Initiated the regression test setup

tools/regression-tests/config.yaml

@@ -0,0 +1,10 @@
+---
+  lmp_binary: ""
+  nprocs: "4"
+  args: "-sc none -cite none"
+  mpiexec: "mpirun"
+  mpiexec_numproc_flag: "-n"
+  accelerator_supported:
+    - omp
+
+

tools/regression-tests/in.lj

@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt
+
+variable        x index 1
+variable        y index 1
+variable        z index 1
+
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
+
+units           lj
+atom_style      atomic
+
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+fix             1 all nve
+                #REG:ADD thermo 10
+                #REG:ADD thermo_style yaml
+run             100

tools/regression-tests/in.lj.test

@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt
+
+variable        x index 1
+variable        y index 1
+variable        z index 1
+
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
+
+units           lj
+atom_style      atomic
+
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
+
+velocity        all create 1.44 87287 loop geom
+
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
+
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
+
+fix             1 all nve
+                 thermo 10
+                 thermo_style yaml
+run             100

tools/regression-tests/in.rhodo

@@ -0,0 +1,27 @@
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1   #REG:ADD check no
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+fix             2 all npt temp 300.0 300.0 100.0 &
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+thermo          50            #REG:SUB thermo 20
+thermo_style    multi         #REG:SUB thermo_style yaml
+timestep        2.0
+
+run             100           #REG:SUB run 200 post no

tools/regression-tests/in.rhodo.test

@@ -0,0 +1,27 @@
+# Rhodopsin model
+
+units           real
+neigh_modify    delay 5 every 1    check no
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data       data.rhodo
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+fix             2 all npt temp 300.0 300.0 100.0 &
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+
+special_bonds   charmm
+
+ thermo 20
+ thermo_style yaml
+timestep        2.0
+
+ run 200 post no

tools/regression-tests/run_tests.py

@@ -0,0 +1,172 @@
+'''
+UPDATE: Oct 25, 2023:
+  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.
+
+  python3 run_tests.py /path/to/lmp_binary
+
+Original plan: using the LAMMPS Python module
+  The following steps are for setting up regression tests with the LAMMPS Python module
+
+  0) Create a virtual environment, and activate it
+
+    python -m venv lmp-venv
+    source lmp-venv/bin/activate
+    PYTHON_EXECUTABLE=`which python`
+    INSTALL_PREFIX=$(${PYTHON_EXECUTABLE} -c "import sys; print(sys.prefix)")
+
+  1) Build LAMMPS as a shared lib and install the LAMMPS python module into the virtual environment
+
+    git clone https://github.com/lammps/lammps.git lammps
+    cd lammps
+    mkdir build && cd build
+    cmake ../cmake/presets/basic.cmake -DBUILD_SHARED_LIBS=on -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX
+    make -j4
+    make install-python
+
+  2) Run this script, after activating the virtual environment and having the input scripts with markers ready:
+
+    source lmp-venv/bin/activate
+    python3 run_tests.py
+
+'''
+
+#from lammps import lammps
+import sys
+import re, yaml
+import subprocess
+
+try:
+    from yaml import CSafeLoader as Loader
+except ImportError:
+    from yaml import SafeLoader as Loader
+
+'''
+  inputFileName:  input file with comments #REG:ADD and #REG:SUB as markers
+  outputFileName: modified input file ready for testing
+'''
+def processing_markers(inputFileName, outputFileName):
+  # read in the script
+  with open(inputFileName, 'r') as file:
+    data = file.read()
+
+    # replace #REG:ADD with empty string (i.e. adding the text at the end of the line)
+    data = data.replace("#REG:ADD", "")
+
+    # replace the line contaning #REG:SUB with a line with the text that follows this marker 
+    data = data.splitlines()
+    separator="#REG:SUB"
+    out = []
+    for line in data:
+      s = line.split(separator)
+      if len(s) < 2:
+        out.append(line)
+      else:
+        out.append(s[1])
+
+  # write data to the new script
+  with open(outputFileName, 'w') as file:
+    for line in out:
+      file.write(line + "\n")
+
+'''
+  yamlFileName: input YAML file with thermo structured as described in https://docs.lammps.org/Howto_structured_data.html
+  return: thermo, which is a list containing a dictionary for each run where the tag "keywords" maps to the list
+    of thermo header strings and the tag “data” has a list of lists where the outer list represents the lines
+    of output and the inner list the values of the columns matching the header keywords for that step.
+'''
+def extract_thermo(yamlFileName):
+  docs = ""
+  with open(yamlFileName) as f:
+      for line in f:
+          m = re.search(r"^(keywords:.*$|data:$|---$|\.\.\.$|  - \[.*\]$)", line)
+          if m: docs += m.group(0) + '\n'
+
+  thermo = list(yaml.load_all(docs, Loader=Loader))
+  return thermo
+
+'''
+  launch LAMMPS using the configuration defined in the dictionary config with an input file
+  TODO:
+    - generate new reference values if needed
+    - wrap subprocess with try/catch to handle exceptions
+'''
+def execute(lmp_binary, config, input_file_name, generate_ref_yaml=False):
+  cmd_str = config['mpiexec'] + " " + config['mpiexec_numproc_flag'] + " " + config['nprocs'] + " "
+  cmd_str += lmp_binary + " -in " + input_file_name + " " + config['args']
+  print(f"Execute: {cmd_str}")
+  p = subprocess.run(cmd_str, shell=True, text=True, capture_output=True)
+  output = p.stdout.split('\n')
+
+'''
+  TODO:
+    - process "lmp -h" to get the list of installed packages
+    - automate tagging the example input scripts of the installed packages
+'''
+if __name__ == "__main__":
+
+  lmp_binary = ""
+  # if lmp binary is specified in the command line
+  if len(sys.argv) >= 2:
+    lmp_binary = sys.argv[1]
+
+  # list of input scripts with markers #REG:SUB and #REG:ADD
+  input_list=['in.lj', 'in.rhodo']
+
+  # read in the configuration of the tests
+  with open("config.yaml", 'r') as f:
+    config = yaml.load(f, Loader=Loader)
+    print(config)
+ 
+  # check if lmp_binary is specified in the config yaml
+  if lmp_binary == "":
+    if config['lmp_binary'] == "":
+       print("Needs a valid LAMMPS binary")
+       exit
+    else:
+       lmp_binary = config['lmp_binary']
+  
+  # iterative over the input scripts
+  for input in input_list:
+    input_test=input + '.test'
+    processing_markers(input, input_test)
+    
+    str_t = "Running " + input_test
+    print(str_t)
+    print(f"-"*len(str_t))
+
+    # using the LAMMPS python module (for single-proc runs)
+    #  lmp = lammps()
+    #  lmp.file(input_test)
+    
+    # or more customizable with config.yaml
+    execute(lmp_binary, config, input_test)
+
+    # process thermo output
+    thermo = extract_thermo("log.lammps")
+
+    num_runs = len(thermo)
+    if num_runs == 0:
+       print(f"Failed with {input_test}\n")
+       continue 
+
+    print(f"Number of runs: {num_runs}")
+
+    # read in the thermo yaml output  
+    thermo_ref_file = 'thermo.' + input + '.yaml'
+    thermo_ref = extract_thermo(thermo_ref_file)
+
+    # comparing output vs reference values
+    width = 20
+    print("Quantities".ljust(width) + "Output".center(width) + "Reference".center(width) + "Diff.".center(width))
+    irun = 0
+    num_fields = len(thermo[irun]['keywords'])
+    for i in range(num_fields):
+       val = thermo[irun]['data'][2][i]
+       ref = thermo[0]['data'][2][i]
+       diff = float(val) - float(ref)
+       print(f"{thermo[0]['keywords'][i].ljust(width)} {str(val).rjust(20)} {str(ref).rjust(20)} {str(diff).rjust(20)}")
+    print("-"*(4*width+3))
+
+
+

tools/regression-tests/thermo.in.lj.yaml

@@ -0,0 +1,15 @@
+---
+keywords: ['Step', 'Temp', 'KinEng', 'PotEng', 'E_bond', 'E_angle', 'E_dihed', 'E_impro', 'E_vdwl', 'E_coul', 'E_long', 'Press', ]
+data:
+  - [0, 1.44000000000001, 2.15993250000001, -6.77336805323422, 0, 0, 0, 0, -6.77336805323422, 0, 0, -5.01970725908556, ]
+  - [10, 1.12539487029313, 1.68803955255514, -6.30005271976029, 0, 0, 0, 0, -6.30005271976029, 0, 0, -2.55968522600129, ]
+  - [20, 0.625793798302192, 0.938661363368992, -5.55655653922756, 0, 0, 0, 0, -5.55655653922756, 0, 0, 0.973517658007722, ]
+  - [30, 0.745927295413064, 1.11885597777762, -5.73951278150759, 0, 0, 0, 0, -5.73951278150759, 0, 0, 0.339284096694852, ]
+  - [40, 0.731026217827733, 1.09650505988764, -5.71764564663628, 0, 0, 0, 0, -5.71764564663628, 0, 0, 0.388973418756238, ]
+  - [50, 0.740091517740786, 1.11010258482128, -5.73150426762886, 0, 0, 0, 0, -5.73150426762886, 0, 0, 0.335273324523691, ]
+  - [60, 0.750500641591031, 1.12571578266897, -5.74713299283555, 0, 0, 0, 0, -5.74713299283555, 0, 0, 0.26343139026926, ]
+  - [70, 0.755436366857812, 1.13311913920702, -5.75480059117447, 0, 0, 0, 0, -5.75480059117447, 0, 0, 0.224276619217515, ]
+  - [80, 0.759974280364828, 1.13992579675285, -5.76187162670983, 0, 0, 0, 0, -5.76187162670983, 0, 0, 0.191626237124102, ]
+  - [90, 0.760464250735042, 1.14066072934081, -5.76280209529731, 0, 0, 0, 0, -5.76280209529731, 0, 0, 0.189478083345243, ]
+  - [100, 0.757453103239936, 1.13614414924569, -5.75850548601596, 0, 0, 0, 0, -5.75850548601596, 0, 0, 0.207261053624723, ]
+...

tools/regression-tests/thermo.in.rhodo.yaml

@@ -0,0 +1,15 @@
+---
+keywords: ['Step', 'Temp', 'KinEng', 'PotEng', 'E_bond', 'E_angle', 'E_dihed', 'E_impro', 'E_vdwl', 'E_coul', 'E_long', 'Press', 'Volume', ]
+data:
+  - [0, 299.039674593374, 21444.8312841477, -46801.0376681541, 2537.99401058653, 10921.3742085766, 5211.78649955145, 213.511585445475, -2307.86341545531, 207025.89272923, -270403.733286089, -149.330107246328, 307995.0335, ]
+  - [20, 299.99775596386, 21513.5375298139, -46857.6878168353, 2540.16808710553, 10813.4472821057, 5184.14211975371, 221.342010137235, -2204.37204196886, 206976.604587209, -270389.019861177, 477.300972239503, 307985.712575511, ]
+  - [40, 300.820676434129, 21572.5510726462, -46903.9535613665, 2554.70824060399, 10802.5198367863, 5193.55697621983, 227.543745597181, -2099.98472913888, 206823.579169277, -270405.876800712, 139.994267989278, 308012.644819437, ]
+  - [60, 299.2331882218, 21458.7085969772, -46780.429323943, 2596.24317980854, 10780.8170148765, 5226.16290108029, 222.228413660505, -2104.75642217625, 206899.797834027, -270400.92224522, 127.22108251404, 308056.810003531, ]
+  - [80, 300.46072237423, 21546.737928972, -46847.0583926036, 2536.59042271716, 10924.8018010137, 5186.04740702919, 222.7881900458, -2041.9411984891, 206726.747509985, -270402.092524906, -413.008542107374, 308097.593860177, ]
+  - [100, 301.090606450347, 21591.9083825557, -46882.6386958151, 2567.98068348825, 10781.9571167463, 5198.74922392828, 216.786418763304, -1902.66178448095, 206659.522653541, -270404.973007801, 6.7406473046388, 308134.228503829, ]
+  - [120, 300.685941196944, 21562.8888950994, -46837.9522831012, 2541.01730379153, 10831.9758258843, 5226.65101853851, 223.572832322853, -1975.83494841013, 206719.093753221, -270404.42806845, 428.656137442736, 308222.498901718, ]
+  - [140, 298.380498037274, 21397.5601986261, -46664.8022666901, 2493.80367285064, 10925.8992265538, 5266.80649683893, 219.398357899592, -1911.54569787679, 206747.9911322, -270407.155455156, -173.318924696789, 308402.211640527, ]
+  - [160, 297.736178370372, 21351.3545352186, -46582.6109596667, 2492.19606551665, 11004.0458067009, 5281.49837380749, 213.676293532578, -2047.52570313019, 206880.475440937, -270406.977237031, 42.9380783207654, 308627.866482533, ]
+  - [180, 299.513482118553, 21478.8091248888, -46647.4003388357, 2471.17948439442, 11079.0862594569, 5266.33520079545, 227.130563582703, -2320.66315429553, 207032.450828902, -270402.919521672, 36.7672752293621, 308836.815084476, ]
+  - [200, 300.804014463663, 21571.356203952, -46650.2048512757, 2488.69566833254, 11073.4385663243, 5221.75299737997, 232.855292128454, -2167.74358296738, 206902.920361046, -270402.124153519, 20.6683483419149, 308997.56038946, ]
+...