Coverage for /builds/hweiske/ase/ase/gui/view.py: 63.27%

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 set_atoms(self, atoms): 

143 natoms = len(atoms) 

144 

145 if self.showing_cell(): 

146 B1, B2 = get_cell_coordinates(atoms.cell, 

147 self.config['shift_cell']) 

148 else: 

149 B1 = B2 = np.zeros((0, 3)) 

150 

151 if self.showing_bonds(): 

152 atomscopy = atoms.copy() 

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

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

155 else: 

156 bonds = np.empty((0, 5), int) 

157 

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

159 # like bonds and cell segments. 

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

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

162 

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

164 

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

166 self.X_pos = self.X[:natoms] 

167 self.X_pos[:] = atoms.positions 

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

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

170 

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

172 cell = atoms.cell 

173 ncellparts = len(B1) 

174 nbonds = len(bonds) 

175 

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

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

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

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

180 

181 if nbonds > 0: 

182 P = atoms.positions 

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

184 a = P[bonds[:, 0]] 

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

186 d = (b**2).sum(1)**0.5 

187 r = 0.65 * self.get_covalent_radii() 

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

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

190 self.X_bonds[:] = a + b * x0 

191 b *= 1.0 - x0 - x1 

192 b[bonds[:, 2:].any(1)] *= 0.5 

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

194 

195 def showing_bonds(self): 

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

197 

198 def showing_cell(self): 

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

200 

201 def toggle_show_unit_cell(self, key=None): 

202 self.set_frame() 

203 

204 def update_labels(self): 

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

206 if index == 0: 

207 self.labels = None 

208 elif index == 1: 

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

210 elif index == 2: 

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

212 elif index == 4: 

213 Q = self.atoms.get_initial_charges() 

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

215 else: 

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

217 

218 def show_labels(self): 

219 self.update_labels() 

220 self.draw() 

221 

222 def toggle_show_axes(self, key=None): 

223 self.draw() 

224 

225 def toggle_show_bonds(self, key=None): 

226 self.set_frame() 

227 

228 def toggle_show_velocities(self, key=None): 

229 self.draw() 

230 

231 def get_forces(self): 

232 if self.atoms.calc is not None: 

233 try: 

234 return self.atoms.get_forces() 

235 except PropertyNotImplementedError: 

236 pass 

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

238 

239 def toggle_show_forces(self, key=None): 

240 self.draw() 

241 

242 def hide_selected(self): 

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

244 self.draw() 

245 

246 def show_selected(self): 

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

248 self.draw() 

249 

250 def repeat_window(self, key=None): 

251 return Repeat(self) 

252 

253 def rotate_window(self): 

254 return Rotate(self) 

255 

256 def colors_window(self, key=None): 

257 win = ColorWindow(self) 

258 self.register_vulnerable(win) 

259 return win 

260 

261 def focus(self, x=None): 

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

263 self.images[0].cell.any()) 

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

265 self.scale = 20.0 

266 self.center = np.zeros(3) 

267 self.draw() 

268 return 

269 

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

271 # including the covalent_radii used for drawing the atoms 

272 P = np.dot(self.X, self.axes) 

273 n = len(self.atoms) 

274 covalent_radii = self.get_covalent_radii() 

275 P[:n] -= covalent_radii[:, None] 

276 P1 = P.min(0) 

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

278 P2 = P.max(0) 

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

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

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

282 S = 1.3 * (P2 - P1) 

283 w, h = self.window.size 

284 if S[0] * h < S[1] * w: 

285 self.scale = h / S[1] 

286 elif S[0] > 0.0001: 

287 self.scale = w / S[0] 

288 else: 

289 self.scale = 1.0 

290 self.draw() 

291 

292 def reset_view(self, menuitem): 

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

294 self.set_frame() 

295 self.focus(self) 

296 

297 def set_view(self, key): 

298 if key == 'Z': 

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

300 elif key == 'X': 

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

302 elif key == 'Y': 

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

304 elif key == 'Alt+Z': 

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

306 elif key == 'Alt+X': 

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

308 elif key == 'Alt+Y': 

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

310 else: 

311 if key == '3': 

312 i, j = 0, 1 

313 elif key == '1': 

314 i, j = 1, 2 

315 elif key == '2': 

316 i, j = 2, 0 

317 elif key == 'Alt+3': 

318 i, j = 1, 0 

319 elif key == 'Alt+1': 

320 i, j = 2, 1 

321 elif key == 'Alt+2': 

322 i, j = 0, 2 

323 

324 A = complete_cell(self.atoms.cell) 

325 x1 = A[i] 

326 x2 = A[j] 

327 

328 norm = np.linalg.norm 

329 

330 x1 = x1 / norm(x1) 

331 x2 = x2 - x1 * np.dot(x1, x2) 

332 x2 /= norm(x2) 

333 x3 = np.cross(x1, x2) 

334 

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

336 

337 self.set_frame() 

338 

339 def get_colors(self, rgb=False): 

340 if rgb: 

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

342 for _rgb in self.get_colors()] 

343 

344 if self.colormode == 'jmol': 

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

346 

347 if self.colormode == 'neighbors': 

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

349 for Z in self.get_color_scalars()] 

350 

351 colorscale, cmin, cmax = self.colormode_data 

352 N = len(colorscale) 

353 colorswhite = colorscale + ['#ffffff'] 

354 if cmin == cmax: 

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

356 else: 

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

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

359 0.5).astype(int), 

360 0, N - 1).filled(N) 

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

362 

363 def get_color_scalars(self, frame=None): 

364 if self.colormode == 'tag': 

365 return self.atoms.get_tags() 

366 if self.colormode == 'force': 

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

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

369 elif self.colormode == 'velocity': 

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

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

372 return self.atoms.get_initial_charges() 

373 elif self.colormode == 'magmom': 

374 return get_magmoms(self.atoms) 

375 elif self.colormode == 'neighbors': 

376 from ase.neighborlist import NeighborList 

377 n = len(self.atoms) 

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

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

380 nl.update(self.atoms) 

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

382 else: 

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

384 dtype=float) 

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

386 

387 def get_covalent_radii(self, atoms=None): 

388 if atoms is None: 

389 atoms = self.atoms 

390 return self.images.get_radii(atoms) 

391 

392 def draw(self, status=True): 

393 self.window.clear() 

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

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

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

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

398 n = len(self.atoms) 

399 

400 # The indices enumerate drawable objects in z order: 

401 self.indices = X[:, 2].argsort() 

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

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

404 r *= 0.65 

405 P = self.P = X[:n, :2] 

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

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

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

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

410 axes)).round().astype(int) 

411 d = (2 * r).round().astype(int) 

412 

413 vector_arrays = [] 

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

415 # Scale ugly? 

416 v = self.atoms.get_velocities() 

417 if v is not None: 

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

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

420 f = self.get_forces() 

421 vector_arrays.append(f * self.force_vector_scale) 

422 

423 for array in vector_arrays: 

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

425 

426 colors = self.get_colors() 

427 circle = self.window.circle 

428 arc = self.window.arc 

429 line = self.window.line 

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

431 

432 selected = self.images.selected 

433 visible = self.images.visible 

434 ncell = len(self.X_cell) 

435 bond_linewidth = self.scale * 0.15 

436 

437 self.update_labels() 

438 

439 if self.arrowkey_mode == self.ARROWKEY_MOVE: 

440 movecolor = GREEN 

441 elif self.arrowkey_mode == self.ARROWKEY_ROTATE: 

442 movecolor = PURPLE 

443 

444 for a in self.indices: 

445 if a < n: 

446 ra = d[a] 

447 if visible[a]: 

448 try: 

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

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

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

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

453 fill = '#ffffff' 

454 circle(fill, selected[a], 

455 A[a, 0], A[a, 1], 

456 A[a, 0] + ra, A[a, 1] + ra) 

457 start = 0 

458 # start with the dominant species 

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

460 key=lambda x: x[1], 

461 reverse=True): 

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

463 circle(colors[a], selected[a], 

464 A[a, 0], A[a, 1], 

465 A[a, 0] + ra, A[a, 1] + ra) 

466 else: 

467 # jmol colors for the moment 

468 extent = 360. * occ 

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

470 selected[a], 

471 start, extent, 

472 A[a, 0], A[a, 1], 

473 A[a, 0] + ra, A[a, 1] + ra) 

474 start += extent 

475 except KeyError: 

476 # legacy behavior 

477 # Draw the atoms 

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

479 and self.move_atoms_mask[a]): 

480 circle(movecolor, False, 

481 A[a, 0] - 4, A[a, 1] - 4, 

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

483 

484 circle(colors[a], selected[a], 

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

486 

487 # Draw labels on the atoms 

488 if self.labels is not None: 

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

490 A[a, 1] + ra / 2, 

491 str(self.labels[a])) 

492 

493 # Draw cross on constrained atoms 

494 if constrained[a]: 

495 R1 = int(0.14644 * ra) 

496 R2 = int(0.85355 * ra) 

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

498 A[a, 0] + R2, A[a, 1] + R2)) 

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

500 A[a, 0] + R1, A[a, 1] + R2)) 

501 

502 # Draw velocities and/or forces 

503 for v in vector_arrays: 

504 assert not np.isnan(v).any() 

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

506 width=2) 

507 else: 

508 # Draw unit cell and/or bonds: 

509 a -= n 

510 if a < ncell: 

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

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

513 else: 

514 line((X1[a, 0], X1[a, 1], 

515 X2[a, 0], X2[a, 1]), 

516 width=bond_linewidth) 

517 

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

519 self.draw_axes() 

520 

521 if len(self.images) > 1: 

522 self.draw_frame_number() 

523 

524 self.window.update() 

525 

526 if status: 

527 self.status(self.atoms) 

528 

529 def arrow(self, coords, width): 

530 line = self.window.line 

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

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

533 line(coords, width) 

534 

535 vec = end - begin 

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

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

538 

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

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

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

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

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

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

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

546 

547 def draw_axes(self): 

548 axes_length = 15 

549 

550 rgb = ['red', 'green', 'blue'] 

551 

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

553 a = 20 

554 b = self.window.size[1] - 20 

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

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

557 self.window.line((a, b, c, d)) 

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

559 

560 def draw_frame_number(self): 

561 x, y = self.window.size 

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

563 anchor='SE') 

564 

565 def release(self, event): 

566 if event.button in [4, 5]: 

567 self.scroll_event(event) 

568 return 

569 

570 if event.button != self.b1: 

571 return 

572 

573 selected = self.images.selected 

574 selected_ordered = self.images.selected_ordered 

575 

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

577 d = self.P - self.xy 

578 r = self.get_covalent_radii() 

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

580 for a in self.indices[::-1]: 

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

582 if event.modifier == 'ctrl': 

583 selected[a] = not selected[a] 

584 if selected[a]: 

585 selected_ordered += [a] 

586 elif len(selected_ordered) > 0: 

587 if selected_ordered[-1] == a: 

588 selected_ordered = selected_ordered[:-1] 

589 else: 

590 selected_ordered = [] 

591 else: 

592 selected[:] = False 

593 selected[a] = True 

594 selected_ordered = [a] 

595 break 

596 else: 

597 selected[:] = False 

598 selected_ordered = [] 

599 self.draw() 

600 else: 

601 A = (event.x, event.y) 

602 C1 = np.minimum(A, self.xy) 

603 C2 = np.maximum(A, self.xy) 

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

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

606 if event.modifier != 'ctrl': 

607 selected[:] = False 

608 selected[indices] = True 

609 if (len(indices) == 1 and 

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

611 selected_ordered += [indices[0]] 

612 elif len(indices) > 1: 

613 selected_ordered = [] 

614 self.draw() 

615 

616 # XXX check bounds 

617 natoms = len(self.atoms) 

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

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

620 selected_ordered = [] 

621 self.images.selected_ordered = selected_ordered 

622 

623 def press(self, event): 

624 self.button = event.button 

625 self.xy = (event.x, event.y) 

626 self.t0 = event.time 

627 self.axes0 = self.axes 

628 self.center0 = self.center 

629 

630 def move(self, event): 

631 x = event.x 

632 y = event.y