The result is a number which is mapped to the following different lattice structures:
-The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms diff -Naur lammps-7Nov08/doc/compute_ackland_atom.txt lammps-20Nov08/doc/compute_ackland_atom.txt --- lammps-7Nov08/doc/compute_ackland_atom.txt 2008-05-15 16:05:51.000000000 -0600 +++ lammps-20Nov08/doc/compute_ackland_atom.txt 2008-11-17 07:56:58.000000000 -0700 @@ -34,11 +34,11 @@ The result is a number which is mapped to the following different lattice structures: -1 = UNKNOWN -2 = BCC -3 = FCC -4 = HCP -5 = ICO :ul +0 = UNKNOWN +1 = BCC +2 = FCC +3 = HCP +4 = ICO :ul The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms diff -Naur lammps-7Nov08/doc/fix_indent.html lammps-20Nov08/doc/fix_indent.html --- lammps-7Nov08/doc/fix_indent.html 2008-10-01 10:01:49.000000000 -0600 +++ lammps-20Nov08/doc/fix_indent.html 2008-11-13 08:34:21.000000000 -0700 @@ -75,12 +75,14 @@ cylinder extends infinitely along its axis.
A planar indenter is really an axis-aligned infinite-extent wall -exerting the same force on atoms in the system, where r is the -distance from the plane. If the side parameter of the plane is -specified as lo then it will indent from the lo end of the -simulation box, meaning that atoms with a coordinate less than the -plane's current position will be pushed towards the hi end of the box. -Vice versa if side is specified as hi. +exerting the same force on atoms in the system, where R is the +position of the plane and r-R is the distance from the plane. If +the side parameter of the plane is specified as lo then it will +indent from the lo end of the simulation box, meaning that atoms with +a coordinate less than the plane's current position will be pushed +towards the hi end of the box and atoms with a coordinate higher than +the plane's current position will feel no force. Vice versa if side +is specified as hi.
If the vel keyword is specified, the center (or axis or position) of the spherical (or cylindrical or planar) indenter will move during the diff -Naur lammps-7Nov08/doc/fix_indent.txt lammps-20Nov08/doc/fix_indent.txt --- lammps-7Nov08/doc/fix_indent.txt 2008-10-01 10:01:49.000000000 -0600 +++ lammps-20Nov08/doc/fix_indent.txt 2008-11-13 08:34:21.000000000 -0700 @@ -66,12 +66,14 @@ cylinder extends infinitely along its axis. A planar indenter is really an axis-aligned infinite-extent wall -exerting the same force on atoms in the system, where {r} is the -distance from the plane. If the {side} parameter of the plane is -specified as {lo} then it will indent from the lo end of the -simulation box, meaning that atoms with a coordinate less than the -plane's current position will be pushed towards the hi end of the box. -Vice versa if {side} is specified as {hi}. +exerting the same force on atoms in the system, where {R} is the +position of the plane and {r-R} is the distance from the plane. If +the {side} parameter of the plane is specified as {lo} then it will +indent from the lo end of the simulation box, meaning that atoms with +a coordinate less than the plane's current position will be pushed +towards the hi end of the box and atoms with a coordinate higher than +the plane's current position will feel no force. Vice versa if {side} +is specified as {hi}. If the {vel} keyword is specified, the center (or axis or position) of the spherical (or cylindrical or planar) indenter will move during the diff -Naur lammps-7Nov08/doc/pair_eam.html lammps-20Nov08/doc/pair_eam.html --- lammps-7Nov08/doc/pair_eam.html 2008-10-09 08:47:45.000000000 -0600 +++ lammps-20Nov08/doc/pair_eam.html 2008-11-17 07:56:58.000000000 -0700 @@ -65,11 +65,11 @@
The cutoff distance and the tabulated values of the functionals F, rho, and phi are listed in one or more files which are specified by the pair_coeff command. These are ASCII text files -in a DYNAMO-style format which is described below. DYNAMO is a serial -MD code. Several DYNAMO potential files for different metals are -included in the "potentials" directory of the LAMMPS distribution. -All of these files are parameterized in terms of LAMMPS metal -units. +in a DYNAMO-style format which is described below. DYNAMO was the +original serial EAM MD code, written by the EAM originators. Several +DYNAMO potential files for different metals are included in the +"potentials" directory of the LAMMPS distribution. All of these files +are parameterized in terms of LAMMPS metal units.
IMPORTANT NOTE: The eam style reads single-element EAM potentials in the DYNAMO funcfl format. Either single element or alloy systems @@ -81,6 +81,19 @@ as described below. These files require no mixing since they specify alloy interactions explicitly.
+There are several WWW sites that distribute and document EAM +potentials stored in DYNAMO or other formats: +
+http://www.ctcms.nist.gov/potentials +http://cst-www.nrl.navy.mil/ccm6/ap +http://enpub.fulton.asu.edu/cms/potentials/main/main.htm ++
These potentials should be usable with LAMMPS, though the alternate +formats would need to be converted to the DYNAMO format used by LAMMPS +and described on this page. +
+For style eam, potential values are read from a file that is in the DYNAMO single-element funcfl format. If the DYNAMO file was created by a Fortran program, it cannot have "D" values in it for exponents. @@ -356,17 +369,6 @@
-Here are several WWW sites that discuss EAM potentials stored in -either the original DYNAMO or other formats: -
-http://www.ims.uconn.edu/centers/simul/pot -http://cst-www.nrl.navy.mil/ccm6/ap -http://enpub.fulton.asu.edu/cms/potentials/main/main.htm --
In principle, these potentials could be used with LAMMPS, though the -alternate formats would need to be converted to the DYNAMO format used -by LAMMPS and described above. -
Default: none
This command operates similar to the replicate tool in the tools -sub-directory of the LAMMPS distribution which creates new data files -from old ones. -
Restrictions:
A 2d simulation cannot be replicated in the z dimension. diff -Naur lammps-7Nov08/doc/replicate.txt lammps-20Nov08/doc/replicate.txt --- lammps-7Nov08/doc/replicate.txt 2008-10-08 09:02:35.000000000 -0600 +++ lammps-20Nov08/doc/replicate.txt 2008-11-19 07:19:15.000000000 -0700 @@ -37,10 +37,6 @@ atoms with image flags that differ by 1. This will allow them to be unwrapped appropriately. -This command operates similar to the replicate tool in the tools -sub-directory of the LAMMPS distribution which creates new data files -from old ones. - [Restrictions:] A 2d simulation cannot be replicated in the z dimension. diff -Naur lammps-7Nov08/src/displace_atoms.cpp lammps-20Nov08/src/displace_atoms.cpp --- lammps-7Nov08/src/displace_atoms.cpp 2008-01-18 10:18:46.000000000 -0700 +++ lammps-20Nov08/src/displace_atoms.cpp 2008-11-20 08:39:05.000000000 -0700 @@ -135,7 +135,7 @@ if (strcmp(arg[5],"x") == 0) coord_dim = 0; else if (strcmp(arg[5],"y") == 0) coord_dim = 1; else if (strcmp(arg[5],"z") == 0) coord_dim = 2; - else error->all("Illegal velocity ramp command"); + else error->all("Illegal displace_atoms ramp command"); double coord_lo,coord_hi; if (coord_dim == 0) { diff -Naur lammps-7Nov08/src/lattice.cpp lammps-20Nov08/src/lattice.cpp --- lammps-7Nov08/src/lattice.cpp 2008-04-11 14:05:42.000000000 -0600 +++ lammps-20Nov08/src/lattice.cpp 2008-11-13 20:48:36.000000000 -0700 @@ -94,8 +94,8 @@ } else if (style == HCP) { add_basis(0.0,0.0,0.0); add_basis(0.5,0.5,0.0); - add_basis(0.5,0.25,0.5); - add_basis(0.0,0.75,0.5); + add_basis(0.5,5.0/6.0,0.5); + add_basis(0.0,1.0/3.0,0.5); } else if (style == SQ) { add_basis(0.0,0.0,0.0); } else if (style == SQ2) {