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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1613 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2008-03-18 20:18:54 +00:00
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18
doc/Section_errors.html
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@ -374,7 +374,7 @@ are too far apart to make a valid bond.
<DT><I>Bond atoms %d %d missing on proc %d at step %d</I>
<DD>One or more of 2 atoms needed to compute a particular bond are
<DD>One or both of 2 atoms needed to compute a particular bond are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the bond has blown apart and an atom is
too far away.
@ -514,7 +514,7 @@ or create_box command.
<DT><I>Cannot fix deform on a non-periodic boundary</I>
<DD>Only a periodiic boundary can be modified.
<DD>Only a periodic boundary can be modified.
<DT><I>Cannot have both pair_modify shift and tail set to yes</I>
@ -1036,6 +1036,10 @@ does not exist.
<DD>A group ID used in the dump command does not exist.
<DT><I>Could not find dump_modify ID</I>
<DD>Self-explanatory.
<DT><I>Could not find fix ID to delete</I>
<DD>Self-explanatory.
@ -1136,10 +1140,6 @@ does not exist.
<DD>If using a Kspace solver, all Coulomb cutoffs of long pair styles must
be the same.
<DT><I>Cound not find dump_modify ID</I>
<DD>Self-explanatory.
<DT><I>Create_atoms command before simulation box is defined</I>
<DD>The create_atoms command cannot be used before a read_data,
@ -1187,7 +1187,7 @@ read_restart, or create_box command.
<DT><I>Deposition region extends outside simulation box</I>
<DD>Self-explatory.
<DD>Self-explanatory.
<DT><I>Did not assign all atoms correctly</I>
@ -2387,7 +2387,7 @@ orthogonal.
<DD>The three specified lattice orientation vectors must create a
right-handed coordinate system such that a1 cross a2 = a3.
<DT><I>Lattice primitive vectors are colinear</I>
<DT><I>Lattice primitive vectors are collinear</I>
<DD>The specified lattice primitive vectors do not for a unit cell with
non-zero volume.
@ -3104,7 +3104,7 @@ outside a non-periodic simulation box.
<DD>Fix poems will only work with bodies (collections of atoms) that have
non-zero principal moments of inertia. This means they must be 3 or
more non-colinear atoms, even with joint atoms removed.
more non-collinear atoms, even with joint atoms removed.
<DT><I>Rigid fix must come before NPT/NPH fix</I>

18
doc/Section_errors.txt
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@ -371,7 +371,7 @@ are too far apart to make a valid bond. :dd
{Bond atoms %d %d missing on proc %d at step %d} :dt
One or more of 2 atoms needed to compute a particular bond are
One or both of 2 atoms needed to compute a particular bond are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the bond has blown apart and an atom is
too far away. :dd
@ -511,7 +511,7 @@ Group ID used in the delete_bonds command does not exist. :dd
{Cannot fix deform on a non-periodic boundary} :dt
Only a periodiic boundary can be modified. :dd
Only a periodic boundary can be modified. :dd
{Cannot have both pair_modify shift and tail set to yes} :dt
@ -1033,6 +1033,10 @@ Self-explanatory. :dd
A group ID used in the dump command does not exist. :dd
{Could not find dump_modify ID} :dt
Self-explanatory. :dd
{Could not find fix ID to delete} :dt
Self-explanatory. :dd
@ -1133,10 +1137,6 @@ does not exist. :dd
If using a Kspace solver, all Coulomb cutoffs of long pair styles must
be the same. :dd
{Cound not find dump_modify ID} :dt
Self-explanatory. :dd
{Create_atoms command before simulation box is defined} :dt
The create_atoms command cannot be used before a read_data,
@ -1184,7 +1184,7 @@ No atoms are yet defined so the delete_bonds command cannot be used. :dd
{Deposition region extends outside simulation box} :dt
Self-explatory. :dd
Self-explanatory. :dd
{Did not assign all atoms correctly} :dt
@ -2384,7 +2384,7 @@ orthogonal. :dd
The three specified lattice orientation vectors must create a
right-handed coordinate system such that a1 cross a2 = a3. :dd
{Lattice primitive vectors are colinear} :dt
{Lattice primitive vectors are collinear} :dt
The specified lattice primitive vectors do not for a unit cell with
non-zero volume. :dd
@ -3101,7 +3101,7 @@ A region ID cannot be used twice. :dd
Fix poems will only work with bodies (collections of atoms) that have
non-zero principal moments of inertia. This means they must be 3 or
more non-colinear atoms, even with joint atoms removed. :dd
more non-collinear atoms, even with joint atoms removed. :dd
{Rigid fix must come before NPT/NPH fix} :dt

10
doc/Section_howto.html
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@ -319,10 +319,16 @@ place:
the following commands:
</P>
<UL><LI><A HREF = "atom_style.html">atom_style</A> granular
<LI><A HREF = "fix_nve_gran.html">fix nve/gran</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_gravity.html">fix gravity</A>
<LI><A HREF = "thermo_style.html">thermo_style</A> gran
</UL>
<P>This compute
</P>
<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</UL>
<P>will calculate rotational kinetic energy which can then be <A HREF = "">output
with thermodynamic info</A>.
</P>
<P>Use one of these 3 pair potentials:
</P>
<UL><LI><A HREF = "pair_style.html">pair_style</A> gran/history

12
doc/Section_howto.txt
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@ -315,9 +315,15 @@ To run a simulation of a granular model, you will want to use
the following commands:
"atom_style"_atom_style.html granular
"fix nve/gran"_fix_nve_gran.html
"fix gravity"_fix_gravity.html
"thermo_style"_thermo_style.html gran :ul
"fix nve/sphere"_fix_nve_sphere.html
"fix gravity"_fix_gravity.html :ul
This compute
"compute erotate/sphere"_compute_erotate_sphere.html :ul
will calculate rotational kinetic energy which can then be "output
with thermodynamic info"_.
Use one of these 3 pair potentials:

4
doc/Section_intro.html
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@ -128,8 +128,8 @@ commands)
<LI> angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS)
<LI> dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
<LI> improper potentials: harmonic, cvff, class 2 (COMPASS)
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simlulation
<LI> overlayed potentials: superposition of multiple pair potentials
<LI> hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
<LI> overlaid potentials: superposition of multiple pair potentials
<LI> polymer potentials: all-atom, united-atom, bead-spring, breakable
<LI> water potentials: TIP3P, TIP4P, SPC
<LI> implicit solvent potentials: hydrodynamic lubrication, Debye

4
doc/Section_intro.txt
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@ -129,8 +129,8 @@ commands)
class 2 (COMPASS), OPLS
improper potentials: harmonic, cvff, class 2 (COMPASS)
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simlulation
overlayed potentials: superposition of multiple pair potentials
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials
polymer potentials: all-atom, united-atom, bead-spring, breakable
water potentials: TIP3P, TIP4P, SPC
implicit solvent potentials: hydrodynamic lubrication, Debye

2
doc/Section_modify.html
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@ -14,7 +14,7 @@ Section</A>
<H3>8. Modifying & extending LAMMPS
</H3>
<P>LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% if its source code
extend with new functionality. In fact, about 75% of its source code
is files added in this fashion.
</P>
<P>In this section, changes and additions users can make are listed along

2
doc/Section_modify.txt
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@ -11,7 +11,7 @@ Section"_Section_errors.html :c
8. Modifying & extending LAMMPS :h3
LAMMPS is designed in a modular fashion so as to be easy to modify and
extend with new functionality. In fact, about 75% if its source code
extend with new functionality. In fact, about 75% of its source code
is files added in this fashion.
In this section, changes and additions users can make are listed along

2
doc/Section_tools.html
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@ -65,7 +65,7 @@ own sub-directories with their own Makefiles.
<H4><A NAME = "amber"></A>amber2lmp tool
</H4>
<P>The amber2lmp sub-directory contain two Python scripts for converting
<P>The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
README file in amber2lmp for more information.
</P>

2
doc/Section_tools.txt
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@ -61,7 +61,7 @@ own sub-directories with their own Makefiles.
amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contain two Python scripts for converting
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
README file in amber2lmp for more information.

2
doc/angle_coeff.html
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@ -32,7 +32,7 @@ Angle coefficients can also be set in the data file read by the
<A HREF = "read_data.html">read_data</A> command or in a restart file.
</P>
<P>N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
be used, as in the 1st example above. Or a wild-card asterisk 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 asterisk with no numeric values means all types from 1 to N. A

2
doc/angle_coeff.txt
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@ -29,7 +29,7 @@ Angle coefficients can also be set in the data file read by the
"read_data"_read_data.html command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
be used, as in the 1st example above. Or a wild-card asterisk 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 asterisk with no numeric values means all types from 1 to N. A

2
doc/fix_langevin.html
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@ -119,7 +119,7 @@ include that dimension. The default is 1 for all 3 dimensions.
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
specifying a ratio of 2 increases the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the <A HREF = "fix_viscous.html">fix viscous</A> command, since the damp factor in

2
doc/fix_langevin.txt
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@ -109,7 +109,7 @@ The keyword {scale} allows the damp factor to be scaled up or down by
the specified factor for atoms of that type. This can be useful when
different atom types have different sizes or masses. It can be used
multiple times to adjust damp for several atom types. Note that
specifying a ratio of 2 increase the relaxation time which is
specifying a ratio of 2 increases the relaxation time which is
equivalent to the the solvent's viscosity acting on particles with 1/2
the diameter. This is the opposite effect of scale factors used by
the "fix viscous"_fix_viscous.html command, since the damp factor in

2
doc/fix_poems.html
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@ -59,7 +59,7 @@ a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
</P>
<P>Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-colinear atoms. Which atoms are in which
must contain at least 3 non-collinear 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

2
doc/fix_poems.txt
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@ -52,7 +52,7 @@ a constant-energy time integration, so you should not update the same
atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
Each body must have a non-degenerate inertia tensor, which means if
must contain at least 3 non-colinear atoms. Which atoms are in which
must contain at least 3 non-collinear 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

2
doc/jump.html
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@ -52,7 +52,7 @@ jump in.lj loop
<P>If the jump <I>file</I> argument is a variable, the jump command can be
used to cause different processor partitions to run different input
scripts. In this example, LAMMPS is run on 40 processors, with 4
partions of 10 procs each. An in.file containing the example variable
partitions of 10 procs each. An in.file containing the example variable
and jump command will cause each partition to run a different
simulation.
</P>

2
doc/jump.txt
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@ -49,7 +49,7 @@ jump in.lj loop :pre
If the jump {file} argument is a variable, the jump command can be
used to cause different processor partitions to run different input
scripts. In this example, LAMMPS is run on 40 processors, with 4
partions of 10 procs each. An in.file containing the example variable
partitions of 10 procs each. An in.file containing the example variable
and jump command will cause each partition to run a different
simulation.

4
doc/mass.html
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@ -36,7 +36,7 @@ individual atoms, not types. <A HREF = "pair_eam.html">Pair_style eam</A> defin
the masses of atom types in the EAM potential file.
</P>
<P>I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
be used, as in the 1st example above. Or a wild-card asterisk 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
asterisk with no numeric values means all types from 1 to N. A leading
@ -46,7 +46,7 @@ types from m to n (inclusive).
</P>
<P>A line in a data file that specifies mass uses the same format as the
arguments of the mass command in an input script, except that no
wild-card asterik can be used. For example, under the "Masses"
wild-card asterisk can be used. For example, under the "Masses"
section of a data file, the line that corresponds to the 1st example
above would be listed as
</P>

4
doc/mass.txt
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@ -33,7 +33,7 @@ individual atoms, not types. "Pair_style eam"_pair_eam.html defines
the masses of atom types in the EAM potential file.
I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
be used, as in the 1st example above. Or a wild-card asterisk 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
asterisk with no numeric values means all types from 1 to N. A leading
@ -43,7 +43,7 @@ types from m to n (inclusive).
A line in a data file that specifies mass uses the same format as the
arguments of the mass command in an input script, except that no
wild-card asterik can be used. For example, under the "Masses"
wild-card asterisk can be used. For example, under the "Masses"
section of a data file, the line that corresponds to the 1st example
above would be listed as

6
doc/pair_airebo.html
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@ -80,9 +80,9 @@ LAMMPS atom types:
<UL><LI>filename
<LI>N element names = mapping of AIREBO elements to atom types
</UL>
<P>As an example, if your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be C, and the 4th to be H, you would use the
following pair_coeff command:
<P>As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:
</P>
<PRE>pair_coeff * * CH.airebo C C C H
</PRE>

6
doc/pair_airebo.txt
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@ -77,9 +77,9 @@ LAMMPS atom types:
filename
N element names = mapping of AIREBO elements to atom types :ul
As an example, if your LAMMPS simulation has 4 atoms types and you
want the 1st 3 to be C, and the 4th to be H, you would use the
following pair_coeff command:
As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:
pair_coeff * * CH.airebo C C C H :pre

2
doc/pair_gran.html
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@ -44,7 +44,7 @@ apart when r is less than the contact distance d.
<CENTER><IMG SRC = "Eqs/pair_granular.jpg">
</CENTER>
<P>The 1st term is a normal force and the 2nd term is a tangential force.
The other quantites are as follows:
The other quantities are as follows:
</P>
<UL><LI>delta = d - r
<LI>f(x) = 1 for Hookean contacts used in pair styles <I>history</I> and <I>no_history</I>

2
doc/pair_gran.txt
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@ -34,7 +34,7 @@ apart when r is less than the contact distance d.
:c,image(Eqs/pair_granular.jpg)
The 1st term is a normal force and the 2nd term is a tangential force.
The other quantites are as follows:
The other quantities are as follows:
delta = d - r
f(x) = 1 for Hookean contacts used in pair styles {history} and {no_history}

2
doc/pair_soft.html
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@ -65,7 +65,7 @@ always mixed via a <I>geometric</I> rule. The cutoff is mixed according to
the pair_modify mix value. The default mix value is <I>geometric</I>. See
the "pair_modify" command for details.
</P>
<P>This pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option, since the pair interaction goes to 0.0 at the cutoff.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not

2
doc/pair_soft.txt
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@ -62,7 +62,7 @@ always mixed via a {geometric} rule. The cutoff is mixed according to
the pair_modify mix value. The default mix value is {geometric}. See
the "pair_modify" command for details.
This pair styles does not support the "pair_modify"_pair_modify.html
This pair style does not support the "pair_modify"_pair_modify.html
shift option, since the pair interaction goes to 0.0 at the cutoff.
The "pair_modify"_pair_modify.html table and tail options are not

24
doc/pair_sw.html
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@ -85,19 +85,17 @@ for both two-body and three-body interactions. gamma is used only in the
three-body interactions, but is defined for pairs of atoms.
The non-annotated parameters are unitless.
</P>
<P>LAMMPS introduces an additional performance-optimization parameter
tol that is used for
both two-body and three-body interactions.
In the Stillinger-Weber potential, the
interaction energies become negligibly small at atomic separations
substantially less than the theoretical cutoff
distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol.
The use of the virtual cutoff distance in constructing atom neighbor
lists can significantly reduce the neighbor list sizes and therefore the
computational cost. LAMMPS provide a tol value for each of the three-body
entries so that they can be separately controlled. If tol = 0.0, then
the standard Stillinger-Weber cutoff is used.
<P>LAMMPS introduces an additional performance-optimization parameter tol
that is used for both two-body and three-body interactions. In the
Stillinger-Weber potential, the interaction energies become negligibly
small at atomic separations substantially less than the theoretical
cutoff distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol. The use of the virtual cutoff
distance in constructing atom neighbor lists can significantly reduce
the neighbor list sizes and therefore the computational cost. LAMMPS
provides a <I>tol</I> value for each of the three-body entries so that they
can be separately controlled. If tol = 0.0, then the standard
Stillinger-Weber cutoff is used.
</P>
<P>The Stillinger-Weber potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain

24
doc/pair_sw.txt
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@ -82,19 +82,17 @@ for both two-body and three-body interactions. gamma is used only in the
three-body interactions, but is defined for pairs of atoms.
The non-annotated parameters are unitless.
LAMMPS introduces an additional performance-optimization parameter
tol that is used for
both two-body and three-body interactions.
In the Stillinger-Weber potential, the
interaction energies become negligibly small at atomic separations
substantially less than the theoretical cutoff
distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol.
The use of the virtual cutoff distance in constructing atom neighbor
lists can significantly reduce the neighbor list sizes and therefore the
computational cost. LAMMPS provide a tol value for each of the three-body
entries so that they can be separately controlled. If tol = 0.0, then
the standard Stillinger-Weber cutoff is used.
LAMMPS introduces an additional performance-optimization parameter tol
that is used for both two-body and three-body interactions. In the
Stillinger-Weber potential, the interaction energies become negligibly
small at atomic separations substantially less than the theoretical
cutoff distances. LAMMPS therefore defines a virtual cutoff distance
based on a user defined tolerance tol. The use of the virtual cutoff
distance in constructing atom neighbor lists can significantly reduce
the neighbor list sizes and therefore the computational cost. LAMMPS
provides a {tol} value for each of the three-body entries so that they
can be separately controlled. If tol = 0.0, then the standard
Stillinger-Weber cutoff is used.
The Stillinger-Weber potential file must contain entries for all the
elements listed in the pair_coeff command. It can also contain