forked from lijiext/lammps
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This commit is contained in:
sjplimp
parent
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commit
1138cacffd
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@ -502,7 +502,7 @@ or create_box command.
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<DT><I>Cannot displace_box on a non-periodic boundary</I>
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<DD>Self-explantory.
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<DD>Self-explanatory.
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<DT><I>Cannot dump scaled coords with triclinic box</I>
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@ -2150,9 +2150,9 @@ or cause multiple files to be written.
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<DD>Filenames used with the dump xyz style cannot be binary or cause files
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to be written by each processor.
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<DT><I>Invalid dump_modify threshhold operator</I>
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<DT><I>Invalid dump_modify threshold operator</I>
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<DD>Operator keyword used for threshhold specification in not recognized.
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<DD>Operator keyword used for threshold specification in not recognized.
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<DT><I>Invalid fix ID in variable formula</I>
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@ -499,7 +499,7 @@ or create_box command. :dd
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{Cannot displace_box on a non-periodic boundary} :dt
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Self-explantory. :dd
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Self-explanatory. :dd
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{Cannot dump scaled coords with triclinic box} :dt
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@ -2147,9 +2147,9 @@ or cause multiple files to be written. :dd
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Filenames used with the dump xyz style cannot be binary or cause files
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to be written by each processor. :dd
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{Invalid dump_modify threshhold operator} :dt
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{Invalid dump_modify threshold operator} :dt
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Operator keyword used for threshhold specification in not recognized. :dd
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Operator keyword used for threshold specification in not recognized. :dd
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{Invalid fix ID in variable formula} :dt
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@ -35,7 +35,7 @@ Site</A>.
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<TR><TD >crack</TD><TD > crack propagation in a 2d solid</TD></TR>
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<TR><TD >dipole</TD><TD > point dipolar particles, 2d system</TD></TR>
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<TR><TD >ellipse</TD><TD > ellipsoidal particles in spherical solvent, 2d system</TD></TR>
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<TR><TD >flow</TD><TD > Couette and Poisseuille flow in a 2d channel</TD></TR>
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<TR><TD >flow</TD><TD > Couette and Poiseuille flow in a 2d channel</TD></TR>
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<TR><TD >friction</TD><TD > frictional contact of spherical asperities between 2d surfaces</TD></TR>
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<TR><TD >indent</TD><TD > spherical indenter into a 2d solid</TD></TR>
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<TR><TD >meam</TD><TD > MEAM test for SiC and shear (same as shear examples)</TD></TR>
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@ -31,7 +31,7 @@ colloid: big colloid particles in a small particle solvent, 2d system
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crack: crack propagation in a 2d solid
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dipole: point dipolar particles, 2d system
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poisseuille flow in a 2d channel
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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indent: spherical indenter into a 2d solid
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meam: MEAM test for SiC and shear (same as shear examples)
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@ -556,17 +556,17 @@ functions:
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<PRE>void lammps_open(int, char **, MPI_Comm, void **);
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void lammps_close(void *);
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void lammps_file(void *, char *);
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char *lammps_command(doivd *, char *);
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char *lammps_command(void *, char *);
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</PRE>
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<P>The functions contain C++ code you could write in a C++ application
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that was invoking LAMMPS directly. Note that LAMMPS classes are
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defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
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defined within a LAMMPS namespace (LAMMPS_NS) if you use them
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from another C++ application.
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</P>
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<P>Two of the routines in library.cpp are of particular note. The
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lammps_open() function initiates LAMMPS and takes an MPI communicator
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as an argument. It returns a pointer to a LAMMPS "object". As with
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C++, the lammps_open() function can be called mutliple times, to
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C++, the lammps_open() function can be called multiple times, to
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create multiple instances of LAMMPS.
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</P>
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<P>LAMMPS will run on the set of processors in the communicator. This
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@ -604,7 +604,7 @@ create files in several formats. The native LAMMPS dump format is a
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text file (see "dump atom" or "dump custom") which can be visualized
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by the <A HREF = "Section_tools.html#xmovie">xmovie</A> program, included with the
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LAMMPS package. This produces simple, fast 2d projections of 3d
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systems, and can be useful for rapid debugging of simulation geoemtry
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systems, and can be useful for rapid debugging of simulation geometry
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and atom trajectories.
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</P>
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<P>Several programs included with LAMMPS as auxiliary tools can convert
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@ -613,7 +613,7 @@ native LAMMPS dump files to other formats. See the
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the <A HREF = "Section_tools.html#charmm">ch2lmp tool</A>, which contains a
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lammps2pdb Perl script which converts LAMMPS dump files into PDB
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files. The second is the <A HREF = "Section_tools.html#arc">lmp2arc tool</A> which
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converts LAMMPS dump files into Accelrys's Insight MD program files.
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converts LAMMPS dump files into Accelrys' Insight MD program files.
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The third is the <A HREF = "Section_tools.html#cfg">lmp2cfg tool</A> which converts
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LAMMPS dump files into CFG files which can be read into the
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<A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A> visualizer.
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@ -723,9 +723,9 @@ the xy, xz, and yz tilt factors as a simulation runs.
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<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
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used to measure a fluid's rheological properties such as viscosity.
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In LAMMPS, such simulations can be performed by first setting up a
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non-orthogonal simulation box (see the preceeding Howto section).
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non-orthogonal simulation box (see the preceding Howto section).
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</P>
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<P>A shear strain can be applied to the simuaation box at a desired
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<P>A shear strain can be applied to the simulation box at a desired
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strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
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<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
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the sheared fluid and integrate the SLLOD equations of motion for the
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@ -765,7 +765,7 @@ The <A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used t
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define a Gay-Berne (GB) potential for how ellipsoidal particles
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interact with each other and with spherical particles. The GB
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potential is like a Lennard-Jones (LJ) potential, generalized for
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orientiation-dependent interactions.
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orientation-dependent interactions.
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</P>
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<P>The orientation of ellipsoidal particles is stored as a quaternion.
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See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions
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@ -821,9 +821,9 @@ generate values that can be output with these commands.
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<P>The frequency and format of thermodynamic output is set by the
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<A HREF = "thermo.html">thermo</A>, <A HREF = "thermo_style.html">thermo_style</A>, and
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<A HREF = "thermo_modify.html">thermo_modify</A> commands. The
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<A HREF = "themo_style.html">thermo_style</A> command also specifies what values are
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<A HREF = "thermo_style.html">thermo_style</A> command also specifies what values are
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calculated and written out. Pre-defined keywords can be specified
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(e.g. press, etotal, etc). Three addtional kinds of keywords can also
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(e.g. press, etotal, etc). Three additional kinds of keywords can also
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be specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or
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<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the value to be
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output. Each of these are described in turn.
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@ -948,7 +948,7 @@ options for how it performs time averaging. The per-layer values it
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produces can be used in two ways. First, they can be written directly
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to a file. Note that the averaging parameters can be specified in
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such a way that time averaging is not done, in which case this is a
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convenient means of simply outputting desired quanitities (summed over
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convenient means of simply outputting desired quantities (summed over
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atoms within a 1d layer) directly to a separate file. Like other
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fixes that produce global quantities, the results of this fix can also
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be used as input by any command that accesses global quantities,
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|
|
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@ -552,17 +552,17 @@ functions:
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void lammps_open(int, char **, MPI_Comm, void **);
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void lammps_close(void *);
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void lammps_file(void *, char *);
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char *lammps_command(doivd *, char *); :pre
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char *lammps_command(void *, char *); :pre
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The functions contain C++ code you could write in a C++ application
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that was invoking LAMMPS directly. Note that LAMMPS classes are
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defined wihin a LAMMPS namespace (LAMMPS_NS) if you use them
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defined within a LAMMPS namespace (LAMMPS_NS) if you use them
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from another C++ application.
|
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Two of the routines in library.cpp are of particular note. The
|
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lammps_open() function initiates LAMMPS and takes an MPI communicator
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as an argument. It returns a pointer to a LAMMPS "object". As with
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C++, the lammps_open() function can be called mutliple times, to
|
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C++, the lammps_open() function can be called multiple times, to
|
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create multiple instances of LAMMPS.
|
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LAMMPS will run on the set of processors in the communicator. This
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|
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@ -600,7 +600,7 @@ create files in several formats. The native LAMMPS dump format is a
|
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text file (see "dump atom" or "dump custom") which can be visualized
|
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by the "xmovie"_Section_tools.html#xmovie program, included with the
|
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LAMMPS package. This produces simple, fast 2d projections of 3d
|
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systems, and can be useful for rapid debugging of simulation geoemtry
|
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systems, and can be useful for rapid debugging of simulation geometry
|
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and atom trajectories.
|
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|
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Several programs included with LAMMPS as auxiliary tools can convert
|
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|
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@ -609,7 +609,7 @@ native LAMMPS dump files to other formats. See the
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the "ch2lmp tool"_Section_tools.html#charmm, which contains a
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lammps2pdb Perl script which converts LAMMPS dump files into PDB
|
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files. The second is the "lmp2arc tool"_Section_tools.html#arc which
|
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converts LAMMPS dump files into Accelrys's Insight MD program files.
|
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converts LAMMPS dump files into Accelrys' Insight MD program files.
|
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The third is the "lmp2cfg tool"_Section_tools.html#cfg which converts
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LAMMPS dump files into CFG files which can be read into the
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"AtomEye"_atomeye visualizer.
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|
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@ -716,9 +716,9 @@ Another use of non-orthogonal boxes is to perform non-equilibrium MD
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Non-equilibrium molecular dynamics or NEMD simulations are typically
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used to measure a fluid's rheological properties such as viscosity.
|
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In LAMMPS, such simulations can be performed by first setting up a
|
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non-orthogonal simulation box (see the preceeding Howto section).
|
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non-orthogonal simulation box (see the preceding Howto section).
|
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|
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A shear strain can be applied to the simuaation box at a desired
|
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A shear strain can be applied to the simulation box at a desired
|
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strain rate by using the "fix deform"_fix_deform.html command. The
|
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"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
|
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the sheared fluid and integrate the SLLOD equations of motion for the
|
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|
|
@ -758,7 +758,7 @@ The "pair_style gayberne"_pair_gayberne.html command can be used to
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define a Gay-Berne (GB) potential for how ellipsoidal particles
|
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interact with each other and with spherical particles. The GB
|
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potential is like a Lennard-Jones (LJ) potential, generalized for
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orientiation-dependent interactions.
|
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orientation-dependent interactions.
|
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The orientation of ellipsoidal particles is stored as a quaternion.
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See the "set"_set.html command for a brief explanation of quaternions
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@ -814,9 +814,9 @@ Thermodynamic output :h5
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The frequency and format of thermodynamic output is set by the
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"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
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"thermo_modify"_thermo_modify.html commands. The
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"thermo_style"_themo_style.html command also specifies what values are
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"thermo_style"_thermo_style.html command also specifies what values are
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calculated and written out. Pre-defined keywords can be specified
|
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(e.g. press, etotal, etc). Three addtional kinds of keywords can also
|
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(e.g. press, etotal, etc). Three additional kinds of keywords can also
|
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be specified (c_ID, f_ID, v_name), where a "compute"_compute.html or
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"fix"_fix.html or "variable"_variable.html provides the value to be
|
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output. Each of these are described in turn.
|
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|
|
@ -941,7 +941,7 @@ options for how it performs time averaging. The per-layer values it
|
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produces can be used in two ways. First, they can be written directly
|
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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
|
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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
|
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fixes that produce global quantities, the results of this fix can also
|
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be used as input by any command that accesses global quantities,
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|
|
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@ -180,7 +180,7 @@ commands)
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</H4>
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<P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands)
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</P>
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<UL><LI> log file of thermodynanmic info
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<UL><LI> log file of thermodynamic info
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<LI> text dump files of atom coords, velocities, other per-atom quantities
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<LI> binary restart files
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<LI> per-atom quantities (energy, stress, centro-symmetry parameter, etc)
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@ -507,11 +507,11 @@ the list.
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<TR><TD >radial distribution functions</TD><TD > Paul Crozier & Jeff Greathouse (Sandia)</TD></TR>
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<TR><TD >force tables for long-range Coulombics</TD><TD > Paul Crozier (Sandia)</TD></TR>
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<TR><TD >targeted molecular dynamics (TMD)</TD><TD > Paul Crozier (Sandia) and Christian Burisch (Bochum University, Germany)</TD></TR>
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<TR><TD >FFT support for SGI SCLS (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
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<TR><TD >FFT support for SGI SCSL (Altix)</TD><TD > Jim Shepherd (Ga Tech)</TD></TR>
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<TR><TD >lmp2cfg and lmp2traj tools</TD><TD > Ara Kooser, Jeff Greathouse, Andrey Kalinichev (Sandia)</TD></TR>
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<TR><TD >parallel tempering</TD><TD > Mark Sears (Sandia)</TD></TR>
|
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<TR><TD >embedded atom method (EAM) potential</TD><TD > Stephen Foiles (Sandia)</TD></TR>
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<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Putz (Sandia)</TD></TR>
|
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<TR><TD >multi-harmonic dihedral potential</TD><TD > Mathias Puetz (Sandia)</TD></TR>
|
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<TR><TD >granular force fields and BC</TD><TD > Leo Silbert & Gary Grest (Sandia)</TD></TR>
|
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<TR><TD >2d Ewald/PPPM</TD><TD > Paul Crozier (Sandia)</TD></TR>
|
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<TR><TD >CHARMM force fields</TD><TD > Paul Crozier (Sandia)</TD></TR>
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|
|
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@ -178,7 +178,7 @@ Integrators: :h4
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Output: :h4
|
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("dump"_dump.html, "restart"_restart.html commands)
|
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|
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log file of thermodynanmic info
|
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log file of thermodynamic info
|
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text dump files of atom coords, velocities, other per-atom quantities
|
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binary restart files
|
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per-atom quantities (energy, stress, centro-symmetry parameter, etc)
|
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|
|
@ -504,12 +504,12 @@ radial distribution functions: Paul Crozier & Jeff Greathouse (Sandia)
|
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force tables for long-range Coulombics: Paul Crozier (Sandia)
|
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targeted molecular dynamics (TMD): Paul Crozier (Sandia) and \
|
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Christian Burisch (Bochum University, Germany)
|
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FFT support for SGI SCLS (Altix): Jim Shepherd (Ga Tech)
|
||||
FFT support for SGI SCSL (Altix): Jim Shepherd (Ga Tech)
|
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lmp2cfg and lmp2traj tools: Ara Kooser, Jeff Greathouse, \
|
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Andrey Kalinichev (Sandia)
|
||||
parallel tempering: Mark Sears (Sandia)
|
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embedded atom method (EAM) potential: Stephen Foiles (Sandia)
|
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multi-harmonic dihedral potential: Mathias Putz (Sandia)
|
||||
multi-harmonic dihedral potential: Mathias Puetz (Sandia)
|
||||
granular force fields and BC: Leo Silbert & Gary Grest (Sandia)
|
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2d Ewald/PPPM: Paul Crozier (Sandia)
|
||||
CHARMM force fields: Paul Crozier (Sandia)
|
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|
|
|
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|
|
@ -88,7 +88,7 @@ in the LAMMPS distribution.
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<LI><A HREF = "#bond">Bond, angle, dihedral, improper potentials</A>
|
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<LI><A HREF = "#compute">Compute styles</A>
|
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<LI><A HREF = "#dump">Dump styles</A>
|
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<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
|
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<LI><A HREF = "#command">Input script commands</A>
|
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<LI><A HREF = "#kspace">Kspace computations</A>
|
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|
|
@ -373,7 +373,7 @@ needed.
|
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<A NAME = "kspace"></A><H4>Kspace computations
|
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</H4>
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<P>Classes that compute long-range Coulombic interactions via K-space
|
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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.
|
||||
</P>
|
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<P>Ewald.cpp is an example of computing K-space interactions.
|
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|
|
@ -469,7 +469,7 @@ thermodynamic info is output. See the
|
|||
quantities.
|
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</P>
|
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<P>The thermo styles (one, multi, etc) are simply lists of keywords.
|
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Adding a new style thus only requies defining a new list of keywords.
|
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Adding a new style thus only requires defining a new list of keywords.
|
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Search for the word "customize" with references to "thermo style" in
|
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thermo.cpp to see the two locations where code will need to be added.
|
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</P>
|
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|
|
@ -503,7 +503,7 @@ group functions = mass(group), xcm(group,x), ...
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atom values = x<B>123</B>, y<B>3</B>, vx<B>34</B>, ...
|
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compute values = c_mytemp<B>0</B>, c_thermo_press<B>3</B>, ...
|
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</P>
|
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<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
|
||||
<A HREF = "Section_modify.html#thermo">here</A> on this page.
|
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</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
|
||||
example of how to do this.
|
||||
</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
|
||||
feature.
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -85,7 +85,7 @@ in the LAMMPS distribution.
|
|||
"Bond, angle, dihedral, improper potentials"_#bond
|
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"Compute styles"_#compute
|
||||
"Dump styles"_#dump
|
||||
"Dump custom output optoins"_#dump
|
||||
"Dump custom output options"_#dump
|
||||
"Fix styles"_#fix which include integrators, \
|
||||
temperature and pressure control, force constraints, \
|
||||
boundary conditions, diagnostic output, etc
|
||||
|
|
@ -358,7 +358,7 @@ needed.
|
|||
Kspace computations :link(kspace),h4
|
||||
|
||||
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.
|
||||
|
||||
Ewald.cpp is an example of computing K-space interactions.
|
||||
|
|
@ -446,7 +446,7 @@ thermodynamic info is output. See the
|
|||
quantities.
|
||||
|
||||
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
|
||||
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], ...
|
||||
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
|
||||
"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
|
||||
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
|
||||
feature.
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
|
||||
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
|
||||
files available. See the Restrictions section of the <A HREF = "dump.html">dump</A>
|
||||
command for details.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
FFTs (in the PPPM solver) on some platforms. The -DPACK_ARRAY setting
|
||||
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
|
||||
files available. See the Restrictions section of the "dump"_dump.html
|
||||
command for details.
|
||||
|
|
|
|||
|
|
@ -153,8 +153,8 @@ produce are in the potentials directory.
|
|||
<H4><A NAME = "arc"></A>lmp2arc tool
|
||||
</H4>
|
||||
<P>The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys's Insight MD code (formerly
|
||||
MSI/Biosysm and its Discover MD code). See the README file for more
|
||||
files to the format for Accelrys' Insight MD code (formerly
|
||||
MSI/Biosym and its Discover MD code). See the README file for more
|
||||
information.
|
||||
</P>
|
||||
<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>
|
||||
<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.
|
||||
</P>
|
||||
<P>This tool was written by John Carpenter (Cray), Michael Peachey
|
||||
|
|
|
|||
|
|
@ -149,8 +149,8 @@ The source files and potentials were provided by Gerolf Ziegenhain
|
|||
lmp2arc tool :h4,link(arc)
|
||||
|
||||
The lmp2arc sub-directory contains a tool for converting LAMMPS output
|
||||
files to the format for Accelrys's Insight MD code (formerly
|
||||
MSI/Biosysm and its Discover MD code). See the README file for more
|
||||
files to the format for Accelrys' Insight MD code (formerly
|
||||
MSI/Biosym and its Discover MD code). See the README file for more
|
||||
information.
|
||||
|
||||
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)
|
||||
|
||||
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.
|
||||
|
||||
This tool was written by John Carpenter (Cray), Michael Peachey
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
</P>
|
||||
<PRE>angle_coeff N args
|
||||
</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
|
||||
</UL>
|
||||
<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
|
||||
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,
|
||||
then an asterik 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 means all types from n to N (inclusive). A middle asterisk
|
||||
then an asterisk with no numeric values means all types from 1 to N. A
|
||||
leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
</P>
|
||||
<P>Note that using an angle_coeff command can override a previous setting
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ angle_coeff command :h3
|
|||
|
||||
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
|
||||
|
||||
[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
|
||||
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,
|
||||
then an asterik 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 means all types from n to N (inclusive). A middle asterisk
|
||||
then an asterisk with no numeric values means all types from 1 to N. A
|
||||
leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
|
||||
Note that using an angle_coeff command can override a previous setting
|
||||
|
|
|
|||
|
|
@ -51,7 +51,7 @@ you will need to choose them carefully so they form a suitable bond
|
|||
potential.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ you will need to choose them carefully so they form a suitable bond
|
|||
potential.
|
||||
|
||||
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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -52,7 +52,7 @@ orthogonal box.
|
|||
ave/spatial</A> or <A HREF = "fix_deform.html">fix deform</A> be
|
||||
active. This is because these commands test whether the simulation
|
||||
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>
|
||||
command is also used to turn them off.
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
active. This is because these commands test whether the simulation
|
||||
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
|
||||
command is also used to turn them off.
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
via the <A HREF = "compute_reduce.html">compute reduce</A> command.
|
||||
</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
|
||||
potential energy is the sum of pair, bond, angle, dihedral, improper,
|
||||
and kspace (long-range) energy. If any extra keywords are listed,
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
potential energy is the sum of pair, bond, angle, dihedral, improper,
|
||||
and kspace (long-range) energy. If any extra keywords are listed,
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ and long-range interactions. <A HREF = "fix.html">Fixes</A> that impose constra
|
|||
virial term.
|
||||
</P>
|
||||
<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
|
||||
<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
|
||||
|
|
@ -95,7 +95,7 @@ the simulation.
|
|||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_stress_atom.html">compute
|
||||
stress/atom</A>,
|
||||
<A HREF = "themo_style.html">thermo_style</A>,
|
||||
<A HREF = "thermo_style.html">thermo_style</A>,
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -45,7 +45,7 @@ and long-range interactions. "Fixes"_fix.html that impose constraints
|
|||
virial term.
|
||||
|
||||
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
|
||||
"compute"_compute.html and "fix"_fix.html commands. The equation for
|
||||
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
|
||||
stress/atom"_compute_stress_atom.html,
|
||||
"thermo_style"_themo_style.html,
|
||||
"thermo_style"_thermo_style.html,
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -28,7 +28,7 @@ compute myTemp mobile temp/dipole
|
|||
<P>Define a computation that calculates the temperature of a group of
|
||||
particles that include a point dipole. The computation is similar to
|
||||
<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
|
||||
KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is
|
||||
the angular velocity.
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ compute myTemp mobile temp/dipole :pre
|
|||
Define a computation that calculates the temperature of a group of
|
||||
particles that include a point dipole. The computation is similar to
|
||||
"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
|
||||
KE_rotational = 1/2 I w^2, where I is the moment of inertia and w is
|
||||
the angular velocity.
|
||||
|
|
|
|||
|
|
@ -87,7 +87,7 @@ styles and values.
|
|||
</P>
|
||||
<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.
|
||||
See the discsussion of the units keyword below.
|
||||
See the discussion of the units keyword below.
|
||||
</P>
|
||||
<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
|
||||
|
|
@ -134,7 +134,7 @@ units keyword below.
|
|||
</P>
|
||||
<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
|
||||
the discsussion of the units keyword below.
|
||||
the discussion of the units keyword below.
|
||||
</P>
|
||||
<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
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ styles and values.
|
|||
|
||||
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.
|
||||
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
|
||||
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
|
||||
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,
|
||||
tilt factors (xy,xz,yz) for triclinic boxes are always bounded by half
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@
|
|||
attribute = same attributes (x,fy,etotal,sxx,etc) used by dump custom style
|
||||
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
|
||||
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>
|
||||
|
||||
|
|
@ -105,15 +105,15 @@ shape, and it can be the "union" or "intersection" of a series of
|
|||
simpler regions.
|
||||
</P>
|
||||
<P>The <I>thresh</I> keyword only applies to the dump <I>custom</I> style.
|
||||
Multiple threshholds can be specified. Specifying "none" turns off
|
||||
all threshhold criteria. If theshholds are specified, only atoms
|
||||
whose attributes meet all the threshhold criteria are written to the
|
||||
Multiple thresholds can be specified. Specifying "none" turns off
|
||||
all threshold criteria. If thresholds are specified, only atoms
|
||||
whose attributes meet all the threshold criteria are written to 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>
|
||||
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
|
||||
whose energy is above some threshhold.
|
||||
whose energy is above some threshold.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
operation = "<" or "<=" or ">" or ">=" or "==" or "!="
|
||||
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
|
||||
:ule
|
||||
|
||||
|
|
@ -98,15 +98,15 @@ shape, and it can be the "union" or "intersection" of a series of
|
|||
simpler regions.
|
||||
|
||||
The {thresh} keyword only applies to the dump {custom} style.
|
||||
Multiple threshholds can be specified. Specifying "none" turns off
|
||||
all threshhold criteria. If theshholds are specified, only atoms
|
||||
whose attributes meet all the threshhold criteria are written to the
|
||||
Multiple thresholds can be specified. Specifying "none" turns off
|
||||
all threshold criteria. If thresholds are specified, only atoms
|
||||
whose attributes meet all the threshold criteria are written to 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
|
||||
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
|
||||
whose energy is above some threshhold.
|
||||
whose energy is above some threshold.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@
|
|||
filename = file to write results to
|
||||
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
|
||||
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>
|
||||
|
||||
|
|
@ -99,13 +99,13 @@ produce global quantities.
|
|||
timesteps the layer values will be generated in order to contribute to
|
||||
the average. The final averaged quantities are generated every
|
||||
<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
|
||||
even if <I>Nrepeat</I> is 1.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
averaging is done; values are simply generated on timesteps
|
||||
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
|
||||
and the per-atom property is calculated for the first time, the number
|
||||
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
|
||||
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
|
||||
|
|
@ -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
|
||||
another output command or written to a file.
|
||||
</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;
|
||||
they are output as-is without further averaging.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
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
|
||||
via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ keyword = {norm} or {units} or {file} or {ave} :l
|
|||
filename = file to write results to
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
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
|
||||
: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
|
||||
the average. The final averaged quantities are generated every
|
||||
{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
|
||||
even if {Nrepeat} is 1.
|
||||
|
||||
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
|
||||
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
|
||||
averaging is done; values are simply generated on timesteps
|
||||
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
|
||||
and the per-atom property is calculated for the first time, the number
|
||||
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
|
||||
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
|
||||
|
|
@ -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
|
||||
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;
|
||||
they are output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the layer values produced on
|
||||
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
|
||||
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
|
||||
via the "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@
|
|||
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>
|
||||
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>
|
||||
|
||||
|
|
@ -94,13 +94,13 @@ since they produce per-atom values.
|
|||
timesteps the values will be generated in order to contribute to the
|
||||
average. The final averaged quantities are generated every <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.
|
||||
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
|
||||
even if <I>Nrepeat</I> is 1.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
averaging is done; values are simply generated on timesteps
|
||||
100,200,etc.
|
||||
|
|
@ -158,8 +158,8 @@ output as-is without further averaging.
|
|||
</P>
|
||||
<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
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value produced on that timestep with all preceeding
|
||||
cumulative sense before being output. Each output value is thus the
|
||||
average of the value produced on that timestep with all preceding
|
||||
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>
|
||||
command, or by re-defining the fix by re-specifying it.
|
||||
|
|
|
|||
|
|
@ -31,7 +31,7 @@ keyword = {file} or {ave} :l
|
|||
filename = name of file to output time averages to
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
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
|
||||
: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
|
||||
average. The final averaged quantities are generated every {Nfreq}
|
||||
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
|
||||
even if {Nrepeat} is 1.
|
||||
|
||||
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
|
||||
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
|
||||
averaging is done; values are simply generated on timesteps
|
||||
100,200,etc.
|
||||
|
|
@ -145,8 +145,8 @@ output as-is without further averaging.
|
|||
|
||||
If the {ave} setting is {running}, then the values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value produced on that timestep with all preceeding
|
||||
cumulative sense before being output. Each output value is thus the
|
||||
average of the value produced on that timestep with all preceding
|
||||
values. This running average begins when the fix is defined; it can
|
||||
only be restarted by deleting the fix via the "unfix"_unfix.html
|
||||
command, or by re-defining the fix by re-specifying it.
|
||||
|
|
|
|||
|
|
@ -126,7 +126,7 @@ value.
|
|||
</P>
|
||||
<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.
|
||||
See the discsussion of the units keyword below.
|
||||
See the discussion of the units keyword below.
|
||||
</P>
|
||||
<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
|
||||
|
|
@ -233,13 +233,13 @@ units keyword below.
|
|||
</P>
|
||||
<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
|
||||
the discsussion of the units keyword below.
|
||||
the discussion of the units keyword below.
|
||||
</P>
|
||||
<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
|
||||
"engineering shear strain rate", where rate = V/L0 and L0 is 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
|
||||
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
|
||||
|
|
@ -304,7 +304,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
|||
... are all equivalent.
|
||||
</P>
|
||||
<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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -116,7 +116,7 @@ value.
|
|||
|
||||
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.
|
||||
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
|
||||
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
|
||||
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
|
||||
specified in units of distance/time. This is effectively an
|
||||
"engineering shear strain rate", where rate = V/L0 and L0 is 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
|
||||
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
|
||||
|
|
@ -294,7 +294,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
|||
... are all equivalent.
|
||||
|
||||
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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@ normalizing factor each time temperature is computed.
|
|||
</P>
|
||||
<P>Care must be taken that inserted particles are not too near existing
|
||||
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
|
||||
escaping the surface and flying upward should be considered, since the
|
||||
particle may be lost or the box size may grow infinitely large. A
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ normalizing factor each time temperature is computed.
|
|||
|
||||
Care must be taken that inserted particles are not too near existing
|
||||
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
|
||||
escaping the surface and flying upward should be considered, since the
|
||||
particle may be lost or the box size may grow infinitely large. A
|
||||
|
|
|
|||
|
|
@ -68,7 +68,7 @@ files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|||
are relevant to this fix.
|
||||
</P>
|
||||
<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
|
||||
<A HREF = "Section_howto.html#4_15">output commands</A>. The scalar and vector
|
||||
values calculated by this fix are "intensive", meaning they are
|
||||
|
|
@ -80,7 +80,7 @@ minimization</A>.
|
|||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</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
|
||||
<A HREF = "reset_timestep.html">reset_timestep</A> command while this fix is defined
|
||||
will mess up the time accumulation.
|
||||
|
|
|
|||
|
|
@ -64,7 +64,7 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
|||
are relevant to 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
|
||||
"output commands"_Section_howto.html#4_15. The scalar and vector
|
||||
values calculated by this fix are "intensive", meaning they are
|
||||
|
|
@ -76,7 +76,7 @@ minimization"_minimize.html.
|
|||
|
||||
[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
|
||||
"reset_timestep"_reset_timestep.html command while this fix is defined
|
||||
will mess up the time accumulation.
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
term acting on the macroscopic particles. More generally, it can
|
||||
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
|
||||
adds the same force to each atom, independent of its mass. This
|
||||
command imparts the same acceleration to each atom (force/mass).
|
||||
|
|
|
|||
|
|
@ -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"
|
||||
term acting on the macroscopic particles. More generally, it can
|
||||
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
|
||||
adds the same force to each atom, independent of its mass. This
|
||||
command imparts the same acceleration to each atom (force/mass).
|
||||
|
|
|
|||
|
|
@ -67,7 +67,7 @@ user.
|
|||
</P>
|
||||
<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
|
||||
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
|
||||
timestep size, and damp is the damping factor. Random numbers are
|
||||
used to randomize the direction and magnitude of this force as
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ user.
|
|||
|
||||
Fr is a force due to solvent atoms at a temperature T randomly bumping
|
||||
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
|
||||
timestep size, and damp is the damping factor. Random numbers are
|
||||
used to randomize the direction and magnitude of this force as
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ default method for computing P.
|
|||
</P>
|
||||
<P>For fixes that calculate a contribution to the potential energy of the
|
||||
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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ default method for computing P.
|
|||
|
||||
For fixes that calculate a contribution to the potential energy of the
|
||||
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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> or
|
||||
<I>thermo_press</I> will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} or
|
||||
{thermo_press} will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> or
|
||||
<I>thermo_press</I> will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} or
|
||||
{thermo_press} will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> or
|
||||
<I>thermo_press</I> will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix's temperature or pressure via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} or
|
||||
{thermo_press} will have no effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
affected, except that updates occur at both the beginning and end of 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
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
affected, except that updates occur at both the beginning and end of 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
|
||||
various "output commands"_Section_howto.html#4_15. The scalar value
|
||||
calculated by this fix is "extensive", meaning it scales with the
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
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
|
||||
(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
|
||||
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
|
||||
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>The derivative of this energy expression gives the force on each atom
|
||||
which thus depends on the orientation of its neighbors relative to the
|
||||
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.
|
||||
</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
|
||||
it is possible two different neighbors will use the same reference
|
||||
vector. In such cases, the atom in question is far from a perfect
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
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
|
||||
(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
|
||||
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
|
||||
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
|
||||
which thus depends on the orientation of its neighbors relative to the
|
||||
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.
|
||||
|
||||
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
|
||||
it is possible two different neighbors will use the same reference
|
||||
vector. In such cases, the atom in question is far from a perfect
|
||||
|
|
|
|||
|
|
@ -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).
|
||||
</P>
|
||||
<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.
|
||||
</P>
|
||||
<P>For option <I>group</I>, each of the listed groups is treated as a rigid
|
||||
|
|
|
|||
|
|
@ -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).
|
||||
|
||||
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.
|
||||
|
||||
For option {group}, each of the listed groups is treated as a rigid
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix print line is output. Equal-style variables calculate formulas
|
||||
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 = "variable.html">variables</A>.
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
fix print line is output. Equal-style variables calculate formulas
|
||||
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
|
||||
"variables"_variable.html.
|
||||
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@
|
|||
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
||||
<LI>rdf = style name of this fix command
|
||||
<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>itypeN = central atom type for RDF pair N
|
||||
<LI>jtypeN = distribution atom type for RDF pair N
|
||||
|
|
|
|||
|
|
@ -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
|
||||
rdf = style name of this fix command
|
||||
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
|
||||
itypeN = central atom type for RDF pair N
|
||||
jtypeN = distribution atom type for RDF pair N :ul
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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
|
||||
chain.
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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
|
||||
chain.
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
<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.
|
||||
It also means that changing attributes of <I>thermo_temp</I> will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
(e.g. its degrees-of-freedom) via the
|
||||
"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.
|
||||
It also means that changing attributes of {thermo_temp} will have no
|
||||
effect on this fix.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
yields a momentum flux. The ratio of momentum flux to the slope of
|
||||
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.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
|
||||
|
|
@ -73,7 +73,7 @@ the Nevery parameter.
|
|||
</P>
|
||||
<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
|
||||
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
|
||||
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
|
||||
|
|
@ -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
|
||||
are relevant to this fix.
|
||||
</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
|
||||
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
|
||||
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
|
||||
|
|
@ -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.
|
||||
</P>
|
||||
<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.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
yields a momentum flux. The ratio of momentum flux to the slope of
|
||||
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.
|
||||
|
||||
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
|
||||
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
|
||||
system using a "PPPM solver"_kspace_style.html since PPPM does not
|
||||
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
|
||||
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
|
||||
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
|
||||
by various "output commands"_Section_howto.html#4_15, such as
|
||||
"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.
|
||||
|
||||
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.
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -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
|
||||
times to adjust gamma for several atom types.
|
||||
</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
|
||||
diffusion coefficient. D can be written as kT / (6 pi eta d), where
|
||||
eta = viscosity of the frictional fluid and d = diameter of particle.
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
diffusion coefficient. D can be written as kT / (6 pi eta d), where
|
||||
eta = viscosity of the frictional fluid and d = diameter of particle.
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
</P>
|
||||
<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>
|
||||
<UL><LI>K (energy/radian^2)
|
||||
<LI>X0 (degrees)
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
||||
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)
|
||||
X0 (degrees) :ul
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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"
|
||||
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.
|
||||
</P>
|
||||
<PRE>variable a loop 10
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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"
|
||||
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.
|
||||
|
||||
variable a loop 10
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
script as discussed in the "jump"_jump.html commmand.
|
||||
script as discussed in the "jump"_jump.html command.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ either 2d or 3d problems.
|
|||
cell, and a set of transformation parameters (scale, origin, orient)
|
||||
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
|
||||
"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
|
||||
minimum volume.
|
||||
</P>
|
||||
|
|
@ -191,7 +191,7 @@ in the min/max of the y and z coordinates.
|
|||
</P>
|
||||
<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
|
||||
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
|
||||
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
|
||||
3*sqrt(3.0) in y.
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
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
|
||||
"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
|
||||
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
|
||||
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
|
||||
factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
|
||||
3*sqrt(3.0) in y.
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
</P>
|
||||
<PRE>mass I value
|
||||
</PRE>
|
||||
<UL><LI>I = atom type (see asterik form below)
|
||||
<UL><LI>I = atom type (see asterisk form below)
|
||||
<LI>value = mass
|
||||
</UL>
|
||||
<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
|
||||
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
|
||||
asterik 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
|
||||
means all types from n to N (inclusive). A middle asterik means all
|
||||
asterisk with no numeric values means all types from 1 to N. A leading
|
||||
asterisk means all types from 1 to n (inclusive). A trailing asterisk
|
||||
means all types from n to N (inclusive). A middle asterisk means all
|
||||
types from m to n (inclusive).
|
||||
</P>
|
||||
<P>A line in a data file that specifies mass uses the same format as the
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ mass command :h3
|
|||
|
||||
mass I value :pre
|
||||
|
||||
I = atom type (see asterik form below)
|
||||
I = atom type (see asterisk form below)
|
||||
value = mass :ul
|
||||
|
||||
[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
|
||||
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
|
||||
asterik 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
|
||||
means all types from n to N (inclusive). A middle asterik means all
|
||||
asterisk with no numeric values means all types from 1 to N. A leading
|
||||
asterisk means all types from 1 to n (inclusive). A trailing asterisk
|
||||
means all types from n to N (inclusive). A middle asterisk means all
|
||||
types from m to n (inclusive).
|
||||
|
||||
A line in a data file that specifies mass uses the same format as the
|
||||
|
|
|
|||
|
|
@ -37,7 +37,7 @@ min_modify lineiter 5
|
|||
</P>
|
||||
<P>This command sets parameters that affect the minimization algorithms.
|
||||
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.
|
||||
</P>
|
||||
<P>The <I>linestyle</I> sets the algorithm used for 1d line searches at each
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ min_modify lineiter 5 :pre
|
|||
|
||||
This command sets parameters that affect the minimization algorithms.
|
||||
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.
|
||||
|
||||
The {linestyle} sets the algorithm used for 1d line searches at each
|
||||
|
|
|
|||
|
|
@ -103,7 +103,7 @@ contribute to the potential energy which is probably not what is
|
|||
desired.
|
||||
</P>
|
||||
<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
|
||||
(i.e. allow the box dimensions to change), but this has not yet been
|
||||
implemented.
|
||||
|
|
|
|||
|
|
@ -100,7 +100,7 @@ contribute to the potential energy which is probably not what is
|
|||
desired.
|
||||
|
||||
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
|
||||
(i.e. allow the box dimensions to change), but this has not yet been
|
||||
implemented.
|
||||
|
|
|
|||
|
|
@ -104,7 +104,7 @@ both atoms are in the specified group and in the same molecule, as
|
|||
determined by their molecule ID.
|
||||
</P>
|
||||
<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.
|
||||
The other exclude options are more expensive if specified multiple
|
||||
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
|
||||
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
|
||||
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
|
||||
atom can have.
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -98,7 +98,7 @@ both atoms are in the specified group and in the same molecule, as
|
|||
determined by their molecule ID.
|
||||
|
||||
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.
|
||||
The other exclude options are more expensive if specified multiple
|
||||
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
|
||||
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
|
||||
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
|
||||
atom can have.
|
||||
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
|
|||
would be 10.2 Angstroms.
|
||||
</P>
|
||||
<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>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
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ factor of 3.0 (the argument in pair_style), the resulting E_LJ cutoff
|
|||
would be 10.2 Angstroms.
|
||||
|
||||
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
|
||||
specifies an AIREBO potential file with parameters for C and H. These
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@
|
|||
<PRE> <I>long</I> = use Kspace long-range summation for the Coulombic term 1/r
|
||||
<I>off</I> = omit the Coulombic term
|
||||
</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)
|
||||
</UL>
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@ flag_buck = {long} or {cut} :ulb,l
|
|||
flag_coul = {long} or {off} :l
|
||||
{long} = use Kspace long-range summation for the Coulombic term 1/r
|
||||
{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
|
||||
|
||||
[Examples:]
|
||||
|
|
|
|||
|
|
@ -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/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_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/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
|
||||
|
|
|
|||
|
|
@ -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/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
|
||||
"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/no_history"_pair_gran.html - granular potential without history effects
|
||||
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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.
|
||||
</P>
|
||||
<HR>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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
|
||||
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.
|
||||
|
||||
:line
|
||||
|
|
|
|||
|
|
@ -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
|
||||
different atom types to model an alloy system. The mixing to create
|
||||
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.
|
||||
</P>
|
||||
<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
|
||||
electron density.
|
||||
</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>
|
||||
<UL><LI>embedding function F(rho) (Nrho 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
|
||||
density function rho are the same as for drho (see above, electron
|
||||
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
|
||||
expression as r*phi, in units of eV-Angstroms, via the formula
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -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
|
||||
different atom types to model an alloy system. The mixing to create
|
||||
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.
|
||||
|
||||
{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
|
||||
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)
|
||||
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
|
||||
density function rho are the same as for drho (see above, electron
|
||||
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
|
||||
expression as r*phi, in units of eV-Angstroms, via the formula
|
||||
|
||||
|
|
|
|||
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Reference in New Issue