From 2cd2d6f5065ade2eacab31a1bee880afb14cbed9 Mon Sep 17 00:00:00 2001
From: Martin Diehl <mail@martin-diehl.net>
Date: Sat, 21 Dec 2019 18:07:04 +0100
Subject: [PATCH] cell_2_node/node_2_cell work only for periodic data

hence, coordinates and displacements cannot be converted easily
---
 python/damask/grid_filters.py     | 67 ++++++++++++++++++++++++++++++-
 python/tests/test_grid_filters.py |  7 ++++
 2 files changed, 72 insertions(+), 2 deletions(-)

diff --git a/python/damask/grid_filters.py b/python/damask/grid_filters.py
index 664198630..69e7dd6b1 100644
--- a/python/damask/grid_filters.py
+++ b/python/damask/grid_filters.py
@@ -97,6 +97,8 @@ def cell_coord0(grid,size,origin=np.zeros(3)):
         number of grid points.
     size : numpy.ndarray
         physical size of the periodic field. 
+    origin : numpy.ndarray, optional
+        physical origin of the periodic field. Default is [0.0,0.0,0.0].
 
     """
     start = origin + size/grid*.5
@@ -149,6 +151,36 @@ def cell_displacement_avg(size,F):
     F_avg = np.average(F,axis=(0,1,2))
     return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
 
+def cell_displacement(size,F):
+    """
+    Cell center displacement field from deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
+
+def cell_coord(size,F,origin=np.zeros(3)):
+    """
+    Cell center positions.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+    origin : numpy.ndarray, optional
+        physical origin of the periodic field. Default is [0.0,0.0,0.0].
+
+    """
+    return cell_coord0(F.shape[:3][::-1],size,origin) + cell_displacement(size,F)
+
 def cell_coord0_2_DNA(coord0,ordered=True):
     """
     Return grid 'DNA', i.e. grid, size, and origin from array of cell positions.
@@ -196,6 +228,8 @@ def node_coord0(grid,size,origin=np.zeros(3)):
         number of grid points.
     size : numpy.ndarray
         physical size of the periodic field. 
+    origin : numpy.ndarray, optional
+        physical origin of the periodic field. Default is [0.0,0.0,0.0].
 
     """
     x, y, z = np.meshgrid(np.linspace(origin[2],size[2]+origin[2],1+grid[2]),
@@ -234,9 +268,38 @@ def node_displacement_avg(size,F):
     F_avg = np.average(F,axis=(0,1,2))
     return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
 
+def node_displacement(size,F):
+    """
+    Nodal displacement field from deformation gradient field.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+
+    """
+    return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
+
+def node_coord(size,F,origin=np.zeros(3)):
+    """
+    Nodal positions.
+
+    Parameters
+    ----------
+    size : numpy.ndarray
+        physical size of the periodic field. 
+    F : numpy.ndarray
+        deformation gradient field.
+    origin : numpy.ndarray, optional
+        physical origin of the periodic field. Default is [0.0,0.0,0.0].
+
+    """
+    return node_coord0(F.shape[:3][::-1],size,origin) + node_displacement(size,F)
 
 def cell_2_node(cell_data):
-    """Interpolate cell data to nodal data."""
+    """Interpolate periodic cell data to nodal data."""
     n = (  cell_data + np.roll(cell_data,1,(0,1,2))
          + np.roll(cell_data,1,(0,))  + np.roll(cell_data,1,(1,))  + np.roll(cell_data,1,(2,))
          + np.roll(cell_data,1,(0,1)) + np.roll(cell_data,1,(1,2)) + np.roll(cell_data,1,(2,0)))*0.125
@@ -244,7 +307,7 @@ def cell_2_node(cell_data):
     return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
 
 def node_2_cell(node_data):
-    """Interpolate nodal data to cell data."""
+    """Interpolate periodic nodal data to cell data."""
     c = (  node_data + np.roll(node_data,1,(0,1,2))
          + np.roll(node_data,1,(0,))  + np.roll(node_data,1,(1,))  + np.roll(node_data,1,(2,))
          + np.roll(node_data,1,(0,1)) + np.roll(node_data,1,(1,2)) + np.roll(node_data,1,(2,0)))*0.125
diff --git a/python/tests/test_grid_filters.py b/python/tests/test_grid_filters.py
index b23fad549..c8442eee4 100644
--- a/python/tests/test_grid_filters.py
+++ b/python/tests/test_grid_filters.py
@@ -35,6 +35,13 @@ class TestGridFilters:
          _grid,_size,_origin = eval('grid_filters.{}_coord0_2_DNA(coord0.reshape((-1,3)))'.format(mode))
          assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
 
+    def test_displacement_fluct_equivalence(self):
+         size = np.random.random(3)
+         grid = np.random.randint(8,32,(3))
+         F    = np.random.random(tuple(grid)+(3,3))
+         assert np.allclose(grid_filters.node_displacement_fluct(size,F),
+                            grid_filters.cell_2_node(grid_filters.cell_displacement_fluct(size,F)))
+
 
     @pytest.mark.parametrize('mode',[('cell'),('node')])
     def test_displacement_avg_vanishes(self,mode):