From f4000efd8a43e8131a3669e445da62699e253c6e Mon Sep 17 00:00:00 2001
From: jtclemm <jtclemm@sandia.gov>
Date: Mon, 17 Jul 2023 11:52:06 -0600
Subject: [PATCH] Adding reference section to doc pages, update misc error
 messages

---
 doc/src/fix_nonaffine_displacement.rst       | 12 +++++++++++-
 src/EXTRA-FIX/fix_nonaffine_displacement.cpp |  8 +++-----
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/doc/src/fix_nonaffine_displacement.rst b/doc/src/fix_nonaffine_displacement.rst
index 466a7b1ab0..99d98b451b 100644
--- a/doc/src/fix_nonaffine_displacement.rst
+++ b/doc/src/fix_nonaffine_displacement.rst
@@ -70,7 +70,9 @@ displacement. A deformation gradient tensor is then calculated as
     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.
+is the identity tensor. This calculation is only performed on timesteps that
+are a multiple of *nevery* (including timestep zero). Data accessed before
+this occurs will simply be zeroed.
 
 The *integrated* style simply integrates the velocity of particles
 every timestep to calculate a displacement. This style only works if
@@ -78,6 +80,14 @@ 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>`.
 
+Both of these methods require defining a reference state. With the *fixed* reference
+style, the user picks a specific timestep *nstep* from which particle positions are saved.
+If peratom data is accessed from this compute prior to this timestep, it will simply be
+zeroed. The *update* reference style implies the reference state will be updated every
+*nstep* timesteps. The *offset* reference only applies to the *d2min* metric and will
+update the reference state *nstep* timesteps before a multiple of *nevery* timesteps.
+
+
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
diff --git a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp
index f18fdd2c4a..bb5c2ca0c3 100755
--- a/src/EXTRA-FIX/fix_nonaffine_displacement.cpp
+++ b/src/EXTRA-FIX/fix_nonaffine_displacement.cpp
@@ -116,6 +116,9 @@ FixNonaffineDisplacement::FixNonaffineDisplacement(LAMMPS *lmp, int narg, char *
     if (cut_style == RADIUS && (!atom->radius_flag))
       error->all(FLERR, "Fix nonaffine/displacement radius style requires atom attribute radius");
 
+  if (nad_style == INTEGRATED && reference_style == OFFSET)
+    error->all(FLERR, "Fix nonaffine/displacement cannot use the integrated style with an offset reference state");
+
   peratom_flag = 1;
   peratom_freq = nevery;
   nmax = -1;
@@ -347,11 +350,6 @@ void FixNonaffineDisplacement::save_reference_state()
 
 void FixNonaffineDisplacement::calculate_D2Min()
 {
-  if (!reference_saved) {
-    error->warning(FLERR, "Calculating D2Min without a saved reference state");
-    return;
-  }
-
   // invoke half neighbor list (will copy or build if necessary)
   neighbor->build_one(list);