Merge pull request #317 from libAtoms/vasp_simplify

simplify Vasp wrapper to minimize mangling to ASE Vasp calculator keywords

docs/source/overview.queued.md

@@ -70,7 +70,7 @@ cat<<EOF > remoteinfo.json
      "resources": { "num_nodes" : 1, "max_time": "24h" },
      "num_inputs_per_queued_job" : 1,
      "input_files": ["POTCARs"],
-     "env_vars": ["VASP_COMMAND=${vasp_path}", "VASP_PP_PATH=POTCARs",
+     "env_vars": ["ASE_VASP_COMMAND=${vasp_path}", "VASP_PP_PATH=POTCARs",
                   "WFL_NUM_PYTHON_SUBPROCESSES=\${EXPYRE_NCORES_PER_NODE}",
                   "WFL_VASP_KWARGS='{ \"ncore\": '\${EXPYRE_NCORES_PER_NODE}'}'" ]
    }

tests/calculators/test_vasp.py

@@ -31,21 +31,20 @@ def test_vasp_gamma(tmp_path, monkeypatch):
         output_prefix='TEST_',
     )
 
-    run_dir = list(tmp_path.glob('run_VASP_*'))
-    nfiles = len(list(os.scandir(run_dir[0])))
+    for run_dir in tmp_path.glob('run_VASP_*'):
+        nfiles = len(list(os.scandir(run_dir)))
 
-    assert nfiles == 18
+        assert nfiles == 18
 
-    ats = list(configs_eval)
-    assert 'TEST_energy' in ats[0].info
-    assert 'TEST_forces' in ats[0].arrays
-    # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
-    with open(Path(run_dir[0]) / "OUTCAR") as fin:
-        l = fin.readline()
-        assert "gamma-only" in l
+        ats = list(configs_eval)
+        assert 'TEST_energy' in ats[0].info
+        assert 'TEST_forces' in ats[0].arrays
+        # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
+        with open(Path(run_dir) / "OUTCAR") as fin:
+            l = fin.readline()
+            assert "gamma-only" in l
 
     # try with command_gamma
-
     command_gamma = os.environ["ASE_VASP_COMMAND_GAMMA"]
     for cmd in Vasp.env_commands:
         monkeypatch.delenv(cmd + "_GAMMA", raising=False)
@@ -57,18 +56,72 @@ def test_vasp_gamma(tmp_path, monkeypatch):
         output_prefix='TEST_',
     )
 
-    run_dir = list(tmp_path.glob('run_VASP_*'))
-    nfiles = len(list(os.scandir(run_dir[0])))
+    for run_dir in tmp_path.glob('run_VASP_*'):
+        nfiles = len(list(os.scandir(run_dir)))
 
-    assert nfiles == 18
+        assert nfiles == 18
 
-    ats = list(configs_eval)
-    assert 'TEST_energy' in ats[0].info
-    assert 'TEST_forces' in ats[0].arrays
-    # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
-    with open(Path(run_dir[0]) / "OUTCAR") as fin:
-        l = fin.readline()
-        assert "gamma-only" in l
+        ats = list(configs_eval)
+        assert 'TEST_energy' in ats[0].info
+        assert 'TEST_forces' in ats[0].arrays
+        # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
+        with open(Path(run_dir) / "OUTCAR") as fin:
+            l = fin.readline()
+            assert "gamma-only" in l
+
+
+def test_vasp_gamma_auto(tmp_path):
+    ase.io.write(tmp_path / 'vasp_in.xyz', Atoms('Si', cell=(6, 2, 2), pbc=[True] * 3), format='extxyz')
+
+    # try with not large enough kspacing
+    configs_eval = generic.calculate(
+        inputs=ConfigSet(tmp_path / 'vasp_in.xyz'),
+        outputs=OutputSpec('vasp_out.auto_gamma_no.xyz', file_root=tmp_path),
+        calculator=Vasp(workdir=tmp_path, encut=200, pp=os.environ['PYTEST_VASP_POTCAR_DIR'],
+                        keep_files=True, kspacing=2),
+        output_prefix='TEST_',
+    )
+
+    for run_dir in tmp_path.glob('run_VASP_*'):
+        nfiles = len(list(os.scandir(run_dir)))
+
+        assert nfiles == 18
+
+        for at in configs_eval:
+            assert 'TEST_energy' in at.info
+            assert 'TEST_forces' in at.arrays
+        # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
+        with open(Path(run_dir) / "OUTCAR") as fin:
+            l = fin.readline()
+            assert "gamma-only" not in l
+
+        print("BOB clean non-gamma", run_dir)
+        shutil.rmtree(run_dir)
+
+    # try with large enough kspacing
+    configs_eval = generic.calculate(
+        inputs=ConfigSet(tmp_path / 'vasp_in.xyz'),
+        outputs=OutputSpec('vasp_out.auto_gamma_yes.xyz', file_root=tmp_path),
+        calculator=Vasp(workdir=tmp_path, encut=200, pp=os.environ['PYTEST_VASP_POTCAR_DIR'],
+                        keep_files=True, kspacing=4),
+        output_prefix='TEST_',
+    )
+
+    for run_dir in tmp_path.glob('run_VASP_*'):
+        nfiles = len(list(os.scandir(run_dir)))
+
+        assert nfiles == 18
+
+        for at in configs_eval:
+            assert 'TEST_energy' in at.info
+            assert 'TEST_forces' in at.arrays
+        # ase.io.write(sys.stdout, list(configs_eval), format='extxyz')
+        with open(Path(run_dir) / "OUTCAR") as fin:
+            l = fin.readline()
+            assert "gamma-only" in l
+
+        print("BOB clean gamma", run_dir)
+        shutil.rmtree(run_dir)
 
 
 def test_vasp(tmp_path):

tests/local_scripts/complete_pytest.tin

@@ -65,7 +65,7 @@ l=`egrep '^=.*(passed|failed|skipped|xfailed)' complete_pytest.tin.out`
 echo "summary line $l"
 lp=$( echo $l | sed -E -e 's/ in .*//' -e 's/\s*,\s*/\n/g' )
 
-declare -A expected_n=( ["passed"]="175" ["skipped"]="21" ["warnings"]=823 ["xfailed"]=2 ["xpassed"]=1 )
+declare -A expected_n=( ["passed"]="176" ["skipped"]="21" ["warnings"]=823 ["xfailed"]=2 ["xpassed"]=1 )
 IFS=$'\n'
 for out in $lp; do
     out_n=$(echo $out | sed -e 's/^=* //' -e 's/ .*//' -e 's/,//')

wfl/calculators/vasp.py

@@ -31,6 +31,10 @@ class Vasp(WFLFileIOCalculator, ASE_Vasp):
     Notes
     -----
     "directory" argument cannot be present. Use rundir_prefix and workdir instead.
+
+    "command_gamma" (or ASE_VASP_COMMAND_GAMMA) is used when non-periodic cells or large
+    enough kspacing are detected
+
     "pp" defaults to ".", so VASP_PP_PATH env var is absolute path to "<elem name>/POTCAR" files
 
     Parameters
@@ -48,11 +52,8 @@ class Vasp(WFLFileIOCalculator, ASE_Vasp):
     scratchdir: str / Path, default None
         temporary directory to execute calculations in and delete or copy back results (set by
         "keep_files") if needed.  For example, directory on a local disk with fast file I/O.
-    calculator_exec: str
-        executable to run (without ASE-specific command line arguments). Mutually exclusive with ASE-built-in "command"
-    calculator_exec_gamma: str
-        executable to run for nonperiodic systems (overrides ASE_VASP_COMMAND_GAMMA, VASP_COMMAND_GAMMA, VASP_SCRIPT_GAMMA).
-        Mutually exclusive with ASE-built-in "command" and "command_gamma"
+    command_gamma: str, default None
+        command to use when gamma-only calculations are detected (e.g. large kspacing, or pbc=False)
     **kwargs: arguments for ase.calculators.vasp.vasp.Vasp
         remaining arguments to ASE's Vasp calculator constructor
     """
@@ -70,8 +71,7 @@ class Vasp(WFLFileIOCalculator, ASE_Vasp):
     })
 
     def __init__(self, keep_files="default", rundir_prefix="run_VASP_",
-                 workdir=None, scratchdir=None,
-                 calculator_exec=None, calculator_exec_gamma=None,
+                 workdir=None, scratchdir=None, command_gamma=None,
                  **kwargs):
 
         # get initialparams from env var
@@ -91,16 +91,7 @@ def __init__(self, keep_files="default", rundir_prefix="run_VASP_",
         if "pp" not in kwargs_use:
             kwargs_use["pp"] = "."
 
-        if calculator_exec is not None:
-            if "command" in kwargs_use or "command_gamma" in kwargs_use:
-                raise ValueError("Cannot specify both calculator_exec and command or command_gamma")
-            self.command = calculator_exec
-        if calculator_exec_gamma is not None:
-            if "command" in kwargs_use or "command_gamma" in kwargs_use:
-                raise ValueError("Cannot specify both calculator_exec_gamma and command or command_gamma")
-            self._command_gamma = calculator_exec_gamma
-        else:
-            self._command_gamma = kwargs_use.pop("command_gamma", None)
+        self._command_gamma = command_gamma
 
         self.universal_kspacing = kwargs_use.pop("universal_kspacing", None)
 
@@ -132,11 +123,22 @@ def per_config_setup(self, atoms):
         self._orig_command = self.command
         self._orig_kspacing = self.float_params["kspacing"]
         self._orig_kgamma = self.bool_params["kgamma"]
-        if np.all(~self._orig_pbc):
+        use_gamma_exec = np.all(~self._orig_pbc)
+        # gamma centered if kgamma is undefined (default) or True
+        if self._orig_kgamma is None or self._orig_kgamma:
+            try:
+                n_k = np.maximum(1, np.ceil(np.linalg.norm(atoms.cell.reciprocal(), axis=1) * 2.0 * np.pi / self._orig_kspacing))
+                use_gamma_exec |= np.all(n_k == 1)
+            except TypeError:
+                pass
+
+        if use_gamma_exec:
             # set command
             if self._command_gamma is not None:
+                # from constructor argument that was saved
                 command_gamma = self._command_gamma
             else:
+                # from env var
                 command_gamma = None
                 for env_var in self.env_commands:
                     if env_var + "_GAMMA" in os.environ:
@@ -145,7 +147,7 @@ def per_config_setup(self, atoms):
             if command_gamma is not None:
                 self.command = command_gamma
 
-            # set k-points for nonperiodic systems
+            # explicitly set k-points for nonperiodic systems
             self.float_params["kspacing"] = 1.0e8
             self.bool_params["kgamma"] = True