Fixed remaining discrepancies between lists of keywords and doc of them
This commit is contained in:
@ -17,7 +17,7 @@ Syntax
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.. parsed-literal::
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.. parsed-literal::
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*replace* arg = name of per-atom variable
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*refresh* arg = name of per-atom variable
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Examples
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Examples
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""""""""
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""""""""
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@ -13,7 +13,7 @@ Syntax
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* voronoi/atom = style name of this compute command
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* voronoi/atom = style name of this compute command
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
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* keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
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.. parsed-literal::
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.. parsed-literal::
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@ -28,7 +28,7 @@ Syntax
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region-ID = create atoms within this region, use NULL for entire simulation box
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region-ID = create atoms within this region, use NULL for entire simulation box
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *overlap* or *maxtry* or *units*
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* 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*
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.. parsed-literal::
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.. parsed-literal::
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@ -26,6 +26,13 @@ Syntax
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* zero or more keywords may be appended
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* zero or more keywords may be appended
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* keyword = *any* or *undo* or *remove* or *special*
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* keyword = *any* or *undo* or *remove* or *special*
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.. parsed-literal::
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*any* arg = none = turn off interactions if any atoms are in the group (or on if *undo* is also used)
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*undo* arg = none = turn specified bonds on instead of off
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*remove* arg = permanently remove bonds that have been turned off
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*special* arg = recompute pairwise 1-2, 1-3, and 1-4 lists
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Examples
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Examples
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""""""""
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""""""""
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@ -101,13 +108,13 @@ Several keywords can be appended to the argument list to alter the
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default behaviors.
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default behaviors.
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The *any* keyword changes the requirement that all atoms in the bond
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The *any* keyword changes the requirement that all atoms in the bond
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(angle, etc) must be in the specified group in order to turn off the
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(angle, etc.) must be in the specified group in order to turn off the
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interaction. Instead, if any of the atoms in the interaction are in
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interaction. Instead, if any of the atoms in the interaction are in
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the specified group, it will be turned off (or on if the *undo*
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the specified group, it will be turned off (or on if the *undo*
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keyword is used).
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keyword is used).
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The *undo* keyword inverts the delete_bonds command so that the
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The *undo* keyword inverts the delete_bonds command so that the
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specified bonds, angles, etc are turned on if they are currently
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specified bonds, angles, etc. are turned on if they are currently
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turned off. This means a negative value is toggled to positive. For
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turned off. This means a negative value is toggled to positive. For
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example, for style *angle*, if *type* is specified as 2, then all
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example, for style *angle*, if *type* is specified as 2, then all
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angles with current type = :math:`-2` are reset to type = :math:`2`.
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angles with current type = :math:`-2` are reset to type = :math:`2`.
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@ -11,7 +11,7 @@ Syntax
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kspace_modify keyword value ...
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kspace_modify keyword value ...
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* one or more keyword/value pairs may be listed
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* one or more keyword/value pairs may be listed
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* 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*
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* 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*
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.. parsed-literal::
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.. parsed-literal::
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@ -18,7 +18,7 @@ Syntax
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* compute-ID = ID of the compute used for event detection
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* compute-ID = ID of the compute used for event detection
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* random_seed = random # seed (positive integer)
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* random_seed = random # seed (positive integer)
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *min* or *temp* or *vel*
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* keyword = *min* or *temp* or *vel* or *time*
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.. parsed-literal::
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.. parsed-literal::
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@ -18,18 +18,17 @@ Syntax
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*grid* arg = gstyle params ...
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*grid* arg = gstyle params ...
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gstyle = *onelevel* or *twolevel* or *numa* or *custom*
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gstyle = *onelevel* or *twolevel* or *numa* or *custom*
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onelevel params = none
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*onelevel* params = none
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twolevel params = Nc Cx Cy Cz
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*twolevel* params = Nc Cx Cy Cz
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Nc = number of cores per node
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Nc = number of cores per node
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Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
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Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
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numa params = none
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*numa* params = none
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custom params = infile
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*custom* params = infile
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infile = file containing grid layout
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infile = file containing grid layout
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*map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
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*map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
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cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
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cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
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cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
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cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
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xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
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xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
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*numa* arg = none
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*part* args = Psend Precv cstyle
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*part* args = Psend Precv cstyle
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Psend = partition # (1 to Np) which will send its processor layout
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Psend = partition # (1 to Np) which will send its processor layout
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Precv = partition # (1 to Np) which will recv the processor layout
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Precv = partition # (1 to Np) which will recv the processor layout
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@ -18,7 +18,7 @@ Syntax
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* tmax = reciprocal of lowest expected pre-exponential factor (time units)
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* tmax = reciprocal of lowest expected pre-exponential factor (time units)
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* compute-ID = ID of the compute used for event detection
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* compute-ID = ID of the compute used for event detection
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *min* or *neb* or *min_style* or *neb_style* or *neb_log*
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* keyword = *min* or *neb* or *neb_style* or *neb_step* or *neb_log*
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.. parsed-literal::
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.. parsed-literal::
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@ -33,7 +33,7 @@ Syntax
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*angular* = zero the angular momentum
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*angular* = zero the angular momentum
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *units*
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* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *rigid* or *units*
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.. parsed-literal::
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.. parsed-literal::
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