Merge pull request #4540 from evoyiatzis/fix-adapt-dihedral

extend fix adapt to treat dihedrals

unittest/force-styles/test_dihedral_style.cpp

@@ -746,3 +746,44 @@ TEST(DihedralStyle, numdiff)
     cleanup_lammps(lmp, test_config);
     if (!verbose) ::testing::internal::GetCapturedStdout();
 }
+
+TEST(DihedralStyle, extract)
+{
+    if (test_config.skip_tests.count(test_info_->name())) GTEST_SKIP();
+
+    LAMMPS::argv args = {"DihedralStyle", "-log", "none", "-echo", "screen", "-nocite"};
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    LAMMPS *lmp = nullptr;
+    try {
+        lmp = init_lammps(args, test_config, true);
+    } catch (std::exception &e) {
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+        FAIL() << e.what();
+    }
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    if (!lmp) {
+        std::cerr << "One or more prerequisite styles are not available "
+                     "in this LAMMPS configuration:\n";
+        for (auto prerequisite : test_config.prerequisites) {
+            std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
+        }
+        GTEST_SKIP();
+    }
+
+    auto *dihedral = lmp->force->dihedral;
+    void *ptr   = nullptr;
+    int dim     = 0;
+    for (auto extract : test_config.extract) {
+        ptr = dihedral->extract(extract.first.c_str(), dim);
+        EXPECT_NE(ptr, nullptr);
+        EXPECT_EQ(dim, extract.second);
+    }
+    ptr = dihedral->extract("does_not_exist", dim);
+    EXPECT_EQ(ptr, nullptr);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    cleanup_lammps(lmp, test_config);
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+}

unittest/force-styles/tests/dihedral-charmm.yaml

@@ -19,7 +19,10 @@ dihedral_coeff: ! |
   3  56.0 0 110 0.0
   4  23.0 1 180 0.5
   5  19.0 3  90 1.0
-extract: ! ""
+extract: ! |
+  k 1
+  n 1
+  d 1
 natoms: 29
 init_energy: 1317.959844120986
 init_stress: ! |2-

unittest/force-styles/tests/dihedral-charmmfsw.yaml

@@ -19,7 +19,10 @@ dihedral_coeff: ! |
   3  56.0 0 110 0.0
   4  23.0 1 180 0.5
   5  19.0 3  90 1.0
-extract: ! ""
+extract: ! |
+  k 1
+  n 1
+  d 1
 natoms: 29
 init_energy: 1317.959844120986
 init_stress: ! |2-

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

@@ -17,7 +17,13 @@ dihedral_coeff: ! |
   *  at   75 42 31 75 42 31 120 50
   *  aat  75 120 160
   *  bb13 75 1.4 1.4
-extract: ! ""
+extract: ! |
+  k1 1
+  k2 1
+  k3 1
+  phi1 1
+  phi2 1
+  phi3 1
 natoms: 29
 init_energy: 3355.0074717375933
 init_stress: ! |2-

unittest/force-styles/tests/dihedral-cosine_squared_restricted.yaml

@@ -16,7 +16,9 @@ dihedral_coeff: ! |
   3  15.0 -10.0
   4  12.0 0.0
   5  11.0 45.0
-extract: ! ""
+extract: ! |
+  k 1
+  phi0 1
 natoms: 29
 init_energy: 10643.96352037142
 init_stress: ! |2-

unittest/force-styles/tests/dihedral-helix.yaml

@@ -16,7 +16,10 @@ dihedral_coeff: ! |
   3  56 10 32
   4  23 80 61
   5  19 90 13
-extract: ! ""
+extract: ! |
+  a 1
+  b 1
+  c 1
 natoms: 29
 init_energy: 4634.436545707672
 init_stress: ! |-

unittest/force-styles/tests/dihedral-multi_harmonic.yaml

@@ -16,7 +16,12 @@ dihedral_coeff: ! |
   3  56 10 32 84 52
   4  23 80 61 83 74
   5  19 90 13 15 58
-extract: ! ""
+extract: ! |
+  a1 1
+  a2 1
+  a3 1
+  a4 1
+  a5 1
 natoms: 29
 init_energy: 2854.9857316566695
 init_stress: ! |2-

unittest/force-styles/tests/dihedral-opls.yaml

@@ -16,7 +16,11 @@ dihedral_coeff: ! |
   3  56 10 32 84
   4  23 80 61 83
   5  19 90 13 15
-extract: ! ""
+extract: ! |
+  k1 1
+  k2 1
+  k3 1
+  k4 1
 natoms: 29
 init_energy: 2260.6834525285753
 init_stress: ! |-

unittest/force-styles/tests/dihedral-quadratic.yaml

@@ -17,7 +17,9 @@ dihedral_coeff: ! |
   3  25 100
   4  35 110
   5  85 120
-extract: ! ""
+extract: ! |
+  k 1
+  phi0 1
 natoms: 29
 init_energy: 6216.314347066598
 init_stress: ! |2-