refactor neb module 🎷 (#386)

src/simmate/apps/vasp/workflows/__init__.py

@@ -2,6 +2,8 @@
 
 from .diffusion import (
     Diffusion__Vasp__NebAllPathsMit,
+    Diffusion__Vasp__NebAllPathsWarrenLab,
+    Diffusion__Vasp__NebAllPathsWarrenLabQuick,
     Diffusion__Vasp__NebFromEndpointsMit,
     Diffusion__Vasp__NebFromImagesMit,
     Diffusion__Vasp__NebFromImagesMvlCi,

src/simmate/apps/vasp/workflows/diffusion/__init__.py

@@ -4,8 +4,13 @@
 # circular imports errors, so we prevent isort from changing this file.
 # isort: skip_file
 
-from .neb_all_paths_mit import Diffusion__Vasp__NebAllPathsMit
-from .neb_from_endpoints_mit import Diffusion__Vasp__NebFromEndpointsMit
-from .neb_from_images_mit import Diffusion__Vasp__NebFromImagesMit
-from .neb_from_images_mvl_ci import Diffusion__Vasp__NebFromImagesMvlCi
-from .neb_single_path_mit import Diffusion__Vasp__NebSinglePathMit
+from .mit import (
+    Diffusion__Vasp__NebAllPathsMit,
+    Diffusion__Vasp__NebFromEndpointsMit,
+    Diffusion__Vasp__NebFromImagesMit,
+    Diffusion__Vasp__NebFromImagesMvlCi,
+    Diffusion__Vasp__NebSinglePathMit,
+)
+
+from .warren_lab import Diffusion__Vasp__NebAllPathsWarrenLab
+from .warren_lab_quick import Diffusion__Vasp__NebAllPathsWarrenLabQuick

src/simmate/apps/vasp/workflows/diffusion/mit/__init__.py

@@ -0,0 +1,11 @@
+# -*- coding: utf-8 -*-
+
+# The order that we import these different modules is important to prevent
+# circular imports errors, so we prevent isort from changing this file.
+# isort: skip_file
+
+from .from_images import Diffusion__Vasp__NebFromImagesMit
+from .from_images_mvl_ci import Diffusion__Vasp__NebFromImagesMvlCi
+from .from_endpoints import Diffusion__Vasp__NebFromEndpointsMit
+from .single_path import Diffusion__Vasp__NebSinglePathMit
+from .all_paths import Diffusion__Vasp__NebAllPathsMit

src/simmate/apps/vasp/workflows/diffusion/neb_all_paths_mit.py → src/simmate/apps/vasp/workflows/diffusion/mit/all_paths.py

@@ -1,9 +1,7 @@
 # -*- coding: utf-8 -*-
 
-from simmate.apps.vasp.workflows.diffusion.neb_all_paths_base import NebAllPathsWorkflow
-from simmate.apps.vasp.workflows.diffusion.neb_single_path_mit import (
-    Diffusion__Vasp__NebSinglePathMit,
-)
+from simmate.apps.vasp.workflows.diffusion.mit import Diffusion__Vasp__NebSinglePathMit
+from simmate.apps.vasp.workflows.diffusion.neb_base import NebAllPathsWorkflow
 from simmate.apps.vasp.workflows.relaxation.mit import Relaxation__Vasp__Mit
 from simmate.apps.vasp.workflows.static_energy.mit import StaticEnergy__Vasp__Mit
 

src/simmate/apps/vasp/workflows/diffusion/neb_from_endpoints_mit.py → src/simmate/apps/vasp/workflows/diffusion/mit/from_endpoints.py

@@ -1,11 +1,7 @@
 # -*- coding: utf-8 -*-
 
-from simmate.apps.vasp.workflows.diffusion.neb_from_endpoints_base import (
-    NebFromEndpointWorkflow,
-)
-from simmate.apps.vasp.workflows.diffusion.neb_from_images_mit import (
-    Diffusion__Vasp__NebFromImagesMit,
-)
+from simmate.apps.vasp.workflows.diffusion.mit import Diffusion__Vasp__NebFromImagesMit
+from simmate.apps.vasp.workflows.diffusion.neb_base import NebFromEndpointWorkflow
 from simmate.apps.vasp.workflows.relaxation.mvl_neb_endpoint import (
     Relaxation__Vasp__MvlNebEndpoint,
 )

src/simmate/apps/vasp/workflows/diffusion/neb_from_images_mit.py → src/simmate/apps/vasp/workflows/diffusion/mit/from_images.py

@@ -1,9 +1,7 @@
 # -*- coding: utf-8 -*-
 
-from simmate.apps.vasp.error_handlers import Walltime
-from simmate.apps.vasp.workflows.diffusion.neb_from_images_base import (
-    VaspNebFromImagesWorkflow,
-)
+from simmate.apps.vasp.error_handlers import Frozen, Unconverged, Walltime
+from simmate.apps.vasp.workflows.diffusion.neb_base import VaspNebFromImagesWorkflow
 from simmate.apps.vasp.workflows.relaxation.mit import Relaxation__Vasp__Mit
 
 
@@ -39,5 +37,5 @@ class Diffusion__Vasp__NebFromImagesMit(
     error_handlers = [
         handler
         for handler in Relaxation__Vasp__Mit.error_handlers
-        if type(handler) not in [Walltime]
+        if type(handler) not in [Walltime, Unconverged, Frozen]
     ]

src/simmate/apps/vasp/workflows/diffusion/neb_from_images_mvl_ci.py → src/simmate/apps/vasp/workflows/diffusion/mit/from_images_mvl_ci.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
 
-from simmate.apps.vasp.workflows.diffusion.neb_from_images_mit import (
-    Diffusion__Vasp__NebFromImagesMit,
-)
+from simmate.apps.vasp.workflows.diffusion.mit import Diffusion__Vasp__NebFromImagesMit
 
 
 class Diffusion__Vasp__NebFromImagesMvlCi(Diffusion__Vasp__NebFromImagesMit):

src/simmate/apps/vasp/workflows/diffusion/neb_single_path_mit.py → src/simmate/apps/vasp/workflows/diffusion/mit/single_path.py

@@ -1,11 +1,7 @@
 # -*- coding: utf-8 -*-
 
-from simmate.apps.vasp.workflows.diffusion.neb_from_images_mit import (
-    Diffusion__Vasp__NebFromImagesMit,
-)
-from simmate.apps.vasp.workflows.diffusion.neb_single_path_base import (
-    SinglePathWorkflow,
-)
+from simmate.apps.vasp.workflows.diffusion.mit import Diffusion__Vasp__NebFromImagesMit
+from simmate.apps.vasp.workflows.diffusion.neb_base import SinglePathWorkflow
 from simmate.apps.vasp.workflows.relaxation.mvl_neb_endpoint import (
     Relaxation__Vasp__MvlNebEndpoint,
 )

src/simmate/apps/vasp/workflows/diffusion/neb_base/__init__.py

@@ -0,0 +1,10 @@
+# -*- coding: utf-8 -*-
+
+# The order that we import these different modules is important to prevent
+# circular imports errors, so we prevent isort from changing this file.
+# isort: skip_file
+
+from .all_paths import NebAllPathsWorkflow
+from .from_endpoints import NebFromEndpointWorkflow
+from .from_images import VaspNebFromImagesWorkflow
+from .single_path import SinglePathWorkflow

src/simmate/apps/vasp/workflows/diffusion/warren_lab.py

@@ -0,0 +1,211 @@
+# -*- coding: utf-8 -*-
+
+from simmate.apps.vasp.inputs.potcar_mappings import PBE_ELEMENT_MAPPINGS
+from simmate.apps.vasp.workflows.base import VaspWorkflow
+from simmate.apps.vasp.workflows.diffusion.neb_base import (
+    NebAllPathsWorkflow,
+    SinglePathWorkflow,
+    VaspNebFromImagesWorkflow,
+)
+
+# -----------------------------------------------------------------------------
+
+# BULK UNITCELL RELAXATION
+
+
+class Relaxation__Vasp__WarrenLab(VaspWorkflow):
+    functional = "PBE"
+    potcar_mappings = PBE_ELEMENT_MAPPINGS
+    incar = dict(
+        ALGO="Fast",
+        EDIFF=1e-06,
+        ENCUT=520,  # TODO: set dynamically to be 1.3x highest elemental ENMAX
+        IBRION=2,
+        ICHARG=1,
+        ISIF=3,
+        ISPIN=2,
+        ISYM=0,
+        IVDW=12,
+        LORBIT=11,
+        LREAL="Auto",
+        LWAVE=False,
+        # MAGMOM = # TODO: set dynamically
+        NELM=200,
+        NELMIN=4,
+        NSW=99,
+        PREC="Accurate",
+        ISMEAR=0,
+        SIGMA=0.05,
+        KSPACING=0.35,
+        LMAXMIX=4,
+    )
+    error_handlers = []
+
+
+# -----------------------------------------------------------------------------
+
+# BULK UNITCELL STATIC ENERGY
+
+
+class StaticEnergy__Vasp__WarrenLab(VaspWorkflow):
+    functional = "PBE"
+    potcar_mappings = PBE_ELEMENT_MAPPINGS
+    incar = dict(
+        ALGO="Fast",
+        EDIFF=1e-06,
+        ENCUT=520,  # TODO: set dynamically to be 1.3x highest elemental ENMAX
+        IBRION=-1,
+        ICHARG=1,
+        ISIF=3,
+        ISPIN=2,
+        ISYM=0,
+        IVDW=12,
+        LORBIT=11,
+        LREAL="Auto",
+        LWAVE=False,
+        # MAGMOM = # TODO: set dynamically
+        NELM=200,
+        NELMIN=4,
+        NSW=0,
+        PREC="Accurate",
+        ISMEAR=0,
+        SIGMA=0.05,
+        KSPACING=0.35,
+        LMAXMIX=4,
+    )
+    error_handlers = []
+
+
+# -----------------------------------------------------------------------------
+
+# ENDPOINT SUPERCELL RELAXATIONS
+
+
+class Relaxation__Vasp__WarrenLabNebEndpoint(VaspWorkflow):
+    functional = "PBE"
+    potcar_mappings = PBE_ELEMENT_MAPPINGS
+    incar = dict(
+        ALGO="Fast",
+        EDIFF=5e-05,
+        EDIFFG=-0.01,
+        ENCUT=520,  # TODO: set dynamically to be 1.3x highest elemental ENMAX
+        IBRION=2,
+        ICHARG=1,
+        ISIF=2,
+        ISPIN=2,
+        ISYM=0,
+        IVDW=12,
+        LORBIT=11,
+        LREAL="Auto",
+        LWAVE=False,
+        LCHARG=False,
+        # MAGMOM = # TODO: set dynamically
+        NELM=200,
+        NSW=99,
+        PREC="Accurate",
+        ISMEAR=0,
+        SIGMA=0.05,
+        KSPACING=0.4,
+        LMAXMIX=4,
+    )
+    error_handlers = []
+
+
+# -----------------------------------------------------------------------------
+
+# ENDPOINT SUPERCELL STATIC ENERGY
+
+
+class StaticEnergy__Vasp__WarrenLabNebEndpoint(VaspWorkflow):
+    functional = "PBE"
+    potcar_mappings = PBE_ELEMENT_MAPPINGS
+    incar = dict(
+        ALGO="Fast",
+        EDIFF=5e-05,
+        EDIFFG=-0.01,
+        ENCUT=520,  # TODO: set dynamically to be 1.3x highest elemental ENMAX
+        IBRION=-1,
+        ICHARG=1,
+        ISIF=2,
+        ISPIN=2,
+        ISYM=0,
+        IVDW=12,
+        LORBIT=11,
+        LREAL="Auto",
+        LWAVE=False,
+        LCHARG=False,
+        # MAGMOM = # TODO: set dynamically
+        NELM=200,
+        NSW=0,
+        PREC="Accurate",
+        ISMEAR=0,
+        SIGMA=0.05,
+        KSPACING=0.4,
+        LMAXMIX=4,
+    )
+    error_handlers = []
+
+
+# -----------------------------------------------------------------------------
+
+# NEB FROM IMAGES
+
+
+class Diffusion__Vasp__WarrenLabCiNebFromImages(VaspNebFromImagesWorkflow):
+    functional = "PBE"
+    potcar_mappings = PBE_ELEMENT_MAPPINGS
+    incar = dict(
+        ALGO="Fast",
+        EDIFF=5e-05,
+        EDIFFG=-0.01,
+        ENCUT=520,  # TODO: set dynamically to be 1.3x highest elemental ENMAX
+        IBRION=3,
+        ICHARG=1,
+        ISIF=2,
+        ISPIN=2,
+        ISYM=0,
+        IVDW=12,
+        LORBIT=11,
+        LREAL="Auto",
+        LWAVE=False,
+        LCHARG=False,
+        # MAGMOM = # TODO: set dynamically
+        NELM=200,
+        NSW=99,
+        PREC="Accurate",
+        ISMEAR=0,
+        SIGMA=0.05,
+        KSPACING=0.4,
+        LMAXMIX=4,
+        NIMAGES=5,
+        LCLIMB=True,
+        SPRING=-5,
+        POTIM=0,
+        IOPT=1,
+    )
+    error_handlers = []
+
+
+# -----------------------------------------------------------------------------
+
+# SINGLE PATH NEB
+
+
+class Diffusion__Vasp__WarrenLabNebSinglePath(SinglePathWorkflow):
+    endpoint_relaxation_workflow = Relaxation__Vasp__WarrenLabNebEndpoint
+    endpoint_energy_workflow = StaticEnergy__Vasp__WarrenLabNebEndpoint
+    from_images_workflow = Diffusion__Vasp__WarrenLabCiNebFromImages
+
+
+# -----------------------------------------------------------------------------
+
+# ALL PATHS NEB
+
+
+class Diffusion__Vasp__NebAllPathsWarrenLab(NebAllPathsWorkflow):
+    bulk_relaxation_workflow = Relaxation__Vasp__WarrenLab
+    bulk_static_energy_workflow = StaticEnergy__Vasp__WarrenLab
+    single_path_workflow = Diffusion__Vasp__WarrenLabNebSinglePath
+
+
+# -----------------------------------------------------------------------------