Added documentation, added an example, avoided position round off, added in...

.. 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

# LAMMPS FIX NUMDIFF EXAMPLE

## Numerical Difference Fix

This directory contains the ingredients to run an NVE simulation using the numerical difference fix and calculate error in forces.

Example:

```

NP=4 #number of processors

mpirun -np $NP lmp_mpi -in.numdiff

```

## Required LAMMPS packages: MOLECULE package

#############################

#Atoms types - mass - charge#

#############################

#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#

variable Ar equal 1

#############

#Atom Masses#

#############

mass ${Ar}      39.903

###########################

#Pair Potentials - Tersoff#

###########################

pair_style      lj/cubic

pair_coeff      * * 0.0102701 3.42

# Numerical difference calculation of error in forces

units   	metal

atom_style      full

boundary 	p p p

read_data argon.lmp

include ff-argon.lmp

velocity all create 10 2357 mom yes dist gaussian

neighbor 1 bin

timestep 0.001

fix numdiff all numdiff 200 0.0001

fix nve all nve

variable errx atom fx-f_numdiff[1]

variable erry atom fy-f_numdiff[2]

variable errz atom fz-f_numdiff[3]

dump forces all custom 200 force_error.dump v_errx v_erry v_errz

thermo 200

run 2000