Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="12 Oct 2016 version"> <META NAME="docnumber" CONTENT="18 Oct 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 12 Oct 2016 version :c,h4 18 Oct 2016 version :c,h4 Version info: :h4 Loading doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -573,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, "gravity (o)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, Loading doc/src/dump_modify.txt +8 −8 Original line number Diff line number Diff line Loading @@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o id = sort per-atom lines by atom ID N = sort per-atom lines in ascending order by the Nth column -N = sort per-atom lines in descending order by the Nth column {thresh} args = attribute operation value {thresh} args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding {unwrap} arg = {yes} or {no} :pre Loading Loading @@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold. If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values which may be useful for the comparision operation. Boolean values can which may be useful for the comparision operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the "variable"_variable.html command doc page for details. Loading Loading @@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump. E.g. due to reactions and subsequent charge equilibration in a reactive force field. The choice of operations are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. :line Loading doc/src/fix_halt.txt 0 → 100644 +121 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix halt command :h3 [Syntax:] fix ID group-ID halt N attribute operator avalue keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l halt = style name of this fix command :l N = check halt condition every N steps :l attribute = hstyle or v_name :l hstyle = {bondmax} v_name = name of "equal-style variable"_variable.html :pre operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l avalue = numeric value to compare attribute to :l string = text string to print with optional variable names :l zero or more keyword/value pairs may be appended :l keyword = {error} :l {error} value = {hard} or {soft} or {continue} :pre :ule [Examples:] fix 10 all halt 1 bondmax > 1.5 fix 10 all print 10 v_myCheck != 0 error soft :pre [Description:] Check a condition every N steps during a simulation run. N must be >= 1. If the condition is met, exit the run immediately. In this context a "run" can be dynamics or minimization iterations, as specified by the "run"_run.html or "minimize"_minimize.html command. The specified group-ID is ignored by this fix. The specified {attribute} can be one of the {hstyle} options listed above, or an "equal-style variable"_variable.html referenced as {v_name}, where "name" is the name of a variable that has been defined previously in the input script. The only {hstyle} option currently implemented is {bondmax}. This will loop over all bonds in the system, compute their current lengths, and set {attribute} to the longest bond distance. Equal-style variables evaluate to a numeric value. See the "variable"_variable.html command for a description. They calculate formulas which can involve mathematical operations, atom properties, group properties, thermodynamic properties, global values calculated by a "compute"_compute.html or "fix"_fix.html, or references to other "variables"_variable.html. Thus they are a very general means of computing some attribute of the current system. For example, the following "bondmax" variable will calculate the same quantity as the hstyle = bondmax option. compute bdist all bond/local dist compute bmax all reduce max c_bdist variable bondmax equal c_bmax :pre Thus these two versions of a fix halt command will do the same thing: fix 10 all halt 1 bondmax > 1.5 fix 10 all halt 1 v_bondmax > 1.5 :pre The version with "bondmax" will just run somewhat faster, due to less overhead in computing bond lengths and not storing them in a separate compute. The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or avalue is 0.0 and the other is non-zero, then the result is "true". Otherwise it is "false". The specified {avalue} must be a numeric value. :line The optional {error} keyword determines how the current run is halted. If its value is {hard}, then LAMMPS will stop with an error message. If its value is {soft}, LAMMPS will exit the current run, but continue to execute subsequent commands in the input script. However, additional "run"_run.html or "minimize"_minimize.html commands will be skipped. For example, this allows a script to output the current state of the system, e.g. via a "write_dump"_write_dump.html or "write_restart"_write_restart.html command. If its value is {continue}, the behavior is the same as for {soft}, except subsequent subsequent "run"_run.html or "minimize"_minimize.html commands are executed. This allows your script to remedy the condition that triggered the halt, if necessary. Note that you may wish use the "unfix"_unfix.html command on the fix halt ID, so that the same condition is not immediately triggered in a subsequent run. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none [Related commands:] "variable"_variable.html [Default:] The option defaults are error = hard. doc/src/minimize.txt +5 −0 Original line number Diff line number Diff line Loading @@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0 the number of outer iterations or timesteps exceeds {maxiter} the number of total force evaluations exceeds {maxeval} :ul NOTE: You can also use the "fix halt"_fix_halt.html command to specify a general criterion for exiting a minimization, that is a calculation performed on the state of the current system, as defined by an "equal-style variable"_variable.html. For the first criterion, the specified energy tolerance {etol} is unitless; it is met when the energy change between successive iterations divided by the energy magnitude is less than or equal to Loading Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="12 Oct 2016 version"> <META NAME="docnumber" CONTENT="18 Oct 2016 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ <H1></H1> LAMMPS Documentation :c,h3 12 Oct 2016 version :c,h4 18 Oct 2016 version :c,h4 Version info: :h4 Loading
doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -573,6 +573,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, "gravity (o)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, "langevin (k)"_fix_langevin.html, Loading
doc/src/dump_modify.txt +8 −8 Original line number Diff line number Diff line Loading @@ -47,9 +47,9 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o id = sort per-atom lines by atom ID N = sort per-atom lines in ascending order by the Nth column -N = sort per-atom lines in descending order by the Nth column {thresh} args = attribute operation value {thresh} args = attribute operator value attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style operation = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" value = numeric value to compare to, or LAST these 3 args can be replaced by the word "none" to turn off thresholding {unwrap} arg = {yes} or {no} :pre Loading Loading @@ -470,7 +470,7 @@ stress of atoms whose energy is above some threshold. If an atom-style variable is used as the attribute, then it can produce continuous numeric values or effective Boolean 0/1 values which may be useful for the comparision operation. Boolean values can which may be useful for the comparision operator. Boolean values can be generated by variable formulas that use comparison or Boolean math operators or special functions like gmask() and rmask() and grmask(). See the "variable"_variable.html command doc page for details. Loading Loading @@ -503,11 +503,11 @@ less than 1/2 to greater than 1/2 (or vice versa) since the last dump. E.g. due to reactions and subsequent charge equilibration in a reactive force field. The choice of operations are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or value is 0.0 and the other is non-zero, then the result is "true" and the threshold criterion is met. Otherwise it is not met. :line Loading
doc/src/fix_halt.txt 0 → 100644 +121 −0 Original line number Diff line number Diff line "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line fix halt command :h3 [Syntax:] fix ID group-ID halt N attribute operator avalue keyword value ... :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l halt = style name of this fix command :l N = check halt condition every N steps :l attribute = hstyle or v_name :l hstyle = {bondmax} v_name = name of "equal-style variable"_variable.html :pre operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^" :l avalue = numeric value to compare attribute to :l string = text string to print with optional variable names :l zero or more keyword/value pairs may be appended :l keyword = {error} :l {error} value = {hard} or {soft} or {continue} :pre :ule [Examples:] fix 10 all halt 1 bondmax > 1.5 fix 10 all print 10 v_myCheck != 0 error soft :pre [Description:] Check a condition every N steps during a simulation run. N must be >= 1. If the condition is met, exit the run immediately. In this context a "run" can be dynamics or minimization iterations, as specified by the "run"_run.html or "minimize"_minimize.html command. The specified group-ID is ignored by this fix. The specified {attribute} can be one of the {hstyle} options listed above, or an "equal-style variable"_variable.html referenced as {v_name}, where "name" is the name of a variable that has been defined previously in the input script. The only {hstyle} option currently implemented is {bondmax}. This will loop over all bonds in the system, compute their current lengths, and set {attribute} to the longest bond distance. Equal-style variables evaluate to a numeric value. See the "variable"_variable.html command for a description. They calculate formulas which can involve mathematical operations, atom properties, group properties, thermodynamic properties, global values calculated by a "compute"_compute.html or "fix"_fix.html, or references to other "variables"_variable.html. Thus they are a very general means of computing some attribute of the current system. For example, the following "bondmax" variable will calculate the same quantity as the hstyle = bondmax option. compute bdist all bond/local dist compute bmax all reduce max c_bdist variable bondmax equal c_bmax :pre Thus these two versions of a fix halt command will do the same thing: fix 10 all halt 1 bondmax > 1.5 fix 10 all halt 1 v_bondmax > 1.5 :pre The version with "bondmax" will just run somewhat faster, due to less overhead in computing bond lengths and not storing them in a separate compute. The choice of operators listed above are the usual comparison operators. The XOR operation (exclusive or) is also included as "|^". In this context, XOR means that if either the attribute or avalue is 0.0 and the other is non-zero, then the result is "true". Otherwise it is "false". The specified {avalue} must be a numeric value. :line The optional {error} keyword determines how the current run is halted. If its value is {hard}, then LAMMPS will stop with an error message. If its value is {soft}, LAMMPS will exit the current run, but continue to execute subsequent commands in the input script. However, additional "run"_run.html or "minimize"_minimize.html commands will be skipped. For example, this allows a script to output the current state of the system, e.g. via a "write_dump"_write_dump.html or "write_restart"_write_restart.html command. If its value is {continue}, the behavior is the same as for {soft}, except subsequent subsequent "run"_run.html or "minimize"_minimize.html commands are executed. This allows your script to remedy the condition that triggered the halt, if necessary. Note that you may wish use the "unfix"_unfix.html command on the fix halt ID, so that the same condition is not immediately triggered in a subsequent run. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] none [Related commands:] "variable"_variable.html [Default:] The option defaults are error = hard.
doc/src/minimize.txt +5 −0 Original line number Diff line number Diff line Loading @@ -103,6 +103,11 @@ the line search fails because the step distance backtracks to 0.0 the number of outer iterations or timesteps exceeds {maxiter} the number of total force evaluations exceeds {maxeval} :ul NOTE: You can also use the "fix halt"_fix_halt.html command to specify a general criterion for exiting a minimization, that is a calculation performed on the state of the current system, as defined by an "equal-style variable"_variable.html. For the first criterion, the specified energy tolerance {etol} is unitless; it is met when the energy change between successive iterations divided by the energy magnitude is less than or equal to Loading
