Adding d2min doc

doc/src/fix_nonaffine_displacement.rst

@@ -8,129 +8,114 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group nonaffine/displacement style args reference/style args
+   fix ID group nonaffine/displacement style args reference/style nstep
 
 * ID, group are documented in :doc:`fix <fix>` command
-* gravity = style name of this fix command
+* nonaffine/displacement = style name of this fix command
-* magnitude = size of acceleration (force/mass units)
+* nevery = calculate nonaffine displacement every this many timesteps
-* magnitude can be a variable (see below)
+* style = *d2min* or *integrated*
-* style = *chute* or *spherical* or *gradient* or *vector*
 
   .. parsed-literal::
 
-       *chute* args = angle
+       *d2min* args = cutoff args
-         angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
+         cutoff = *type* or *radius* or *custom*
-         angle can be a variable (see below)
+           *type* args = none, cutoffs determined by atom types
-       *spherical* args = phi theta
+           *radius* args = none, cutoffs determined based on atom diameters (atom style sphere)
-         phi = azimuthal angle from +x axis (in degrees)
+           *custom* args = *rmax*, cutoff set by a constant numeric value *rmax*
-         theta = angle from +z or +y axis in 3d/2d (in degrees)
+       *integrated* args = none
-         phi or theta can be a variable (see below)
+
-       *vector* args = x y z
+* reference/style = *fixed* or *update* or *offset*
-         x y z = vector direction to apply the acceleration
+
-         x or y or z can be a variable (see below)
+  .. parsed-literal::
+
+       *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
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   fix 1 all gravity 1.0 chute 24.0
+   fix 1 all nonaffine/displacement 100 integrated update 100
-   fix 1 all gravity v_increase chute 24.0
+   fix 1 all nonaffine/displacement 1000 d2min type fixed 0
-   fix 1 all gravity 1.0 spherical 0.0 -180.0
+   fix 1 all nonaffine/displacement 1000 d2min custom 2.0 offset 100
-   fix 1 all gravity 10.0 spherical v_phi v_theta
-   fix 1 all gravity 100.0 vector 1 1 0
 
 Description
 """""""""""
 
-Impose an additional acceleration on each particle in the group.  This
+This fix computes different metrics of the nonaffine displacement of
-fix is typically used with granular systems to include a "gravity"
+particles. The first metric, *d2min* calculates the :math:`D^2_\mathrm{min}`
-term acting on the macroscopic particles.  More generally, it can
+nonaffine displacement by Falk and Langer in :ref:`(Falk) <d2min-Falk>`.
-represent any kind of driving field, e.g. a pressure gradient inducing
+For each atom, the fix computes the two tensors
-a Poiseuille flow in a fluid.  Note that this fix operates differently
-than the :doc:`fix addforce <fix_addforce>` 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).
 
-The *magnitude* of the acceleration is specified in force/mass units.
+.. math::
-For granular systems (LJ units) this is typically 1.0.  See the
-:doc:`units <units>` command for details.
 
-Style *chute* is typically used for simulations of chute flow where
+   X = \sum_{\mathrm{neighbors}} \vec{r} \left(\vec{r}_{0} \right)^T
-the specified *angle* is the chute angle, with flow occurring in the +x
-direction.  For 3d systems, the tilt is away from the z axis; for 2d
-systems, the tilt is away from the y axis.
 
-Style *spherical* allows an arbitrary 3d direction to be specified for
+and
-the acceleration vector.  *Phi* and *theta* are defined in the usual
-spherical coordinates.  Thus for acceleration acting in the -z
-direction, *theta* would be 180.0 (or -180.0).  *Theta* = 90.0 and
-*phi* = -90.0 would mean acceleration acts in the -y direction.  For
-2d systems, *phi* is ignored and *theta* is an angle in the xy plane
-where *theta* = 0.0 is the y-axis.
 
-Style *vector* imposes an acceleration in the vector direction given
+.. math::
-by (x,y,z).  Only the direction of the vector is important; it's
-length is ignored.  For 2d systems, the *z* component is ignored.
 
-Any of the quantities *magnitude*, *angle*, *phi*, *theta*, *x*, *y*,
+   Y = \sum_{\mathrm{neighbors}} \vec{r}_0 \left(\vec{r}_{0} \right)^T
-*z* which define the gravitational magnitude and direction, can be
-specified as an equal-style :doc:`variable <variable>`.  If the value is
-a variable, it should be specified as v_name, where name is the
-variable name.  In this case, the variable will be evaluated each
-timestep, and its value used to determine the quantity.  You should
-insure that the variable calculates a result in the appropriate units,
-e.g. force/mass or degrees.
 
-Equal-style variables can specify formulas with various mathematical
+where the neighbors include all other atoms within the distance criterion
-functions, and include :doc:`thermo_style <thermo_style>` command
+set by the cutoff option, discussed below, :math:`\vec{r}` is the current
-keywords for the simulation box parameters and timestep and elapsed
+displacement between particles, and :math:`\vec{r}_0` is the reference
-time.  Thus it is easy to specify a time-dependent gravitational
+displacement. A deformation gradient tensor is then calculated as
-field.
+:math:`F = X Y^{-1}` from which
 
-----------
+.. math::
 
-.. include:: accel_styles.rst
+    D^2_\mathrm{min} = \sum_{\mathrm{neighbors}} \left| \vec{r} - F \vec{r}_0 \right|^2
+
+and a strain tensor is calculated :math:`E = F F^{T} - I` where :math:`I`
+is the identity tensor.
+
+The *integrated* style simply integrates the velocity of particles
+every timestep to calculate a displacement. This style only works if
+used in conjunction with another fix that deforms the box and displaces
+atom positions such as :doc:`the remap x option of fix deform <fix_deform>`,
+:doc:`fix press/berendsen <fix_press_berendsen>`, or :doc:`fix nh <fix_nh>`.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+The reference state is saved to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this
-this fix to add the gravitational potential energy of the system to
+fix.
-the global potential energy of the system as part of
-:doc:`thermodynamic output <thermo_style>`.  The default setting for
-this fix is :doc:`fix_modify energy no <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+This fix computes a peratom array with 3 columns, which can be accessed
-fix. This allows to set at which level of the :doc:`r-RESPA
+by indices 1-3 using any command that uses per-atom values from a fix
-<run_style>` integrator the fix is adding its forces. Default is the
+as input.
-outermost level.
 
-This fix computes a global scalar which can be accessed by various
+For the *integrated* style, the three columns are the nonaffine
-:doc:`output commands <Howto_output>`.  This scalar is the
+displacements in the x, y, and z directions. For the *d2min* style,
-gravitational potential energy of the particles in the defined field,
+the three columns are the calculated :math:`D^2_\mathrm{min}`, the
-namely mass \* (g dot x) for each particles, where x and mass are the
+volumetric strain, and the deviatoric strain.
-particles position and mass, and g is the gravitational field.  The
-scalar value calculated by this fix is "extensive".
-
-No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during
-:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
- none
+
+This compute is part of the EXTRA-FIX package.  It is only enabled if
+LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`atom_style sphere <atom_style>`, :doc:`fix addforce <fix_addforce>`
+none
 
 Default
 """""""
 
 none
+
+----------
+
+.. _nh-Martyna:
+
+**(Martyna)** Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).

src/GRANULAR/compute_fabric.cpp

@@ -11,6 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+/* ----------------------------------------------------------------------
+   Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
 #include "compute_fabric.h"
 
 #include "atom.h"

src/compute_rattlers.cpp

@@ -11,6 +11,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+/* ----------------------------------------------------------------------
+   Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
 #include "compute_rattlers.h"
 
 #include "atom.h"

src/fix_nonaffine_displacement.cpp

@@ -12,6 +12,10 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
+/* ----------------------------------------------------------------------
+   Contributing authors: Joel Clemmer (SNL), Ishan Srivastava (LBNL)
+------------------------------------------------------------------------- */
+
 #include "fix_nonaffine_displacement.h"
 
 #include "atom.h"
@@ -63,31 +67,30 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char *
 {
   if (narg < 4) error->all(FLERR,"Illegal fix nonaffine/displacement command");
 
-  int iarg = 3;
+  nevery = utils::inumeric(FLERR, arg[3], false, lmp);
+  if (nevery <= 0) error->all(FLERR,"Illegal nevery value {} in fix nonaffine/displacement", nevery);
+
+  int iarg = 4;
   if (strcmp(arg[iarg], "integrated") == 0) {
     nad_style = INTEGRATED;
     nevery = 1;
     iarg += 1;
   } else if (strcmp(arg[iarg], "d2min") == 0) {
-    if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+    if (iarg + 1 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
-
     nad_style = D2MIN;
-    nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
+    if (strcmp(arg[iarg + 1], "type") == 0) {
-    if (nevery <= 0) error->all(FLERR,"Illegal nevery value {} in fix nonaffine/displacement", nevery);
-
-    if (strcmp(arg[iarg + 2], "type") == 0) {
       cut_style = TYPE;
-    } else if (strcmp(arg[iarg + 2], "radius") == 0) {
+    } else if (strcmp(arg[iarg + 1], "radius") == 0) {
       cut_style = RADIUS;
-    } else if (strcmp(arg[iarg + 2], "custom") == 0) {
+    } else if (strcmp(arg[iarg + 1], "custom") == 0) {
-      if (iarg + 3 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
+      if (iarg + 2 > narg) error->all(FLERR,"Illegal fix nonaffine/displacement command");
       cut_style = CUSTOM;
-      cutoff_custom = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
+      cutoff_custom = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
       cutsq_custom = cutoff_custom * cutoff_custom;
       if (cutoff_custom <= 0)
-        error->all(FLERR, "Illegal custom cutoff length {}", arg[iarg + 3]);
+        error->all(FLERR, "Illegal custom cutoff length {}", arg[iarg + 2]);
       iarg += 1;
-    } else error->all(FLERR,"Illegal cutoff style {} in fix nonaffine/displacement", arg[iarg + 2]);
+    } else error->all(FLERR,"Illegal cutoff style {} in fix nonaffine/displacement", arg[iarg + 1]);
     iarg += 3;
   }