From 57940c47b65c0bbfb812b359cf9aa66ad6dc7bc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Edoardo=20Apr=C3=A0?= Date: Wed, 1 Nov 2023 12:19:14 -0700 Subject: [PATCH] formatting --- Keywords-for-the-GEOMETRY-directive.md | 72 ++++++++++++++++---------- 1 file changed, 46 insertions(+), 26 deletions(-) diff --git a/Keywords-for-the-GEOMETRY-directive.md b/Keywords-for-the-GEOMETRY-directive.md index 7efd0dec..a0ac9d3b 100644 --- a/Keywords-for-the-GEOMETRY-directive.md +++ b/Keywords-for-the-GEOMETRY-directive.md @@ -18,13 +18,16 @@ form, All of the keywords and input on this line are optional. The following list describes all options and their defaults. - - `` - user-supplied name for the geometry; the default name is +### NAME +`` is a user-supplied name for the geometry; the default name is geometry, and all NWChem modules look for a geometry with this name. However, multiple geometries may be specified by using a different name for each. Subsequently, the user can direct a module to a named geometry by using the [SET](SET.md) directive (see the example in the [SET Section](SET.md)) to associate the default name of geometry with the alternate name. - - `units` - keyword specifying that a value will be entered by the user + + ### UNITS + The `units` keyword specifies what value will be entered by the user for the string variable . The default units for the geometry input are Angstrøms (Note: atomic units or Bohr are used within the code, regardless of the option specified for the input units. The @@ -32,35 +35,45 @@ list describes all options and their defaults. to Bohr is 1.8897265 which may be overidden with the `angstrom_to_au` keyword described below.). The code recognizes the - following possible values for the string variable : - - `angstroms` or `an` -- Angstroms , the default (converts to A.U. - using the Angstrom to A.U. conversion factor) - - `au` or `atomic` or `bohr` -- Atomic units (A.U.) - - `nm` or `nanometers` -- nanometers (converts to A.U. using a - conversion factor computed as 10.0 times the Angstrom to A.U. - conversion factor) - - `pm` or `picometers` -- `picometers` (converts to A.U. using a - conversion factor computed as 0.01 times the Angstrom to A.U. - conversion factor) - - `angstrom_to_au` - may also be specified as `ang2au`. This enables the + following possible values for the string variable : +* `angstroms` or `an`: Angstrøms , the default (converts to A.U. + using the Angstrøm to A.U. conversion factor) +* `au` or `atomic` or `bohr`: Atomic units (A.U.) +* `nm` or `nanometers`: nanometers (converts to A.U. using a + conversion factor computed as 10.0 times the Angstrøm to A.U. + conversion factor) +* `pm` or `picometers`: `picometers` (converts to A.U. using a + conversion factor computed as 0.01 times the Angstrøm to A.U. + conversion factor) + +### ANGSTROM_TO_AU + The `angstrom_to_au` option may also be specified as `ang2au`. This enables the user to modify the conversion factors used to convert between - Angstrom and A.U.. The default value is 1.8897265. - - `bqbq` - keyword to specify the treatment of interactions between + Angstrøm and A.U.. The default value is 1.8897265. + + ### BQBQ + The `bqbq` keyword specifies the treatment of interactions between dummy centers. The default in NWChem is to ignore such interactions when computing energies or energy derivatives. These interactions will be included if the keyword `bqbq` is specified. - - `print` and `noprint` - complementary keyword pair to enable or disable + + ### PRINT/NOPRINT + `print` and `noprint` is a complementary keyword pair to enable or disable printing of the geometry. The default is to print the output associated with the geometry. In addition, the keyword print may be qualified by the additional keyword xyz, which specifies that the coordinates should be printed in the XYZ format of molecular graphics program XMol - - `center` and `nocenter` - complementary keyword pair to enable or + + ### CENTER/NOCENTER + `center` and `nocenter` is a complementary keyword pair to enable or disable translation of the center of nuclear charge to the origin. With the origin at this position, all three components of the nuclear dipole are zero. The default is to move the center of nuclear charge to the origin. - - `autosym` and `noautosym` - keyword to specify that the symmetry of the + + ### AUTOSYM/NOAUTOSYM + `autosym` and `noautosym` are keywords to specify that the symmetry of the geometric system should be automatically determined. This option is on by default, but can be turned off with noautosym. Only groups up to and including Oh are recognized. Occasionally NWChem will @@ -77,7 +90,10 @@ list describes all options and their defaults. tags might be assigned different basis sets, for example, after which they are no longer symmetry equivalent. Therefore autosym chooses to make the save choice. - - `noautoz` - by default NWChem (release 3.3 and later) will generate + + ### NOAUTOZ + +`noautoz` - by default NWChem (release 3.3 and later) will generate redundant internal coordinates from user input Cartesian coordinates. The internal coordinates will be used in geometry optimizations. The `noautoz` keyword disables use of internal @@ -87,19 +103,23 @@ list describes all options and their defaults. a more detailed description of redundant internal coordinates, including how to force the definition of specific internal variables in combination with automatically generated variables. - - `adjust` - This indicates that an existing geometry is to be adjusted. + + ### ADJUST + Use of the `adjust` keyword indicates that an existing geometry is to be adjusted. Only new input for the redundant internal coordinates may be provided ([ZCOORD: Forcing internal coordinates](ZCOORD-Forcing-internal-coordinates.md)). It is not possible to define new centers or to modify the point group using this keyword. See the section [use of the adjust keyword](ZCOORD-Forcing-internal-coordinates.md#how-to-use-the-adjust-keyword) for an example of its usage. - - `nucleus` - keyword to specify the default model for the nuclear - charge distribution. The following values are recognized: - - `point` or `pt` -- point nuclear charge distribution. This is the - default. - - `finite` or `fi` -- finite nuclear charge distribution with a - Gaussian shape. The RMS radius of the Gaussian is determined + + ### NUCLEUS + The `nucleus` keyword to specifies the default model for the nuclear + charge distribution. The following values are recognized: +* `point` or `pt`: point nuclear charge distribution. This is the default. +* `finite` or `fi`: finite nuclear charge distribution with a + Gaussian shape. +The RMS radius of the Gaussian is determined from the nuclear mass number A by the expression 
r RMS = 0.836*A1/3+0.57 fm