From fc8a048662107dc9185331264e59edb1cd07caa2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 7 Mar 2023 21:22:57 -0500
Subject: [PATCH] add unit test

---
 src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp |  4 +-
 unittest/force-styles/test_bond_style.cpp     |  2 +-
 .../tests/bond-harmonic_restrain.yaml         | 90 +++++++++++++++++++
 3 files changed, 93 insertions(+), 3 deletions(-)
 create mode 100644 unittest/force-styles/tests/bond-harmonic_restrain.yaml

diff --git a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
index 2054884e3e..a15642f90b 100644
--- a/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
+++ b/src/EXTRA-MOLECULE/bond_harmonic_restrain.cpp
@@ -163,7 +163,7 @@ void BondHarmonicRestrain::init_style()
 
     // create internal fix to store initial positions
     initial = dynamic_cast<FixPropertyAtom *>(
-      modify->add_fix("BOND_RESTRAIN_X0 all property/atom d2_BOND_RESTRAIN_X0 3 ghost yes"));
+        modify->add_fix("BOND_RESTRAIN_X0 all property/atom d2_BOND_RESTRAIN_X0 3 ghost yes"));
     if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
 
     natoms = atom->natoms;
@@ -182,7 +182,7 @@ void BondHarmonicRestrain::init_style()
           modify->add_fix("BOND_RESTRAIN_X0 all property/atom d2_BOND_RESTRAIN_X0 3 ghost yes"));
       if (!initial) error->all(FLERR, "Failure to create internal per-atom storage");
     }
-  } 
+  }
 
   // must not add  atoms
   if (natoms < atom->natoms)
diff --git a/unittest/force-styles/test_bond_style.cpp b/unittest/force-styles/test_bond_style.cpp
index d056fdc876..c723541366 100644
--- a/unittest/force-styles/test_bond_style.cpp
+++ b/unittest/force-styles/test_bond_style.cpp
@@ -123,7 +123,7 @@ LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool new
 
     command("run 0 post no");
     command("write_restart " + cfg.basename + ".restart");
-    command("write_data " + cfg.basename + ".data");
+    command("write_data " + cfg.basename + ".data nofix");
     command("write_coeff " + cfg.basename + "-coeffs.in");
 
     return lmp;
diff --git a/unittest/force-styles/tests/bond-harmonic_restrain.yaml b/unittest/force-styles/tests/bond-harmonic_restrain.yaml
new file mode 100644
index 0000000000..1fd04b818e
--- /dev/null
+++ b/unittest/force-styles/tests/bond-harmonic_restrain.yaml
@@ -0,0 +1,90 @@
+---
+lammps_version: 8 Feb 2023
+tags: generated
+date_generated: Tue Mar  7 21:07:27 2023
+epsilon: 2.5e-13
+skip_tests: extract
+prerequisites: ! |
+  atom full
+  bond harmonic/restrain
+pre_commands: ! ""
+post_commands: ! ""
+input_file: in.fourmol
+bond_style: harmonic/restrain
+bond_coeff: ! |
+  1 250.0
+  2 300.0
+  3 350.0
+  4 650.0
+  5 450.0
+equilibrium: 5 -1 -1 -1 -1 -1
+extract: ! |
+  k 1
+natoms: 29
+init_energy: 0
+init_stress: ! |2-
+   0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+init_forces: ! |2
+    1  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    2  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    3  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    4  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    5  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    6  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    7  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    8  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+    9  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   10  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   11  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   12  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   13  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   14  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   15  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   16  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   17  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   18  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   19  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   20  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   21  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   22  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   23  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   24  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   25  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   26  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   27  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   28  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+   29  0.0000000000000000e+00  0.0000000000000000e+00  0.0000000000000000e+00
+run_energy: 0.009384424442608962
+run_stress: ! |2-
+   1.3334287184173488e+00  3.1110677999939773e-01 -1.4064657849540130e+00  2.6546279385354110e-01  1.5492956756466219e+00  7.2358876924785698e-01
+run_forces: ! |2
+    1  1.1485941046856593e-01  1.4088049450172524e-01 -8.5852076971833030e-02
+    2 -9.3217481807658653e-02 -7.6867386712704044e-02  1.0932532178570745e-01
+    3 -2.3741413942894266e-01 -8.5667734110971339e-02 -8.2143831089792743e-02
+    4  2.3324188168788909e-01 -6.5094431822773302e-02  1.6591701889629748e-01
+    5  2.6793200848186677e-02  4.1227376782380774e-02 -1.3685685314886964e-01
+    6  2.4862628338772436e-01 -3.6125357500552457e-01 -7.8230634578348013e-01
+    7 -3.8706943762359766e-02  1.9888379369193138e-01  9.8933719851963053e-01
+    8 -3.5267248957722913e-01  4.2911503092501313e-01  1.0190469073820968e-01
+    9 -5.1632048293607458e-02 -5.5343430872859360e-02 -2.2821606693951479e-01
+   10  1.2860877826855494e-01 -7.5971599169706849e-01 -5.5343112593256227e-01
+   11  1.6956002318038377e-01  4.2001247662003161e-01  6.8896503378985918e-01
+   12  3.4231534762621078e-02 -2.4857235824638585e-01 -6.3964642589377518e-01
+   13 -2.7815178906130594e-01  1.0946454990993748e-01  5.1669158882660616e-03
+   14  2.2738751895410908e-01 -4.5437525741145839e-02  5.8956676893113813e-01
+   15 -4.6207378210972273e-03  1.6438094307388113e-01  5.8917445017986604e-02
+   16 -1.1399994473799732e-02  1.1329499720204761e-01 -5.0720152745025260e-01
+   17 -1.1549300733203431e-01  8.0692771502484495e-02  3.0655385964298520e-01
+   18  1.9145703373728828e+00  1.8373130373081787e+00 -3.9519344330792983e-01
+   19 -4.7317441908503255e-01 -3.0353033418925196e-01 -5.7175303978447201e-01
+   20 -1.4413959182878502e+00 -1.5337827031189268e+00  9.6694648309240183e-01
+   21 -3.3244533656237202e-01 -3.0309080808086836e-01  6.5775553694406208e-01
+   22 -2.9549353211149859e-01 -7.2150425050573716e-02 -4.6194669575592789e-01
+   23  6.2793886867387061e-01  3.7524123313144209e-01 -1.9580884118813421e-01
+   24  8.2698432709098157e-01 -1.4448474780063469e+00  1.2133188519739595e+00
+   25 -1.5417378702379472e+00  2.4470962384652978e-01 -1.2964818258023694e+00
+   26  7.1475354314696560e-01  1.2001378541598171e+00  8.3162973828409884e-02
+   27  2.1885007758012770e-01 -5.7423924185981945e-01  2.7745249319135684e-01
+   28 -5.2036258696458004e-01  2.2330647386191435e-01 -3.5136945845348061e-01
+   29  3.0151250938445234e-01  3.5093276799790507e-01  7.3916965262123782e-02
+...