Add unittests for command

examples/ex02_h2_comparison.py

@@ -20,7 +20,7 @@
 
 d = 0.9575
 h2_root = Atoms("H2", positions=[(d, 0, 0), (0, 0, 0)], cell=[8, 8, 8], pbc=True)
-rootdir = Path(__file__).parents[1] / "sandbox"
+rootdir = Path(__file__).resolve().parents[1] / "sandbox"
 fmax = 0.005
 ediff = 1e-7
 

examples/worker-cpu-spec.yml

@@ -5,15 +5,15 @@ metadata:
 spec:
   restartPolicy: Never
   containers:
-  - image: ulissigroup/kubeflow_vasp:amptorch
+  - image: ulissigroup/kubeflow_vasp:beef_vdw
     imagePullPolicy: Always
     args: [dask-worker, --nthreads, '1', --no-dashboard, --memory-limit, 2GB, --death-timeout, '60']
     name: dask
     env:
     - name: PYTHONPATH
       value: "/home/jovyan/data/vasp-interactive-test:/home/jovyan/data/vasp-interactive-test/examples"
     - name: ASE_VASP_COMMAND
-      value: "mpirun -np 4 --mca btl_vader_single_copy_mechanism none /opt/vasp.6.1.2_pgi_mkl/bin/vasp_std"
+      value: "mpirun -np 4 --mca btl_vader_single_copy_mechanism none /opt/vasp.6.1.2_pgi_mkl/bin/vasp_gam"
     resources:
       limits:
         cpu: "4"

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="vasp-interactive",
-    version="0.0.1",
+    version="0.0.2",
     packages=["vasp_interactive", "vasp_interactive.kubernetes"],
     install_requires=[
         "ase",

tests/test_class.py

@@ -11,7 +11,7 @@ def test_class():
 
     """Test if VaspInteractive correctly write inputs
     """
-    atoms = molecule("C2H2", vacuum=5)
+    atoms = molecule("C2H2", vacuum=5, pbc=True)
     with tempfile.TemporaryDirectory() as tempdir:
         tempdir = Path(tempdir)
         calc = VaspInteractive(xc="pbe", directory=tempdir)
@@ -56,7 +56,7 @@ def test_output():
 
     """Test if VaspInteractive correctly write inputs
     """
-    atoms = molecule("C2H2", vacuum=5)
+    atoms = molecule("C2H2", vacuum=5, pbc=True)
     with tempfile.TemporaryDirectory() as tempdir:
         # No value provided, default to vasp.out
         calc = VaspInteractive(xc="pbe", directory=tempdir)

tests/test_command.py

@@ -0,0 +1,53 @@
+"""Testing if environmental variable correctly passes to process
+"""
+import pytest
+from vasp_interactive import VaspInteractive
+import tempfile
+from pathlib import Path
+import os
+import sys
+
+
+def test_command_env():
+    from ase.build import molecule
+
+    # When testing under the github action system, it should be
+    # `mpirun -np 1 <options> <path>/vasp_gam`
+    default_command = os.environ["VASP_COMMAND"]
+
+    """Test if VaspInteractive correctly catches command if env changes
+    """
+    atoms = molecule("H2", vacuum=5, pbc=True)
+    with tempfile.TemporaryDirectory() as tempdir:
+        tempdir = Path(tempdir)
+        calc = VaspInteractive(xc="pbe", directory=tempdir)
+        with calc:
+            atoms.calc = calc
+            assert calc.command is None
+            command = calc.make_command()
+            assert command == default_command
+            atoms.get_potential_energy()
+            # calc.process the shell mode, so args is a string
+            assert calc.process.args == default_command
+
+            # Harmless change
+            new_command = default_command.replace("-np", "-n")
+            calc.command = new_command
+            # Should be no change
+            assert calc.process.args == default_command
+
+        with calc:
+            atoms.rattle()
+            atoms.get_potential_energy()
+            print(calc.process.args)
+            assert calc.process.args == new_command
+
+        with calc:
+            # reset the environ
+            os.environ["VASP_COMMAND"] = "echo TEST && " + default_command
+            atoms.rattle()
+            calc.command = None
+            atoms.get_potential_energy()
+            assert calc.command is None
+            print(calc.process.args)
+            assert "TEST" in calc.process.args

vasp_interactive/vasp_interactive.py

@@ -86,12 +86,6 @@ def __init__(
         self.process = None
         self.allow_restart_process = allow_restart_process
 
-        # Make command a list of args for Popen
-        cmd = self.make_command(self.command)
-        if isinstance(cmd, str):
-            cmd = cmd.split()
-        self._args = cmd
-
         # Ionic steps counter. Note this number will be 1 more than that in ase.optimize
         self.steps = 0
         # Is the relaxation finished?
@@ -196,7 +190,6 @@ def _stdin(self, text, out=None, ending="\n"):
             raise RuntimeError("VaspInteractive does not have the VASP process.")
 
     def _stdout(self, text, out=None):
-        """ """
         if out is not None:
             out.write(text)
 
@@ -240,9 +233,11 @@ def _run(self, atoms, out):
             self.initialize(atoms)
             self.write_input(atoms)
             self._stdout("Starting VASP for initial step...\n", out=out)
-            # Drop py2 support
+            # Dynamic generation of command args
+            command = self.make_command(self.command)
             self.process = Popen(
-                self._args,
+                command,
+                shell=True,
                 stdout=PIPE,
                 stdin=PIPE,
                 stderr=PIPE,