Added documentation, added an example, avoided position round off, added in compute_pe's compute_scalar, now fix produces per-atom array instead of global array

doc/src/fix_num_diff.rst

@@ -0,0 +1,78 @@
+.. index:: fix numdiff
+
+fix numdiff command
+====================
+
+Syntax
+""""""
+
+
+.. parsed-literal::
+
+   fix ID group-ID numdiff Nevery Delta
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* numdiff = style name of this fix command
+* Nevery = calculate force by finite difference every this many timesteps
+* Delta = finite difference displacement length (distance units)
+  
+
+Examples
+""""""""
+
+
+.. parsed-literal::
+
+   fix 1 all numdiff 1 0.0001
+   fix 1 all numdiff 10 1e-6
+   fix 1 all numdiff 100 0.01
+
+Description
+"""""""""""
+
+Calculate forces through finite difference of energy versus position.
+The resulting per-atom forces can be used by :doc:`dump custom <dump>`.
+
+The group specified with the command means only atoms within the group
+have their averages computed.  Results are set to 0.0 for atoms not in
+the group.
+
+
+----------
+
+
+The *Nevery*\ argument specifies on what timesteps the force will 
+be used calculated by finite difference.
+
+The *Delta*\ argument specifies the positional displacement each
+atom will undergo.
+
+
+----------
+
+
+**Restart, fix\_modify, output, run start/stop, minimize info:**
+
+No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+are relevant to this fix.  No global scalar or vector quantities are
+stored by this fix for access by various :doc:`output commands <Howto_output>`.
+
+This fix produces a per-atom array which can be accessed by
+various :doc:`output commands <Howto_output>`.  .  This fix produces
+a per-atom array of the forces calculated by finite difference. The
+per-atom values should only be accessed on timesteps that are multiples
+of *Nfreq* since that is when the finite difference forces are calculated.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+ none
+
+Related commands
+""""""""""""""""
+
+:doc:`dynamical_matrix <dynamical_matrix>`,
+
+**Default:** none