Merge pull request #749 from akohlmey/collected-bugfixes-and-updates

:pre

Note that 3 symbolic (soft) links, "includelink" and "liblink" and

"filelink", are created in lib/latte to point into the LATTE home dir.

"filelink.o", are created in lib/latte to point into the LATTE home dir.

When LAMMPS builds in src it will use these links.  You should 

also check that the Makefile.lammps file you create is appropriate

for the compiler you use on your system to build LATTE.

during the NEB relaxation, so these replicas simply relax toward their

respective local minima.  By using the key word {end}, additional

forces can be applied to the first and/or last replicas, to enable

them to relax toward a MEP while constraining their energy.

them to relax toward a MEP while constraining their energy E to the

target energy ETarget.

The interatomic force Fi for the specified replica becomes:

If ETarget>E, the interatomic force Fi for the specified replica becomes:

Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T',  {when} Grad(V) dot T' < 0

Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0

:pre

where E is the current energy of the replica and ETarget is the target

energy.  The "spring" constant on the difference in energies is the

specified {Kspring3} value.

The "spring" constant on the difference in energies is the specified

{Kspring3} value.

When {estyle} is specified as {first}, the force is applied to the

first replica.  When {estyle} is specified as {last}, the force is

have a larger energy than the first replica. If this is not the case,

the path is probably not a MEP.

Finally, note that if the last replica converges toward a local

minimum which has a larger energy than the energy of the first

replica, a NEB calculation using an {estyle} of {last/efirst} or

{last/efirst/middle} cannot reach final convergence.

Finally, note that the last replica may never reach the target energy

if it is stuck in a local minima which has a larger energy than the

target energy.

[Restart, fix_modify, output, run start/stop, minimize info:]

that can be invoked from within a "pair style"_pair_style.html or

"fix"_fix.html or "compute"_compute.html that you write.

NOTE: If this fix is defined [after] the simulation box is created,

a 'run 0' command should be issued to properly initialize the storage

created by this fix.

:line

This fix is one of a small number that can be defined in an input

fix prop all property/atom mol

variable cluster atom ((id-1)/10)+1

set id * mol v_cluster :pre

set atom * mol v_cluster :pre

The "atom-style variable"_variable.html will create values for atoms

with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9.  When the

  lmp = lammps(ptr=lmpptr)

  natoms = lmp.get_natoms()

  try:

    for i in range(N):

      cut = cut0 + i*0.1

      pe = lmp.extract_compute("thermo_pe",0,0)   # extract total PE from LAMMPS

      print("PE",pe/natoms,thresh)

      if pe/natoms < thresh: return

  except Exception as e:

    print("LOOP error:", e)

from __future__ import print_function

def simple():

  foo = 0

  print("Inside simple function")

  try:

    foo += 1