Add Testsuite

.gitignore

@@ -81,3 +81,5 @@ documentation_carousel.md
 # Annoying OSX files
 .DS_Store
 fortls_debug.log
+
+__pycache__

CONTRIBUTING.md

@@ -23,4 +23,4 @@ In order to contribute code to `TDEP`, please follow the usual steps for [prepar
 
   This will format the code with an indent (`-i`) of 4 characters, without enforcing line breaks (`-l 500` allows up to 500 characters per line - please use less.)
 
-- Please _document_ and _test_ your changes by providing an example in the `examples` folder. 
+- Please _document_ and _test_ your changes by providing an example in the [`./examples`](./examples) or [`./tests`](./tests) folder.

INSTALL.md

@@ -31,11 +31,28 @@ Then run the build script via
 bash build_things.sh --nthreads_make 4
 ```
 
+If everything works find, the last lines of the output should be something like:
+
+```bash
+...
+
+Printing bashrc_tdep, append these lines to your .bashrc for stuff to work nicely
+MANPATH=$MANPATH:/path/to/tdep/man
+PATH=$PATH:/path/to/tdep/bin
+export MANPATH
+export PATH
+alias gnuplot='gnuplot -persist'
+
+Everything should be set up and good to go!
+```
+
+i.e., add the respective lines to your `.bashrc` and you are all set up!
+
 **If problems occur, please look at the [Troubleshooting section below](#Troubleshooting). If you cannot fix the error, please reach out, e.g., via the [issue tracker](https://github.com/tdep-developers/tdep/issues).**
 
 ## Check your installation
 
-We advise to run the examples in `tdep/examples` to test your installation after compilation.
+We advise to run the tests in [`./tests`](./tests)  to check your installation.
 
 ## HDF5
 
@@ -157,4 +174,4 @@ If you see the error
 ... error: unrecognized command line option '-fallow-argument-mismatch'; did you mean '-Wno-argument-mismatch'?
 ```
 
-it likely means that you are using an older Fortran version, and should replace `-fallow-argument-mismatch` with `-Wno-argument-mismatch` in your `important_settings` as suggested.
+it likely means that you are using an older Fortran version, and should replace `-fallow-argument-mismatch` with `-Wno-argument-mismatch` in your `important_settings` as suggested.

tests/Makefile

@@ -0,0 +1,17 @@
+testfiles:
+	bash make_all_testfiles.sh
+
+test:
+	pytest
+
+all: clean testfiles
+	pytest
+
+clean:
+	rm -f */outfile*
+	rm -rf */__pycache__/
+	rm -rf *.pytest_cache/
+	rm -f */contcar*
+	rm -f */*.dat
+	rm -f */*.log
+

tests/README.md

@@ -0,0 +1,42 @@
+Test suite
+===
+
+## Run binaries and create test files
+
+```bash
+make testfiles
+```
+
+will run the TDEP binaries **from your current PATH** and create their output.
+
+## Run tests
+
+To check the files that were created against reference data, please run
+
+```bash
+make test
+```
+
+This will run python scripts in each folder to check the produced output. **Please note that this requires some python dependencies which you find in `requirements.txt` and install via `pip install -r requirements.txt`**.
+
+Run
+
+```bash
+make all
+```
+
+to run everything.
+
+## Clean up
+
+Use
+
+```bash
+make clean
+```
+
+to clean test files.
+
+## Reference files
+
+Were created with TDEP commit `8c01e0343e4098f1d160efc141f8af6ae7f54941` on a macbook with M1 chip.

tests/anharmonic_free_energy/Makefile

@@ -0,0 +1,2 @@
+testfiles:
+	anharmonic_free_energy

tests/anharmonic_free_energy/infile.forceconstant

@@ -0,0 +1 @@
+../infiles/infile.forceconstant

tests/anharmonic_free_energy/infile.forceconstant_thirdorder

@@ -0,0 +1 @@
+../infiles/infile.forceconstant_thirdorder

tests/anharmonic_free_energy/infile.forces

@@ -0,0 +1 @@
+../infiles/infile.forces

tests/anharmonic_free_energy/infile.meta

@@ -0,0 +1 @@
+../infiles/infile.meta

tests/anharmonic_free_energy/infile.positions

@@ -0,0 +1 @@
+../infiles/infile.positions

tests/anharmonic_free_energy/infile.ssposcar

@@ -0,0 +1 @@
+../infiles/infile.ssposcar

tests/anharmonic_free_energy/infile.stat

@@ -0,0 +1 @@
+../infiles/infile.stat

tests/anharmonic_free_energy/infile.ucposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar

tests/anharmonic_free_energy/reference/outfile.anharmonic_free_energy

@@ -0,0 +1,7 @@
+ # Lowest order approximation to the free energy: (eV/atom)
+ # Calculated as <U - U_second - U_polar> + F_phonon
+ F        =   -3744.8107316589626     
+ # Absolute bound on error:   0.0000000000000000     
+ # Components of the Free energy
+ U0       =  -3744.8468307109688     
+ F_phonon =   3.6099052005669353E-002

tests/anharmonic_free_energy/test_anharmonic_free_energy.py

@@ -0,0 +1,29 @@
+import numpy as np
+from pathlib import Path
+
+parent = Path(__file__).parent
+folder = parent / "reference"
+
+
+def _read_file(file):
+    with open(file) as f:
+        next(f)
+        next(f)
+        F = float(next(f).split()[2])
+        next(f)
+        next(f)
+        U0 = float(next(f).split()[2])
+        Fp = float(next(f).split()[2])
+
+    return np.array([F, U0, Fp])
+
+
+def test_output(file="outfile.anharmonic_free_energy"):
+    data_ref = _read_file(folder / file)
+    data_new = _read_file(parent / file)
+
+    np.testing.assert_allclose(data_ref, data_new, err_msg=(parent / file).absolute())
+
+
+if __name__ == "__main__":
+    test_output()

tests/atomic_distribution/Makefile

@@ -0,0 +1,3 @@
+testfiles:
+	rm -f outfile.*
+	atomic_distribution

tests/atomic_distribution/infile.forces

@@ -0,0 +1 @@
+../infiles/infile.forces

tests/atomic_distribution/infile.meta

@@ -0,0 +1 @@
+../infiles/infile.meta

tests/atomic_distribution/infile.positions

@@ -0,0 +1 @@
+../infiles/infile.positions

tests/atomic_distribution/infile.ssposcar

@@ -0,0 +1 @@
+../infiles/infile.ssposcar

tests/atomic_distribution/infile.stat

@@ -0,0 +1 @@
+../infiles/infile.stat

tests/atomic_distribution/infile.ucposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar

tests/atomic_distribution/reference/outfile.mean_square_displacement

@@ -0,0 +1,24 @@
+      0.0000000000E+00     0.1324324513E-01     0.7575131815E-02     0.5668113312E-02
+      0.1000000000E+01     0.1325716124E-01     0.6431467011E-02     0.6825694228E-02
+      0.2000000000E+01     0.1521220719E-01     0.8681552719E-02     0.6530654468E-02
+      0.3000000000E+01     0.1354675923E-01     0.7593830527E-02     0.5952928702E-02
+      0.4000000000E+01     0.1350535340E-01     0.7621549108E-02     0.5883804293E-02
+      0.5000000000E+01     0.1451778889E-01     0.7683050491E-02     0.6834738404E-02
+      0.6000000000E+01     0.1366543408E-01     0.7647978904E-02     0.6017455175E-02
+      0.7000000000E+01     0.1374110908E-01     0.7262810932E-02     0.6478298147E-02
+      0.8000000000E+01     0.1420842632E-01     0.7729059346E-02     0.6479366977E-02
+      0.9000000000E+01     0.1478612211E-01     0.7998269465E-02     0.6787852645E-02
+      0.1000000000E+02     0.1342004651E-01     0.7007244616E-02     0.6412801889E-02
+      0.1100000000E+02     0.1204463696E-01     0.6593592776E-02     0.5451044183E-02
+      0.1200000000E+02     0.1456863041E-01     0.8343406443E-02     0.6225223967E-02
+      0.1300000000E+02     0.1381476779E-01     0.7974751335E-02     0.5840016458E-02
+      0.1400000000E+02     0.1250360305E-01     0.6971732195E-02     0.5531870852E-02
+      0.1500000000E+02     0.1343391609E-01     0.7125686577E-02     0.6308229517E-02
+      0.1600000000E+02     0.1203339223E-01     0.6173066149E-02     0.5860326077E-02
+      0.1700000000E+02     0.1346966481E-01     0.7444351019E-02     0.6025313793E-02
+      0.1800000000E+02     0.1280969769E-01     0.6846304693E-02     0.5963392995E-02
+      0.1900000000E+02     0.1403983413E-01     0.8144062000E-02     0.5895772131E-02
+      0.2000000000E+02     0.1221906310E-01     0.6789029898E-02     0.5430033200E-02
+      0.2100000000E+02     0.1301751363E-01     0.6752937241E-02     0.6264576394E-02
+      0.2200000000E+02     0.1412698324E-01     0.6992694849E-02     0.7134288387E-02
+      0.2300000000E+02     0.1359467381E-01     0.7785864242E-02     0.5808809569E-02

tests/atomic_distribution/test_atomic_distribution.py

@@ -0,0 +1,41 @@
+import numpy as np
+import xarray as xr
+from pathlib import Path
+
+parent = Path(__file__).parent
+folder = parent / "reference"
+
+files_hdf5 = [
+    "outfile.mean_square_displacement.hdf5",
+    "outfile.pair_distribution.hdf5",
+    "outfile.powder_diffraction.hdf5",
+]
+
+
+def test_mean_square_displacement(file="outfile.mean_square_displacement"):
+    file_ref = folder / file
+    file_new = parent / file
+
+    data_ref = np.loadtxt(file_ref)
+    data_new = np.loadtxt(file_new)
+
+    np.testing.assert_allclose(data_ref, data_new, err_msg=file_new.absolute())
+
+
+def test_hdf5(files=files_hdf5, decimals=7):
+    for file in files:
+        file_ref = folder / file
+        file_new = parent / file
+
+        ds_ref = xr.load_dataset(file_ref)
+        ds_new = xr.load_dataset(file_new)
+
+        for var in ds_ref.data_vars:
+            x = ds_ref[var].round(decimals=decimals)
+            y = ds_new[var].round(decimals=decimals)
+            np.testing.assert_allclose(x, y, err_msg=var)
+
+
+if __name__ == "__main__":
+    test_mean_square_displacement()
+    test_hdf5()

tests/canonical_configuration/Makefile

@@ -0,0 +1,6 @@
+testfiles:
+	canonical_configuration --modes | tail -n 12 | tee canonical_configuration.dat
+	rm contcar*
+
+test: testfiles
+	pytest

tests/canonical_configuration/infile.forceconstant

@@ -0,0 +1 @@
+../infiles/infile.forceconstant

tests/canonical_configuration/infile.ssposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar

tests/canonical_configuration/infile.ucposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar

tests/canonical_configuration/reference/canonical_configuration.dat

@@ -0,0 +1,12 @@
+    1     +        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    2     -        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    3     +        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    4     -        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    5     +        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    6     -        0.00000        0.00000            NaN        0.00000        0.00000       0.00000000
+    7     +       50.00000       50.00000        1.00000       50.00000        7.14286       0.00397797
+    8     -       50.00000       50.00000        1.00000       50.00000       12.50000       0.00696145
+    9     +       50.00000       50.00000        1.00000       50.00000       16.66667       0.00928193
+   10     -       50.00000       50.00000        1.00000       50.00000       20.00000       0.01113832
+   11     +       50.00000       20.79236        1.13229       35.39618       21.39965       0.01175817
+   12     -       50.00000       20.79236        1.24180       35.39618       22.56603       0.01227471

tests/canonical_configuration/test_canonical_configuration.py

@@ -0,0 +1,33 @@
+import numpy as np
+from pathlib import Path
+
+parent = Path(__file__).parent
+folder = parent / "reference"
+
+
+def _check_numeric(character):
+    try:
+        float(character)
+        return True
+    except ValueError:
+        return False
+
+
+def _read_log(file):
+    rows = []
+    with open(file) as f:
+        for line in f:
+            rows.append([s for s in line.split() if _check_numeric(s)])
+
+    return np.nan_to_num(np.array(rows, dtype=float))
+
+
+def test_log(file="canonical_configuration.dat"):
+    data_ref = _read_log(folder / file)
+    data_new = _read_log(parent / file)
+
+    np.testing.assert_allclose(data_ref, data_new, err_msg=(parent / file).absolute())
+
+
+if __name__ == "__main__":
+    test_log()

tests/crystal_structure_info/Makefile

@@ -0,0 +1,5 @@
+testfiles:
+	crystal_structure_info
+
+test: testfiles
+	pytest

tests/crystal_structure_info/infile.ucposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar

tests/crystal_structure_info/reference/outfile.qpoints_dispersion

@@ -0,0 +1,7 @@
+FCC                         ! Bravais lattice type
+  100                       ! Number of points on each path
+    4                       ! Number paths between special points
+GM  X                       ! Starting and ending special point
+X   U                       !
+K   GM                      !
+GM  L                       !

tests/crystal_structure_info/test_crystal_structure_info.py

@@ -0,0 +1,16 @@
+from pathlib import Path
+import filecmp
+
+parent = Path(__file__).parent
+folder = parent / "reference"
+
+
+def test_output(file="outfile.qpoints_dispersion"):
+    file_ref = folder / file
+    file_new = parent / file
+
+    assert filecmp.cmp(file_ref, file_new), file_new.absolute()
+
+
+if __name__ == "__main__":
+    test_output()

tests/extract_forceconstants/Makefile

@@ -0,0 +1,2 @@
+testfiles:
+	extract_forceconstants -rc2 0 -rc3 0 --polar

tests/extract_forceconstants/infile.lotosplitting

@@ -0,0 +1 @@
+../infiles/infile.lotosplitting

tests/extract_forceconstants/infile.sim.hdf5

@@ -0,0 +1 @@
+../infiles/infile.sim.hdf5

tests/extract_forceconstants/infile.ssposcar

@@ -0,0 +1 @@
+../infiles/infile.ssposcar

tests/extract_forceconstants/infile.ucposcar

@@ -0,0 +1 @@
+../infiles/infile.ucposcar