Modifiers for structure analysis.

autogabi/analysis.py

@@ -166,6 +166,87 @@ def perform_voroni_analysis(self):
         # https://tess.readthedocs.io/en/stable/
         # https://github.com/materialsproject/pymatgen/blob/v2022.0.14/pymatgen/analysis/structure_analyzer.py#L61-L174
 
+    def perform_ptm(self, enabled: list = ['fcc', 'hpc', 'bcc'], compute: bool=True, *args, **kwargs):
+        """
+
+        Args:
+            enabled (list): List of strings for enabled structure types. Possible values:
+                fcc-hcp-bcc-ico-sc-dcub-dhex-graphene
+
+                output_deformation_gradient = False
+                output_interatomic_distance = False
+                output_ordering = False
+                output_orientation = False
+                output_rmsd = False
+                rmsd_cutoff = 0.1
+
+        Returns:
+
+        """
+
+        if self.backend == 'ovito':
+
+            from ovito.plugins.ParticlesPython import PolyhedralTemplateMatchingModifier
+            ptm = PolyhedralTemplateMatchingModifier(*args, **kwargs)
+
+            # Enabled by default: FCC, HCP, BCC
+            if 'fcc' not in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.FCC].enabled = False
+            if 'hcp' not in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.HCP].enabled = False
+            if 'bcc' not in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.BCC].enabled = False
+            if 'ico' in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.ICO].enabled = True
+            if 'sc' in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.SC].enabled = True
+            if 'dcub' in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.CUBIC_DIAMOND].enabled = True
+            if 'dhex' in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.HEX_DIAMOND].enabled = True
+            if 'graphene' in enabled:
+                ptm.structures[PolyhedralTemplateMatchingModifier.Type.GRAPHENE].enabled = True
+
+            self.pipeline.modifiers.append(ptm)
+
+            if compute:
+                self.data = self.pipeline.compute()
+
+        elif self.backend == 'lammps':
+            # https://docs.lammps.org/compute_ptm_atom.html
+            pass
+        else:
+            # print error
+            pass
+
+    def perform_ajm(self):
+        # AcklandJonesModifier
+        pass
+
+    def get_distinct_grains(self, *args, **kwargs):
+        """
+        Get distinct grains from the structure.
+        Args:
+            ovito:
+                    algorithm = GrainSegmentationModifier.Algorithm.GraphClusteringAuto
+                    color_particles = True
+                    handle_stacking_faults = True
+                    merging_threshold = 0.0
+                    min_grain_size = 100
+                    orphan_adoption = True
+
+        Returns:
+
+        """
+
+        if self.backend == 'ovito':
+            from ovito.plugins.CrystalAnalysisPython import GrainSegmentationModifier
+            gsm = GrainSegmentationModifier(*args, **kwargs)
+            self.pipeline.modifiers.append(gsm)
+            self.data = self.pipeline.compute()
+
+
+
     def set_analysis(self):
 
         if self.backend == 'ovito':

autogabi/minimiser.py

@@ -1 +1 @@
-# Minimiser for lammps, vasp, gulp
+# Minimiser for lammps, vasp, gulp

autogabi/orientation.py

@@ -1,18 +1,19 @@
-# Get grain orientation
-
-# https://github.com/paulhof/GraDe-A
-# Centrosymetric parameter
-
-
-# Polyhedral template matching is implemented in ovito, ASAP, and LAMMPS
-# P. M. Larsen, S. Schmidt, J. Schiøtz, Modelling Simul. Mater. Sci. Eng. 2016, 24, 055007.
-# https://docs.lammps.org/compute_ptm_atom.html
-
-def get_grain_orientation(backend):
-    if backend == 'ovito':
-        # First, perform PTM
-        # Iterate over all ions to get grains
-        #   Pick one fcc ion, if > 2 ffc neighbors, count to grain, otherwise disregard
-        # Get average
-
-        return None
+# Get grain orientation
+
+# https://github.com/paulhof/GraDe-A
+# Centrosymetric parameter
+
+
+# Polyhedral template matching is implemented in ovito, ASAP, and LAMMPS
+# P. M. Larsen, S. Schmidt, J. Schiøtz, Modelling Simul. Mater. Sci. Eng. 2016, 24, 055007.
+# https://docs.lammps.org/compute_ptm_atom.html
+
+def get_grain_orientation(backend):
+    if backend == 'ovito':
+
+        # First, perform PTM
+        # Iterate over all ions to get grains
+        #   Pick one fcc ion, if > 2 ffc neighbors, count to grain, otherwise disregard
+        # Get average
+
+        return None

examples/grain_analysis.ipynb

@@ -0,0 +1,93 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": true,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "This notebook demonstrates how Auto-GABI can be used to get distinct grains and their properties"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "outputs": [],
+   "source": [
+    "from analysis import GBStructure\n",
+    "import numpy as np"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "outputs": [],
+   "source": [
+    "gb = GBStructure('ovito', 'LSF_supercell_md3.lmp')\n",
+    "gb.delete_particles('O')\n",
+    "gb.perform_ptm(\n",
+    "    enabled = ['bcc'],\n",
+    "    output_orientation=True,\n",
+    "    rmsd_cutoff = 0.15)\n",
+    "gb.set_analysis()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "outputs": [],
+   "source": [
+    "gb.get_distinct_grains(min_grain_size=10)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   }
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "name": "pycharm-1f46a509",
+   "language": "python",
+   "display_name": "PyCharm (03_postprocessing)"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}