of whitespace on each side of the atoms 

284 S = 1.3 * (P2 - P1) 

285 w, h = self.window.size 

286 if S[0] * h < S[1] * w: 

287 self.scale = h / S[1] 

288 elif S[0] > 0.0001: 

289 self.scale = w / S[0] 

290 else: 

291 self.scale = 1.0 

292 self.draw() 

293 

294 def reset_view(self, menuitem): 

295 self.axes = rotate('0.0x,0.0y,0.0z') 

296 self.set_frame() 

297 self.focus(self) 

298 

299 def set_view(self, key): 

300 if key == 'Z': 

301 self.axes = rotate('0.0x,0.0y,0.0z') 

302 elif key == 'X': 

303 self.axes = rotate('-90.0x,-90.0y,0.0z') 

304 elif key == 'Y': 

305 self.axes = rotate('90.0x,0.0y,90.0z') 

306 elif key == 'Alt+Z': 

307 self.axes = rotate('180.0x,0.0y,90.0z') 

308 elif key == 'Alt+X': 

309 self.axes = rotate('0.0x,90.0y,0.0z') 

310 elif key == 'Alt+Y': 

311 self.axes = rotate('-90.0x,0.0y,0.0z') 

312 else: 

313 if key == '3': 

314 i, j = 0, 1 

315 elif key == '1': 

316 i, j = 1, 2 

317 elif key == '2': 

318 i, j = 2, 0 

319 elif key == 'Alt+3': 

320 i, j = 1, 0 

321 elif key == 'Alt+1': 

322 i, j = 2, 1 

323 elif key == 'Alt+2': 

324 i, j = 0, 2 

325 

326 A = complete_cell(self.atoms.cell) 

327 x1 = A[i] 

328 x2 = A[j] 

329 

330 norm = np.linalg.norm 

331 

332 x1 = x1 / norm(x1) 

333 x2 = x2 - x1 * np.dot(x1, x2) 

334 x2 /= norm(x2) 

335 x3 = np.cross(x1, x2) 

336 

337 self.axes = np.array([x1, x2, x3]).T 

338 

339 self.set_frame() 

340 

341 def get_colors(self, rgb=False): 

342 if rgb: 

343 return [tuple(int(_rgb[i:i + 2], 16) / 255 for i in range(1, 7, 2)) 

344 for _rgb in self.get_colors()] 

345 

346 if self.colormode == 'jmol': 

347 return [self.colors.get(Z, BLACKISH) for Z in self.atoms.numbers] 

348 

349 if self.colormode == 'neighbors': 

350 return [self.colors.get(Z, BLACKISH) 

351 for Z in self.get_color_scalars()] 

352 

353 colorscale, cmin, cmax = self.colormode_data 

354 N = len(colorscale) 

355 colorswhite = colorscale + ['#ffffff'] 

356 if cmin == cmax: 

357 indices = [N // 2] * len(self.atoms) 

358 else: 

359 scalars = np.ma.array(self.get_color_scalars()) 

360 indices = np.clip(((scalars - cmin) / (cmax - cmin) * N + 

361 0.5).astype(int), 

362 0, N - 1) 

363 return [colorswhite[i] for i in indices.filled(N)] 

364 

365 def get_color_scalars(self, frame=None): 

366 if self.colormode == 'tag': 

367 return self.atoms.get_tags() 

368 if self.colormode == 'force': 

369 f = (self.get_forces()**2).sum(1)**0.5 

370 return f * self.images.get_dynamic(self.atoms) 

371 elif self.colormode == 'velocity': 

372 return (self.atoms.get_velocities()**2).sum(1)**0.5 

373 elif self.colormode == 'initial charge': 

374 return self.atoms.get_initial_charges() 

375 elif self.colormode == 'magmom': 

376 return get_magmoms(self.atoms) 

377 elif self.colormode == 'neighbors': 

378 from ase.neighborlist import NeighborList 

379 n = len(self.atoms) 

380 nl = NeighborList(self.get_covalent_radii(self.atoms) * 1.5, 

381 skin=0, self_interaction=False, bothways=True) 

382 nl.update(self.atoms) 

383 return [len(nl.get_neighbors(i)[0]) for i in range(n)] 

384 else: 

385 scalars = np.array(self.atoms.get_array(self.colormode), 

386 dtype=float) 

387 return np.ma.array(scalars, mask=np.isnan(scalars)) 

388 

389 def get_covalent_radii(self, atoms=None): 

390 if atoms is None: 

391 atoms = self.atoms 

392 return self.images.get_radii(atoms) 

393 

394 def draw(self, status=True): 

395 self.window.clear() 

396 axes = self.scale * self.axes * (1, -1, 1) 

397 offset = np.dot(self.center, axes) 

398 offset[:2] -= 0.5 * self.window.size 

399 X = np.dot(self.X, axes) - offset 

400 n = len(self.atoms) 

401 

402 # The indices enumerate drawable objects in z order: 

403 self.indices = X[:, 2].argsort() 

404 r = self.get_covalent_radii() * self.scale 

405 if self.window['toggle-show-bonds']: 

406 r *= 0.65 

407 P = self.P = X[:n, :2] 

408 A = (P - r[:, None]).round().astype(int) 

409 X1 = X[n:, :2].round().astype(int) 

410 X2 = (np.dot(self.B, axes) - offset).round().astype(int) 

411 disp = (np.dot(self.atoms.get_celldisp().reshape((3,)), 

412 axes)).round().astype(int) 

413 d = (2 * r).round().astype(int) 

414 

415 vector_arrays = [] 

416 if self.window['toggle-show-velocities']: 

417 # Scale ugly? 

418 v = self.atoms.get_velocities() 

419 if v is not None: 

420 vector_arrays.append(v * 10.0 * self.velocity_vector_scale) 

421 if self.window['toggle-show-forces']: 

422 f = self.get_forces() 

423 vector_arrays.append(f * self.force_vector_scale) 

424 

425 for array in vector_arrays: 

426 array[:] = np.dot(array, axes) + X[:n] 

427 

428 colors = self.get_colors() 

429 circle = self.window.circle 

430 arc = self.window.arc 

431 line = self.window.line 

432 constrained = ~self.images.get_dynamic(self.atoms) 

433 

434 selected = self.images.selected 

435 visible = self.images.visible 

436 ncell = len(self.X_cell) 

437 bond_linewidth = self.scale * 0.15 

438 

439 self.update_labels() 

440 

441 if self.arrowkey_mode == self.ARROWKEY_MOVE: 

442 movecolor = GREEN 

443 elif self.arrowkey_mode == self.ARROWKEY_ROTATE: 

444 movecolor = PURPLE 

445 

446 for a in self.indices: 

447 if a < n: 

448 ra = d[a] 

449 if visible[a]: 

450 try: 

451 kinds = self.atoms.arrays['spacegroup_kinds'] 

452 site_occ = self.atoms.info['occupancy'][str(kinds[a])] 

453 # first an empty circle if a site is not fully occupied 

454 if (np.sum([v for v in site_occ.values()])) < 1.0: 

455 fill = '#ffffff' 

456 circle(fill, selected[a], 

457 A[a, 0], A[a, 1], 

458 A[a, 0] + ra, A[a, 1] + ra) 

459 start = 0 

460 # start with the dominant species 

461 for sym, occ in sorted(site_occ.items(), 

462 key=lambda x: x[1], 

463 reverse=True): 

464 if np.round(occ, decimals=4) == 1.0: 

465 circle(colors[a], selected[a], 

466 A[a, 0], A[a, 1], 

467 A[a, 0] + ra, A[a, 1] + ra) 

468 else: 

469 # jmol colors for the moment 

470 extent = 360. * occ 

471 arc(self.colors[atomic_numbers[sym]], 

472 selected[a], 

473 start, extent, 

474 A[a, 0], A[a, 1], 

475 A[a, 0] + ra, A[a, 1] + ra) 

476 start += extent 

477 except KeyError: 

478 # legacy behavior 

479 # Draw the atoms 

480 if (self.moving and a < len(self.move_atoms_mask) 

481 and self.move_atoms_mask[a]): 

482 circle(movecolor, False, 

483 A[a, 0] - 4, A[a, 1] - 4, 

484 A[a, 0] + ra + 4, A[a, 1] + ra + 4) 

485 

486 circle(colors[a], selected[a], 

487 A[a, 0], A[a, 1], A[a, 0] + ra, A[a, 1] + ra) 

488 

489 # Draw labels on the atoms 

490 if self.labels is not None: 

491 self.window.text(A[a, 0] + ra / 2, 

492 A[a, 1] + ra / 2, 

493 str(self.labels[a])) 

494 

495 # Draw cross on constrained atoms 

496 if constrained[a]: 

497 R1 = int(0.14644 * ra) 

498 R2 = int(0.85355 * ra) 

499 line((A[a, 0] + R1, A[a, 1] + R1, 

500 A[a, 0] + R2, A[a, 1] + R2)) 

501 line((A[a, 0] + R2, A[a, 1] + R1, 

502 A[a, 0] + R1, A[a, 1] + R2)) 

503 

504 # Draw velocities and/or forces 

505 for v in vector_arrays: 

506 assert not np.isnan(v).any() 

507 self.arrow((X[a, 0], X[a, 1], v[a, 0], v[a, 1]), 

508 width=2) 

509 else: 

510 # Draw unit cell and/or bonds: 

511 a -= n 

512 if a < ncell: 

513 line((X1[a, 0] + disp[0], X1[a, 1] + disp[1], 

514 X2[a, 0] + disp[0], X2[a, 1] + disp[1])) 

515 else: 

516 line((X1[a, 0], X1[a, 1], 

517 X2[a, 0], X2[a, 1]), 

518 width=bond_linewidth) 

519 

520 if self.window['toggle-show-axes']: 

521 self.draw_axes() 

522 

523 if len(self.images) > 1: 

524 self.draw_frame_number() 

525 

526 self.window.update() 

527 

528 if status: 

529 self.status(self.atoms) 

530 

531 def arrow(self, coords, width): 

532 line = self.window.line 

533 begin = np.array((coords[0], coords[1])) 

534 end = np.array((coords[2], coords[3])) 

535 line(coords, width) 

536 

537 vec = end - begin 

538 length = np.sqrt((vec[:2]**2).sum()) 

539 length = min(length, 0.3 * self.scale) 

540 

541 angle = np.arctan2(end[1] - begin[1], end[0] - begin[0]) + np.pi 

542 x1 = (end[0] + length * np.cos(angle - 0.3)).round().astype(int) 

543 y1 = (end[1] + length * np.sin(angle - 0.3)).round().astype(int) 

544 x2 = (end[0] + length * np.cos(angle + 0.3)).round().astype(int) 

545 y2 = (end[1] + length * np.sin(angle + 0.3)).round().astype(int) 

546 line((x1, y1, end[0], end[1]), width) 

547 line((x2, y2, end[0], end[1]), width) 

548 

549 def draw_axes(self): 

550 axes_length = 15 

551 

552 rgb = ['red', 'green', 'blue'] 

553 

554 for i in self.axes[:, 2].argsort(): 

555 a = 20 

556 b = self.window.size[1] - 20 

557 c = int(self.axes[i][0] * axes_length + a) 

558 d = int(-self.axes[i][1] * axes_length + b) 

559 self.window.line((a, b, c, d)) 

560 self.window.text(c, d, 'XYZ'[i], color=rgb[i]) 

561 

562 def draw_frame_number(self): 

563 x, y = self.window.size 

564 self.window.text(x, y, '{}'.format(self.frame), 

565 anchor='SE') 

566 

567 def release(self, event): 

568 if event.button in [4, 5]: 

569 self.scroll_event(event) 

570 return 

571 

572 if event.button != self.b1: 

573 return 

574 

575 selected = self.images.selected 

576 selected_ordered = self.images.selected_ordered 

577 

578 if event.time < self.t0 + 200: # 200 ms 

579 d = self.P - self.xy 

580 r = self.get_covalent_radii() 

581 hit = np.less((d**2).sum(1), (self.scale * r)**2) 

582 for a in self.indices[::-1]: 

583 if a < len(self.atoms) and hit[a]: 

584 if event.modifier == 'ctrl': 

585 selected[a] = not selected[a] 

586 if selected[a]: 

587 selected_ordered += [a] 

588 elif len(selected_ordered) > 0: 

589 if selected_ordered[-1] == a: 

590 selected_ordered = selected_ordered[:-1] 

591 else: 

592 selected_ordered = [] 

593 else: 

594 selected[:] = False 

595 selected[a] = True 

596 selected_ordered = [a] 

597 break 

598 else: 

599 selected[:] = False 

600 selected_ordered = [] 

601 self.draw() 

602 else: 

603 A = (event.x, event.y) 

604 C1 = np.minimum(A, self.xy) 

605 C2 = np.maximum(A, self.xy) 

606 hit = np.logical_and(self.P > C1, self.P < C2) 

607 indices = np.compress(hit.prod(1), np.arange(len(hit))) 

608 if event.modifier != 'ctrl': 

609 selected[:] = False 

610 selected[indices] = True 

611 if (len(indices) == 1 and 

612 indices[0] not in self.images.selected_ordered): 

613 selected_ordered += [indices[0]] 

614 elif len(indices) > 1: 

615 selected_ordered = [] 

616 self.draw() 

617 

618 # XXX check bounds 

619 natoms = len(self.atoms) 

620 indices = np.arange(natoms)[self.images.selected[:natoms]] 

621 if len(indices) != len(selected_ordered): 

622 selected_ordered = [] 

623 self.images.selected_ordered = selected_ordered 

624 

625 def press(self, event): 

626 self.button = event.button 

627 self.xy = (event.x, event.y) 

628 self.t0 = event.time 

629 self.axes0 = self.axes 

630 self.center0 = self.center 

631 

632 def move(self, event):