ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Updated run_tests.py for testing inplace input scripts

Browse Source
This commit is contained in:
Trung Nguyen
2023-12-10 16:56:47 -06:00
parent bcd0eac78a
commit fbbdd5bcad
3 changed files with 64 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/melt/in.melt
View File

@ -30,4 +30,6 @@ fix 1 all nve
#dump_modify 3 pad 3 #dump_modify 3 pad 3
thermo 50 thermo 50
#REG:ADD thermo 10
#REG:ADD thermo_style yaml
run 250 run 250

30
examples/melt/thermo.in.melt.yaml Normal file
View File

@ -0,0 +1,30 @@
---
keywords: ['Step', 'Temp', 'KinEng', 'PotEng', 'E_bond', 'E_angle', 'E_dihed', 'E_impro', 'E_vdwl', 'E_coul', 'E_long', 'Press', ]
data:
- [0, 3, 4.498875, -6.77336805325309, 0, 0, 0, 0, -6.77336805325309, 0, 0, -3.70335042008559, ]
- [10, 2.10321748289327, 3.15403751778382, -5.43205056762964, 0, 0, 0, 0, -5.43205056762964, 0, 0, 2.44664612874199, ]
- [20, 1.66698827387667, 2.4998572902123, -4.78557898994314, 0, 0, 0, 0, -4.78557898994314, 0, 0, 5.7194842453284, ]
- [30, 1.64463591181311, 2.46633712925273, -4.75014983253114, 0, 0, 0, 0, -4.75014983253114, 0, 0, 5.83511134604229, ]
- [40, 1.65983694888923, 2.48913298447801, -4.77212731730918, 0, 0, 0, 0, -4.77212731730918, 0, 0, 5.71855964813656, ]
- [50, 1.68428652677302, 2.52579818271199, -4.80824944183235, 0, 0, 0, 0, -4.80824944183235, 0, 0, 5.5666131491923, ]
- [60, 1.66815815080248, 2.50161166689717, -4.78367061989279, 0, 0, 0, 0, -4.78367061989279, 0, 0, 5.67528005338882, ]
- [70, 1.66402179226008, 2.49540868021802, -4.77686685471957, 0, 0, 0, 0, -4.77686685471957, 0, 0, 5.71440814999079, ]
- [80, 1.6463068175025, 2.46884286119719, -4.7503425133881, 0, 0, 0, 0, -4.7503425133881, 0, 0, 5.82878230162724, ]
- [90, 1.65213476173072, 2.47758259206044, -4.75887395274472, 0, 0, 0, 0, -4.75887395274472, 0, 0, 5.78857522212723, ]
- [100, 1.67125773589965, 2.50625988219851, -4.78756088755821, 0, 0, 0, 0, -4.78756088755821, 0, 0, 5.66139134808918, ]
- [110, 1.63826089869192, 2.45677700020087, -4.73847959372321, 0, 0, 0, 0, -4.73847959372321, 0, 0, 5.83433671147024, ]
- [120, 1.66397998337157, 2.49534598256359, -4.77733017817545, 0, 0, 0, 0, -4.77733017817545, 0, 0, 5.7161276162825, ]
- [130, 1.64420426664086, 2.46568982336129, -4.74721609415452, 0, 0, 0, 0, -4.74721609415452, 0, 0, 5.85416096284122, ]
- [140, 1.63799069414866, 2.45637179471268, -4.73761038924631, 0, 0, 0, 0, -4.73761038924631, 0, 0, 5.8924664923107, ]
- [150, 1.64447506913092, 2.46609592554545, -4.74710336860059, 0, 0, 0, 0, -4.74710336860059, 0, 0, 5.86142109924274, ]
- [160, 1.66028563222537, 2.48980584122597, -4.77053696912806, 0, 0, 0, 0, -4.77053696912806, 0, 0, 5.78149200803179, ]
- [170, 1.64800156341178, 2.47138434453138, -4.75152678764742, 0, 0, 0, 0, -4.75152678764742, 0, 0, 5.87559878509103, ]
- [180, 1.61506777079168, 2.42199600577348, -4.70280109442303, 0, 0, 0, 0, -4.70280109442303, 0, 0, 6.06457648357222, ]
- [190, 1.65753628644168, 2.48568285355511, -4.76714288367232, 0, 0, 0, 0, -4.76714288367232, 0, 0, 5.81285286411193, ]
- [200, 1.64715424139984, 2.47011367925923, -4.75090528585447, 0, 0, 0, 0, -4.75090528585447, 0, 0, 5.88054312674685, ]
- [210, 1.63561771848911, 2.45281322108923, -4.73307042686537, 0, 0, 0, 0, -4.73307042686537, 0, 0, 5.98187394543464, ]
- [220, 1.63598264224576, 2.4533604698778, -4.73411363245931, 0, 0, 0, 0, -4.73411363245931, 0, 0, 5.99506689751106, ]
- [230, 1.64254851953143, 2.46320682360233, -4.74376812701158, 0, 0, 0, 0, -4.74376812701158, 0, 0, 5.92494093901652, ]
- [240, 1.64699582794229, 2.46987611847796, -4.75091222082099, 0, 0, 0, 0, -4.75091222082099, 0, 0, 5.8750140904026, ]
- [250, 1.66455966684989, 2.49621529039977, -4.77743273563228, 0, 0, 0, 0, -4.77743273563228, 0, 0, 5.75260890051261, ]
...

44
tools/regression-tests/run_tests.py
View File

@ -1,10 +1,15 @@
''' '''
UPDATE: Oct 25, 2023: UPDATE: Dec 10, 2023:
Launching the LAMMPS binary under testing using a configuration defined in a yaml file (e.g. config.yaml) Launching the LAMMPS binary under testing using a configuration defined in a yaml file (e.g. config.yaml).
this way we can launch LAMMPS with mpirun with more flexibility. Also it simplifies the build configuration. This way we can:
+ launch tests with mpirun with multiple procs
+ specify what LAMMPS binary version to test
+ simplify the build configuration
Example usage:
python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=config.yaml --gen-ref=False python3 run_tests.py --lmp-bin=/path/to/lmp_binary --config-file=config.yaml --gen-ref=False
--------------------------------------------------------------------------------------------------------------
Original plan: using the LAMMPS Python module Original plan: using the LAMMPS Python module
The following steps are for setting up regression tests with the LAMMPS Python module The following steps are for setting up regression tests with the LAMMPS Python module
@ -158,12 +163,12 @@ def has_markers(input):
''' '''
Iterate over a list of input files Iterate over a list of input files
''' '''
def iterate(input_list): def iterate(input_list, removeAnnotatedInput=False):
num_tests = len(input_list) num_tests = len(input_list)
test_id = 0 test_id = 0
# iterative over the input scripts # iterative over the input scripts
for input in input_list: for input in input_list:
input_test = input + '.test' input_test = 'test.' + input
if os.path.isfile(input) == True: if os.path.isfile(input) == True:
if has_markers(input): if has_markers(input):
@ -233,9 +238,15 @@ def iterate(input_list):
test_id = test_id + 1 test_id = test_id + 1
# remove the annotated input script
if removeAnnotatedInput == True:
cmd_str = "rm " + input_test
os.system(cmd_str)
''' '''
TODO: TODO:
- automate tagging the example input scripts of the installed packages - automate annotating the example input scripts of the installed packages
''' '''
if __name__ == "__main__": if __name__ == "__main__":
@ -275,26 +286,28 @@ if __name__ == "__main__":
packages = get_installed_packages(lmp_binary) packages = get_installed_packages(lmp_binary)
print(f"List of installed packages: {packages}") print(f"List of installed packages: {packages}")
# list of input scripts with markers #REG:SUB and #REG:ADD # Using inplace input scripts
#input_list=['in.lj', 'in.rhodo', 'in.eam']
#iterate(input_list)
automated = True inplace_input = True
if automated == True: if inplace_input == True:
# save current working dir # save current working dir
p = subprocess.run("pwd", shell=True, text=True, capture_output=True) p = subprocess.run("pwd", shell=True, text=True, capture_output=True)
pwd = p.stdout.split('\n')[0] pwd = p.stdout.split('\n')[0]
print("Working dir" + pwd) print("Working dir" + pwd)
# change dir to an example # change dir to a folder under examples/
# TODO: loop through the subfolders under examples/, depending on the installed packages
directory = "../../examples/melt" directory = "../../examples/melt"
print("Entering " + directory) print("Entering " + directory)
os.chdir(directory) os.chdir(directory)
# create a symbolic link to the lammps binary at the present directory # create a symbolic link to the lammps binary at the present directory
cmd_str = "ln -s " + lmp_binary + " lmp" cmd_str = "ln -s " + lmp_binary + " lmp"
os.system(cmd_str) os.system(cmd_str)
input_list=['in.melt'] input_list=['in.melt']
# iterate through the input scripts
iterate(input_list) iterate(input_list)
# unlink the symbolic link # unlink the symbolic link
@ -303,3 +316,8 @@ if __name__ == "__main__":
# get back to the working dir # get back to the working dir
cmd_str = "cd " + pwd cmd_str = "cd " + pwd
os.system(cmd_str) os.system(cmd_str)
else:
# or using the input scripts in the working directory
input_list=['in.lj', 'in.rhodo', 'in.eam']
iterate(input_list)