Merge branch 'develop' into alphataubio-kokkos-fixes

unittest/force-styles/tests/angle-amoeba.yaml

@@ -20,7 +20,13 @@ angle_coeff: ! |
   * ub 0.0 0.0
   4 ub -7.6 1.5537
 equilibrium: 4 1.9320794819577227 1.9687313962496038 2.1676989309769574 1.8936822384138474
-extract: ! ""
+extract: ! |
+  k2 1
+  k3 1
+  k4 1
+  k5 1
+  k6 1
+  theta0 1
 natoms: 29
 init_energy: 22.644137017730763
 init_stress: ! |2-

unittest/force-styles/tests/angle-class2_p6.yaml

@@ -23,7 +23,13 @@ angle_coeff: ! |
   3  ba  10.0 10.0 1.5 1.5
   4  ba   0.0 20.0 1.5 1.5
 equilibrium: 4 1.9216075064457565 1.9373154697137058 2.0943951023931953 1.8936822384138474
-extract: ! ""
+extract: ! |
+  k2 1
+  k3 1
+  k4 1
+  k5 1
+  k6 1
+  theta0 1
 natoms: 29
 init_energy: 46.44080287964778
 init_stress: ! |2-

unittest/force-styles/tests/angle-cross.yaml

@@ -16,7 +16,13 @@ angle_coeff: ! |
   3 100.0 150.0 120.0 1.45 1.35  98.2
   4 250.0  90.0 110.0 1.05 1.20  99.9
 equilibrium: 4 1.8675022996339325 1.911135530933791 1.7139133254584316 1.7435839227423353
-extract: ! ""
+extract: ! |
+  r00 1
+  r01 1
+  kss 1
+  kbs0 1
+  kbs1 1
+  theta0 1
 natoms: 29
 init_energy: -138.93227715361755
 init_stress: ! |-

unittest/force-styles/tests/angle-gaussian.yaml

@@ -16,7 +16,10 @@ angle_coeff: ! |
   3  300.0 2 0.2189  8.66 88.1 0.5439  9.94 142.7
   4  300.0 2 0.0214 14.29 85.3 0.3934 18.22 118.1
 equilibrium: 4 1.5376350710070041 1.4887658519511628 1.5376350710070041 1.4887658519511628
-extract: ! ""
+extract: ! |
+  alpha 2
+  width 2
+  theta0 2
 natoms: 29
 init_energy: 57.794009158943744
 init_stress: ! |2-

unittest/force-styles/tests/bond-class2.yaml

@@ -18,6 +18,9 @@ bond_coeff: ! |
   5 0.97   532.50 -1282.90  2004.76
 equilibrium: 5 1.42 1.1 1.3 1.2 0.97
 extract: ! |
+  k2 1
+  k3 1
+  k4 1
   r0 1
 natoms: 29
 init_energy: 26.429859642132705

unittest/force-styles/tests/bond-gaussian.yaml

@@ -17,7 +17,10 @@ bond_coeff: ! |
   4 300.0 1 0.0100 0.098 2.45
   5 300.0 1 0.0100 0.098 2.85
 equilibrium: 5 1.45 1.37 1.61 2.45 2.85
-extract: ! ""
+extract: ! |
+  alpha 2
+  width 2
+  r0 2
 natoms: 29
 init_energy: 4638.6541482649545
 init_stress: ! |2-

unittest/force-styles/tests/bond-morse.yaml

@@ -18,6 +18,8 @@ bond_coeff: ! |
   5 7000.0 0.3 1.0
 equilibrium: 5 1.5 1.1 1.3 1.2 1
 extract: ! |
+  d0 1
+  alpha 1
   r0 1
 natoms: 29
 init_energy: 5.607154540709207

unittest/force-styles/tests/bond-nonlinear.yaml

@@ -17,7 +17,10 @@ bond_coeff: ! |
   4 650.0 1.2 1.4
   5 450.0 1.0 1.1
 equilibrium: 5 1.5 1.1 1.3 1.2 1
-extract: ! ""
+extract: ! |
+  lamda 1
+  epsilon 1
+  r0 1
 natoms: 29
 init_energy: 1.9451728032820943
 init_stress: ! |-