• OOF Home
  • Mailing List
  • Newsletters
  • Presentations
  • Credits and Disclaimer
• OOF1
• OOF2
  • Download
  • OOF2 Manual
  • OOF2 Reference Manual
  • Bugs
  • Run OOF2 online
• OOF3D
• oofcanvas
• gtklogger
• VSB
• OOF Working Group
  • Steve Langer
  • Andrew Reid
  • Günay Doğan
• NIST Links
  • Applied and Computational Mathematics Division
  • Information Technology Laboratory
  • Center for Theoretical and Computational Materials Science
  • Material Measurement Laboratory
  • Privacy / Security / Accessibility

OOF: Finite Element Analysis of Microstructures

Binary Format

The beginning and end of the binary .goof files are actually ASCII. The data in the middle, however, is all binary. This means that it consists of nothing but numbers written by the C fwrite() function. The exact order in which the numbers are written is crucial. The number of bytes used for each number in principle depends on the type of computer that's reading and writing the file, so this manual will only specify the C data type. The types and their usual sizes are

C	Fortran	size (bytes)
double	double precision	8
float	real	4
int	integer	4
char	character	1

Header

The header is all ASCII.

The file must begin with the line

version number = 5

The version number may change in future releases. This manual describes only version 5.

The next two lines specify the number of elements and nodes in the grid.

Nelements = <n>
Nnodes = <n>

If these lines are omitted, or if the numbers are wrong, the program will still work, but memory will not be used efficiently.

The next line tells OOF that this is a binary file. This line is required.

type = b

The bulk of the header consists of lists of names of element types, node types, and node and element groups. The purpose of the lists is to establish an order for the names, so that in the binary section of the file they can be referred to by number. The first item in each list is number 0, the second is number 1, etc. Each item in the lists must appear on its own line, and each list must end with a line containing only -1. The four lists can appear in any order, and only the first two are required.

Element Types

Begin this list with the line

elements

Each element type that appears in the grid must be listed, but types that don't appear don't have to be listed. The name of the type is the name that appears in the menus (Section 4.5). For example, the list

empty
isotropic
-1

indicates that empty elements are type 0, isotropic elements are type 1, and no other element types are present.

Node Types

Begin this list with the line

nodes

followed by a list of the node types used in the file. The types are xy and linear.

Node Groups

Begin this list with the line

nodegroups

Element Groups

Begin this list with the line

elementgroups

End the header with another -1, indicating that there are no more lists to follow.

For example, here is the header from the file example2.goof used in Section 2.2:

version number = 5
type = b
elements
isotropic
empty
cubic
damisotropic
hexagonal
orthorhombic
eds_el
damage
-1
nodes
xy
linear
-1
nodegroups
right
left
top
bottom
upperleft
lowerleft
upperright
lowerright
-1
elementgroups
stones
u2
rem
doors
zepplin
negativland
nirvana
stage
-1
-1

Binary Data

From here on, until instructed otherwise, everything in the file is binary. The data must appear in the file in the order in which they appear in the tables below. Names are provided just for reference, they aren't actually used. The sizes, order, and meaning are what matters.

Nodes

The two different node types have different representations. Both begin with an int type, which is the position of that type of node in the name list in the header. Because the amount of data needed for each node type is known, no special termination is needed between nodes.

XY Nodes
type	int	The position of xy in the node name list.
flag	char	0 or 1. See below.
index	int	The node index. Must be unique, and all integers from 0 up to the number of nodes must be accounted for.
x	float	The node's undistorted $x$ position.
y	float	The node's undistorted $y$ position.

If flag is 1, then the node displacement is also specified:

dx	float	The node's $x$ displacement.
dy	float	The node's $y$ displacement.

Linear Nodes
type	int	The position of linear in the node name list.
flag	char	See below.
index	int	The node index. Must be unique, and all integers from 0 up to the number of nodes must be accounted for.
x	float	The node's undistorted $x$ position.
y	float	The node's undistorted $y$ position.

If the low bit of flag is 1, then the node displacement is also specified:

dx	float	The node's $x$ displacement.
dy	float	The node's $y$ displacement.

If the second bit of flag is 1 (i.e, flag=2 or flag=3, then the transformation matrix $T$ is also specified. $T$ is the matrix that transforms a 2-vector in the node's coordinate system into the OOF coordinate system.

t00	float	The $xx$ component of $T$.
t01	float	The $xy$ component of $T$.
t10	float	The $yx$ component of $T$.
t11	float	The $yy$ component of $T$.

The list of nodes must end with a binary integer $-1$:

End List
EOL	int	$-1$

Elements

Each element type has a different binary representation. This section of the file lists the data for each element. Because the amount of data for each type of element is known, no special termination is needed between elements.

Element Index

Unlike the ASCII data file, the binary data file does not contain an explicit index labeling each element. Instead, the index is inferred from the order in which the elements appear in the file. The first element is number 0, the second is 1, and so on. This index is used to specify clones and element groups.

Element Type

The element type is stored as an integer, indicating the position of this type in the list of element types in the header. The first element type in the list is 0, the second is 1, and so on.

Flag

All elements other than the empty element have an integer flag parameter. The low bit (0x1) of flag is 1 if the element is in plane strain, 0 if it's in plane stress. The second bit (0x2) is 1 if the local stiffness matrix and thermal forces are stored. The third bit (0x4) is 1 if this element is a clone (see below), and the fourth bit (0x8) is 1 if the element has been mutated.

Clones

The third bit (0x4) of flag is 1 if this element is a clone. To save space and time, elements can be flagged as being clones of other elements that have already been read. Clones must have identical geometries, orientations, and thermoelastic parameters. They can differ only in their node indices and gray value.^6.3 The big advantage of clones is that their local stiffness matrices do not have to be stored or computed; they can simply be copied from another element. The clone index appearing in the tables below is the element index of the element whose stiffness matrix is to be copied.

In no case can both the clone index and the stiffness matrix $K$ be specified at the same time. The notation ``(conditional)'' in the tables means that the datum in question is present only if flag is set appropriately.

Mutated Elements

The fourth bit (0x8) of flag is 1 if the element has been mutated. The notation ``(mutated)'' in the tables indicates that the datum in question is present only if the element has been mutated.

Additional Data Types

If stiffness matrices or thermal forces are provided in the data file, then the data type in the file below is listed as stiffness or force. The exact form of these is listed at the end of this section.

Termination

The list of elements must end with a binary integer $-1$.

Data Details for Elements

The data for each element type is as follows:

Isotropic Element (Section 4.5.1)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
poisson	float	Poisson's ratio.
young	float	Young's modulus.
alpha	float	Thermal expansion coefficient.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).

empty Element (Section 4.5.2)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.

cubic Element (Section 4.5.3)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
poisson	float	Poisson's ratio.
young	float	Young's modulus.
alpha	float	Thermal expansion coefficient.
A	float	Anisotropy.

hexagonal Element (Section 4.5.4)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
c11	float	Elastic coefficient.
c12	float	Elastic coefficient.
c13	float	Elastic coefficient.
c33	float	Elastic coefficient.
c44	float	Elastic coefficient.
alpha11	float	Thermal expansion coefficient.
alpha33	float	Thermal expansion coefficient.

orthorhombic Element (Section 4.5.5)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
c11	float	Elastic coefficient.
c12	float	Elastic coefficient.
c13	float	Elastic coefficient.
c22	float	Elastic coefficient.
c23	float	Elastic coefficient.
c33	float	Elastic coefficient.
c55	float	Elastic coefficient.
c66	float	Elastic coefficient.
alpha11	float	Thermal expansion coefficient.
alpha22	float	Thermal expansion coefficient.
alpha33	float	Thermal expansion coefficient.

trigonalA Element (Section 4.5.7)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
c11	float	Elastic coefficient.
c12	float	Elastic coefficient.
c13	float	Elastic coefficient.
c14	float	Elastic coefficient.
c15	float	Elastic coefficient.
c33	float	Elastic coefficient.
c44	float	Elastic coefficient.
alpha11	float	Thermal expansion coefficient.
alpha33	float	Thermal expansion coefficient.

trigonalB Element (Section 4.5.8)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
c11	float	Elastic coefficient.
c12	float	Elastic coefficient.
c13	float	Elastic coefficient.
c14	float	Elastic coefficient.
c33	float	Elastic coefficient.
c44	float	Elastic coefficient.
alpha11	float	Thermal expansion coefficient.
alpha33	float	Thermal expansion coefficient.

eds_el Element (Section 4.5.6)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
poisson	float	Poisson's ratio.
young	float	Young's modulus.
a1	float	Thermal expansion coefficient.
a2	float	Thermal expansion coefficient.
a3	float	Thermal expansion coefficient.

damisotropic Element (Section 4.5.9)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
poisson	float	Poisson's ratio.
young	float	Young's modulus.
alpha	float	Thermal expansion coefficient.
max_s	float	Maximum stress.
min_s	float	Minimum stress.
max_kd	float	Maximum knockdown factor.
min_kd	float	Minimum knockdown factor.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
total_kd	float	Product of all applied knockdowns (mutated.)
oldgray	float	Gray value before mutation (mutated).

damage Element (Section 4.5.10)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
poisson	float	Poisson's ratio.
young	float	Young's modulus.
alpha	float	Thermal expansion coefficient.
max_s	float	Maximum stress.
kd_1	float	First knockdown factor.
kd_2	float	Second knockdown factor.
only_once	int	Mutate only once?
oldgray	float	Gray value before mutation (mutated).
C_ijkl	stiffness	Mutated 3-D stiffness matrix (mutated).

griffith and griffith2 Elements (Section 4.5.11)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
poisson	float	Poisson's ratio of unmutated element.
young	float	Young's modulus of unmutated element.
alpha	float	Thermal expansion coefficient.
gamma	float	Surface energy density.
kd_1	float	First knockdown factor.
kd_2	float	Second knockdown factor.
only_once	int	Mutate only once?
oldgray	float	Gray value before mutation (mutated).
C_ijkl	stiffness	Mutated 3-D stiffness matrix (mutated).

zimmer and zimmer2 Elements (Section 4.5.13)
type	int	Element type.
gray	float	Gray value used to display the element.
node1	int	Index of first node, going counterclockwise around the element.
node2	int	Index of second node.
node3	int	Index of third node.
L	float	Latitude (See Section 4.3).
R	float	Rotation.
S	float	Spin.
flag	int	See above.
K	stiffness	Stiffness matrix (conditional).
F	force	Thermal forces (conditional).
clone	int	Clone index (conditional).
c11	float	Elastic coefficient.
c12	float	Elastic coefficient.
c13	float	Elastic coefficient.
c33	float	Elastic coefficient.
c44	float	Elastic coefficient.
alpha11	float	Thermal expansion coefficient.
alpha33	float	Thermal expansion coefficient.
gamma	float	Surface energy density.
kd_1	float	First knockdown factor.
kd_2	float	Second knockdown factor.
only_once	int	Mutate only once?
oldgray	float	Gray value before mutation (mutated).
C_ijkl	stiffness	Mutated 3-D stiffness matrix (mutated).

The local stiffness matrix is a $6\times6$ symmetric matrix $K$, giving the element's contribution to the global stiffness $K_{\rm global}$. It's easiest by far to leave it out of the file. If you are writing your own binary .goof file, and really really want to include the stiffness matrices, it's best to write the file without them, load it into OOF and use /output/grid/binary (Section 3.31.2) with ${\sf save\_stiffness}={\tt true}$ to write a new .goof file. For completeness, though, here is the binary format used to save the local stiffness matrix and thermal forces:

Stiffness Matrices
k00	double	$K_{00}$: only the lower triangular part of $K$ is stored.
k10	double	$K_{10}$
k11	double	$K_{11}$
k20	double	$K_{20}$
k21	double	$K_{21}$
k22	double	$K_{22}$
k30	double	$K_{30}$
k31	double	$K_{31}$
k32	double	$K_{32}$
k33	double	$K_{33}$
k40	double	$K_{40}$
k41	double	$K_{41}$
k42	double	$K_{42}$
k43	double	$K_{43}$
k44	double	$K_{44}$
k50	double	$K_{50}$
k51	double	$K_{51}$
k52	double	$K_{52}$
k53	double	$K_{53}$
k54	double	$K_{54}$
k55	double	$K_{55}$

Thermal Forces
F0x	double	$x$ component of thermal force on node 0.
F0y	double	$y$ component of thermal force on node 0.
F1x	double	$x$ component of thermal force on node 1.
F1y	double	$y$ component of thermal force on node 1.
F2x	double	$x$ component of thermal force on node 2.
F2y	double	$y$ component of thermal force on node 2.

Node Groups

Each of the node groups is listed after the elements, in the order in which they appear in the node group name list in the header. Each list is a sequence of integers, giving the indices of the nodes in the group. Each list must end with a binary integer $-1$.

Node Groups
n1	int	Index of first node in first node group.
...
nn	int	Index of last node in first node group.
EOL	int	$-1$
n1	int	Index of first node in second node group.
...		etc.

Element Groups

The element groups are written in an analogous way to the node groups. The groups must be listed in the order in which they appear in the element group name list in the header. Each list is a sequence of integers giving the element indices of the elements in the group. Each list must end with a binary integer $-1$.

Element Groups
e1	int	Index of first element in first element group.
...
en	int	Index of last element in first element group.
EOL	int	$-1$
e1	int	Index of first element in second element group.
...		etc.

Startup Commands

This final section of the binary data file is again in ASCII. It is identical to the Startup Commands section of the ASCII data file: a series of arbitrary OOF commands, each preceded by the word oof.

Send comments to the OOF team.

Last updated: Monday, 26 January 2009 14:42:21 EST