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Doc and gitignore updates

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jtclemm
2023-07-15 22:12:10 -06:00
parent 7fa1f4b3b4
commit a80739c537
3 changed files with 10 additions and 6 deletions
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10
doc/src/compute_rattlers.rst
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@ -20,7 +20,7 @@ Syntax
*radius* = cutoffs determined based on atom diameters (atom style sphere)
* zmin = minimum coordination for a non-rattler particle
* ntries = maximum number of interations to remove rattlers
* ntries = maximum number of iterations to remove rattlers
Examples
""""""""
@ -35,12 +35,12 @@ Description
Define a compute that identifies rattlers in a system. Rattlers are
identified using an interative approach. The coordination number of
all atoms is first calculated. The *type* and *radius* settings are
used to select whether interactions cutoffs are determined by atom
used to select whether interaction cutoffs are determined by atom
types or by the sum of atomic radii (atom style sphere), respectively.
Rattlers are then identified as particles with a coordination number
less than *zmin* and are removed from consideration. A coordination
number is then recalaculated, excluding previously identified rattlers,
to identify new rattlers. This process is looped, up to a maximum
less than *zmin* and are removed from consideration. Atomic coordination
numbers are then recalculated, excluding previously identified rattlers,
to identify a new set of rattlers. This process is iterated, up to a maximum
of *ntries*, until no new rattlers are identified and the remaining
atoms form a stable network of contacts.

2
doc/src/fix_nonaffine_displacement.rst
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@ -30,7 +30,7 @@ Syntax
*fixed* = use a fixed reference frame at *nstep*
*update* = update the reference frame every *nstep* timesteps
*offset* = update the reference frame *nstep* timesteps before calculating the non/affine displacement
*offset* = update the reference frame *nstep* timesteps before calculating the nonaffine displacement
Examples
""""""""

4
src/.gitignore vendored
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@ -598,6 +598,8 @@
/compute_pressure_grem.h
/compute_ptm_atom.cpp
/compute_ptm_atom.h
/compute_rattlers.cpp
/compute_rattlers.h
/compute_rigid_local.cpp
/compute_rigid_local.h
/compute_smd_triangle_vertices.cpp
@ -889,6 +891,8 @@
/fix_nvt_sllod_eff.h
/fix_nve_tri.cpp
/fix_nve_tri.h
/fix_nonaffine_displacement.cpp
/fix_nonaffine_displacement.h
/fix_oneway.cpp
/fix_oneway.h
/fix_orient_bcc.cpp