intro.xml

<Section><Heading>Abstract and Notation</Heading>

<Package>HAPcryst</Package> is an extension for "Homological Algebra
Programming" (<Package>HAP</Package>, <Cite Key="hap"></Cite>) by Graham
Ellis. It uses geometric methods to calculate resolutions for
crystallographic groups. 

In this manual, we will use the terms "space group" and
"crystallographic group" synonymous. As usual in &GAP;, group elements
are supposed to act from the right. To emphasize this fact, some
functions have names ending in "OnRight" (namely those, which rely on
the action from the right). This is also meant to make work with
<Package>HAPcryst</Package> and <Package>cryst</Package> <Cite Key="cryst"></Cite> easier.<P></P>

The functions called "somethingStandardSpaceGroup" are supposed to work for
standard crystallographic groups on left and right some time in the
future. Currently only the versions acting on right are implemented.

As in <Package>cryst</Package> <Cite Key="cryst"></Cite>, space groups
are represented as affine linear groups. For the computations in
<Package>HAPcryst</Package>, crystallographic  groups have to be in
"standard form". That is, the translation basis has to be the standard
basis of the space. This implies that the linear part of a group
element need not be orthogonal with respect to the usual scalar
product.


<Subsection><Heading>The natural action of crystallographic groups</Heading>
<Index>action of crystallographic groups</Index>

There is some confusion about the way crystallographic groups are
written. This concerns the question if we act on left or on right and if
vectors are of the form <C>[1,...]</C> or <C>[...,1]</C>. <P></P>

As mentioned, <Package>HAPcryst</Package> handles affine crystallographic
groups on right (and maybe later also on left) acting on vectors of the form
<M>[...,1]</M>.
<P></P>
<B>BUT:</B> The functions in <Package>HAPcryst</Package> do not take augmented
vectors as input (no leading or ending ones). The handling of vectors is done
internally. So in <Package>HAPcryst</Package>, a crystallographic group is a
group of <M>n\times n</M> matrices which acts on a vector space of dimension
<M>n-1</M> whose elements are vectors of length <M>n-1</M> (not <M>n</M>).
Example:

<Example>
gap> G:=SpaceGroup(3,4); #This group acts on 3-Space
SpaceGroupOnRightBBNWZ( 3, 2, 1, 1, 2 )
gap> Display(Representative(G));
[ [  1,  0,  0,  0 ],
  [  0,  1,  0,  0 ],
  [  0,  0,  1,  0 ],
  [  0,  0,  0,  1 ] ]
gap> OrbitStabilizerInUnitCubeOnRight(G,[1/2,0,0]);
rec( orbit := [ [ 1/2, 0, 0 ], [ 1/2, 1/2, 0 ] ],
  stabilizer := Group([ [ [ 1, 0, 0, 0 ], [ 0, 1, 0, 0 ], [ 0, 0, 1, 0 ],
          [ 0, 0, 0, 1 ] ] ]) )
</Example>

</Subsection>

</Section>


<Section><Heading>Requirements</Heading><Index>installation</Index>

The following &GAP; packages are required

<List>

<Item>
 <Package>polymaking</Package> which in turn depends on the computational
   geometry software polymake.
</Item>

<Item> <Package>HAP</Package> </Item>
<Item> <Package>Cryst</Package> </Item>

</List>

The following &GAP; packages are not required but highly recommended:

<List>
<Item><Package>carat</Package></Item>
<Item><Package>CrystCat</Package></Item>
<Item><Package>GAPDoc</Package> is needed to display the online manual</Item>
</List> 

<Subsection><Heading>Recommendation concerning polymake</Heading>
<Index>polymake</Index>

Calculating resolutions of Bieberbach groups involves convex hull
computations. polymake by default uses cdd to compute convex
hulls. Experiments suggest that lrs is the more suitable algorithm for
the computations done in HAPcryst than the default cdd. You can change the
behaviour of by editing the file "yourhomedirectory/.polymake/prefer.pl". It
should contain a section like this (just make sure lrs is before cdd,
the position of beneath_beyond does not matter):

<Listing>
#########################################
application polytope;

prefer "*.convex_hull  lrs, beneath_beyond, cdd";
</Listing>

</Subsection>

</Section>

<Section><Heading>Global Variables</Heading>

<!-- 
The following global variables are used to influence the behavior of
<Package>HAPcryst</Package>. They can be found in the files
<File>lib/environment.gd</File> and <File>lib/environment.gi</File> of
the package directory.

<ManSection>
    <Var Name="HAPCRYST_TMPDIR"/>
 <Description>
  For the interaction with <K>polymake</K>, files have to be
  written. This variable determines which directory will be used for
  this.<P></P>
  All data files for <K>polymake</K> are written to this directory. If
  it is not set (which is the default), a temporary directory is
  created using <Code>DirectoryTemporary()</Code> at the first time a
  method tries to write a file.
  <P></P>
  You can set the variable by either adding the line
<Code>HAPCRYST_TMPDIR:=Directory("nameofdir");</Code> to your <F>.gaprc</F>
file or by using <Ref Var="SetHAPcrystDataDirectory"/>.
 </Description>
</ManSection>

<ManSection>
   <Meth Name="SetHAPcrystDataDirectory" Arg="dir"/>
 <Description>
  Sets the value of the global variable <Ref Var="HAPCRYST_TMPDIR"/> to
  <A>dir</A>. Note that <A>dir</A> must be a directory you must be allowed to
  read from and write to (permissions are not checked).
 </Description>
</ManSection>
-->

<Package>HAPcryst</Package> itself does only have one global variable, namely
<Ref InfoClass="InfoHAPcryst"/>. 
The location of files generated for interaction with polymake are determined by
the value of <Ref Var="POLYMAKE_DATA_DIR" BookName="polymaking"/> which is a
global variable of <Package>polymaking</Package>.

<ManSection>
    <InfoClass Name="InfoHAPcryst"/>
  <Description>
   At a level of 1, only the most important messages are printed. At level 2,
   additional information is displayed, and level 3 is even more verbose. At
level 0, <Package>HAPcryst</Package> remains silent.
  </Description>
</ManSection>

</Section>