Merge branch 'master' into magnetism-workflow-staging

Author: mkhorton

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.5"
+__version__ = "0.8.7"

atomate/vasp/firetasks/parse_outputs.py

@@ -1093,7 +1093,7 @@ def run_task(self, fw_spec):
 
         polarization = Polarization(p_elecs, p_ions, structures)
 
-        p_change = polarization.get_polarization_change().A1.tolist()
+        p_change = np.ravel(polarization.get_polarization_change()).tolist()
         p_norm = polarization.get_polarization_change_norm()
         polarization_max_spline_jumps = polarization.max_spline_jumps()
         same_branch = polarization.get_same_branch_polarization_data(convert_to_muC_per_cm2=True)
@@ -1108,7 +1108,7 @@ def run_task(self, fw_spec):
         def split_abc(var, var_name):
             d = {}
             for i, j in enumerate('abc'):
-                d.update({var_name + "_{}".format(j): var[:, i].A1.tolist()})
+                d.update({var_name + "_{}".format(j): np.ravel(var[:, i]).tolist()})
             return d
 
         # Add some sort of id for the structures? Like cid but more general?

atomate/vasp/firetasks/run_calc.py

@@ -205,7 +205,8 @@ def run_task(self, fw_spec):
         c.run()
 
         if os.path.exists(zpath("custodian.json")):
-            return FWAction(stored_data=loadfn(zpath("custodian.json")))
+            stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
+            return FWAction(stored_data=stored_custodian_data)
 
 
 @explicit_serialize

atomate/vasp/firetasks/tests/test_polarization_to_db.py

@@ -60,7 +60,7 @@ def test_polarizationtodb(self):
         # Check recovered change in polarization
         coll = self.get_task_collection("polarization_tasks")
         d = coll.find_one()
-        self.assertAlmostEqual(d['polarization_change_norm'], 46.288752795325244)
+        self.assertAlmostEqual(d['polarization_change_norm'], 46.288752795325244, 5)
 
 
 

atomate/vasp/firetasks/write_inputs.py

@@ -314,7 +314,7 @@ def run_task(self, fw_spec):
             sym_prec=self.get("sym_prec", 0.1),
             international_monoclinic=self.get("international_monoclinic", True),
             mode=self.get("mode", "uniform"),
-            nedos=self.get("nedos", 601),
+            nedos=self.get("nedos", 2001),
             optics=self.get("optics", False),
             **self.get("other_params", {}))
         vis.write_input(".")

atomate/vasp/fireworks/core.py

@@ -236,14 +236,16 @@ def __init__(self, parents=None, prev_calc_dir=None, structure=None, mode="gap",
 
 class NonSCFFW(Firework):
 
-    def __init__(self, parents=None, prev_calc_dir=None, structure=None, name="nscf", mode="uniform", vasp_cmd="vasp",
-                 copy_vasp_outputs=True, db_file=None,  **kwargs):
+    def __init__(self, parents=None, prev_calc_dir=None, structure=None,
+                 name="nscf", mode="uniform", vasp_cmd="vasp",
+                 copy_vasp_outputs=True, db_file=None,
+                 input_set_overrides=None, **kwargs):
         """
-        Standard NonSCF Calculation Firework supporting both
-        uniform and line modes.
+        Standard NonSCF Calculation Firework supporting uniform and line modes.
 
         Args:
-            structure (Structure): Input structure - used only to set the name of the FW.
+            structure (Structure): Input structure - used only to set the name
+                of the FW.
             name (str): Name for the Firework.
             mode (str): "uniform" or "line" mode.
             vasp_cmd (str): Command to run vasp.
@@ -253,36 +255,48 @@ def __init__(self, parents=None, prev_calc_dir=None, structure=None, name="nscf"
             db_file (str): Path to file specifying db credentials.
             parents (Firework): Parents of this particular Firework.
                 FW or list of FWS.
+            input_set_overrides (dict): Arguments passed to the
+                "from_prev_calc" method of the MPNonSCFSet. This parameter
+                allows a user to modify the default values of the input set.
+                For example, passing the key value pair
+                    {'reciprocal_density': 1000}
+                will override default k-point meshes for uniform calculations.
             \*\*kwargs: Other kwargs that are passed to Firework.__init__.
         """
-        fw_name = "{}-{} {}".format(structure.composition.reduced_formula if structure else "unknown", name,
-                                    mode)
+        input_set_overrides = input_set_overrides or {}
+
+        fw_name = "{}-{} {}".format(structure.composition.reduced_formula if
+                                    structure else "unknown", name, mode)
         t = []
 
         if prev_calc_dir:
-            t.append(CopyVaspOutputs(calc_dir=prev_calc_dir, additional_files=["CHGCAR"]))
+            t.append(CopyVaspOutputs(calc_dir=prev_calc_dir,
+                                     additional_files=["CHGCAR"]))
         elif parents:
-            t.append(CopyVaspOutputs(calc_loc=True, additional_files=["CHGCAR"]))
+            t.append(CopyVaspOutputs(calc_loc=True,
+                                     additional_files=["CHGCAR"]))
         else:
             raise ValueError("Must specify previous calculation for NonSCFFW")
 
         mode = mode.lower()
         if mode == "uniform":
             t.append(
                 WriteVaspNSCFFromPrev(prev_calc_dir=".", mode="uniform",
-                                      reciprocal_density=1000))
+                                      **input_set_overrides))
         else:
             t.append(WriteVaspNSCFFromPrev(prev_calc_dir=".", mode="line",
-                                           reciprocal_density=20))
+                                           **input_set_overrides))
 
-        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd, auto_npar=">>auto_npar<<"))
+        t.append(RunVaspCustodian(vasp_cmd=vasp_cmd,
+                                  auto_npar=">>auto_npar<<"))
         t.append(PassCalcLocs(name=name))
         t.append(VaspToDb(db_file=db_file,
                           additional_fields={"task_label": name + " " + mode},
                           parse_dos=(mode == "uniform"),
                           bandstructure_mode=mode))
 
-        super(NonSCFFW, self).__init__(t, parents=parents, name=fw_name, **kwargs)
+        super(NonSCFFW, self).__init__(t, parents=parents, name=fw_name,
+                                       **kwargs)
 
 
 class LepsFW(Firework):

atomate/vasp/workflows/base/library/bandstructure_no_opt.yaml

@@ -0,0 +1,12 @@
+# A typical band structure
+# Author: Alex Ganose ([email protected])
+fireworks:
+- fw: atomate.vasp.fireworks.core.StaticFW
+- fw: atomate.vasp.fireworks.core.NonSCFFW
+  params:
+    parents: 0
+    mode: uniform
+- fw: atomate.vasp.fireworks.core.NonSCFFW
+  params:
+    parents: 0
+    mode: line

atomate/vasp/workflows/presets/core.py

@@ -53,6 +53,29 @@ def wf_bandstructure(structure, c=None):
 
     return wf
 
+
+def wf_bandstructure_no_opt(structure, c=None):
+
+    c = c or {}
+    vasp_cmd = c.get("VASP_CMD", VASP_CMD)
+    db_file = c.get("DB_FILE", DB_FILE)
+
+    wf = get_wf(structure, "bandstructure_no_opt.yaml",
+                vis=MPStaticSet(structure, force_gamma=True),
+                common_params={"vasp_cmd": vasp_cmd, "db_file": db_file})
+
+    wf = add_common_powerups(wf, c)
+
+    if c.get("SMALLGAP_KPOINT_MULTIPLY", SMALLGAP_KPOINT_MULTIPLY):
+        wf = add_small_gap_multiply(wf, 0.5, 5, "static")
+        wf = add_small_gap_multiply(wf, 0.5, 5, "nscf")
+
+    if c.get("ADD_WF_METADATA", ADD_WF_METADATA):
+        wf = add_wf_metadata(wf, structure)
+
+    return wf
+
+
 def wf_bandstructure_hse(structure, c=None):
 
     c = c or {}