add single test to angle_style, add support for equilibrium data

unittest/force-styles/angle_style.cpp

@@ -766,3 +766,152 @@ TEST(AngleStyle, omp) {
     if (!verbose) ::testing::internal::GetCapturedStdout();
 };
 
+TEST(AngleStyle, single) {
+    const char *args[] = {"AngleStyle", "-log", "none", "-echo", "screen", "-nocite" };
+    char **argv = (char **)args;
+    int argc = sizeof(args)/sizeof(char *);
+
+    // create a LAMMPS instance with standard settings to detect the number of atom types
+    if (!verbose) ::testing::internal::CaptureStdout();
+    LAMMPS *lmp = init_lammps(argc,argv,test_config);
+    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();
+    }
+
+    // gather some information and skip if unsupported
+    int nangletypes = lmp->atom->nangletypes;
+    int molecular = lmp->atom->molecular;
+    if (molecular != 1) {
+        std::cerr << "Only simple molecular atom styles are supported\n";
+        if (!verbose) ::testing::internal::CaptureStdout();
+        cleanup_lammps(lmp,test_config);
+        if (!verbose) ::testing::internal::GetCapturedStdout();
+        GTEST_SKIP();
+    }
+
+    // utility lambda to improve readability
+    auto command = [&](const std::string & line) {
+        lmp->input->one(line.c_str());
+    };
+
+    // now start over
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("clear");
+    command("variable newton_bond delete");
+    command("variable newton_bond index on");
+
+    command("variable input_dir index " + INPUT_FOLDER);
+
+    for (auto& pre_command : test_config.pre_commands) {
+        command(pre_command);
+    }
+
+    command("atom_style molecular");
+    command("units ${units}");
+    command("boundary p p p");
+    command("newton ${newton_pair} ${newton_bond}");
+    command("special_bonds lj/coul "
+            "${bond_factor} ${angle_factor} ${dihedral_factor}");
+
+    command("atom_modify map array");
+    command("region box block -10.0 10.0 -10.0 10.0 -10.0 10.0 units box");
+
+    char buf[10];
+    std::string cmd("create_box 1 box");
+    cmd += " angle/types ";
+    snprintf(buf,10,"%d",nangletypes);
+    cmd += buf;
+    cmd += " extra/angle/per/atom 2";
+    cmd += " extra/special/per/atom 2";
+    command(cmd);
+
+    command("pair_style zero 8.0");
+    command("pair_coeff * *");
+
+    command("angle_style " + test_config.angle_style);
+    Angle *angle = lmp->force->angle;
+
+    for (auto& angle_coeff : test_config.angle_coeff) {
+        command("angle_coeff " + angle_coeff);
+    }
+
+    // create (only) three atoms and one angle
+    command("mass * 1.0");
+    command("create_atoms 1 single  5.0 -0.75  0.4 units box");
+    command("create_atoms 1 single  5.5  0.25 -0.1 units box");
+    command("create_atoms 1 single  5.0  0.75  0.4 units box");
+    command("create_bonds single/angle 1 1 2 3");
+
+    for (auto& post_command : test_config.post_commands) {
+        command(post_command);
+    }
+
+    command("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    int idx1 = lmp->atom->map(1);
+    int idx2 = lmp->atom->map(2);
+    int idx3 = lmp->atom->map(3);
+    double epsilon = test_config.epsilon;
+    double eangle[4], esingle[4];
+
+    eangle[0] = angle->energy;
+    esingle[0] = angle->single(1, idx1, idx2, idx3);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("displace_atoms all random 0.5 0.5 0.5 23456");
+    command("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    idx1 = lmp->atom->map(1);
+    idx2 = lmp->atom->map(2);
+    idx3 = lmp->atom->map(3);
+    eangle[1] = angle->energy;
+    esingle[1] = angle->single(1, idx1, idx2, idx3);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("displace_atoms all random 0.5 0.5 0.5 456963");
+    command("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    idx1 = lmp->atom->map(1);
+    idx2 = lmp->atom->map(2);
+    idx3 = lmp->atom->map(3);
+    eangle[2] = angle->energy;
+    esingle[2] = angle->single(1, idx1, idx2, idx3);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    command("displace_atoms all random 0.5 0.5 0.5 9726532");
+    command("run 0 post no");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    idx1 = lmp->atom->map(1);
+    idx2 = lmp->atom->map(2);
+    idx3 = lmp->atom->map(3);
+    eangle[3] = angle->energy;
+    esingle[3] = angle->single(1, idx1, idx2, idx3);
+
+    ErrorStats stats;
+    EXPECT_FP_LE_WITH_EPS(eangle[0], esingle[0], epsilon);
+    EXPECT_FP_LE_WITH_EPS(eangle[1], esingle[1], epsilon);
+    EXPECT_FP_LE_WITH_EPS(eangle[2], esingle[2], epsilon);
+    EXPECT_FP_LE_WITH_EPS(eangle[3], esingle[3], epsilon);
+    if (print_stats)
+        std::cerr << "single_energy  stats:" << stats << std::endl;
+
+    int i = 0;
+    for (auto &dist : test_config.equilibrium)
+        EXPECT_NEAR(dist,angle->equilibrium_angle(++i),0.00001);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    cleanup_lammps(lmp,test_config);
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+}

unittest/force-styles/bond_style.cpp

@@ -778,7 +778,7 @@ TEST(BondStyle, single) {
     if (!lmp) {
         std::cerr << "One or more prerequisite styles are not available "
             "in this LAMMPS configuration:\n";
-        for (auto prerequisite : test_config.prerequisites) {
+        for (auto& prerequisite : test_config.prerequisites) {
             std::cerr << prerequisite.first << "_style "
                       << prerequisite.second << "\n";
         }
@@ -801,8 +801,6 @@ TEST(BondStyle, single) {
         lmp->input->one(line.c_str());
     };
 
-    Bond *bond = lmp->force->bond;
-
     // now start over
     if (!verbose) ::testing::internal::CaptureStdout();
     command("clear");
@@ -838,9 +836,9 @@ TEST(BondStyle, single) {
     command("pair_coeff * *");
 
     command("bond_style " + test_config.bond_style);
-    bond = lmp->force->bond;
+    Bond *bond = lmp->force->bond;
 
-    for (auto bond_coeff : test_config.bond_coeff) {
+    for (auto& bond_coeff : test_config.bond_coeff) {
         command("bond_coeff " + bond_coeff);
     }
 
@@ -1020,6 +1018,10 @@ TEST(BondStyle, single) {
     if (print_stats)
         std::cerr << "single_energy  stats:" << stats << std::endl;
 
+    int i = 0;
+    for (auto &dist : test_config.equilibrium)
+        EXPECT_NEAR(dist,bond->equilibrium_distance(++i),0.00001);
+
     if (!verbose) ::testing::internal::CaptureStdout();
     cleanup_lammps(lmp,test_config);
     if (!verbose) ::testing::internal::GetCapturedStdout();

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

@@ -1,6 +1,6 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Tue May 19 19:19:41 202
+date_generated: Thu May 28 22:02:50 202
 epsilon: 2.5e-13
 prerequisites: ! |
   atom full
@@ -14,6 +14,7 @@ angle_coeff: ! |
   2  46.1 111.3   0.0 0.000
   3  40.0 120.0  35.0 2.410
   4  33.0 108.5  30.0 2.163
+equilibrium: 1.92161 1.94255 2.0944 1.89368
 extract: ! ""
 natoms: 29
 init_energy: 85.4248638845977

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

@@ -1,6 +1,6 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Tue May 19 19:00:35 202
+date_generated: Thu May 28 22:02:43 202
 epsilon: 2.5e-13
 prerequisites: ! |
   atom full
@@ -14,6 +14,7 @@ angle_coeff: ! |
   2  45.0 111.0
   3  50.0 120.0
   4 100.0 108.5
+equilibrium: 1.92161 1.93732 2.0944 1.89368
 extract: ! ""
 natoms: 29
 init_energy: 41.530817896491

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

@@ -1,7 +1,7 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:02:55 202
-epsilon: 1.0e-14
+epsilon: 1e-14
 prerequisites: ! |
   atom full
   angle zero
@@ -14,6 +14,7 @@ angle_coeff: ! |
   2 111
   3 120
   4 108.5
+equilibrium: 1.92161 1.93732 2.0944 1.89368
 extract: ! ""
 natoms: 29
 init_energy: 0

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

@@ -1,7 +1,7 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:04:42 202
-epsilon: 1.0e-13
+epsilon: 1e-13
 prerequisites: ! |
   atom full
   bond class2
@@ -15,6 +15,7 @@ bond_coeff: ! |
   3 1.3    299.67  -501.77   679.81
   4 1.2    345.00  -691.89   844.60
   5 0.97   532.50 -1282.90  2004.76
+equilibrium: 1.42 1.1 1.3 1.2 0.97
 extract: ! |
   r0 1
 natoms: 29

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

@@ -1,6 +1,6 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:04:14 202
 epsilon: 2.5e-13
 prerequisites: ! |
   atom full
@@ -15,7 +15,8 @@ bond_coeff: ! |
   3 350.0 1.3
   4 650.0 1.2
   5 450.0 1.0
-extract: !
+equilibrium: 1.5 1.1 1.3 1.2 1
+extract: ! |
   kappa 1
   r0 1
 natoms: 29

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

@@ -1,6 +1,6 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:04:30 202
 epsilon: 2.5e-13
 prerequisites: ! |
   atom full
@@ -16,6 +16,7 @@ bond_coeff: ! |
   3 morse    7000.0 0.2 1.3
   4 harmonic  650.0 1.2
   5 harmonic  450.0 1.0
+equilibrium: 1.5 1.1 1.3 1.2 1
 extract: ! ""
 natoms: 29
 init_energy: 4.63957309438403

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

@@ -1,6 +1,6 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:04:25 202
 epsilon: 2.5e-13
 prerequisites: ! |
   atom full
@@ -15,6 +15,7 @@ bond_coeff: ! |
   3 7000.0 0.2 1.3
   4 7500.0 0.4 1.2
   5 7000.0 0.3 1.0
+equilibrium: 1.5 1.1 1.3 1.2 1
 extract: ! |
   r0 1
 natoms: 29

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

@@ -1,7 +1,7 @@
 ---
 lammps_version: 5 May 2020
-date_generated: Mon May 18 18:18:26 202
+date_generated: Thu May 28 22:03:25 202
-epsilon: 1.0e-14
+epsilon: 1e-14
 prerequisites: ! |
   atom full
   bond zero
@@ -15,6 +15,7 @@ bond_coeff: ! |
   3 1.3
   4 1.2
   5 1.0
+equilibrium: 1.5 1.1 1.3 1.2 1
 extract: ! |
   r0 1
 natoms: 29