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add support for testing virial contributions from fixes (as an option)

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This commit is contained in:
Axel Kohlmeyer
2020-08-09 16:39:31 -04:00
parent f1da1ed180
commit 4b7356f5af
10 changed files with 194 additions and 14 deletions
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14
doc/src/Build_development.rst
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@ -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
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

152
unittest/force-styles/test_fix_timestep.cpp
View File

@ -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

5
unittest/force-styles/tests/fix-timestep-rattle_angle.yaml
View File

@ -1,6 +1,6 @@
---
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

5
unittest/force-styles/tests/fix-timestep-rattle_bond.yaml
View File

@ -1,6 +1,6 @@
---
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

5
unittest/force-styles/tests/fix-timestep-rigid-group.yaml
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@ -1,6 +1,6 @@
---
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

5
unittest/force-styles/tests/fix-timestep-rigid-molecule.yaml
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@ -1,6 +1,6 @@
---
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 solvent rigid molecule
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-4.9200116134790363e+01 -2.6907707565987732e+01 -6.0080860422282560e+00 -2.5620423972101747e+01 -1.3450224059984075e+01 -1.4947288487004844e+00
global_scalar: 18.3405601674144
run_pos: ! |2
1 -2.7993683669226832e-01 2.4726588069312840e+00 -1.7200860244148433e-01

5
unittest/force-styles/tests/fix-timestep-rigid-single.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:12:16 202
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 solute rigid single
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-1.3754817466835852e+03 -1.4228425246165939e+03 -3.6087196201913630e+03 8.7407043149698166e+02 2.1665316519768876e+02 -6.0480791462031175e+02
global_scalar: 4.53142303857031
run_pos: ! |2
1 -2.7899546859693181e-01 2.4731857340428789e+00 -1.7290667720876129e-01

5
unittest/force-styles/tests/fix-timestep-shake_angle.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:39:26 202
date_generated: Sun Aug 9 16:30:22 202
epsilon: 1e-14
prerequisites: ! |
atom full
@ -9,8 +9,11 @@ pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solvent shake 1.0e-5 20 4 b 5 a 1
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |-
-6.7489461181454146e+01 -3.6466852749734755e+01 -4.1453635345326461e+01 -3.0881721833345594e+01 -2.8271651455044346e+01 1.8512237607314627e-01
run_pos: ! |2
1 -2.7045559935221097e-01 2.4912159904412490e+00 -1.6695851634760922e-01
2 3.1004029578877490e-01 2.9612354630874571e+00 -8.5466363025011627e-01

5
unittest/force-styles/tests/fix-timestep-shake_bond.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:37:51 202
date_generated: Sun Aug 9 16:30:22 202
epsilon: 1e-14
prerequisites: ! |
atom full
@ -9,8 +9,11 @@ pre_commands: ! ""
post_commands: ! |
fix move all nve
fix test solute shake 1.0e-5 20 4 m 4.00794
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
4.1327164284089424e+00 4.1298776885725212e+00 7.7065049821613400e+01 7.3427739401911385e-01 3.1021321349896283e+01 3.0482918118325731e+01
run_pos: ! |2
1 -2.6863205200661111e-01 2.4924200251053290e+00 -1.6940797171639235e-01
2 3.0314855494326542e-01 2.9555142432097057e+00 -8.4661597718762593e-01

5
unittest/force-styles/tests/fix-timestep-wall-harmonic_const.yaml
View File

@ -1,6 +1,6 @@
---
lammps_version: 21 Jul 2020
date_generated: Sun Aug 9 07:21:00 202
date_generated: Sun Aug 9 16:30:22 202
epsilon: 1e-14
prerequisites: ! |
atom full
@ -10,8 +10,11 @@ pre_commands: ! |
post_commands: ! |
fix move all nve
fix test solute wall/harmonic ylo EDGE 100.0 0.0 5.0 yhi EDGE 100.0 0.0 5.0
fix_modify test virial yes
input_file: in.fourmol
natoms: 29
run_stress: ! |2-
0.0000000000000000e+00 7.2422093200265749e+02 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
global_scalar: 42.6997744353244
global_vector: ! |-
2 0.0 161.92409617466126