LAMMPS-ICMS Documentation
-
22 Jul 2016 version
+27 Jul 2016 version
Version info:
diff --git a/doc/html/_sources/Manual.txt b/doc/html/_sources/Manual.txt index 2665bfcc56..fb8d854257 100644 --- a/doc/html/_sources/Manual.txt +++ b/doc/html/_sources/Manual.txt @@ -5,7 +5,7 @@ LAMMPS Documentation ==================== -22 Jul 2016 version +27 Jul 2016 version ------------------- Version info: diff --git a/doc/html/_sources/compute_centro_atom.txt b/doc/html/_sources/compute_centro_atom.txt index 176644ee7f..f2c4222f57 100644 --- a/doc/html/_sources/compute_centro_atom.txt +++ b/doc/html/_sources/compute_centro_atom.txt @@ -8,11 +8,20 @@ Syntax .. parsed-literal:: - compute ID group-ID centro/atom lattice + compute ID group-ID centro/atom lattice keyword value ... * ID, group-ID are documented in :doc:`computecompute centro/atom command
Syntax
-compute ID group-ID centro/atom lattice
+compute ID group-ID centro/atom lattice keyword value ...
-
-
- ID, group-ID are documented in compute command -
- centro/atom = style name of this compute command -
- lattice = fcc or bcc or N = # of neighbors per atom to include +
- ID, group-ID are documented in compute command +centro/atom = style name of this compute command +lattice = fcc or bcc or N = # of neighbors per atom to include +
- zero or more keyword/value pairs may be appended +
- keyword = axes
+axes value = no or yes
+ no = do not calulate 3 symmetry axes
+ yes = calulate 3 symmetry axes
+
Examples
@@ -149,17 +156,18 @@Description
Define a computation that calculates the centro-symmetry parameter for -each atom in the group. In solid-state systems the centro-symmetry -parameter is a useful measure of the local lattice disorder around an -atom and can be used to characterize whether the atom is part of a -perfect lattice, a local defect (e.g. a dislocation or stacking -fault), or at a surface.
+each atom in the group, for either FCC or BCC lattices, depending on +the choice of the lattice argument. In solid-state systems the +centro-symmetry parameter is a useful measure of the local lattice +disorder around an atom and can be used to characterize whether the +atom is part of a perfect lattice, a local defect (e.g. a dislocation +or stacking fault), or at a surface.The value of the centro-symmetry parameter will be 0.0 for atoms not in the specified compute group.
This parameter is computed using the following formula from (Kelchner)
-where the N nearest neighbors or each atom are identified and Ri and +
where the N nearest neighbors of each atom are identified and Ri and Ri+N/2 are vectors from the central atom to a particular pair of nearest neighbors. There are N*(N-1)/2 possible neighbor pairs that can contribute to this formula. The quantity in the sum is computed @@ -179,6 +187,20 @@ larger positive value. An atom at a surface will have a large positive parameter. If the atom does not have N neighbors (within the potential cutoff), then its centro-symmetry parameter is set to 0.0.
+If the keyword axes has the setting yes, then this compute also +estimates three symmetry axes for each atom’s local neighborhood. The +first two of these are the vectors joining the two pairs of neighbor +atoms with smallest contributions to the centrosymmetry parameter, +i.e. the two most symmetric pairs of atoms. The third vector is +normal to the first two by the right-hand rule. All three vectors are +normalized to unit length. For FCC crystals, the first two vectors +will lie along a <110> direction, while the third vector will lie +along either a <100> or <111> direction. For HCP crystals, the first +two vectors will lie along <1000> directions, while the third vector +will lie along <0001>. This provides a simple way to measure local +orientation in HCP structures. In general, the axes keyword can be +used to estimate the orientation of symmetry axes in the neighborhood +of any atom.
Only atoms within the cutoff of the pairwise neighbor list are considered as possible neighbors. Atoms not in the compute group are included in the N neighbors used in this calculation.
@@ -188,15 +210,21 @@ is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each with a centro/atom style.Output info:
-This compute calculates a per-atom vector, which can be accessed by -any command that uses per-atom values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options.
-The per-atom vector values are unitless values >= 0.0. Their -magnitude depends on the lattice style due to the number of -contibuting neighbor pairs in the summation in the formula above. And -it depends on the local defects surrounding the central atom, as -described above.
+By default, this compute calculates the centrosymmetry value for each +atom as a per-atom vector, which can be accessed by any command that +uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +options.
+If the axes keyword setting is yes, then a per-atom array is +calculated. The first column is the centrosymmetry parameter. The +next three columns are the x, y, and z components of the first +symmetry axis, followed by the second, and third symmetry axes in +columns 5-7 and 8-10.
+The centrosymmetry values are unitless values >= 0.0. Their magnitude +depends on the lattice style due to the number of contibuting neighbor +pairs in the summation in the formula above. And it depends on the +local defects surrounding the central atom, as described above. For +the axes yes case, the vector components are also unitless, since +they represent spatial directions.
Here are typical centro-symmetry values, from a a nanoindentation simulation into gold (FCC). These were provided by Jon Zimmerman (Sandia):
@@ -226,7 +254,10 @@ of 12. +
+
diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html
index dde99ea67c..ff55e4e302 100644
--- a/doc/html/fix_nh.html
+++ b/doc/html/fix_nh.html
@@ -198,7 +198,9 @@ keyword = temp or iso or aniso or tri or flip value = yes or no = allow or disallow box flips when it becomes highly skewed
fixedpoint values = x y z
x,y,z = perform barostat dilation/contraction around this point (distance units)
- update value = dipole update dipole orientation (only for sphere variants)
+ update value = dipole or dipole/dlm
+ dipole = update dipole orientation (only for sphere variants)
+ dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants)
Default
+The default value for the optional keyword is axes = no.
(Kelchner) Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
@@ -451,6 +453,12 @@ orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to finite-size particles,
e.g. spheroids via use of the atom_style hybrid sphere dipole command.
+
diff --git a/doc/html/fix_nve_sphere.html b/doc/html/fix_nve_sphere.html
index 763917f0a1..e0e8bf5189 100644
--- a/doc/html/fix_nve_sphere.html
+++ b/doc/html/fix_nve_sphere.html
@@ -138,17 +138,19 @@
The default dipole orientation integrator can be changed to the +Dullweber-Leimkuhler-McLachlan integration scheme +(Dullweber) when using update with the value +dipole/dlm. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost.
Note
@@ -715,6 +723,8 @@ not coupled to barostat, otherwise no.(Tuckerman) Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006).
(Shinoda) Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
+(Dullweber) Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997).
-update value = dipole - dipole = update orientation of dipole moment during integration +keyword = update + update value = dipole or dipole/dlm + dipole = update orientation of dipole moment during integration + dipole/dlm = use DLM integrator to update dipole orientation
Examples
fix 1 all nve/sphere
fix 1 all nve/sphere update dipole
+fix 1 all nve/sphere update dipole/dlm
The default dipole orientation integrator can be changed to the +Dullweber-Leimkuhler-McLachlan integration scheme +(Dullweber) when using update with the value +dipole/dlm. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost.
Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. @@ -205,6 +213,9 @@ be point particles.
Related commands
Default: none
++
(Dullweber) Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997).