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.  
  60. .. index:: .RADIAL
  61. .. _VISUAL_.RADIAL:
  62.  
  63. .RADIAL
  64. -------
  65.  
  66. Compute radial distributions
  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.  
  75.    .RADIAL
  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.  
  85.    pam --get=plot.radial.scalar ...
  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
  112. using Gauss-Lobatto quadrature.
  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.  
  151. .. index:: .3D_ADD
  152. .. _VISUAL_.3D_ADD:
  153.  
  154. .3D_ADD
  155. -------
  156.  
  157. Add space around the cube file.
  158. Default (coordinates in bohr)::
  159.  
  160.   .3D_ADD
  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.  
  508. .. index:: .READJB
  509. .. _VISUAL_.READJB:
  510.  
  511. .READJB
  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.  
  518.   .READJB
  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.

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