Fixed remaining discrepancies between lists of keywords and doc of them

This commit is contained in:
Karl Hammond
2022-10-13 23:00:13 -05:00
parent edcdedc574
commit e3c78b70ed
9 changed files with 20 additions and 14 deletions

View File

@ -17,7 +17,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*replace* arg = name of per-atom variable *refresh* arg = name of per-atom variable
Examples Examples
"""""""" """"""""

View File

@ -13,7 +13,7 @@ Syntax
* ID, group-ID are documented in :doc:`compute <compute>` command * ID, group-ID are documented in :doc:`compute <compute>` command
* voronoi/atom = style name of this compute command * voronoi/atom = style name of this compute command
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom* * keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
.. parsed-literal:: .. parsed-literal::

View File

@ -28,7 +28,7 @@ Syntax
region-ID = create atoms within this region, use NULL for entire simulation box region-ID = create atoms within this region, use NULL for entire simulation box
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *overlap* or *maxtry* or *units* * keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *radscale* or *meshmode* or *rotate* or *overlap* or *maxtry* or *units*
.. parsed-literal:: .. parsed-literal::

View File

@ -26,6 +26,13 @@ Syntax
* zero or more keywords may be appended * zero or more keywords may be appended
* keyword = *any* or *undo* or *remove* or *special* * keyword = *any* or *undo* or *remove* or *special*
.. parsed-literal::
*any* arg = none = turn off interactions if any atoms are in the group (or on if *undo* is also used)
*undo* arg = none = turn specified bonds on instead of off
*remove* arg = permanently remove bonds that have been turned off
*special* arg = recompute pairwise 1-2, 1-3, and 1-4 lists
Examples Examples
"""""""" """"""""
@ -101,13 +108,13 @@ Several keywords can be appended to the argument list to alter the
default behaviors. default behaviors.
The *any* keyword changes the requirement that all atoms in the bond The *any* keyword changes the requirement that all atoms in the bond
(angle, etc) must be in the specified group in order to turn off the (angle, etc.) must be in the specified group in order to turn off the
interaction. Instead, if any of the atoms in the interaction are in interaction. Instead, if any of the atoms in the interaction are in
the specified group, it will be turned off (or on if the *undo* the specified group, it will be turned off (or on if the *undo*
keyword is used). keyword is used).
The *undo* keyword inverts the delete_bonds command so that the The *undo* keyword inverts the delete_bonds command so that the
specified bonds, angles, etc are turned on if they are currently specified bonds, angles, etc. are turned on if they are currently
turned off. This means a negative value is toggled to positive. For turned off. This means a negative value is toggled to positive. For
example, for style *angle*, if *type* is specified as 2, then all example, for style *angle*, if *type* is specified as 2, then all
angles with current type = :math:`-2` are reset to type = :math:`2`. angles with current type = :math:`-2` are reset to type = :math:`2`.

View File

@ -11,7 +11,7 @@ Syntax
kspace_modify keyword value ... kspace_modify keyword value ...
* one or more keyword/value pairs may be listed * one or more keyword/value pairs may be listed
* keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol* * keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol* or *wire*
.. parsed-literal:: .. parsed-literal::

View File

@ -18,7 +18,7 @@ Syntax
* compute-ID = ID of the compute used for event detection * compute-ID = ID of the compute used for event detection
* random_seed = random # seed (positive integer) * random_seed = random # seed (positive integer)
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *min* or *temp* or *vel* * keyword = *min* or *temp* or *vel* or *time*
.. parsed-literal:: .. parsed-literal::

View File

@ -18,18 +18,17 @@ Syntax
*grid* arg = gstyle params ... *grid* arg = gstyle params ...
gstyle = *onelevel* or *twolevel* or *numa* or *custom* gstyle = *onelevel* or *twolevel* or *numa* or *custom*
onelevel params = none *onelevel* params = none
twolevel params = Nc Cx Cy Cz *twolevel* params = Nc Cx Cy Cz
Nc = number of cores per node Nc = number of cores per node
Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
numa params = none *numa* params = none
custom params = infile *custom* params = infile
infile = file containing grid layout infile = file containing grid layout
*map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx* *map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0 cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1 cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
*numa* arg = none
*part* args = Psend Precv cstyle *part* args = Psend Precv cstyle
Psend = partition # (1 to Np) which will send its processor layout Psend = partition # (1 to Np) which will send its processor layout
Precv = partition # (1 to Np) which will recv the processor layout Precv = partition # (1 to Np) which will recv the processor layout

View File

@ -18,7 +18,7 @@ Syntax
* tmax = reciprocal of lowest expected pre-exponential factor (time units) * tmax = reciprocal of lowest expected pre-exponential factor (time units)
* compute-ID = ID of the compute used for event detection * compute-ID = ID of the compute used for event detection
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *min* or *neb* or *min_style* or *neb_style* or *neb_log* * keyword = *min* or *neb* or *neb_style* or *neb_step* or *neb_log*
.. parsed-literal:: .. parsed-literal::

View File

@ -33,7 +33,7 @@ Syntax
*angular* = zero the angular momentum *angular* = zero the angular momentum
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *units* * keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *rigid* or *units*
.. parsed-literal:: .. parsed-literal::