These are fix styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 74af2e5a0e..b018906a35 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -389,7 +389,6 @@ of each style or click on the style itself for a full description: "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, -"coord/original"_fix_coord_original.html, "deform"_fix_deform.html, "deposit"_fix_deposit.html, "drag"_fix_drag.html, @@ -432,6 +431,8 @@ of each style or click on the style itself for a full description: "spring"_fix_spring.html, "spring/rg"_fix_spring_rg.html, "spring/self"_fix_spring_self.html, +"store/coord"_fix_store_coord.html, +"store/force"_fix_store_force.html, "temp/berendsen"_fix_temp_berendsen.html, "temp/rescale"_fix_temp_rescale.html, "thermal/conductivity"_fix_thermal_conductivity.html, diff --git a/doc/compute_displace_atom.html b/doc/compute_displace_atom.html index c3998f89f5..6d4a4bf83f 100644 --- a/doc/compute_displace_atom.html +++ b/doc/compute_displace_atom.html @@ -35,20 +35,20 @@ dz*dz).
The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "coord/original", as if this +the compute creates its own fix of style "store/coord", as if this command had been issued:
-fix compute-ID_coord_original group-ID coord/original +fix compute-ID_store_coord group-ID store/coord-See the fix coord/original command for -details. Note that the ID of the new fix is the compute-ID + -underscore + "coord_original", and the group for the new fix is -the same as the compute group. +
See the fix store/coord command for details. +Note that the ID of the new fix is the compute-ID + underscore + +"store_coord", and the group for the new fix is the same as the +compute group.
The value of the displacement will be 0.0 for atoms not in the specified compute group.
-IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +
IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the dump custom command for a discussion of "unwrapped" coordinates. See the Atoms section of the @@ -83,8 +83,8 @@ overview of LAMMPS output options.
Related commands:
-compute msd, dump custom, fix -coord/original +
compute msd, dump custom, fix +store/coord
Default: none
diff --git a/doc/compute_displace_atom.txt b/doc/compute_displace_atom.txt index 39a11639ad..ee3c4880bd 100644 --- a/doc/compute_displace_atom.txt +++ b/doc/compute_displace_atom.txt @@ -32,20 +32,20 @@ dz*dz). The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "coord/original", as if this +the compute creates its own fix of style "store/coord", as if this command had been issued: -fix compute-ID_coord_original group-ID coord/original :pre +fix compute-ID_store_coord group-ID store/coord :pre -See the "fix coord/original"_fix_coord_original.html command for -details. Note that the ID of the new fix is the compute-ID + -underscore + "coord_original", and the group for the new fix is -the same as the compute group. +See the "fix store/coord"_fix_coord_original.html command for details. +Note that the ID of the new fix is the compute-ID + underscore + +"store_coord", and the group for the new fix is the same as the +compute group. The value of the displacement will be 0.0 for atoms not in the specified compute group. -IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of "unwrapped" coordinates. See the Atoms section of the @@ -81,6 +81,6 @@ overview of LAMMPS output options. [Related commands:] "compute msd"_compute_msd.html, "dump custom"_dump.html, "fix -coord/original"_fix_coord_original.html +store/coord"_fix_store_coord.html [Default:] none diff --git a/doc/compute_msd.html b/doc/compute_msd.html index 57c549c89d..901e1ad38c 100644 --- a/doc/compute_msd.html +++ b/doc/compute_msd.html @@ -49,22 +49,22 @@ proportional to the diffusion coefficient of the diffusing atoms.The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "coord/original", as if this +the compute creates its own fix of style "store/coord", as if this command had been issued:
-fix compute-ID_coord_original group-ID coord/original +fix compute-ID_store_coord group-ID store/coord-See the fix coord/original command for +
See the fix store/coord command for details. Note that the ID of the new fix is the compute-ID + -underscore + "coord_original", and the group for the new fix is +underscore + "store_coord", and the group for the new fix is the same as the compute group.
If the com option is set to yes then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. The com option -is also passed to the created fix coord/original. +is also passed to the created fix store/coord.
-IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +
IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the dump custom command for a discussion of "unwrapped" coordinates. See the Atoms section of the @@ -102,8 +102,8 @@ number of atoms in the simulation.
Related commands:
-compute displace_atom, fix -coord/original, compute +
compute displace_atom, fix +store/coord, compute msd/molecule
Default: diff --git a/doc/compute_msd.txt b/doc/compute_msd.txt index 796d0cca8f..09930883f0 100644 --- a/doc/compute_msd.txt +++ b/doc/compute_msd.txt @@ -41,22 +41,22 @@ proportional to the diffusion coefficient of the diffusing atoms. The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, -the compute creates its own fix of style "coord/original", as if this +the compute creates its own fix of style "store/coord", as if this command had been issued: -fix compute-ID_coord_original group-ID coord/original :pre +fix compute-ID_store_coord group-ID store/coord :pre -See the "fix coord/original"_fix_coord_original.html command for +See the "fix store/coord"_fix_store_coord.html command for details. Note that the ID of the new fix is the compute-ID + -underscore + "coord_original", and the group for the new fix is +underscore + "store_coord", and the group for the new fix is the same as the compute group. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calcluated. The {com} option -is also passed to the created fix coord/original. +is also passed to the created fix store/coord. -IMPORTANT NOTE: Fix coord/original stores the initial coordinates in +IMPORTANT NOTE: Fix store/coord stores the initial coordinates in "unwrapped" form, by using the image flags associated with each atom. See the "dump custom"_dump.html command for a discussion of "unwrapped" coordinates. See the Atoms section of the @@ -95,7 +95,7 @@ number of atoms in the simulation. [Related commands:] "compute displace_atom"_compute_displace_atom.html, "fix -coord/original"_fix_coord_original.html, "compute +store/coord"_fix_store_coord.html, "compute msd/molecule"_compute_msd_molecule.html [Default:] diff --git a/doc/compute_pair_local.html b/doc/compute_pair_local.html index 224260db8e..d0cebf538a 100644 --- a/doc/compute_pair_local.html +++ b/doc/compute_pair_local.html @@ -9,54 +9,55 @@
-compute bond/local command +
compute pair/local command
Syntax:
-compute ID group-ID bond/local input1 input2 ... +compute ID group-ID pair/local input1 input2 ...
- ID, group-ID are documented in compute command -
- bond/local = style name of this compute command +
- pair/local = style name of this compute command
- zero or more keywords may be appended -
- keyword = dist or eng +
- keyword = dist or eng or force -
dist = tabulate bond distances - eng = tablutate bond energies +dist = tabulate pairwise distances + eng = tablutate pairwise energies + eng = tablutate pairwise forcesExamples:
-compute 1 all bond/local eng -compute 1 all bond/local dist eng +compute 1 all pair/local eng +compute 1 all pair/local dist eng forceDescription:
-Define a computation that calculates properties of individual bond +
Define a computation that calculates properties of individual pairwise interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system. +processors, equals the number of pairwise interactions in the system.
-The local data stored by this command is generated by looping over all -the atoms owned on a processor and their bonds. A bond will only be -included if both atoms in the bond are in the specified compute group. -Any bonds that have been broken (see the bond_style -command) by setting their bond type to 0 are not included. Bonds that -have been turned off (see the fix shake or -delete_bonds commands) by setting their bond type -negative are written into the file, but their energy will be 0.0. +
The local data stored by this command is generated by looping over the +pairwise neighbor list. Info about an individual pairwise interaction +will only be included if both atoms in the pair are in the specified +compute group, and if the current pairwise distance is less than the +force cutoff distance for that interaction, as defined by the +pair_style and pair_coeff +commands.
The output dist will be in distance units. The output -eng will be in energy units. +eng will be in energy units. The output force will +be in force units.
Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, bond output from the compute +For example, pair output from the compute property/local command can be combined with data from this command and output by the dump local command in a consistent way. @@ -65,7 +66,7 @@ command in a consistent way.
This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the -array is the number of bonds. If a single keyword is specified, a +array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that diff --git a/doc/compute_pair_local.txt b/doc/compute_pair_local.txt index 79aeedbf73..b4326af53b 100644 --- a/doc/compute_pair_local.txt +++ b/doc/compute_pair_local.txt @@ -6,49 +6,50 @@ :line -compute bond/local command :h3 +compute pair/local command :h3 [Syntax:] -compute ID group-ID bond/local input1 input2 ... :pre +compute ID group-ID pair/local input1 input2 ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l -bond/local = style name of this compute command :l +pair/local = style name of this compute command :l zero or more keywords may be appended :l -keyword = {dist} or {eng} :l - {dist} = tabulate bond distances - {eng} = tablutate bond energies :pre +keyword = {dist} or {eng} or {force} :l + {dist} = tabulate pairwise distances + {eng} = tablutate pairwise energies + {eng} = tablutate pairwise forces :pre :ule [Examples:] -compute 1 all bond/local eng -compute 1 all bond/local dist eng :pre +compute 1 all pair/local eng +compute 1 all pair/local dist eng force :pre [Description:] -Define a computation that calculates properties of individual bond +Define a computation that calculates properties of individual pairwise interactions. The number of datums generated, aggregated across all -processors, equals the number of bonds in the system. +processors, equals the number of pairwise interactions in the system. -The local data stored by this command is generated by looping over all -the atoms owned on a processor and their bonds. A bond will only be -included if both atoms in the bond are in the specified compute group. -Any bonds that have been broken (see the "bond_style"_bond_style.html -command) by setting their bond type to 0 are not included. Bonds that -have been turned off (see the "fix shake"_fix_shake.html or -"delete_bonds"_delete_bonds.html commands) by setting their bond type -negative are written into the file, but their energy will be 0.0. +The local data stored by this command is generated by looping over the +pairwise neighbor list. Info about an individual pairwise interaction +will only be included if both atoms in the pair are in the specified +compute group, and if the current pairwise distance is less than the +force cutoff distance for that interaction, as defined by the +"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html +commands. The output {dist} will be in distance "units"_units.html. The output -{eng} will be in energy "units"_units.html. +{eng} will be in energy "units"_units.html. The output {force} will +be in force "units"_units.html. Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, bond output from the "compute +For example, pair output from the "compute property/local"_compute_property_local.html command can be combined with data from this command and output by the "dump local"_dump.html command in a consistent way. @@ -57,7 +58,7 @@ command in a consistent way. This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the -array is the number of bonds. If a single keyword is specified, a +array is the number of pairs. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that diff --git a/doc/compute_property_local.html b/doc/compute_property_local.html index be8a812690..769facb6e8 100644 --- a/doc/compute_property_local.html +++ b/doc/compute_property_local.html @@ -60,21 +60,22 @@ attributes can be specified together, or angle attributes, etc. Bond and angle attributes can not be mixed in the same compute property/local command.
-The local data is generated by looping over all the atoms owned on a -processor and extracting bond, angle, etc info. For bonds, info about -an individual bond will only be included if both atoms in the bond are -in the specified compute group. Likewise for angles, dihedrals, etc. +
If the inputs are pair attributes, the local data is generated by +looping over the pairwise neighbor list. Info about an individual +pairwise interaction will only be included if both atoms in the pair +are in the specified compute group, and if the current pairwise +distance is less than the force cutoff distance for that interaction, +as defined by the pair_style and +pair_coeff commands.
-In the case of pairs, the local data is generated by looping over the -pairwise neighbor list. Info about an individual pairwise interaction -will only be included if both atoms in the pair are in the specified -compute group, and if the current pairwise distance is less than the -force cutoff distance for that interaction, as defined by the -pair_style and pair_coeff -commands. +
If the inputs are bond, angle, etc attributes, the local data is +generated by looping over all the atoms owned on a processor and +extracting bond, angle, etc info. For bonds, info about an individual +bond will only be included if both atoms in the bond are in the +specified compute group. Likewise for angles, dihedrals, etc.
-As atoms migrate from processor to processor, there will be no -consistent ordering of the entries within the local vector or array +
Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. diff --git a/doc/compute_property_local.txt b/doc/compute_property_local.txt index d45b2b0699..726568aa6b 100644 --- a/doc/compute_property_local.txt +++ b/doc/compute_property_local.txt @@ -53,21 +53,22 @@ attributes can be specified together, or angle attributes, etc. Bond and angle attributes can not be mixed in the same compute property/local command. -The local data is generated by looping over all the atoms owned on a -processor and extracting bond, angle, etc info. For bonds, info about -an individual bond will only be included if both atoms in the bond are -in the specified compute group. Likewise for angles, dihedrals, etc. +If the inputs are pair attributes, the local data is generated by +looping over the pairwise neighbor list. Info about an individual +pairwise interaction will only be included if both atoms in the pair +are in the specified compute group, and if the current pairwise +distance is less than the force cutoff distance for that interaction, +as defined by the "pair_style"_pair_style.html and +"pair_coeff"_pair_coeff.html commands. -In the case of pairs, the local data is generated by looping over the -pairwise neighbor list. Info about an individual pairwise interaction -will only be included if both atoms in the pair are in the specified -compute group, and if the current pairwise distance is less than the -force cutoff distance for that interaction, as defined by the -"pair_style"_pair_style.html and "pair_coeff"_pair_coeff.html -commands. +If the inputs are bond, angle, etc attributes, the local data is +generated by looping over all the atoms owned on a processor and +extracting bond, angle, etc info. For bonds, info about an individual +bond will only be included if both atoms in the bond are in the +specified compute group. Likewise for angles, dihedrals, etc. -As atoms migrate from processor to processor, there will be no -consistent ordering of the entries within the local vector or array +Note that as atoms migrate from processor to processor, there will be +no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. diff --git a/doc/fix.html b/doc/fix.html index 0952769f8b..255ef467c7 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -168,7 +168,6 @@ list of fix styles available in LAMMPS:
bond/create - create bonds on the fly bond/swap - Monte Carlo bond swapping box/relax - relax box size during energy minimization - coord/original - store original coords of each atom deform - change the simulation box size/shape deposit - add new atoms above a surface drag - drag atoms towards a defined coordinate @@ -210,6 +209,8 @@ list of fix styles available in LAMMPS: spring - apply harmonic spring force to group of atoms spring/rg - spring on radius of gyration of group of atoms spring/self - spring from each atom to its origin + store/coord - store coords of each atom + store/force - store force on each atom temp/berendsen - temperature control by Berendsen thermostat temp/rescale - temperature control by velocity rescaling thermal/conductivity - Muller-Plathe kinetic energy exchange for thermal conductivity calculation diff --git a/doc/fix.txt b/doc/fix.txt index 13048baf99..11a48c5034 100644 --- a/doc/fix.txt +++ b/doc/fix.txt @@ -163,7 +163,6 @@ list of fix styles available in LAMMPS: "bond/create"_fix_bond_create.html - create bonds on the fly "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization -"coord/original"_fix_coord_original.html - store original coords of each atom "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface "drag"_fix_drag.html - drag atoms towards a defined coordinate @@ -211,6 +210,8 @@ list of fix styles available in LAMMPS: "spring/rg"_fix_spring_rg.html - spring on radius of gyration of \ group of atoms "spring/self"_fix_spring_self.html - spring from each atom to its origin +"store/coord"_fix_store_coord.html - store coords of each atom +"store/force"_fix_store_force.html - store force on each atom "temp/berendsen"_fix_temp_berendsen.html - temperature control by \ Berendsen thermostat "temp/rescale"_fix_temp_rescale.html - temperature control by \ diff --git a/doc/fix_coord_original.html b/doc/fix_store_coord.html similarity index 100% rename from doc/fix_coord_original.html rename to doc/fix_store_coord.html diff --git a/doc/fix_coord_original.txt b/doc/fix_store_coord.txt similarity index 100% rename from doc/fix_coord_original.txt rename to doc/fix_store_coord.txt