From e3c78b70ed02f41171ff68d593f79f85b1e8dd00 Mon Sep 17 00:00:00 2001 From: Karl Hammond Date: Thu, 13 Oct 2022 23:00:13 -0500 Subject: [PATCH] Fixed remaining discrepancies between lists of keywords and doc of them --- doc/src/compute_displace_atom.rst | 2 +- doc/src/compute_voronoi_atom.rst | 2 +- doc/src/create_atoms.rst | 2 +- doc/src/delete_bonds.rst | 11 +++++++++-- doc/src/kspace_modify.rst | 2 +- doc/src/prd.rst | 2 +- doc/src/processors.rst | 9 ++++----- doc/src/tad.rst | 2 +- doc/src/velocity.rst | 2 +- 9 files changed, 20 insertions(+), 14 deletions(-) diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 5d52ab947d..a2b1d946ae 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -17,7 +17,7 @@ Syntax .. parsed-literal:: - *replace* arg = name of per-atom variable + *refresh* arg = name of per-atom variable Examples """""""" diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index 19914997a3..274be1b702 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -13,7 +13,7 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * voronoi/atom = style name of this compute command * 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:: diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 95d0abd240..8a0cc8812f 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -28,7 +28,7 @@ Syntax region-ID = create atoms within this region, use NULL for entire simulation box * 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:: diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index ac2ffb3452..0b30ae5588 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -26,6 +26,13 @@ Syntax * zero or more keywords may be appended * 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 """""""" @@ -101,13 +108,13 @@ Several keywords can be appended to the argument list to alter the default behaviors. 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 the specified group, it will be turned off (or on if the *undo* keyword is used). 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 example, for style *angle*, if *type* is specified as 2, then all angles with current type = :math:`-2` are reset to type = :math:`2`. diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index b1d6efa86c..3c6fccc285 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -11,7 +11,7 @@ Syntax kspace_modify keyword value ... * 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:: diff --git a/doc/src/prd.rst b/doc/src/prd.rst index 758aa4f570..0f6e9e481f 100644 --- a/doc/src/prd.rst +++ b/doc/src/prd.rst @@ -18,7 +18,7 @@ Syntax * compute-ID = ID of the compute used for event detection * random_seed = random # seed (positive integer) * 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:: diff --git a/doc/src/processors.rst b/doc/src/processors.rst index d717fa9b73..e4279c00ea 100644 --- a/doc/src/processors.rst +++ b/doc/src/processors.rst @@ -18,18 +18,17 @@ Syntax *grid* arg = gstyle params ... gstyle = *onelevel* or *twolevel* or *numa* or *custom* - onelevel params = none - twolevel params = Nc Cx Cy Cz + *onelevel* params = none + *twolevel* params = Nc Cx Cy Cz Nc = number of cores per node Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node - numa params = none - custom params = infile + *numa* params = none + *custom* params = infile infile = file containing grid layout *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/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 - *numa* arg = none *part* args = Psend Precv cstyle Psend = partition # (1 to Np) which will send its processor layout Precv = partition # (1 to Np) which will recv the processor layout diff --git a/doc/src/tad.rst b/doc/src/tad.rst index b36ad2e431..cc6d52d415 100644 --- a/doc/src/tad.rst +++ b/doc/src/tad.rst @@ -18,7 +18,7 @@ Syntax * tmax = reciprocal of lowest expected pre-exponential factor (time units) * compute-ID = ID of the compute used for event detection * 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:: diff --git a/doc/src/velocity.rst b/doc/src/velocity.rst index cd283de399..c1afaf2edc 100644 --- a/doc/src/velocity.rst +++ b/doc/src/velocity.rst @@ -33,7 +33,7 @@ Syntax *angular* = zero the angular momentum * 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::