diff --git a/.binder/requirements.txt b/.binder/requirements.txt
index 23b291b..5d59e8c 100644
--- a/.binder/requirements.txt
+++ b/.binder/requirements.txt
@@ -1 +1 @@
-cipher-parse==0.5.0
+cipher-parse==0.6.0a1
diff --git a/CHANGELOG-dev.md b/CHANGELOG-dev.md
index 147a996..b34aae7 100644
--- a/CHANGELOG-dev.md
+++ b/CHANGELOG-dev.md
@@ -1,4 +1,75 @@
 
+<a name="v0.6.0a1"></a>
+## [v0.6.0a1](https://github.com/LightForm-group/cipher-parse/compare/v0.6.0a0...v0.6.0a1) - 2024.03.28
+
+### 🐛 Bug Fixes
+
+* use pyvista to resample VTU files onto a grid
+
+
+<a name="v0.6.0a0"></a>
+## [v0.6.0a0](https://github.com/LightForm-group/cipher-parse/compare/v0.5.1a4...v0.6.0a0) - 2024.03.28
+
+### ✨ Features
+
+* add to/from_zarr (without CIPHERGeometry support for now
+
+
+<a name="v0.5.1a4"></a>
+## [v0.5.1a4](https://github.com/LightForm-group/cipher-parse/compare/v0.5.1a3...v0.5.1a4) - 2024.01.08
+
+### 🐛 Bug Fixes
+
+* more reasonable time in notebook examples
+
+
+<a name="v0.5.1a3"></a>
+## [v0.5.1a3](https://github.com/LightForm-group/cipher-parse/compare/v0.5.1a2...v0.5.1a3) - 2024.01.08
+
+### 🐛 Bug Fixes
+
+* clear notebook outputs
+* interface width is now expected within the interface definitions
+
+
+<a name="v0.5.1a2"></a>
+## [v0.5.1a2](https://github.com/LightForm-group/cipher-parse/compare/v0.5.1a1...v0.5.1a2) - 2023.09.05
+
+### ✨ Features
+
+* support separate text files for mappings
+
+### 🐛 Bug Fixes
+
+* DefDAP uses P=+1 for quat ops where we were assuming P=-1
+* tests
+* try indenting
+* func args
+* func args
+
+
+<a name="v0.5.1a1"></a>
+## [v0.5.1a1](https://github.com/LightForm-group/cipher-parse/compare/v0.5.1a0...v0.5.1a1) - 2023.07.21
+
+### ✨ Features
+
+* use DefDAP to compute CIPHERGeometry.misorientation_matrix - much faster
+
+
+<a name="v0.5.1a0"></a>
+## [v0.5.1a0](https://github.com/LightForm-group/cipher-parse/compare/v0.5.0...v0.5.1a0) - 2023.06.01
+
+### 🐛 Bug Fixes
+
+* cast pyvista_ndarray to numpy ndarray
+* get_time_linear_subset_indices should return primitive types
+* get_incremental_data if original_viz dir exists
+
+
+<a name="v0.5.0"></a>
+## [v0.5.0](https://github.com/LightForm-group/cipher-parse/compare/v0.5.0a3...v0.5.0) - 2023.05.15
+
+
 <a name="v0.5.0a3"></a>
 ## [v0.5.0a3](https://github.com/LightForm-group/cipher-parse/compare/v0.5.0a2...v0.5.0a3) - 2023.05.15
 
diff --git a/cipher_parse/_version.py b/cipher_parse/_version.py
index 3d18726..c6422df 100644
--- a/cipher_parse/_version.py
+++ b/cipher_parse/_version.py
@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "0.6.0a1"
diff --git a/cipher_parse/cipher_input.py b/cipher_parse/cipher_input.py
index f1e17fa..9639dbc 100644
--- a/cipher_parse/cipher_input.py
+++ b/cipher_parse/cipher_input.py
@@ -2,6 +2,7 @@
 import json
 from pathlib import Path
 from dataclasses import dataclass
+from textwrap import indent
 from typing import Optional, List, Union, Tuple, Dict
 
 import numpy as np
@@ -17,11 +18,9 @@
 
 
 def compress_1D_array(arr):
-
     vals = []
     nums = []
     for idx, i in enumerate(arr):
-
         if idx == 0:
             vals.append(i)
             nums.append(1)
@@ -129,6 +128,52 @@ def from_JSON(cls, data, quiet=True):
         }
         return cls(**data, quiet=quiet)
 
+    @classmethod
+    def get_input_maps_from_files(
+        cls,
+        inp_file_str,
+        directory,
+        get_voxel_phase=True,
+        get_phase_material=True,
+        get_interface=True,
+    ):
+        directory = Path(directory)
+        voxel_phase_file = Path(directory / "voxel_phase_mapping.txt")
+        phase_material_file = Path(directory / "phase_material_mapping.txt")
+        interface_file = Path(directory / "interface_mapping.txt")
+
+        inp_dat = None
+        voxel_phase = None
+        phase_material = None
+        interface_map = None
+        if any(
+            i.exists() for i in (voxel_phase_file, phase_material_file, interface_file)
+        ):
+            inp_dat = cls.read_input_YAML_string(
+                file_str=inp_file_str,
+                parse_interface_map=False,
+            )
+        if get_voxel_phase and voxel_phase_file.exists():
+            with voxel_phase_file.open("rt") as fp:
+                voxel_phase_str = "".join(fp.readlines())
+                voxel_phase = decompress_1D_array_string(voxel_phase_str)
+                voxel_phase = voxel_phase.reshape(inp_dat["grid_size"], order="F") - 1
+
+        if get_phase_material and phase_material_file.exists():
+            with phase_material_file.open("rt") as fp:
+                phase_material_str = "".join(fp.readlines())
+                phase_material = decompress_1D_array_string(phase_material_str) - 1
+
+        if get_interface and interface_file.exists():
+            num_phases = inp_dat["num_phases"]
+            with interface_file.open("rt") as fp:
+                interface_str = "".join(fp.readlines())
+                interface_map = decompress_1D_array_string(interface_str)
+                interface_map = interface_map.reshape((num_phases, num_phases)) - 1
+                interface_map[np.tril_indices(num_phases)] = -1  # only need one half
+
+        return (voxel_phase, phase_material, interface_map)
+
     @classmethod
     def from_input_YAML_file(cls, path):
         """Generate a CIPHERInput object from a CIPHER input YAML file."""
@@ -136,19 +181,31 @@ def from_input_YAML_file(cls, path):
         with Path(path).open("rt") as fp:
             file_str = "".join(fp.readlines())
 
-        return cls.from_input_YAML_str(file_str)
+        (
+            voxel_phase,
+            phase_material,
+            interface_map,
+        ) = CIPHERInput.get_input_maps_from_files(
+            inp_file_str=file_str,
+            directory=path.parent,
+        )
+
+        return cls.from_input_YAML_str(
+            file_str=file_str,
+            input_map_voxel_phase=voxel_phase,
+            input_map_phase_material=phase_material,
+            input_map_interface=interface_map,
+        )
 
     @classmethod
     def read_input_YAML_file(cls, path):
-
         with Path(path).open("rt") as fp:
             file_str = "".join(fp.readlines())
 
-        return cls.read_input_YAML_string(file_str)
+        return cls.read_input_YAML_string(file_str=file_str)
 
     @staticmethod
     def read_input_YAML_string(file_str, parse_interface_map=True):
-
         yaml = YAML(typ="safe")
         data = yaml.load(file_str)
 
@@ -157,23 +214,30 @@ def read_input_YAML_string(file_str, parse_interface_map=True):
         size = header["size"]
         num_phases = header["n_phases"]
 
-        voxel_phase = decompress_1D_array_string(data["mappings"]["voxel_phase_mapping"])
-        voxel_phase = voxel_phase.reshape(grid_size, order="F") - 1
-
-        unique_phase_IDs = np.unique(voxel_phase)
-        assert len(unique_phase_IDs) == num_phases
+        voxel_phase = None
+        unique_phase_IDs = None
+        if data["mappings"]["voxel_phase_mapping"] != "voxel_phase_mapping.txt":
+            voxel_phase = decompress_1D_array_string(
+                data["mappings"]["voxel_phase_mapping"]
+            )
+            voxel_phase = voxel_phase.reshape(grid_size, order="F") - 1
+            unique_phase_IDs = np.unique(voxel_phase)
+            assert len(unique_phase_IDs) == num_phases
 
         interface_map = None
-        if parse_interface_map:
-            interface_map = decompress_1D_array_string(
-                data["mappings"]["interface_mapping"]
-            )
-            interface_map = interface_map.reshape((num_phases, num_phases)) - 1
-            interface_map[np.tril_indices(num_phases)] = -1  # only need one half
+        if data["mappings"]["interface_mapping"] != "interface_mapping.txt":
+            if parse_interface_map:
+                interface_map = decompress_1D_array_string(
+                    data["mappings"]["interface_mapping"]
+                )
+                interface_map = interface_map.reshape((num_phases, num_phases)) - 1
+                interface_map[np.tril_indices(num_phases)] = -1  # only need one half
 
-        phase_material = (
-            decompress_1D_array_string(data["mappings"]["phase_material_mapping"]) - 1
-        )
+        phase_material = None
+        if data["mappings"]["phase_material_mapping"] != "phase_material_mapping.txt":
+            phase_material = (
+                decompress_1D_array_string(data["mappings"]["phase_material_mapping"]) - 1
+            )
 
         return {
             "header": header,
@@ -190,10 +254,27 @@ def read_input_YAML_string(file_str, parse_interface_map=True):
         }
 
     @classmethod
-    def from_input_YAML_str(cls, file_str, quiet=False):
+    def from_input_YAML_str(
+        cls,
+        file_str,
+        input_map_voxel_phase=None,
+        input_map_phase_material=None,
+        input_map_interface=None,
+        quiet=False,
+    ):
         """Generate a CIPHERInput object from a CIPHER input YAML file string."""
 
         yaml_dat = cls.read_input_YAML_string(file_str)
+        if input_map_voxel_phase is not None:
+            yaml_dat["voxel_phase"] = input_map_voxel_phase
+            yaml_dat["unique_phase_IDs"] = np.unique(input_map_voxel_phase)
+
+        if input_map_phase_material is not None:
+            yaml_dat["phase_material"] = input_map_phase_material
+
+        if input_map_interface is not None:
+            yaml_dat["interface_map"] = input_map_interface
+
         materials = [
             MaterialDefinition(
                 name=name,
@@ -252,8 +333,8 @@ def from_voronoi(
         num_phases=None,
         random_seed=None,
         is_periodic=False,
+        combine_phases=None,
     ):
-
         geometry = CIPHERGeometry.from_voronoi(
             num_phases=num_phases,
             seeds=seeds,
@@ -263,6 +344,7 @@ def from_voronoi(
             size=size,
             random_seed=random_seed,
             is_periodic=is_periodic,
+            combine_phases=combine_phases,
         )
 
         inp = cls(
@@ -286,8 +368,8 @@ def from_seed_voronoi(
         solution_parameters,
         random_seed=None,
         is_periodic=False,
+        combine_phases=None,
     ):
-
         return cls.from_voronoi(
             seeds=seeds,
             grid_size=grid_size,
@@ -299,6 +381,7 @@ def from_seed_voronoi(
             solution_parameters=solution_parameters,
             random_seed=random_seed,
             is_periodic=is_periodic,
+            combine_phases=combine_phases,
         )
 
     @classmethod
@@ -314,8 +397,8 @@ def from_random_voronoi(
         solution_parameters,
         random_seed=None,
         is_periodic=False,
+        combine_phases=None,
     ):
-
         return cls.from_voronoi(
             num_phases=num_phases,
             grid_size=grid_size,
@@ -327,6 +410,7 @@ def from_random_voronoi(
             solution_parameters=solution_parameters,
             random_seed=random_seed,
             is_periodic=is_periodic,
+            combine_phases=combine_phases,
         )
 
     @classmethod
@@ -340,14 +424,15 @@ def from_voxel_phase_map(
         outputs,
         solution_parameters,
         random_seed=None,
+        combine_phases=None,
     ):
-
         geometry = CIPHERGeometry(
             voxel_phase=voxel_phase,
             materials=materials,
             interfaces=interfaces,
             size=size,
             random_seed=random_seed,
+            combine_phases=combine_phases,
         )
         inp = cls(
             geometry=geometry,
@@ -368,8 +453,8 @@ def from_dream3D(
         solution_parameters,
         container_labels=None,
         phase_type_map=None,
+        combine_phases=None,
     ):
-
         default_container_labels = {
             "SyntheticVolumeDataContainer": "SyntheticVolumeDataContainer",
             "CellData": "CellData",
@@ -389,7 +474,6 @@ def from_dream3D(
         container_labels = {**default_container_labels, **container_labels}
 
         with h5py.File(path, "r") as fp:
-
             voxel_phase_path = "/".join(
                 (
                     "DataContainers",
@@ -484,6 +568,7 @@ def from_dream3D(
             components=components,
             outputs=outputs,
             solution_parameters=solution_parameters,
+            combine_phases=combine_phases,
         )
 
     @property
@@ -517,11 +602,48 @@ def get_header(self):
     def get_interfaces(self):
         return {i.name: i.properties for i in self.geometry.interfaces}
 
-    def write_yaml(self, path):
-        """Write the CIPHER input YAML file."""
+    def write_yaml(self, path, separate_mappings=False):
+        """Write the CIPHER input YAML file.
+
+        Parameters
+        ----------
+        separate_mappings
+            If True, write separate text files for the mappings.
+
+        """
 
         self.geometry._validate_interface_map()
 
+        phase_mat_str = compress_1D_array_string(self.geometry.phase_material + 1)
+        vox_phase_str = compress_1D_array_string(
+            self.geometry.voxel_phase.flatten(order="F") + 1
+        )
+        int_str = compress_1D_array_string(self.geometry.interface_map_int.flatten() + 1)
+
+        if not separate_mappings:
+            # CIPHER does not like trailing new lines in the mapping text files:
+            phase_mat_str += "\n"
+            vox_phase_str += "\n"
+            int_str += "\n"
+
+        if separate_mappings:
+            phase_mat_map = "phase_material_mapping.txt"
+            vox_phase_map = "voxel_phase_mapping.txt"
+            int_map = "interface_mapping.txt"
+            with Path(phase_mat_map).open("wt") as fh:
+                fh.write(indent(phase_mat_str, "    "))
+
+            with Path(vox_phase_map).open("wt") as fh:
+                fh.write(indent(vox_phase_str, "    "))
+
+            with Path(int_map).open("wt") as fh:
+                fh.write(indent(int_str, "    "))
+
+        else:
+            phase_mat_map = LiteralScalarString(phase_mat_str)
+            vox_phase_map = LiteralScalarString(vox_phase_str)
+            int_map = LiteralScalarString(int_str)
+
         cipher_input_data = {
             "header": self.get_header(),
             "solution_parameters": dict(sorted(self.solution_parameters.items())),
@@ -530,21 +652,9 @@ def write_yaml(self, path):
             },
             "interface": {k: copy.deepcopy(v) for k, v in self.get_interfaces().items()},
             "mappings": {
-                "phase_material_mapping": LiteralScalarString(
-                    compress_1D_array_string(self.geometry.phase_material + 1) + "\n"
-                ),
-                "voxel_phase_mapping": LiteralScalarString(
-                    compress_1D_array_string(
-                        self.geometry.voxel_phase.flatten(order="F") + 1
-                    )
-                    + "\n"
-                ),
-                "interface_mapping": LiteralScalarString(
-                    compress_1D_array_string(
-                        self.geometry.interface_map_int.flatten() + 1
-                    )
-                    + "\n"
-                ),
+                "phase_material_mapping": phase_mat_map,
+                "voxel_phase_mapping": vox_phase_map,
+                "interface_mapping": int_map,
             },
         }
 
@@ -565,6 +675,7 @@ def bin_interfaces_by_misorientation_angle(
         B=5,
         bin_width=5,
         degrees=True,
+        **kwargs,
     ):
         if energy_range is None and mobility_range is None:
             raise ValueError(
@@ -572,7 +683,7 @@ def bin_interfaces_by_misorientation_angle(
             )
 
         if self.geometry.misorientation_matrix is None:
-            misori_matrix = self.geometry.get_misorientation_matrix()
+            misori_matrix = self.geometry.get_misorientation_matrix(**kwargs)
         else:
             misori_matrix = self.geometry.misorientation_matrix
 
@@ -619,7 +730,6 @@ def bin_interfaces_by_misorientation_angle(
             )
 
         for int_name in base_interface_name:
-
             base_defn, phase_pairs = self.geometry.remove_interface(int_name)
 
             phase_pairs_bin_idx = bin_idx[phase_pairs[0], phase_pairs[1]]
@@ -630,7 +740,6 @@ def bin_interfaces_by_misorientation_angle(
             print("Preparing new interface defintions...")
             new_int_idx = 0
             for bin_idx_i, bin_i in enumerate(misori_bins, start=1):
-
                 phase_pairs_bin_i_idx = np.where(phase_pairs_bin_idx == bin_idx_i)[0]
                 if not phase_pairs_bin_i_idx.size:
                     continue
@@ -789,7 +898,6 @@ def apply_interface_property(
         num_existing_int_defns = len(self.geometry.interfaces)
         print("Preparing new interface defintions...", end="")
         for idx, i in enumerate(new_interfaces_data):
-
             props = copy.deepcopy(base_defn.properties)
             for name, val in zip(property_name, i["values"]):
                 new_value = val.item()  #  convert from numpy to native
diff --git a/cipher_parse/cipher_output.py b/cipher_parse/cipher_output.py
index 7a37e0d..86aa1f2 100644
--- a/cipher_parse/cipher_output.py
+++ b/cipher_parse/cipher_output.py
@@ -1,3 +1,4 @@
+import copy
 import json
 import shutil
 from subprocess import run, PIPE
@@ -10,8 +11,9 @@
 import pyvista as pv
 import pandas as pd
 import plotly.express as px
+import zarr
 
-from cipher_parse.cipher_input import CIPHERInput
+from cipher_parse.cipher_input import CIPHERInput, decompress_1D_array_string
 from cipher_parse.geometry import CIPHERGeometry
 from cipher_parse.utilities import (
     get_subset_indices,
@@ -20,7 +22,6 @@
 )
 from cipher_parse.derived_outputs import num_voxels_per_phase
 
-DEFAULT_PARAVIEW_EXE = "pvbatch"
 INC_DATA_NON_ARRAYS = (
     "increment",
     "time",
@@ -107,53 +108,6 @@ def parse_cipher_stdout(path_or_string, is_string=False):
     return out
 
 
-def generate_VTI_files_from_VTU_files(
-    sampling_dimensions,
-    paraview_exe=DEFAULT_PARAVIEW_EXE,
-):
-    """Generate a 'ParaView-python' script for generating VTI files from VTU files and
-    execute that script."""
-
-    script_name = "vtu2vti.py"
-    if len(sampling_dimensions) == 2:
-        sampling_dimensions += [1]
-
-    with Path(script_name).open("wt") as fp:
-        fp.write(
-            dedent(
-                f"""
-            import os
-
-            from paraview.simple import *
-
-            vtu_files = []
-            for root, dirs, files in os.walk("."):
-                for f in files:
-                    if f.endswith(".vtu"):
-                        vtu_files.append(f)
-            
-            for file_i_path in vtu_files:
-                file_i_base_name = file_i_path.split(".")[0]
-                vtu_data_i = XMLUnstructuredGridReader(
-                    FileName=[os.getcwd() + os.path.sep + file_i_path]
-                )
-                resampleToImage1 = ResampleToImage(Input=vtu_data_i)
-                resampleToImage1.SamplingDimensions = {sampling_dimensions!r}
-                SetActiveSource(resampleToImage1)
-                SaveData(file_i_base_name + ".vti", resampleToImage1)
-        """
-            )
-        )
-
-    proc = run(f"{paraview_exe} {script_name}", shell=True, stdout=PIPE, stderr=PIPE)
-    stdout = proc.stdout.decode()
-    stderr = proc.stderr.decode()
-    if stdout:
-        print(stdout)
-    if stderr:
-        print(stderr)
-
-
 class CIPHEROutput:
     """Class to hold output information from a CIPHER simulation."""
 
@@ -166,17 +120,13 @@ def __init__(
         input_YAML_file_str,
         stdout_file_str,
         incremental_data,
+        input_map_voxel_phase=None,
+        input_map_phase_material=None,
+        input_map_interface=None,
         quiet=False,
         cipher_input=None,
     ):
-
         default_options = {
-            "paraview_exe": DEFAULT_PARAVIEW_EXE,
-            "delete_VTIs": True,
-            "delete_VTUs": False,
-            "use_existing_VTIs": False,
-            "num_VTU_files": None,
-            "VTU_files_time_interval": None,
             "derive_outputs": None,
             "save_outputs": None,
         }
@@ -185,6 +135,9 @@ def __init__(
         self.options = {**default_options, **options}
         self.input_YAML_file_name = input_YAML_file_name
         self.input_YAML_file_str = input_YAML_file_str
+        self.input_map_voxel_phase = input_map_voxel_phase
+        self.input_map_phase_material = input_map_phase_material
+        self.input_map_interface = input_map_interface
         self.stdout_file_name = stdout_file_name
         self.stdout_file_str = stdout_file_str
         self.incremental_data = incremental_data
@@ -194,15 +147,7 @@ def __init__(
         self._cipher_stdout = None
         self._geometries = None  # assigned by set_geometries
 
-        if (
-            options.get("VTU_files_time_interval") is not None
-            and options.get("num_VTU_files") is not None
-        ):
-            raise ValueError(
-                "Specify at most one of 'num_VTU_files' and 'VTU_files_time_interval'."
-            )
-
-        for idx, i in enumerate(options["save_outputs"]):
+        for idx, i in enumerate(options["save_outputs"] or ()):
             if i.get("number") is not None and i.get("time_interval") is not None:
                 raise ValueError(
                     f"Specify at most one of 'number' and 'time_interval' for save "
@@ -216,6 +161,9 @@ def parse(
         options=None,
         input_YAML_file_name="cipher_input.yaml",
         stdout_file_name="stdout.log",
+        get_voxel_phase=True,
+        get_phase_material=True,
+        get_interface=True,
     ):
         directory = Path(directory)
 
@@ -227,11 +175,26 @@ def parse(
         with stdout_path.open("rt") as fp:
             stdout_file_str = "".join(fp.readlines())
 
+        (
+            voxel_phase,
+            phase_material,
+            interface_map,
+        ) = CIPHERInput.get_input_maps_from_files(
+            inp_file_str=input_YAML_file_str,
+            directory=directory,
+            get_voxel_phase=get_voxel_phase,
+            get_phase_material=get_phase_material,
+            get_interface=get_interface,
+        )
+
         obj = cls(
             directory=directory,
             options=options,
             input_YAML_file_name=input_YAML_file_name,
             input_YAML_file_str=input_YAML_file_str,
+            input_map_voxel_phase=voxel_phase,
+            input_map_phase_material=phase_material,
+            input_map_interface=interface_map,
             stdout_file_name=stdout_file_name,
             stdout_file_str=stdout_file_str,
             incremental_data=None,
@@ -254,131 +217,130 @@ def get_incremental_data(self):
         """Generate temporary VTI files to parse requested cipher outputs on a uniform
         grid."""
 
-        cipher_input = self.cipher_input
-
-        if not self.options["use_existing_VTIs"]:
-            generate_VTI_files_from_VTU_files(
-                sampling_dimensions=cipher_input.geometry.grid_size.tolist(),
-                paraview_exe=self.options["paraview_exe"],
-            )
+        inp_dat = self.get_input_YAML_data()
+        grid_size = inp_dat["grid_size"]
+        grid_size_3D = grid_size if len(grid_size) == 3 else [*grid_size, 1]
 
-        outfile_base = cipher_input.solution_parameters["outfile"]
+        outfile_base = inp_dat["solution_parameters"]["outfile"]
         output_lookup = {
             i: f"{outfile_base} output.{idx}"
-            for idx, i in enumerate(self.cipher_input.outputs)
+            for idx, i in enumerate(inp_dat["header"]["outputs"])
         }
         vtu_file_list = sorted(
             list(self.directory.glob(f"{outfile_base}_*.vtu")),
             key=lambda x: int(re.search(r"\d+", x.name).group()),
         )
-        vti_file_list = sorted(
-            list(self.directory.glob(f"{outfile_base}_*.vti")),
-            key=lambda x: int(re.search(r"\d+", x.name).group()),
-        )
-
-        # Move all VTU files to a sub-directory:
-        viz_dir = Path("original_viz")
-        viz_dir.mkdir()
-        vtu_orig_file_list = []
-        for viz_file_i in vtu_file_list:
-            dst_i = viz_dir.joinpath(viz_file_i.name).with_suffix(
-                ".viz" + viz_file_i.suffix
-            )
-            shutil.move(viz_file_i, dst_i)
-            vtu_orig_file_list.append(dst_i)
-
-        # Copy back to the root directory VTU files that we want to keep:
-        if self.options["num_VTU_files"]:
-            viz_files_keep_idx = get_subset_indices(
-                len(vti_file_list),
-                self.options["num_VTU_files"],
-            )
-        elif self.options["VTU_files_time_interval"]:
-            viz_files_keep_idx = self._get_time_linear_subset_indices(
-                time_interval=self.options["VTU_files_time_interval"]
-            )
-        else:
-            viz_files_keep_idx = []
-
-        for i in viz_files_keep_idx:
-            viz_file_i = vtu_orig_file_list[i]
-            dst_i = Path("").joinpath(viz_file_i.name).with_suffix("").with_suffix(".vtu")
-            shutil.copy(viz_file_i, dst_i)
-
-        if self.options["delete_VTUs"]:
-            print(f"Deleting original VTU files in directory: {viz_dir}")
-            shutil.rmtree(viz_dir)
 
         # get which files to include for each output/derived output
         outputs_keep_idx = {}
-        for save_out_i in self.options["save_outputs"]:
+        for save_out_i in self.options["save_outputs"] or ():
             if "number" in save_out_i:
-                keep_idx = get_subset_indices(len(vti_file_list), save_out_i["number"])
+                keep_idx = get_subset_indices(len(vtu_file_list), save_out_i["number"])
             elif "time_interval" in save_out_i:
                 keep_idx = self._get_time_linear_subset_indices(
                     time_interval=save_out_i["time_interval"]
                 )
             else:
-                keep_idx = list(range(len(vti_file_list)))
+                keep_idx = list(range(len(vtu_file_list)))
             outputs_keep_idx[save_out_i["name"]] = keep_idx
 
         incremental_data = []
-        for file_i_idx, file_i in enumerate(vti_file_list):
+        for file_i_idx, file_i in enumerate(vtu_file_list):
+            print(f"Reading VTU file {file_i.name}...", flush=True)
+            try:
+                mesh = pv.get_reader(file_i).read()
+            except Exception:
+                print(f"Failed to read VTU file {file_i.name}.", flush=True)
+                continue
+            vtu_file_name = file_i.name
+
+            img_data = pv.ImageData(dimensions=grid_size_3D)
+
+            print(
+                f"Resampling VTU file {file_i.name} onto an image-data mesh...",
+                flush=True,
+            )
+            try:
+                img_mesh = img_data.sample(mesh)
+            except Exception:
+                print(
+                    f"Failed to re-sample VTU file {file_i.name} onto an image "
+                    f"data grid.",
+                    flush=True,
+                )
+                continue
 
-            mesh = pv.get_reader(file_i).read()
-            vtu_file_name = file_i.name.replace("vti", "vtu")
             inc_data_i = {
-                "increment": int(re.search(r"\d+", file_i.name).group()),
+                "increment": int(re.search(r"\d+", vtu_file_name).group()),
                 "time": self.cipher_stdout["outputs"][vtu_file_name],
-                "dimensions": list(mesh.dimensions),
-                "spacing": list(mesh.spacing),
-                "number_VTI_cells": mesh.number_of_cells,
-                "number_VTI_points": mesh.number_of_points,
+                "dimensions": list(img_mesh.dimensions),
+                "spacing": list(img_mesh.spacing),
+                "number_VTI_cells": img_mesh.number_of_cells,
+                "number_VTI_points": img_mesh.number_of_points,
             }
 
             standard_outputs = {}
             for name in output_lookup:
-                arr_flat = mesh.get_array(output_lookup[name])
-                arr = arr_flat.reshape(mesh.dimensions, order="F")
+                try:
+                    arr_flat = img_mesh.get_array(output_lookup[name])
+                except KeyError:
+                    print(
+                        f"Failed to get array {output_lookup[name]} from file "
+                        f"{file_i.name}",
+                        flush=True,
+                    )
+                    continue
+                arr = arr_flat.reshape(img_mesh.dimensions, order="F")
                 if name in STANDARD_OUTPUTS_TYPES:
                     arr = arr.astype(STANDARD_OUTPUTS_TYPES[name])
-                standard_outputs[name] = arr
+                standard_outputs[name] = np.array(arr)  # convert from pyvista_ndarray
 
             derived_outputs = {}
-            for derive_out_i in self.options["derive_outputs"]:
+            for derive_out_i in self.options["derive_outputs"] or ():
                 name_i = derive_out_i["name"]
                 func = DERIVED_OUTPUTS_FUNCS[name_i]
-                func_args = {"cipher_input": cipher_input}
-                func_args.update(
-                    {i: standard_outputs[i] for i in DERIVED_OUTPUTS_REQUIREMENTS[name_i]}
-                )
+                func_args = {"input_data": inp_dat}
+                try:
+                    func_args.update(
+                        {
+                            i: standard_outputs[i]
+                            for i in DERIVED_OUTPUTS_REQUIREMENTS[name_i]
+                        }
+                    )
+                except KeyError:
+                    print(
+                        f"Failed to prepare arguments for derived output function "
+                        f"{func.__name__!r}.",
+                        flush=True,
+                    )
+                    continue
                 derived_outputs[name_i] = func(**func_args)
 
             for out_name, keep_idx in outputs_keep_idx.items():
                 if file_i_idx in keep_idx:
-                    if out_name in DERIVED_OUTPUTS_REQUIREMENTS:
-                        # a derived output:
-                        inc_data_i[out_name] = derived_outputs[out_name]
-                    else:
-                        # a standard output:
-                        inc_data_i[out_name] = standard_outputs[out_name]
+                    try:
+                        if out_name in DERIVED_OUTPUTS_REQUIREMENTS:
+                            # a derived output:
+                            inc_data_i[out_name] = derived_outputs[out_name]
+                        else:
+                            # a standard output:
+                            inc_data_i[out_name] = standard_outputs[out_name]
+                    except KeyError:
+                        continue
 
             incremental_data.append(inc_data_i)
 
-        if self.options["delete_VTIs"] and not self.options["use_existing_VTIs"]:
-            for file_i in vti_file_list:
-                print(f"Deleting temporary VTI file: {file_i}")
-                os.remove(file_i)
-
-        outputs_keep_idx["VTU_files"] = viz_files_keep_idx
-
         return incremental_data, outputs_keep_idx
 
     @property
     def cipher_input(self):
         if not self._cipher_input:
             self._cipher_input = CIPHERInput.from_input_YAML_str(
-                self.input_YAML_file_str, quiet=self.quiet
+                file_str=self.input_YAML_file_str,
+                quiet=self.quiet,
+                input_map_voxel_phase=self.input_map_voxel_phase,
+                input_map_phase_material=self.input_map_phase_material,
+                input_map_interface=self.input_map_interface,
             )
         return self._cipher_input
 
@@ -399,9 +361,21 @@ def cipher_stdout(self):
     def get_input_YAML_data(self, parse_interface_map=False):
         """Get some basic input details (using the YAML input file) without initialising
         the CIPHERInput object, which can take a while depending on the grid size."""
-        return CIPHERInput.read_input_YAML_string(
-            self.input_YAML_file_str, parse_interface_map=parse_interface_map
+        dat = CIPHERInput.read_input_YAML_string(
+            file_str=self.input_YAML_file_str,
+            parse_interface_map=parse_interface_map,
         )
+        if self.input_map_voxel_phase is not None:
+            dat["voxel_phase"] = self.input_map_voxel_phase
+            dat["unique_phase_IDs"] = np.unique(self.input_map_voxel_phase)
+
+        if self.input_map_phase_material is not None:
+            dat["phase_material"] = self.input_map_phase_material
+
+        if self.input_map_interface is not None:
+            dat["interface_map"] = self.input_map_interface
+
+        return dat
 
     def to_JSON(self, keep_arrays=False):
         data = {
@@ -409,6 +383,9 @@ def to_JSON(self, keep_arrays=False):
             "options": self.options,
             "input_YAML_file_name": self.input_YAML_file_name,
             "input_YAML_file_str": self.input_YAML_file_str,
+            "input_map_voxel_phase": self.input_map_voxel_phase,
+            "input_map_phase_material": self.input_map_phase_material,
+            "input_map_interface": self.input_map_interface,
             "stdout_file_name": self.stdout_file_name,
             "stdout_file_str": self.stdout_file_str,
             "incremental_data": self.incremental_data,
@@ -418,24 +395,54 @@ def to_JSON(self, keep_arrays=False):
             for inc_idx, inc_i in enumerate(data["incremental_data"] or []):
                 for key in inc_i:
                     if key not in INC_DATA_NON_ARRAYS:
-                        as_list_val = data["incremental_data"][inc_idx][key].tolist()
+                        as_list_val = np.copy(
+                            data["incremental_data"][inc_idx][key]
+                        ).tolist()
                         data["incremental_data"][inc_idx][key] = as_list_val
 
+            if data["input_map_voxel_phase"] is not None:
+                data["input_map_voxel_phase"] = np.copy(
+                    data["input_map_voxel_phase"]
+                ).tolist()
+
+            if data["input_map_phase_material"] is not None:
+                data["input_map_phase_material"] = np.copy(
+                    data["input_map_phase_material"]
+                ).tolist()
+
+            if data["input_map_interface"] is not None:
+                data["input_map_interface"] = np.copy(
+                    data["input_map_interface"]
+                ).tolist()
+
         return data
 
     @classmethod
     def from_JSON(cls, data, cipher_input=None, quiet=True):
-
         attrs = {
             "directory": data["directory"],
             "options": data["options"],
             "input_YAML_file_name": data["input_YAML_file_name"],
             "input_YAML_file_str": data["input_YAML_file_str"],
+            "input_map_voxel_phase": data.get("input_map_voxel_phase"),
+            "input_map_phase_material": data.get("input_map_phase_material"),
+            "input_map_interface": data.get("input_map_interface"),
             "stdout_file_name": data["stdout_file_name"],
             "stdout_file_str": data["stdout_file_str"],
             "incremental_data": data["incremental_data"],
         }
 
+        if attrs["input_map_voxel_phase"]:
+            attrs["input_map_voxel_phase"] = np.array(attrs["input_map_voxel_phase"])
+
+        if attrs["input_map_phase_material"]:
+            attrs["input_map_phase_material"] = np.array(
+                attrs["input_map_phase_material"]
+            )
+
+        if attrs["input_map_interface"]:
+            attrs["input_map_interface"] = np.array(attrs["input_map_interface"])
+
         for inc_idx, inc_i in enumerate(attrs["incremental_data"] or []):
             for key, val in inc_i.items():
                 if key not in INC_DATA_NON_ARRAYS and not isinstance(val, np.ndarray):
@@ -463,6 +470,84 @@ def from_JSON_file(cls, path):
             data = json.load(fp)
         return cls.from_JSON(data)
 
+    def to_zarr(self, path, overwrite=False, close_store=None):
+        """Save to a persistent zarr store.
+
+        This does not yet save `geometries`.
+
+        """
+        out_group = zarr.open_group(store=path)
+        out_group.attrs.put(
+            {
+                "directory": str(self.directory),
+                "options": self.options,
+                "input_YAML_file_name": self.input_YAML_file_name,
+                "input_map_voxel_phase": self.input_map_voxel_phase,
+                "input_map_phase_material": self.input_map_phase_material,
+                "input_map_interface": self.input_map_interface,
+                "stdout_file_name": self.stdout_file_name,
+            }
+        )
+        out_group.create_dataset(
+            name="stdout_file_str",
+            data=self.stdout_file_str.splitlines(),
+            overwrite=overwrite,
+        )
+        out_group.create_dataset(
+            name="input_YAML_file_str",
+            data=self.input_YAML_file_str.splitlines(),
+            overwrite=overwrite,
+        )
+        inc_dat_group = out_group.create_group("incremental_data", overwrite=True)
+        for idx, inc_dat_i in enumerate(self.incremental_data):
+            inc_dat_i_group = inc_dat_group.create_group(f"{idx}")
+            inc_dat_i_group.attrs.put({k: inc_dat_i[k] for k in INC_DATA_NON_ARRAYS})
+            for k in inc_dat_i:
+                if k not in INC_DATA_NON_ARRAYS:
+                    inc_dat_i_group.create_dataset(
+                        name=k, data=inc_dat_i[k], overwrite=overwrite
+                    )
+
+        if path.endswith(".zip") and close_store is None:
+            close_store = True
+
+        if close_store:
+            out_group.store.close()
+
+        return out_group
+
+    @classmethod
+    def from_zarr(cls, path, cipher_input=None, quiet=True):
+        """Load from a persistent zarr store.
+
+        This does not yet load `geometries`.
+
+        """
+        group = zarr.open_group(store=path, mode="r")
+        attrs = group.attrs.asdict()
+        kwargs = {
+            "directory": attrs["directory"],
+            "options": attrs["options"],
+            "input_YAML_file_name": attrs["input_YAML_file_name"],
+            "input_map_voxel_phase": attrs["input_map_voxel_phase"],
+            "input_map_phase_material": attrs["input_map_phase_material"],
+            "input_map_interface": attrs["input_map_interface"],
+            "stdout_file_name": attrs["stdout_file_name"],
+            "stdout_file_str": "\n".join(group.get("stdout_file_str")[:]),
+            "input_YAML_file_str": "\n".join(group.get("input_YAML_file_str")[:]),
+        }
+        inc_data = []
+        for inc_dat_i_group in group.get("incremental_data").values():
+            inc_dat_i_group_attrs = inc_dat_i_group.attrs.asdict()
+            inc_data_i = {k: inc_dat_i_group_attrs[k] for k in INC_DATA_NON_ARRAYS}
+            for name, dataset in inc_dat_i_group.items():
+                inc_data_i[name] = dataset[:]
+            inc_data.append(inc_data_i)
+        kwargs["incremental_data"] = inc_data
+
+        obj = cls(**kwargs, cipher_input=cipher_input, quiet=quiet)
+        return obj
+
     @classmethod
     def compare_phase_size_dist_evolution(
         cls,
@@ -480,7 +565,6 @@ def compare_phase_size_dist_evolution(
         label_name=None,
         layout_args=None,
     ):
-
         if len(cipher_outputs) > 1 and not (row_labels or col_labels or labels):
             raise TypeError(
                 "Multiple cipher outputs but not labels/row_labels/col_labels "
@@ -712,7 +796,6 @@ def _prepare_phase_size_dist_evolution_dataframe(
                     }
                 )
             else:
-
                 if inc_idx == 0:
                     initial_bins = bins[bin_indices_i - 1]
 
@@ -831,7 +914,6 @@ def show_misorientation_dist_evolution(
         bin_size=None,
         layout_args=None,
     ):
-
         all_misori_vox = []
         inc_dat_indices = []
         incs = []
@@ -1014,21 +1096,28 @@ def show_slice_evolution(
 
     def get_average_radius_evolution(self, exclude=None):
         """Get an evolution proportional to the average radius across all phases."""
+
+        inp_dat = self.get_input_YAML_data()
+        num_phases = inp_dat["num_phases"]
+        dimension = len(inp_dat["grid_size"])
         exclude = exclude or []
-        all_phases_num_voxels = [[] for _ in range(self.geometries[0].num_phases)]
+
+        num_voxel_inc_idx = []
         times = []
-        for dat_i in self.incremental_data:
-            if "num_voxels_per_phase" in dat_i:
-                for idx, i in enumerate(dat_i["num_voxels_per_phase"]):
-                    if idx in exclude:
-                        i = 0
-                    all_phases_num_voxels[idx].append(i)
-                times.append(dat_i["time"])
-
-        power = 1 / self.geometries[0].dimension
-        all_phases_prop_radius = np.array(
-            [np.power(i, power) for i in all_phases_num_voxels]
-        )
+        for idx, i in enumerate(self.incremental_data):
+            if "num_voxels_per_phase" in i:
+                num_voxel_inc_idx.append(idx)
+                times.append(i["time"])
+
+        all_phases_num_voxels = np.ones((num_phases, len(num_voxel_inc_idx))) * np.nan
+        for idx, inc_i_idx in enumerate(num_voxel_inc_idx):
+            num_voxels = np.copy(self.incremental_data[inc_i_idx]["num_voxels_per_phase"])
+            if exclude:
+                num_voxels[exclude] = 0
+            all_phases_num_voxels[:, idx] = num_voxels
+
+        power = 1 / dimension
+        all_phases_prop_radius = np.power(all_phases_num_voxels, power)
         all_phases_prop_radius[np.isclose(all_phases_prop_radius, 0)] = np.nan
         prop_avg_radius = np.nanmean(all_phases_prop_radius, axis=0)
 
diff --git a/cipher_parse/derived_outputs.py b/cipher_parse/derived_outputs.py
index f6a4e29..c60a176 100644
--- a/cipher_parse/derived_outputs.py
+++ b/cipher_parse/derived_outputs.py
@@ -1,9 +1,8 @@
 import numpy as np
 
 
-def num_voxels_per_phase(cipher_input, phaseid):
-    voxel_phase = cipher_input.geometry.voxel_phase
-    num_initial_phases = len(np.unique(voxel_phase))
+def num_voxels_per_phase(input_data, phaseid):
+    num_initial_phases = input_data["num_phases"]
     num_voxels_per_phase = np.zeros(num_initial_phases, dtype=int)
     uniq, counts = np.unique(phaseid.astype(int), return_counts=True)
     num_voxels_per_phase[uniq] = counts
diff --git a/cipher_parse/geometry.py b/cipher_parse/geometry.py
index 5b29f22..5f1b035 100644
--- a/cipher_parse/geometry.py
+++ b/cipher_parse/geometry.py
@@ -1,3 +1,5 @@
+import random
+
 from damask import Orientation
 import pyvista as pv
 import numpy as np
@@ -16,7 +18,11 @@
     GeometryVoxelPhaseError,
 )
 from cipher_parse.utilities import generate_interface_energies_plot
-from cipher_parse.quats import quat_angle_between
+from cipher_parse.quats import (
+    compute_misorientation_matrix,
+    quat_angle_between,
+    compute_misorientation_matrix_damask,
+)
 
 
 class CIPHERGeometry:
@@ -35,6 +41,7 @@ def __init__(
         time=None,
         increment=None,
         incremental_data_idx=None,
+        combine_phases=None,
     ):
         """
         Parameters
@@ -103,6 +110,22 @@ def __init__(
 
         self._ensure_phase_assignment(random_seed)
 
+        if combine_phases:
+            # combine multiple phases into the same phase to reduce the computational cost
+            self.voxel_phase = self.combine_phases_per_phase_type(
+                voxel_map,
+                materials,
+                combine_phases,
+            )
+            self.voxel_map = VoxelMap(
+                region_ID=voxel_phase,
+                size=size,
+                is_periodic=is_periodic,
+                quiet=quiet,
+            )
+            all_phases = self.present_phases
+            self._num_phases = all_phases.size
+
         self._phase_material = self._get_phase_material()
         self._validate_interfaces()
         self._check_interface_phase_pairs()
@@ -127,6 +150,93 @@ def __init__(
         self._misorientation_matrix = None
         self._misorientation_matrix_is_degrees = None
 
+    @staticmethod
+    def combine_phases_per_phase_type(voxel_map, materials, combine_phases):
+
+        print(f"combining phases according to {combine_phases}")
+
+        voxel_phase_new = voxel_map.region_ID
+        neighbours = voxel_map.neighbour_list
+
+        for mat in materials:
+            for pt_i in mat.phase_types:
+                print(f"{pt_i.name=}")
+                max_phases_i = combine_phases.get(pt_i.name)
+                if max_phases_i:
+
+                    n_phases = pt_i.phases.size
+                    group_size = int(np.ceil(n_phases / max_phases_i))
+
+                    print(f" n_phases: {n_phases}")
+                    print(f" max_phases_i: {max_phases_i}")
+                    print(f" group_size: {group_size}")
+
+                    voxel_phase_new = np.copy(voxel_phase_new)
+
+                    reassignment = {}
+                    reassignment_inv = {}
+                    possible_IDs_idx = set(range(max_phases_i, n_phases))
+                    possible_IDs = set(pt_i.phases[list(possible_IDs_idx)])
+                    count = 0
+                    kept_IDs = []
+                    for root_ID_idx in range(int(np.ceil(n_phases / group_size))):
+
+                        root_ID = pt_i.phases[root_ID_idx]
+                        kept_IDs.append(root_ID)
+
+                        neighbours_i = set(neighbours[:, neighbours[0] == root_ID][1])
+                        possible_IDs -= {root_ID}
+                        possible_IDs_i = possible_IDs - neighbours_i
+                        shared_IDs = [root_ID]
+                        count += 1
+
+                        for _ in range(1, group_size):
+                            if count >= n_phases:
+                                break
+                            try:
+                                sampled_ID = random.sample(possible_IDs_i, 1)[0]
+                            except ValueError:
+                                print(
+                                    f"No non-neighbouring samples left for root_ID: {root_ID}."
+                                )
+                                # allow touching phase IDs within this group:
+                                possible_IDs_i = possible_IDs - set(shared_IDs)
+
+                                if possible_IDs_i:
+                                    sampled_ID = random.sample(possible_IDs_i, 1)[0]
+                                else:
+                                    raise ValueError(
+                                        f"Cannot find non-neighbouring root IDs"
+                                    ) from None
+
+                            neighbours_sampled = set(
+                                neighbours[:, neighbours[0] == sampled_ID][1]
+                            )
+                            possible_IDs_i -= neighbours_sampled
+                            possible_IDs_i -= {sampled_ID}
+                            possible_IDs -= {sampled_ID}
+                            shared_IDs.append(sampled_ID)
+                            count += 1
+
+                        for i in shared_IDs:
+                            reassignment[i] = root_ID
+                            voxel_phase_new[voxel_phase_new == i] = root_ID
+
+                        reassignment_inv[root_ID] = shared_IDs
+
+                    pt_i.phases = kept_IDs  # modify phase type phases
+
+                    # reindex phases across all materials to maintain consecutive phase IDs:
+                    voxel_phase_new_flat = voxel_phase_new.reshape(-1)
+                    uniq, inv = np.unique(voxel_phase_new_flat, return_inverse=True)
+                    reindex = dict(zip(uniq, range(len(uniq))))
+                    voxel_phase_new = inv.reshape(voxel_phase_new.shape)
+                    for mat_j in materials:
+                        for pt_j in mat_j.phase_types:
+                            pt_j.phases = np.array([reindex[i] for i in pt_j.phases])
+
+        return voxel_phase_new
+
     def __eq__(self, other):
         # Note we don't check seeds (not stored in YAML file)
         if not isinstance(other, self.__class__):
@@ -379,7 +489,6 @@ def _check_interface_phase_pairs(self):
         the specified phases of associated material."""
 
         for i in self.interfaces:
-
             # assign materials as well as phase_types if materials not assigned to
             # interface:
             if not i.materials:
@@ -453,7 +562,7 @@ def _get_phase_material(self):
                 "Not all phases are accounted for in the phase type definitions."
             )  # TODO: test raise
 
-        # check all phase indices form a consequtive range:
+        # check all phase indices form a consecutive range:
         num_phases_range = set(np.arange(self.num_phases))
         known_phases = set(np.hstack(all_phase_idx))
         miss_phase_idx = num_phases_range - known_phases
@@ -522,7 +631,6 @@ def _get_interface_map(self, upper_tri_only=False, quiet=False):
             ints_by_phase_type_pair[int_def.phase_types].append(int_def)
 
         for pt_pair, int_defs in ints_by_phase_type_pair.items():
-
             names = [i.name for i in int_defs]
             if len(set(names)) < len(names):
                 raise ValueError(
@@ -660,7 +768,7 @@ def _validate_interface_map(self):
                 f"definition: {phase_idx_int_is_nan}."
             )
 
-    def get_misorientation_matrix(self, degrees=True, overwrite=False):
+    def get_misorientation_matrix(self, degrees=True, overwrite=False, method="defdap"):
         """Given phase type definitions that include orientation lists, get the
         misorientation matrix between all pairs."""
 
@@ -670,7 +778,6 @@ def get_misorientation_matrix(self, degrees=True, overwrite=False):
             )
             return
 
-        misori_matrix = np.zeros((self.num_phases, self.num_phases), dtype=float)
         all_oris = np.ones((self.num_phases, 4)) * np.nan
         for i in self.phase_types:
             all_oris[i.phases] = i.orientations
@@ -680,23 +787,10 @@ def get_misorientation_matrix(self, degrees=True, overwrite=False):
                 "Not all orientations are accounted for in the phase type definitions."
             )
 
-        all_oris = Orientation(all_oris, family="cubic")  # TODO: generalise symmetry
-
-        misori_matrix = np.zeros((self.num_phases, self.num_phases), dtype=float)
-        for idx in range(self.num_phases):
-            print(
-                f"Finding misorientation for orientation {idx + 1}/{len(all_oris)}",
-                flush=True,
-            )
-            ori_i = all_oris[idx : idx + 1]
-            other_oris = all_oris[idx + 1 :]
-            if other_oris.size:
-                disori_i = ori_i.disorientation(other_oris).as_axis_angle()[..., -1]
-                misori_matrix[idx, idx + 1 :] = disori_i
-                misori_matrix[idx + 1 :, idx] = disori_i
-
-        if degrees:
-            misori_matrix = np.rad2deg(misori_matrix)
+        if method == "defdap":
+            misori_matrix = compute_misorientation_matrix(all_oris, degrees)
+        elif method == "damask":
+            misori_matrix = compute_misorientation_matrix_damask(all_oris, degrees)
 
         self._misorientation_matrix = misori_matrix
         self._misorientation_matrix_is_degrees = degrees
@@ -706,7 +800,7 @@ def get_misorientation_matrix(self, degrees=True, overwrite=False):
     def get_pyvista_grid(self):
         """Experimental!"""
 
-        grid = pv.UniformGrid()
+        grid = pv.ImageData()
 
         grid.dimensions = self.grid_size_3D + 1  # +1 to inject values on cell data
         grid.spacing = self.size_3D / self.grid_size_3D
@@ -728,7 +822,6 @@ def assign_phase_material_randomly(
         volume_fractions,
         random_seed=None,
     ):
-
         print(
             "Randomly assigning phases to materials according to volume_fractions...",
             end="",
@@ -753,8 +846,8 @@ def from_voronoi(
         num_phases=None,
         random_seed=None,
         is_periodic=False,
+        combine_phases=None,
     ):
-
         if sum(i is not None for i in (seeds, num_phases)) != 1:
             raise ValueError(f"Specify exactly one of `seeds` and `num_phases`")
 
@@ -783,6 +876,7 @@ def from_voronoi(
             size=size,
             seeds=seeds,
             random_seed=random_seed,
+            combine_phases=combine_phases,
         )
 
     @classmethod
@@ -880,7 +974,6 @@ def get_slice(
         include=None,
         misorientation_matrix=None,
     ):
-
         allowed_data = [
             "phase",
             "material",
@@ -939,7 +1032,6 @@ def show_slice(
         layout_args=None,
         **kwargs,
     ):
-
         if "misorientation_matrix" in kwargs:
             slice_dat = self.get_slice(
                 slice_index,
@@ -996,7 +1088,6 @@ def show(self):
         pl.show()
 
     def write_VTK(self, path):
-
         grid = self.get_pyvista_grid()
 
         grid.cell_data["interface_idx"] = self.voxel_interface_idx_3D.flatten(order="F")
diff --git a/cipher_parse/quats.py b/cipher_parse/quats.py
index 946c627..4a4bce2 100644
--- a/cipher_parse/quats.py
+++ b/cipher_parse/quats.py
@@ -1,5 +1,8 @@
 import numpy as np
 
+from defdap.quat import Quat
+from damask import Orientation
+
 
 def quat_conjugate(quats_arr):
     quats_copy = np.copy(quats_arr)
@@ -264,3 +267,73 @@ def quat_sample_random(number):
     ).T
 
     return quats
+
+
+def compute_misorientation_matrix(quat_comps, degrees=False, quiet=False):
+    """Use DefDAP to calculate an N-by-N symmetric matrix of disorientation angles between
+    an array of N quaternions.
+
+    Parameter
+    ---------
+    degrees
+        If True, return the misorientation array in degrees rather than radians.
+
+    """
+
+    # DefDAP uses P=+1, but we assume P=-1 for now (same as DAMASK):
+    quat_comps[:, 1:] *= -1
+    num_quats = len(quat_comps)
+    quat_objs = np.empty(num_quats, dtype=Quat)
+
+    for i in range(len(quat_comps)):
+        quat_objs[i] = Quat(quat_comps[i])
+
+    quat_comps_sym = Quat.calcSymEqvs(quat_objs, "cubic")
+
+    misori_matrix = np.zeros((num_quats, num_quats))
+    for idx, ref_ori in enumerate(quat_objs):
+        if not quiet and idx % 100 == 0:
+            print(f"Finding misorientations {idx}/{num_quats}", flush=True)
+        misori, _ = Quat.calcMisOri(quat_comps_sym, ref_ori)
+        misori_matrix[:, idx] = 2 * np.arccos(misori)
+
+    # make precisely symmetric
+    misori_matrix = np.triu(misori_matrix)
+    misori_matrix = misori_matrix + misori_matrix.T - np.diag(np.diag(misori_matrix))
+
+    if degrees:
+        misori_matrix = np.rad2deg(misori_matrix)
+
+    return misori_matrix
+
+
+def compute_misorientation_matrix_damask(quat_comps, degrees=False, quiet=False):
+    """Use DefDAP to calculate an N-by-N symmetric matrix of disorientation angles between
+    an array of N quaternions.
+
+    Parameter
+    ---------
+    degrees
+        If True, return the misorientation array in degrees rather than radians.
+
+    """
+    num_quats = len(quat_comps)
+    all_oris = Orientation(quat_comps, family="cubic")
+
+    misori_matrix = np.zeros((num_quats, num_quats), dtype=float)
+    for idx in range(num_quats):
+        print(
+            f"Finding misorientation for orientation {idx + 1}/{len(all_oris)}",
+            flush=True,
+        )
+        ori_i = all_oris[idx : idx + 1]
+        other_oris = all_oris[idx + 1 :]
+        if other_oris.size:
+            disori_i = ori_i.disorientation(other_oris).as_axis_angle()[..., -1]
+            misori_matrix[idx, idx + 1 :] = disori_i
+            misori_matrix[idx + 1 :, idx] = disori_i
+
+    if degrees:
+        misori_matrix = np.rad2deg(misori_matrix)
+
+    return misori_matrix
diff --git a/cipher_parse/utilities.py b/cipher_parse/utilities.py
index 031e55a..6340ae2 100644
--- a/cipher_parse/utilities.py
+++ b/cipher_parse/utilities.py
@@ -538,7 +538,7 @@ def get_time_linear_subset_indices(time_interval, max_time, times):
         num=int(((max_time + time_interval) / time_interval)),
         endpoint=True,
     )
-    return list(set(np.argmin(np.abs(times - intervals[:, None]), axis=1)))
+    return list(set(np.argmin(np.abs(times - intervals[:, None]), axis=1).tolist()))
 
 
 def sample_from_orientations_gradient(phase_centroids, max_misorientation_deg):
diff --git a/cipher_parse/voxel_map.py b/cipher_parse/voxel_map.py
index dcdd61a..b16518c 100644
--- a/cipher_parse/voxel_map.py
+++ b/cipher_parse/voxel_map.py
@@ -353,7 +353,7 @@ def size_3D(self):
     def get_pyvista_grid(self, include_region_ID=False):
         """Experimental!"""
 
-        grid = pv.UniformGrid()
+        grid = pv.ImageData()
 
         grid.dimensions = self.grid_size_3D + 1  # +1 to inject values on cell data
         grid.spacing = self.spacing_3D
diff --git a/notebooks/demo_cipher_inputs.ipynb b/notebooks/demo_cipher_inputs.ipynb
index 978c7f2..8e9e4ae 100644
--- a/notebooks/demo_cipher_inputs.ipynb
+++ b/notebooks/demo_cipher_inputs.ipynb
@@ -51,10 +51,12 @@
                 "}\n",
                 "\n",
                 "int_props_1 = {\n",
+                "    'width': 4,\n",
                 "    'energy': {'e0': 5e+8},\n",
                 "    'mobility': {'m0': 1e-11},\n",
                 "}\n",
                 "int_props_2 = {\n",
+                "    'width': 4,\n",
                 "    'energy': {'e0': 5e+8},\n",
                 "    'mobility': {'m0': 1e-11},\n",
                 "}\n",
@@ -65,7 +67,6 @@
                 "  'initblocksize': [1, 1, 1],\n",
                 "  'initcoarsen': 6,\n",
                 "  'initrefine': 7,\n",
-                "  'interfacewidth': 4,\n",
                 "  'interpolation': 'cubic',\n",
                 "  'maxnrefine': 7,\n",
                 "  'minnrefine': 0,\n",
@@ -74,7 +75,7 @@
                 "  'petscoptions': '-ts_adapt_monitor -ts_rk_type 2a',\n",
                 "  'random_seed': 1579993586,\n",
                 "  'reltol': 0.0001,\n",
-                "  'time': 100000000,\n",
+                "  'time': 4000,\n",
                 "}\n",
                 "\n",
                 "solution_params_2 = {**solution_params_1}\n",
diff --git a/poetry.lock b/poetry.lock
index 47ace93..95df795 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4841 +1,8451 @@
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-
-[[package]]
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+]
+
+[package.dependencies]
+cffi = {version = ">=1.11", markers = "platform_python_implementation == \"PyPy\""}
+
+[package.extras]
+cffi = ["cffi (>=1.11)"]
+
+[extras]
+hickle = []
+matflow = []
+notebook = ["notebook"]
+
+[metadata]
+lock-version = "2.1"
+python-versions = ">=3.8,<3.11"
+content-hash = "8a7fbbae86d1331103591049cf21db70be87540acb703b3292272e0f723521bc"
diff --git a/pyproject.toml b/pyproject.toml
index e1267dd..48385b3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cipher-parse"
-version = "0.5.0"
+version = "0.6.0a1"
 description = "Pre- and post-processing for the phase-field code CIPHER."
 authors = ["aplowman <adam.plowman@manchester.ac.uk>"]
 license = "MIT"
@@ -12,25 +12,23 @@ include = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.11"
-numpy = "1.21"
-h5py = "2.10.0"
+numpy = "<2"
 "ruamel.yaml" = "^0.17.21"
-damask = "^3.0.0-alpha.6"
+damask = "3.0.0-alpha.7post0"
 plotly = "^5.9.0"
 vecmaths = "^0.1.6"
 nbformat = "^5.4.0"
 itkwidgets = ">=0.25.2"
-hickle = {version = "4.0.4", optional = true}
-matflow = {version = "^0.2.26", optional = true}
 notebook = {version = "^6.5.1", optional = true}
 pandas = "^1.5.1"
 parse = "^1.19.0"
 ipywidgets = "<8.0.0"
-sqlalchemy = {version = "<2.0.0", optional = true}
-pyvista = "^0.39.0"
 trame = "^2.4.2"
+defdap = "^0.93.5"
+zarr = "^2.16.0"
+pyvista = {extras = ["all", "trame"], version = "^0.43.4"}
 
-[tool.poetry.dev-dependencies]
+[tool.poetry.group.dev.dependencies]
 pylint = "^2.12.2"
 ipykernel = "^6.6.1"
 pytest = "^6.2.5"
@@ -49,7 +47,7 @@ notebook = ["notebook"]
 
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "0.5.0"
+version = "0.6.0a1"
 tag_format = "v$version"
 version_files = [ 
     "pyproject.toml:version",