TEXT   11

peqm

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  1. :orphan:
  2.  
  3. .. index:: *PEQM
  4. .. _*PEQM:
  5.  
  6. ======
  7. \*PEQM
  8. ======
  9.  
  10. Polarizable embedding model
  11.  
  12. This input section controls calculations using the polarizable embedding (PE) model.
  13. In DIRAC it is possible to include the effects from a structured environment on a core
  14. molecular system using the polarizable embedding (PE) model. The current implemen-
  15. tation is a layered QM/MM-type embedding model capable of using advanced potentials
  16. that include an electrostatic component as well as an induction (polarization) component.
  17. The effects of the environment are included through effective operators that contain an em-
  18. bedding potential, which is a representation of the environment, thereby directly affecting
  19. the molecular properties of the core system. The wave function of the core system is opti-
  20. mized while taking into account the explicit electrostatic interactions and induction effects
  21. from the environment in a fully self-consistent manner. The electrostatic and induction
  22. components are modeled using Cartesian multipole moments and anisotropic dipole-dipole
  23. polarizabilities, respectively. The electrostatic part models the permanent charge distribu-
  24. tion of the environment and will polarize the core system, while the induction part also
  25. allows polarization of the environment. The environment response is included in the effec-
  26. tive operator as induced dipoles, which arise due to the electric fields from the electrons and
  27. nuclei in the core system as well as from the environment itself. It is therefore necessary
  28. to recalculate the induced dipoles according to the changes in the electron density of the
  29. core system as they occur in a wave function optimization. Furthermore, since the induced
  30. dipoles are coupled through the electric fields, it is necessary to solve a set of coupled linear
  31. equations. This can be done using either an iterative or a direct solver. This also means
  32. that we include many-body effects of the total system.
  33.  
  34. The multipoles and polarizabilities can be obtained in many different ways. It is
  35. possible to use the molecular properties, however, usually distributed/localized properties
  36. are used because of the better convergence of the multipole expansion. These are typically
  37. centered on all atomic sites in the environment (and sometimes also bond-midpoints), how-
  38. ever, the implementation is general in this sense so they can be placed anywhere in space.
  39. Currently, the PE library supports multipole moments up to fifth order and anisotropic
  40. dipole-dipole polarizabilities are supported. For multipoles up to and including third order
  41. (octopoles) the trace will be removed if present. Note, that the fourth and fifth order multi-
  42. pole moments are expected to be traceless. In case polarizabilities are included it might be
  43. necessary to use an exclusion list to ensure that only relevant sites can polarize each other.
  44. The format of the POTENTIAL.INP file is demonstrated below.
  45.  
  46. Keywords
  47. ========
  48.  
  49. .. index:: .POTENTIAL
  50. .. _PEQM_.POTENTIAL:
  51.  
  52. .POTENTIAL
  53. ----------
  54.  
  55. This option can be used to specify a non-default name of the POTENTIAL.INP in-
  56. put file that contains the embedding potential parameters, e.g.::
  57.  
  58.    .POTENT
  59.    peqm.pot
  60.  
  61. The default name is POTENTIAL.INP.
  62.  
  63. .. index:: .DIRECT
  64. .. _PEQM_.DIRECT:
  65.  
  66. .DIRECT
  67. -------
  68.  
  69. Use the direct solver to determine the induced dipole moments. It will explicitly build
  70. a classical response matrix of size :math:`3S(3S + 1)/2`, where :math:`S` is the number of polarizable
  71. sites and is therefore only recommendable for smaller molecular systems. Note that
  72. this solver is not parallelized. The default is to use the iterative solver
  73.  
  74. .. index:: .ITERATIVE
  75. .. _PEQM_.ITERATIVE:
  76.  
  77. .ITERATIVE
  78. ----------
  79.  
  80. Use the iterative solver to determine the induced dipole moments. This is the
  81. default. The convergence threshold defaults to :math:`1.0\cdot 10^{-8}>\sum^S_{s=1}|\mu^{(k)}_s-\mu^{(k-1)}_s|`, where :math:`k` is the
  82. current iteration, but can also be provided with this option::
  83.  
  84.   READ (LUCMD, *) THRITER (optional)
  85.  
  86. .. index:: .BORDER
  87. .. _PEQM_.BORDER:
  88.  
  89. .BORDER
  90. -------
  91.  
  92. Controls the handling of the border between the core molecular system and its en-
  93. vironment described by the embedding potential.::
  94.  
  95.    1) READ (LUCMD, *) BORDER_TYPE, RMIN, AUORAA
  96.    2) READ (LUCMD, *) BORDER_TYPE, REDIST_ORDER, RMIN, AUORAA, NREDIST
  97.  
  98. There are two mutually exclusive schemes:
  99.    1) BORDER_TYPE = REMOVE
  100.    2) BORDER_TYPE = REDIST
  101.  
  102. The first option will remove all multipoles and polarizabilities that are within the given distance "RMIN" from any atom in the core molecular system. The "AUORAA" variable specifies
  103. whether the distance threshold is given in ångström ("AA") or bohr ("AU"). The second
  104. option will redistribute parameters that are within the given threshold "RMIN" from any
  105. atom in the core system to nearest sites in the environment. The order of multipoles
  106. up to which will be redistributed is determined by the "REDIST_ORDER" variable, e.g.
  107. "REDIST_ORDER = 1" means that only charges will be redistributed and all other pa-
  108. rameters removed, "REDIST_ORDER = 2" means charges and dipoles are redistributed
  109. and so on. The sign of "REDIST_ORDER" specifies if the polarizabilities are redistributed.
  110. Positive means that the polarizabilities are removed and negative means redistributed.
  111. The number of sites that parameters on a given site are redistributed to is determined
  112. by the "NREDIST" variable which can be between 1 and 3. The default is to redistribute
  113. charges within 2.2 bohr to its nearest site and removing all other parameters.
  114.  
  115. .. index:: .DAMP INDUCED
  116. .. _PEQM_.DAMP INDUCED:
  117.  
  118. .DAMP INDUCED
  119. -------------
  120.  
  121. Damp the electric fields from induced dipole moments using Thole’s exponential damp-
  122. ing scheme.::
  123.  
  124.   READ (LUCMD, *) IND_DAMP (optional)
  125.  
  126. The default damping coefficient is the standard 2.1304.
  127.  
  128. .. index:: .DAMP MULTIPOLE
  129. .. _PEQM_.DAMP MULTIPOLE:
  130.  
  131. .DAMP MULTIPOLE
  132. ---------------
  133.  
  134. Damp the electric fields from permanent multipole moments using Thole’s expo-
  135. nential damping scheme.::
  136.  
  137.   READ (LUCMD, *) MUL_DAMP (optional)
  138.  
  139. This option requires polarizabilities on all sites with permanent multipole moments. The default damping coefficient is the standard 2.1304.
  140.  
  141. .. index:: .DAMP CORE
  142. .. _PEQM_.DAMP CORE:
  143.  
  144. .DAMP CORE
  145. ----------
  146.  
  147. Damp the electric fields from the electrons and nuclei in the core region based on
  148. Thole’s exponential damping scheme::
  149.  
  150.    READ (LUCMD, *) CORE_DAMP (optional)
  151.    READ (LUCMD, *) NALPHAS
  152.    DO I = 1, NALPHAS
  153.       READ (LUCMD, *) ISO_ALPHA(I)
  154.    END DO
  155.  
  156. The damping coefficient is optional unless isotropic polarizabilities are present. The default damping coefficient is the standard 2.1304. Standard polarizabilities from :cite:`vanduijnen1998`
  157. have been implemented and will be used if none are given as input. However, only H, C, N, O, F, S, Cl, Br and I are available.
  158.  
  159. .. index:: .GSPOL
  160. .. _PEQM_.GSPOL:
  161.  
  162. .GSPOL
  163. ------
  164.  
  165. Activate the ground-state polarization approximation, i.e. freeze the embedding po-
  166. tential according to the ground-state density. This means that the polarizable envi-
  167. ronment is self-consistently relaxed during the optimization of the ground-state den-
  168. sity/wave function of the core molecular system and then kept frozen in any following
  169. response calculations
  170.  
  171. .. index:: .NOMB
  172. .. _PEQM_.NOMB:
  173.  
  174. .NOMB
  175. -----
  176.  
  177. Remove many-body effects in the environment. This is done by deactivating interac-
  178. tions between inducible dipole moments.
  179.  
  180. .. index:: .RESTART
  181. .. _PEQM_.RESTART:
  182.  
  183. .RESTART
  184. --------
  185.  
  186. Use any existing files to restart calculation.
  187.  
  188. .. index:: .CUBE
  189. .. _PEQM_.CUBE:
  190.  
  191. .CUBE
  192. -----
  193.  
  194. Create cube file for the core molecular system containing the electrostatic potential due
  195. to the final converged polarizable embedding potential.::
  196.  
  197.    1) READ (LUCMD, *) STD_GRID
  198.    2) READ (LUCMD, *) OPTION
  199.    2) IF (OPTION == ’GRID’) THEN
  200.    2)    READ (LUCMD, *) XSIZE, XGRID, YSIZE, YGRID, ZSIZE, ZGRID
  201.    2) END IF
  202.    IF (OPTION == ’FIELD’) THEN
  203.       FIELD = .TRUE.
  204.    END IF
  205.  
  206. The grid density can be spec-
  207. ified either using 1) standard grids (COARSE (3 points/bohr), MEDIUM (6 points/bohr)
  208. or FINE (12 points/bohr) and in all cases 8.0 bohr are added in each direction) or
  209. 2) the GRID option which gives full control of the cube size and density, and requires
  210. an additional input line specifying the extent added (in bohr) in each direction and
  211. density (in points/bohr). The default grid density is MEDIUM and default cube size
  212. is the extent of the molecule plus 8.0 bohr in plus and minus each Cartesian coordi-
  213. nate. If the FIELD option is given then also three cube files containing the Cartesian
  214. components of the electric field from the embedding potential will be created.  
  215.  
  216. .. index:: .ISOPOL
  217. .. _PEQM_.ISOPOL:
  218.  
  219. .ISOPOL
  220. -------
  221.  
  222. Converts all anisotropic polarizabilities into isotropic polarizabilities.
  223.  
  224. .. index:: .ZEROPOL
  225. .. _PEQM_.ZEROPOL:
  226.  
  227. .ZEROPOL
  228. --------
  229.  
  230. Remove all polarizabilities
  231.  
  232. .. index:: .ZEROMUL
  233. .. _PEQM_.ZEROMUL:
  234.  
  235. .ZEROMUL
  236. --------
  237.  
  238. Remove all multipoles of order ZEROMUL_ORDER and up.::
  239.  
  240.    READ (LUCMD, *) ZEROMUL_ORDER (optional)
  241.  
  242. Remove all multipoles of order ZEROMUL_ORDER and up. The default is to remove all
  243. dipoles and higher-order multipoles (i.e. ZEROMUL_ORDER = 1).
  244.  
  245. .. index:: .VERBOSE
  246. .. _PEQM_.VERBOSE:
  247.  
  248. .VERBOSE
  249. --------
  250.  
  251. Verbose output. Currently this will print the final converged induced dipole moments.
  252.  
  253. .. index:: .DEBUG
  254. .. _PEQM_.DEBUG:
  255.  
  256. .DEBUG
  257. ------
  258.  
  259. Debug output. Prints the total electric field and the induced dipole moments in each
  260. iteration. WARNING: for large systems this will produce very large output files.
  261.  
  262.  
  263.    
  264. The potential input format
  265. ==========================
  266.  
  267. The POTENTIAL.INP file is split into three sections: @COORDINATES, @MULTIPOLES and
  268. @POLARIZABILITIES. The format is perhaps best illustrated using an example:
  269.  
  270. .. literalinclude:: ../tutorials/polarizable_embedding/3_h2o.pot
  271.  
  272. @COORDINATES
  273. ------------
  274.  
  275. The coordinates section follows the standard XYZ file format so that the environment can
  276. be easily visualized using standard programs. The first line in gives the total number of
  277. sites in the environment and the second line specifies whether the coordinates are given in
  278. ångström (AA) or bohr (AU). The rest of the coordinates section is a list of the sites in the
  279. environment where each line contains the element symbol and x-, y- and z-coordinates of
  280. a site. If a site is not located on an atom, e.g. if it is a bond-midpoint, then the element
  281. symbol should be specified as X. The listing also gives an implicit numbering of the sites,
  282. so that the first line is site number one, the second line is site number two and so on. This
  283. numbering is important and used in the following sections.
  284.  
  285. @MULTIPOLES
  286. -----------
  287. The multipoles section is subdivided into the orders of the multipoles, i.e. ORDER 0
  288. for monopoles/charges, ORDER 1 for dipoles and so on. For each order there is a number
  289. specifying the number of multipoles of that specific order. Note, that this number does
  290. not have to be equal to the total number of sites. This is followed by a list of multipoles
  291. where each line gives the multipole of a site. The lines begin with a number that specifies
  292. which site the multipole is placed. Only the symmetry-independent Cartesian multipoles
  293. (given in a.u.) should be provided using an ordering such that the components are stepped
  294. from the right, e.g. xx xy xz yy yz zz or xxx xxy xxz xyy xyz xzz yyy yyz yzz zzz.
  295. Note, that the multipoles should in general be traceless, however, for multipoles up to and
  296. including octopoles (i.e. ORDER 3) the trace is removed if present. Furthermore, the current
  297. implementation is limited to fifth order multipoles.
  298.  
  299. @POLARIZABILITIES
  300. -----------------
  301.  
  302. The polarizabilities section is also subdivided into orders, i.e. ORDER 1 1 for dipole-dipole
  303. polarizabilities, which is the only type supported in the current release. The format is the
  304. same as for multipoles, i.e. first line contains number of polarizabilities which is followed by
  305. a list of the polarizabilities using the same ordering as the multipoles. The polarizabilities
  306. should also be given in a.u. In addition, there is also the exclusion lists (EXCLISTS section).
  307. Here the first line gives the number of lists (i.e. the number of lines) and the length of the
  308. exclusion lists (i.e. the number of entries per line). The exclusion lists specify the polar-
  309. ization rules. There is a list attached to each polarizable site that specifies which sites are
  310. not allowed to polarize it, e.g. 1 2 3 4 5 means that site number 1 cannot be polarized by
  311. si

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