diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 74ae16820c..b753fdbe5f 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -10,7 +10,7 @@ Syntax atom_style style args -* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid* +* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *mesont* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid* .. parsed-literal:: diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index 42a5ca9301..9d36827c25 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -15,7 +15,7 @@ Syntax .. parsed-literal:: - style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name + style = *bin/1d* or *bin/2d* or *bin/3d* or *bin/sphere* or *bin/cylinder* or *type* or *molecule* or c_ID, c_ID[I], f_ID, f_ID[I], v_name *bin/1d* args = dim origin delta dim = *x* or *y* or *z* origin = *lower* or *center* or *upper* or coordinate value (distance units) @@ -49,7 +49,7 @@ Syntax v_name = per-atom vector calculated by an atom-style variable with name * zero or more keyword/values pairs may be appended -* keyword = *region* or *nchunk* or *static* or *compress* or *bound* or *discard* or *pbc* or *units* +* keyword = *region* or *nchunk* or *limit* or *ids* or *compress* or *discard* or *bound* or *pbc* or *units* .. parsed-literal:: @@ -74,7 +74,7 @@ Syntax no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID mixed = keep or discard such atoms according to spatial binning rule *bound* values = x/y/z lo hi - x/y/z = *x* or *y* or *z* to bound sptial bins in this dimension + x/y/z = *x* or *y* or *z* to bound spatial bins in this dimension lo = *lower* or coordinate value (distance units) hi = *upper* or coordinate value (distance units) *pbc* value = *no* or *yes* diff --git a/doc/src/compute_orientorder_atom.rst b/doc/src/compute_orientorder_atom.rst index bc608e21d7..82c7c57495 100644 --- a/doc/src/compute_orientorder_atom.rst +++ b/doc/src/compute_orientorder_atom.rst @@ -19,12 +19,12 @@ Syntax .. parsed-literal:: - keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize* + keyword = *cutoff* or *nnn* or *degrees* or *wl* or *wl/hat* or *components* or *chunksize* *cutoff* value = distance cutoff *nnn* value = number of nearest neighbors *degrees* values = nlvalues, l1, l2,... - *wl* value = yes or no - *wl/hat* value = yes or no + *wl* value = *yes* or *no* + *wl/hat* value = *yes* or *no* *components* value = ldegree *chunksize* value = number of atoms in each pass diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 37ee302f8f..6704d8f0d6 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -41,8 +41,8 @@ Examples compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo - fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed - fix saed/vtk 1 1 1 c_2 file Ni_000.saed + fix 1 all saed/vtk 1 1 1 c_1 file Al2O3_001.saed + fix 2 all saed/vtk 1 1 1 c_2 file Ni_000.saed Description """"""""""" diff --git a/doc/src/compute_smd_triangle_vertices.rst b/doc/src/compute_smd_triangle_vertices.rst index 9f478b7262..d1aebfb29e 100644 --- a/doc/src/compute_smd_triangle_vertices.rst +++ b/doc/src/compute_smd_triangle_vertices.rst @@ -18,7 +18,7 @@ Examples .. code-block:: LAMMPS - compute 1 all smd/triangle/mesh/vertices + compute 1 all smd/triangle/vertices Description """"""""""" diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 664d870cb0..1f468dd42a 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -10,7 +10,7 @@ Syntax create_bonds style args ... keyword value ... -* style = *many* or *single/bond* or *single/angle* or *single/dihedral* +* style = *many* or *single/bond* or *single/angle* or *single/dihedral* or *single/improper* .. parsed-literal:: diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 9777f16cc9..f70570c040 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -55,7 +55,7 @@ Examples delete_atoms random fraction 0.1 yes all cube 482793 bond yes delete_atoms random fraction 0.3 no polymer NULL 482793 bond yes delete_atoms random count 500 no ions NULL 482793 - detele_atoms variable checkers + delete_atoms variable checkers Description """"""""""" diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 0f481f917d..8c741faaf3 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -8,7 +8,10 @@ Syntax .. code-block:: LAMMPS - dihedral_style zero [nocoeff] + dihedral_style zero keyword + +* zero or more keywords may be appended +* keyword = *nocoeff* Examples """""""" diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 9916126dad..fb9239d9de 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -36,7 +36,7 @@ Syntax .. parsed-literal:: keyword = *units* - value = *box* or *lattice* + *units* value = *box* or *lattice* Examples """""""" diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 778b6f6682..b0b7b7abae 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -61,7 +61,7 @@ Syntax * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be dumped -* style = *atom* or *atom/gz* or *atom/zstd or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* +* style = *atom* or *atom/gz* or *atom/zstd* or *atom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *dcd* or *h5md* or *image* or *local* or *local/gz* or *local/zstd* or *molfile* or *movie* or *netcdf* or *netcdf/mpiio* or *vtk* or *xtc* or *xyz* or *xyz/gz* or *xyz/zstd* or *xyz/mpiio* or *yaml* * N = dump every this many timesteps * file = name of file to write dump info to * args = list of arguments for a particular style @@ -96,7 +96,7 @@ Syntax *xyz/mpiio* args = none *yaml* args = same as *custom* args, see below -* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes +* *custom* or *custom/gz* or *custom/zstd* or *custom/mpiio* or *cfg* or *cfg/gz* or *cfg/zstd* or *cfg/mpiio* or *cfg/uef* or *netcdf* or *netcdf/mpiio* or *yaml* args = list of atom attributes .. parsed-literal:: diff --git a/doc/src/dump_h5md.rst b/doc/src/dump_h5md.rst index 202d5fb89d..37fc7ad600 100644 --- a/doc/src/dump_h5md.rst +++ b/doc/src/dump_h5md.rst @@ -6,31 +6,31 @@ dump h5md command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dump ID group-ID h5md N file.h5 args * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be imaged -* h5md = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) +* *h5md* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file.h5 = name of file to write to +* args = *position* options or *image* or *velocity* options or *force* options or *species* options or *file_from* ID or *box* value or *create_group* value or *author* value = list of data elements to dump, with their dump "sub-intervals" -.. parsed-literal:: + .. parsed-literal:: - args = list of data elements to dump, with their dump "sub-intervals" - position options - image - velocity options - force options - species options - file_from ID: do not open a new file, re-use the already opened file from dump ID - box value = *yes* or *no* - create_group value = *yes* or *no* - author value = quoted string + *position* options + *image* + *velocity* options + *force* options + *species* options + *file_from* ID = do not open a new file, re-use the already opened file from dump ID + *box* value = *yes* or *no* + *create_group* value = *yes* or *no* + *author* value = quoted string -Note that at least one element must be specified and image may only be -present if position is specified first. +Note that at least one element must be specified and that *image* may only be +present if *position* is specified first. For the elements *position*, *velocity*, *force* and *species*, a sub-interval may be specified to write the data only every N_element @@ -39,7 +39,7 @@ specified by this option directly following the element declaration: .. parsed-literal:: - every N_element + options = *every* N_element Examples """""""" diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 9b16a7c133..a243b0b839 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -56,7 +56,7 @@ Syntax phi = azimuthal view angle (degrees) theta or phi can be a variable (see below) *center* values = flag Cx Cy Cz = center point of image - flag = "s" for static, "d" for dynamic + flag = *s* for static, *d* for dynamic Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box) Cx,Cy,Cz can be variables (see below) *up* values = Ux Uy Uz = direction that is "up" in image @@ -110,13 +110,13 @@ Syntax *amap* args = lo hi style delta N entry1 entry2 ... entryN lo = number or *min* = lower bound of range of color map hi = number or *max* = upper bound of range of color map - style = 2 letters = "c" or "d" or "s" plus "a" or "f" - "c" for continuous - "d" for discrete - "s" for sequential - "a" for absolute - "f" for fractional - delta = binsize (only used for style "s", otherwise ignored) + style = 2 letters = *c* or *d* or *s* plus *a* or *f* + *c* for continuous + *d* for discrete + *s* for sequential + *a* for absolute + *f* for fractional + delta = binsize (only used for style *s*, otherwise ignored) binsize = range is divided into bins of this width N = # of subsequent entries entry = value color (for continuous style) diff --git a/doc/src/fix_electrode_conp.rst b/doc/src/fix_electrode_conp.rst index 75b099995f..e070433c07 100644 --- a/doc/src/fix_electrode_conp.rst +++ b/doc/src/fix_electrode_conp.rst @@ -25,38 +25,47 @@ Syntax .. parsed-literal:: - fix ID group-ID electrode/conp potential eta keyword values ... - fix ID group-ID electrode/conq charge eta keyword values ... - fix ID group-ID electrode/thermo potential eta temp T_v tau_v rng_v keyword values ... + fix ID group-ID style args keyword value ... -* ID, group-ID are documented in fix command -* mode = electrode/conp or electrode/conq or electrode/thermo -* potential = electrode potential -* charge = electrode charge -* eta = reciprocal width of electrode charge smearing -* T_v = temperature of thermo-potentiostat -* tau_v = time constant of thermo-potentiostat -* rng_v = integer used to initialize random number generator +* ID, group-ID are documented in :doc:`fix ` command +* style = *electrode/conp* or *electrode/conq* or *electrode/thermo* +* args = arguments used by a particular style + + .. parsed-literal:: + + *electrode/conp* args = potential eta + *electrode/conq* args = charge eta + *electrode/thermo* args = potential eta *temp* values + potential = electrode potential + charge = electrode charge + eta = reciprocal width of electrode charge smearing + *temp* values = T_v tau_v rng_v + T_v = temperature of thermo-potentiostat + tau_v = time constant of thermo-potentiostat + rng_v = integer used to initialize random number generator + +* zero or more keyword/value pairs may be appended +* keyword = *symm* or *couple* or *etypes* or *ffield* or *write_mat* or *write_inv* or *read_mat* or *read_inv* .. parsed-literal:: - *symm(etry) on/off* + *symm* value = *on* or *off* turn on/off charge neutrality constraint for the electrodes - *couple group-ID value* + *couple* values = group-ID val group-ID = group of atoms treated as additional electrode - value = electric potential or charge on this electrode - *etypes values = atom types* - specify atom types exclusive to the electrode for optimized neighbor lists - *ffield on/off* + val = electric potential or charge on this electrode + *etypes* values = type + type = atom type (can be a range) exclusive to the electrode for optimized neighbor lists + *ffield* value = *on* or *off* turn on/off finite-field implementation - *write_mat filename* - write elastance matrix to file - *write_inv filename* - write inverted matrix to file - *read_mat filename* - read elastance matrix from file - *read_inv filename* - read inverted matrix from file + *write_mat* value = filename + filename = file to which to write elastance matrix + *write_inv* value = filename + filename = file to which to write inverted matrix + *read_mat* value = filename + filename = file from which to read elastance matrix + *read_inv* value = filename + filename = file from which to read inverted matrix Examples """""""" diff --git a/doc/src/fix_flow_gauss.rst b/doc/src/fix_flow_gauss.rst index 3697142a37..87ab283923 100644 --- a/doc/src/fix_flow_gauss.rst +++ b/doc/src/fix_flow_gauss.rst @@ -24,9 +24,9 @@ Syntax .. parsed-literal:: - *energy* value = no or yes - no = do not compute work done by this fix - yes = compute work done by this fix + *energy* value = *no* or *yes* + *no* = do not compute work done by this fix + *yes* = compute work done by this fix Examples """""""" diff --git a/doc/src/fix_ipi.rst b/doc/src/fix_ipi.rst index bd4b4d84e8..6ddd6976a2 100644 --- a/doc/src/fix_ipi.rst +++ b/doc/src/fix_ipi.rst @@ -14,8 +14,14 @@ Syntax * ipi = style name of this fix command * address = internet address (FQDN or IP), or UNIX socket name * port = port number (ignored for UNIX sockets) -* optional keyword = *unix*, if present uses a unix socket -* optional keyword = *reset*, if present reset electrostatics at each call + +* zero or more keywords may be appended +* keyword = *unix* or *reset* + + .. parsed-literal:: + + *unix* args = none = use a unix socket + *reset* args = none = reset electrostatics at each call Examples """""""" diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index b51e232a3c..64d406ee64 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -22,13 +22,14 @@ Syntax .. parsed-literal:: - keyword = *ext* or *strain* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk* + keyword = *erate* or *ext* or *strain* or *temp* or *iso* or *x* or *y* or *z* or *tchain* or *pchain* or *tloop* or *ploop* or *mtk* + *erate* values = e_x e_y = engineering strain rates (required) *ext* value = *x* or *y* or *z* or *xy* or *yz* or *xz* = external dimensions sets the external dimensions used to calculate the scalar pressure *strain* values = e_x e_y = initial strain usually not needed, but may be needed to resume a run with a data file. - *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk* keywords - documented by the :doc:`fix npt ` command + *temp*, *iso*, *x*, *y*, *z*, *tchain*, *pchain*, *tloop*, *ploop*, *mtk* + keywords documented by the :doc:`fix npt ` command Examples """""""" diff --git a/doc/src/fix_oneway.rst b/doc/src/fix_oneway.rst index 4c5afb29cf..272797fa17 100644 --- a/doc/src/fix_oneway.rst +++ b/doc/src/fix_oneway.rst @@ -21,9 +21,9 @@ Examples .. code-block:: LAMMPS - fix ions oneway 10 semi -x - fix all oneway 1 left -z - fix all oneway 1 right z + fix 1 ions oneway 10 semi -x + fix 2 all oneway 1 left -z + fix 3 all oneway 1 right z Description """"""""""" diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index 09286cca38..3eb9365f57 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -15,18 +15,18 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * property/atom = style name of this fix command -* name1,name2,... = *mol* or *q* or *rmass* or *i_name* or *d_name* or *i2_name* or *d2_name* +* name1,name2,... = *mol* or *q* or *rmass* or i_name or d_name or i2_name or d2_name .. parsed-literal:: *mol* = molecule IDs *q* = charge *rmass* = per-atom mass - *i_name* = new integer vector referenced by name - *d_name* = new floating-point vector referenced by name - *i2_name* = new integer array referenced by name + i_name = new integer vector referenced by name + d_name = new floating-point vector referenced by name + i2_name = new integer array referenced by name i2_name arg = N = number of columns in the array - *d2_name* = new floating-point array referenced by name + d2_name = new floating-point array referenced by name d2_name arg = N = number of columns in the array * zero of more keyword/value pairs may be appended diff --git a/doc/src/fix_rigid.rst b/doc/src/fix_rigid.rst index 1f722aff7b..445b86466c 100644 --- a/doc/src/fix_rigid.rst +++ b/doc/src/fix_rigid.rst @@ -88,7 +88,7 @@ Syntax Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) seed = random number seed to use for white noise (positive integer) - *reinit* = *yes* or *no* + *reinit* value = *yes* or *no* *temp* values = Tstart Tstop Tdamp Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) @@ -98,7 +98,7 @@ Syntax *x* or *y* or *z* values = Pstart Pstop Pdamp Pstart,Pstop = external stress tensor component at start/end of run (pressure units) Pdamp = stress damping parameter (time units) - *couple* = *none* or *xyz* or *xy* or *yz* or *xz* + *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* *tparam* values = Tchain Titer Torder Tchain = length of Nose/Hoover thermostat chain Titer = number of thermostat iterations performed diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 7d66db367b..e465c4629f 100644 --- a/doc/src/group2ndx.rst +++ b/doc/src/group2ndx.rst @@ -1,4 +1,5 @@ .. index:: group2ndx +.. index:: ndx2group group2ndx command ================= diff --git a/doc/src/if.rst b/doc/src/if.rst index 91b001fbdc..d40eca0ba8 100644 --- a/doc/src/if.rst +++ b/doc/src/if.rst @@ -25,7 +25,7 @@ Examples if "${steps} > 1000" then quit if "${myString} == a10" then quit - if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y" + if "$x <= $y" then "print 'X is smaller = $x'" else "print 'Y is smaller = $y'" if "(${eng} > 0.0) || ($n < 1000)" then & "timestep 0.005" & elif $n<10000 & diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index 7c070d2e9c..a829d9989c 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -17,7 +17,7 @@ Examples .. code-block:: LAMMPS - improper_style hybrid harmonic helix + improper_style hybrid harmonic cvff improper_coeff 1 harmonic 120.0 30 improper_coeff 2 cvff 20.0 -1 2 diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index d6fa12f713..d99a3187aa 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -22,24 +22,24 @@ Syntax *check* value = *yes* or *no* *yes* = only build if some atom has moved half the skin distance or more *no* = always build on 1st step that *every* and *delay* are satisfied - *once* + *once* value = *yes* or *no* *yes* = only build neighbor list once at start of run and never rebuild *no* = rebuild neighbor list according to other settings - *cluster* + *cluster* value = *yes* or *no* *yes* = check bond,angle,etc neighbor list for nearby clusters *no* = do not check bond,angle,etc neighbor list for nearby clusters *include* value = group-ID group-ID = only build pair neighbor lists for atoms in this group *exclude* values: - type M N + *type* M N M,N = exclude if one atom in pair is type M, other is type N - group group1-ID group2-ID + *group* group1-ID group2-ID group1-ID,group2-ID = exclude if one atom is in 1st group, other in 2nd - molecule/intra group-ID + *molecule/intra* group-ID group-ID = exclude if both atoms are in the same molecule and in group - molecule/inter group-ID + *molecule/inter* group-ID group-ID = exclude if both atoms are in different molecules and in group - none + *none* delete all exclude settings *page* value = N N = number of pairs stored in a single neighbor page diff --git a/doc/src/package.rst b/doc/src/package.rst index 0810bd5b6b..84dab41ab3 100644 --- a/doc/src/package.rst +++ b/doc/src/package.rst @@ -18,16 +18,16 @@ Syntax *gpu* args = Ngpu keyword value ... Ngpu = # of GPUs per node zero or more keyword/value pairs may be appended - keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *platform* or *device_type* or *ocl_args* + keywords = *neigh* or *newton* or *pair/only* or *binsize* or *split* or *gpuID* or *tpa* or *blocksize* or *omp* or *platform* or *device_type* or *ocl_args* *neigh* value = *yes* or *no* - yes = neighbor list build on GPU (default) - no = neighbor list build on CPU + *yes* = neighbor list build on GPU (default) + *no* = neighbor list build on CPU *newton* = *off* or *on* - off = set Newton pairwise flag off (default and required) - on = set Newton pairwise flag on (currently not allowed) + *off* = set Newton pairwise flag off (default and required) + *on* = set Newton pairwise flag on (currently not allowed) *pair/only* = *off* or *on* - off = apply "gpu" suffix to all available styles in the GPU package (default) - on = apply "gpu" suffix only pair styles + *off* = apply "gpu" suffix to all available styles in the GPU package (default) + *on* = apply "gpu" suffix only pair styles *binsize* value = size size = bin size for neighbor list construction (distance units) *split* = fraction @@ -42,7 +42,7 @@ Syntax id = For OpenCL, platform ID for the GPU or accelerator *gpuID* values = id id = ID of first GPU to be used on each node - *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom,val1,val2,...* + *device_type* value = *intelgpu* or *nvidiagpu* or *amdgpu* or *applegpu* or *generic* or *custom*,val1,val2,... val1,val2,... = custom OpenCL accelerator configuration parameters (see below for details) *ocl_args* value = args args = List of additional OpenCL compiler arguments delimited by colons @@ -57,13 +57,13 @@ Syntax *omp* value = Nthreads Nthreads = number of OpenMP threads to use on CPU (default = 0) *lrt* value = *yes* or *no* - yes = use additional thread dedicated for some PPPM calculations - no = do not dedicate an extra thread for some PPPM calculations + *yes* = use additional thread dedicated for some PPPM calculations + *no* = do not dedicate an extra thread for some PPPM calculations *balance* value = split split = fraction of work to offload to co-processor, -1 for dynamic *ghost* value = *yes* or *no* - yes = include ghost atoms for offload - no = do not include ghost atoms for offload + *yes* = include ghost atoms for offload + *no* = do not include ghost atoms for offload *tpc* value = Ntpc Ntpc = max number of co-processor threads per co-processor core (default = 4) *tptask* value = Ntptask @@ -71,7 +71,7 @@ Syntax *no_affinity* values = none *kokkos* args = keyword value ... zero or more keyword/value pairs may be appended - keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* *comm/pair/forward* *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only* + keywords = *neigh* or *neigh/qeq* or *neigh/thread* or *neigh/transpose* or *newton* or *binsize* or *comm* or *comm/exchange* or *comm/forward* or *comm/pair/forward* or *comm/fix/forward* or *comm/reverse* or *comm/pair/reverse* or *gpu/aware* or *pair/only* *neigh* value = *full* or *half* full = full neighbor list half = half neighbor list built in thread-safe manner @@ -79,14 +79,14 @@ Syntax full = full neighbor list half = half neighbor list built in thread-safe manner *neigh/thread* value = *off* or *on* - off = thread only over atoms - on = thread over both atoms and neighbors + *off* = thread only over atoms + *on* = thread over both atoms and neighbors *neigh/transpose* value = *off* or *on* - off = use same memory layout for GPU neigh list build as pair style - on = use transposed memory layout for GPU neigh list build + *off* = use same memory layout for GPU neigh list build as pair style + *on* = use transposed memory layout for GPU neigh list build *newton* = *off* or *on* - off = set Newton pairwise and bonded flags off - on = set Newton pairwise and bonded flags on + *off* = set Newton pairwise and bonded flags off + *on* = set Newton pairwise and bonded flags on *binsize* value = size size = bin size for neighbor list construction (distance units) *comm* value = *no* or *host* or *device* @@ -96,23 +96,25 @@ Syntax *comm/pair/forward* value = *no* or *device* *comm/fix/forward* value = *no* or *device* *comm/reverse* value = *no* or *host* or *device* + *no* = perform communication pack/unpack in non-KOKKOS mode + *host* = perform pack/unpack on host (e.g. with OpenMP threading) + *device* = perform pack/unpack on device (e.g. on GPU) *comm/pair/reverse* value = *no* or *device* - no = perform communication pack/unpack in non-KOKKOS mode - host = perform pack/unpack on host (e.g. with OpenMP threading) - device = perform pack/unpack on device (e.g. on GPU) + *no* = perform communication pack/unpack in non-KOKKOS mode + *device* = perform pack/unpack on device (e.g. on GPU) *gpu/aware* = *off* or *on* - off = do not use GPU-aware MPI - on = use GPU-aware MPI (default) + *off* = do not use GPU-aware MPI + *on* = use GPU-aware MPI (default) *pair/only* = *off* or *on* - off = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default) - on = use device acceleration only for pair styles (and host acceleration for others) + *off* = use device acceleration (e.g. GPU) for all available styles in the KOKKOS package (default) + *on* = use device acceleration only for pair styles (and host acceleration for others) *omp* args = Nthreads keyword value ... Nthreads = # of OpenMP threads to associate with each MPI process zero or more keyword/value pairs may be appended keywords = *neigh* *neigh* value = *yes* or *no* - yes = threaded neighbor list build (default) - no = non-threaded neighbor list build + *yes* = threaded neighbor list build (default) + *no* = non-threaded neighbor list build Examples """""""" diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 780a181a69..162187210d 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -36,7 +36,7 @@ Examples .. code-block:: LAMMPS - pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) + pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 # (assuming radius = 1) pair_coeff 1 1 2.05 2.8 pair_coeff * * diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index 147b9177ec..9b9bedd63d 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -24,7 +24,7 @@ Examples pair_coeff * * 1.0 1.0 pair_coeff * * nialhjea 1 1 2 pair_coeff * 3 morse.table ENTRY1 - pair_coeff 1 2 lj/cut 1.0 1.0 2.5 (for pair_style hybrid) + pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid) Description """"""""""" diff --git a/doc/src/pair_rann.rst b/doc/src/pair_rann.rst index a9ad5d9236..5bfac561ba 100644 --- a/doc/src/pair_rann.rst +++ b/doc/src/pair_rann.rst @@ -17,8 +17,8 @@ Examples .. code-block:: LAMMPS pair_style rann - pair_coeff ** Mg.rann Mg - pair_coeff ** MgAlalloy.rann Mg Mg Al Mg + pair_coeff * * Mg.rann Mg + pair_coeff * * MgAlalloy.rann Mg Mg Al Mg Description """"""""""" diff --git a/doc/src/thermo_modify.rst b/doc/src/thermo_modify.rst index 10b3a44f4f..2600b337bc 100644 --- a/doc/src/thermo_modify.rst +++ b/doc/src/thermo_modify.rst @@ -11,7 +11,7 @@ Syntax thermo_modify keyword value ... * one or more keyword/value pairs may be listed -* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *format* or *temp* or *press* +* keyword = *lost* or *lost/bond* or *warn* or *norm* or *flush* or *line* or *colname* or *format* or *temp* or *press* .. parsed-literal:: diff --git a/src/UEF/fix_nh_uef.cpp b/src/UEF/fix_nh_uef.cpp index e1342adc17..720c960252 100644 --- a/src/UEF/fix_nh_uef.cpp +++ b/src/UEF/fix_nh_uef.cpp @@ -121,7 +121,7 @@ FixNHUef::FixNHUef(LAMMPS *lmp, int narg, char **arg) : } if (!erate_flag) - error->all(FLERR,"Keyword erate must be set for fix npt/npt/uef command"); + error->all(FLERR,"Keyword erate must be set for fix nvt/npt/uef command"); if (mtchain_default_flag) mtchain=1;