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 the_cosmo_model [2020/06/11 18:17] – external edit 127.0.0.1 the_cosmo_model [2022/08/16 14:15] (current) – external edit 127.0.0.1 2022/08/16 14:15 external edit2020/06/15 17:07 may add examples2020/06/15 14:56 qianli 2020/06/15 14:52 qianli [GOPENMOL — calculate grids for visualization in gOpenMol] 2020/06/11 18:17 external edit 2022/08/16 14:15 external edit2020/06/15 17:07 may add examples2020/06/15 14:56 qianli 2020/06/15 14:52 qianli [GOPENMOL — calculate grids for visualization in gOpenMol] 2020/06/11 18:17 external edit Line 51: Line 51: The non vanishing electron density outside the cavity causes an error that can be corrected by the outlying charge correction. This correction uses the potential on the so called outer surface (defined by the radii $R_i+\mbox{rsolv} \times \mbox{routf}$) to estimate a correction term for the screening charges and the energies (A. Klamt and V. Jonas, [[https://dx.doi.org/10.1063/1.472829|J. Chem. Phys.]] **105**, 9972-9981(1996)). The correction will be performed once at the end of a converged SCF calculation. All corrected values can be found in the COSMO output file. The non vanishing electron density outside the cavity causes an error that can be corrected by the outlying charge correction. This correction uses the potential on the so called outer surface (defined by the radii $R_i+\mbox{rsolv} \times \mbox{routf}$) to estimate a correction term for the screening charges and the energies (A. Klamt and V. Jonas, [[https://dx.doi.org/10.1063/1.472829|J. Chem. Phys.]] **105**, 9972-9981(1996)). The correction will be performed once at the end of a converged SCF calculation. All corrected values can be found in the COSMO output file. - ===== CUBE — dump density or orbital values ===== + Three example inputs can be found in {{:examples:cosmo_water1.inp}}, {{:examples:cosmo_water2.inp}} and {{:examples:cosmo_water3.inp}}. - + - ''CUBE'',//filename,iflag,//$n_1$,$n_2$,$n_3$ + - + - calls a module which dumps the values of various properties on a spatial parallelopipedal grid to an external file. The purpose is to allow plotting of orbitals, densities and other quantities by external programs. The format of the file is intended to be the same as that produced by other programs. + - + - * **//filename//** is the unix path name of the file to be written, and its specification is mandatory. + - * **//iflag//** If //iflag// is negative (default), a formatted file will be written, otherwise unformatted fortran i/o will be used. + - * **$n_1$,$n_2$,$n_3$** specify the number of grid points in each of three dimensions. If not specified, sensible defaults are chosen. + - + - By default, the last density computed is evaluated on the grid, and written to //filename//. This behaviour can be modified by one or more of the following subcommands. + - + - ==== STEP — setting the point spacing ==== + - + - ''STEP'',[//stepx//],[//stepy//], [//stepz//]\\ + - //stepx,stepy, stepz// specify the point spacing in each of three axis directions. By default, the value of //stepx,stepy, stepz// is determined by the number of grid points, the Bragg radii of the atoms, and some related parameters. + - + - ==== DENSITY — source of density ==== + - + - ''DENSITY'',[//density-source//]\\ + - ''GRADIENT'',[//density-source//]\\ + - ''LAPLACIAN'',[//density-source//] + - + - Compute the density and, optionally, its gradient and laplacian. //$<$density-source$>$// may be a record number containing the required density, and may contain further qualification, such as set or state number, in the usual way. By default, the last computed density is taken. + - + - Example: + - + - + - {multi;wf,spin=0,symmetry=1;state,2;dm;orbital,2140.2} + - {cube,multi_1;density,2140.2,state=1.1}   ! cube for state 1 + - {cube,multi_2;density,2140.2,state=2.1}   ! cube for state 2 + - {mrci;wf,spin=0,symmetry=1;state,2;dm,3000.2}   !save densities in record 3000.2 + - {cube,mrci_1;density,3000.2,state=1.1}    ! cube for state 1 + - {cube,mrci_2;density,3000.2,state=2.1}    ! cube for state 2 + - + - ==== ORBITAL — source of orbitals ==== + - + - ''ORBITAL'',[//orbital-list//],[''RECORD=''//orbital-source//] + - + - //$<$orbital-list$>$// is a list of one or more orbital numbers of the form //number.symmetry// or keywords chosen from ''HOMO'', ''LUMO'', ''OCC'' (all occupied orbitals), ''ALL''. If nothing is specified, the default is ''HOMO''. //$<$orbital-source$>$// may be a record number containing the required density, and may contain further qualification, such as set number, in the usual way. By default, the last computed orbitals are taken. + - + - Note that the CUBE file format precludes simultaneous orbital and density dumps, but that this may be achieved in the GOPENMOL format (see [[the COSMO model#GOPENMOL --- calculate grids for visualization in gOpenMol|GOPENMOL --- calculate grids for visualization in gOpenMol]]). + - + - ==== AXIS — direction of grid axes ==== + - + - ''AXIS'',//x,y,z// + - + - //x,y,z// specify the unnormalised direction cosines of one of the three axes defining the grid. Up to three ''AXIS'' commands can be given, but none is required. Axes need not be orthogonal. By default, the first axis is the cartesian $x$, the second is orthogonal to the first and to the cartesian $z$, and the third is orthogonal to the first two. + - + - ==== BRAGG — spatial extent of grid ==== + - + - Based on the direction of the coordinate axes, a parallelopiped (in the usual case of orthogonal axes, a cuboid) is constructed to contain the molecule completely. The atoms are assumed to be spherical, with an extent proportional to their Bragg radii, and the constant of proportionality can be changed from the default value using + - + - ''BRAGG'',//scale// + - + - After the parallelopiped has been constructed, the grid is laid out with equal spacing to cover it using the number of points specified on the ''CUBE'' command. + - + - ==== ORIGIN — centroid of grid ==== + - + - ''ORIGIN'',//x,y,z// + - + - //x,y,z// specify the centroid of the grid. It is usually not necessary to use this option, since the default should suffice for most purposes. + - + - ==== TITLE — user defined title ==== + - + - ''TITLE'',//title// + - + - Set a user defined title in the cube file. + - + - ==== DESCRIPTION — user defined description ==== + - + - ''DESCRIPTION'',//description// + - + - Set a user defined description in the cube file. + - + - ==== Format of cube file ==== + - + - The formatted cube file contains the following records + - + - * **''%%(A)%%''** job title. + - * **''%%(A)%%''** brief description of the file contents. + - * **''%%(I5,3F12.6)%%''** number of atoms, coordinates of grid origin (bohr). + - * **''%%(I5,3F12.6)%%''** number of grid points $n_1$, step vector for first grid dimension. + - * **''%%(I5,3F12.6)%%''** number of grid points $n_2$, step vector for second grid dimension. + - * **''%%(I5,3F12.6)%%''** number of grid points $n_3$, step vector for third grid dimension. + - * **''%%(I5,4F12.6)%%''** atomic number, charge and coordinates; one such record for each atom. + - * **''%%(6E13.5)%%''** $n_1 \times n_2$ records of length $n_3$ containing the values of the density or orbital at each grid point. With default choice of the axes, the inner loop will be over $n_3$ points along the cartesian $z$ axis, and the outer loop over $n_1$ points along the cartesian $x$ axis.\\ + - In the case of a number of orbitals $m$, the record length is $m \times n_3$, with the data for a single grid point grouped together. In the case of the density gradient, there is first a record of length $n_3$ containing the density, then one of length $3n_3$ containing the gradient, with the three cartesian components contiguous. For the laplacian, there is a further record of length $n_3$. + - + - ===== GOPENMOL — calculate grids for visualization in gOpenMol ===== + - + - ''GOPENMOL'',//filename,iflag,//$n_1$,$n_2$,$n_3$ + - + - The syntax and sub-options are exactly the same as for CUBE, except that the files produced are in a format that can be used directly in the [[http://www.csc.fi/~laaksone/gopenmol/gopenmol.html|gOpenMol]] visualization program. The following should be noted. + - + - * Only the base name (up to the last ’.’) in //filename// is used, and is appended by different suffices to create several different files: + - * **.crd** A CHARMm CRD-format file containing the coordinates is always produced, and may be used in the invocation of gOpenMol: ''rungOpenMol'' ''-i''//filename//''.crd'' + - * **''_density.plt''** If ''DENSITY'' is given, then the file //filename//''_density.plt'' is produced and contains the density grid in gOpenMol internal format. + - * **''_orbital_''//number//''.''//symmetry//''.plt''** If ''ORBITAL'' is given, then for each orbital //number//''.''//symmetry// specified, the file //filename//''_orbital_''//number//''.''//symmetry//''.plt'' is produced and contains the orbital grid in gOpenMol internal format. + - * The default is not to produce any orbitals or densities, and so only the atomic coordinates are dumped. + - * The default is to use unformatted binary files, and this should not normally be changed. + - * The ''ORIGIN'' and ''AXIS'' commands should not be used. + - * If ''INTERACT'' is given in the input, when all the grids have been calculated, an attempt is made to start gOpenMol by executing the Unix command ''rungOpenMol''. If ''rungOpenMol'' is not in ''%%\$PATH%%'', then nothing happens. Otherwise, gOpenMol should start and display the molecule. Any ''.plt'' files produced can be added to the display by following the ''Plot'';''Contour'' menu item. The name of the Unix command may be changed from the default ''rungOpenMol'' by specifying it as the first argument to the ''INTERACT'' directive. By default, gOpenMol is not started, and this is equivalent to giving the command ''BATCH''. +