From c10f59aa181995a68bdfb211cbbdd0152d9e5f0b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 2 Jan 2008 19:25:15 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1273 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 7 +- doc/Section_commands.txt | 6 +- doc/Section_howto.html | 253 ++++++++++++++++---------- doc/Section_howto.txt | 250 ++++++++++++++++---------- doc/compute.html | 79 ++++---- doc/compute.txt | 77 ++++---- doc/compute_attribute_atom.html | 75 -------- doc/compute_attribute_atom.txt | 70 -------- doc/compute_pe.html | 5 + doc/compute_pe.txt | 5 + doc/compute_pressure.html | 7 + doc/compute_pressure.txt | 7 + doc/compute_rotate_dipole.html | 5 + doc/compute_rotate_dipole.txt | 5 + doc/compute_rotate_gran.html | 5 + doc/compute_rotate_gran.txt | 5 + doc/compute_sum.html | 86 ++++++--- doc/compute_sum.txt | 81 ++++++--- doc/compute_sum_atom.html | 54 ------ doc/compute_sum_atom.txt | 49 ----- doc/compute_temp.html | 7 + doc/compute_temp.txt | 7 + doc/compute_temp_asphere.html | 7 + doc/compute_temp_asphere.txt | 7 + doc/compute_temp_deform.html | 7 + doc/compute_temp_deform.txt | 7 + doc/compute_temp_dipole.html | 7 + doc/compute_temp_dipole.txt | 7 + doc/compute_temp_partial.html | 7 + doc/compute_temp_partial.txt | 7 + doc/compute_temp_ramp.html | 7 + doc/compute_temp_ramp.txt | 7 + doc/compute_temp_region.html | 7 + doc/compute_temp_region.txt | 7 + doc/compute_variable.html | 55 ------ doc/compute_variable.txt | 50 ------ doc/compute_variable_atom.html | 65 ------- doc/compute_variable_atom.txt | 60 ------- doc/dump.html | 55 +++--- doc/dump.txt | 55 +++--- doc/fix.html | 62 ++++--- doc/fix.txt | 62 ++++--- doc/fix_ave_atom.html | 134 ++++++++++---- doc/fix_ave_atom.txt | 126 +++++++++---- doc/fix_ave_spatial.html | 214 ++++++++++++---------- doc/fix_ave_spatial.txt | 212 ++++++++++++---------- doc/fix_ave_time.html | 191 +++++++++++--------- doc/fix_ave_time.txt | 186 +++++++++++-------- doc/fix_drag.html | 4 +- doc/fix_drag.txt | 4 +- doc/fix_dt_reset.html | 4 +- doc/fix_dt_reset.txt | 4 +- doc/fix_indent.html | 4 +- doc/fix_indent.txt | 4 +- doc/fix_nph.html | 12 +- doc/fix_nph.txt | 10 +- doc/fix_npt.html | 12 +- doc/fix_npt.txt | 10 +- doc/fix_npt_asphere.html | 8 +- doc/fix_npt_asphere.txt | 6 +- doc/fix_nvt.html | 11 +- doc/fix_nvt.txt | 9 +- doc/fix_nvt_asphere.html | 8 +- doc/fix_nvt_asphere.txt | 8 +- doc/fix_nvt_sllod.html | 6 +- doc/fix_nvt_sllod.txt | 4 +- doc/fix_orient_fcc.html | 4 +- doc/fix_orient_fcc.txt | 4 +- doc/fix_print.html | 10 +- doc/fix_print.txt | 11 +- doc/fix_setforce.html | 4 +- doc/fix_setforce.txt | 4 +- doc/fix_spring.html | 4 +- doc/fix_spring.txt | 4 +- doc/fix_temp_rescale.html | 11 +- doc/fix_temp_rescale.txt | 9 +- doc/fix_viscosity.html | 4 +- doc/fix_viscosity.txt | 4 +- doc/fix_wall_lj126.html | 4 +- doc/fix_wall_lj126.txt | 4 +- doc/fix_wall_lj93.html | 4 +- doc/fix_wall_lj93.txt | 4 +- doc/print.html | 7 +- doc/print.txt | 7 +- doc/run.html | 44 ++--- doc/run.txt | 44 ++--- doc/thermo_style.html | 93 +++++----- doc/thermo_style.txt | 93 +++++----- doc/variable.html | 301 ++++++++++++++++++------------- doc/variable.txt | 308 ++++++++++++++++++-------------- 90 files changed, 2077 insertions(+), 1793 deletions(-) delete mode 100644 doc/compute_attribute_atom.html delete mode 100644 doc/compute_attribute_atom.txt delete mode 100644 doc/compute_sum_atom.html delete mode 100644 doc/compute_sum_atom.txt delete mode 100644 doc/compute_variable.html delete mode 100644 doc/compute_variable.txt delete mode 100644 doc/compute_variable_atom.html delete mode 100644 doc/compute_variable_atom.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 19e6018e47..67ae662f1e 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -333,10 +333,9 @@ descriptions of each style or click on the style itself for a full description:

- - - - + +
attribute/atomcentro/atomcoord/atomke/atompepe/atom
pressurerotate/dipolerotate/granstress/atomsumsum/atom
temptemp/aspheretemp/deformtemp/dipoletemp/partialtemp/ramp
temp/regionvariablevariable/atom +
centro/atomcoord/atomke/atompepe/atompressure
rotate/dipolerotate/granstress/atomsumtemptemp/asphere
temp/deformtemp/dipoletemp/partialtemp/ramptemp/region

These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 91b93d4ce9..aa60e9fb4a 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -437,7 +437,6 @@ Compute styles. See the "compute"_compute.html command for one-line descriptions of each style or click on the style itself for a full description: -"attribute/atom"_compute_attribute_atom.html, "centro/atom"_compute_centro_atom.html, "coord/atom"_compute_coord_atom.html, "ke/atom"_compute_ke_atom.html, @@ -448,16 +447,13 @@ description: "rotate/gran"_compute_rotate_gran.html, "stress/atom"_compute_stress_atom.html, "sum"_compute_sum.html, -"sum/atom"_compute_sum_atom.html, "temp"_compute_temp.html, "temp/asphere"_compute_temp_asphere.html, "temp/deform"_compute_temp_deform.html, "temp/dipole"_compute_temp_dipole.html, "temp/partial"_compute_temp_partial.html, "temp/ramp"_compute_temp_ramp.html, -"temp/region"_compute_temp_region.html, -"variable"_compute_variable.html, -"variable/atom"_compute_variable_atom.html :tb(c=6,ea=c) +"temp/region"_compute_temp_region.html :tb(c=6,ea=c) These are compute styles contributed by users, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#2_3. diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 0e8dbfc392..5fe33645d0 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -805,131 +805,198 @@ which is a list of quantities printed every few timesteps to the screen and logfile. The second is dump files, which contain snapshots of atoms and various per-atom values and are written at a specified frequency. A simulation prints one set of -thermodynamic output; it may generate zero, or one, or multiple dump -files. LAMMPS gives you a variety of ways to determine what +thermodynamic output; it may generate any number of dump files. As +discussed below, LAMMPS gives you a variety of ways to determine what quantities are computed and printed when thermodynamic info or dump files are output. There are also three fixes which can do their own -output of user-defined quantities: fix ave/time -for time averaging, fix ave/spatial for spatial -averaging, and fix print. These are described below. +output of user-chosen quantities: fix ave/time for +time averaging, fix ave/spatial for spatial +averaging, and fix print. These are also described +below. Throughout this discussion, note that users can add their own +computes and fixes to LAMMPS which can then +generate values that can be output with these commands.

+
Thermodynamic output +

The frequency and format of thermodynamic output is set by the thermo, thermo_style, and thermo_modify commands. The thermo_style command also specifies what values are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc) which include time-averaged versions of -temperature, pressure, and a few other variables (tave, pave, etc). -Three addtional kinds of keywords can also be specified (c_ID, f_ID, -v_name), where a compute or fix or -variable provides the value(s) to be output. Each of -these are described in turn. +(e.g. press, etotal, etc). Three addtional kinds of keywords can also +be specified (c_ID, f_ID, v_name), where a compute or +fix or variable provides the value to be +output. Each of these are described in turn.

In LAMMPS, a compute comes in two flavors: ones that -compute one or more global values (e.g. temperature, kinetic energy -tensor) and ones that compute one or more per-atom values. There is a -compute sum command which sums per-atom quantities -into a global scalar or vector. +compute global values (e.g. temperature, pressure tensor) and ones +that compute per-atom values. Only global quantities from a compute +can be used for thermodynamic output. The user-defined ID of the +compute is used along with an optional subscript as part of the +thermo_style command. E.g. c_myTemp outputs the +single scalar value generated by the compute; c_myTemp[2] outputs +the 2nd vector value. Note that there is a compute +sum command which sums per-atom quantities into a +global scalar or vector.

-

Only global quantities from a compute can be used for thermodynamic -output. The user-defined ID of the compute is used along with an -optional subscript as part of the thermo_style -command. E.g. c_myTemp outputs the single scalar value generated by -the compute; c_myTemp[2] would output the 2nd vector value. +

Fixes can generate global scalar or vector values which can +be output with thermodynamic output, e.g. the energy of an indenter's +interaction with the simulation atoms. These values are accessed via +the same format as a compute's values, as f_ID or f_ID[N]. See the +doc pages for individual fix commands to see which ones generate +global values that can be output with thermodynamic info. The fix +ave/time command generates time-averaged global +quantities which can be accessed for thermodynamic output, e.g. a +time-averaged pressure.

-

Fixes can also generate global scalar or vector values -which can be output with thermodynamic output, e.g. the energy of an -indenter's interaction with the simulation atoms. These values are -accessed via the same format as a compute's values, as f_ID or -f_ID[N]. See the doc pages for individual fix commands to see which -ones generate global values that can be output with thermodynamic -info. The fix ave/time command generates -time-averaged global quantities which can be accessed for -thermodynamic output. -

-

Input script variables of various kinds are defined by the -variable command. All kinds except the atom-style -variable can be used for thermodynamic output. A variable with name +

Variables can be defined in the input script. All +styles except the atom-style variable can be used for thermodynamic +output, since it generates per-atom values. A variable with the name "abc" is referenced in a thermo_style command as v_abc.

-

The variable formula defined in the input script can contain math -functions (add, exp, etc), atom values (x[N], fx[N]), groups -quantities (mass(), vcm(), etc), references to thermodynamic -quantities (e.g. temp, volume, etc), or references to other variables -or computes or fixes. Thus a variable is -the most general way to define some quantity you want calculated and -output with thermodynamic info. +

The formula associated with equal-style variables can contain math +operations and functions (x+y,x*y,(),sqrt,exp,etc), atom values +(x[N],fx[N],etc), group functions (mass(),vcm(),etc), references +to thermodynamic quantities (temp,press,vol,etc), references to +computes that generate global values, references to +fixes that generate global values, or references to other +variables. Thus an equal-style variable is the most +general way to define some quantity to calculate and include with +thermodynamic output.

+
Dump file output +

Dump file output is specified by the dump and dump_modify commands. There are several pre-defined formats (dump atom, dump xtc, etc). There is also a dump -custom format where you specify what values are output with -each atom. Pre-defined keywords can be specified (e.g. tag, type, x, -etc). Two additional kinds of keywords can also be specified (c_ID, -f_ID), where a compute or fix provides the -values to be output. +custom format where the user specifies what values are +output with each atom. Pre-defined keywords can be specified (tag, x, +fx, etc). Three additional kinds of keywords can also be specified +(c_ID, f_ID, v_name), where a compute or fix +or variable provides the value to be output. Each of +these are described in turn.

-

Computes that generate per-atom values can be accessed -by the dump custom command. These are computes that have the word -"atom" in their style name, e.g. ke/atom, stress/atom, etc. The -values are accessed as c_myKE for a scalar per-atom quantity or as -c_myStress[2] for a component of a vector per-atom quantity. The -compute variable/atom command takes a -user-defined atom-style variable as input and -calculates its value for each atom. Since this compute can be -accessed by the dump custom command, this is a general way to define -some quantity you want calculated and output in a dump file. +

Computes that generate one or more per-atom values can +be accessed by the dump custom command. These are computes that have +the word "atom" in their style name, e.g. ke/atom, stress/atom, etc. +The values are accessed as c_myKE for a scalar per-atom quantity or as +c_myStress[2] for a component of a vector per-atom quantity.

-

Fixes can also generate per-atom values to output to dump -files. For example, the fix ave/atom command -calculates time-averages of compute quantities. As indicated in the -preceeding paragraph, a compute quantity can be a -calculated value such as energy or -stress or it can be a value calculated by -an atom-style variable, or it can be an atom -attribute such as velocity or force. +

Fixes can generate per-atom values to output to dump files. +For example, the fix ave/atom command calculates +time-averages of per-atom quantities, such as per-atom +computes and atom-style variables. These per-atom fix values are accessed by the dump custom -command as f_myKE for a scalar per-atom quantity or as f_myStress[2] -for a component of a vector per-atom quantity. +command via the same format as a compute's values, as f_myKE or +f_myStress[2].

+

Variables can be defined in the input script. Only +atom-style variables can be used for dump custom output, since only +they produce per-atom values. A variable with the name "abc" is +referenced in a dump custom command as v_abc. +

+

Just like equal-style variables, the formula associated with +atom-style variables can contain math operations and functions +(x+y,x*y,(),sqrt,exp,etc), atom values (x[N],fx[N],etc), group +functions (mass(),vcm(),etc), references to thermodynamic quantities +(temp,press,vol,etc), references to computes that +generate global values, references to fixes that generate +global values, or references to non atom-style variables that generate +global values. In addition, an atom-style variable can reference +vectors of atom values (x[],fx[],etc), computes +that generate per-atom values, fixes that generate per-atom +values, or other atom-style variables. Thus an atom-style variable is +the most general way to define some quantity to calculate and output +to a dump file. +

+
Fix output +

Three other fixes are of particular note for output: fix ave/time, fix ave/spatial, and fix print.

The fix ave/time command enables time-averaging of -global quantities like temperature or pressure. The global quantities -are calculated by a compute or a fix. The -compute or fix must generate global scalar or vector quantities. Note -that this includes the "compute sum" command which computes global -values by summing per-atom quantities. The time-averaged values -generated by fix ave/time can be written directly -to a file and/or accessed by any output command that uses fixes as a -source of input, e.g. the thermo_style custom -command. Fix ave/time options allow for running cummulative averages -or moving time-windowed averages to be output. +any global quantity, like those output with thermodynamic info. The +user specifies one or more quantities to time average. These can be +global compute values, global fix values, or +variables of any style except the atom style which +produces per-atom values. Since a variable can refer to keywords used +by the thermo_style custom command (like temp or +press), any thermodynamic quantity can be time averaged in this way. +

+

The fix ave/time command offers several options +for how it performs time averaging. The results it produces can be +used in two ways. First, they can be written directly to a file, one +line per timestamp. Note that the averaging parameters can be +specified in such a way that averaging is not done at all, in which +case this is simply a convenient means of outputting desired +quantities directly to a separate file. Like other fixes that produce +global quantities, the results of this fix can also be used as input +to any command that accesses global quantities, e.g. by the +thermo_style custom command, by a variable, etc.

The fix ave/spatial command enables -spatial-averaging of per-atom quantities like per-atom energy or -stress. The per-atom quantities can be atom density (mass or number) -or be calculated by a compute or a fix. The -compute or fix must generate per-atom scalar or vector quantities. -Note that if you use the fix ave/atom command with -fix ave/spatial, it means you are effectively calculating a time -average of a spatial average of a time-averaged per-atom quantity. -The time-averaged values generated by fix -ave/spatial can be written directly to a file -and/or accessed by any output command that uses fixes as a source of -input, e.g. the thermo_style custom command. Fix -ave/spatial options allow for running cummulative averages or moving -time-windowed averages to be output. +spatial-averaging of per-atom quantities like those output in dump +files, within 1d layers of the simulation box. The per-atom +quantities can be atom density (mass or number) or atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a compute, by a +fix, or by an atom-style variable. +

+

The fix ave/spatial command offers several +options for how it performs time averaging. The per-layer values it +produces can be used in two ways. First, they can be written directly +to a file. Note that the averaging parameters can be specified in +such a way that time averaging is not done, in which case this is a +convenient means of simply outputting desired quanitities (summed over +atoms within a 1d layer) directly to a separate file. Like other +fixes that produce global quantities, the results of this fix can also +be used as input by any command that accesses global quantities, +e.g. by the thermo_style custom command, by a +variable, etc. See the doc page for fix +ave/spatial for a description of how these +values are indexed.

The fix print command can generate a line of output -written to the screen and log file periodically during a running -simulation. Since the line can contain one or more -variable quantities, this command is a means to output -desired calculated quantities that are not part of thermodynamic or -dump file output. +written to the screen and log file or to a separate file, periodically +during a running simulation. The line can contain one or more +variable values (for any style variable except the +atom style), and as explained above, variables themselves can contain +references to global values generated by thermodynamic +keywords, computes, +fixes, or other variables. Thus the fix +print command is a means to output any desired +calculated quantity separate from normal thermodynamic or dump file +output.

+

This table summarizes the various output options, specifying what +their inputs and outputs are. The frequency with which they are +invoked and produce output is also listed. Basically, any two +commands can be hooked together so long as one produces output that +matches the input needs of the other. A "match" means that the +frequencies and global vs per-atom attributes are the same. +

+
+ + + + + + + + + + + + + + + +
Command Input Input Freq Output Output Freq
thermo_style custom thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable nthermo screen, log nthermo
dump custom keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable dump freq file dump freq
global fixes N/A N/A global scalar/vector 1 or nevery
peratom fixes N/A N/A peratom scalar/vector 1 or nevery
fix ave/time global scalar/vector fix, global scalar/vector compute, equal variable nevery global scalar/vector, file nfreq
fix ave/spatial peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number nevery global vector nfreq, file
fix ave/atom peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector nevery peratom scalar/vector nfreq
fix print any variable nevery screen, file nevery
global computes N/A N/A global scalar/vector N/A
peratom computes N/A N/A peratom scalar/vector N/A
compute sum peratom scalar/vector compute, peratom scalar/vector fix, atom variable N/A global scalar/vector N/A
variable equal thermo keywords, atom value vx[123], global scalar/vector compute, global scalar/vector fix, non-atom variable N/A global scalar N/A
variable atom thermo keywords, atom value vx[123], atom vector vx[], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable N/A peratom scalar N/A
print any variable N/A screen, log between runs
run every any variable nevery screen, log nevery +
+ +
+
diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 35b69c95f3..3dc650e6f9 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -798,131 +798,195 @@ which is a list of quantities printed every few timesteps to the screen and logfile. The second is "dump files"_dump.html, which contain snapshots of atoms and various per-atom values and are written at a specified frequency. A simulation prints one set of -thermodynamic output; it may generate zero, or one, or multiple dump -files. LAMMPS gives you a variety of ways to determine what +thermodynamic output; it may generate any number of dump files. As +discussed below, LAMMPS gives you a variety of ways to determine what quantities are computed and printed when thermodynamic info or dump files are output. There are also three fixes which can do their own -output of user-defined quantities: "fix ave/time"_fix_ave_time.html -for time averaging, "fix ave/spatial"_fix_ave_spatial.html for spatial -averaging, and "fix print"_fix_print.html. These are described below. +output of user-chosen quantities: "fix ave/time"_fix_ave_time.html for +time averaging, "fix ave/spatial"_fix_ave_spatial.html for spatial +averaging, and "fix print"_fix_print.html. These are also described +below. Throughout this discussion, note that users can "add their own +computes and fixes to LAMMPS"_Section_modify.html which can then +generate values that can be output with these commands. + +Thermodynamic output :h5 The frequency and format of thermodynamic output is set by the "thermo"_thermo.html, "thermo_style"_thermo_style.html, and "thermo_modify"_thermo_modify.html commands. The "thermo_style"_themo_style.html command also specifies what values are calculated and written out. Pre-defined keywords can be specified -(e.g. press, etotal, etc) which include time-averaged versions of -temperature, pressure, and a few other variables (tave, pave, etc). -Three addtional kinds of keywords can also be specified (c_ID, f_ID, -v_name), where a "compute"_compute.html or "fix"_fix.html or -"variable"_variable.html provides the value(s) to be output. Each of -these are described in turn. +(e.g. press, etotal, etc). Three addtional kinds of keywords can also +be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or +"fix"_fix.html or "variable"_variable.html provides the value to be +output. Each of these are described in turn. In LAMMPS, a "compute"_compute.html comes in two flavors: ones that -compute one or more global values (e.g. temperature, kinetic energy -tensor) and ones that compute one or more per-atom values. There is a -"compute sum"_compute_sum.html command which sums per-atom quantities -into a global scalar or vector. +compute global values (e.g. temperature, pressure tensor) and ones +that compute per-atom values. Only global quantities from a compute +can be used for thermodynamic output. The user-defined ID of the +compute is used along with an optional subscript as part of the +"thermo_style"_thermo_style.html command. E.g. c_myTemp outputs the +single scalar value generated by the compute; c_myTemp\[2\] outputs +the 2nd vector value. Note that there is a "compute +sum"_compute_sum.html command which sums per-atom quantities into a +global scalar or vector. -Only global quantities from a compute can be used for thermodynamic -output. The user-defined ID of the compute is used along with an -optional subscript as part of the "thermo_style"_thermo_style.html -command. E.g. c_myTemp outputs the single scalar value generated by -the compute; c_myTemp\[2\] would output the 2nd vector value. +"Fixes"_fix.html can generate global scalar or vector values which can +be output with thermodynamic output, e.g. the energy of an indenter's +interaction with the simulation atoms. These values are accessed via +the same format as a compute's values, as f_ID or f_ID\[N\]. See the +doc pages for individual fix commands to see which ones generate +global values that can be output with thermodynamic info. The "fix +ave/time"_fix_ave_time.html command generates time-averaged global +quantities which can be accessed for thermodynamic output, e.g. a +time-averaged pressure. -"Fixes"_fix.html can also generate global scalar or vector values -which can be output with thermodynamic output, e.g. the energy of an -indenter's interaction with the simulation atoms. These values are -accessed via the same format as a compute's values, as f_ID or -f_ID\[N\]. See the doc pages for individual fix commands to see which -ones generate global values that can be output with thermodynamic -info. The "fix ave/time"_fix_ave_time.html command generates -time-averaged global quantities which can be accessed for -thermodynamic output. - -Input script variables of various kinds are defined by the -"variable"_variable.html command. All kinds except the atom-style -variable can be used for thermodynamic output. A variable with name +"Variables"_variable.html can be defined in the input script. All +styles except the atom-style variable can be used for thermodynamic +output, since it generates per-atom values. A variable with the name "abc" is referenced in a thermo_style command as v_abc. -The variable formula defined in the input script can contain math -functions (add, exp, etc), atom values (x\[N\], fx\[N\]), groups -quantities (mass(), vcm(), etc), references to thermodynamic -quantities (e.g. temp, volume, etc), or references to other variables -or "computes"_compute.html or "fixes"_fix.html. Thus a variable is -the most general way to define some quantity you want calculated and -output with thermodynamic info. +The formula associated with equal-style variables can contain math +operations and functions (x+y,x*y,(),sqrt,exp,etc), atom values +(x\[N\],fx\[N\],etc), group functions (mass(),vcm(),etc), references +to thermodynamic quantities (temp,press,vol,etc), references to +"computes"_compute.html that generate global values, references to +"fixes"_fix.html that generate global values, or references to other +"variables"_variable.html. Thus an equal-style variable is the most +general way to define some quantity to calculate and include with +thermodynamic output. + +Dump file output :h5 Dump file output is specified by the "dump"_dump.html and "dump_modify"_dump_modify.html commands. There are several pre-defined formats (dump atom, dump xtc, etc). There is also a "dump -custom"_dump.html format where you specify what values are output with -each atom. Pre-defined keywords can be specified (e.g. tag, type, x, -etc). Two additional kinds of keywords can also be specified (c_ID, -f_ID), where a "compute"_compute.html or "fix"_fix.html provides the -values to be output. +custom"_dump.html format where the user specifies what values are +output with each atom. Pre-defined keywords can be specified (tag, x, +fx, etc). Three additional kinds of keywords can also be specified +(c_ID, f_ID, v_name), where a "compute"_compute.html or "fix"_fix.html +or "variable"_variable.html provides the value to be output. Each of +these are described in turn. -"Computes"_compute.html that generate per-atom values can be accessed -by the dump custom command. These are computes that have the word -"atom" in their style name, e.g. ke/atom, stress/atom, etc. The -values are accessed as c_myKE for a scalar per-atom quantity or as -c_myStress\[2\] for a component of a vector per-atom quantity. The -"compute variable/atom"_compute_variable_atom.html command takes a -user-defined atom-style "variable"_variable.html as input and -calculates its value for each atom. Since this compute can be -accessed by the dump custom command, this is a general way to define -some quantity you want calculated and output in a dump file. +"Computes"_compute.html that generate one or more per-atom values can +be accessed by the dump custom command. These are computes that have +the word "atom" in their style name, e.g. ke/atom, stress/atom, etc. +The values are accessed as c_myKE for a scalar per-atom quantity or as +c_myStress\[2\] for a component of a vector per-atom quantity. -"Fixes"_fix.html can also generate per-atom values to output to dump -files. For example, the "fix ave/atom"_fix_ave_atom.html command -calculates time-averages of compute quantities. As indicated in the -preceeding paragraph, a "compute quantity"_compute.html can be a -calculated value such as "energy"_compute_epair_atom.html or -"stress"_compute_stress_atom.html or it can be a value calculated by -an atom-style "variable"_variable.html, or it can be an "atom -attribute"_compute_attribute_atom.html such as velocity or force. +"Fixes"_fix.html can generate per-atom values to output to dump files. +For example, the "fix ave/atom"_fix_ave_atom.html command calculates +time-averages of per-atom quantities, such as per-atom +"computes"_compute.html and atom-style "variables"_variable.html. These per-atom fix values are accessed by the "dump custom"_dump.html -command as f_myKE for a scalar per-atom quantity or as f_myStress\[2\] -for a component of a vector per-atom quantity. +command via the same format as a compute's values, as f_myKE or +f_myStress\[2\]. + +"Variables"_variable.html can be defined in the input script. Only +atom-style variables can be used for dump custom output, since only +they produce per-atom values. A variable with the name "abc" is +referenced in a dump custom command as v_abc. + +Just like equal-style variables, the formula associated with +atom-style variables can contain math operations and functions +(x+y,x*y,(),sqrt,exp,etc), atom values (x\[N\],fx\[N\],etc), group +functions (mass(),vcm(),etc), references to thermodynamic quantities +(temp,press,vol,etc), references to "computes"_compute.html that +generate global values, references to "fixes"_fix.html that generate +global values, or references to non atom-style variables that generate +global values. In addition, an atom-style variable can reference +vectors of atom values (x\[\],fx\[\],etc), "computes"_compute.html +that generate per-atom values, "fixes"_fix.html that generate per-atom +values, or other atom-style variables. Thus an atom-style variable is +the most general way to define some quantity to calculate and output +to a dump file. + +Fix output :h5 Three other fixes are of particular note for output: "fix ave/time"_fix_ave_time.html, "fix ave/spatial"_fix_ave_spatial.html, and "fix print"_fix_print.html. The "fix ave/time"_fix_ave_time.html command enables time-averaging of -global quantities like temperature or pressure. The global quantities -are calculated by a "compute"_compute.html or a "fix"_fix.html. The -compute or fix must generate global scalar or vector quantities. Note -that this includes the "compute sum" command which computes global -values by summing per-atom quantities. The time-averaged values -generated by "fix ave/time"_fix_ave_time.html can be written directly -to a file and/or accessed by any output command that uses fixes as a -source of input, e.g. the "thermo_style custom"_thermo_style.html -command. Fix ave/time options allow for running cummulative averages -or moving time-windowed averages to be output. +any global quantity, like those output with thermodynamic info. The +user specifies one or more quantities to time average. These can be +global "compute"_compute.html values, global "fix"_fix.html values, or +"variables"_variable.html of any style except the atom style which +produces per-atom values. Since a variable can refer to keywords used +by the "thermo_style custom"_thermo_style.html command (like temp or +press), any thermodynamic quantity can be time averaged in this way. + +The "fix ave/time"_fix_ave_time.html command offers several options +for how it performs time averaging. The results it produces can be +used in two ways. First, they can be written directly to a file, one +line per timestamp. Note that the averaging parameters can be +specified in such a way that averaging is not done at all, in which +case this is simply a convenient means of outputting desired +quantities directly to a separate file. Like other fixes that produce +global quantities, the results of this fix can also be used as input +to any command that accesses global quantities, e.g. by the +"thermo_style custom"_thermo_style.html command, by a variable, etc. The "fix ave/spatial"_fix_ave_spatial.html command enables -spatial-averaging of per-atom quantities like per-atom energy or -stress. The per-atom quantities can be atom density (mass or number) -or be calculated by a "compute"_compute.html or a "fix"_fix.html. The -compute or fix must generate per-atom scalar or vector quantities. -Note that if you use the "fix ave/atom"_fix_ave_atom.html command with -fix ave/spatial, it means you are effectively calculating a time -average of a spatial average of a time-averaged per-atom quantity. -The time-averaged values generated by "fix -ave/spatial"_fix_ave_spatial.html can be written directly to a file -and/or accessed by any output command that uses fixes as a source of -input, e.g. the "thermo_style custom"_thermo_style.html command. Fix -ave/spatial options allow for running cummulative averages or moving -time-windowed averages to be output. +spatial-averaging of per-atom quantities like those output in dump +files, within 1d layers of the simulation box. The per-atom +quantities can be atom density (mass or number) or atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a "compute"_compute.html, by a +"fix"_fix.html, or by an atom-style "variable"_variable.html. + +The "fix ave/spatial"_fix_ave_spatial.html command offers several +options for how it performs time averaging. The per-layer values it +produces can be used in two ways. First, they can be written directly +to a file. Note that the averaging parameters can be specified in +such a way that time averaging is not done, in which case this is a +convenient means of simply outputting desired quanitities (summed over +atoms within a 1d layer) directly to a separate file. Like other +fixes that produce global quantities, the results of this fix can also +be used as input by any command that accesses global quantities, +e.g. by the "thermo_style custom"_thermo_style.html command, by a +variable, etc. See the doc page for "fix +ave/spatial"_fix_ave_spatial.html for a description of how these +values are indexed. The "fix print"_fix_print.html command can generate a line of output -written to the screen and log file periodically during a running -simulation. Since the line can contain one or more -"variable"_variable.html quantities, this command is a means to output -desired calculated quantities that are not part of thermodynamic or -dump file output. +written to the screen and log file or to a separate file, periodically +during a running simulation. The line can contain one or more +"variable"_variable.html values (for any style variable except the +atom style), and as explained above, variables themselves can contain +references to global values generated by "thermodynamic +keywords"_thermo_style.html, "computes"_compute.html, +"fixes"_fix.html, or other "variables"_variable.html. Thus the "fix +print"_fix_print.html command is a means to output any desired +calculated quantity separate from normal thermodynamic or dump file +output. +This table summarizes the various output options, specifying what +their inputs and outputs are. The frequency with which they are +invoked and produce output is also listed. Basically, any two +commands can be hooked together so long as one produces output that +matches the input needs of the other. A "match" means that the +frequencies and global vs per-atom attributes are the same. + +Command: Input: Input Freq: Output: Output Freq +thermo_style custom: thermo keyword, global scalar/vector compute, global scalar/vector fix, equal variable: nthermo: screen, log: nthermo +dump custom: keyword, peratom scalar/vector compute, peratom scalar/vector fix, atom variable: dump freq: file: dump freq +global fixes: N/A: N/A: global scalar/vector: 1 or nevery +peratom fixes: N/A: N/A: peratom scalar/vector: 1 or nevery +fix ave/time: global scalar/vector fix, global scalar/vector compute, equal variable: nevery: global scalar/vector, file: nfreq +fix ave/spatial: peratom scalar/vector fix, peratom scalar/vector compute, atom vector, atom variable, density mass/number: nevery: global vector: nfreq, file +fix ave/atom: peratom scalar/vector compute, peratom scalar/vector fix, atom variable, atom vector: nevery: peratom scalar/vector: nfreq +fix print: any variable: nevery: screen, file: nevery +global computes: N/A: N/A: global scalar/vector: N/A +peratom computes: N/A: N/A: peratom scalar/vector: N/A +compute sum: peratom scalar/vector compute, peratom scalar/vector fix, atom variable: N/A: global scalar/vector: N/A +variable equal: thermo keywords, atom value vx\[123\], global scalar/vector compute, global scalar/vector fix, non-atom variable: N/A: global scalar: N/A +variable atom: thermo keywords, atom value vx\[123\], atom vector vx\[\], global scalar/vector compute, peratom scalar/vector compute, global scalar/vector fix, peratom scalar/vector fix, any variable: N/A: peratom scalar: N/A +print: any variable: N/A: screen, log: between runs +run every: any variable: nevery: screen, log: nevery :tb(s=:) + +:line :line :link(Cornell) diff --git a/doc/compute.html b/doc/compute.html index 0d0b60d86b..ac7382b791 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -29,31 +29,50 @@ compute 3 all ke/atom

Description:

Create a computation that will be performed on a group of atoms. +Quantities calculated by a compute are instantaneous values, meaning +they are calculated from information about atoms on the current +timestep or iteration. There are two kinds of computes, "global" +computes that calculate one or more values for the entire group of +atoms, and "per-atom" computes that calculate one or more values for +each atom in the group. The latter has the word "atom" in its style +name.

-

In LAMMPS, a "compute" is used in several ways. There are two kinds -of computes, "global" computes that calculate one or more values for -the entire group of atoms, and "per-atom" computes that calculate one -or more values for each atom in the group. The latter has the word -"atom" in its style name. -

-

The results of global computes can be output via the thermo_style +

In LAMMPS, a "compute" can be used in several ways. The results of +global computes can be output via the thermo_style custom or fix ave/time command. -Or the values can be referenced in a variable equal -command. The results of computes that calculate a global temperature -or pressure can be used by fixes that do thermostatting or -barostatting and when atom velocities are created. +Or the values can be referenced in a variable equal or +variable atom command. The results of computes that +calculate a global temperature or pressure can be used by fixes that +do thermostatting or barostatting and when atom velocities are +created.

The results of per-atom computes can be output via the dump custom command or the fix ave/spatial command. Or the per-atom values can be time-averaged via the fix ave/atom command and then output via the dump custom or fix -ave/spatial commands. Note that the value of -per-atom computes will be 0.0 for atoms not in the specified compute -group. +ave/spatial commands. Or the per-atom values +can be referenced in a variable atom command. Note +that the value of per-atom computes will be 0.0 for atoms not in the +specified compute group.

See this howto section for a summary of -various LAMMPS output options. +various LAMMPS output options, many of which involve computes. +

+

The ID of a compute can only contain alphanumeric characters and +underscores. +

+

The results of computes that calculate global quantities can be either +"intensive" or "extensive" values. Intensive means the value is +independent of the number of atoms in the simulation, +e.g. temperature. Extensive means the value scales with the number of +atoms in the simulation, e.g. total rotational kinetic energy. +Thermodynamic output will normalize extensive +values depending on the "thermo_modify norm" setting. But if a +compute value is accessed in another way, e.g. by a +variable, you may need to know whether it is an +intensive or extensive value. See the doc page for individual +computes for further info.

LAMMPS creates its own global computes for thermodynamic output. Three computes are always created, named "thermo_temp", @@ -64,20 +83,20 @@ invoked in the input script: compute thermo_pressure all pressure thermo_temp compute thermo_pe all pe -

Additional computes are created if the thermo style requires it. See -the documentation for the thermo_style command. +

Additional computes for other quantities are created if the thermo +style requires it. See the documentation for the +thermo_style command.

-

The dumping of atom snapshots and fixes that compute temperature or -pressure also create computes as required. These are discussed in the -documentation for the dump custom and specific -fix commands. +

Fixes that calculate temperature or pressure, i.e. for thermostatting +or barostatting, may also create computes. These are discussed in the +documentation for specific fix commands.

In all these cases, the default computes can be replaced by computes defined by the user in the input script, as described by the -thermo_modify, fix modify, and -dump commands. +thermo_modify and fix modify +commands.

-

Properties of either a default of user-defined compute can be modified +

Properties of either a default or user-defined compute can be modified via the compute_modify command.

Computes can be deleted with the uncompute command. @@ -88,29 +107,25 @@ calculations accessed in the various ways described above.

Each compute style has its own doc page which describes its arguments and what it does. Here is an alphabetic list of compute styles -defined in LAMMPS: +available in LAMMPS:

- @@ -80,18 +80,19 @@ information for atoms in the specified group is dumped. The included. Not all styles support all these options; see details below.

-

Note that because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box. +

IMPORTANT NOTE: Vecause periodic boundary conditions are enforced only +on timesteps when neighbor lists are rebuilt, the coordinates of an +atom written to a dump file may be slightly outside the simulation +box.

-

Also note that when LAMMPS is running in parallel, the atom -information written to dump files (typically one line per atom) may be -written in an indeterminate order. This is because data for a single -snapshot is collected from multiple processors. This is always the -case for the atom, bond, and custom styles. It is also the case -for the xyz style if the dump group is not all. It is not the -case for the dcd and xtc styles which always write atoms in sorted -order. So does the xyz style if the dump group is all. +

When LAMMPS is running in parallel, the atom information written to +dump files (typically one line per atom) may be written in an +indeterminate order. This is because data for a single snapshot is +collected from multiple processors. This is always the case for the +atom, bond, and custom styles. It is also the case for the +xyz style if the dump group is not all. It is not the case for +the dcd and xtc styles which always write atoms in sorted order. +So does the xyz style if the dump group is all.

@@ -240,9 +241,9 @@ rotational torque on the particle. 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. +compute command for details. There are per-atom +computes for calculating the energy, stress, centro-symmetry +parameter, and coordination number of individual atoms.

Note that computes which calculate global scalar and vector quantities, as opposed to per-atom quantities, cannot be output in a @@ -251,8 +252,8 @@ 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 -in the range from 1-M will print the Nth component of the M-length -per-atom vector calculated by the compute. +must be in the range from 1-M, which 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 @@ -265,22 +266,22 @@ produced by any compute, fix

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. +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 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. +referenced, since it is the only style 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. +very general means of creating 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 +on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files.

diff --git a/doc/dump.txt b/doc/dump.txt index fad4505682..5640e62f65 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -44,11 +44,11 @@ args = list of arguments for a particular style :l mux,muy,muz = orientation of dipolar atom quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on aspherical particles - 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 - v_name = atom-style variable that calculates a per-atom quantity :pre + c_ID = per-atom scalar value calculated by a compute with ID + c_ID\[N\] = Nth component of per-atom vector calculated by a compute with ID + f_ID = per-atom scalar value calculated by a fix with ID + f_ID\[N\] = Nth component of per-atom vector calculated by a fix with ID + v_name = per-atom value calculated by an atom-style variable with name :pre :ule [Examples:] @@ -70,18 +70,19 @@ information for atoms in the specified group is dumped. The included. Not all styles support all these options; see details below. -Note that because periodic boundary conditions are enforced only on -timesteps when neighbor lists are rebuilt, the coordinates of an atom -written to a dump file may be slightly outside the simulation box. +IMPORTANT NOTE: Vecause periodic boundary conditions are enforced only +on timesteps when neighbor lists are rebuilt, the coordinates of an +atom written to a dump file may be slightly outside the simulation +box. -Also note that when LAMMPS is running in parallel, the atom -information written to dump files (typically one line per atom) may be -written in an indeterminate order. This is because data for a single -snapshot is collected from multiple processors. This is always the -case for the {atom}, {bond}, and {custom} styles. It is also the case -for the {xyz} style if the dump group is not {all}. It is not the -case for the {dcd} and {xtc} styles which always write atoms in sorted -order. So does the {xyz} style if the dump group is {all}. +When LAMMPS is running in parallel, the atom information written to +dump files (typically one line per atom) may be written in an +indeterminate order. This is because data for a single snapshot is +collected from multiple processors. This is always the case for the +{atom}, {bond}, and {custom} styles. It is also the case for the +{xyz} style if the dump group is not {all}. It is not the case for +the {dcd} and {xtc} styles which always write atoms in sorted order. +So does the {xyz} style if the dump group is {all}. :line @@ -230,9 +231,9 @@ The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector per-atom 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. +"compute"_compute.html command for details. There are per-atom +computes for calculating the energy, stress, centro-symmetry +parameter, and coordination number of individual atoms. Note that computes which calculate global scalar and vector quantities, as opposed to per-atom quantities, cannot be output in a @@ -241,8 +242,8 @@ 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 -in the range from 1-M will print the Nth component of the M-length -per-atom vector calculated by the compute. +must be in the range from 1-M, which 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"_fix.html to be output. The ID in the @@ -255,22 +256,22 @@ produced by any "compute"_compute.html, "fix"_fix.html, or atom-style 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. +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 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. +referenced, since it is the only style 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. +very general means of creating 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 +on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities which could then be output into dump files. :line diff --git a/doc/fix.html b/doc/fix.html index 67a4c11791..9a33878555 100644 --- a/doc/fix.html +++ b/doc/fix.html @@ -34,23 +34,26 @@ timestepping or minimization. Examples include updating of atom positions and velocities due to time integration, controlling temperature, applying constraint forces to atoms, enforcing boundary conditions, computing diagnostics, etc. There are dozens of fixes -defined in LAMMPS and new ones can be added - see this +defined in LAMMPS and new ones can be added; see this section for a discussion.

-

Each fix style has its own documentation page which describes its -arguments and what it does, as listed below. -

Fixes perform their operations at different stages of the timestep. -If 2 or more fixes both operate at the same stage of the timestep, -they are invoked in the order they were specified in the input script. +If 2 or more fixes operate at the same stage of the timestep, they are +invoked in the order they were specified in the input script.

-

Fixes can be deleted with the unfix command. Note that -this is the only way to turn off a fix; simply specifying a new fix -with a similar style will not turn off the first one. For example, -using a fix nve command for a second run after using a -fix nvt command for the first run, will not cancel out -the NVT time integration invoked by the "fix nvt" command. Thus two -time integrators would be in place! +

The ID of a fix can only contain alphanumeric characters and +underscores. +

+

Fixes can be deleted with the unfix command. +

+

IMPORTANT NOTE: The unfix command is the only way to turn +off a fix; simply specifying a new fix with a similar style will not +turn off the first one. This is especially important to realize for +integration fixes. For example, using a fix nve +command for a second run after using a fix nvt command +for the first run, will not cancel out the NVT time integration +invoked by the "fix nvt" command. Thus two time integrators would be +in place!

If you specify a new fix with the same ID and style as an existing fix, the old fix is deleted and the new one is created (presumably @@ -64,12 +67,29 @@ made to the old fix via the fix_modify command. fixes to be reset. See the doc page for individual fixes for details.

Some fixes calculate a global scalar or vector quantity which can be -accessed by various output commands, including -variables, thermo_style custom, -and fix ave/time. See this howto -section for a summary of various LAMMPS -output options. See the doc pages for individual fixes for info on -which ones calculate these quantities. +accessed by various commands for output, including equal- and +atom-style variables, thermo_style +custom, and fix ave/time. +

+

Some fixes calculate a per-atom scalar or vector quantity which can be +accessed by various commands for output, including atom-style +variables, dump_style custom, and fix +ave/spatial. +

+

The results of fixes that calculate global quantities can be either +"intensive" or "extensive" values. Intensive means the value is +independent of the number of atoms in the simulation, e.g. timestep +size. Extensive means the value scales with the number of atoms in +the simulation, e.g. total force applied by the fix. Thermodynamic +output will normalize extensive values depending on +the "thermo_modify norm" setting. But if a fix value is accessed in +another way, e.g. by a variable, you may need to know +whether it is an intensive or extensive value. See the doc page for +individual fixes for further info. +

+

See this howto section for a summary of +various LAMMPS output options. See the doc pages for individual fixes +for info on which ones calculate these quantities.

Some fixes store an internal "state" which is written to binary restart files via the restart or @@ -79,7 +99,9 @@ continue on with its calculations in a restarted simulation. See the a fix in an input script that reads a restart file. See the doc pages for individual fixes for info on which ones can be restarted.

-

Here is an alphabetic list of fix styles available in LAMMPS: +

Each fix style has its own documentation page which describes its +arguments and what it does, as listed below. Here is an alphabetic +list of fix styles available in LAMMPS: