Coverage for /builds/alexhroom/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 i: ('#{:02X}{:02X}{:02X}'.format(*(int(x * 255) for x in rgb))) 

97 for i, rgb in enumerate(jmol_colors) 

98 } 

99 # scaling factors for vectors 

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

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

102 

103 # buttons 

104 self.b1 = 1 # left 

105 self.b3 = 3 # right 

106 if self.config['swap_mouse']: 

107 self.b1 = 3 

108 self.b3 = 1 

109 

110 @property 

111 def atoms(self): 

112 return self.images[self.frame] 

113 

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

115 if frame is None: 

116 frame = self.frame 

117 assert frame < len(self.images) 

118 self.frame = frame 

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

120 

121 fname = self.images.filenames[frame] 

122 if fname is None: 

123 header = 'ase.gui' 

124 else: 

125 # fname is actually not necessarily the filename but may 

126 # contain indexing like filename@0 

127 header = basename(fname) 

128 

129 images_loaded_text = ngettext( 

130 'one image loaded', 

131 '{} images loaded', 

132 len(self.images) 

133 ).format(len(self.images)) 

134 

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

136 

137 if focus: 

138 self.focus() 

139 else: 

140 self.draw() 

141 

142 def get_bonds(self, atoms): 

143 # this method exists rather than just using the standalone function 

144 # so that it can be overridden by external libraries 

145 return get_bonds(atoms, self.get_covalent_radii(atoms)) 

146 

147 def set_atoms(self, atoms): 

148 natoms = len(atoms) 

149 

150 if self.showing_cell(): 

151 B1, B2 = get_cell_coordinates(atoms.cell, 

152 self.config['shift_cell']) 

153 else: 

154 B1 = B2 = np.zeros((0, 3)) 

155 

156 if self.showing_bonds(): 

157 atomscopy = atoms.copy() 

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

159 bonds = self.get_bonds(atomscopy) 

160 else: 

161 bonds = np.empty((0, 5), int) 

162 

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

164 # like bonds and cell segments. 

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

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

167 

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

169 

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

171 self.X_pos = self.X[:natoms] 

172 self.X_pos[:] = atoms.positions 

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

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

175 

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

177 cell = atoms.cell 

178 ncellparts = len(B1) 

179 nbonds = len(bonds) 

180 

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

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

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

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

185 

186 if nbonds > 0: 

187 P = atoms.positions 

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

189 a = P[bonds[:, 0]] 

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

191 d = (b**2).sum(1)**0.5 

192 r = 0.65 * self.get_covalent_radii() 

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

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

195 self.X_bonds[:] = a + b * x0 

196 b *= 1.0 - x0 - x1 

197 b[bonds[:, 2:].any(1)] *= 0.5 

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

199 

200 def showing_bonds(self): 

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

202 

203 def showing_cell(self): 

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

205 

206 def toggle_show_unit_cell(self, key=None): 

207 self.set_frame() 

208 

209 def update_labels(self): 

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

211 if index == 0: 

212 self.labels = None 

213 elif index == 1: 

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

215 elif index == 2: 

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

217 elif index == 4: 

218 Q = self.atoms.get_initial_charges() 

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

220 else: 

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

222 

223 def show_labels(self): 

224 self.update_labels() 

225 self.draw() 

226 

227 def toggle_show_axes(self, key=None): 

228 self.draw() 

229 

230 def toggle_show_bonds(self, key=None): 

231 self.set_frame() 

232 

233 def toggle_show_velocities(self, key=None): 

234 self.draw() 

235 

236 def get_forces(self): 

237 if self.atoms.calc is not None: 

238 try: 

239 return self.atoms.get_forces() 

240 except PropertyNotImplementedError: 

241 pass 

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

243 

244 def toggle_show_forces(self, key=None): 

245 self.draw() 

246 

247 def hide_selected(self): 

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

249 self.draw() 

250 

251 def show_selected(self): 

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

253 self.draw() 

254 

255 def repeat_window(self, key=None): 

256 return Repeat(self) 

257 

258 def rotate_window(self): 

259 return Rotate(self) 

260 

261 def colors_window(self, key=None): 

262 win = ColorWindow(self) 

263 self.register_vulnerable(win) 

264 return win 

265 

266 def focus(self, x=None): 

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

268 self.images[0].cell.any()) 

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

270 self.scale = 20.0 

271 self.center = np.zeros(3) 

272 self.draw() 

273 return 

274 

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

276 # including the covalent_radii used for drawing the atoms 

277 P = np.dot(self.X, self.axes) 

278 n = len(self.atoms) 

279 covalent_radii = self.get_covalent_radii() 

280 P[:n] -= covalent_radii[:, None] 

281 P1 = P.min(0) 

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

283 P2 = P.max(0) 

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

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

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

287 S = 1.3 * (P2 - P1) 

288 w, h = self.window.size 

289 if S[0] * h < S[1] * w: 

290 self.scale = h / S[1] 

291 elif S[0] > 0.0001: 

292 self.scale = w / S[0] 

293 else: 

294 self.scale = 1.0 

295 self.draw() 

296 

297 def reset_view(self, menuitem): 

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

299 self.set_frame() 

300 self.focus(self) 

301 

302 def set_view(self, key): 

303 if key == 'Z': 

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

305 elif key == 'X': 

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

307 elif key == 'Y': 

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

309 elif key == 'Alt+Z': 

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

311 elif key == 'Alt+X': 

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

313 elif key == 'Alt+Y': 

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

315 else: 

316 if key == '3': 

317 i, j = 0, 1 

318 elif key == '1': 

319 i, j = 1, 2 

320 elif key == '2': 

321 i, j = 2, 0 

322 elif key == 'Alt+3': 

323 i, j = 1, 0 

324 elif key == 'Alt+1': 

325 i, j = 2, 1 

326 elif key == 'Alt+2': 

327 i, j = 0, 2 

328 

329 A = complete_cell(self.atoms.cell) 

330 x1 = A[i] 

331 x2 = A[j] 

332 

333 norm = np.linalg.norm 

334 

335 x1 = x1 / norm(x1) 

336 x2 = x2 - x1 * np.dot(x1, x2) 

337 x2 /= norm(x2) 

338 x3 = np.cross(x1, x2) 

339 

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

341 

342 self.set_frame() 

343 

344 def get_colors(self, rgb=False): 

345 if rgb: 

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

347 for _rgb in self.get_colors()] 

348 

349 if self.colormode == 'jmol': 

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

351 

352 if self.colormode == 'neighbors': 

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

354 for Z in self.get_color_scalars()] 

355 

356 colorscale, cmin, cmax = self.colormode_data 

357 N = len(colorscale) 

358 colorswhite = colorscale + ['#ffffff'] 

359 if cmin == cmax: 

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

361 else: 

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

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

364 0.5).astype(int), 

365 0, N - 1).filled(N) 

366 return [colorswhite[i] for i in indices] 

367 

368 def get_color_scalars(self, frame=None): 

369 if self.colormode == 'tag': 

370 return self.atoms.get_tags() 

371 if self.colormode == 'force': 

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

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

374 elif self.colormode == 'velocity': 

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

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

377 return self.atoms.get_initial_charges() 

378 elif self.colormode == 'magmom': 

379 return get_magmoms(self.atoms) 

380 elif self.colormode == 'neighbors': 

381 from ase.neighborlist import NeighborList 

382 n = len(self.atoms) 

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

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

385 nl.update(self.atoms) 

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

387 else: 

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

389 dtype=float) 

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

391 

392 def get_covalent_radii(self, atoms=None): 

393 if atoms is None: 

394 atoms = self.atoms 

395 return self.images.get_radii(atoms) 

396 

397 def draw(self, status=True): 

398 self.window.clear() 

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

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

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

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

403 n = len(self.atoms) 

404 

405 # The indices enumerate drawable objects in z order: 

406 self.indices = X[:, 2].argsort() 

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

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

409 r *= 0.65 

410 P = self.P = X[:n, :2] 

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

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

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

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

415 axes)).round().astype(int) 

416 d = (2 * r).round().astype(int) 

417 

418 vector_arrays = [] 

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

420 # Scale ugly? 

421 v = self.atoms.get_velocities() 

422 if v is not None: 

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

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

425 f = self.get_forces() 

426 vector_arrays.append(f * self.force_vector_scale) 

427 

428 for array in vector_arrays: 

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

430 

431 colors = self.get_colors() 

432 circle = self.window.circle 

433 arc = self.window.arc 

434 line = self.window.line 

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

436 

437 selected = self.images.selected 

438 visible = self.images.visible 

439 ncell = len(self.X_cell) 

440 bond_linewidth = self.scale * 0.15 

441 

442 self.update_labels() 

443 

444 if self.arrowkey_mode == self.ARROWKEY_MOVE: 

445 movecolor = GREEN 

446 elif self.arrowkey_mode == self.ARROWKEY_ROTATE: 

447 movecolor = PURPLE 

448 

449 for a in self.indices: 

450 if a < n: 

451 ra = d[a] 

452 if visible[a]: 

453 try: 

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

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

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

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

458 fill = '#ffffff' 

459 circle(fill, selected[a], 

460 A[a, 0], A[a, 1], 

461 A[a, 0] + ra, A[a, 1] + ra) 

462 start = 0 

463 # start with the dominant species 

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

465 key=lambda x: x[1], 

466 reverse=True): 

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

468 circle(colors[a], selected[a], 

469 A[a, 0], A[a, 1], 

470 A[a, 0] + ra, A[a, 1] + ra) 

471 else: 

472 # jmol colors for the moment 

473 extent = 360. * occ 

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

475 selected[a], 

476 start, extent, 

477 A[a, 0], A[a, 1], 

478 A[a, 0] + ra, A[a, 1] + ra) 

479 start += extent 

480 except KeyError: 

481 # legacy behavior 

482 # Draw the atoms 

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

484 and self.move_atoms_mask[a]): 

485 circle(movecolor, False, 

486 A[a, 0] - 4, A[a, 1] - 4, 

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

488 

489 circle(colors[a], selected[a], 

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

491 

492 # Draw labels on the atoms 

493 if self.labels is not None: 

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

495 A[a, 1] + ra / 2, 

496 str(self.labels[a])) 

497 

498 # Draw cross on constrained atoms 

499 if constrained[a]: 

500 R1 = int(0.14644 * ra) 

501 R2 = int(0.85355 * ra) 

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

503 A[a, 0] + R2, A[a, 1] + R2)) 

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

505 A[a, 0] + R1, A[a, 1] + R2)) 

506 

507 # Draw velocities and/or forces 

508 for v in vector_arrays: 

509 assert not np.isnan(v).any() 

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

511 width=2) 

512 else: 

513 # Draw unit cell and/or bonds: 

514 a -= n 

515 if a < ncell: 

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

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

518 else: 

519 line((X1[a, 0], X1[a, 1], 

520 X2[a, 0], X2[a, 1]), 

521 width=bond_linewidth) 

522 

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

524 self.draw_axes() 

525 

526 if len(self.images) > 1: 

527 self.draw_frame_number() 

528 

529 self.window.update() 

530 

531 if status: 

532 self.status(self.atoms) 

533 

534 def arrow(self, coords, width): 

535 line = self.window.line 

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

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

538 line(coords, width) 

539 

540 vec = end - begin 

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

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

543 

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

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

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

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

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

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

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

551 

552 def draw_axes(self): 

553 axes_length = 15 

554 

555 rgb = ['red', 'green', 'blue'] 

556 

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

558 a = 20 

559 b = self.window.size[1] - 20 

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

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

562 self.window.line((a, b, c, d)) 

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

564 

565 def draw_frame_number(self): 

566 x, y = self.window.size 

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

568 anchor='SE') 

569 

570 def release(self, event): 

571 if event.button in [4, 5]: 

572 self.scroll_event(event) 

573 return 

574 

575 if event.button != self.b1: 

576 return 

577 

578 selected = self.images.selected 

579 selected_ordered = self.images.selected_ordered 

580 

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

582 d = self.P - self.xy 

583 r = self.get_covalent_radii() 

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

585 for a in self.indices[::-1]: 

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

587 if event.modifier == 'ctrl': 

588 selected[a] = not selected[a] 

589 if selected[a]: 

590 selected_ordered += [a] 

591 elif len(selected_ordered) > 0: 

592 if selected_ordered[-1] == a: 

593 selected_ordered = selected_ordered[:-1] 

594 else: 

595 selected_ordered = [] 

596 else: 

597 selected[:] = False 

598 selected[a] = True 

599 selected_ordered = [a] 

600 break 

601 else: 

602 selected[:] = False 

603 selected_ordered = [] 

604 self.draw() 

605 else: 

606 A = (event.x, event.y) 

607 C1 = np.minimum(A, self.xy) 

608 C2 = np.maximum(A, self.xy) 

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

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

611 if event.modifier != 'ctrl': 

612 selected[:] = False 

613 selected[indices] = True 

614 if (len(indices) == 1 and 

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

616 selected_ordered += [indices[0]] 

617 elif len(indices) > 1: 

618 selected_ordered = [] 

619 self.draw() 

620 

621 # XXX check bounds 

622 natoms = len(self.atoms) 

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

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

625 selected_ordered = [] 

626 self.images.selected_ordered = selected_ordered 

627 

628 def press(self, event): 

629 self.button = event.button 

630 self.xy = (event.x, event.y) 

631 self.t0 = event.time 

632 self.axes0 = self.axes