TEXT   13

visual

Guest on 19th May 2022 03:22:35 PM

1. :orphan:
2.
3.
4. .. warning::
5.
6.    Only the calculation of the density is tested for open shell configurations
7.    (and relies on a correct .OCCUPATION). All other properties are only
8.    tested for closed shell systems and should not be trusted for open shell systems
9.    without a thorough testing.
10.
11.
12. .. index:: **VISUAL
13. .. _**VISUAL:
14.
15. ==========
16. \*\*VISUAL
17. ==========
18.
19. Sampling
20. ========
21.
22. .. index:: .LIST
23. .. _VISUAL_.LIST:
24.
25. .LIST
26. -----
27.
28. Calculate various densities in few points. Example (3 points; coordinates in
29. bohr)::
30.
31.   .LIST
32.    3
33.    1.0 0.0 0.0
34.    0.0 1.0 0.0
35.    0.0 0.0 1.0
36.
37.
38. .. index:: .LINE
39. .. _VISUAL_.LINE:
40.
41. .LINE
42. -----
43.
44. Calculate various densities along a line.
45. Example (line connecting two points; 200 steps; coordinates in bohr)::
46.
47.   .LINE
48.    0.0 0.0 0.0
49.    0.0 0.0 5.0
50.    200
51.
52. Scalar and vector densities are written to files plot.line.scalar and plot.line.vector, respectively,
53. and should be saved after calculation, e.g. ::
54.
55.    pam --get=plot.line.scalar ...
56.
57. The first three columns of the output files gives the coordinates (x, y, z) of the point.
58. It is then followed by one/three columns giving the value of the scalar/vector density in that point.
59.
62.
64. -------
65.
67.
68. .. math::
69.
70.    f(r) = \int_{0}^{2\pi}\int_{0}^{\pi}f(\mathbf{r})r^2\sin\theta d\theta d\phi
71.
72. by performing Lebedev angular integration over a specified number of even-spaced radial shells out to some specified distance
73. from a specified initial point. Example (coordinates and distance in bohr)::
74.
76.    0.0 0.0 0.0
77.    10.0
78.    200
79.
80. The first line after the keyword specifies the initial point, here chosen to be the origin.
81. The second and third line is the distance and step size, respectively.
82. Scalar and vector densities are written to files plot.radial.scalar and plot.radial.vector, respectively,
83. and should be saved after calculation, e.g. ::
84.
86.
87. .. index:: .2D
88. .. _VISUAL_.2D:
89.
90. .2D
91. ---
92.
93. Calculate various densities in a plane.
94. The plane is specified using 3 points that have to form a right angle.
95. Example (coordinates in bohr)::
96.
97.   .2D
98.    0.0  0.0  0.0     !origin
99.    0.0  0.0 10.0     !"right"
100.    200               !nr of points origin-"right"
101.    0.0 10.0  0.0     !"top"
102.    200               !nr of points origin-"top"
103.
104.
105. .. index:: .2D_INT
106. .. _VISUAL_.2D_INT:
107.
108. .2D_INT
109. -------
110.
111. Integrate various densities in a plane
113. The plane is specified using 3 points that have to form a right angle.
114. Example (coordinates in bohr)::
115.
116.   .2D_INT
117.    0.0  0.0  0.0     !origin
118.    0.0  0.0 10.0     !"right"
119.    10                !nr of tiles to the "right"
120.    0.0 10.0  0.0     !"top"
121.    10                !nr of tiles to the "right"
122.    5                 !order of the Legendre polynomial for each tile
123.
124.
125. .. index:: .3D
126. .. _VISUAL_.3D:
127.
128. .3D
129. ---
130.
131. Calculate various densities in 3D and write to cube file format.
132. Example (coordinates in bohr)::
133.
134.   .3D
135.    40 40 40          ! 40 x 40 x 40 points
136.
137.
138. .. index:: .3DFAST
139. .. _VISUAL_.3DFAST:
140.
141. .3DFAST
142. -------
143.
144. Fast evaluation of the molecular electrostatic potential.
145. Example (coordinates in bohr)::
146.
147.   .3DFAST
148.    40 40 40          ! 40 x 40 x 40 points
149.
150.
153.
155. -------
156.
157. Add space around the cube file.
158. Default (coordinates in bohr)::
159.
161.    4.0
162.
163.
164. .. index:: .3D_IMP
165. .. _VISUAL_.3D_IMP:
166.
167. .3D_IMP
168. -------
169.
170. Calculate various densities in 3D on an imported grid (does not have to be regular)
171. Example::
172.
173.   .3D_IMP
174.    grid_file        ! a file with x,y,z-coordinates of grid points
175.
176.
177. .. index:: .3D_INT
178. .. _VISUAL_.3D_INT:
179.
180. .3D_INT
181. -------
182.
183. Integrate densities in 3D.
184.
185. Modification of densities
186. =========================
187.
188. .. index:: .CARPOW
189. .. _VISUAL_.CARPOW:
190.
191. .CARPOW
192. -------
193.
194. Scale densities by Cartesian product :math:x^iy^jz^k. The keyword is followed by three integers specifying the exponents :math:(i,j,k). Example::
195.
196.   .DENSITY
197.   .CARPOW
198.   1 0 0
199.
200. is equivalent to the specification::
201.
202.    .EDIPX
203.
204. .. index:: .SCALE
205. .. _VISUAL_.SCALE:
206.
207. .SCALE
208. ------
209.
210. Scale densities by a factor.
211. Default::
212.
213.   .SCALE
214.    1.0
215.
216. .. index:: .DSCALE
217. .. _VISUAL_.DSCALE:
218.
219. .DSCALE
220. -------
221.
222. Scale densities *down* by a factor.
223. Default::
224.
225.   .DSCALE
226.    1.0
227.
228. Densities
229. =========
230.
231. .. index:: .DENSITY
232. .. _VISUAL_.DENSITY:
233.
234. .DENSITY
235. --------
236.
237. Compute number density :math:n(\mathbf{r}) .
238. Example (unperturbed density)::
239.
240.   .DENSITY
241.    DFCOEF
242.
243. Another example (perturbed density, first response vector)::
244.
245.   .DENSITY
246.    PAMXVC 1
247.
248.
249. .. index:: .ELF
250. .. _VISUAL_.ELF:
251.
252. .ELF
253. ----
254.
255. Compute the electron localization function. Example::
256.
257.   .ELF
258.    DFCOEF
259.
260.
261. .. index:: .GAMMA5
262. .. _VISUAL_.GAMMA5:
263.
264. .GAMMA5
265. -------
266.
267. Compute the electron chirality density. Example::
268.
269.   .GAMMA5
270.    DFCOEF
271.
272.
273. .. index:: .J
274. .. _VISUAL_.J:
275.
276. .J
277. --
278.
279. Compute the current density :math:\mathbf{j}(\mathbf{r})=-e\psi_{i}^{\ast}c\boldsymbol{\alpha}\psi_{i}. Example (use first response vector)::
280.
281.   .J
282.    PAMXVC 1
283.
284. .. index:: .JDIA
285. .. _VISUAL_.JDIA:
286.
287. .JDIA
288. -----
289.
290. Compute the nonrelativistic diamagnetic current density. Example::
291.
292.   .JDIA
293.    DFCOEF
294.
295.
296. .. index:: .JX
297. .. _VISUAL_.JX:
298.
299. .JX
300. ---
301.
302. Compute the x-component :math:j_{x}(\mathbf{r})=-e\psi_{i}^{\ast}c\alpha_{x}\psi_{i} of the current density. Example (use first response vector)::
303.
304.   .JX
305.    PAMXVC 1
306.
307. .. index:: .JY
308. .. _VISUAL_.JY:
309.
310. .JY
311. ---
312.
313. Compute the y-component :math:j_{y}(\mathbf{r})=-e\psi_{i}^{\ast}c\alpha_{y}\psi_{i} of the current density. Example (use first response vector)::
314.
315.   .JY
316.    PAMXVC 1
317.
318. .. index:: .JZ
319. .. _VISUAL_.JZ:
320.
321. .JZ
322. ---
323.
324. Compute the z-component :math:j_{z}(\mathbf{r})=-e\psi_{i}^{\ast}c\alpha_{z}\psi_{i} of the current density. Example (use first response vector)::
325.
326.   .JZ
327.    PAMXVC 1
328.
329. .. index:: .DIVJ
330. .. _VISUAL_.DIVJ:
331.
332. .DIVJ
333. -----
334.
335. Compute the divergence of the current density. Example (use first response vector)::
336.
337.   .DIVJ
338.    PAMXVC 1
339.
340.
341. .. index:: .ROTJ
342. .. _VISUAL_.ROTJ:
343.
344. .ROTJ
345. -----
346.
347. Compute the curl of the current density. Example (use first response vector)::
348.
349.   .ROTJ
350.    PAMXVC 1
351.
352. .. index:: .BDIPX
353. .. _VISUAL_.BDIPX:
354.
355. .BDIPX
356. ------
357.
358. Compute the x-component :math:m^{[1]}_{x}(\mathbf{r})=-\frac{1}{2}(\mathbf{r}\times\mathbf{j})_{x} of the magnetic dipole operator. Example (use first response vector)::
359.
360.   .BDIPX
361.    PAMXVC 1
362.
363. .. index:: .BDIPY
364. .. _VISUAL_.BDIPY:
365.
366. .BDIPY
367. ------
368.
369. Compute the y-component :math:m^{[1]}_{y}(\mathbf{r})=-\frac{1}{2}(\mathbf{r}\times\mathbf{j})_{y} of the magnetic dipole operator. Example (use first response vector)::
370.
371.   .BDIPY
372.    PAMXVC 1
373.
374. .. index:: .BDIPZ
375. .. _VISUAL_.BDIPZ:
376.
377. .BDIPZ
378. ------
379.
380. Compute the z-component :math:m^{[1]}_{z}(\mathbf{r})=-\frac{1}{2}(\mathbf{r}\times\mathbf{j})_{z} of the magnetic dipole operator. Example (use first response vector)::
381.
382.   .BDIPZ
383.    PAMXVC 1
384.
385. .. index:: .EDIPX
386. .. _VISUAL_.EDIPX:
387.
388. .EDIPX
389. ------
390.
391. Compute the x-component :math:Q^{[1]}_{x}(\mathbf{r})=xn(\mathbf{r}) of the electric dipole.
392.
393. .. index:: .EDIPY
394. .. _VISUAL_.EDIPY:
395.
396. .EDIPY
397. ------
398.
399. Compute the y-component :math:Q^{[1]}_{y}(\mathbf{r})=yn(\mathbf{r}) of the electric dipole.
400.
401. .. index:: .EDIPZ
402. .. _VISUAL_.EDIPZ:
403.
404. .EDIPZ
405. ------
406.
407. Compute the z-component :math:Q^{[1]}_{z}(\mathbf{r})=zn(\mathbf{r}) of the electric dipole.
408.
409. .. index:: .ESP
410. .. _VISUAL_.ESP:
411.
412. .ESP
413. ----
414.
415. Compute the electrostatic potential. Example::
416.
417.   .ESP
418.    DFCOEF
419.
420.
421. .. index:: .ESPE
422. .. _VISUAL_.ESPE:
423.
424. .ESPE
425. -----
426.
427. Compute the electronic part of the electrostatic potential.
428.
429.
430. .. index:: .ESPN
431. .. _VISUAL_.ESPN:
432.
433. .ESPN
434. -----
435.
436. Compute the nuclear part of the electrostatic potential.
437.
438.
439. .. index:: .ESPRHO
440. .. _VISUAL_.ESPRHO:
441.
442. .ESPRHO
443. -------
444.
445. Compute the electrostatic potential times density.
446.
447.
448. .. index:: .ESPERHO
449. .. _VISUAL_.ESPERHO:
450.
451. .ESPERHO
452. --------
453.
454. Compute the electronic part of the electrostatic potential times density.
455.
456.
457. .. index:: .ESPNRHO
458. .. _VISUAL_.ESPNRHO:
459.
460. .ESPNRHO
461. --------
462.
463. Compute the nuclear part of the electrostatic potential times density.
464.
465.
466. .. index:: .NDIPX
467. .. _VISUAL_.NDIPX:
468.
469. .NDIPX
470. ------
471.
472. Compute the NMR shielding density, with the "X"-component of the nuclear magnetic dipole moment and
473. the selected component of the magnetically-induced current density (by the chosen record on PAMXVC file) as perturbing operators.
474.
475. .. index:: .NDIPY
476. .. _VISUAL_.NDIPY:
477.
478. .NDIPY
479. ------
480.
481. Compute the NMR shielding density, with the "Y"-component of the nuclear magnetic dipole moment and
482. the selected component of the magnetically-induced current density (by the chosen record on PAMXVC file) as perturbing operators.
483.
484. .. index:: .NDIPZ
485. .. _VISUAL_.NDIPZ:
486.
487. .NDIPZ
488. ------
489.
490. Compute the NMR shielding density, with the "Z"-component of the nuclear magnetic dipole moment and
491. the selected component of the magnetically-induced current density (by the chosen record on PAMXVC file) as perturbing operators.
492.
493. .. index:: .NICS
494. .. _VISUAL_.NICS :
495.
496. .NICS
497. ------
498.
499. Compute the NMR shielding density in a selected point in space. Is used to calculate NICS.
500. Example::
501.
502.   .NICS
503.    1.2 -1.0 2.0
504.
505. will calculate the NMR shielding in point (1.2, -1.0, 2.0). This keyword can be used only with one of: NDIPX, NDIPY, NDIPZ keywords.
506.
507.
510.
512. -------
513.
514. Use the grid and the magnetically-induced current density (jB) from a file to calculate the jB-dependent densities,
515. e.g. the NMR shielding density or the magnetizability density.
516. Example::
517.
519.    file_name        ! a file with x,y,z-coordinates of grid points and jB vector field
520.
521.
522. .. index:: .GAUGE
523. .. _VISUAL_.GAUGE:
524.
525. .GAUGE
526. ------
527.
528. Specify gauge origin. Example::
529.
530.   .GAUGE
531.    0.0 0.0 0.0
532.
533.
534. .. index:: .SMALLAO
535. .. _VISUAL_.SMALLAO:
536.
537. .SMALLAO
538. --------
539.
540. Force evaluation of small component basis functions.
541.
542.
543. .. index:: .OCCUPATION
544. .. _VISUAL_.OCCUPATION:
545.
546. .OCCUPATION
547. -----------
548.
549. Specify occupation of orbitals.
550. Example (neon atom)::
551.
552.   .OCCUPATION
553.    2
554.    1 1-2 1.0
555.    2 1-3 1.0
556.
557. The first line after the keyword gives the number of subsequent lines to read.
558. In each line, the first number is the fermion ircop. In molecules with inversion symmetry
559. there are two fermion ircops: gerade (1) and ungerade (2). Otherwise there is a single fermion ircop (1).
560. The specification of the fermion ircop is followed by the range of selected orbitals and their occupation.
561. If a single orbital is specified a single number is given instead of the range.
562.
563. Another example (water)::
564.
565.   .OCCUPATION
566.    1
567.    1 1-5 1.0
568.
569. Another example (nitrogen atom)::
570.
571.   .OCCUPATION
572.    2
573.    1 1-2 1.0
574.    2 1-3 0.5
575.
576.
577. .. index:: .LONDON
578. .. _VISUAL_.LONDON:
579.
580. .LONDON
581. -------
582.
583. Activate LAO contribution.
584. This keyword is followed by a letter "X", "Y" or "Z" indicating the component of an external perturbing magnetic field.
585. For example::
586.
587.   .LONDON
588.    X
589.
590.
591. .. index:: .NONE
592. .. _VISUAL_.NONE:
593.
594. .NONE
595. -----
596.
597. Select "none" connection when
598. when plotting LAO perturbed densities.
599.
600.
601. .. index:: .NODIRECT
602. .. _VISUAL_.NODIRECT:
603.
604. .NODIRECT
605. ---------
606.
607. Skip direct LAO contribution
608. when plotting perturbed densities.
609.
610.
611. .. index:: .NOREORTHO
612. .. _VISUAL_.NOREORTHO:
613.
614. .NOREORTHO
615. ----------
616.
617. Skip LAO reorthonormalization contribution
618. when plotting perturbed densities.
619.
620.
621. .. index:: .NOKAPPA
622. .. _VISUAL_.NOKAPPA:
623.
624. .NOKAPPA
625. --------
626.
627. Skip orbital relaxation contribution
628. when plotting perturbed densities.