add support for testing virial contributions from fixes (as an option) (4b7356f5) · Commits · 郑智淋 / lammps

doc/src/Build_development.rst

+9 −5

Original line number	Diff line number	Diff line
		@@ -294,14 +294,18 @@ YAML format test inputs.
		- The fix to be tested must be specified in the ``post_commands:``
		section with the fix-ID ``test``. This section may contain other
		commands and other fixes (e.g. an instance of fix nve for testing
		thermostat or force manipulation fixes)
		a thermostat or force manipulation fix)
		- For fixes that can tally contributions to the global virial, the
		line ``fix_modify test virial yes`` should be included in the
		``post_commands:`` section of the test input.
		- For thermostat fixes the target temperature should be ramped from
		an arbitrary value (e.g. 50K) to a pre-defined target temperature
		entered as ``${t_target}``.
		- For fixes that may or may not do thermostatting depending on
		the flags in use (e.g. fix rigid), the ``post_commands:`` section
		should contain ``variable t_target delete`` to disable the target
		temperature ramp check in case the thermostat is not enabled
		- For fixes that have thermostatting support included, but do not
		have it enabled in the input (e.g. fix rigid with default settings),
		the ``post_commands:`` section should contain the line
		``variable t_target delete`` to disable the target temperature ramp
		check to avoid false positives.

		Use custom linker for faster link times when ENABLE_TESTING is active
		^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

unittest/force-styles/test_fix_timestep.cpp

+153 −1

Original line number	Diff line number	Diff line
		@@ -239,6 +239,15 @@ void generate_yaml_file(const char *outfile, const TestConfig &config)
		} else {
		Fix *fix = lmp->modify->fix[ifix];

		// run_stress, if enabled
		if (fix->thermo_virial) {
		auto stress = fix->virial;
		block = fmt::format("{:23.16e} {:23.16e} {:23.16e} "
		"{:23.16e} {:23.16e} {:23.16e}",
		stress[0], stress[1], stress[2], stress[3], stress[4], stress[5]);
		writer.emit_block("run_stress", block);
		}

		// global scalar
		if (fix->scalar_flag) {
		double value = fix->compute_scalar();
		@@ -338,8 +347,19 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress normal run, verlet: " << stats << std::endl;
		}

		stats.reset();
		// global scalar
		if (fix->scalar_flag) {
		double value = fix->compute_scalar();
		@@ -402,6 +422,18 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress restart, verlet: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -453,6 +485,18 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress rmass, verlet: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -510,6 +554,18 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress normal run, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -561,6 +617,18 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress restart, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -612,6 +680,18 @@ TEST(FixTimestep, plain)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress rmass, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -701,6 +781,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress normal run, verlet: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -765,6 +857,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress restart, verlet: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -816,6 +920,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress rmass, verlet: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -873,6 +989,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress normal run, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -924,6 +1052,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress restart, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar
		@@ -975,6 +1115,18 @@ TEST(FixTimestep, omp)
		FAIL() << "ERROR: no fix defined with fix ID 'test'\n";
		} else {
		Fix *fix = lmp->modify->fix[ifix];
		if (fix->thermo_virial) {
		stats.reset();
		auto stress = fix->virial;
		EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
		EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
		if (print_stats) std::cerr << "run_stress rmass, respa: " << stats << std::endl;
		}

		stats.reset();

		// global scalar

unittest/force-styles/tests/fix-timestep-rattle_angle.yaml

+4 −1

Original line number	Diff line number	Diff line
		---
		lammps_version: 21 Jul 2020
		date_generated: Sun Aug 9 13:57:28 202
		date_generated: Sun Aug 9 16:30:21 202
		epsilon: 1e-14
		prerequisites: ! \|
		atom full
		@@ -9,8 +9,11 @@ pre_commands: ! ""
		post_commands: ! \|
		fix move all nve
		fix test solvent rattle 1.0e-5 20 4 b 5 a 1
		fix_modify test virial yes
		input_file: in.fourmol
		natoms: 29
		run_stress: ! \|-
		-6.7489444076122581e+01 -3.6466857275816793e+01 -4.1453650662488030e+01 -3.0881715538687999e+01 -2.8271646386126275e+01 1.8512924155867125e-01
		run_pos: ! \|2
		1 -2.7045559935221097e-01 2.4912159904412490e+00 -1.6695851634760922e-01
		2 3.1004029578877490e-01 2.9612354630874571e+00 -8.5466363025011627e-01

unittest/force-styles/tests/fix-timestep-rattle_bond.yaml

+4 −1

Original line number	Diff line number	Diff line
		---
		lammps_version: 21 Jul 2020
		date_generated: Sun Aug 9 13:57:18 202
		date_generated: Sun Aug 9 16:30:21 202
		epsilon: 1e-14
		prerequisites: ! \|
		atom full
		@@ -9,8 +9,11 @@ pre_commands: ! ""
		post_commands: ! \|
		fix move all nve
		fix test solute rattle 1.0e-5 20 4 m 4.00794
		fix_modify test virial yes
		input_file: in.fourmol
		natoms: 29
		run_stress: ! \|2-
		3.9891557115890999e+00 3.7983351717152480e+00 7.6152694943743228e+01 5.7163462651523300e-01 3.0839737670745507e+01 3.0066936263232019e+01
		run_pos: ! \|2
		1 -2.6863205200662160e-01 2.4924200251053037e+00 -1.6940797171640173e-01
		2 3.0314855494325726e-01 2.9555142432096928e+00 -8.4661597718762538e-01

unittest/force-styles/tests/fix-timestep-rigid-group.yaml

+4 −1

Original line number	Diff line number	Diff line
		---
		lammps_version: 21 Jul 2020
		date_generated: Sun Aug 9 07:12:15 202
		date_generated: Sun Aug 9 16:30:21 202
		epsilon: 2.5e-13
		prerequisites: ! \|
		atom full
		@@ -9,8 +9,11 @@ pre_commands: ! ""
		post_commands: ! \|
		variable t_target delete
		fix test all rigid group 2 solute solvent
		fix_modify test virial yes
		input_file: in.fourmol
		natoms: 29
		run_stress: ! \|-
		-1.4245356937318927e+03 -1.4496493315649675e+03 -3.6144360984224963e+03 8.4840626828643849e+02 2.0318336761611764e+02 -6.0622397707969685e+02
		global_scalar: 15.7115214231781
		run_pos: ! \|2
		1 -2.7899546863891622e-01 2.4731857340328216e+00 -1.7290667740241872e-01

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