Loading doc/src/balance.rst +12 −6 Original line number Diff line number Diff line Loading @@ -465,12 +465,18 @@ atom-style variables can reference the position of a particle, its velocity, the volume of its Voronoi cell, etc. The *store* weight style does not compute a weight factor. Instead it stores the current accumulated weights in a custom per-atom property specified by *name*\ . This must be a property defined as *d_name* via the :doc:`fix property/atom <fix_property_atom>` command. Note that these custom per-atom properties can be output in a :doc:`dump <dump>` file, so this is a way to examine, debug, or visualize the per-particle weights computed during the load-balancing operation. stores the current accumulated weights in a custom per-atom vector specified by *name*\ . This must be a vector defined as *d_name* via the :doc:`fix property/atom <fix_property_atom>` command. This means the values in the vector can be read as part of a data file with the :doc:`read_data <read_data>` command or specified with the :doc:`set <set>` command. These weights can also be output in a :doc:`dump <dump>` file, so this is a way to examine, debug, or visualize the per-particle weights used during the load-balancing operation. Note that the name of the custom per-atom vector is specified just as *name*, not as *d_name* as it is for other commands that use different kinds of custom atom vectors or arrays as arguments. ---------- Loading doc/src/compute_property_atom.rst +62 −55 Original line number Diff line number Diff line Loading @@ -20,7 +20,8 @@ Syntax x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, sp, spx, spy, spz, fmx, fmy, fmz, spx, spy, spz, sp, fmx, fmy, fmz, nbonds, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, Loading @@ -29,42 +30,42 @@ Syntax corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, nbonds, buckling, vfrac, s0, spin, eradius, ervel, erforce, rho, drho, e, de, cv, i_name, d_name i_name, d_name, i2_name[I], d2_name[I], vfrac, s0, spin, eradius, ervel, erforce, rho, drho, e, de, cv, buckling .. parsed-literal:: id = atom ID mol = molecule ID proc = ID of processor that owns atom type = atom type mass = atom mass x,y,z = unscaled atom coordinates xs,ys,zs = scaled atom coordinates xu,yu,zu = unwrapped atom coordinates ix,iy,iz = box image that the atom is in vx,vy,vz = atom velocities fx,fy,fz = forces on atoms q = atom charge mux,muy,muz = orientation of dipole moment of atom mu = magnitude of dipole moment of atom sp = atomic magnetic spin moment spx, spy, spz = direction of the atomic magnetic spin fmx, fmy, fmz = magnetic force radius,diameter = radius,diameter of spherical particle omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle shapex,shapey,shapez = 3 diameters of aspherical particle quatw,quati,quatj,quatk = quaternion components for aspherical or body particles tqx,tqy,tqz = torque on finite-size particles end12x, end12y, end12z = end points of line segment corner123x, corner123y, corner123z = corner points of triangle nbonds = number of bonds assigned to an atom buckling = buckling flag used in mesoscopic simulation of nanotubes *id* = atom ID *mol* = molecule ID *proc* = ID of processor that owns atom *type* = atom type *mass* = atom mass *x,y,z* = unscaled atom coordinates *xs,ys,zs* = scaled atom coordinates *xu,yu,zu* = unwrapped atom coordinates *ix,iy,iz* = box image that the atom is in *vx,vy,vz* = atom velocities *fx,fy,fz* = forces on atoms *q* = atom charge *mux,muy,muz* = orientation of dipole moment of atom *mu* = magnitude of dipole moment of atom *spx, spy, spz* = direction of the atomic magnetic spin *sp* = magintude of atomic magnetic spin moment *fmx, fmy, fmz* = magnetic force *nbonds* = number of bonds assigned to an atom *radius,diameter* = radius,diameter of spherical particle *omegax,omegay,omegaz* = angular velocity of spherical particle *angmomx,angmomy,angmomz* = angular momentum of aspherical particle *shapex,shapey,shapez* = 3 diameters of aspherical particle *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles *tqx,tqy,tqz* = torque on finite-size particles *end12x, end12y, end12z* = end points of line segment *corner123x, corner123y, corner123z* = corner points of triangle *i_name* = custom integer vector with name *d_name* = custom floating point vector with name *i2_name[I]* = Ith column of custom integer array with name *d2_name[I]* = Ith column of custom floating-point array with name .. parsed-literal:: Loading @@ -91,9 +92,8 @@ Syntax .. parsed-literal:: :doc:`fix property/atom <fix_property_atom>` per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with name USER-MESONT package per-atom properties: buckling = buckling flag used in mesoscopic simulation of nanotubes Examples """""""" Loading @@ -104,6 +104,7 @@ Examples compute 2 all property/atom type compute 1 all property/atom ix iy iz compute 3 all property/atom sp spx spy spz compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3] Description """"""""""" Loading @@ -116,20 +117,37 @@ ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>` commands. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. Basically, this augmented list gives an input script access to any per-atom quantity stored by LAMMPS. The list of possible attributes is essentially the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. The goal of this augmented list gives an input script access to any per-atom quantity stored by LAMMPS. The values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group or for quantities that are not defined for a particular particle in the group (e.g. *shapex* if the particle is not an ellipsoid). Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom per-atom integer and floating-point vectors or arrays that have been added via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are the "name" portion of these attributes. For arrays *i2_name* and *d2_name*, the column of the array must also be included following the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. The additional quantities only accessible via this command, and not directly via the :doc:`dump custom <dump>` command, are as follows. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the :doc:`newton bond <newton>` command is set to *on*\ , which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off <newton>` is set, it will be tallied with both atom I and atom J. *Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles and define the 3d shape of each particle. Loading @@ -146,19 +164,8 @@ line segment. *corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for triangular particles and define the corner points of each triangle. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the :doc:`newton bond <newton>` command is set to *on*\ , which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off <newton>` is set, it will be tallied with both atom I and atom J. The *i_name* and *d_name* attributes refer to custom integer and floating-point properties that have been added to each atom via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are what is specified as the "name" portion of *i_name* or *d_name*. In addition, the various per-atom quantities listed above for specific packages are only accessible by this command. Output info """"""""""" Loading doc/src/dump.rst +26 −19 Original line number Diff line number Diff line Loading @@ -78,7 +78,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID, c_ID[I], f_ID, f_ID[I], v_name, i_name, d_name, i2_name[I], d2_name[I] .. parsed-literal:: Loading Loading @@ -108,8 +109,10 @@ Syntax f_ID = per-atom vector calculated by a fix with ID 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 i_name = custom integer vector with name d_name = custom floating point vector with name i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below) d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below) * *local* args = list of local attributes Loading @@ -134,7 +137,7 @@ Examples dump 2 subgroup atom 50 dump.run.mpiio.bin dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] dump 1 all xtc 1000 file.xtc Loading Loading @@ -465,16 +468,15 @@ styles. ---------- Note that in the discussion which follows, for styles which can reference values from a compute or fix, like the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = scalar) or the number of columns in the array (for *mode* = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). reference values from a compute or fix or custom atom property, like the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of columns in the array, then an asterisk with no numeric values means all column indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual columns of the array had been listed one by one. E.g. these 2 dump commands are Loading Loading @@ -512,8 +514,9 @@ bonds and angles. Note that computes which calculate global or per-atom quantities, as opposed to local quantities, cannot be output in a dump local command. Instead, global quantities can be output by the :doc:`thermo_style custom <thermo_style>` command, and per-atom quantities can be output by the dump custom command. Instead, global quantities can be output by the :doc:`thermo_style custom <thermo_style>` command, and per-atom quantities can be output by the dump custom command. If *c_ID* is used as a attribute, then the local vector calculated by the compute is printed. If *c_ID[I]* is used, then I must be in the Loading Loading @@ -660,9 +663,13 @@ 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 :doc:`fix property/atom <fix_property_atom>`. The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to per-atom integer and floating-point vectors or arrays that have been added via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are the "name" portion of these keywords. For arrays *i2_name* and *d2_name*, the column of the array must also be included following the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. See the :doc:`Modify <Modify>` doc page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities Loading doc/src/fix_property_atom.rst +142 −120 File changed.Preview size limit exceeded, changes collapsed. Show changes doc/src/fix_store_state.rst +20 −15 Original line number Diff line number Diff line Loading @@ -23,8 +23,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name, d_name, i_name c_ID, c_ID[I], f_ID, f_ID[I], v_name, d_name, i_name, i2_name[I], d2_name[I], .. parsed-literal:: Loading @@ -46,13 +46,15 @@ Syntax omegax,omegay,omegaz = angular velocity of spherical particle 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[I] = Ith column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID f_ID[I] = Ith column of per-atom array calculated by a fix with ID v_name = per-atom vector calculated by an atom-style variable with name d_name = per-atom floating point vector name, managed by fix property/atom i_name = per-atom integer vector name, managed by fix property/atom *c_ID* = per-atom vector calculated by a compute with ID *c_ID[I]* = Ith column of per-atom array calculated by a compute with ID *f_ID* = per-atom vector calculated by a fix with ID *f_ID[I]* = Ith column of per-atom array calculated by a fix with ID *v_name* = per-atom vector calculated by an atom-style variable with name *i_name* = custom integer vector with name *d_name* = custom floating point vector with name *i2_name[I]* = Ith column of custom integer array with name *d2_name[I]* = Ith column of custom floating-point array with name * zero or more keyword/value pairs may be appended * keyword = *com* Loading Loading @@ -92,7 +94,8 @@ steps. those attributes may require quantities that are not defined in between runs. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning. If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu* inputs store the position of each atom relative to the center-of-mass Loading @@ -105,10 +108,11 @@ group. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the :doc:`fix_modify <fix_modify>` options are relevant to this Loading @@ -121,7 +125,8 @@ can be accessed by various :doc:`output commands <Howto_output>`. The per-atom values be accessed on any timestep. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. Restrictions """""""""""" Loading Loading
doc/src/balance.rst +12 −6 Original line number Diff line number Diff line Loading @@ -465,12 +465,18 @@ atom-style variables can reference the position of a particle, its velocity, the volume of its Voronoi cell, etc. The *store* weight style does not compute a weight factor. Instead it stores the current accumulated weights in a custom per-atom property specified by *name*\ . This must be a property defined as *d_name* via the :doc:`fix property/atom <fix_property_atom>` command. Note that these custom per-atom properties can be output in a :doc:`dump <dump>` file, so this is a way to examine, debug, or visualize the per-particle weights computed during the load-balancing operation. stores the current accumulated weights in a custom per-atom vector specified by *name*\ . This must be a vector defined as *d_name* via the :doc:`fix property/atom <fix_property_atom>` command. This means the values in the vector can be read as part of a data file with the :doc:`read_data <read_data>` command or specified with the :doc:`set <set>` command. These weights can also be output in a :doc:`dump <dump>` file, so this is a way to examine, debug, or visualize the per-particle weights used during the load-balancing operation. Note that the name of the custom per-atom vector is specified just as *name*, not as *d_name* as it is for other commands that use different kinds of custom atom vectors or arrays as arguments. ---------- Loading
doc/src/compute_property_atom.rst +62 −55 Original line number Diff line number Diff line Loading @@ -20,7 +20,8 @@ Syntax x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, sp, spx, spy, spz, fmx, fmy, fmz, spx, spy, spz, sp, fmx, fmy, fmz, nbonds, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, Loading @@ -29,42 +30,42 @@ Syntax corner1x, corner1y, corner1z, corner2x, corner2y, corner2z, corner3x, corner3y, corner3z, nbonds, buckling, vfrac, s0, spin, eradius, ervel, erforce, rho, drho, e, de, cv, i_name, d_name i_name, d_name, i2_name[I], d2_name[I], vfrac, s0, spin, eradius, ervel, erforce, rho, drho, e, de, cv, buckling .. parsed-literal:: id = atom ID mol = molecule ID proc = ID of processor that owns atom type = atom type mass = atom mass x,y,z = unscaled atom coordinates xs,ys,zs = scaled atom coordinates xu,yu,zu = unwrapped atom coordinates ix,iy,iz = box image that the atom is in vx,vy,vz = atom velocities fx,fy,fz = forces on atoms q = atom charge mux,muy,muz = orientation of dipole moment of atom mu = magnitude of dipole moment of atom sp = atomic magnetic spin moment spx, spy, spz = direction of the atomic magnetic spin fmx, fmy, fmz = magnetic force radius,diameter = radius,diameter of spherical particle omegax,omegay,omegaz = angular velocity of spherical particle angmomx,angmomy,angmomz = angular momentum of aspherical particle shapex,shapey,shapez = 3 diameters of aspherical particle quatw,quati,quatj,quatk = quaternion components for aspherical or body particles tqx,tqy,tqz = torque on finite-size particles end12x, end12y, end12z = end points of line segment corner123x, corner123y, corner123z = corner points of triangle nbonds = number of bonds assigned to an atom buckling = buckling flag used in mesoscopic simulation of nanotubes *id* = atom ID *mol* = molecule ID *proc* = ID of processor that owns atom *type* = atom type *mass* = atom mass *x,y,z* = unscaled atom coordinates *xs,ys,zs* = scaled atom coordinates *xu,yu,zu* = unwrapped atom coordinates *ix,iy,iz* = box image that the atom is in *vx,vy,vz* = atom velocities *fx,fy,fz* = forces on atoms *q* = atom charge *mux,muy,muz* = orientation of dipole moment of atom *mu* = magnitude of dipole moment of atom *spx, spy, spz* = direction of the atomic magnetic spin *sp* = magintude of atomic magnetic spin moment *fmx, fmy, fmz* = magnetic force *nbonds* = number of bonds assigned to an atom *radius,diameter* = radius,diameter of spherical particle *omegax,omegay,omegaz* = angular velocity of spherical particle *angmomx,angmomy,angmomz* = angular momentum of aspherical particle *shapex,shapey,shapez* = 3 diameters of aspherical particle *quatw,quati,quatj,quatk* = quaternion components for aspherical or body particles *tqx,tqy,tqz* = torque on finite-size particles *end12x, end12y, end12z* = end points of line segment *corner123x, corner123y, corner123z* = corner points of triangle *i_name* = custom integer vector with name *d_name* = custom floating point vector with name *i2_name[I]* = Ith column of custom integer array with name *d2_name[I]* = Ith column of custom floating-point array with name .. parsed-literal:: Loading @@ -91,9 +92,8 @@ Syntax .. parsed-literal:: :doc:`fix property/atom <fix_property_atom>` per-atom properties: i_name = custom integer vector with name d_name = custom integer vector with name USER-MESONT package per-atom properties: buckling = buckling flag used in mesoscopic simulation of nanotubes Examples """""""" Loading @@ -104,6 +104,7 @@ Examples compute 2 all property/atom type compute 1 all property/atom ix iy iz compute 3 all property/atom sp spx spy spz compute 1 all property/atom i_myFlag d_Sxyz[1] d_Sxyz[3] Description """"""""""" Loading @@ -116,20 +117,37 @@ ave/atom <fix_ave_atom>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix ave/chunk <fix_ave_chunk>`, and :doc:`atom-style variable <variable>` commands. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. Basically, this augmented list gives an input script access to any per-atom quantity stored by LAMMPS. The list of possible attributes is essentially the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning, with some additional quantities that are only defined for certain :doc:`atom styles <atom_style>`. The goal of this augmented list gives an input script access to any per-atom quantity stored by LAMMPS. The values are stored in a per-atom vector or array as discussed below. Zeroes are stored for atoms not in the specified group or for quantities that are not defined for a particular particle in the group (e.g. *shapex* if the particle is not an ellipsoid). Attributes *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom per-atom integer and floating-point vectors or arrays that have been added via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are the "name" portion of these attributes. For arrays *i2_name* and *d2_name*, the column of the array must also be included following the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. The additional quantities only accessible via this command, and not directly via the :doc:`dump custom <dump>` command, are as follows. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the :doc:`newton bond <newton>` command is set to *on*\ , which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off <newton>` is set, it will be tallied with both atom I and atom J. *Shapex*\ , *shapey*\ , and *shapez* are defined for ellipsoidal particles and define the 3d shape of each particle. Loading @@ -146,19 +164,8 @@ line segment. *corner2z*\ , *corner3x*\ , *corner3y*\ , *corner3z*\ , are defined for triangular particles and define the corner points of each triangle. *Nbonds* is available for all molecular atom styles and refers to the number of explicit bonds assigned to an atom. Note that if the :doc:`newton bond <newton>` command is set to *on*\ , which is the default, then every bond in the system is assigned to only one of the two atoms in the bond. Thus a bond between atoms I,J may be tallied for either atom I or atom J. If :doc:`newton bond off <newton>` is set, it will be tallied with both atom I and atom J. The *i_name* and *d_name* attributes refer to custom integer and floating-point properties that have been added to each atom via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are what is specified as the "name" portion of *i_name* or *d_name*. In addition, the various per-atom quantities listed above for specific packages are only accessible by this command. Output info """"""""""" Loading
doc/src/dump.rst +26 −19 Original line number Diff line number Diff line Loading @@ -78,7 +78,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID, c_ID[I], f_ID, f_ID[I], v_name, i_name, d_name, i2_name[I], d2_name[I] .. parsed-literal:: Loading Loading @@ -108,8 +109,10 @@ Syntax f_ID = per-atom vector calculated by a fix with ID 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 i_name = custom integer vector with name d_name = custom floating point vector with name i2_name[I] = Ith column of custom integer array with name, I can include wildcard (see below) d2_name[I] = Ith column of custom floating point vector with name, I can include wildcard (see below) * *local* args = list of local attributes Loading @@ -134,7 +137,7 @@ Examples dump 2 subgroup atom 50 dump.run.mpiio.bin dump 4a all custom 100 dump.myforce.* id type x y vx fx dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[\*] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2] dump 1 all xtc 1000 file.xtc Loading Loading @@ -465,16 +468,15 @@ styles. ---------- Note that in the discussion which follows, for styles which can reference values from a compute or fix, like the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the size of the vector (for *mode* = scalar) or the number of columns in the array (for *mode* = vector), then an asterisk with no numeric values means all indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). reference values from a compute or fix or custom atom property, like the *custom*\ , *cfg*\ , or *local* styles, the bracketed index I can be specified using a wildcard asterisk with the index to effectively specify multiple values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of columns in the array, then an asterisk with no numeric values means all column indices from 1 to N. A leading asterisk means all indices from 1 to n (inclusive). A trailing asterisk means all indices from n to N (inclusive). A middle asterisk means all indices from m to n (inclusive). Using a wildcard is the same as if the individual columns of the array had been listed one by one. E.g. these 2 dump commands are Loading Loading @@ -512,8 +514,9 @@ bonds and angles. Note that computes which calculate global or per-atom quantities, as opposed to local quantities, cannot be output in a dump local command. Instead, global quantities can be output by the :doc:`thermo_style custom <thermo_style>` command, and per-atom quantities can be output by the dump custom command. Instead, global quantities can be output by the :doc:`thermo_style custom <thermo_style>` command, and per-atom quantities can be output by the dump custom command. If *c_ID* is used as a attribute, then the local vector calculated by the compute is printed. If *c_ID[I]* is used, then I must be in the Loading Loading @@ -660,9 +663,13 @@ 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 :doc:`fix property/atom <fix_property_atom>`. The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to per-atom integer and floating-point vectors or arrays that have been added via the :doc:`fix property/atom <fix_property_atom>` command. When that command is used specific names are given to each attribute which are the "name" portion of these keywords. For arrays *i2_name* and *d2_name*, the column of the array must also be included following the name in brackets: e.g. d2_xyz[2], i2_mySpin[3]. See the :doc:`Modify <Modify>` doc page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities Loading
doc/src/fix_property_atom.rst +142 −120 File changed.Preview size limit exceeded, changes collapsed. Show changes
doc/src/fix_store_state.rst +20 −15 Original line number Diff line number Diff line Loading @@ -23,8 +23,8 @@ Syntax q, mux, muy, muz, mu, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, tqx, tqy, tqz, c_ID, c_ID[N], f_ID, f_ID[N], v_name, d_name, i_name c_ID, c_ID[I], f_ID, f_ID[I], v_name, d_name, i_name, i2_name[I], d2_name[I], .. parsed-literal:: Loading @@ -46,13 +46,15 @@ Syntax omegax,omegay,omegaz = angular velocity of spherical particle 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[I] = Ith column of per-atom array calculated by a compute with ID f_ID = per-atom vector calculated by a fix with ID f_ID[I] = Ith column of per-atom array calculated by a fix with ID v_name = per-atom vector calculated by an atom-style variable with name d_name = per-atom floating point vector name, managed by fix property/atom i_name = per-atom integer vector name, managed by fix property/atom *c_ID* = per-atom vector calculated by a compute with ID *c_ID[I]* = Ith column of per-atom array calculated by a compute with ID *f_ID* = per-atom vector calculated by a fix with ID *f_ID[I]* = Ith column of per-atom array calculated by a fix with ID *v_name* = per-atom vector calculated by an atom-style variable with name *i_name* = custom integer vector with name *d_name* = custom floating point vector with name *i2_name[I]* = Ith column of custom integer array with name *d2_name[I]* = Ith column of custom floating-point array with name * zero or more keyword/value pairs may be appended * keyword = *com* Loading Loading @@ -92,7 +94,8 @@ steps. those attributes may require quantities that are not defined in between runs. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning. The list of possible attributes is the same as that used by the :doc:`dump custom <dump>` command, which describes their meaning. If the *com* keyword is set to *yes* then the *xu*\ , *yu*\ , and *zu* inputs store the position of each atom relative to the center-of-mass Loading @@ -105,10 +108,11 @@ group. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an This fix writes the per-atom values it stores to :doc:`binary restart files <restart>`, so that the values can be restored when a simulation is restarted. See the :doc:`read_restart <read_restart>` command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. None of the :doc:`fix_modify <fix_modify>` options are relevant to this Loading @@ -121,7 +125,8 @@ can be accessed by various :doc:`output commands <Howto_output>`. The per-atom values be accessed on any timestep. No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. Restrictions """""""""""" Loading
