add single test to angle_style, add support for equilibrium data (08ee1cb4) · Commits · 郑智淋 / lammps

unittest/force-styles/angle_style.cpp

+149 −0

Original line number	Diff line number	Diff line
		@@ -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

+7 −5

Original line number	Diff line number	Diff line
		@@ -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

+2 −1

Original line number	Diff line number	Diff line
		---
		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

+2 −1

Original line number	Diff line number	Diff line
		---
		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

+3 −2

Original line number	Diff line number	Diff line
		---
		lammps_version: 5 May 2020
		date_generated: Mon May 18 18:18:26 202
		epsilon: 1.0e-14
		date_generated: Thu May 28 22:02:55 202
		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

Admin message