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63
doc/Section_howto.html
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@ -796,18 +796,20 @@ lj/cut</A>.
<A NAME = "4_15"></A><H4>4.15 Output from LAMMPS <A NAME = "4_15"></A><H4>4.15 Output from LAMMPS
</H4> </H4>
<P>There are two basic kinds of LAMMPS output. The first is <P>Aside from <A HREF = "restart.html">restart files</A>, there are two basic kinds of
thermodynamic output, which is a list of quantities printed every few LAMMPS output. The first is <A HREF = "thermo_style.html">thermodynamic output</A>,
timesteps to the screen and logfile. The second is dump files, which which is a list of quantities printed every few timesteps to the
screen and logfile. The second is <A HREF = "dump.html">dump files</A>, which
contain snapshots of atoms and various per-atom values and are written contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and files are output. There are also two fixes which perform time and
spatial averaging of user-defined quantities, fix ave/time and fix spatial averaging of user-defined quantities, <A HREF = "fix_ave_time.html">fix
ave/spatial. These produce their own output files and are described ave/time</A> and <A HREF = "fix_ave_spatial.html">fix
below. ave/spatial</A>. These produce their own output
files and are described below.
</P> </P>
<P>The frequency and format of thermodynamic output is set by the <P>The frequency and format of thermodynamic output is set by the
<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and <A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
@ -830,12 +832,13 @@ the compute is used along with an optional subscript as part of the
single scalar value generated by the compute; c_myTemp[2] would single scalar value generated by the compute; c_myTemp[2] would
output the 2nd vector value. output the 2nd vector value.
</P> </P>
<P><A HREF = "fix.html">Fixes</A> can also generate values to output with thermodynamic <P><A HREF = "fix.html">Fixes</A> can also generate global scalar or vector values
output, e.g. the energy of an indenter's interaction with the which can be output with thermodynamic output, e.g. the energy of an
simulation atoms. These values are accessed via the same format as indenter's interaction with the simulation atoms. These values are
compute's values, as f_ID or f_ID[N]. See the doc pages for accessed via the same format as a compute's values, as f_ID or
individual fix commands to see which ones generate global values that f_ID[N]. See the doc pages for individual fix commands to see which
can be output with thermodynamic info. ones generate global values that can be output with thermodynamic
info.
</P> </P>
<P>Input script variables of various kinds are defined by the <P>Input script variables of various kinds are defined by the
<A HREF = "variable.html">variable</A> command. All kinds except the atom-style <A HREF = "variable.html">variable</A> command. All kinds except the atom-style
@ -846,9 +849,9 @@ variable can be used for thermodynamic output. A variable with name
functions (add, exp, etc), atom values (x[N], fx[N]), groups functions (add, exp, etc), atom values (x[N], fx[N]), groups
quantities (mass(), vcm(), etc), references to thermodynamic quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables quantities (e.g. temp, volume, etc), or references to other variables
or <A HREF = "compute.html">computes</A>. Thus a variable is the most general way or <A HREF = "compute.html">computes</A> or <A HREF = "fix.html">fixes</A>. Thus a variable is
to define some quantity you want calculated and output with the most general way to define some quantity you want calculated and
thermodynamic info. output with thermodynamic info.
</P> </P>
<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and <P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
<A HREF = "dump_modify.html">dump_modify</A> commands. There are several <A HREF = "dump_modify.html">dump_modify</A> commands. There are several
@ -862,34 +865,38 @@ values to be output.
<P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed <P><A HREF = "compute.html">Computes</A> that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word 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 "atom" in their style name, e.g. ke/atom, stress/atom, etc. The
values are accessed as described above: c_myKE or c_myStress[2]. values are accessed as c_myKE for a scalar per-atom quantity or as
The <A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a c_myStress[2] for a component of a vector per-atom quantity. The
<A HREF = "compute_variable_atom.html">compute variable/atom</A> command takes a
user-defined atom-style <A HREF = "variable.html">variable</A> as input and user-defined atom-style <A HREF = "variable.html">variable</A> as input and
calculates its value for each atom. Since this compute can be calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file. some quantity you want calculated and output in a dump file.
</P> </P>
<P><A HREF = "fix.html">Fixes</A> can also generate values to output to dump files. <P><A HREF = "fix.html">Fixes</A> can also generate per-atom values to output to dump
For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does files. For example, the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command does
time-averaging of atom quantites, such as velocity or energy or stress time-averaging of atom quantities, such as velocity or energy or
which can then be output in a dump file. These values are accessed as stress which can then be output in a dump file. These values are
describe above, as f_ID or f_ID[N]. accessed as f_myKE for a scalar per-atom quantity or as
f_myStress[2] for a component of a vector per-atom quantity.
</P> </P>
<P>Two other fixes are of particular note for output. Neither produces <P>Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output, rather they output their values for thermodynamic or dump output. Instead they output their
results directly to a file. results directly to a file.
</P> </P>
<P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of <P>The <A HREF = "fix_ave_time.html">fix ave/time</A> command enables time-averaging of
global quantities like temperature or pressure. The global quantities global quantities like temperature or pressure. The global quantities
are calculated by a <A HREF = "compute.html">compute</A>. are calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
compute or fix must generate global scalar or vector quantities.
</P> </P>
<P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables <P>The <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command enables
spatial-averaging of per-atom quantities like per-atom energy or spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number) stress. The per-atom quantities can be atom density (mass or number)
or be calculated by a by a <A HREF = "compute.html">compute</A>. They can also be or be calculated by a <A HREF = "compute.html">compute</A> or a <A HREF = "fix.html">fix</A>. The
quantities calculated by <A HREF = "fix_ave_atom.html">fix ave/atom</A>, which means compute or fix must generate per-atom scalar or vector quantities.
you are effectively calculating a time average of a spatial average of Note that if you use the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command with
a time-averaged per-atom quantity. fix ave/spatial, it means you are effectively calculating a time
average of a spatial average of a time-averaged per-atom quantity.
</P> </P>
<HR> <HR>

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@ -789,18 +789,20 @@ lj/cut"_pair_lj.html.
4.15 Output from LAMMPS :link(4_15),h4 4.15 Output from LAMMPS :link(4_15),h4
There are two basic kinds of LAMMPS output. The first is Aside from "restart files"_restart.html, there are two basic kinds of
thermodynamic output, which is a list of quantities printed every few LAMMPS output. The first is "thermodynamic output"_thermo_style.html,
timesteps to the screen and logfile. The second is dump files, which 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 contain snapshots of atoms and various per-atom values and are written
at a specified frequency. A simulation prints one set of at a specified frequency. A simulation prints one set of
thermodynamic output; it may generate zero, or one, or multiple dump thermodynamic output; it may generate zero, or one, or multiple dump
files. LAMMPS gives you a variety of ways to determine what files. LAMMPS gives you a variety of ways to determine what
quantities are computed and printed when thermodynamic info or dump quantities are computed and printed when thermodynamic info or dump
files are output. There are also two fixes which perform time and files are output. There are also two fixes which perform time and
spatial averaging of user-defined quantities, fix ave/time and fix spatial averaging of user-defined quantities, "fix
ave/spatial. These produce their own output files and are described ave/time"_fix_ave_time.html and "fix
below. ave/spatial"_fix_ave_spatial.html. These produce their own output
files and are described below.
The frequency and format of thermodynamic output is set by the The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and "thermo"_thermo.html, "thermo_style"_thermo_style.html, and
@ -823,12 +825,13 @@ the compute is used along with an optional subscript as part of the
single scalar value generated by the compute; c_myTemp\[2\] would single scalar value generated by the compute; c_myTemp\[2\] would
output the 2nd vector value. output the 2nd vector value.
"Fixes"_fix.html can also generate values to output with thermodynamic "Fixes"_fix.html can also generate global scalar or vector values
output, e.g. the energy of an indenter's interaction with the which can be output with thermodynamic output, e.g. the energy of an
simulation atoms. These values are accessed via the same format as indenter's interaction with the simulation atoms. These values are
compute's values, as f_ID or f_ID\[N\]. See the doc pages for accessed via the same format as a compute's values, as f_ID or
individual fix commands to see which ones generate global values that f_ID\[N\]. See the doc pages for individual fix commands to see which
can be output with thermodynamic info. ones generate global values that can be output with thermodynamic
info.
Input script variables of various kinds are defined by the Input script variables of various kinds are defined by the
"variable"_variable.html command. All kinds except the atom-style "variable"_variable.html command. All kinds except the atom-style
@ -839,9 +842,9 @@ The variable formula defined in the input script can contain math
functions (add, exp, etc), atom values (x\[N\], fx\[N\]), groups functions (add, exp, etc), atom values (x\[N\], fx\[N\]), groups
quantities (mass(), vcm(), etc), references to thermodynamic quantities (mass(), vcm(), etc), references to thermodynamic
quantities (e.g. temp, volume, etc), or references to other variables quantities (e.g. temp, volume, etc), or references to other variables
or "computes"_compute.html. Thus a variable is the most general way or "computes"_compute.html or "fixes"_fix.html. Thus a variable is
to define some quantity you want calculated and output with the most general way to define some quantity you want calculated and
thermodynamic info. output with thermodynamic info.
Dump file output is specified by the "dump"_dump.html and Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several "dump_modify"_dump_modify.html commands. There are several
@ -855,34 +858,38 @@ values to be output.
"Computes"_compute.html that generate per-atom values can be accessed "Computes"_compute.html that generate per-atom values can be accessed
by the dump custom command. These are computes that have the word 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 "atom" in their style name, e.g. ke/atom, stress/atom, etc. The
values are accessed as described above: c_myKE or c_myStress\[2\]. values are accessed as c_myKE for a scalar per-atom quantity or as
The "compute variable/atom"_compute_variable_atom.html command takes a 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 user-defined atom-style "variable"_variable.html as input and
calculates its value for each atom. Since this compute can be calculates its value for each atom. Since this compute can be
accessed by the dump custom command, this is a general way to define accessed by the dump custom command, this is a general way to define
some quantity you want calculated and output in a dump file. some quantity you want calculated and output in a dump file.
"Fixes"_fix.html can also generate values to output to dump files. "Fixes"_fix.html can also generate per-atom values to output to dump
For example, the "fix ave/atom"_fix_ave_atom.html command does files. For example, the "fix ave/atom"_fix_ave_atom.html command does
time-averaging of atom quantites, such as velocity or energy or stress time-averaging of atom quantities, such as velocity or energy or
which can then be output in a dump file. These values are accessed as stress which can then be output in a dump file. These values are
describe above, as f_ID or f_ID\[N\]. accessed as f_myKE for a scalar per-atom quantity or as
f_myStress\[2\] for a component of a vector per-atom quantity.
Two other fixes are of particular note for output. Neither produces Two other fixes are of particular note for output. Neither produces
values for thermodynamic or dump output, rather they output their values for thermodynamic or dump output. Instead they output their
results directly to a file. results directly to a file.
The "fix ave/time"_fix_ave_time.html command enables time-averaging of The "fix ave/time"_fix_ave_time.html command enables time-averaging of
global quantities like temperature or pressure. The global quantities global quantities like temperature or pressure. The global quantities
are calculated by a "compute"_compute.html. are calculated by a "compute"_compute.html or a "fix"_fix.html. The
compute or fix must generate global scalar or vector quantities.
The "fix ave/spatial"_fix_ave_spatial.html command enables The "fix ave/spatial"_fix_ave_spatial.html command enables
spatial-averaging of per-atom quantities like per-atom energy or spatial-averaging of per-atom quantities like per-atom energy or
stress. The per-atom quantities can be atom density (mass or number) stress. The per-atom quantities can be atom density (mass or number)
or be calculated by a by a "compute"_compute.html. They can also be or be calculated by a "compute"_compute.html or a "fix"_fix.html. The
quantities calculated by "fix ave/atom"_fix_ave_atom.html, which means compute or fix must generate per-atom scalar or vector quantities.
you are effectively calculating a time average of a spatial average of Note that if you use the "fix ave/atom"_fix_ave_atom.html command with
a time-averaged per-atom quantity. fix ave/spatial, it means you are effectively calculating a time
average of a spatial average of a time-averaged per-atom quantity.
:line :line

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@ -50,6 +50,9 @@ be time-averaged via the <A HREF = "fix_ave_atom.html">fix ave/atom</A> command
then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix then output via the <A HREF = "dump.html">dump custom</A> or <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> commands. ave/spatial</A> commands.
</P> </P>
<P>See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
various LAMMPS output options.
</P>
<P>LAMMPS creates its own global computes for thermodynamic output. Two <P>LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked: "thermo_pressure", as if these commands had been invoked:

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@ -47,6 +47,9 @@ be time-averaged via the "fix ave/atom"_fix_ave_atom.html command and
then output via the "dump custom"_dump.html or "fix then output via the "dump custom"_dump.html or "fix
ave/spatial"_fix_ave_spatial.html commands. ave/spatial"_fix_ave_spatial.html commands.
See this "howto section"_Section_howto.html#4_15 for a summary of
various LAMMPS output options.
LAMMPS creates its own global computes for thermodynamic output. Two LAMMPS creates its own global computes for thermodynamic output. Two
computes are always created, named "thermo_temp" and computes are always created, named "thermo_temp" and
"thermo_pressure", as if these commands had been invoked: "thermo_pressure", as if these commands had been invoked:

2
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@ -43,7 +43,7 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
</UL> </UL>
<P>The weighting factor is applied to pairwise interaction between the <P>The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is 1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the <A HREF = "doc/special_bonds.html">special unrelated to the weighting factor specified by the <A HREF = "special_bonds.html">special
bonds</A> command which applies to all 1-4 bonds</A> command which applies to all 1-4
interactions in the system. interactions in the system.
</P> </P>

2
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@ -41,7 +41,7 @@ weighting factor (0.0 to 1.0) :ul
The weighting factor is applied to pairwise interaction between the The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is 1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the "special unrelated to the weighting factor specified by the "special
bonds"_doc/special_bonds.html command which applies to all 1-4 bonds"_special_bonds.html command which applies to all 1-4
interactions in the system. interactions in the system.
For CHARMM force fields, the special_bonds 1-4 weighting factor should For CHARMM force fields, the special_bonds 1-4 weighting factor should

8
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@ -63,6 +63,14 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
<P>The <A HREF = "fix_modify.html">fix modify</A> command allows settings for some <P>The <A HREF = "fix_modify.html">fix modify</A> command allows settings for some
fixes to be reset. See the doc page for individual fixes for details. fixes to be reset. See the doc page for individual fixes for details.
</P> </P>
<P>Some fixes calculate a global scalar or vector quantity which can be
accessed by various output commands, including
<A HREF = "variable.html">variables</A>, <A HREF = "thermo_style.html">thermo_style custom</A>,
and <A HREF = "fix_ave_time.html">fix ave/time</A>. See this <A HREF = "Section_howto.html#4_15">howto
section</A> for a summary of various LAMMPS
output options. See the doc pages for individual fixes for info on
which ones calculate these quantities.
</P>
<P>Some fixes store an internal "state" which is written to binary <P>Some fixes store an internal "state" which is written to binary
restart files via the <A HREF = "restart.html">restart</A> or restart files via the <A HREF = "restart.html">restart</A> or
<A HREF = "write_restart.html">write_restart</A> commands. This allows the fix to <A HREF = "write_restart.html">write_restart</A> commands. This allows the fix to

8
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@ -60,6 +60,14 @@ made to the old fix via the "fix_modify"_fix_modify.html command.
The "fix modify"_fix_modify.html command allows settings for some The "fix modify"_fix_modify.html command allows settings for some
fixes to be reset. See the doc page for individual fixes for details. 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"_variable.html, "thermo_style custom"_thermo_style.html,
and "fix ave/time"_fix_ave_time.html. See this "howto
section"_Section_howto.html#4_15 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 Some fixes store an internal "state" which is written to binary
restart files via the "restart"_restart.html or restart files via the "restart"_restart.html or
"write_restart"_write_restart.html commands. This allows the fix to "write_restart"_write_restart.html commands. This allows the fix to

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@ -13,43 +13,51 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file <PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file
</PRE> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command <LI>ave/time = style name of this fix command
<LI>Nevery = calculate property every this many timesteps <LI>Nevery = calculate property every this many timesteps
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging <LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
<LI>Nfreq = timestep frequency at which the average value is written to file <LI>Nfreq = timestep frequency at which the average value is written to file
<LI>compute-ID = ID of compute that performs the calculation <LI>style = <I>compute</I> or <I>fix</I>
<LI>ID = ID of compute or fix that performs the calculation
<LI>flag = 0 for scalar quantity, 1 for vector quantity, 2 for both <LI>flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
<LI>file = filename to write results to <LI>file = filename to write results to
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats <PRE>fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
</PRE>
<PRE>fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Calculate one or more instantaneous quantities every few timesteps, <P>Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file. average them over a longer timescale, and print the results to a file.
This can be used to time-average any "compute" entity in LAMMPS which This can be used to time-average a <A HREF = "compute.html">compute</A> which
calculates a global quantity such as a temperature or pressure. calculates a global quantity such as a temperature or pressure or a
Per-atom computes cannot be used with this fix. <A HREF = "fix.html">fix</A> which calculates such a global quantity. Note that
per-atom computes cannot be used with this fix; their values can be
averaged by the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
ave/atom</A> commands.
</P> </P>
<P>The <I>compute-ID</I> specifies a <A HREF = "compute.html">compute</A> which calculates <P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which
the desired property. The compute must be a "global" compute that calculates the desired property. The compute must be a "global"
calculates one or more global properties rather than a "per-atom" compute that calculates one or more global properties rather than a
compute. The compute can be previously defined in the input script. "per-atom" compute. The fix must be previously defined in the input
Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic script. Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nvt.html">fix output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. Users nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. Users
can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to can write code for their own compute styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>. LAMMPS</A>.
</P> </P>
<P>In all these cases, the fix ave/time command uses the global scalar or <P>For style <I>fix</I> the <I>ID</I> specifies a <A HREF = "fix.html">fix</A> which calculates
vector calculated by the compute. See the <A HREF = "fix_ave_spatial.html">fix the desired property. The fix must calculate a global scalar or
ave/spatial</A> command if you wish to average vector quantity, which only a few fixes do. See the doc page for
spatially, e.g. via a compute that calculates per-atom quantities. individual fix commands for details. The fix must be previously
defined in the input script. Users can write code for their own fix
styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
</P> </P>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the <P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
property will be time-averaged. The final averaged value(s) are property will be time-averaged. The final averaged value(s) are
@ -61,22 +69,23 @@ final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc. timesteps 190,192,194,196,198,200 on timestep 200, etc.
</P> </P>
<P>The <I>flag</I> argument chooses whether the scalar and/or vector <P>The <I>flag</I> argument chooses whether the scalar and/or vector
calculation of the compute is invoked. The former computes a single calculation of the compute or fix is invoked. The former computes a
global value. The latter computes N global values, where N is defined single global value. The latter computes N global values, where N is
by the compute, e.g. 6 pressure tensor components. In the vector defined by the compute or fix, e.g. 6 pressure tensor components. In
case, each of the N values is averaged independently and N values are the vector case, each of the N values is averaged independently and N
written to the file at each output. values are written to the file at each output.
</P> </P>
<P>Since the calculation is performed by the compute which stores its own <P>Since the calculation is performed by the compute or fix which stores
"group" definition, the group specified for this fix is ignored. its own "group" definition, the group specified for with the fix
ave/time command is ignored.
</P> </P>
<P>If the compute calculates pressure, it will cause the force <P>If the style is <I>compute</I> and the compute calculates pressure, it will
computations performed by LAMMPS (pair, bond, angle, etc) to calculate cause the force computations performed by LAMMPS (pair, bond, angle,
virial terms each Nevery timesteps. If this is more frequent than etc) to calculate virial terms each Nevery timesteps. If this is more
thermodynamic output, this adds extra cost to a simulation. However, frequent than thermodynamic output, this adds extra cost to a
if a constant pressure simulation is being run (<A HREF = "fix_npt.html">fix npt</A> simulation. However, if a constant pressure simulation is being run
or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already calculating virial terms (<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already
for the pressure every timestep. calculating virial terms for the pressure every timestep.
</P> </P>
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B> <P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
</P> </P>
@ -92,7 +101,8 @@ minimization</A>.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> <P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

71
doc/fix_ave_time.txt
View File

@ -10,43 +10,50 @@ fix ave/time command :h3
[Syntax:] [Syntax:]
fix ID group-ID ave/time Nevery Nrepeat Nfreq compute-ID flag file :pre fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID flag file :pre
ID, group-ID are documented in "fix"_fix.html command ID, group-ID are documented in "fix"_fix.html command
ave/time = style name of this fix command ave/time = style name of this fix command
Nevery = calculate property every this many timesteps Nevery = calculate property every this many timesteps
Nrepeat = # of times to repeat the Nevery calculation before averaging Nrepeat = # of times to repeat the Nevery calculation before averaging
Nfreq = timestep frequency at which the average value is written to file Nfreq = timestep frequency at which the average value is written to file
compute-ID = ID of compute that performs the calculation style = {compute} or {fix}
ID = ID of compute or fix that performs the calculation
flag = 0 for scalar quantity, 1 for vector quantity, 2 for both flag = 0 for scalar quantity, 1 for vector quantity, 2 for both
file = filename to write results to :ul file = filename to write results to :ul
[Examples:] [Examples:]
fix 1 all ave/time 100 5 1000 myTemp 0 temp.stats :pre fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats :pre
fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent :pre
[Description:] [Description:]
Calculate one or more instantaneous quantities every few timesteps, Calculate one or more instantaneous quantities every few timesteps,
average them over a longer timescale, and print the results to a file. average them over a longer timescale, and print the results to a file.
This can be used to time-average any "compute" entity in LAMMPS which This can be used to time-average a "compute"_compute.html which
calculates a global quantity such as a temperature or pressure. calculates a global quantity such as a temperature or pressure or a
Per-atom computes cannot be used with this fix. "fix"_fix.html which calculates such a global quantity. Note that
per-atom computes cannot be used with this fix; their values can be
averaged by the "fix ave/spatial"_fix_ave_spatial.html or "fix
ave/atom"_fix_ave_atom.html commands.
The {compute-ID} specifies a "compute"_compute.html which calculates For style {compute} the {ID} specifies a "compute"_compute.html which
the desired property. The compute must be a "global" compute that calculates the desired property. The compute must be a "global"
calculates one or more global properties rather than a "per-atom" compute that calculates one or more global properties rather than a
compute. The compute can be previously defined in the input script. "per-atom" compute. The fix must be previously defined in the input
Or it can be a compute defined by "thermodynamic script. Or it can be a compute defined by "thermodynamic
output"_thermo_style.html or other fixes such as "fix output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html. Users
can also write code for their own compute styles and "add them to can write code for their own compute styles and "add them to
LAMMPS"_Section_modify.html. LAMMPS"_Section_modify.html.
In all these cases, the fix ave/time command uses the global scalar or For style {fix} the {ID} specifies a "fix"_fix.html which calculates
vector calculated by the compute. See the "fix the desired property. The fix must calculate a global scalar or
ave/spatial"_fix_ave_spatial.html command if you wish to average vector quantity, which only a few fixes do. See the doc page for
spatially, e.g. via a compute that calculates per-atom quantities. individual fix commands for details. The fix must be previously
defined in the input script. Users can write code for their own fix
styles and "add them to LAMMPS"_Section_modify.html.
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
property will be time-averaged. The final averaged value(s) are property will be time-averaged. The final averaged value(s) are
@ -58,22 +65,23 @@ final average written to the file on timestep 100. Similary for
timesteps 190,192,194,196,198,200 on timestep 200, etc. timesteps 190,192,194,196,198,200 on timestep 200, etc.
The {flag} argument chooses whether the scalar and/or vector The {flag} argument chooses whether the scalar and/or vector
calculation of the compute is invoked. The former computes a single calculation of the compute or fix is invoked. The former computes a
global value. The latter computes N global values, where N is defined single global value. The latter computes N global values, where N is
by the compute, e.g. 6 pressure tensor components. In the vector defined by the compute or fix, e.g. 6 pressure tensor components. In
case, each of the N values is averaged independently and N values are the vector case, each of the N values is averaged independently and N
written to the file at each output. values are written to the file at each output.
Since the calculation is performed by the compute which stores its own Since the calculation is performed by the compute or fix which stores
"group" definition, the group specified for this fix is ignored. its own "group" definition, the group specified for with the fix
ave/time command is ignored.
If the compute calculates pressure, it will cause the force If the style is {compute} and the compute calculates pressure, it will
computations performed by LAMMPS (pair, bond, angle, etc) to calculate cause the force computations performed by LAMMPS (pair, bond, angle,
virial terms each Nevery timesteps. If this is more frequent than etc) to calculate virial terms each Nevery timesteps. If this is more
thermodynamic output, this adds extra cost to a simulation. However, frequent than thermodynamic output, this adds extra cost to a
if a constant pressure simulation is being run ("fix npt"_fix_npt.html simulation. However, if a constant pressure simulation is being run
or "fix nph"_fix_nph.html), LAMMPS is already calculating virial terms ("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already
for the pressure every timestep. calculating virial terms for the pressure every timestep.
[Restart, fix_modify, thermo output, run start/stop, minimize info:] [Restart, fix_modify, thermo output, run start/stop, minimize info:]
@ -89,6 +97,7 @@ minimization"_minimize.html.
[Related commands:] [Related commands:]
"compute"_compute.html, "fix ave/spatial"_fix_ave_spatial.html "compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/spatial"_fix_ave_spatial.html
[Default:] none [Default:] none

7
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View File

@ -105,10 +105,9 @@ the system's potential energy as part of <A HREF = "thermo_style.html">thermodyn
output</A>. The energy of each particle interacting output</A>. The energy of each particle interacting
with the indenter is K/3 (r - R)^3. with the indenter is K/3 (r - R)^3.
</P> </P>
<P>The atom/indenter interaction energy can be printed as part of <P>This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of indenter), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for commands</A>.
details.
</P> </P>
<P>This fix can adjust the indenter position and radius over multiple <P>This fix can adjust the indenter position and radius over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>

7
doc/fix_indent.txt
View File

@ -96,10 +96,9 @@ the system's potential energy as part of "thermodynamic
output"_thermo_style.html. The energy of each particle interacting output"_thermo_style.html. The energy of each particle interacting
with the indenter is K/3 (r - R)^3. with the indenter is K/3 (r - R)^3.
The atom/indenter interaction energy can be printed as part of This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of indenter), which can be accessed by various "output
this fix. See the "thermo_style custom"_thermo_style.html command for commands"_Section_howto.html#4_15.
details.
This fix can adjust the indenter position and radius over multiple This fix can adjust the indenter position and radius over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html runs, using the {start} and {stop} keywords of the "run"_run.html

6
doc/fix_nph.html
View File

@ -168,9 +168,9 @@ fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target pressure over multiple runs, using the <P>This fix can ramp its target pressure over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the

6
doc/fix_nph.txt
View File

@ -158,9 +158,9 @@ fix to add the energy change induced by Nose/Hoover barostatting to
the system's potential energy as part of "thermodynamic the system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target pressure over multiple runs, using the This fix can ramp its target pressure over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the {start} and {stop} keywords of the "run"_run.html command. See the

6
doc/fix_npt.html
View File

@ -171,9 +171,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>. <A HREF = "thermo_style.html">thermodynamic output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target temperature and pressure over multiple <P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>

6
doc/fix_npt.txt
View File

@ -160,9 +160,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html. "thermodynamic output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html runs, using the {start} and {stop} keywords of the "run"_run.html

6
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View File

@ -172,9 +172,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of barostatting to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>. <A HREF = "thermo_style.html">thermodynamic output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target temperature and pressure over multiple <P>This fix can ramp its target temperature and pressure over multiple
runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>

6
doc/fix_npt_asphere.txt
View File

@ -161,9 +161,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting and
barostatting to the system's potential energy as part of barostatting to the system's potential energy as part of
"thermodynamic output"_thermo_style.html. "thermodynamic output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target temperature and pressure over multiple This fix can ramp its target temperature and pressure over multiple
runs, using the {start} and {stop} keywords of the "run"_run.html runs, using the {start} and {stop} keywords of the "run"_run.html

6
doc/fix_nvt.html
View File

@ -99,9 +99,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target temperature over multiple runs, using the <P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the

6
doc/fix_nvt.txt
View File

@ -90,9 +90,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic the system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the {start} and {stop} keywords of the "run"_run.html command. See the

6
doc/fix_nvt_asphere.html
View File

@ -100,9 +100,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target temperature over multiple runs, using the <P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the

6
doc/fix_nvt_asphere.txt
View File

@ -91,9 +91,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic the system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the {start} and {stop} keywords of the "run"_run.html command. See the

6
doc/fix_nvt_sllod.html
View File

@ -126,9 +126,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic the system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
<A HREF = "thermo_style.html">thermo_style custom</A> command for details. commands</A>.
</P> </P>
<P>This fix can ramp its target temperature over multiple runs, using the <P>This fix can ramp its target temperature over multiple runs, using the
<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the

6
doc/fix_nvt_sllod.txt
View File

@ -117,9 +117,9 @@ fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic the system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The energy change can be printed as part of thermodynamic output via The potential energy change due to this fix is stored as a scalar
the keyword f_ID, where ID is the fix-ID of this fix. See the quantity, which can be accessed by various "output
"thermo_style custom"_thermo_style.html command for details. commands"_Section_howto.html#4_15.
This fix can ramp its target temperature over multiple runs, using the This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command. See the {start} and {stop} keywords of the "run"_run.html command. See the

7
doc/fix_orient_fcc.html
View File

@ -126,10 +126,9 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of boundary driving force to the system's potential energy as part of
<A HREF = "thermo_style.html">thermodynamic output</A>. <A HREF = "thermo_style.html">thermodynamic output</A>.
</P> </P>
<P>The atom/grain-boundary interaction energy can be printed as part of <P>The potential energy change due to this fix is stored as a scalar
thermodynamic output via the keyword f_ID, where ID is the fix-ID of quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for commands</A>.
details.
</P> </P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy

7
doc/fix_orient_fcc.txt
View File

@ -123,10 +123,9 @@ fix to add the potential energy of atom interactions with the grain
boundary driving force to the system's potential energy as part of boundary driving force to the system's potential energy as part of
"thermodynamic output"_thermo_style.html. "thermodynamic output"_thermo_style.html.
The atom/grain-boundary interaction energy can be printed as part of The potential energy change due to this fix is stored as a scalar
thermodynamic output via the keyword f_ID, where ID is the fix-ID of quantity, which can be accessed by various "output
this fix. See the "thermo_style custom"_thermo_style.html command for commands"_Section_howto.html#4_15.
details.
No parameter of this fix can be used with the {start/stop} keywords of 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 the "run"_run.html command. This fix is not invoked during "energy

13
doc/fix_setforce.html
View File

@ -41,15 +41,10 @@ alter the force component in that dimension.
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. are relevant to this fix.
</P> </P>
<P>The total vector force on the group of atoms before it is reset is <P>This fix computes a 3-vector of forces, which can be accessed by
stored by the fix and its components can be printed as part of various <A HREF = "Section_howto.html#4_15">output commands</A>. This is the total
thermodynamic output via the keywords f_ID[N] where ID is the fix-ID force on the group of atoms before the forces on individual atoms are
of this fix and N = 1,2,3. See the <A HREF = "thermo_style.html">thermo_style reset by the fix.
custom</A> command for details. Note that the fix
stores the total force on the group of atoms, but the printed value
may be normalized by the total number of atoms in the simulation
depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A> option being
used.
</P> </P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. the <A HREF = "run.html">run</A> command.

13
doc/fix_setforce.txt
View File

@ -38,15 +38,10 @@ No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. are relevant to this fix.
The total vector force on the group of atoms before it is reset is This fix computes a 3-vector of forces, which can be accessed by
stored by the fix and its components can be printed as part of various "output commands"_Section_howto.html#4_15. This is the total
thermodynamic output via the keywords f_ID\[N\] where ID is the fix-ID force on the group of atoms before the forces on individual atoms are
of this fix and N = 1,2,3. See the "thermo_style reset by the fix.
custom"_thermo_style.html command for details. Note that the fix
stores the total force on the group of atoms, but the printed value
may be normalized by the total number of atoms in the simulation
depending on the "thermo_modify norm"_thermo_modify.html option being
used.
No parameter of this fix can be used with the {start/stop} keywords of No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. the "run"_run.html command.

7
doc/fix_temp_rescale.html
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@ -111,8 +111,11 @@ fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. Note that because this fix is invoked output</A>. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that every N steps and thermodynamic info is printed every M steps, that
unless M is a multiple of N, the energy contribution will not be for unless M is a multiple of N, the energy contribution will be zero.
the current timestep. </P>
<P>The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
commands</A>.
</P> </P>
<P>The energy change can be printed as part of thermodynamic output via <P>The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the the keyword f_ID, where ID is the fix-ID of this fix. See the

7
doc/fix_temp_rescale.txt
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@ -107,8 +107,11 @@ fix to add the energy change implied by a velocity rescaling to the
system's potential energy as part of "thermodynamic system's potential energy as part of "thermodynamic
output"_thermo_style.html. Note that because this fix is invoked output"_thermo_style.html. Note that because this fix is invoked
every N steps and thermodynamic info is printed every M steps, that every N steps and thermodynamic info is printed every M steps, that
unless M is a multiple of N, the energy contribution will not be for unless M is a multiple of N, the energy contribution will be zero.
the current timestep.
The potential energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15.
The energy change can be printed as part of thermodynamic output via The energy change can be printed as part of thermodynamic output via
the keyword f_ID, where ID is the fix-ID of this fix. See the the keyword f_ID, where ID is the fix-ID of this fix. See the

7
doc/fix_wall_lj126.html
View File

@ -54,10 +54,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The atom/wall interaction energy can be printed as part of <P>This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for commands</A>.
details.
</P> </P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. the <A HREF = "run.html">run</A> command.

7
doc/fix_wall_lj126.txt
View File

@ -51,10 +51,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The atom/wall interaction energy can be printed as part of This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of wall), which can be accessed by various "output
this fix. See the "thermo_style custom"_thermo_style.html command for commands"_Section_howto.html#4_15.
details.
No parameter of this fix can be used with the {start/stop} keywords of No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. the "run"_run.html command.

7
doc/fix_wall_lj93.html
View File

@ -55,10 +55,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic system's potential energy as part of <A HREF = "thermo_style.html">thermodynamic
output</A>. output</A>.
</P> </P>
<P>The atom/wall interaction energy can be printed as part of <P>This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of wall), which can be accessed by various <A HREF = "Section_howto.html#4_15">output
this fix. See the <A HREF = "thermo_style.html">thermo_style custom</A> command for commands</A>.
details.
</P> </P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. the <A HREF = "run.html">run</A> command.

7
doc/fix_wall_lj93.txt
View File

@ -52,10 +52,9 @@ fix to add the energy of interaction between atoms and the wall to the
system's potential energy as part of "thermodynamic system's potential energy as part of "thermodynamic
output"_thermo_style.html. output"_thermo_style.html.
The atom/wall interaction energy can be printed as part of This fix computes a scalar energy and a 3-vector of forces (on the
thermodynamic output via the keyword f_ID, where ID is the fix-ID of wall), which can be accessed by various "output
this fix. See the "thermo_style custom"_thermo_style.html command for commands"_Section_howto.html#4_15.
details.
No parameter of this fix can be used with the {start/stop} keywords of No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. the "run"_run.html command.

2
doc/run.html
View File

@ -48,7 +48,7 @@ run 100000 every 1000 NULL
</P> </P>
<P>Run or continue dynamics for a specified number of timesteps. <P>Run or continue dynamics for a specified number of timesteps.
</P> </P>
<P>When the <A HREF = "doc/run_style.html">run style</A> is <I>respa</I>, N refers to outer <P>When the <A HREF = "run_style.html">run style</A> is <I>respa</I>, N refers to outer
loop (largest) timesteps. loop (largest) timesteps.
</P> </P>
<P>A value of N = 0 is acceptable; only the thermodynamics of the system <P>A value of N = 0 is acceptable; only the thermodynamics of the system

2
doc/run.txt
View File

@ -41,7 +41,7 @@ run 100000 every 1000 NULL :pre
Run or continue dynamics for a specified number of timesteps. Run or continue dynamics for a specified number of timesteps.
When the "run style"_doc/run_style.html is {respa}, N refers to outer When the "run style"_run_style.html is {respa}, N refers to outer
loop (largest) timesteps. loop (largest) timesteps.
A value of N = 0 is acceptable; only the thermodynamics of the system A value of N = 0 is acceptable; only the thermodynamics of the system

55
doc/thermo_style.html
View File

@ -200,33 +200,44 @@ timesteps), where N is the value set by the <I>window</I> option of the
</P> </P>
<HR> <HR>
<P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow scalar or vector quantities <P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow global scalar or vector
calculated by a compute to be output. The ID in the keyword should be quantities calculated by a compute to be output. The ID in the
replaced by the actual ID of the compute that has been defined keyword should be replaced by the actual ID of the compute that has
elsewhere in the input script. See the <A HREF = "compute.html">compute</A> command been defined elsewhere in the input script. See the
for details. Note that only global scalar or vector quantites <A HREF = "compute.html">compute</A> command for details. Note that only global
calculated by a compute can be output as thermodynamic data; per-atom scalar or vector quantites calculated by a compute can be output as
quantities calcalated by a compute are output by the <A HREF = "dump.html">dump thermodynamic data; per-atom quantities calcalated by a compute are
custom</A> command. output by the <A HREF = "dump.html">dump custom</A> command. Note that computes
typically calculate global quantities that are summed over all atoms
in the compute group. However the value printed by thermo_style
custom may be normalized by the total number of atoms in the
simulation depending on the <A HREF = "thermo_modify.html">thermo_modify norm</A>
option being used.
</P> </P>
<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by <P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
the compute is printed. If <I>c_ID[N]</I> is used, then N in the range the compute is printed. If <I>c_ID[N]</I> is used, then the compute must
from 1-M will print the Nth component of the M-length vector calculate a vector quantity and N must be an index from 1 to M where M
calculated by the compute. See the doc pages for individual compute is the length of the vector calculated by the compute. See the doc
styles for info on what these quantities are. pages for individual compute styles for info on what these quantities
are.
</P> </P>
<P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow scalar or vector quantities <P>The <I>f_ID</I> and <I>f_ID[N]</I> keywords allow global scalar or vector
calculated by a fix to be output. The ID in the keyword should be quantities calculated by a fix to be output. The ID in the keyword
replaced by the actual ID of the fix that has been defined elsewhere should be replaced by the actual ID of the fix that has been defined
in the input script. elsewhere in the input script. Note that fixes typically calculate
global quantities that are summed over all atoms in the fix group.
However the value printed by thermo_style custom may be normalized by
the total number of atoms in the simulation depending on the
<A HREF = "thermo_modify.html">thermo_modify norm</A> option being used.
</P> </P>
<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by <P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
the fix is printed. If <I>f_ID[N]</I> is used, then N in the range from the fix is printed. If <I>f_ID[N]</I> is used, then the fix must
1-M will print the Nth component of the M-length vector calculated by calculate a vector quantity and N must be an index from 1 to M where M
the fix. See the doc pages for individual fix styles for info on what is the length of the vector calculated by the fix. See the doc pages
these quantities are. For fixes that compute a contribution to the for individual fix styles for info on which fixes calculate these
potential energy of the system, the scalar quantity f_ID is typically global quantities and what they quantities are. For fixes that
that quantity. compute a contribution to the potential energy of the system, the
scalar quantity f_ID is typically that quantity.
</P> </P>
<P>The <I>v_name</I> keyword allow the current value of a variable to be <P>The <I>v_name</I> keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd output. The name in the keyword should be replaced by the actual namd

55
doc/thermo_style.txt
View File

@ -194,33 +194,44 @@ timesteps), where N is the value set by the {window} option of the
:line :line
The {c_ID} and {c_ID\[N\]} keywords allow scalar or vector quantities The {c_ID} and {c_ID\[N\]} keywords allow global scalar or vector
calculated by a compute to be output. The ID in the keyword should be quantities calculated by a compute to be output. The ID in the
replaced by the actual ID of the compute that has been defined keyword should be replaced by the actual ID of the compute that has
elsewhere in the input script. See the "compute"_compute.html command been defined elsewhere in the input script. See the
for details. Note that only global scalar or vector quantites "compute"_compute.html command for details. Note that only global
calculated by a compute can be output as thermodynamic data; per-atom scalar or vector quantites calculated by a compute can be output as
quantities calcalated by a compute are output by the "dump thermodynamic data; per-atom quantities calcalated by a compute are
custom"_dump.html command. output by the "dump custom"_dump.html command. Note that computes
typically calculate global quantities that are summed over all atoms
in the compute group. However the value printed by thermo_style
custom may be normalized by the total number of atoms in the
simulation depending on the "thermo_modify norm"_thermo_modify.html
option being used.
If {c_ID} is used as a keyword, then the scalar quantity calculated by If {c_ID} is used as a keyword, then the scalar quantity calculated by
the compute is printed. If {c_ID\[N\]} is used, then N in the range the compute is printed. If {c_ID\[N\]} is used, then the compute must
from 1-M will print the Nth component of the M-length vector calculate a vector quantity and N must be an index from 1 to M where M
calculated by the compute. See the doc pages for individual compute is the length of the vector calculated by the compute. See the doc
styles for info on what these quantities are. pages for individual compute styles for info on what these quantities
are.
The {f_ID} and {f_ID\[N\]} keywords allow scalar or vector quantities The {f_ID} and {f_ID\[N\]} keywords allow global scalar or vector
calculated by a fix to be output. The ID in the keyword should be quantities calculated by a fix to be output. The ID in the keyword
replaced by the actual ID of the fix that has been defined elsewhere should be replaced by the actual ID of the fix that has been defined
in the input script. elsewhere in the input script. Note that fixes typically calculate
global quantities that are summed over all atoms in the fix group.
However the value printed by thermo_style custom may be normalized by
the total number of atoms in the simulation depending on the
"thermo_modify norm"_thermo_modify.html option being used.
If {f_ID} is used as a keyword, then the scalar quantity calculated by If {f_ID} is used as a keyword, then the scalar quantity calculated by
the fix is printed. If {f_ID\[N\]} is used, then N in the range from the fix is printed. If {f_ID\[N\]} is used, then the fix must
1-M will print the Nth component of the M-length vector calculated by calculate a vector quantity and N must be an index from 1 to M where M
the fix. See the doc pages for individual fix styles for info on what is the length of the vector calculated by the fix. See the doc pages
these quantities are. For fixes that compute a contribution to the for individual fix styles for info on which fixes calculate these
potential energy of the system, the scalar quantity f_ID is typically global quantities and what they quantities are. For fixes that
that quantity. compute a contribution to the potential energy of the system, the
scalar quantity f_ID is typically that quantity.
The {v_name} keyword allow the current value of a variable to be The {v_name} keyword allow the current value of a variable to be
output. The name in the keyword should be replaced by the actual namd output. The name in the keyword should be replaced by the actual namd

25
doc/variable.html
View File

@ -39,6 +39,7 @@
vx[], vy[], vz[], vx[], vy[], vz[],
fx[], fy[], fz[] fx[], fy[], fz[]
compute references = c_ID[0], c_ID[N] compute references = c_ID[0], c_ID[N]
fix references = f_ID[0], f_ID[N]
other variables = v_abc, v_x, etc other variables = v_abc, v_x, etc
</PRE> </PRE>
@ -211,6 +212,7 @@ variables; the syntax of Atom vector references is different.
<TR><TD >Atom vectors for <I>equal</I></TD><TD > mass[N], x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR> <TR><TD >Atom vectors for <I>equal</I></TD><TD > mass[N], x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
<TR><TD >Atom vectors for <I>atom</I></TD><TD > mass[], x[], y[], z[], vx[], vy[], vz[], fx[], fy[], fz[]</TD></TR> <TR><TD >Atom vectors for <I>atom</I></TD><TD > mass[], x[], y[], z[], vx[], vy[], vz[], fx[], fy[], fz[]</TD></TR>
<TR><TD >Compute references</TD><TD > c_ID[0], c_ID[N]</TD></TR> <TR><TD >Compute references</TD><TD > c_ID[0], c_ID[N]</TD></TR>
<TR><TD >Fix references</TD><TD > f_ID[0], f_ID[N]</TD></TR>
<TR><TD >Other variables</TD><TD > v_abc, v_x, etc <TR><TD >Other variables</TD><TD > v_abc, v_x, etc
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
@ -252,9 +254,26 @@ per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities. way, but only global scalar or vector quantities.
</P> </P>
<P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity <P>If <I>c_ID[0]</I> is used as a keyword, then the scalar quantity
calculated by the compute is printed. If <I>c_ID[N]</I> is used, then N calculated by the compute is used. If <I>c_ID[N]</I> is used, then one
in the range from 1-M will print the Mth component of the N-length component of the vector quantity calculated by the compute is used. N
vector calculated by the compute. should be an integer from 1-M, where M is the length of the vector
calculated by the compute.
</P>
<P>Fix references access scalar or vector quantities calculated by a
<A HREF = "fix.html">fix</A>. See the doc pages for individual fixes to see which
ones compute a scalar or vector quantity. Since the fix may not be
invoked every timestep and compute its quantities, you should insure
the variable is only evaluated on appropriate timesteps. The ID in
the reference should be replaced by the actual ID of the fix defined
elsewhere in the input script. See the <A HREF = "fix.html">fix</A> command for
details. Note that per-atom quantities calculated by a fix cannot be
accessed this way, but only global scalar or vector quantities.
</P>
<P>If <I>f_ID[0]</I> is used as a keyword, then the scalar quantity
calculated by the fix is used. If <I>f_ID[N]</I> is used, then one
component of the vector quantity calculated by the fix is used. N
should be an integer from 1-M, where M is the length of the vector
calculated by the fix.
</P> </P>
<P>The current values of other variables can be accessed by prepending a <P>The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be "v_" to the variable name. This will cause the other variable to be

25
doc/variable.txt
View File

@ -34,6 +34,7 @@ style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {ato
vx\[\], vy\[\], vz\[\], vx\[\], vy\[\], vz\[\],
fx\[\], fy\[\], fz\[\] fx\[\], fy\[\], fz\[\]
compute references = c_ID\[0\], c_ID\[N\] compute references = c_ID\[0\], c_ID\[N\]
fix references = f_ID\[0\], f_ID\[N\]
other variables = v_abc, v_x, etc :pre other variables = v_abc, v_x, etc :pre
:ule :ule
@ -210,6 +211,7 @@ Atom vectors for {atom}: mass\[\], x\[\], y\[\], z\[\], \
vx\[\], vy\[\], vz\[\], \ vx\[\], vy\[\], vz\[\], \
fx\[\], fy\[\], fz\[\] fx\[\], fy\[\], fz\[\]
Compute references: c_ID\[0\], c_ID\[N\] Compute references: c_ID\[0\], c_ID\[N\]
Fix references: f_ID\[0\], f_ID\[N\]
Other variables: v_abc, v_x, etc :tb(s=:) Other variables: v_abc, v_x, etc :tb(s=:)
The thermo keywords allowed in the equation are those defined by the The thermo keywords allowed in the equation are those defined by the
@ -250,9 +252,26 @@ per-atom quantities calculated by a compute cannot be accessed this
way, but only global scalar or vector quantities. way, but only global scalar or vector quantities.
If {c_ID\[0\]} is used as a keyword, then the scalar quantity If {c_ID\[0\]} is used as a keyword, then the scalar quantity
calculated by the compute is printed. If {c_ID\[N\]} is used, then N calculated by the compute is used. If {c_ID\[N\]} is used, then one
in the range from 1-M will print the Mth component of the N-length component of the vector quantity calculated by the compute is used. N
vector calculated by the compute. should be an integer from 1-M, where M is the length of the vector
calculated by the compute.
Fix references access scalar or vector quantities calculated by a
"fix"_fix.html. See the doc pages for individual fixes to see which
ones compute a scalar or vector quantity. Since the fix may not be
invoked every timestep and compute its quantities, you should insure
the variable is only evaluated on appropriate timesteps. The ID in
the reference should be replaced by the actual ID of the fix defined
elsewhere in the input script. See the "fix"_fix.html command for
details. Note that per-atom quantities calculated by a fix cannot be
accessed this way, but only global scalar or vector quantities.
If {f_ID\[0\]} is used as a keyword, then the scalar quantity
calculated by the fix is used. If {f_ID\[N\]} is used, then one
component of the vector quantity calculated by the fix is used. N
should be an integer from 1-M, where M is the length of the vector
calculated by the fix.
The current values of other variables can be accessed by prepending a The current values of other variables can be accessed by prepending a
"v_" to the variable name. This will cause the other variable to be "v_" to the variable name. This will cause the other variable to be