diff --git a/doc/dump.html b/doc/dump.html index 1b073135f1..c90c89fe80 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -56,7 +56,8 @@ c_ID = scalar per-atom quantity calculated by a compute identified by its ID c_ID[N] = Nth per-atom vector quantity calculated by a compute identified by its ID f_ID = scalar per-atom quantity calculated by a fix identified by its ID - f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID + f_ID[N] = Nth per-atom vector quantity calculated by a fix identified by its ID + v_name = variable of atom style that calculates a per-atom quantity @@ -65,7 +66,7 @@ 
dump myDump all atom 100 dump.atom
 dump 2 subgroup atom 50 dump.run.bin
 dump 4a all custom 100 dump.myforce.* tag type x y vx fx
-dump 4b flow custom 100 dump.%.myforce tag type c_myF[3]
+dump 4b flow custom 100 dump.%.myforce tag type c_myF[3] v_ke
 dump 1 all xtc 1000 file.xtc 100.0

Description: @@ -125,9 +126,9 @@ file.

Style custom allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are -listed above and will appear in the order specified. Be careful not -to specify a quantity that is not defined for a particular simulation -- such as q for atom style bond, since that atom style doesn't +listed above and will appear in the order specified. You cannot +specify a quantity that is not defined for a particular simulation - +such as q for atom style bond, since that atom style doesn't assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the dump custom quantities is given @@ -236,20 +237,17 @@ define the orientiation of the particle. The final 3 give the rotational torque on the particle.

The c_ID and c_ID[N] keywords allow scalar or vector per-atom -quantities calculated by a compute to be output. The ID in the -keyword should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -compute command for details. There are pre-defined -computes for calculating the energy, stress, centro-symmetry -parameter, and coordination number of individual atoms. The "compute -variable/atom" command will evaluate a per-atom formula you define via -the variable atom command, for each atom, which can -then be dumped. +quantities calculated by a compute to be output. The +ID in the keyword should be replaced by the actual ID of the compute +that has been defined previously in the input script. See the +compute command for details. There are computes for +calculating the energy, stress, centro-symmetry parameter, and +coordination number of individual atoms.

-

Note that scalar and vector quantities that are not calculated on a -per-atom basis by a compute (e.g. global temperature or pressure) -cannot be output in a dump. Rather, these quantities can be output by -the thermo_style custom command. +

Note that computes which calculate global scalar and vector +quantities, as opposed to per-atom quantities, cannot be output in a +dump. Instead, these quantities can be output by the thermo_style +custom command.

If c_ID is used as a keyword, then the scalar per-atom quantity calculated by the compute is printed. If c_ID[N] is used, then N @@ -257,23 +255,33 @@ in the range from 1-M will print the Nth component of the M-length per-atom vector calculated by the compute.

The f_ID and f_ID[N] keywords allow scalar or vector per-atom -quantities calculated by a fix to be output. The ID in the keyword -should be replaced by the actual ID of the fix that has been defined -previously in the input script. Currently the fix +quantities calculated by a fix to be output. The ID in the +keyword should be replaced by the actual ID of the fix that has been +defined previously in the input script. Currently the fix ave/atom command is the only fix that calculates -per-atom quantities. Since it takes a per-atom compute -as an argument it effectively time-averages any of the previously -described compute quantities so the time-averaged result can be -written to a dump file. +per-atom quantities. Since it can time-average per-atom quantities +produced by any compute, fix, or atom-style +variable, this allows those time-averaged results to +be written to a dump file.

If f_ID is used as a keyword, then the scalar per-atom quantity calculated by the fix is printed. If f_ID[N] is used, then N in the range from 1-M will print the Nth component of the M-length per-atom vector calculated by the fix.

+

The v_name keyword allows per-atom quantities calculated by a +variable to be output. The name in the keyword should +be replaced by the actual name of the variable that has been defined +previously in the input script. Only an atom-style variable can be +referenced, since it is the only one that generates per-atom values. +Variables of style atom can reference individual atom attributes, +per-atom atom attributes, thermodynamic keywords, or invoke other +computes, fixes, or variables when they are evaluated, so this is a +very general means of generating quantities to output to a dump file. +

See this section of the manual for information on how to add new compute and fix styles to LAMMPS that calculate -per-atom quantities which could then be output with these keywords. +per-atom quantities which could then be output into dump files.

diff --git a/doc/dump.txt b/doc/dump.txt index 473490023b..ee1d6e2718 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -47,7 +47,8 @@ args = list of arguments for a particular style :l c_ID = scalar per-atom quantity calculated by a compute identified by its ID c_ID\[N\] = Nth per-atom vector quantity calculated by a compute identified by its ID f_ID = scalar per-atom quantity calculated by a fix identified by its ID - f_ID\[N\] = Nth per-atom vector quantity calculated by a fix identified by its ID :pre + f_ID\[N\] = Nth per-atom vector quantity calculated by a fix identified by its ID + v_name = variable of atom style that calculates a per-atom quantity :pre :ule [Examples:] @@ -55,7 +56,7 @@ args = list of arguments for a particular style :l dump myDump all atom 100 dump.atom dump 2 subgroup atom 50 dump.run.bin dump 4a all custom 100 dump.myforce.* tag type x y vx fx -dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\] +dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\] v_ke dump 1 all xtc 1000 file.xtc 100.0 :pre [Description:] @@ -115,9 +116,9 @@ file. Style {custom} allows you to specify a list of atom attributes to be written to the dump file for each atom. Possible attributes are -listed above and will appear in the order specified. Be careful not -to specify a quantity that is not defined for a particular simulation -- such as {q} for atom style {bond}, since that atom style doesn't +listed above and will appear in the order specified. You cannot +specify a quantity that is not defined for a particular simulation - +such as {q} for atom style {bond}, since that atom style doesn't assign charges. Dumps occur at the very end of a timestep, so atom attributes will include effects due to fixes that are applied during the timestep. An explanation of the dump custom quantities is given @@ -226,20 +227,17 @@ define the orientiation of the particle. The final 3 give the rotational torque on the particle. The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom -quantities calculated by a compute to be output. The ID in the -keyword should be replaced by the actual ID of the compute that has -been defined previously in the input script. See the -"compute"_compute.html command for details. There are pre-defined -computes for calculating the energy, stress, centro-symmetry -parameter, and coordination number of individual atoms. The "compute -variable/atom" command will evaluate a per-atom formula you define via -the "variable atom"_variable.html command, for each atom, which can -then be dumped. +quantities calculated by a "compute"_compute.html to be output. The +ID in the keyword should be replaced by the actual ID of the compute +that has been defined previously in the input script. See the +"compute"_compute.html command for details. There are computes for +calculating the energy, stress, centro-symmetry parameter, and +coordination number of individual atoms. -Note that scalar and vector quantities that are not calculated on a -per-atom basis by a compute (e.g. global temperature or pressure) -cannot be output in a dump. Rather, these quantities can be output by -the "thermo_style custom"_thermo_style.html command. +Note that computes which calculate global scalar and vector +quantities, as opposed to per-atom quantities, cannot be output in a +dump. Instead, these quantities can be output by the "thermo_style +custom"_thermo_style.html command. If {c_ID} is used as a keyword, then the scalar per-atom quantity calculated by the compute is printed. If {c_ID\[N\]} is used, then N @@ -247,23 +245,33 @@ in the range from 1-M will print the Nth component of the M-length per-atom vector calculated by the compute. The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector per-atom -quantities calculated by a fix to be output. The ID in the keyword -should be replaced by the actual ID of the fix that has been defined -previously in the input script. Currently the "fix +quantities calculated by a "fix"_fix.html to be output. The ID in the +keyword should be replaced by the actual ID of the fix that has been +defined previously in the input script. Currently the "fix ave/atom"_fix_ave_atom.html command is the only fix that calculates -per-atom quantities. Since it takes a per-atom "compute"_compute.html -as an argument it effectively time-averages any of the previously -described compute quantities so the time-averaged result can be -written to a dump file. +per-atom quantities. Since it can time-average per-atom quantities +produced by any "compute"_compute.html, "fix"_fix.html, or atom-style +"variable"_variable.html, this allows those time-averaged results to +be written to a dump file. If {f_ID} is used as a keyword, then the scalar per-atom quantity calculated by the fix is printed. If {f_ID\[N\]} is used, then N in the range from 1-M will print the Nth component of the M-length per-atom vector calculated by the fix. +The {v_name} keyword allows per-atom quantities calculated by a +"variable"_variable.html to be output. The name in the keyword should +be replaced by the actual name of the variable that has been defined +previously in the input script. Only an atom-style variable can be +referenced, since it is the only one that generates per-atom values. +Variables of style {atom} can reference individual atom attributes, +per-atom atom attributes, thermodynamic keywords, or invoke other +computes, fixes, or variables when they are evaluated, so this is a +very general means of generating quantities to output to a dump file. + See "this section"_Section_modify.html of the manual for information on how to add new compute and fix styles to LAMMPS that calculate -per-atom quantities which could then be output with these keywords. +per-atom quantities which could then be output into dump files. :line