diff --git a/doc/src/dump_custom_vtk.txt b/doc/src/dump_custom_vtk.txt index f15d20f849692cd49176d0ce39d0619dc1f28900..d4c16193d89f22eb956f0bdcc99b64c6b72ba8b5 100644 --- a/doc/src/dump_custom_vtk.txt +++ b/doc/src/dump_custom_vtk.txt @@ -26,7 +26,6 @@ args = list of arguments for a particular style :l q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, - spin, eradius, ervel, erforce, c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre id = atom ID @@ -51,17 +50,18 @@ args = list of arguments for a particular style :l angmomx,angmomy,angmomz = angular momentum of aspherical particle tqx,tqy,tqz = torque on finite-size particles c_ID = per-atom vector calculated by a compute with ID - c_ID\[N\] = Nth column of per-atom array calculated by a compute with ID + c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) f_ID = per-atom vector calculated by a fix with ID - f_ID\[N\] = Nth column of per-atom array calculated by a fix with ID - v_name = per-atom vector calculated by an atom-style variable with name :pre + f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below) + v_name = per-atom vector calculated by an atom-style variable with name + d_name = per-atom floating point vector with name, managed by fix property/atom + i_name = per-atom integer vector with name, managed by fix property/atom :pre :ule [Examples:] dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx -dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke -dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce :pre +dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre The style {custom/vtk} is similar to the "custom"_dump.html style but uses the VTK library to write data to VTK simple legacy or XML format @@ -199,32 +199,38 @@ part of the {custom/vtk} style. The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx}, {vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory. -{id} is the atom ID. {mol} is the molecule ID, included in the data -file for molecular systems. {type} is the atom type. {element} is -typically the chemical name of an element, which you must assign to -each type via the "dump_modify element"_dump_modify.html command. -More generally, it can be any string you wish to associate with an -atom type. {mass} is the atom mass. {vx}, {vy}, {vz}, {fx}, {fy}, -{fz}, and {q} are components of atom velocity and force and atomic -charge. +{Id} is the atom ID. {Mol} is the molecule ID, included in the data +file for molecular systems. {Proc} is the ID of the processor (0 to +Nprocs-1) that currently owns the atom. {Procp1} is the proc ID+1, +which can be convenient in place of a {type} attribute (1 to Ntypes) +for coloring atoms in a visualization program. {Type} is the atom +type (1 to Ntypes). {Element} is typically the chemical name of an +element, which you must assign to each type via the "dump_modify +element"_dump_modify.html command. More generally, it can be any +string you wish to associated with an atom type. {Mass} is the atom +mass. {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of +atom velocity and force and atomic charge. There are several options for outputting atom coordinates. The {x}, -{y}, {z} attributes are used to write atom coordinates "unscaled", in -the appropriate distance "units"_units.html (Angstroms, sigma, etc). -Additionally, you can use {xs}, {ys}, {zs} if you want to also save the -coordinates "scaled" to the box size, so that each value is 0.0 to -1.0. If the simulation box is triclinic (tilted), then all atom -coords will still be between 0.0 and 1.0. Use {xu}, {yu}, {zu} if you -want the coordinates "unwrapped" by the image flags for each atom. -Unwrapped means that if the atom has passed through a periodic -boundary one or more times, the value is printed for what the -coordinate would be if it had not been wrapped back into the periodic -box. Note that using {xu}, {yu}, {zu} means that the coordinate -values may be far outside the box bounds printed with the snapshot. -Using {xsu}, {ysu}, {zsu} is similar to using {xu}, {yu}, {zu}, except -that the unwrapped coordinates are scaled by the box size. Atoms that -have passed through a periodic boundary will have the corresponding -coordinate increased or decreased by 1.0. +{y}, {z} attributes write atom coordinates "unscaled", in the +appropriate distance "units"_units.html (Angstroms, sigma, etc). Use +{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size, +so that each value is 0.0 to 1.0. If the simulation box is triclinic +(tilted), then all atom coords will still be between 0.0 and 1.0. +I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are +the non-orthogonal vectors of the simulation box edges, as discussed +in "Section 6.12"_Section_howto.html#howto_12. + +Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the +image flags for each atom. Unwrapped means that if the atom has +passed thru a periodic boundary one or more times, the value is +printed for what the coordinate would be if it had not been wrapped +back into the periodic box. Note that using {xu}, {yu}, {zu} means +that the coordinate values may be far outside the box bounds printed +with the snapshot. Using {xsu}, {ysu}, {zsu} is similar to using +{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by +the box size. Atoms that have passed through a periodic boundary will +have the corresponding coordinate increased or decreased by 1.0. The image flags can be printed directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the @@ -255,13 +261,7 @@ The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that can sustain a rotational torque due to interactions with other particles. -The {spin}, {eradius}, {ervel}, and {erforce} attributes are for -particles that represent nuclei and electrons modeled with the -electronic force field (EFF). See "atom_style -electron"_atom_style.html and "pair_style eff"_pair_eff.html for more -details. - -The {c_ID} and {c_ID\[N\]} attributes allow per-atom vectors or arrays +The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays calculated by a "compute"_compute.html to be output. The ID in the attribute should be replaced by the actual ID of the compute that has been defined previously in the input script. See the @@ -275,12 +275,14 @@ command. Instead, global quantities can be output by the "thermo_style custom"_thermo_style.html command, and local quantities can be output by the dump local command. -If {c_ID} is used as an attribute, then the per-atom vector calculated -by the compute is printed. If {c_ID\[N\]} is used, then N must be in -the range from 1-M, which will print the Nth column of the M-length -per-atom array calculated by the compute. +If {c_ID} is used as a attribute, then the per-atom vector calculated +by the compute is printed. If {c_ID\[I\]} is used, then I must be in +the range from 1-M, which will print the Ith column of the per-atom +array with M columns calculated by the compute. See the discussion +above for how I can be specified with a wildcard asterisk to +effectively specify multiple values. -The {f_ID} and {f_ID\[N\]} attributes allow vector or array per-atom +The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom quantities calculated by a "fix"_fix.html to be output. The ID in the attribute should be replaced by the actual ID of the fix that has been defined previously in the input script. The "fix @@ -291,9 +293,11 @@ any "compute"_compute.html, "fix"_fix.html, or atom-style be written to a dump file. If {f_ID} is used as a attribute, then the per-atom vector calculated -by the fix is printed. If {f_ID\[N\]} is used, then N must be in the -range from 1-M, which will print the Nth column of the M-length -per-atom array calculated by the fix. +by the fix is printed. If {f_ID\[I\]} is used, then I must be in the +range from 1-M, which will print the Ith column of the per-atom array +with M columns calculated by the fix. See the discussion above for +how I can be specified with a wildcard asterisk to effectively specify +multiple values. The {v_name} attribute allows per-atom vectors calculated by a "variable"_variable.html to be output. The name in the attribute @@ -306,6 +310,10 @@ invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of creating quantities to output to a dump file. +The {d_name} and {i_name} attributes allow to output custom per atom +floating point or integer properties that are managed by +"fix property/atom"_fix_property_atom.html. + See "Section 10"_Section_modify.html of the manual for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files.