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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1564 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2008-03-01 01:13:20 +00:00
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6
doc/Section_errors.html
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@ -502,7 +502,7 @@ or create_box command.
<DT><I>Cannot displace_box on a non-periodic boundary</I> <DT><I>Cannot displace_box on a non-periodic boundary</I>
<DD>Self-explantory. <DD>Self-explanatory.
<DT><I>Cannot dump scaled coords with triclinic box</I> <DT><I>Cannot dump scaled coords with triclinic box</I>
@ -2150,9 +2150,9 @@ or cause multiple files to be written.
<DD>Filenames used with the dump xyz style cannot be binary or cause files <DD>Filenames used with the dump xyz style cannot be binary or cause files
to be written by each processor. to be written by each processor.
<DT><I>Invalid dump_modify threshhold operator</I> <DT><I>Invalid dump_modify threshold operator</I>
<DD>Operator keyword used for threshhold specification in not recognized. <DD>Operator keyword used for threshold specification in not recognized.
<DT><I>Invalid fix ID in variable formula</I> <DT><I>Invalid fix ID in variable formula</I>

6
doc/Section_errors.txt
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@ -499,7 +499,7 @@ or create_box command. :dd
{Cannot displace_box on a non-periodic boundary} :dt {Cannot displace_box on a non-periodic boundary} :dt
Self-explantory. :dd Self-explanatory. :dd
{Cannot dump scaled coords with triclinic box} :dt {Cannot dump scaled coords with triclinic box} :dt
@ -2147,9 +2147,9 @@ or cause multiple files to be written. :dd
Filenames used with the dump xyz style cannot be binary or cause files Filenames used with the dump xyz style cannot be binary or cause files
to be written by each processor. :dd to be written by each processor. :dd
{Invalid dump_modify threshhold operator} :dt {Invalid dump_modify threshold operator} :dt
Operator keyword used for threshhold specification in not recognized. :dd Operator keyword used for threshold specification in not recognized. :dd
{Invalid fix ID in variable formula} :dt {Invalid fix ID in variable formula} :dt

2
doc/Section_example.html
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@ -35,7 +35,7 @@ Site</A>.
<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR> <TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR> <TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR> <TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
<TR><TD >flow</TD><TD > Couette and Poisseuille flow in a 2d channel</TD></TR> <TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR> <TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR> <TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR> <TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>

2
doc/Section_example.txt
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@ -31,7 +31,7 @@ colloid: big colloid particles in a small particle solvent, 2d system
crack: crack propagation in a 2d solid crack: crack propagation in a 2d solid
dipole: point dipolar particles, 2d system dipole: point dipolar particles, 2d system
ellipse: ellipsoidal particles in spherical solvent, 2d system ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poisseuille flow in a 2d channel flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces friction: frictional contact of spherical asperities between 2d surfaces
indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid
meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples)

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doc/Section_howto.html
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@ -556,17 +556,17 @@ functions:
<PRE>void lammps_open(int, char **, MPI_Comm, void **); <PRE>void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *); void lammps_close(void *);
void lammps_file(void *, char *); void lammps_file(void *, char *);
char *lammps_command(doivd *, char *); char *lammps_command(void *, char *);
</PRE> </PRE>
<P>The functions contain C++ code you could write in a C++ application <P>The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them defined within a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application. from another C++ application.
</P> </P>
<P>Two of the routines in library.cpp are of particular note. The <P>Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. It returns a pointer to a LAMMPS "object". As with as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called mutliple times, to C++, the lammps_open() function can be called multiple times, to
create multiple instances of LAMMPS. create multiple instances of LAMMPS.
</P> </P>
<P>LAMMPS will run on the set of processors in the communicator. This <P>LAMMPS will run on the set of processors in the communicator. This
@ -604,7 +604,7 @@ create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized text file (see "dump atom" or "dump custom") which can be visualized
by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geoemtry systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories. and atom trajectories.
</P> </P>
<P>Several programs included with LAMMPS as auxiliary tools can convert <P>Several programs included with LAMMPS as auxiliary tools can convert
@ -613,7 +613,7 @@ native LAMMPS dump files to other formats. See the
the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
converts LAMMPS dump files into Accelrys's Insight MD program files. converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
LAMMPS dump files into CFG files which can be read into the LAMMPS dump files into CFG files which can be read into the
<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer. <A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
@ -723,9 +723,9 @@ the xy, xz, and yz tilt factors as a simulation runs.
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically <P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity. used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section). non-orthogonal simulation box (see the preceding Howto section).
</P> </P>
<P>A shear strain can be applied to the simuaation box at a desired <P>A shear strain can be applied to the simulation box at a desired
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the the sheared fluid and integrate the SLLOD equations of motion for the
@ -765,7 +765,7 @@ The <A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used t
define a Gay-Berne (GB) potential for how ellipsoidal particles define a Gay-Berne (GB) potential for how ellipsoidal particles
interact with each other and with spherical particles. The GB interact with each other and with spherical particles. The GB
potential is like a Lennard-Jones (LJ) potential, generalized for potential is like a Lennard-Jones (LJ) potential, generalized for
orientiation-dependent interactions. orientation-dependent interactions.
</P> </P>
<P>The orientation of ellipsoidal particles is stored as a quaternion. <P>The orientation of ellipsoidal particles is stored as a quaternion.
See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions
@ -821,9 +821,9 @@ generate values that can be output with these commands.
<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
<A HREF = "thermo_modify.html">thermo_modify</A> commands. The <A HREF = "thermo_modify.html">thermo_modify</A> commands. The
<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are <A HREF = "thermo_style.html">thermo_style</A> command also specifies what values are
calculated and written out. Pre-defined keywords can be specified calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three addtional kinds of keywords can also (e.g. press, etotal, etc). Three additional kinds of keywords can also
be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
output. Each of these are described in turn. output. Each of these are described in turn.
@ -948,7 +948,7 @@ options for how it performs time averaging. The per-layer values it
produces can be used in two ways. First, they can be written directly produces can be used in two ways. First, they can be written directly
to a file. Note that the averaging parameters can be specified in to a file. Note that the averaging parameters can be specified in
such a way that time averaging is not done, in which case this is a such a way that time averaging is not done, in which case this is a
convenient means of simply outputting desired quanitities (summed over convenient means of simply outputting desired quantities (summed over
atoms within a 1d layer) directly to a separate file. Like other atoms within a 1d layer) directly to a separate file. Like other
fixes that produce global quantities, the results of this fix can also fixes that produce global quantities, the results of this fix can also
be used as input by any command that accesses global quantities, be used as input by any command that accesses global quantities,

22
doc/Section_howto.txt
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@ -552,17 +552,17 @@ functions:
void lammps_open(int, char **, MPI_Comm, void **); void lammps_open(int, char **, MPI_Comm, void **);
void lammps_close(void *); void lammps_close(void *);
void lammps_file(void *, char *); void lammps_file(void *, char *);
char *lammps_command(doivd *, char *); :pre char *lammps_command(void *, char *); :pre
The functions contain C++ code you could write in a C++ application The functions contain C++ code you could write in a C++ application
that was invoking LAMMPS directly. Note that LAMMPS classes are that was invoking LAMMPS directly. Note that LAMMPS classes are
defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them defined within a LAMMPS namespace (LAMMPS_NS) if you use them
from another C++ application. from another C++ application.
Two of the routines in library.cpp are of particular note. The Two of the routines in library.cpp are of particular note. The
lammps_open() function initiates LAMMPS and takes an MPI communicator lammps_open() function initiates LAMMPS and takes an MPI communicator
as an argument. It returns a pointer to a LAMMPS "object". As with as an argument. It returns a pointer to a LAMMPS "object". As with
C++, the lammps_open() function can be called mutliple times, to C++, the lammps_open() function can be called multiple times, to
create multiple instances of LAMMPS. create multiple instances of LAMMPS.
LAMMPS will run on the set of processors in the communicator. This LAMMPS will run on the set of processors in the communicator. This
@ -600,7 +600,7 @@ create files in several formats. The native LAMMPS dump format is a
text file (see "dump atom" or "dump custom") which can be visualized text file (see "dump atom" or "dump custom") which can be visualized
by the "xmovie"_Section_tools.html#xmovie program, included with the by the "xmovie"_Section_tools.html#xmovie program, included with the
LAMMPS package. This produces simple, fast 2d projections of 3d LAMMPS package. This produces simple, fast 2d projections of 3d
systems, and can be useful for rapid debugging of simulation geoemtry systems, and can be useful for rapid debugging of simulation geometry
and atom trajectories. and atom trajectories.
Several programs included with LAMMPS as auxiliary tools can convert Several programs included with LAMMPS as auxiliary tools can convert
@ -609,7 +609,7 @@ native LAMMPS dump files to other formats. See the
the "ch2lmp tool"_Section_tools.html#charmm, which contains a the "ch2lmp tool"_Section_tools.html#charmm, which contains a
lammps2pdb Perl script which converts LAMMPS dump files into PDB lammps2pdb Perl script which converts LAMMPS dump files into PDB
files. The second is the "lmp2arc tool"_Section_tools.html#arc which files. The second is the "lmp2arc tool"_Section_tools.html#arc which
converts LAMMPS dump files into Accelrys's Insight MD program files. converts LAMMPS dump files into Accelrys' Insight MD program files.
The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
LAMMPS dump files into CFG files which can be read into the LAMMPS dump files into CFG files which can be read into the
"AtomEye"_atomeye visualizer. "AtomEye"_atomeye visualizer.
@ -716,9 +716,9 @@ Another use of non-orthogonal boxes is to perform non-equilibrium MD
Non-equilibrium molecular dynamics or NEMD simulations are typically Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity. used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section). non-orthogonal simulation box (see the preceding Howto section).
A shear strain can be applied to the simuaation box at a desired A shear strain can be applied to the simulation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The strain rate by using the "fix deform"_fix_deform.html command. The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat "fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the the sheared fluid and integrate the SLLOD equations of motion for the
@ -758,7 +758,7 @@ The "pair_style gayberne"_pair_gayberne.html command can be used to
define a Gay-Berne (GB) potential for how ellipsoidal particles define a Gay-Berne (GB) potential for how ellipsoidal particles
interact with each other and with spherical particles. The GB interact with each other and with spherical particles. The GB
potential is like a Lennard-Jones (LJ) potential, generalized for potential is like a Lennard-Jones (LJ) potential, generalized for
orientiation-dependent interactions. orientation-dependent interactions.
The orientation of ellipsoidal particles is stored as a quaternion. The orientation of ellipsoidal particles is stored as a quaternion.
See the "set"_set.html command for a brief explanation of quaternions See the "set"_set.html command for a brief explanation of quaternions
@ -814,9 +814,9 @@ Thermodynamic output :h5
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
"thermo_modify"_thermo_modify.html commands. The "thermo_modify"_thermo_modify.html commands. The
"thermo_style"_themo_style.html command also specifies what values are "thermo_style"_thermo_style.html command also specifies what values are
calculated and written out. Pre-defined keywords can be specified calculated and written out. Pre-defined keywords can be specified
(e.g. press, etotal, etc). Three addtional kinds of keywords can also (e.g. press, etotal, etc). Three additional kinds of keywords can also
be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or
"fix"_fix.html or "variable"_variable.html provides the value to be "fix"_fix.html or "variable"_variable.html provides the value to be
output. Each of these are described in turn. output. Each of these are described in turn.
@ -941,7 +941,7 @@ options for how it performs time averaging. The per-layer values it
produces can be used in two ways. First, they can be written directly produces can be used in two ways. First, they can be written directly
to a file. Note that the averaging parameters can be specified in to a file. Note that the averaging parameters can be specified in
such a way that time averaging is not done, in which case this is a such a way that time averaging is not done, in which case this is a
convenient means of simply outputting desired quanitities (summed over convenient means of simply outputting desired quantities (summed over
atoms within a 1d layer) directly to a separate file. Like other atoms within a 1d layer) directly to a separate file. Like other
fixes that produce global quantities, the results of this fix can also fixes that produce global quantities, the results of this fix can also
be used as input by any command that accesses global quantities, be used as input by any command that accesses global quantities,

6
doc/Section_intro.html
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@ -180,7 +180,7 @@ commands)
</H4> </H4>
<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands) <P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
</P> </P>
<UL><LI> log file of thermodynanmic info <UL><LI> log file of thermodynamic info
<LI> text dump files of atom coords, velocities, other per-atom quantities <LI> text dump files of atom coords, velocities, other per-atom quantities
<LI> binary restart files <LI> binary restart files
<LI> per-atom quantities (energy, stress, centro-symmetry parameter, etc) <LI> per-atom quantities (energy, stress, centro-symmetry parameter, etc)
@ -507,11 +507,11 @@ the list.
<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR> <TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR> <TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR> <TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR>
<TR><TD >FFT support for SGI SCLS (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR> <TR><TD >FFT support for SGI SCSL (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR> <TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR> <TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
<TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR> <TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR>
<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Putz (Sandia)</TD></TR> <TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Puetz (Sandia)</TD></TR>
<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR> <TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR> <TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR> <TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>

6
doc/Section_intro.txt
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@ -178,7 +178,7 @@ Integrators: :h4
Output: :h4 Output: :h4
("dump"_dump.html, "restart"_restart.html commands) ("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynanmic info log file of thermodynamic info
text dump files of atom coords, velocities, other per-atom quantities text dump files of atom coords, velocities, other per-atom quantities
binary restart files binary restart files
per-atom quantities (energy, stress, centro-symmetry parameter, etc) per-atom quantities (energy, stress, centro-symmetry parameter, etc)
@ -504,12 +504,12 @@ radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
force tables for long-range Coulombics: Paul Crozier (Sandia) force tables for long-range Coulombics: Paul Crozier (Sandia)
targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \ targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
Christian Burisch (Bochum University, Germany) Christian Burisch (Bochum University, Germany)
FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech) FFT support for SGI SCSL (Altix): Jim Shepherd (Ga Tech)
lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \ lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
Andrey Kalinichev (Sandia) Andrey Kalinichev (Sandia)
parallel tempering: Mark Sears (Sandia) parallel tempering: Mark Sears (Sandia)
embedded atom method (EAM) potential: Stephen Foiles (Sandia) embedded atom method (EAM) potential: Stephen Foiles (Sandia)
multi-harmonic dihedral potential: Mathias Putz (Sandia) multi-harmonic dihedral potential: Mathias Puetz (Sandia)
granular force fields and BC: Leo Silbert & Gary Grest (Sandia) granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
2d Ewald/PPPM: Paul Crozier (Sandia) 2d Ewald/PPPM: Paul Crozier (Sandia)
CHARMM force fields: Paul Crozier (Sandia) CHARMM force fields: Paul Crozier (Sandia)

10
doc/Section_modify.html
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@ -88,7 +88,7 @@ in the LAMMPS distribution.
<LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A> <LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A>
<LI><A HREF = "#compute">Compute styles</A> <LI><A HREF = "#compute">Compute styles</A>
<LI><A HREF = "#dump">Dump styles</A> <LI><A HREF = "#dump">Dump styles</A>
<LI><A HREF = "#dump">Dump custom output optoins</A> <LI><A HREF = "#dump">Dump custom output options</A>
<LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc <LI><A HREF = "#fix">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc
<LI><A HREF = "#command">Input script commands</A> <LI><A HREF = "#command">Input script commands</A>
<LI><A HREF = "#kspace">Kspace computations</A> <LI><A HREF = "#kspace">Kspace computations</A>
@ -373,7 +373,7 @@ needed.
<A NAME = "kspace"></A><H4>Kspace computations <A NAME = "kspace"></A><H4>Kspace computations
</H4> </H4>
<P>Classes that compute long-range Coulombic interactions via K-space <P>Classes that compute long-range Coulombic interactions via K-space
represenations (Ewald, PPPM) are derived from the KSpace class. New representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS. styles can be created to add new K-space options to LAMMPS.
</P> </P>
<P>Ewald.cpp is an example of computing K-space interactions. <P>Ewald.cpp is an example of computing K-space interactions.
@ -469,7 +469,7 @@ thermodynamic info is output. See the
quantities. quantities.
</P> </P>
<P>The thermo styles (one, multi, etc) are simply lists of keywords. <P>The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requies defining a new list of keywords. Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added. thermo.cpp to see the two locations where code will need to be added.
</P> </P>
@ -503,7 +503,7 @@ group functions = mass(group), xcm(group,x), ...
atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ... atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ... compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
</P> </P>
<P>Adding keywords for the <A HREF = "themo_style.html">thermo_style custom</A> command <P>Adding keywords for the <A HREF = "thermo_style.html">thermo_style custom</A> command
(which can then be accessed by variables) was discussed (which can then be accessed by variables) was discussed
<A HREF = "Section_modify.html#thermo">here</A> on this page. <A HREF = "Section_modify.html#thermo">here</A> on this page.
</P> </P>
@ -590,7 +590,7 @@ should indicate that your feature is only available if LAMMPS is built
with the "user-foo" package. See other user package files for an with the "user-foo" package. See other user package files for an
example of how to do this. example of how to do this.
</P> </P>
<P>Note that the more clear and self-exaplantory you make your doc and <P>Note that the more clear and self-explanatory you make your doc and
README files, the more likely it is that users will try out your new README files, the more likely it is that users will try out your new
feature. feature.
</P> </P>

10
doc/Section_modify.txt
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@ -85,7 +85,7 @@ in the LAMMPS distribution.
"Bond, angle, dihedral, improper potentials"_#bond "Bond, angle, dihedral, improper potentials"_#bond
"Compute styles"_#compute "Compute styles"_#compute
"Dump styles"_#dump "Dump styles"_#dump
"Dump custom output optoins"_#dump "Dump custom output options"_#dump
"Fix styles"_#fix which include integrators, \ "Fix styles"_#fix which include integrators, \
temperature and pressure control, force constraints, \ temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc boundary conditions, diagnostic output, etc
@ -358,7 +358,7 @@ needed.
Kspace computations :link(kspace),h4 Kspace computations :link(kspace),h4
Classes that compute long-range Coulombic interactions via K-space Classes that compute long-range Coulombic interactions via K-space
represenations (Ewald, PPPM) are derived from the KSpace class. New representations (Ewald, PPPM) are derived from the KSpace class. New
styles can be created to add new K-space options to LAMMPS. styles can be created to add new K-space options to LAMMPS.
Ewald.cpp is an example of computing K-space interactions. Ewald.cpp is an example of computing K-space interactions.
@ -446,7 +446,7 @@ thermodynamic info is output. See the
quantities. quantities.
The thermo styles (one, multi, etc) are simply lists of keywords. The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requies defining a new list of keywords. Adding a new style thus only requires defining a new list of keywords.
Search for the word "customize" with references to "thermo style" in Search for the word "customize" with references to "thermo style" in
thermo.cpp to see the two locations where code will need to be added. thermo.cpp to see the two locations where code will need to be added.
@ -480,7 +480,7 @@ group functions = mass(group), xcm(group,x), ...
atom values = x[123], y[3], vx[34], ... atom values = x[123], y[3], vx[34], ...
compute values = c_mytemp[0], c_thermo_press[3], ... compute values = c_mytemp[0], c_thermo_press[3], ...
Adding keywords for the "thermo_style custom"_themo_style.html command Adding keywords for the "thermo_style custom"_thermo_style.html command
(which can then be accessed by variables) was discussed (which can then be accessed by variables) was discussed
"here"_Section_modify.html#thermo on this page. "here"_Section_modify.html#thermo on this page.
@ -567,7 +567,7 @@ should indicate that your feature is only available if LAMMPS is built
with the "user-foo" package. See other user package files for an with the "user-foo" package. See other user package files for an
example of how to do this. example of how to do this.
Note that the more clear and self-exaplantory you make your doc and Note that the more clear and self-explanatory you make your doc and
README files, the more likely it is that users will try out your new README files, the more likely it is that users will try out your new
feature. feature.

2
doc/Section_start.html
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@ -191,7 +191,7 @@ support the "popen" command. Using one of the -DPACK_ARRAY,
-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel -DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
is the default. If you compile with -DLAMMPS_XDR, the build will is the default. If you compile with -DLAMMPS_XDR, the build will
include XDR compatability files for doing particle dumps in XTC include XDR compatibility files for doing particle dumps in XTC
format. This is only necessary if your platform does have its own XDR format. This is only necessary if your platform does have its own XDR
files available. See the Restrictions section of the <A HREF = "dump.html">dump</A> files available. See the Restrictions section of the <A HREF = "dump.html">dump</A>
command for details. command for details.

2
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@ -186,7 +186,7 @@ support the "popen" command. Using one of the -DPACK_ARRAY,
-DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel -DPACK_POINTER, and -DPACK_MEMCPY options can make for faster parallel
FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
is the default. If you compile with -DLAMMPS_XDR, the build will is the default. If you compile with -DLAMMPS_XDR, the build will
include XDR compatability files for doing particle dumps in XTC include XDR compatibility files for doing particle dumps in XTC
format. This is only necessary if your platform does have its own XDR format. This is only necessary if your platform does have its own XDR
files available. See the Restrictions section of the "dump"_dump.html files available. See the Restrictions section of the "dump"_dump.html
command for details. command for details.

6
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@ -153,8 +153,8 @@ produce are in the potentials directory.
<H4><A NAME = "arc"></A>lmp2arc tool <H4><A NAME = "arc"></A>lmp2arc tool
</H4> </H4>
<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output <P>The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys's Insight MD code (formerly files to the format for Accelrys' Insight MD code (formerly
MSI/Biosysm and its Discover MD code). See the README file for more MSI/Biosym and its Discover MD code). See the README file for more
information. information.
</P> </P>
<P>This tool was written by John Carpenter (Cray), Michael Peachey <P>This tool was written by John Carpenter (Cray), Michael Peachey
@ -228,7 +228,7 @@ definition file. This tool was used to create the system for the
<H4><A NAME = "msi"></A>msi2lmp tool <H4><A NAME = "msi"></A>msi2lmp tool
</H4> </H4>
<P>The msi2lmp sub-directory contains a tool for creating LAMMPS input <P>The msi2lmp sub-directory contains a tool for creating LAMMPS input
data files from Accelrys's Insight MD code (formerly MSI/Biosysm and data files from Accelrys' Insight MD code (formerly MSI/Biosym and
its Discover MD code). See the README file for more information. its Discover MD code). See the README file for more information.
</P> </P>
<P>This tool was written by John Carpenter (Cray), Michael Peachey <P>This tool was written by John Carpenter (Cray), Michael Peachey

6
doc/Section_tools.txt
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@ -149,8 +149,8 @@ The source files and potentials were provided by Gerolf Ziegenhain
lmp2arc tool :h4,link(arc) lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys's Insight MD code (formerly files to the format for Accelrys' Insight MD code (formerly
MSI/Biosysm and its Discover MD code). See the README file for more MSI/Biosym and its Discover MD code). See the README file for more
information. information.
This tool was written by John Carpenter (Cray), Michael Peachey This tool was written by John Carpenter (Cray), Michael Peachey
@ -224,7 +224,7 @@ definition file. This tool was used to create the system for the
msi2lmp tool :h4,link(msi) msi2lmp tool :h4,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS input The msi2lmp sub-directory contains a tool for creating LAMMPS input
data files from Accelrys's Insight MD code (formerly MSI/Biosysm and data files from Accelrys' Insight MD code (formerly MSI/Biosym and
its Discover MD code). See the README file for more information. its Discover MD code). See the README file for more information.
This tool was written by John Carpenter (Cray), Michael Peachey This tool was written by John Carpenter (Cray), Michael Peachey

8
doc/angle_coeff.html
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@ -15,7 +15,7 @@
</P> </P>
<PRE>angle_coeff N args <PRE>angle_coeff N args
</PRE> </PRE>
<UL><LI>N = angle type (see asterik form below) <UL><LI>N = angle type (see asterisk form below)
<LI>args = coefficients for one or more angle types <LI>args = coefficients for one or more angle types
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
@ -35,9 +35,9 @@ Angle coefficients can also be set in the data file read by the
be used, as in the 1st example above. Or a wild-card asterik can be be used, as in the 1st example above. Or a wild-card asterik can be
used to set the coefficients for multiple angle types. This takes the used to set the coefficients for multiple angle types. This takes the
form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, form "*" or "*n" or "n*" or "m*n". If N = the number of angle types,
then an asterik with no numeric values means all types from 1 to N. A then an asterisk with no numeric values means all types from 1 to N. A
leading asterik means all types from 1 to n (inclusive). A trailing leading asterisk means all types from 1 to n (inclusive). A trailing
asterik means all types from n to N (inclusive). A middle asterisk asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive). means all types from m to n (inclusive).
</P> </P>
<P>Note that using an angle_coeff command can override a previous setting <P>Note that using an angle_coeff command can override a previous setting

8
doc/angle_coeff.txt
View File

@ -12,7 +12,7 @@ angle_coeff command :h3
angle_coeff N args :pre angle_coeff N args :pre
N = angle type (see asterik form below) N = angle type (see asterisk form below)
args = coefficients for one or more angle types :ul args = coefficients for one or more angle types :ul
[Examples:] [Examples:]
@ -32,9 +32,9 @@ N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be be used, as in the 1st example above. Or a wild-card asterik can be
used to set the coefficients for multiple angle types. This takes the used to set the coefficients for multiple angle types. This takes the
form "*" or "*n" or "n*" or "m*n". If N = the number of angle types, form "*" or "*n" or "n*" or "m*n". If N = the number of angle types,
then an asterik with no numeric values means all types from 1 to N. A then an asterisk with no numeric values means all types from 1 to N. A
leading asterik means all types from 1 to n (inclusive). A trailing leading asterisk means all types from 1 to n (inclusive). A trailing
asterik means all types from n to N (inclusive). A middle asterisk asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive). means all types from m to n (inclusive).
Note that using an angle_coeff command can override a previous setting Note that using an angle_coeff command can override a previous setting

2
doc/bond_quartic.html
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@ -51,7 +51,7 @@ you will need to choose them carefully so they form a suitable bond
potential. potential.
</P> </P>
<P>Rc is the cutoff length at which the bond potential goes smoothly to a <P>Rc is the cutoff length at which the bond potential goes smoothly to a
local maximium. If a bond length ever becomes > Rc, LAMMPS "breaks" local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they pairwise interaction between the two atoms is turned on, since they

2
doc/bond_quartic.txt
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@ -48,7 +48,7 @@ you will need to choose them carefully so they form a suitable bond
potential. potential.
Rc is the cutoff length at which the bond potential goes smoothly to a Rc is the cutoff length at which the bond potential goes smoothly to a
local maximium. If a bond length ever becomes > Rc, LAMMPS "breaks" local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they pairwise interaction between the two atoms is turned on, since they

2
doc/change_box.html
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@ -52,7 +52,7 @@ orthogonal box.
ave/spatial</A> or <A HREF = "fix_deform.html">fix deform</A> be ave/spatial</A> or <A HREF = "fix_deform.html">fix deform</A> be
active. This is because these commands test whether the simulation active. This is because these commands test whether the simulation
box is orthogonal when they are first issued. Note that these box is orthogonal when they are first issued. Note that these
commmands can appear in your script before a change_box command is commands can appear in your script before a change_box command is
issued, so long as an <A HREF = "undump.html">undump</A> or <A HREF = "unfix.html">unfix</A> issued, so long as an <A HREF = "undump.html">undump</A> or <A HREF = "unfix.html">unfix</A>
command is also used to turn them off. command is also used to turn them off.
</P> </P>

2
doc/change_box.txt
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@ -48,7 +48,7 @@ At the point in the input script when this command is issued, no
ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be ave/spatial"_fix_ave_spatial.html or "fix deform"_fix_deform.html be
active. This is because these commands test whether the simulation active. This is because these commands test whether the simulation
box is orthogonal when they are first issued. Note that these box is orthogonal when they are first issued. Note that these
commmands can appear in your script before a change_box command is commands can appear in your script before a change_box command is
issued, so long as an "undump"_undump.html or "unfix"_unfix.html issued, so long as an "undump"_undump.html or "unfix"_unfix.html
command is also used to turn them off. command is also used to turn them off.

2
doc/compute_pe.html
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@ -33,7 +33,7 @@ entire system of atoms. The specified group must be "all". See the
energies. These per-atom values could be summed for a group of atoms energies. These per-atom values could be summed for a group of atoms
via the <A HREF = "compute_reduce.html">compute reduce</A> command. via the <A HREF = "compute_reduce.html">compute reduce</A> command.
</P> </P>
<P>The energy is calulated by the various pair, bond, etc potentials <P>The energy is calculated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper, potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed, and kspace (long-range) energy. If any extra keywords are listed,

2
doc/compute_pe.txt
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@ -30,7 +30,7 @@ entire system of atoms. The specified group must be "all". See the
energies. These per-atom values could be summed for a group of atoms energies. These per-atom values could be summed for a group of atoms
via the "compute reduce"_compute_reduce.html command. via the "compute reduce"_compute_reduce.html command.
The energy is calulated by the various pair, bond, etc potentials The energy is calculated by the various pair, bond, etc potentials
defined for the simulation. If no extra keywords are listed, then the defined for the simulation. If no extra keywords are listed, then the
potential energy is the sum of pair, bond, angle, dihedral, improper, potential energy is the sum of pair, bond, angle, dihedral, improper,
and kspace (long-range) energy. If any extra keywords are listed, and kspace (long-range) energy. If any extra keywords are listed,

4
doc/compute_pressure.html
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@ -48,7 +48,7 @@ and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constra
virial term. virial term.
</P> </P>
<P>A 6-component pressure tensor is also calculated by this compute whose <P>A 6-component pressure tensor is also calculated by this compute whose
componenents can be output by the <A HREF = "thermo_style.html">thermo_style components can be output by the <A HREF = "thermo_style.html">thermo_style
custom</A> command or accessed by other custom</A> command or accessed by other
<A HREF = "compute.html">compute</A> and <A HREF = "fix.html">fix</A> commands. The equation for <A HREF = "compute.html">compute</A> and <A HREF = "fix.html">fix</A> commands. The equation for
the components of the tensor is the same as in above formula, except the components of the tensor is the same as in above formula, except
@ -95,7 +95,7 @@ the simulation.
</P> </P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute <P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute
stress/atom</A>, stress/atom</A>,
<A HREF = "themo_style.html">thermo_style</A>, <A HREF = "thermo_style.html">thermo_style</A>,
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

4
doc/compute_pressure.txt
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@ -45,7 +45,7 @@ and long-range interactions. "Fixes"_fix.html that impose constraints
virial term. virial term.
A 6-component pressure tensor is also calculated by this compute whose A 6-component pressure tensor is also calculated by this compute whose
componenents can be output by the "thermo_style components can be output by the "thermo_style
custom"_thermo_style.html command or accessed by other custom"_thermo_style.html command or accessed by other
"compute"_compute.html and "fix"_fix.html commands. The equation for "compute"_compute.html and "fix"_fix.html commands. The equation for
the components of the tensor is the same as in above formula, except the components of the tensor is the same as in above formula, except
@ -92,6 +92,6 @@ the simulation.
"compute temp"_compute_temp.html, "compute "compute temp"_compute_temp.html, "compute
stress/atom"_compute_stress_atom.html, stress/atom"_compute_stress_atom.html,
"thermo_style"_themo_style.html, "thermo_style"_thermo_style.html,
[Default:] none [Default:] none

2
doc/compute_temp_dipole.html
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@ -28,7 +28,7 @@ compute myTemp mobile temp/dipole
<P>Define a computation that calculates the temperature of a group of <P>Define a computation that calculates the temperature of a group of
particles that include a point dipole. The computation is similar to particles that include a point dipole. The computation is similar to
<A HREF = "compute_temp.html">compute_temp</A>, however, additional degrees of <A HREF = "compute_temp.html">compute_temp</A>, however, additional degrees of
freedom are include to account for the rotational state of the freedom are included to account for the rotational state of the
particles. The associated kinetic energy includes a rotational term particles. The associated kinetic energy includes a rotational term
KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is
the angular velocity. the angular velocity.

2
doc/compute_temp_dipole.txt
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@ -25,7 +25,7 @@ compute myTemp mobile temp/dipole :pre
Define a computation that calculates the temperature of a group of Define a computation that calculates the temperature of a group of
particles that include a point dipole. The computation is similar to particles that include a point dipole. The computation is similar to
"compute_temp"_compute_temp.html, however, additional degrees of "compute_temp"_compute_temp.html, however, additional degrees of
freedom are include to account for the rotational state of the freedom are included to account for the rotational state of the
particles. The associated kinetic energy includes a rotational term particles. The associated kinetic energy includes a rotational term
KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is
the angular velocity. the angular velocity.

4
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@ -87,7 +87,7 @@ styles and values.
</P> </P>
<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension <P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
are specified. The values can be in lattice or box distance units. are specified. The values can be in lattice or box distance units.
See the discsussion of the units keyword below. See the discussion of the units keyword below.
</P> </P>
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries <P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
of a dimension are specified. The values can be in lattice or box of a dimension are specified. The values can be in lattice or box
@ -134,7 +134,7 @@ units keyword below.
</P> </P>
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is <P>For style <I>delta</I>, a plus or minus change in the tilt factor is
specified. The value can be in lattice or box distance units. See specified. The value can be in lattice or box distance units. See
the discsussion of the units keyword below. the discussion of the units keyword below.
</P> </P>
<P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS, <P>All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half

4
doc/displace_box.txt
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@ -79,7 +79,7 @@ styles and values.
For style {final}, the final lo and hi box boundaries of a dimension For style {final}, the final lo and hi box boundaries of a dimension
are specified. The values can be in lattice or box distance units. are specified. The values can be in lattice or box distance units.
See the discsussion of the units keyword below. See the discussion of the units keyword below.
For style {delta}, plus or minus changes in the lo/hi box boundaries For style {delta}, plus or minus changes in the lo/hi box boundaries
of a dimension are specified. The values can be in lattice or box of a dimension are specified. The values can be in lattice or box
@ -126,7 +126,7 @@ units keyword below.
For style {delta}, a plus or minus change in the tilt factor is For style {delta}, a plus or minus change in the tilt factor is
specified. The value can be in lattice or box distance units. See specified. The value can be in lattice or box distance units. See
the discsussion of the units keyword below. the discussion of the units keyword below.
All of these styles change the xy, xz, yz tilt factors. In LAMMPS, All of these styles change the xy, xz, yz tilt factors. In LAMMPS,
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half

12
doc/dump_modify.html
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@ -34,7 +34,7 @@
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!=" operation = "<" or "<=" or ">" or ">=" or "==" or "!="
value = numeric value to compare to value = numeric value to compare to
these 3 args can be replaced by the word "none" to turn off threshholding these 3 args can be replaced by the word "none" to turn off thresholding
</PRE> </PRE>
@ -105,15 +105,15 @@ shape, and it can be the "union" or "intersection" of a series of
simpler regions. simpler regions.
</P> </P>
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> style. <P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> style.
Multiple threshholds can be specified. Specifying "none" turns off Multiple thresholds can be specified. Specifying "none" turns off
all threshhold criteria. If theshholds are specified, only atoms all threshold criteria. If thresholds are specified, only atoms
whose attributes meet all the threshhold criteria are written to the whose attributes meet all the threshold criteria are written to the
dump file. The possible attributes that can be tested for are the dump file. The possible attributes that can be tested for are the
same as those that can be specified in the <A HREF = "dump.html">dump custom</A> same as those that can be specified in the <A HREF = "dump.html">dump custom</A>
command. Note that different attributes can be output by the dump command. Note that different attributes can be output by the dump
custom command than are used as threshhold criteria by the dump_modify custom command than are used as threshold criteria by the dump_modify
command. E.g. you can output the coordinates and stress of atoms command. E.g. you can output the coordinates and stress of atoms
whose energy is above some threshhold. whose energy is above some threshold.
</P> </P>
<P><B>Restrictions:</B> none <P><B>Restrictions:</B> none
</P> </P>

12
doc/dump_modify.txt
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@ -28,7 +28,7 @@ keyword = {format} or {scale} or {image} or {flush} or {unwrap} or {every} or {p
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
operation = "<" or "<=" or ">" or ">=" or "==" or "!=" operation = "<" or "<=" or ">" or ">=" or "==" or "!="
value = numeric value to compare to value = numeric value to compare to
these 3 args can be replaced by the word "none" to turn off threshholding these 3 args can be replaced by the word "none" to turn off thresholding
:pre :pre
:ule :ule
@ -98,15 +98,15 @@ shape, and it can be the "union" or "intersection" of a series of
simpler regions. simpler regions.
The {thresh} keyword only applies to the dump {custom} style. The {thresh} keyword only applies to the dump {custom} style.
Multiple threshholds can be specified. Specifying "none" turns off Multiple thresholds can be specified. Specifying "none" turns off
all threshhold criteria. If theshholds are specified, only atoms all threshold criteria. If thresholds are specified, only atoms
whose attributes meet all the threshhold criteria are written to the whose attributes meet all the threshold criteria are written to the
dump file. The possible attributes that can be tested for are the dump file. The possible attributes that can be tested for are the
same as those that can be specified in the "dump custom"_dump.html same as those that can be specified in the "dump custom"_dump.html
command. Note that different attributes can be output by the dump command. Note that different attributes can be output by the dump
custom command than are used as threshhold criteria by the dump_modify custom command than are used as threshold criteria by the dump_modify
command. E.g. you can output the coordinates and stress of atoms command. E.g. you can output the coordinates and stress of atoms
whose energy is above some threshhold. whose energy is above some threshold.
[Restrictions:] none [Restrictions:] none

14
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View File

@ -53,7 +53,7 @@
filename = file to write results to filename = file to write results to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I> <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output new average value every Nfreq steps one = output new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps window M = output average of M most recent Nfreq steps
</PRE> </PRE>
@ -99,13 +99,13 @@ produce global quantities.
timesteps the layer values will be generated in order to contribute to timesteps the layer values will be generated in order to contribute to
the average. The final averaged quantities are generated every the average. The final averaged quantities are generated every
<I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I> quantities, computed <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I> quantities, computed
in the preceeding portion of the simulation every <I>Nevery</I> timesteps. in the preceding portion of the simulation every <I>Nevery</I> timesteps.
<I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero
even if <I>Nrepeat</I> is 1. even if <I>Nrepeat</I> is 1.
</P> </P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on <P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps averaging is done; values are simply generated on timesteps
100,200,etc. 100,200,etc.
@ -117,7 +117,7 @@ where the layers are in a particular <I>dim</I> and have a thickness given
by <I>delta</I>. Every Nfreq steps, when an averaging is being performed by <I>delta</I>. Every Nfreq steps, when an averaging is being performed
and the per-atom property is calculated for the first time, the number and the per-atom property is calculated for the first time, the number
of layers and the layer boundaries are computed. Thus if the of layers and the layer boundaries are computed. Thus if the
simlation box changes size during a simulation, the number of layers simulation box changes size during a simulation, the number of layers
and their boundaries may also change. Layers are defined relative to and their boundaries may also change. Layers are defined relative to
a specified <I>origin</I>, which may be the lower/upper edge of the box (in a specified <I>origin</I>, which may be the lower/upper edge of the box (in
<I>dim</I>) or its center point, or a specified coordinate value. Starting <I>dim</I>) or its center point, or a specified coordinate value. Starting
@ -232,15 +232,15 @@ quantities. If the value of the <I>units</I> keyword is <I>box</I> or
steps that were multiples of <I>Nfreq</I>, before they are accessed by steps that were multiples of <I>Nfreq</I>, before they are accessed by
another output command or written to a file. another output command or written to a file.
</P> </P>
<P>If the <I>ave</I> setting is <I>one</I>, then the layuer values produced on <P>If the <I>ave</I> setting is <I>one</I>, then the layer values produced on
timesteps that are multiples of <I>Nfreq</I> are independent of each other; timesteps that are multiples of <I>Nfreq</I> are independent of each other;
they are output as-is without further averaging. they are output as-is without further averaging.
</P> </P>
<P>If the <I>ave</I> setting is <I>running</I>, then the layer values produced on <P>If the <I>ave</I> setting is <I>running</I>, then the layer values produced on
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
cummulative sense before being output. Each output layer value is cumulative sense before being output. Each output layer value is
thus the average of the layer value produced on that timestep with all thus the average of the layer value produced on that timestep with all
preceeding values for the same layer. This running average begins preceding values for the same layer. This running average begins
when the fix is defined; it can only be restarted by deleting the fix when the fix is defined; it can only be restarted by deleting the fix
via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
re-specifying it. re-specifying it.

14
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View File

@ -38,7 +38,7 @@ keyword = {norm} or {units} or {file} or {ave} :l
filename = file to write results to filename = file to write results to
{ave} args = {one} or {running} or {window M} {ave} args = {one} or {running} or {window M}
one = output new average value every Nfreq steps one = output new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps :pre window M = output average of M most recent Nfreq steps :pre
:ule :ule
@ -83,13 +83,13 @@ The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the layer values will be generated in order to contribute to timesteps the layer values will be generated in order to contribute to
the average. The final averaged quantities are generated every the average. The final averaged quantities are generated every
{Nfreq} timesteps. The average is over {Nrepeat} quantities, computed {Nfreq} timesteps. The average is over {Nrepeat} quantities, computed
in the preceeding portion of the simulation every {Nevery} timesteps. in the preceding portion of the simulation every {Nevery} timesteps.
{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero
even if {Nrepeat} is 1. even if {Nrepeat} is 1.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps averaging is done; values are simply generated on timesteps
100,200,etc. 100,200,etc.
@ -101,7 +101,7 @@ where the layers are in a particular {dim} and have a thickness given
by {delta}. Every Nfreq steps, when an averaging is being performed by {delta}. Every Nfreq steps, when an averaging is being performed
and the per-atom property is calculated for the first time, the number and the per-atom property is calculated for the first time, the number
of layers and the layer boundaries are computed. Thus if the of layers and the layer boundaries are computed. Thus if the
simlation box changes size during a simulation, the number of layers simulation box changes size during a simulation, the number of layers
and their boundaries may also change. Layers are defined relative to and their boundaries may also change. Layers are defined relative to
a specified {origin}, which may be the lower/upper edge of the box (in a specified {origin}, which may be the lower/upper edge of the box (in
{dim}) or its center point, or a specified coordinate value. Starting {dim}) or its center point, or a specified coordinate value. Starting
@ -216,15 +216,15 @@ The {ave} keyword determines how the layer values produced every
steps that were multiples of {Nfreq}, before they are accessed by steps that were multiples of {Nfreq}, before they are accessed by
another output command or written to a file. another output command or written to a file.
If the {ave} setting is {one}, then the layuer values produced on If the {ave} setting is {one}, then the layer values produced on
timesteps that are multiples of {Nfreq} are independent of each other; timesteps that are multiples of {Nfreq} are independent of each other;
they are output as-is without further averaging. they are output as-is without further averaging.
If the {ave} setting is {running}, then the layer values produced on If the {ave} setting is {running}, then the layer values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a timesteps that are multiples of {Nfreq} are summed and averaged in a
cummulative sense before being output. Each output layer value is cumulative sense before being output. Each output layer value is
thus the average of the layer value produced on that timestep with all thus the average of the layer value produced on that timestep with all
preceeding values for the same layer. This running average begins preceding values for the same layer. This running average begins
when the fix is defined; it can only be restarted by deleting the fix when the fix is defined; it can only be restarted by deleting the fix
via the "unfix"_unfix.html command, or re-defining the fix by via the "unfix"_unfix.html command, or re-defining the fix by
re-specifying it. re-specifying it.

10
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View File

@ -43,7 +43,7 @@
filename = name of file to output time averages to filename = name of file to output time averages to
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I> <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output a new average value every Nfreq steps one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps window M = output average of M most recent Nfreq steps
</PRE> </PRE>
@ -94,13 +94,13 @@ since they produce per-atom values.
timesteps the values will be generated in order to contribute to the timesteps the values will be generated in order to contribute to the
average. The final averaged quantities are generated every <I>Nfreq</I> average. The final averaged quantities are generated every <I>Nfreq</I>
timesteps. The average is over <I>Nrepeat</I> quantities, computed in the timesteps. The average is over <I>Nrepeat</I> quantities, computed in the
preceeding portion of the simulation every <I>Nevery</I> timesteps. preceding portion of the simulation every <I>Nevery</I> timesteps.
<I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero
even if <I>Nrepeat</I> is 1. even if <I>Nrepeat</I> is 1.
</P> </P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on <P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps averaging is done; values are simply generated on timesteps
100,200,etc. 100,200,etc.
@ -158,8 +158,8 @@ output as-is without further averaging.
</P> </P>
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on <P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
cummulative sense before being output. Each output value is thus the cumulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceeding average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A> only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
command, or by re-defining the fix by re-specifying it. command, or by re-defining the fix by re-specifying it.

10
doc/fix_ave_time.txt
View File

@ -31,7 +31,7 @@ keyword = {file} or {ave} :l
filename = name of file to output time averages to filename = name of file to output time averages to
{ave} args = {one} or {running} or {window M} {ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps running = output cumulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps :pre window M = output average of M most recent Nfreq steps :pre
:ule :ule
@ -81,13 +81,13 @@ The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the values will be generated in order to contribute to the timesteps the values will be generated in order to contribute to the
average. The final averaged quantities are generated every {Nfreq} average. The final averaged quantities are generated every {Nfreq}
timesteps. The average is over {Nrepeat} quantities, computed in the timesteps. The average is over {Nrepeat} quantities, computed in the
preceeding portion of the simulation every {Nevery} timesteps. preceding portion of the simulation every {Nevery} timesteps.
{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero
even if {Nrepeat} is 1. even if {Nrepeat} is 1.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps averaging is done; values are simply generated on timesteps
100,200,etc. 100,200,etc.
@ -145,8 +145,8 @@ output as-is without further averaging.
If the {ave} setting is {running}, then the values produced on If the {ave} setting is {running}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a timesteps that are multiples of {Nfreq} are summed and averaged in a
cummulative sense before being output. Each output value is thus the cumulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceeding average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the "unfix"_unfix.html only be restarted by deleting the fix via the "unfix"_unfix.html
command, or by re-defining the fix by re-specifying it. command, or by re-defining the fix by re-specifying it.

8
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View File

@ -126,7 +126,7 @@ value.
</P> </P>
<P>For style <I>final</I>, the final lo and hi box boundaries of a dimension <P>For style <I>final</I>, the final lo and hi box boundaries of a dimension
are specified. The values can be in lattice or box distance units. are specified. The values can be in lattice or box distance units.
See the discsussion of the units keyword below. See the discussion of the units keyword below.
</P> </P>
<P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries <P>For style <I>delta</I>, plus or minus changes in the lo/hi box boundaries
of a dimension are specified. The values can be in lattice or box of a dimension are specified. The values can be in lattice or box
@ -233,13 +233,13 @@ units keyword below.
</P> </P>
<P>For style <I>delta</I>, a plus or minus change in the tilt factor is <P>For style <I>delta</I>, a plus or minus change in the tilt factor is
specified. The value can be in lattice or box distance units. See specified. The value can be in lattice or box distance units. See
the discsussion of the units keyword below. the discussion of the units keyword below.
</P> </P>
<P>For style <I>vel</I>, a velocity at which the tilt factor changes is <P>For style <I>vel</I>, a velocity at which the tilt factor changes is
specified in units of distance/time. This is effectively an specified in units of distance/time. This is effectively an
"engineering shear strain rate", where rate = V/L0 and L0 is the "engineering shear strain rate", where rate = V/L0 and L0 is the
initial box length perpendicular to the direction of shear. The initial box length perpendicular to the direction of shear. The
distance can be in lattice or box distance units. See the discsussion distance can be in lattice or box distance units. See the discussion
of the units keyword below. For example, if the initial tilt factor of the units keyword below. For example, if the initial tilt factor
is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
tilt factor will be 15 Angstroms. After 2 psec, it will be 25 tilt factor will be 15 Angstroms. After 2 psec, it will be 25
@ -304,7 +304,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all equivalent. ... are all equivalent.
</P> </P>
<P>To obey this constraint and allow for large shear deformations to be <P>To obey this constraint and allow for large shear deformations to be
applied via the <I>xy</I>, <I>xz</I>, or <I>yz</I> parameters, the folloiwng applied via the <I>xy</I>, <I>xz</I>, or <I>yz</I> parameters, the following
algorithm is used. If <I>prd</I> is the associated parallel box length (10 algorithm is used. If <I>prd</I> is the associated parallel box length (10
in the example above), then if the tilt factor exceeds the accepted in the example above), then if the tilt factor exceeds the accepted
range of -5 to 5 during the simulation, then the box is re-shaped to range of -5 to 5 during the simulation, then the box is re-shaped to

8
doc/fix_deform.txt
View File

@ -116,7 +116,7 @@ value.
For style {final}, the final lo and hi box boundaries of a dimension For style {final}, the final lo and hi box boundaries of a dimension
are specified. The values can be in lattice or box distance units. are specified. The values can be in lattice or box distance units.
See the discsussion of the units keyword below. See the discussion of the units keyword below.
For style {delta}, plus or minus changes in the lo/hi box boundaries For style {delta}, plus or minus changes in the lo/hi box boundaries
of a dimension are specified. The values can be in lattice or box of a dimension are specified. The values can be in lattice or box
@ -223,13 +223,13 @@ units keyword below.
For style {delta}, a plus or minus change in the tilt factor is For style {delta}, a plus or minus change in the tilt factor is
specified. The value can be in lattice or box distance units. See specified. The value can be in lattice or box distance units. See
the discsussion of the units keyword below. the discussion of the units keyword below.
For style {vel}, a velocity at which the tilt factor changes is For style {vel}, a velocity at which the tilt factor changes is
specified in units of distance/time. This is effectively an specified in units of distance/time. This is effectively an
"engineering shear strain rate", where rate = V/L0 and L0 is the "engineering shear strain rate", where rate = V/L0 and L0 is the
initial box length perpendicular to the direction of shear. The initial box length perpendicular to the direction of shear. The
distance can be in lattice or box distance units. See the discsussion distance can be in lattice or box distance units. See the discussion
of the units keyword below. For example, if the initial tilt factor of the units keyword below. For example, if the initial tilt factor
is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the is 5 Angstroms, and the V is 10 Angstroms/psec, then after 1 psec, the
tilt factor will be 15 Angstroms. After 2 psec, it will be 25 tilt factor will be 15 Angstroms. After 2 psec, it will be 25
@ -294,7 +294,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
... are all equivalent. ... are all equivalent.
To obey this constraint and allow for large shear deformations to be To obey this constraint and allow for large shear deformations to be
applied via the {xy}, {xz}, or {yz} parameters, the folloiwng applied via the {xy}, {xz}, or {yz} parameters, the following
algorithm is used. If {prd} is the associated parallel box length (10 algorithm is used. If {prd} is the associated parallel box length (10
in the example above), then if the tilt factor exceeds the accepted in the example above), then if the tilt factor exceeds the accepted
range of -5 to 5 during the simulation, then the box is re-shaped to range of -5 to 5 during the simulation, then the box is re-shaped to

2
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@ -78,7 +78,7 @@ normalizing factor each time temperature is computed.
</P> </P>
<P>Care must be taken that inserted particles are not too near existing <P>Care must be taken that inserted particles are not too near existing
particles, using the options described below. When inserting particles, using the options described below. When inserting
particles above a surface in a non-perioidic box (see the particles above a surface in a non-periodic box (see the
<A HREF = "boundary.html">boundary</A> command), the possibility of a particle <A HREF = "boundary.html">boundary</A> command), the possibility of a particle
escaping the surface and flying upward should be considered, since the escaping the surface and flying upward should be considered, since the
particle may be lost or the box size may grow infinitely large. A particle may be lost or the box size may grow infinitely large. A

2
doc/fix_deposit.txt
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@ -66,7 +66,7 @@ normalizing factor each time temperature is computed.
Care must be taken that inserted particles are not too near existing Care must be taken that inserted particles are not too near existing
particles, using the options described below. When inserting particles, using the options described below. When inserting
particles above a surface in a non-perioidic box (see the particles above a surface in a non-periodic box (see the
"boundary"_boundary.html command), the possibility of a particle "boundary"_boundary.html command), the possibility of a particle
escaping the surface and flying upward should be considered, since the escaping the surface and flying upward should be considered, since the
particle may be lost or the box size may grow infinitely large. A particle may be lost or the box size may grow infinitely large. A

4
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@ -68,7 +68,7 @@ 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 current timestep size is stored as a scalar quantity by this fix. <P>The current timestep size is stored as a scalar quantity by this fix.
The cummulative simulation time (in time units) is stored as the first The cumulative simulation time (in time units) is stored as the first
element of a vector. Both these quantities can be accessed by various element of a vector. Both these quantities can be accessed by various
<A HREF = "Section_howto.html#4_15">output commands</A>. The scalar and vector <A HREF = "Section_howto.html#4_15">output commands</A>. The scalar and vector
values calculated by this fix are "intensive", meaning they are values calculated by this fix are "intensive", meaning they are
@ -80,7 +80,7 @@ minimization</A>.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>The cummulative time is zeroed when the fix is created and <P>The cumulative time is zeroed when the fix is created and
continuously accrues thereafter. Using the continuously accrues thereafter. Using the
<A HREF = "reset_timestep.html">reset_timestep</A> command while this fix is defined <A HREF = "reset_timestep.html">reset_timestep</A> command while this fix is defined
will mess up the time accumulation. will mess up the time accumulation.

4
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@ -64,7 +64,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. are relevant to this fix.
The current timestep size is stored as a scalar quantity by this fix. The current timestep size is stored as a scalar quantity by this fix.
The cummulative simulation time (in time units) is stored as the first The cumulative simulation time (in time units) is stored as the first
element of a vector. Both these quantities can be accessed by various element of a vector. Both these quantities can be accessed by various
"output commands"_Section_howto.html#4_15. The scalar and vector "output commands"_Section_howto.html#4_15. The scalar and vector
values calculated by this fix are "intensive", meaning they are values calculated by this fix are "intensive", meaning they are
@ -76,7 +76,7 @@ minimization"_minimize.html.
[Restrictions:] [Restrictions:]
The cummulative time is zeroed when the fix is created and The cumulative time is zeroed when the fix is created and
continuously accrues thereafter. Using the continuously accrues thereafter. Using the
"reset_timestep"_reset_timestep.html command while this fix is defined "reset_timestep"_reset_timestep.html command while this fix is defined
will mess up the time accumulation. will mess up the time accumulation.

2
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@ -51,7 +51,7 @@ fix 1 all gravity 100.0 vector 1 1 0
fix is typically used with granular systems to include a "gravity" fix is typically used with granular systems to include a "gravity"
term acting on the macroscopic particles. More generally, it can term acting on the macroscopic particles. More generally, it can
represent any kind of driving field, e.g. a pressure gradient inducing represent any kind of driving field, e.g. a pressure gradient inducing
a Poisselle flow in a fluid. Note that this fix operates differently a Poiseuille flow in a fluid. Note that this fix operates differently
than the <A HREF = "fix_addforce.html">fix addforce</A> command. The addforce fix than the <A HREF = "fix_addforce.html">fix addforce</A> command. The addforce fix
adds the same force to each atom, independent of its mass. This adds the same force to each atom, independent of its mass. This
command imparts the same acceleration to each atom (force/mass). command imparts the same acceleration to each atom (force/mass).

2
doc/fix_gravity.txt
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@ -43,7 +43,7 @@ Impose an additional acceleration on each particle in the group. This
fix is typically used with granular systems to include a "gravity" fix is typically used with granular systems to include a "gravity"
term acting on the macroscopic particles. More generally, it can term acting on the macroscopic particles. More generally, it can
represent any kind of driving field, e.g. a pressure gradient inducing represent any kind of driving field, e.g. a pressure gradient inducing
a Poisselle flow in a fluid. Note that this fix operates differently a Poiseuille flow in a fluid. Note that this fix operates differently
than the "fix addforce"_fix_addforce.html command. The addforce fix than the "fix addforce"_fix_addforce.html command. The addforce fix
adds the same force to each atom, independent of its mass. This adds the same force to each atom, independent of its mass. This
command imparts the same acceleration to each atom (force/mass). command imparts the same acceleration to each atom (force/mass).

2
doc/fix_langevin.html
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@ -67,7 +67,7 @@ user.
</P> </P>
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping <P>Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation into the particle. As derived from the fluctuation/dissipation
theorum, its magnitude is proportional to sqrt(T m / dt damp), where T theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
is the desired temperature, m is the mass of the particle, dt is the is the desired temperature, m is the mass of the particle, dt is the
timestep size, and damp is the damping factor. Random numbers are timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force as used to randomize the direction and magnitude of this force as

2
doc/fix_langevin.txt
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@ -57,7 +57,7 @@ user.
Fr is a force due to solvent atoms at a temperature T randomly bumping Fr is a force due to solvent atoms at a temperature T randomly bumping
into the particle. As derived from the fluctuation/dissipation into the particle. As derived from the fluctuation/dissipation
theorum, its magnitude is proportional to sqrt(T m / dt damp), where T theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
is the desired temperature, m is the mass of the particle, dt is the is the desired temperature, m is the mass of the particle, dt is the
timestep size, and damp is the damping factor. Random numbers are timestep size, and damp is the damping factor. Random numbers are
used to randomize the direction and magnitude of this force as used to randomize the direction and magnitude of this force as

2
doc/fix_modify.html
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@ -57,7 +57,7 @@ default method for computing P.
</P> </P>
<P>For fixes that calculate a contribution to the potential energy of the <P>For fixes that calculate a contribution to the potential energy of the
system, the <I>energy</I> keyword will include that contribution in system, the <I>energy</I> keyword will include that contribution in
thermodyanmic output of potential energy. See the thermodynamic output of potential energy. See the
<A HREF = "thermo_style.html">thermo_style</A> command for info on how potential <A HREF = "thermo_style.html">thermo_style</A> command for info on how potential
energy is output. The contribution by itself can be printed by using energy is output. The contribution by itself can be printed by using
the keyword f_ID in the thermo_style custom command, where ID is the the keyword f_ID in the thermo_style custom command, where ID is the

2
doc/fix_modify.txt
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@ -50,7 +50,7 @@ default method for computing P.
For fixes that calculate a contribution to the potential energy of the For fixes that calculate a contribution to the potential energy of the
system, the {energy} keyword will include that contribution in system, the {energy} keyword will include that contribution in
thermodyanmic output of potential energy. See the thermodynamic output of potential energy. See the
"thermo_style"_thermo_style.html command for info on how potential "thermo_style"_thermo_style.html command for info on how potential
energy is output. The contribution by itself can be printed by using energy is output. The contribution by itself can be printed by using
the keyword f_ID in the thermo_style custom command, where ID is the the keyword f_ID in the thermo_style custom command, where ID is the

2
doc/fix_nph.html
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@ -142,7 +142,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
and <I>thermo_press</I>. This means you can change the attributes of this and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. <I>thermo_press</I> will have no effect on this fix.

2
doc/fix_nph.txt
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@ -132,7 +132,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. {thermo_press} will have no effect on this fix.

2
doc/fix_npt.html
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@ -146,7 +146,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
and <I>thermo_press</I>. This means you can change the attributes of this and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. <I>thermo_press</I> will have no effect on this fix.

2
doc/fix_npt.txt
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@ -135,7 +135,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. {thermo_press} will have no effect on this fix.

2
doc/fix_npt_asphere.html
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@ -145,7 +145,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
and <I>thermo_press</I>. This means you can change the attributes of this and <I>thermo_press</I>. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
or pressure during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> or It also means that changing attributes of <I>thermo_temp</I> or
<I>thermo_press</I> will have no effect on this fix. <I>thermo_press</I> will have no effect on this fix.

2
doc/fix_npt_asphere.txt
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@ -134,7 +134,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}
and {thermo_press}. This means you can change the attributes of this and {thermo_press}. This means you can change the attributes of this
fix's temperature or pressure via the fix's temperature or pressure via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
or pressure during thermodyanmic output via the "thermo_style or pressure during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} or It also means that changing attributes of {thermo_temp} or
{thermo_press} will have no effect on this fix. {thermo_press} will have no effect on this fix.

2
doc/fix_nve_limit.html
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@ -61,7 +61,7 @@ updates of atom's velocity/position were limited by the maximum
distance criterion. This should be roughly the number of atoms so distance criterion. This should be roughly the number of atoms so
affected, except that updates occur at both the beginning and end of a affected, except that updates occur at both the beginning and end of a
timestep in a velocity Verlet timestepping algorithm. This is a timestep in a velocity Verlet timestepping algorithm. This is a
cummulative quantity for the current run, but is re-initialized to cumulative quantity for the current run, but is re-initialized to
zero each time a run is performed. This value can be accessed by zero each time a run is performed. This value can be accessed by
various <A HREF = "Section_howto.html#4_15">output commands</A>. The scalar value various <A HREF = "Section_howto.html#4_15">output commands</A>. The scalar value
calculated by this fix is "extensive", meaning it scales with the calculated by this fix is "extensive", meaning it scales with the

2
doc/fix_nve_limit.txt
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@ -58,7 +58,7 @@ updates of atom's velocity/position were limited by the maximum
distance criterion. This should be roughly the number of atoms so distance criterion. This should be roughly the number of atoms so
affected, except that updates occur at both the beginning and end of a affected, except that updates occur at both the beginning and end of a
timestep in a velocity Verlet timestepping algorithm. This is a timestep in a velocity Verlet timestepping algorithm. This is a
cummulative quantity for the current run, but is re-initialized to cumulative quantity for the current run, but is re-initialized to
zero each time a run is performed. This value can be accessed by zero each time a run is performed. This value can be accessed by
various "output commands"_Section_howto.html#4_15. The scalar value various "output commands"_Section_howto.html#4_15. The scalar value
calculated by this fix is "extensive", meaning it scales with the calculated by this fix is "extensive", meaning it scales with the

2
doc/fix_nvt_asphere.html
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@ -77,7 +77,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. effect on this fix.

2
doc/fix_nvt_asphere.txt
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@ -68,7 +68,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no It also means that changing attributes of {thermo_temp} will have no
effect on this fix. effect on this fix.

2
doc/fix_nvt_sllod.html
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@ -103,7 +103,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. effect on this fix.

2
doc/fix_nvt_sllod.txt
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@ -94,7 +94,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no It also means that changing attributes of {thermo_temp} will have no
effect on this fix. effect on this fix.

6
doc/fix_orient_fcc.html
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@ -61,19 +61,19 @@ and RIj is a vector in the reference (perfect) crystal. That is, if
dir = 0/1, then RIj is a vector to an atom coord from file 0/1. dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
Equation (2) gives the expected value of the order parameter XiIJ in Equation (2) gives the expected value of the order parameter XiIJ in
the other grain. Hi and lo cutoffs are defined in equations (3) and the other grain. Hi and lo cutoffs are defined in equations (3) and
(4), using the input parameters <I>cutlo</I> and <I>cuthi</I> as threshholds to (4), using the input parameters <I>cutlo</I> and <I>cuthi</I> as thresholds to
avoid adding grain boundary energy when the deviation in the order avoid adding grain boundary energy when the deviation in the order
parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
perfect crystal). The added potential energy Ui for atom I is given perfect crystal). The added potential energy Ui for atom I is given
in equation (6) where it is interpolated between 0 and dE using the in equation (6) where it is interpolated between 0 and dE using the
two threshhold Xi values and the Wi value of equation (5). two threshold Xi values and the Wi value of equation (5).
</P> </P>
<P>The derivative of this energy expression gives the force on each atom <P>The derivative of this energy expression gives the force on each atom
which thus depends on the orientation of its neighbors relative to the which thus depends on the orientation of its neighbors relative to the
2 grain orientations. Only atoms near the grain boundary feel a net 2 grain orientations. Only atoms near the grain boundary feel a net
force which tends to drive them to one of the two grain orientations. force which tends to drive them to one of the two grain orientations.
</P> </P>
<P>In equation (1), the reference vector used for each neigbbor is the <P>In equation (1), the reference vector used for each neighbor is the
reference vector closest to the actual neighbor position. This means reference vector closest to the actual neighbor position. This means
it is possible two different neighbors will use the same reference it is possible two different neighbors will use the same reference
vector. In such cases, the atom in question is far from a perfect vector. In such cases, the atom in question is far from a perfect

6
doc/fix_orient_fcc.txt
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@ -58,19 +58,19 @@ and RIj is a vector in the reference (perfect) crystal. That is, if
dir = 0/1, then RIj is a vector to an atom coord from file 0/1. dir = 0/1, then RIj is a vector to an atom coord from file 0/1.
Equation (2) gives the expected value of the order parameter XiIJ in Equation (2) gives the expected value of the order parameter XiIJ in
the other grain. Hi and lo cutoffs are defined in equations (3) and the other grain. Hi and lo cutoffs are defined in equations (3) and
(4), using the input parameters {cutlo} and {cuthi} as threshholds to (4), using the input parameters {cutlo} and {cuthi} as thresholds to
avoid adding grain boundary energy when the deviation in the order avoid adding grain boundary energy when the deviation in the order
parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a parameter from 0 or 1 is small (e.g. due to thermal fluctuations in a
perfect crystal). The added potential energy Ui for atom I is given perfect crystal). The added potential energy Ui for atom I is given
in equation (6) where it is interpolated between 0 and dE using the in equation (6) where it is interpolated between 0 and dE using the
two threshhold Xi values and the Wi value of equation (5). two threshold Xi values and the Wi value of equation (5).
The derivative of this energy expression gives the force on each atom The derivative of this energy expression gives the force on each atom
which thus depends on the orientation of its neighbors relative to the which thus depends on the orientation of its neighbors relative to the
2 grain orientations. Only atoms near the grain boundary feel a net 2 grain orientations. Only atoms near the grain boundary feel a net
force which tends to drive them to one of the two grain orientations. force which tends to drive them to one of the two grain orientations.
In equation (1), the reference vector used for each neigbbor is the In equation (1), the reference vector used for each neighbor is the
reference vector closest to the actual neighbor position. This means reference vector closest to the actual neighbor position. This means
it is possible two different neighbors will use the same reference it is possible two different neighbors will use the same reference
vector. In such cases, the atom in question is far from a perfect vector. In such cases, the atom in question is far from a perfect

2
doc/fix_poems.html
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@ -59,7 +59,7 @@ a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
</P> </P>
<P>Each body must have a non-degenerate inertia tensor, which means if <P>Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-collinear atoms. Which atoms are in which must contain at least 3 non-colinear atoms. Which atoms are in which
bodies can be defined via several options. bodies can be defined via several options.
</P> </P>
<P>For option <I>group</I>, each of the listed groups is treated as a rigid <P>For option <I>group</I>, each of the listed groups is treated as a rigid

2
doc/fix_poems.txt
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@ -52,7 +52,7 @@ a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin). atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
Each body must have a non-degenerate inertia tensor, which means if Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-collinear atoms. Which atoms are in which must contain at least 3 non-colinear atoms. Which atoms are in which
bodies can be defined via several options. bodies can be defined via several options.
For option {group}, each of the listed groups is treated as a rigid For option {group}, each of the listed groups is treated as a rigid

2
doc/fix_print.html
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@ -52,7 +52,7 @@ style variables which are the most useful ones to use with the fix
print command, since they are evaluated afresh each timestep that the print command, since they are evaluated afresh each timestep that the
fix print line is output. Equal-style variables calculate formulas fix print line is output. Equal-style variables calculate formulas
involving mathematical operations, atom properties, group properties, involving mathematical operations, atom properties, group properties,
thermodyanimc properties, global values calculated by a thermodynamic properties, global values calculated by a
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>, or references to other <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A>, or references to other
<A HREF = "variable.html">variables</A>. <A HREF = "variable.html">variables</A>.
</P> </P>

2
doc/fix_print.txt
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@ -42,7 +42,7 @@ style variables which are the most useful ones to use with the fix
print command, since they are evaluated afresh each timestep that the print command, since they are evaluated afresh each timestep that the
fix print line is output. Equal-style variables calculate formulas fix print line is output. Equal-style variables calculate formulas
involving mathematical operations, atom properties, group properties, involving mathematical operations, atom properties, group properties,
thermodyanimc properties, global values calculated by a thermodynamic properties, global values calculated by a
"compute"_compute.html or "fix"_fix.html, or references to other "compute"_compute.html or "fix"_fix.html, or references to other
"variables"_variable.html. "variables"_variable.html.

2
doc/fix_rdf.html
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@ -18,7 +18,7 @@
<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>rdf = style name of this fix command <LI>rdf = style name of this fix command
<LI>N = compute radial distribution function (RDF) every this many timesteps <LI>N = compute radial distribution function (RDF) every this many timesteps
<LI>file = filename to write radial distribution funtion info to <LI>file = filename to write radial distribution function info to
<LI>Nbin = number of RDF bins <LI>Nbin = number of RDF bins
<LI>itypeN = central atom type for RDF pair N <LI>itypeN = central atom type for RDF pair N
<LI>jtypeN = distribution atom type for RDF pair N <LI>jtypeN = distribution atom type for RDF pair N

2
doc/fix_rdf.txt
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@ -15,7 +15,7 @@ fix ID group-ID rdf N file Nbin itype1 jtype1 itype2 jtype2 ... :pre
ID, group-ID are documented in "fix"_fix.html command ID, group-ID are documented in "fix"_fix.html command
rdf = style name of this fix command rdf = style name of this fix command
N = compute radial distribution function (RDF) every this many timesteps N = compute radial distribution function (RDF) every this many timesteps
file = filename to write radial distribution funtion info to file = filename to write radial distribution function info to
Nbin = number of RDF bins Nbin = number of RDF bins
itypeN = central atom type for RDF pair N itypeN = central atom type for RDF pair N
jtypeN = distribution atom type for RDF pair N :ul jtypeN = distribution atom type for RDF pair N :ul

2
doc/fix_shake.html
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@ -65,7 +65,7 @@ defined as a central atom connected to others in the cluster by
constrained bonds. LAMMPS allows for the following kinds of clusters constrained bonds. LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms one central atom bonded to 2 others and the angle between the 3 atoms
also constained. This means water molecules or CH2 or CH3 groups may also constrained. This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer be constrained, but not all the C-C backbone bonds of a long polymer
chain. chain.
</P> </P>

2
doc/fix_shake.txt
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@ -54,7 +54,7 @@ defined as a central atom connected to others in the cluster by
constrained bonds. LAMMPS allows for the following kinds of clusters constrained bonds. LAMMPS allows for the following kinds of clusters
to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or to be constrained: one central atom bonded to 1 or 2 or 3 atoms, or
one central atom bonded to 2 others and the angle between the 3 atoms one central atom bonded to 2 others and the angle between the 3 atoms
also constained. This means water molecules or CH2 or CH3 groups may also constrained. This means water molecules or CH2 or CH3 groups may
be constrained, but not all the C-C backbone bonds of a long polymer be constrained, but not all the C-C backbone bonds of a long polymer
chain. chain.

2
doc/fix_temp_rescale.html
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@ -88,7 +88,7 @@ the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature <A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID. custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix. effect on this fix.

2
doc/fix_temp_rescale.txt
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@ -84,7 +84,7 @@ the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the (e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature "compute_modify"_compute_modify.html command or print this temperature
during thermodyanmic output via the "thermo_style during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID. custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no It also means that changing attributes of {thermo_temp} will have no
effect on this fix. effect on this fix.

10
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View File

@ -62,7 +62,7 @@ swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box quantity by time and the cross-sectional area of the simulation box
yields a momentum flux. The ratio of momentum flux to the slope of yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in the shear velocity profile is the viscosity of the fluid, in
appopriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for appropriate units. See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
details. details.
</P> </P>
<P>IMPORTANT NOTE: After equilibration, if the velocity profile you <P>IMPORTANT NOTE: After equilibration, if the velocity profile you
@ -73,7 +73,7 @@ the Nevery parameter.
</P> </P>
<P>An alternative method for calculating a viscosity is to run a NEMD <P>An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
the manual. NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix the manual. NEMD simulations deform the simulation box via the <A HREF = "fix_deform.html">fix
deform</A> command. Thus they cannot be run on a charged deform</A> command. Thus they cannot be run on a charged
system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does not system using a <A HREF = "kspace_style.html">PPPM solver</A> since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the currently support non-orthogonal boxes. Using fix viscosity keeps the
@ -85,10 +85,10 @@ box orthogonal; thus it does not suffer from this limitation.
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 cummulative momentum transferred between the bottom and middle of <P>The cumulative momentum transferred between the bottom and middle of
the simulation box (in the <I>pdim</I> direction) is stored as a scalar the simulation box (in the <I>pdim</I> direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined quantity by this fix. This quantity is zeroed when the fix is defined
and accumlates thereafter, once every N steps. The units of the and accumulates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be accessed quantity are momentum = mass*velocity. This quantity can be accessed
by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as by various <A HREF = "Section_howto.html#4_15">output commands</A>, such as
<A HREF = "thermo_style.html">thermo_style custom</A>. The scalar value calculated <A HREF = "thermo_style.html">thermo_style custom</A>. The scalar value calculated
@ -115,7 +115,7 @@ See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algori
in a computation of alcohol molecule properties. in a computation of alcohol molecule properties.
</P> </P>
<P>When running a simulation with large, massive particles or molecules <P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen in a background solvent, you may want to only exchange momenta between
solvent particles. solvent particles.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>

10
doc/fix_viscosity.txt
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@ -59,7 +59,7 @@ swaps is computed by the fix and can be output. Dividing this
quantity by time and the cross-sectional area of the simulation box quantity by time and the cross-sectional area of the simulation box
yields a momentum flux. The ratio of momentum flux to the slope of yields a momentum flux. The ratio of momentum flux to the slope of
the shear velocity profile is the viscosity of the fluid, in the shear velocity profile is the viscosity of the fluid, in
appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for appropriate units. See the "Muller-Plathe paper"_#Muller-Plathe for
details. details.
IMPORTANT NOTE: After equilibration, if the velocity profile you IMPORTANT NOTE: After equilibration, if the velocity profile you
@ -70,7 +70,7 @@ the Nevery parameter.
An alternative method for calculating a viscosity is to run a NEMD An alternative method for calculating a viscosity is to run a NEMD
simulation, as described in "this section"_Section_howto.html#4_13 of simulation, as described in "this section"_Section_howto.html#4_13 of
the manual. NEMD simulations deform the simmulation box via the "fix the manual. NEMD simulations deform the simulation box via the "fix
deform"_fix_deform.html command. Thus they cannot be run on a charged deform"_fix_deform.html command. Thus they cannot be run on a charged
system using a "PPPM solver"_kspace_style.html since PPPM does not system using a "PPPM solver"_kspace_style.html since PPPM does not
currently support non-orthogonal boxes. Using fix viscosity keeps the currently support non-orthogonal boxes. Using fix viscosity keeps the
@ -82,10 +82,10 @@ 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 cummulative momentum transferred between the bottom and middle of The cumulative momentum transferred between the bottom and middle of
the simulation box (in the {pdim} direction) is stored as a scalar the simulation box (in the {pdim} direction) is stored as a scalar
quantity by this fix. This quantity is zeroed when the fix is defined quantity by this fix. This quantity is zeroed when the fix is defined
and accumlates thereafter, once every N steps. The units of the and accumulates thereafter, once every N steps. The units of the
quantity are momentum = mass*velocity. This quantity can be accessed quantity are momentum = mass*velocity. This quantity can be accessed
by various "output commands"_Section_howto.html#4_15, such as by various "output commands"_Section_howto.html#4_15, such as
"thermo_style custom"_thermo_style.html. The scalar value calculated "thermo_style custom"_thermo_style.html. The scalar value calculated
@ -112,7 +112,7 @@ See the "Maginn paper"_#Maginn for an example of using this algorithm
in a computation of alcohol molecule properties. in a computation of alcohol molecule properties.
When running a simulation with large, massive particles or molecules When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen in a background solvent, you may want to only exchange momenta between
solvent particles. solvent particles.
[Related commands:] [Related commands:]

2
doc/fix_viscous.html
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@ -56,7 +56,7 @@ optional keyword <I>scale</I> is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types. times to adjust gamma for several atom types.
</P> </P>
<P>In a Brownian dynamics context, gamma = kT / mD, where k = Bolztmann's <P>In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's
constant, T = temperature, m = particle mass, and D = particle constant, T = temperature, m = particle mass, and D = particle
diffusion coefficient. D can be written as kT / (6 pi eta d), where diffusion coefficient. D can be written as kT / (6 pi eta d), where
eta = viscosity of the frictional fluid and d = diameter of particle. eta = viscosity of the frictional fluid and d = diameter of particle.

2
doc/fix_viscous.txt
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@ -46,7 +46,7 @@ optional keyword {scale} is used, gamma can scaled up or down by the
specified factor for atoms of that type. It can be used multiple specified factor for atoms of that type. It can be used multiple
times to adjust gamma for several atom types. times to adjust gamma for several atom types.
In a Brownian dynamics context, gamma = kT / mD, where k = Bolztmann's In a Brownian dynamics context, gamma = kT / mD, where k = Boltzmann's
constant, T = temperature, m = particle mass, and D = particle constant, T = temperature, m = particle mass, and D = particle
diffusion coefficient. D can be written as kT / (6 pi eta d), where diffusion coefficient. D can be written as kT / (6 pi eta d), where
eta = viscosity of the frictional fluid and d = diameter of particle. eta = viscosity of the frictional fluid and d = diameter of particle.

2
doc/improper_class2.html
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@ -56,7 +56,7 @@ the data file or restart files read by the <A HREF = "read_data.html">read_data<
or <A HREF = "read_restart.html">read_restart</A> commands: or <A HREF = "read_restart.html">read_restart</A> commands:
</P> </P>
<P>For this style, coefficients for the Ei formula can be specified in <P>For this style, coefficients for the Ei formula can be specified in
eiher the input script or data file. These are the 2 coefficients: either the input script or data file. These are the 2 coefficients:
</P> </P>
<UL><LI>K (energy/radian^2) <UL><LI>K (energy/radian^2)
<LI>X0 (degrees) <LI>X0 (degrees)

2
doc/improper_class2.txt
View File

@ -53,7 +53,7 @@ the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands: or "read_restart"_read_restart.html commands:
For this style, coefficients for the Ei formula can be specified in For this style, coefficients for the Ei formula can be specified in
eiher the input script or data file. These are the 2 coefficients: either the input script or data file. These are the 2 coefficients:
K (energy/radian^2) K (energy/radian^2)
X0 (degrees) :ul X0 (degrees) :ul

2
doc/jump.html
View File

@ -38,7 +38,7 @@ be used to loop over a portion of the input script, as in this
example. These commands perform 10 runs, each of 10000 steps, and example. These commands perform 10 runs, each of 10000 steps, and
create 10 dump files named file.1, file.2, etc. The <A HREF = "next.html">next</A> create 10 dump files named file.1, file.2, etc. The <A HREF = "next.html">next</A>
command is used to exit the loop after 10 iterations. When the "a" command is used to exit the loop after 10 iterations. When the "a"
variable has been incremented for the 10th time, it will cause the variable has been incremented for the tenth time, it will cause the
next jump command to be skipped. next jump command to be skipped.
</P> </P>
<PRE>variable a loop 10 <PRE>variable a loop 10

2
doc/jump.txt
View File

@ -35,7 +35,7 @@ be used to loop over a portion of the input script, as in this
example. These commands perform 10 runs, each of 10000 steps, and example. These commands perform 10 runs, each of 10000 steps, and
create 10 dump files named file.1, file.2, etc. The "next"_next.html create 10 dump files named file.1, file.2, etc. The "next"_next.html
command is used to exit the loop after 10 iterations. When the "a" command is used to exit the loop after 10 iterations. When the "a"
variable has been incremented for the 10th time, it will cause the variable has been incremented for the tenth time, it will cause the
next jump command to be skipped. next jump command to be skipped.
variable a loop 10 variable a loop 10

2
doc/label.html
View File

@ -30,7 +30,7 @@ command was used previously, this does nothing. But if a
invoking this script file, then all command lines in the script prior invoking this script file, then all command lines in the script prior
to this line will be ignored. I.e. execution of the script will begin to this line will be ignored. I.e. execution of the script will begin
at this line. This is useful for looping over a section of the input at this line. This is useful for looping over a section of the input
script as discussed in the <A HREF = "jump.html">jump</A> commmand. script as discussed in the <A HREF = "jump.html">jump</A> command.
</P> </P>
<P><B>Restrictions:</B> none <P><B>Restrictions:</B> none
</P> </P>

2
doc/label.txt
View File

@ -27,7 +27,7 @@ command was used previously, this does nothing. But if a
invoking this script file, then all command lines in the script prior invoking this script file, then all command lines in the script prior
to this line will be ignored. I.e. execution of the script will begin to this line will be ignored. I.e. execution of the script will begin
at this line. This is useful for looping over a section of the input at this line. This is useful for looping over a section of the input
script as discussed in the "jump"_jump.html commmand. script as discussed in the "jump"_jump.html command.
[Restrictions:] none [Restrictions:] none

4
doc/lattice.html
View File

@ -81,7 +81,7 @@ either 2d or 3d problems.
cell, and a set of transformation parameters (scale, origin, orient) cell, and a set of transformation parameters (scale, origin, orient)
that map the unit cell into the simulation box. The vectors a1,a2,a3 that map the unit cell into the simulation box. The vectors a1,a2,a3
are the edge vectors of the unit cell. This is the nomenclature for are the edge vectors of the unit cell. This is the nomenclature for
"primitive" vectors in solid-state crytallography, but in LAMMPS the "primitive" vectors in solid-state crystallography, but in LAMMPS the
unit cell they determine does not have to be a "primitive cell" of unit cell they determine does not have to be a "primitive cell" of
minimum volume. minimum volume.
</P> </P>
@ -191,7 +191,7 @@ in the min/max of the y and z coordinates.
</P> </P>
<P>Note that if the unit cell is orthogonal with axis-aligned edges (not <P>Note that if the unit cell is orthogonal with axis-aligned edges (not
rotated via the <I>orient</I> keyword), then the lattice spacings in each rotated via the <I>orient</I> keyword), then the lattice spacings in each
dimension are simply the scale factor (descibed above) multiplied by dimension are simply the scale factor (described above) multiplied by
the length of a1,a2,a3. Thus a <I>hex</I> style lattice with a scale the length of a1,a2,a3. Thus a <I>hex</I> style lattice with a scale
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
3*sqrt(3.0) in y. 3*sqrt(3.0) in y.

4
doc/lattice.txt
View File

@ -73,7 +73,7 @@ A lattice consists of a unit cell, a set of basis atoms within that
cell, and a set of transformation parameters (scale, origin, orient) cell, and a set of transformation parameters (scale, origin, orient)
that map the unit cell into the simulation box. The vectors a1,a2,a3 that map the unit cell into the simulation box. The vectors a1,a2,a3
are the edge vectors of the unit cell. This is the nomenclature for are the edge vectors of the unit cell. This is the nomenclature for
"primitive" vectors in solid-state crytallography, but in LAMMPS the "primitive" vectors in solid-state crystallography, but in LAMMPS the
unit cell they determine does not have to be a "primitive cell" of unit cell they determine does not have to be a "primitive cell" of
minimum volume. minimum volume.
@ -183,7 +183,7 @@ in the min/max of the y and z coordinates.
Note that if the unit cell is orthogonal with axis-aligned edges (not Note that if the unit cell is orthogonal with axis-aligned edges (not
rotated via the {orient} keyword), then the lattice spacings in each rotated via the {orient} keyword), then the lattice spacings in each
dimension are simply the scale factor (descibed above) multiplied by dimension are simply the scale factor (described above) multiplied by
the length of a1,a2,a3. Thus a {hex} style lattice with a scale the length of a1,a2,a3. Thus a {hex} style lattice with a scale
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
3*sqrt(3.0) in y. 3*sqrt(3.0) in y.

8
doc/mass.html
View File

@ -15,7 +15,7 @@
</P> </P>
<PRE>mass I value <PRE>mass I value
</PRE> </PRE>
<UL><LI>I = atom type (see asterik form below) <UL><LI>I = atom type (see asterisk form below)
<LI>value = mass <LI>value = mass
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
@ -39,9 +39,9 @@ the masses of atom types in the EAM potential file.
be used, as in the 1st example above. Or a wild-card asterik can be be used, as in the 1st example above. Or a wild-card asterik can be
used to set the mass for multiple atom types. This takes the form "*" used to set the mass for multiple atom types. This takes the form "*"
or "*n" or "n*" or "m*n". If N = the number of atom types, then an or "*n" or "n*" or "m*n". If N = the number of atom types, then an
asterik with no numeric values means all types from 1 to N. A leading asterisk with no numeric values means all types from 1 to N. A leading
asterik means all types from 1 to n (inclusive). A trailing asterik asterisk means all types from 1 to n (inclusive). A trailing asterisk
means all types from n to N (inclusive). A middle asterik means all means all types from n to N (inclusive). A middle asterisk means all
types from m to n (inclusive). types from m to n (inclusive).
</P> </P>
<P>A line in a data file that specifies mass uses the same format as the <P>A line in a data file that specifies mass uses the same format as the

8
doc/mass.txt
View File

@ -12,7 +12,7 @@ mass command :h3
mass I value :pre mass I value :pre
I = atom type (see asterik form below) I = atom type (see asterisk form below)
value = mass :ul value = mass :ul
[Examples:] [Examples:]
@ -36,9 +36,9 @@ I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be be used, as in the 1st example above. Or a wild-card asterik can be
used to set the mass for multiple atom types. This takes the form "*" used to set the mass for multiple atom types. This takes the form "*"
or "*n" or "n*" or "m*n". If N = the number of atom types, then an or "*n" or "n*" or "m*n". If N = the number of atom types, then an
asterik with no numeric values means all types from 1 to N. A leading asterisk with no numeric values means all types from 1 to N. A leading
asterik means all types from 1 to n (inclusive). A trailing asterik asterisk means all types from 1 to n (inclusive). A trailing asterisk
means all types from n to N (inclusive). A middle asterik means all means all types from n to N (inclusive). A middle asterisk means all
types from m to n (inclusive). types from m to n (inclusive).
A line in a data file that specifies mass uses the same format as the A line in a data file that specifies mass uses the same format as the

2
doc/min_modify.html
View File

@ -37,7 +37,7 @@ min_modify lineiter 5
</P> </P>
<P>This command sets parameters that affect the minimization algorithms. <P>This command sets parameters that affect the minimization algorithms.
The various settings may effect the convergence rate and overall The various settings may effect the convergence rate and overall
number of force evaulations required by a minimization, so users can number of force evaluations required by a minimization, so users can
experiment with these parameters to tune their minimizations. experiment with these parameters to tune their minimizations.
</P> </P>
<P>The <I>linestyle</I> sets the algorithm used for 1d line searches at each <P>The <I>linestyle</I> sets the algorithm used for 1d line searches at each

2
doc/min_modify.txt
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@ -32,7 +32,7 @@ min_modify lineiter 5 :pre
This command sets parameters that affect the minimization algorithms. This command sets parameters that affect the minimization algorithms.
The various settings may effect the convergence rate and overall The various settings may effect the convergence rate and overall
number of force evaulations required by a minimization, so users can number of force evaluations required by a minimization, so users can
experiment with these parameters to tune their minimizations. experiment with these parameters to tune their minimizations.
The {linestyle} sets the algorithm used for 1d line searches at each The {linestyle} sets the algorithm used for 1d line searches at each

2
doc/minimize.html
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@ -103,7 +103,7 @@ contribute to the potential energy which is probably not what is
desired. desired.
</P> </P>
<P>The volume of the simulation domain is not allowed to change during a <P>The volume of the simulation domain is not allowed to change during a
minimzation. Ideally we would allow a fix such as <I>npt</I> to impose an minimization. Ideally we would allow a fix such as <I>npt</I> to impose an
external pressure that would be included in the minimization external pressure that would be included in the minimization
(i.e. allow the box dimensions to change), but this has not yet been (i.e. allow the box dimensions to change), but this has not yet been
implemented. implemented.

2
doc/minimize.txt
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@ -100,7 +100,7 @@ contribute to the potential energy which is probably not what is
desired. desired.
The volume of the simulation domain is not allowed to change during a The volume of the simulation domain is not allowed to change during a
minimzation. Ideally we would allow a fix such as {npt} to impose an minimization. Ideally we would allow a fix such as {npt} to impose an
external pressure that would be included in the minimization external pressure that would be included in the minimization
(i.e. allow the box dimensions to change), but this has not yet been (i.e. allow the box dimensions to change), but this has not yet been
implemented. implemented.

4
doc/neigh_modify.html
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@ -104,7 +104,7 @@ both atoms are in the specified group and in the same molecule, as
determined by their molecule ID. determined by their molecule ID.
</P> </P>
<P>Each of the exclude options can be specified multiple times. The <P>Each of the exclude options can be specified multiple times. The
<I>exclude type</I> option is the most efficient option to use; it requries <I>exclude type</I> option is the most efficient option to use; it requires
only a single check, no matter how many times it has been specified. only a single check, no matter how many times it has been specified.
The other exclude options are more expensive if specified multiple The other exclude options are more expensive if specified multiple
times; they require one check for each time they have been specified. times; they require one check for each time they have been specified.
@ -120,7 +120,7 @@ long cutoff is being used, these parameters can be tuned. The indices
of neighboring atoms are stored in "pages", which are allocated one of neighboring atoms are stored in "pages", which are allocated one
after another as they fill up. The size of each page is set by the after another as they fill up. The size of each page is set by the
<I>page</I> value. A new page is allocated when the next atom's neighbors <I>page</I> value. A new page is allocated when the next atom's neighbors
could potentially overflow the list. This threshhold is set by the could potentially overflow the list. This threshold is set by the
<I>one</I> value which tells LAMMPS the maximum number of neighbor's one <I>one</I> value which tells LAMMPS the maximum number of neighbor's one
atom can have. atom can have.
</P> </P>

4
doc/neigh_modify.txt
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@ -98,7 +98,7 @@ both atoms are in the specified group and in the same molecule, as
determined by their molecule ID. determined by their molecule ID.
Each of the exclude options can be specified multiple times. The Each of the exclude options can be specified multiple times. The
{exclude type} option is the most efficient option to use; it requries {exclude type} option is the most efficient option to use; it requires
only a single check, no matter how many times it has been specified. only a single check, no matter how many times it has been specified.
The other exclude options are more expensive if specified multiple The other exclude options are more expensive if specified multiple
times; they require one check for each time they have been specified. times; they require one check for each time they have been specified.
@ -114,7 +114,7 @@ long cutoff is being used, these parameters can be tuned. The indices
of neighboring atoms are stored in "pages", which are allocated one of neighboring atoms are stored in "pages", which are allocated one
after another as they fill up. The size of each page is set by the after another as they fill up. The size of each page is set by the
{page} value. A new page is allocated when the next atom's neighbors {page} value. A new page is allocated when the next atom's neighbors
could potentially overflow the list. This threshhold is set by the could potentially overflow the list. This threshold is set by the
{one} value which tells LAMMPS the maximum number of neighbor's one {one} value which tells LAMMPS the maximum number of neighbor's one
atom can have. atom can have.

2
doc/pair_airebo.html
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@ -69,7 +69,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms. would be 10.2 Angstroms.
</P> </P>
<P>The E_TORSION term is an explicit 4-body potential that describes <P>The E_TORSION term is an explicit 4-body potential that describes
various diheadral angle preferences in hydrocarbon configurations. various dihedral angle preferences in hydrocarbon configurations.
</P> </P>
<P>Only a single pair_coeff command is used with the <I>airebo</I> style which <P>Only a single pair_coeff command is used with the <I>airebo</I> style which
specifies an AIREBO potential file with parameters for C and H. These specifies an AIREBO potential file with parameters for C and H. These

2
doc/pair_airebo.txt
View File

@ -66,7 +66,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
would be 10.2 Angstroms. would be 10.2 Angstroms.
The E_TORSION term is an explicit 4-body potential that describes The E_TORSION term is an explicit 4-body potential that describes
various diheadral angle preferences in hydrocarbon configurations. various dihedral angle preferences in hydrocarbon configurations.
Only a single pair_coeff command is used with the {airebo} style which Only a single pair_coeff command is used with the {airebo} style which
specifies an AIREBO potential file with parameters for C and H. These specifies an AIREBO potential file with parameters for C and H. These

2
doc/pair_buck_coul.html
View File

@ -25,7 +25,7 @@
<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r <PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
<I>off</I> = omit the Coulombic term <I>off</I> = omit the Coulombic term
</PRE> </PRE>
<LI>cutoff = global cutoff for Buckingnham (and Coulombic if only 1 cutoff) (distance units) <LI>cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units) <LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
</UL> </UL>

2
doc/pair_buck_coul.txt
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@ -18,7 +18,7 @@ flag_buck = {long} or {cut} :ulb,l
flag_coul = {long} or {off} :l flag_coul = {long} or {off} :l
{long} = use Kspace long-range summation for the Coulombic term 1/r {long} = use Kspace long-range summation for the Coulombic term 1/r
{off} = omit the Coulombic term :pre {off} = omit the Coulombic term :pre
cutoff = global cutoff for Buckingnham (and Coulombic if only 1 cutoff) (distance units) :l cutoff = global cutoff for Buckingham (and Coulombic if only 1 cutoff) (distance units) :l
cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule cutoff2 = global cutoff for Coulombic (optional) (distance units) :l,ule
[Examples:] [Examples:]

2
doc/pair_coeff.html
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@ -105,7 +105,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM <LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM <LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential <LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertizain interactions <LI><A HREF = "pair_gran.html">pair_style gran/hertzian</A> - granular potential with Hertzian interactions
<LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects <LI><A HREF = "pair_gran.html">pair_style gran/history</A> - granular potential with history effects
<LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects <LI><A HREF = "pair_gran.html">pair_style gran/no_history</A> - granular potential without history effects
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb

2
doc/pair_coeff.txt
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@ -101,7 +101,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM "pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM "pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential "pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gran/hertzian"_pair_gran.html - granular potential with Hertizain interactions "pair_style gran/hertzian"_pair_gran.html - granular potential with Hertzian interactions
"pair_style gran/history"_pair_gran.html - granular potential with history effects "pair_style gran/history"_pair_gran.html - granular potential with history effects
"pair_style gran/no_history"_pair_gran.html - granular potential without history effects "pair_style gran/no_history"_pair_gran.html - granular potential without history effects
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb

2
doc/pair_colloid.html
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@ -109,7 +109,7 @@ sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5 solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diamter + 4 times the small diamter. I.e. 9 = 5 + 4 for the diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case. colloid-solvent cutoff in this case.
</P> </P>
<HR> <HR>

2
doc/pair_colloid.txt
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@ -106,7 +106,7 @@ sizes. E.g. if colloidal particles of diameter 10 are used with
solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5 solvent particles of diameter 1, then a solvent-solvent cutoff of 2.5
would correspond to a colloid-colloid cutoff of 25. A good would correspond to a colloid-colloid cutoff of 25. A good
rule-of-thumb is to use a colloid-solvent cutoff that is half the big rule-of-thumb is to use a colloid-solvent cutoff that is half the big
diamter + 4 times the small diamter. I.e. 9 = 5 + 4 for the diameter + 4 times the small diameter. I.e. 9 = 5 + 4 for the
colloid-solvent cutoff in this case. colloid-solvent cutoff in this case.
:line :line

6
doc/pair_eam.html
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@ -106,7 +106,7 @@ F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
LAMMPS be Cu atoms. Different single-element files can be assigned to LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYANMO code originally did it; you do not same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs. need to specify coefficients for these type pairs.
</P> </P>
<P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS <P><I>Funcfl</I> files in the <I>potentials</I> directory of the LAMMPS
@ -127,7 +127,7 @@ cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of Angstroms; I'm not sure of the units for drho - some measure of
electron density. electron density.
</P> </P>
<P>Following the 3 header lines are 3 arrays of tabulated values: <P>Following the three header lines are three arrays of tabulated values:
</P> </P>
<UL><LI>embedding function F(rho) (Nrho values) <UL><LI>embedding function F(rho) (Nrho values)
<LI>effective charge function Z(r) (Nr values) <LI>effective charge function Z(r) (Nr values)
@ -140,7 +140,7 @@ individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
<P>The units for the embedding function F are eV. The units for the <P>The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For 2 interacting atoms i,j this is used sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula expression as r*phi, in units of eV-Angstroms, via the formula
</P> </P>

6
doc/pair_eam.txt
View File

@ -98,7 +98,7 @@ F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
LAMMPS be Cu atoms. Different single-element files can be assigned to LAMMPS be Cu atoms. Different single-element files can be assigned to
different atom types to model an alloy system. The mixing to create different atom types to model an alloy system. The mixing to create
alloy potentials for type pairs with I != J is done automatically the alloy potentials for type pairs with I != J is done automatically the
same way that the serial DYANMO code originally did it; you do not same way that the serial DYNAMO code originally did it; you do not
need to specify coefficients for these type pairs. need to specify coefficients for these type pairs.
{Funcfl} files in the {potentials} directory of the LAMMPS {Funcfl} files in the {potentials} directory of the LAMMPS
@ -119,7 +119,7 @@ cutoff used by LAMMPS for the potential. The units of dr are
Angstroms; I'm not sure of the units for drho - some measure of Angstroms; I'm not sure of the units for drho - some measure of
electron density. electron density.
Following the 3 header lines are 3 arrays of tabulated values: Following the three header lines are three arrays of tabulated values:
embedding function F(rho) (Nrho values) embedding function F(rho) (Nrho values)
effective charge function Z(r) (Nr values) effective charge function Z(r) (Nr values)
@ -132,7 +132,7 @@ individual Z(r) values are for r = 0,dr,2*dr, ... (Nr-1)*dr.
The units for the embedding function F are eV. The units for the The units for the embedding function F are eV. The units for the
density function rho are the same as for drho (see above, electron density function rho are the same as for drho (see above, electron
density). The units for the effective charge Z are "atomic charge" or density). The units for the effective charge Z are "atomic charge" or
sqrt(Hartree * Bohr-radii). For 2 interacting atoms i,j this is used sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula expression as r*phi, in units of eV-Angstroms, via the formula

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