Merge branch 'develop' into region-lookup-refactor
This commit is contained in:
Axel Kohlmeyer
@ -33,6 +33,7 @@ KOKKOS, o = OPENMP, t = OPT.
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* :doc:`body/local <compute_body_local>`
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* :doc:`body/local <compute_body_local>`
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* :doc:`bond <compute_bond>`
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* :doc:`bond <compute_bond>`
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* :doc:`bond/local <compute_bond_local>`
|
* :doc:`bond/local <compute_bond_local>`
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|
* :doc:`born/matrix <compute_born_matrix>`
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* :doc:`centro/atom <compute_centro_atom>`
|
* :doc:`centro/atom <compute_centro_atom>`
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* :doc:`centroid/stress/atom <compute_stress_atom>`
|
* :doc:`centroid/stress/atom <compute_stress_atom>`
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* :doc:`chunk/atom <compute_chunk_atom>`
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* :doc:`chunk/atom <compute_chunk_atom>`
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@ -214,6 +214,9 @@ Convenience functions
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.. doxygenfunction:: errorurl
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.. doxygenfunction:: errorurl
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:project: progguide
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:project: progguide
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|
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.. doxygenfunction:: missing_cmd_args
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|
:project: progguide
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|
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.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
|
.. doxygenfunction:: flush_buffers(LAMMPS *lmp)
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:project: progguide
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:project: progguide
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|
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@ -18,23 +18,52 @@ At zero temperature, it is easy to estimate these derivatives by
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deforming the simulation box in one of the six directions using the
|
deforming the simulation box in one of the six directions using the
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:doc:`change_box <change_box>` command and measuring the change in the
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:doc:`change_box <change_box>` command and measuring the change in the
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stress tensor. A general-purpose script that does this is given in the
|
stress tensor. A general-purpose script that does this is given in the
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examples/elastic directory described on the :doc:`Examples <Examples>`
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examples/ELASTIC directory described on the :doc:`Examples <Examples>`
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doc page.
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doc page.
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Calculating elastic constants at finite temperature is more
|
Calculating elastic constants at finite temperature is more
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challenging, because it is necessary to run a simulation that performs
|
challenging, because it is necessary to run a simulation that performs
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time averages of differential properties. One way to do this is to
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time averages of differential properties. There are at least
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measure the change in average stress tensor in an NVT simulations when
|
3 ways to do this in LAMMPS. The most reliable way to do this is
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|
by exploiting the relationship between elastic constants, stress
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|
fluctuations, and the Born matrix, the second derivatives of energy
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|
w.r.t. strain :ref:`(Ray) <Ray>`.
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The Born matrix calculation has been enabled by
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|
the :doc:`compute born/matrix <compute_born_matrix>` command,
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which works for any bonded or non-bonded potential in LAMMPS.
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The most expensive part of the calculation is the sampling of
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|
the stress fluctuations. Several examples of this method are
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provided in the examples/ELASTIC_T/BORN_MATRIX directory
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|
described on the :doc:`Examples <Examples>` doc page.
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|
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|
A second way is to measure
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|
the change in average stress tensor in an NVT simulations when
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the cell volume undergoes a finite deformation. In order to balance
|
the cell volume undergoes a finite deformation. In order to balance
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the systematic and statistical errors in this method, the magnitude of
|
the systematic and statistical errors in this method, the magnitude of
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the deformation must be chosen judiciously, and care must be taken to
|
the deformation must be chosen judiciously, and care must be taken to
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fully equilibrate the deformed cell before sampling the stress
|
fully equilibrate the deformed cell before sampling the stress
|
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tensor. Another approach is to sample the triclinic cell fluctuations
|
tensor. An example of this method is provided in the
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|
examples/ELASTIC_T/DEFORMATION directory
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|
described on the :doc:`Examples <Examples>` doc page.
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|
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|
Another approach is to sample the triclinic cell fluctuations
|
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that occur in an NPT simulation. This method can also be slow to
|
that occur in an NPT simulation. This method can also be slow to
|
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converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`
|
converge and requires careful post-processing :ref:`(Shinoda) <Shinoda1>`.
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|
We do not provide an example of this method.
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|
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|
A nice review of the advantages and disadvantages of all of these methods
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|
is provided in the paper by Clavier et al. :ref:`(Clavier) <Clavier>`.
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|
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----------
|
----------
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|
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|
.. _Ray:
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|
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|
**(Ray)** J. R. Ray and A. Rahman, J Chem Phys, 80, 4423 (1984).
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|
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.. _Shinoda1:
|
.. _Shinoda1:
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|
|
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**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
**(Shinoda)** Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
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|
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|
.. _Clavier:
|
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|
|
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|
**(Clavier)** G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
|
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|
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@ -179,6 +179,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
|
* :doc:`body/local <compute_body_local>` - attributes of body sub-particles
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* :doc:`bond <compute_bond>` - energy of each bond sub-style
|
* :doc:`bond <compute_bond>` - energy of each bond sub-style
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* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
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* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
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* :doc:`born/matrix <compute_born_matrix>` - second derivative or potential with respect to strain
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* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
|
* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
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* :doc:`centroid/stress/atom <compute_stress_atom>` - centroid based stress tensor for each atom
|
* :doc:`centroid/stress/atom <compute_stress_atom>` - centroid based stress tensor for each atom
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* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
|
* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
|
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213
doc/src/compute_born_matrix.rst
Normal file
213
doc/src/compute_born_matrix.rst
Normal file
@ -0,0 +1,213 @@
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|
.. index:: compute born/matrix
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|
compute born/matrix command
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|
===========================
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|
Syntax
|
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|
""""""
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.. parsed-literal::
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compute ID group-ID born/matrix keyword value ...
|
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|
* ID, group-ID are documented in :doc:`compute <compute>` command
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|
* born/matrix = style name of this compute command
|
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|
* zero or more keyword/value pairs may be appended
|
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.. parsed-literal::
|
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|
|
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|
keyword = *numdiff*
|
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|
*numdiff* values = delta virial-ID
|
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|
delta = magnitude of strain (dimensionless)
|
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|
virial-ID = ID of pressure compute for virial (string)
|
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|
|
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|
Examples
|
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|
""""""""
|
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|
|
||||||
|
.. code-block:: LAMMPS
|
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|
|
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|
compute 1 all born/matrix
|
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|
compute 1 all born/matrix bond angle
|
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|
compute 1 all born/matrix numdiff 1.0e-4 myvirial
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|
|
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|
Description
|
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|
"""""""""""
|
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|
|
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|
Define a compute that calculates
|
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|
:math:`\frac{\partial{}^2U}{\partial\varepsilon_{i}\partial\varepsilon_{j}}` the
|
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|
second derivatives of the potential energy :math:`U` w.r.t. strain
|
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|
tensor :math:`\varepsilon` elements. These values are related to:
|
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|
|
||||||
|
.. math::
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|
|
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|
C^{B}_{i,j}=\frac{1}{V}\frac{\partial{}^2U}{\partial{}\varepsilon_{i}\partial\varepsilon_{j}}
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|
also called the Born term of elastic constants in the stress-stress fluctuation
|
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formalism. This quantity can be used to compute the elastic constant tensor.
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|
Using the symmetric Voigt notation, the elastic constant tensor can be written
|
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|
as a 6x6 symmetric matrix:
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|
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|
.. math::
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|
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C_{i,j} = \langle{}C^{B}_{i,j}\rangle
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|
+ \frac{V}{k_{B}T}\left(\langle\sigma_{i}\sigma_{j}\rangle\right.
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\left.- \langle\sigma_{i}\rangle\langle\sigma_{j}\rangle\right)
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|
+ \frac{Nk_{B}T}{V}
|
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|
\left(\delta_{i,j}+(\delta_{1,i}+\delta_{2,i}+\delta_{3,i})\right.
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\left.*(\delta_{1,j}+\delta_{2,j}+\delta_{3,j})\right)
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|
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|
In the above expression, :math:`\sigma` stands for the virial stress
|
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|
tensor, :math:`\delta` is the Kronecker delta and the usual notation apply for
|
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|
the number of particle, the temperature and volume respectively :math:`N`,
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|
:math:`T` and :math:`V`. :math:`k_{B}` is the Boltzmann constant.
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|
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|
The Born term is a symmetric 6x6 matrix, as is the matrix of second derivatives
|
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|
of potential energy w.r.t strain,
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|
whose 21 independent elements are output in this order:
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|
|
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|
.. math::
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|
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|
\begin{matrix}
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|
C_{1} & C_{7} & C_{8} & C_{9} & C_{10} & C_{11} \\
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|
C_{7} & C_{2} & C_{12} & C_{13} & C_{14} & C_{15} \\
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|
\vdots & C_{12} & C_{3} & C_{16} & C_{17} & C_{18} \\
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|
\vdots & C_{13} & C_{16} & C_{4} & C_{19} & C_{20} \\
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|
\vdots & \vdots & \vdots & C_{19} & C_{5} & C_{21} \\
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|
\vdots & \vdots & \vdots & \vdots & C_{21} & C_{6}
|
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|
\end{matrix}
|
||||||
|
|
||||||
|
in this matrix the indices of :math:`C_{k}` value are the corresponding element
|
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|
:math:`k` in the global vector output by this compute. Each term comes from the sum
|
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|
of the derivatives of every contribution to the potential energy
|
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|
in the system as explained in :ref:`(VanWorkum)
|
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|
<VanWorkum>`.
|
||||||
|
|
||||||
|
The output can be accessed using usual Lammps routines:
|
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|
|
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|
.. code-block:: LAMMPS
|
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|
|
||||||
|
compute 1 all born/matrix
|
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|
compute 2 all pressure NULL virial
|
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|
variable S1 equal -c_2[1]
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|
variable S2 equal -c_2[2]
|
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|
variable S3 equal -c_2[3]
|
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|
variable S4 equal -c_2[4]
|
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|
variable S5 equal -c_2[5]
|
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|
variable S6 equal -c_2[6]
|
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|
fix 1 all ave/time 1 1 1 v_S1 v_S2 v_S3 v_S4 v_S5 v_S6 c_1[*] file born.out
|
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|
|
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|
In this example, the file *born.out* will contain the information needed to
|
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|
compute the first and second terms of the elastic constant matrix in a post
|
||||||
|
processing procedure. The other required quantities can be accessed using any
|
||||||
|
other *LAMMPS* usual method. Several examples of this method are
|
||||||
|
provided in the examples/ELASTIC_T/BORN_MATRIX directory
|
||||||
|
described on the :doc:`Examples <Examples>` doc page.
|
||||||
|
|
||||||
|
NOTE: In the above :math:`C_{i,j}` computation, the fluctuation
|
||||||
|
term involving the virial stress tensor :math:`\sigma` is the
|
||||||
|
covariance between each elements. In a
|
||||||
|
solid the stress fluctuations can vary rapidly, while average
|
||||||
|
fluctuations can be slow to converge.
|
||||||
|
A detailed analysis of the convergence rate of all the terms in
|
||||||
|
the elastic tensor
|
||||||
|
is provided in the paper by Clavier et al. :ref:`(Clavier) <Clavier2>`.
|
||||||
|
|
||||||
|
Two different computation methods for the Born matrix are implemented in this
|
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|
compute and are mutually exclusive.
|
||||||
|
|
||||||
|
The first one is a direct computation from the analytical formula from the
|
||||||
|
different terms of the potential used for the simulations :ref:`(VanWorkum)
|
||||||
|
<VanWorkum>`. However, the implementation of such derivations must be done
|
||||||
|
for every potential form. This has not been done yet and can be very
|
||||||
|
complicated for complex potentials. At the moment a warning message is
|
||||||
|
displayed for every term that is not supporting the compute at the moment.
|
||||||
|
This method is the default for now.
|
||||||
|
|
||||||
|
The second method uses finite differences of energy to numerically approximate
|
||||||
|
the second derivatives :ref:`(Zhen) <Zhen>`. This is useful when using
|
||||||
|
interaction styles for which the analytical second derivatives have not been
|
||||||
|
implemented. In this cases, the compute applies linear strain fields of
|
||||||
|
magnitude *delta* to all the atoms relative to a point at the center of the
|
||||||
|
box. The strain fields are in six different directions, corresponding to the
|
||||||
|
six Cartesian components of the stress tensor defined by LAMMPS. For each
|
||||||
|
direction it applies the strain field in both the positive and negative senses,
|
||||||
|
and the new stress virial tensor of the entire system is calculated after each.
|
||||||
|
The difference in these two virials divided by two times *delta*, approximates
|
||||||
|
the corresponding components of the second derivative, after applying a
|
||||||
|
suitable unit conversion.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
It is important to choose a suitable value for delta, the magnitude of
|
||||||
|
strains that are used to generate finite difference
|
||||||
|
approximations to the exact virial stress. For typical systems, a value in
|
||||||
|
the range of 1 part in 1e5 to 1e6 will be sufficient.
|
||||||
|
However, the best value will depend on a multitude of factors
|
||||||
|
including the stiffness of the interatomic potential, the thermodynamic
|
||||||
|
state of the material being probed, and so on. The only way to be sure
|
||||||
|
that you have made a good choice is to do a sensitivity study on a
|
||||||
|
representative atomic configuration, sweeping over a wide range of
|
||||||
|
values of delta. If delta is too small, the output values will vary
|
||||||
|
erratically due to truncation effects. If delta is increased beyond a
|
||||||
|
certain point, the output values will start to vary smoothly with
|
||||||
|
delta, due to growing contributions from higher order derivatives. In
|
||||||
|
between these two limits, the numerical virial values should be largely
|
||||||
|
independent of delta.
|
||||||
|
|
||||||
|
The keyword requires the additional arguments *delta* and *virial-ID*.
|
||||||
|
*delta* gives the size of the applied strains. *virial-ID* gives
|
||||||
|
the ID string of the pressure compute that provides the virial stress tensor,
|
||||||
|
requiring that it use the virial keyword e.g.
|
||||||
|
|
||||||
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
|
compute myvirial all pressure NULL virial
|
||||||
|
compute 1 all born/matrix numdiff 1.0e-4 myvirial
|
||||||
|
|
||||||
|
**Output info:**
|
||||||
|
|
||||||
|
This compute calculates a global vector with 21 values that are
|
||||||
|
the second derivatives of the potential energy w.r.t. strain.
|
||||||
|
The values are in energy units.
|
||||||
|
The values are ordered as explained above. These values can be used
|
||||||
|
by any command that uses global values from a compute as input. See
|
||||||
|
the :doc:`Howto output <Howto_output>` doc page for an overview of
|
||||||
|
LAMMPS output options.
|
||||||
|
|
||||||
|
The array values calculated by this compute are all "extensive".
|
||||||
|
|
||||||
|
Restrictions
|
||||||
|
""""""""""""
|
||||||
|
|
||||||
|
This compute is part of the EXTRA-COMPUTE package. It is only enabled if
|
||||||
|
LAMMPS was built with that package. See the :doc:`Build package
|
||||||
|
<Build_package>` page for more info. LAMMPS was built with that package. See
|
||||||
|
the :doc:`Build package <Build_package>` page for more info.
|
||||||
|
|
||||||
|
The Born term can be decomposed as a product of two terms. The first one is a
|
||||||
|
general term which depends on the configuration. The second one is specific to
|
||||||
|
every interaction composing your force field (non-bonded, bonds, angle...).
|
||||||
|
Currently not all LAMMPS interaction styles implement the *born_matrix* method
|
||||||
|
giving first and second order derivatives and LAMMPS will exit with an error if
|
||||||
|
this compute is used with such interactions unless the *numdiff* option is
|
||||||
|
also used. The *numdiff* option cannot be used with any other keyword. In this
|
||||||
|
situation, LAMMPS will also exit with an error.
|
||||||
|
|
||||||
|
Default
|
||||||
|
"""""""
|
||||||
|
|
||||||
|
none
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
.. _VanWorkum:
|
||||||
|
|
||||||
|
**(Van Workum)** K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
|
||||||
|
|
||||||
|
.. _Clavier2:
|
||||||
|
|
||||||
|
**(Clavier)** G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
|
||||||
|
|
||||||
|
.. _Zhen:
|
||||||
|
|
||||||
|
**(Zhen)** Y. Zhen, C. Chu, Computer Physics Communications 183(2012)261-265
|
||||||
@ -76,21 +76,28 @@ velocity for each atom. Note that if there is only one atom in the
|
|||||||
bin, its thermal velocity will thus be 0.0.
|
bin, its thermal velocity will thus be 0.0.
|
||||||
|
|
||||||
After the spatially-averaged velocity field has been subtracted from
|
After the spatially-averaged velocity field has been subtracted from
|
||||||
each atom, the temperature is calculated by the formula KE = (dim\*N
|
each atom, the temperature is calculated by the formula
|
||||||
- dim\*Nx\*Ny\*Nz) k T/2, where KE = total kinetic energy of the group of
|
*KE* = (*dim\*N* - *Ns\*Nx\*Ny\*Nz* - *extra* ) *k* *T*/2, where *KE* = total
|
||||||
atoms (sum of 1/2 m v\^2), dim = 2 or 3 = dimensionality of the
|
kinetic energy of the group of atoms (sum of 1/2 *m* *v*\^2), *dim* = 2
|
||||||
simulation, N = number of atoms in the group, k = Boltzmann constant,
|
or 3 = dimensionality of the simulation, *Ns* = 0, 1, 2 or 3 for
|
||||||
and T = temperature. The dim\*Nx\*Ny\*Nz term are degrees of freedom
|
streaming velocity subtracted in 0, 1, 2 or 3 dimensions, *extra* = extra
|
||||||
subtracted to adjust for the removal of the center-of-mass velocity in
|
degrees-of-freedom, *N* = number of atoms in the group, *k* = Boltzmann
|
||||||
each of Nx\*Ny\*Nz bins, as discussed in the :ref:`(Evans) <Evans1>` paper.
|
constant, and *T* = temperature. The *Ns\*Nx\*Ny\*Nz* term is degrees
|
||||||
|
of freedom subtracted to adjust for the removal of the center-of-mass
|
||||||
|
velocity in each direction of the *Nx\*Ny\*Nz* bins, as discussed in the
|
||||||
|
:ref:`(Evans) <Evans1>` paper. The extra term defaults to (*dim* - *Ns*)
|
||||||
|
and accounts for overall conservation of center-of-mass velocity across
|
||||||
|
the group in directions where streaming velocity is *not* subtracted. This
|
||||||
|
can be altered using the *extra* option of the
|
||||||
|
:doc:`compute_modify <compute_modify>` command.
|
||||||
|
|
||||||
If the *out* keyword is used with a *tensor* value, which is the
|
If the *out* keyword is used with a *tensor* value, which is the
|
||||||
default, a kinetic energy tensor, stored as a 6-element vector, is
|
default, a kinetic energy tensor, stored as a 6-element vector, is
|
||||||
also calculated by this compute for use in the computation of a
|
also calculated by this compute for use in the computation of a
|
||||||
pressure tensor. The formula for the components of the tensor is the
|
pressure tensor. The formula for the components of the tensor is the
|
||||||
same as the above formula, except that v\^2 is replaced by vx\*vy for
|
same as the above formula, except that *v*\^2 is replaced by *vx\*vy* for
|
||||||
the xy component, etc. The 6 components of the vector are ordered xx,
|
the xy component, etc. The 6 components of the vector are ordered *xx,
|
||||||
yy, zz, xy, xz, yz.
|
yy, zz, xy, xz, yz.*
|
||||||
|
|
||||||
If the *out* keyword is used with a *bin* value, the count of atoms
|
If the *out* keyword is used with a *bin* value, the count of atoms
|
||||||
and computed temperature for each bin are stored for output, as an
|
and computed temperature for each bin are stored for output, as an
|
||||||
@ -123,10 +130,20 @@ needed, the subtracted degrees-of-freedom can be altered using the
|
|||||||
.. note::
|
.. note::
|
||||||
|
|
||||||
When using the *out* keyword with a value of *bin*, the
|
When using the *out* keyword with a value of *bin*, the
|
||||||
calculated temperature for each bin does not include the
|
calculated temperature for each bin includes the degrees-of-freedom
|
||||||
degrees-of-freedom adjustment described in the preceding paragraph,
|
adjustment described in the preceding paragraph for fixes that
|
||||||
for fixes that constrain molecular motion. It does include the
|
constrain molecular motion, as well as the adjustment due to
|
||||||
adjustment due to the *extra* option, which is applied to each bin.
|
the *extra* option (which defaults to *dim* - *Ns* as described above),
|
||||||
|
by fractionally applying them based on the fraction of atoms in each
|
||||||
|
bin. As a result, the bin degrees-of-freedom summed over all bins exactly
|
||||||
|
equals the degrees-of-freedom used in the scalar temperature calculation,
|
||||||
|
:math:`\Sigma N_{DOF_i} = N_{DOF}` and the corresponding relation for temperature
|
||||||
|
is also satisfied :math:`\Sigma N_{DOF_i} T_i = N_{DOF} T`.
|
||||||
|
These relations will breakdown in cases where the adjustment
|
||||||
|
exceeds the actual number of degrees-of-freedom in a bin. This could happen
|
||||||
|
if a bin is empty or in situations where rigid molecules
|
||||||
|
are non-uniformly distributed, in which case the reported
|
||||||
|
temperature within a bin may not be accurate.
|
||||||
|
|
||||||
See the :doc:`Howto thermostat <Howto_thermostat>` page for a
|
See the :doc:`Howto thermostat <Howto_thermostat>` page for a
|
||||||
discussion of different ways to compute temperature and perform
|
discussion of different ways to compute temperature and perform
|
||||||
|
|||||||
@ -3599,6 +3599,7 @@ Voronoi
|
|||||||
VORONOI
|
VORONOI
|
||||||
Vorselaars
|
Vorselaars
|
||||||
Voth
|
Voth
|
||||||
|
Voyiatzis
|
||||||
vpz
|
vpz
|
||||||
vratio
|
vratio
|
||||||
Vries
|
Vries
|
||||||
@ -3664,7 +3665,7 @@ Wittmaack
|
|||||||
wn
|
wn
|
||||||
Wolde
|
Wolde
|
||||||
workflow
|
workflow
|
||||||
workflows
|
Workum
|
||||||
Worley
|
Worley
|
||||||
Wriggers
|
Wriggers
|
||||||
Wuppertal
|
Wuppertal
|
||||||
|
|||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
3.36316 1.87373 1.87607 -0.00346 -0.00172 -0.00104
|
||||||
|
1.87373 3.36170 1.87425 0.00443 0.00033 0.00014
|
||||||
|
1.87607 1.87425 3.36573 0.00143 0.00155 0.00127
|
||||||
|
-0.00346 0.00443 0.00143 1.87425 0.00127 0.00033
|
||||||
|
-0.00172 0.00033 0.00155 0.00127 1.87607 -0.00346
|
||||||
|
-0.00104 0.00014 0.00127 0.00033 -0.00346 1.87373
|
||||||
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
Normal file
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
#!/usr/bin/env python3
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
def reduce_Born(Cf):
|
||||||
|
C = np.zeros((6,6), dtype=np.float64)
|
||||||
|
C[0,0] = Cf[0]
|
||||||
|
C[1,1] = Cf[1]
|
||||||
|
C[2,2] = Cf[2]
|
||||||
|
C[3,3] = Cf[3]
|
||||||
|
C[4,4] = Cf[4]
|
||||||
|
C[5,5] = Cf[5]
|
||||||
|
C[0,1] = Cf[6]
|
||||||
|
C[0,2] = Cf[7]
|
||||||
|
C[0,3] = Cf[8]
|
||||||
|
C[0,4] = Cf[9]
|
||||||
|
C[0,5] = Cf[10]
|
||||||
|
C[1,2] = Cf[11]
|
||||||
|
C[1,3] = Cf[12]
|
||||||
|
C[1,4] = Cf[13]
|
||||||
|
C[1,5] = Cf[14]
|
||||||
|
C[2,3] = Cf[15]
|
||||||
|
C[2,4] = Cf[16]
|
||||||
|
C[2,5] = Cf[17]
|
||||||
|
C[3,4] = Cf[18]
|
||||||
|
C[3,5] = Cf[19]
|
||||||
|
C[4,5] = Cf[20]
|
||||||
|
C = np.where(C,C,C.T)
|
||||||
|
return C
|
||||||
|
|
||||||
|
def compute_delta():
|
||||||
|
D = np.zeros((3,3,3,3))
|
||||||
|
for a in range(3):
|
||||||
|
for b in range(3):
|
||||||
|
for m in range(3):
|
||||||
|
for n in range(3):
|
||||||
|
D[a,b,m,n] = (a==m)*(b==n) + (a==n)*(b==m)
|
||||||
|
d = np.zeros((6,6))
|
||||||
|
d[0,0] = D[0,0,0,0]
|
||||||
|
d[1,1] = D[1,1,1,1]
|
||||||
|
d[2,2] = D[2,2,2,2]
|
||||||
|
d[3,3] = D[1,2,1,2]
|
||||||
|
d[4,4] = D[0,2,0,2]
|
||||||
|
d[5,5] = D[0,1,0,1]
|
||||||
|
d[0,1] = D[0,0,1,1]
|
||||||
|
d[0,2] = D[0,0,2,2]
|
||||||
|
d[0,3] = D[0,0,1,2]
|
||||||
|
d[0,4] = D[0,0,0,2]
|
||||||
|
d[0,5] = D[0,0,0,1]
|
||||||
|
d[1,2] = D[1,1,2,2]
|
||||||
|
d[1,3] = D[1,1,1,2]
|
||||||
|
d[1,4] = D[1,1,0,2]
|
||||||
|
d[1,5] = D[1,1,0,1]
|
||||||
|
d[2,3] = D[2,2,1,2]
|
||||||
|
d[2,4] = D[2,2,0,2]
|
||||||
|
d[2,5] = D[2,2,0,1]
|
||||||
|
d[3,4] = D[1,2,0,2]
|
||||||
|
d[3,5] = D[1,2,0,1]
|
||||||
|
d[4,5] = D[0,2,0,1]
|
||||||
|
d = np.where(d,d,d.T)
|
||||||
|
return d
|
||||||
|
|
||||||
|
|
||||||
|
def write_matrix(C, filename):
|
||||||
|
with open(filename, 'w') as f:
|
||||||
|
f.write("# Cij Matrix from post process computation\n")
|
||||||
|
for i in C:
|
||||||
|
f.write("{:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f}\n".format(
|
||||||
|
i[0]*10**-9, i[1]*10**-9, i[2]*10**-9, i[3]*10**-9, i[4]*10**-9, i[5]*10**-9,
|
||||||
|
)
|
||||||
|
)
|
||||||
|
return
|
||||||
|
|
||||||
|
def main():
|
||||||
|
|
||||||
|
N = 500
|
||||||
|
vol = 27.047271**3 * 10**-30 # m^3
|
||||||
|
T = 60 # K
|
||||||
|
kb = 1.380649 * 10**-23 # J/K
|
||||||
|
kbT = T*kb # J
|
||||||
|
kcalmol2J = 4183.9954/(6.022*10**23)
|
||||||
|
|
||||||
|
born = np.loadtxt('born.out')
|
||||||
|
stre = np.loadtxt('vir.out')
|
||||||
|
stre[:, 1:] = -stre[:, 1:]*101325 # -> Pa
|
||||||
|
try:
|
||||||
|
mean_born = np.mean(born[:, 1:], axis=0)
|
||||||
|
except IndexError:
|
||||||
|
mean_born = born[1:]
|
||||||
|
|
||||||
|
CB = kcalmol2J/vol*reduce_Born(mean_born) # -> J/m^3=Pa
|
||||||
|
Cs = vol/kbT*np.cov(stre[:,1:].T)
|
||||||
|
Ct = N*kbT/vol * compute_delta()
|
||||||
|
C = CB - Cs + Ct
|
||||||
|
write_matrix(CB, 'born_matrix.out')
|
||||||
|
write_matrix(Cs, 'stre_matrix.out')
|
||||||
|
write_matrix(Ct, 'temp_matrix.out')
|
||||||
|
write_matrix(C, 'full_matrix.out')
|
||||||
|
C11 = np.mean([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||||
|
C12 = np.mean([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||||
|
C44 = np.mean([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||||
|
eC11 = np.std([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||||
|
eC12 = np.std([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||||
|
eC44 = np.std([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||||
|
print(C*10**-9)
|
||||||
|
print("C11 = {:f} ± {:f}; C12 = {:f} ± {:f}; C44 = {:f} ± {:f}".format(C11, eC11, C12, eC12, C44, eC44))
|
||||||
|
|
||||||
|
return
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
try:
|
||||||
|
main()
|
||||||
|
except KeyboardInterrupt:
|
||||||
|
raise SystemExit("User interruption.")
|
||||||
|
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
2.18161 1.13726 1.16596 -0.01607 -0.02637 0.00291
|
||||||
|
1.13726 2.20242 1.16714 0.00386 -0.05820 0.02644
|
||||||
|
1.16596 1.16714 2.24704 -0.00354 -0.00368 0.02714
|
||||||
|
-0.01607 0.00386 -0.00354 1.43706 0.00210 0.01003
|
||||||
|
-0.02637 -0.05820 -0.00368 0.00210 1.37530 0.01401
|
||||||
|
0.00291 0.02644 0.02714 0.01003 0.01401 1.42403
|
||||||
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov
Normal file
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov
Normal file
@ -0,0 +1,154 @@
|
|||||||
|
# Analytical calculation
|
||||||
|
# of Born matrix
|
||||||
|
|
||||||
|
# Note that because of cubic symmetry and central forces, we have:
|
||||||
|
# C11, pure axial == positive mean value: 1,2,3
|
||||||
|
# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
|
||||||
|
# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
|
||||||
|
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||||
|
|
||||||
|
# adjustable parameters
|
||||||
|
|
||||||
|
units real
|
||||||
|
variable nsteps index 100000 # length of run
|
||||||
|
variable nthermo index 1000 # thermo output interval
|
||||||
|
variable nlat equal 5 # size of box
|
||||||
|
variable T equal 60. # Temperature in K
|
||||||
|
variable rho equal 5.405 # Lattice spacing in A
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc ${rho}
|
||||||
|
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 39.948
|
||||||
|
|
||||||
|
velocity all create ${T} 87287 loop geom
|
||||||
|
velocity all zero linear
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_coeff 1 1 0.238067 3.405
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check no
|
||||||
|
|
||||||
|
variable vol equal vol
|
||||||
|
thermo 100
|
||||||
|
fix aL all ave/time 1 1 1 v_vol ave running
|
||||||
|
fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
|
||||||
|
unfix NPT
|
||||||
|
|
||||||
|
variable newL equal "f_aL^(1./3.)"
|
||||||
|
change_box all x final 0 ${newL} y final 0. ${newL} z final 0. ${newL} remap units box
|
||||||
|
|
||||||
|
unfix aL
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# Conversion variables
|
||||||
|
variable kb equal 1.38065e-23 # J/K
|
||||||
|
variable Myvol equal "vol*10^-30" # Volume in m^3
|
||||||
|
variable kbt equal "v_kb*v_T"
|
||||||
|
variable Nat equal atoms
|
||||||
|
variable Rhokbt equal "v_kbt*v_Nat/v_Myvol"
|
||||||
|
variable at2Pa equal 101325
|
||||||
|
variable kcalmol2J equal "4183.9954/(6.022e23)"
|
||||||
|
variable C1 equal "v_kcalmol2J/v_Myvol" # Convert Cb from energy to pressure units
|
||||||
|
variable C2 equal "v_Myvol/v_kbt" # Factor for Cfl terms
|
||||||
|
variable Pa2GPa equal 1e-9
|
||||||
|
|
||||||
|
# Born compute giving <C^b> terms
|
||||||
|
compute born all born/matrix
|
||||||
|
# The six virial stress component to compute <C^fl>
|
||||||
|
compute VIR all pressure NULL virial
|
||||||
|
variable s1 equal "-c_VIR[1]*v_at2Pa"
|
||||||
|
variable s2 equal "-c_VIR[2]*v_at2Pa"
|
||||||
|
variable s3 equal "-c_VIR[3]*v_at2Pa"
|
||||||
|
variable s6 equal "-c_VIR[4]*v_at2Pa"
|
||||||
|
variable s5 equal "-c_VIR[5]*v_at2Pa"
|
||||||
|
variable s4 equal "-c_VIR[6]*v_at2Pa"
|
||||||
|
variable press equal press
|
||||||
|
|
||||||
|
|
||||||
|
# Average of Born term and vector to store stress
|
||||||
|
# for post processing
|
||||||
|
fix CB all ave/time 1 ${nthermo} ${nthermo} c_born[*] ave running file born.out overwrite
|
||||||
|
fix CPR all ave/time 1 1 1 c_VIR[*] file vir.out
|
||||||
|
fix APR all ave/time 1 1 1 v_press ave running
|
||||||
|
fix VEC all vector 1 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6
|
||||||
|
|
||||||
|
thermo ${nthermo}
|
||||||
|
thermo_style custom step temp press f_APR c_born[1] f_CB[1] c_born[12] f_CB[12] c_born[4] f_CB[4]
|
||||||
|
thermo_modify line multi
|
||||||
|
|
||||||
|
fix 1 all nvt temp $T $T 100
|
||||||
|
|
||||||
|
run ${nsteps}
|
||||||
|
|
||||||
|
# Compute vector averages
|
||||||
|
# Note the indice switch.
|
||||||
|
# LAMMPS convention is NOT the Voigt notation.
|
||||||
|
variable aves1 equal "ave(f_VEC[1])"
|
||||||
|
variable aves2 equal "ave(f_VEC[2])"
|
||||||
|
variable aves3 equal "ave(f_VEC[3])"
|
||||||
|
variable aves4 equal "ave(f_VEC[6])"
|
||||||
|
variable aves5 equal "ave(f_VEC[5])"
|
||||||
|
variable aves6 equal "ave(f_VEC[4])"
|
||||||
|
|
||||||
|
# Computing the covariance through the <s_{i}s_{j}>-<s_i><s_j>
|
||||||
|
# is numerically instable. Here we go through the <(s-<s>)^2>
|
||||||
|
# definition.
|
||||||
|
|
||||||
|
# Computing difference relative to average values
|
||||||
|
variable ds1 vector "f_VEC[1]-v_aves1"
|
||||||
|
variable ds2 vector "f_VEC[2]-v_aves2"
|
||||||
|
variable ds3 vector "f_VEC[3]-v_aves3"
|
||||||
|
variable ds4 vector "f_VEC[4]-v_aves4"
|
||||||
|
variable ds5 vector "f_VEC[5]-v_aves5"
|
||||||
|
variable ds6 vector "f_VEC[6]-v_aves6"
|
||||||
|
|
||||||
|
# Squaring and averaging
|
||||||
|
variable dds1 vector "v_ds1*v_ds1"
|
||||||
|
variable dds2 vector "v_ds2*v_ds2"
|
||||||
|
variable dds3 vector "v_ds3*v_ds3"
|
||||||
|
variable vars1 equal "ave(v_dds1)"
|
||||||
|
variable vars2 equal "ave(v_dds2)"
|
||||||
|
variable vars3 equal "ave(v_dds3)"
|
||||||
|
variable C11 equal "v_Pa2GPa*(v_C1*f_CB[1] - v_C2*v_vars1 + 2*v_Rhokbt)"
|
||||||
|
variable C22 equal "v_Pa2GPa*(v_C1*f_CB[2] - v_C2*v_vars2 + 2*v_Rhokbt)"
|
||||||
|
variable C33 equal "v_Pa2GPa*(v_C1*f_CB[3] - v_C2*v_vars3 + 2*v_Rhokbt)"
|
||||||
|
|
||||||
|
variable dds12 vector "v_ds1*v_ds2"
|
||||||
|
variable dds13 vector "v_ds1*v_ds3"
|
||||||
|
variable dds23 vector "v_ds2*v_ds3"
|
||||||
|
variable vars12 equal "ave(v_dds12)"
|
||||||
|
variable vars13 equal "ave(v_dds13)"
|
||||||
|
variable vars23 equal "ave(v_dds23)"
|
||||||
|
variable C12 equal "v_Pa2GPa*(v_C1*f_CB[7] - v_C2*v_vars12)"
|
||||||
|
variable C13 equal "v_Pa2GPa*(v_C1*f_CB[8] - v_C2*v_vars13)"
|
||||||
|
variable C23 equal "v_Pa2GPa*(v_C1*f_CB[12] - v_C2*v_vars23)"
|
||||||
|
|
||||||
|
variable dds4 vector "v_ds4*v_ds4"
|
||||||
|
variable dds5 vector "v_ds5*v_ds5"
|
||||||
|
variable dds6 vector "v_ds6*v_ds6"
|
||||||
|
variable vars4 equal "ave(v_dds4)"
|
||||||
|
variable vars5 equal "ave(v_dds5)"
|
||||||
|
variable vars6 equal "ave(v_dds6)"
|
||||||
|
variable C44 equal "v_Pa2GPa*(v_C1*f_CB[4] - v_C2*v_vars4 + v_Rhokbt)"
|
||||||
|
variable C55 equal "v_Pa2GPa*(v_C1*f_CB[5] - v_C2*v_vars5 + v_Rhokbt)"
|
||||||
|
variable C66 equal "v_Pa2GPa*(v_C1*f_CB[6] - v_C2*v_vars6 + v_Rhokbt)"
|
||||||
|
|
||||||
|
variable aC11 equal "(v_C11 + v_C22 + v_C33)/3."
|
||||||
|
variable aC12 equal "(v_C12 + v_C13 + v_C23)/3."
|
||||||
|
variable aC44 equal "(v_C44 + v_C55 + v_C66)/3."
|
||||||
|
|
||||||
|
print """
|
||||||
|
C11 = ${aC11}
|
||||||
|
C12 = ${aC12}
|
||||||
|
C44 = ${aC44}
|
||||||
|
"""
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
1.22342 0.73647 0.71011 0.01261 0.02465 -0.00395
|
||||||
|
0.73647 1.20115 0.70711 0.00057 0.05854 -0.02630
|
||||||
|
0.71011 0.70711 1.16055 0.00497 0.00524 -0.02587
|
||||||
|
0.01261 0.00057 0.00497 0.45813 -0.00083 -0.00969
|
||||||
|
0.02465 0.05854 0.00524 -0.00083 0.52170 -0.01747
|
||||||
|
-0.00395 -0.02630 -0.02587 -0.00969 -0.01747 0.47064
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
0.04187 0.00000 0.00000 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.04187 0.00000 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.04187 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.02093 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.00000 0.02093 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.00000 0.00000 0.02093
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
3.35855 1.86892 1.87139 0.00233 0.00218 -0.00179
|
||||||
|
1.86892 3.37104 1.87285 0.00112 0.00085 -0.00007
|
||||||
|
1.87139 1.87285 3.37707 -0.00058 0.00038 -0.00057
|
||||||
|
0.00233 0.00112 -0.00058 1.88326 -0.00039 0.00065
|
||||||
|
0.00218 0.00085 0.00038 -0.00039 1.88229 0.00242
|
||||||
|
-0.00179 -0.00007 -0.00057 0.00065 0.00242 1.87968
|
||||||
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
Normal file
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
#!/usr/bin/env python3
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
|
||||||
|
import sys
|
||||||
|
import numpy as np
|
||||||
|
|
||||||
|
def reduce_Born(Cf):
|
||||||
|
C = np.zeros((6,6), dtype=np.float64)
|
||||||
|
C[0,0] = Cf[0]
|
||||||
|
C[1,1] = Cf[1]
|
||||||
|
C[2,2] = Cf[2]
|
||||||
|
C[3,3] = Cf[3]
|
||||||
|
C[4,4] = Cf[4]
|
||||||
|
C[5,5] = Cf[5]
|
||||||
|
C[0,1] = Cf[6]
|
||||||
|
C[0,2] = Cf[7]
|
||||||
|
C[0,3] = Cf[8]
|
||||||
|
C[0,4] = Cf[9]
|
||||||
|
C[0,5] = Cf[10]
|
||||||
|
C[1,2] = Cf[11]
|
||||||
|
C[1,3] = Cf[12]
|
||||||
|
C[1,4] = Cf[13]
|
||||||
|
C[1,5] = Cf[14]
|
||||||
|
C[2,3] = Cf[15]
|
||||||
|
C[2,4] = Cf[16]
|
||||||
|
C[2,5] = Cf[17]
|
||||||
|
C[3,4] = Cf[18]
|
||||||
|
C[3,5] = Cf[19]
|
||||||
|
C[4,5] = Cf[20]
|
||||||
|
C = np.where(C,C,C.T)
|
||||||
|
return C
|
||||||
|
|
||||||
|
def compute_delta():
|
||||||
|
D = np.zeros((3,3,3,3))
|
||||||
|
for a in range(3):
|
||||||
|
for b in range(3):
|
||||||
|
for m in range(3):
|
||||||
|
for n in range(3):
|
||||||
|
D[a,b,m,n] = (a==m)*(b==n) + (a==n)*(b==m)
|
||||||
|
d = np.zeros((6,6))
|
||||||
|
d[0,0] = D[0,0,0,0]
|
||||||
|
d[1,1] = D[1,1,1,1]
|
||||||
|
d[2,2] = D[2,2,2,2]
|
||||||
|
d[3,3] = D[1,2,1,2]
|
||||||
|
d[4,4] = D[0,2,0,2]
|
||||||
|
d[5,5] = D[0,1,0,1]
|
||||||
|
d[0,1] = D[0,0,1,1]
|
||||||
|
d[0,2] = D[0,0,2,2]
|
||||||
|
d[0,3] = D[0,0,1,2]
|
||||||
|
d[0,4] = D[0,0,0,2]
|
||||||
|
d[0,5] = D[0,0,0,1]
|
||||||
|
d[1,2] = D[1,1,2,2]
|
||||||
|
d[1,3] = D[1,1,1,2]
|
||||||
|
d[1,4] = D[1,1,0,2]
|
||||||
|
d[1,5] = D[1,1,0,1]
|
||||||
|
d[2,3] = D[2,2,1,2]
|
||||||
|
d[2,4] = D[2,2,0,2]
|
||||||
|
d[2,5] = D[2,2,0,1]
|
||||||
|
d[3,4] = D[1,2,0,2]
|
||||||
|
d[3,5] = D[1,2,0,1]
|
||||||
|
d[4,5] = D[0,2,0,1]
|
||||||
|
d = np.where(d,d,d.T)
|
||||||
|
return d
|
||||||
|
|
||||||
|
|
||||||
|
def write_matrix(C, filename):
|
||||||
|
with open(filename, 'w') as f:
|
||||||
|
f.write("# Cij Matrix from post process computation\n")
|
||||||
|
for i in C:
|
||||||
|
f.write("{:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f}\n".format(
|
||||||
|
i[0]*10**-9, i[1]*10**-9, i[2]*10**-9, i[3]*10**-9, i[4]*10**-9, i[5]*10**-9,
|
||||||
|
)
|
||||||
|
)
|
||||||
|
return
|
||||||
|
|
||||||
|
def main():
|
||||||
|
|
||||||
|
N = 500
|
||||||
|
vol = 27.047271**3 * 10**-30 # m^3
|
||||||
|
T = 60 # K
|
||||||
|
kb = 1.380649 * 10**-23 # J/K
|
||||||
|
kbT = T*kb # J
|
||||||
|
kcalmol2J = 4183.9954/(6.022*10**23)
|
||||||
|
|
||||||
|
born = np.loadtxt('born.out')
|
||||||
|
stre = np.loadtxt('vir.out')
|
||||||
|
stre[:, 1:] = -stre[:, 1:]*101325 # -> Pa
|
||||||
|
try:
|
||||||
|
mean_born = np.mean(born[:, 1:], axis=0)
|
||||||
|
except IndexError:
|
||||||
|
mean_born = born[1:]
|
||||||
|
|
||||||
|
CB = kcalmol2J/vol*reduce_Born(mean_born) # -> J/m^3=Pa
|
||||||
|
Cs = vol/kbT*np.cov(stre[:,1:].T)
|
||||||
|
Ct = N*kbT/vol * compute_delta()
|
||||||
|
C = CB - Cs + Ct
|
||||||
|
write_matrix(CB, 'born_matrix.out')
|
||||||
|
write_matrix(Cs, 'stre_matrix.out')
|
||||||
|
write_matrix(Ct, 'temp_matrix.out')
|
||||||
|
write_matrix(C, 'full_matrix.out')
|
||||||
|
C11 = np.mean([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||||
|
C12 = np.mean([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||||
|
C44 = np.mean([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||||
|
eC11 = np.std([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||||
|
eC12 = np.std([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||||
|
eC44 = np.std([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||||
|
print(C*10**-9)
|
||||||
|
print("C11 = {:f} ± {:f}; C12 = {:f} ± {:f}; C44 = {:f} ± {:f}".format(C11, eC11, C12, eC12, C44, eC44))
|
||||||
|
|
||||||
|
return
|
||||||
|
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
try:
|
||||||
|
main()
|
||||||
|
except KeyboardInterrupt:
|
||||||
|
raise SystemExit("User interruption.")
|
||||||
|
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
2.29922 1.17439 1.20854 -0.01653 -0.01684 0.01188
|
||||||
|
1.17439 2.20673 1.21718 -0.00781 -0.00753 0.00867
|
||||||
|
1.20854 1.21718 2.30804 0.01535 -0.01596 0.00426
|
||||||
|
-0.01653 -0.00781 0.01535 1.47647 -0.01355 -0.01601
|
||||||
|
-0.01684 -0.00753 -0.01596 -0.01355 1.37905 0.01975
|
||||||
|
0.01188 0.00867 0.00426 -0.01601 0.01975 1.40170
|
||||||
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov
Normal file
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov
Normal file
@ -0,0 +1,154 @@
|
|||||||
|
# Numerical difference calculation
|
||||||
|
# of Born matrix
|
||||||
|
|
||||||
|
# Note that because of cubic symmetry and central forces, we have:
|
||||||
|
# C11, pure axial == positive mean value: 1,2,3
|
||||||
|
# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
|
||||||
|
# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
|
||||||
|
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||||
|
|
||||||
|
# adjustable parameters
|
||||||
|
|
||||||
|
units real
|
||||||
|
variable nsteps index 100000 # length of run
|
||||||
|
variable nthermo index 1000 # thermo output interval
|
||||||
|
variable nlat equal 5 # size of box
|
||||||
|
variable T equal 60. # Temperature in K
|
||||||
|
variable rho equal 5.405 # Lattice spacing in A
|
||||||
|
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
lattice fcc ${rho}
|
||||||
|
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
|
||||||
|
mass * 39.948
|
||||||
|
|
||||||
|
velocity all create ${T} 87287 loop geom
|
||||||
|
velocity all zero linear
|
||||||
|
|
||||||
|
pair_style lj/cut 12.0
|
||||||
|
pair_coeff 1 1 0.238067 3.405
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check no
|
||||||
|
|
||||||
|
variable vol equal vol
|
||||||
|
thermo 100
|
||||||
|
fix aL all ave/time 1 1 1 v_vol ave running
|
||||||
|
fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
|
||||||
|
unfix NPT
|
||||||
|
|
||||||
|
variable newL equal "f_aL^(1./3.)"
|
||||||
|
change_box all x final 0 ${newL} y final 0. ${newL} z final 0. ${newL} remap units box
|
||||||
|
|
||||||
|
unfix aL
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# Conversion variables
|
||||||
|
variable kb equal 1.38065e-23 # J/K
|
||||||
|
variable Myvol equal "vol*10^-30" # Volume in m^3
|
||||||
|
variable kbt equal "v_kb*v_T"
|
||||||
|
variable Nat equal atoms
|
||||||
|
variable Rhokbt equal "v_kbt*v_Nat/v_Myvol"
|
||||||
|
variable at2Pa equal 101325
|
||||||
|
variable kcalmol2J equal "4183.9954/(6.022e23)"
|
||||||
|
variable C1 equal "v_kcalmol2J/v_Myvol" # Convert Cb from energy to pressure units
|
||||||
|
variable C2 equal "v_Myvol/v_kbt" # Factor for Cfl terms
|
||||||
|
variable Pa2GPa equal 1e-9
|
||||||
|
|
||||||
|
# Born compute giving <C^b> terms
|
||||||
|
# The six virial stress component to compute <C^fl>
|
||||||
|
compute VIR all pressure NULL virial
|
||||||
|
compute born all born/matrix numdiff 1e-6 VIR
|
||||||
|
variable s1 equal "-c_VIR[1]*v_at2Pa"
|
||||||
|
variable s2 equal "-c_VIR[2]*v_at2Pa"
|
||||||
|
variable s3 equal "-c_VIR[3]*v_at2Pa"
|
||||||
|
variable s6 equal "-c_VIR[4]*v_at2Pa"
|
||||||
|
variable s5 equal "-c_VIR[5]*v_at2Pa"
|
||||||
|
variable s4 equal "-c_VIR[6]*v_at2Pa"
|
||||||
|
variable press equal press
|
||||||
|
|
||||||
|
|
||||||
|
# Average of Born term and vector to store stress
|
||||||
|
# for post processing
|
||||||
|
fix CB all ave/time 1 ${nthermo} ${nthermo} c_born[*] ave running file born.out overwrite
|
||||||
|
fix CPR all ave/time 1 1 1 c_VIR[*] file vir.out
|
||||||
|
fix APR all ave/time 1 1 1 v_press ave running
|
||||||
|
fix VEC all vector 1 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6
|
||||||
|
|
||||||
|
thermo ${nthermo}
|
||||||
|
thermo_style custom step temp press f_APR c_born[1] f_CB[1] c_born[12] f_CB[12] c_born[4] f_CB[4]
|
||||||
|
thermo_modify line multi
|
||||||
|
|
||||||
|
fix 1 all nvt temp $T $T 100
|
||||||
|
|
||||||
|
run ${nsteps}
|
||||||
|
|
||||||
|
# Compute vector averages
|
||||||
|
# Note the indice switch.
|
||||||
|
# LAMMPS convention is NOT the Voigt notation.
|
||||||
|
variable aves1 equal "ave(f_VEC[1])"
|
||||||
|
variable aves2 equal "ave(f_VEC[2])"
|
||||||
|
variable aves3 equal "ave(f_VEC[3])"
|
||||||
|
variable aves4 equal "ave(f_VEC[6])"
|
||||||
|
variable aves5 equal "ave(f_VEC[5])"
|
||||||
|
variable aves6 equal "ave(f_VEC[4])"
|
||||||
|
|
||||||
|
# Computing the covariance through the <s_{i}s_{j}>-<s_i><s_j>
|
||||||
|
# is numerically instable. Here we go through the <(s-<s>)^2>
|
||||||
|
# definition.
|
||||||
|
|
||||||
|
# Computing difference relative to average values
|
||||||
|
variable ds1 vector "f_VEC[1]-v_aves1"
|
||||||
|
variable ds2 vector "f_VEC[2]-v_aves2"
|
||||||
|
variable ds3 vector "f_VEC[3]-v_aves3"
|
||||||
|
variable ds4 vector "f_VEC[4]-v_aves4"
|
||||||
|
variable ds5 vector "f_VEC[5]-v_aves5"
|
||||||
|
variable ds6 vector "f_VEC[6]-v_aves6"
|
||||||
|
|
||||||
|
# Squaring and averaging
|
||||||
|
variable dds1 vector "v_ds1*v_ds1"
|
||||||
|
variable dds2 vector "v_ds2*v_ds2"
|
||||||
|
variable dds3 vector "v_ds3*v_ds3"
|
||||||
|
variable vars1 equal "ave(v_dds1)"
|
||||||
|
variable vars2 equal "ave(v_dds2)"
|
||||||
|
variable vars3 equal "ave(v_dds3)"
|
||||||
|
variable C11 equal "v_Pa2GPa*(v_C1*f_CB[1] - v_C2*v_vars1 + 2*v_Rhokbt)"
|
||||||
|
variable C22 equal "v_Pa2GPa*(v_C1*f_CB[2] - v_C2*v_vars2 + 2*v_Rhokbt)"
|
||||||
|
variable C33 equal "v_Pa2GPa*(v_C1*f_CB[3] - v_C2*v_vars3 + 2*v_Rhokbt)"
|
||||||
|
|
||||||
|
variable dds12 vector "v_ds1*v_ds2"
|
||||||
|
variable dds13 vector "v_ds1*v_ds3"
|
||||||
|
variable dds23 vector "v_ds2*v_ds3"
|
||||||
|
variable vars12 equal "ave(v_dds12)"
|
||||||
|
variable vars13 equal "ave(v_dds13)"
|
||||||
|
variable vars23 equal "ave(v_dds23)"
|
||||||
|
variable C12 equal "v_Pa2GPa*(v_C1*f_CB[7] - v_C2*v_vars12)"
|
||||||
|
variable C13 equal "v_Pa2GPa*(v_C1*f_CB[8] - v_C2*v_vars13)"
|
||||||
|
variable C23 equal "v_Pa2GPa*(v_C1*f_CB[12] - v_C2*v_vars23)"
|
||||||
|
|
||||||
|
variable dds4 vector "v_ds4*v_ds4"
|
||||||
|
variable dds5 vector "v_ds5*v_ds5"
|
||||||
|
variable dds6 vector "v_ds6*v_ds6"
|
||||||
|
variable vars4 equal "ave(v_dds4)"
|
||||||
|
variable vars5 equal "ave(v_dds5)"
|
||||||
|
variable vars6 equal "ave(v_dds6)"
|
||||||
|
variable C44 equal "v_Pa2GPa*(v_C1*f_CB[4] - v_C2*v_vars4 + v_Rhokbt)"
|
||||||
|
variable C55 equal "v_Pa2GPa*(v_C1*f_CB[5] - v_C2*v_vars5 + v_Rhokbt)"
|
||||||
|
variable C66 equal "v_Pa2GPa*(v_C1*f_CB[6] - v_C2*v_vars6 + v_Rhokbt)"
|
||||||
|
|
||||||
|
variable aC11 equal "(v_C11 + v_C22 + v_C33)/3."
|
||||||
|
variable aC12 equal "(v_C12 + v_C13 + v_C23)/3."
|
||||||
|
variable aC44 equal "(v_C44 + v_C55 + v_C66)/3."
|
||||||
|
|
||||||
|
print """
|
||||||
|
C11 = ${aC11}
|
||||||
|
C12 = ${aC12}
|
||||||
|
C44 = ${aC44}
|
||||||
|
"""
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
1.10120 0.69454 0.66285 0.01885 0.01902 -0.01367
|
||||||
|
0.69454 1.20617 0.65567 0.00893 0.00839 -0.00873
|
||||||
|
0.66285 0.65567 1.11090 -0.01593 0.01634 -0.00483
|
||||||
|
0.01885 0.00893 -0.01593 0.42772 0.01316 0.01666
|
||||||
|
0.01902 0.00839 0.01634 0.01316 0.52416 -0.01733
|
||||||
|
-0.01367 -0.00873 -0.00483 0.01666 -0.01733 0.49891
|
||||||
@ -0,0 +1,7 @@
|
|||||||
|
# Cij Matrix from post process computation
|
||||||
|
0.04187 0.00000 0.00000 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.04187 0.00000 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.04187 0.00000 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.02093 0.00000 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.00000 0.02093 0.00000
|
||||||
|
0.00000 0.00000 0.00000 0.00000 0.00000 0.02093
|
||||||
13
examples/ELASTIC_T/BORN_MATRIX/Argon/README.md
Normal file
13
examples/ELASTIC_T/BORN_MATRIX/Argon/README.md
Normal file
@ -0,0 +1,13 @@
|
|||||||
|
This repository is a test case for the compute born/matrix. It provides short
|
||||||
|
scripts creating argon fcc crystal and computing the Born term using the two
|
||||||
|
methods described in the documentation.
|
||||||
|
|
||||||
|
In the __Analytical__ directory the terms are computed using the analytical
|
||||||
|
derivation of the Born term for the lj/cut pair style.
|
||||||
|
|
||||||
|
In the __Numdiff__ directory, the Born term is evaluated through small
|
||||||
|
numerical differences of the stress tensor. This method can be used with any
|
||||||
|
interaction potential.
|
||||||
|
|
||||||
|
Both script show examples on how to compute the full Cij elastic stiffness
|
||||||
|
tensor in LAMMPS.
|
||||||
1
examples/ELASTIC_T/BORN_MATRIX/Silicon/Si.sw
Symbolic link
1
examples/ELASTIC_T/BORN_MATRIX/Silicon/Si.sw
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../../potentials/Si.sw
|
||||||
68
examples/ELASTIC_T/BORN_MATRIX/Silicon/final_output.in
Normal file
68
examples/ELASTIC_T/BORN_MATRIX/Silicon/final_output.in
Normal file
@ -0,0 +1,68 @@
|
|||||||
|
# Average moduli for cubic crystals
|
||||||
|
|
||||||
|
variable C11cubic equal (${C11}+${C22}+${C33})/3.0
|
||||||
|
variable C12cubic equal (${C12}+${C13}+${C23})/3.0
|
||||||
|
variable C44cubic equal (${C44}+${C55}+${C66})/3.0
|
||||||
|
|
||||||
|
variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
|
||||||
|
variable shearmodulus1 equal ${C44cubic}
|
||||||
|
variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
|
||||||
|
variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
|
||||||
|
|
||||||
|
# For Stillinger-Weber silicon, the analytical results
|
||||||
|
# are known to be (E. R. Cowley, 1988):
|
||||||
|
# C11 = 151.4 GPa
|
||||||
|
# C12 = 76.4 GPa
|
||||||
|
# C44 = 56.4 GPa
|
||||||
|
|
||||||
|
#print "========================================="
|
||||||
|
#print "Components of the Elastic Constant Tensor"
|
||||||
|
#print "========================================="
|
||||||
|
|
||||||
|
print "Elastic Constant C11 = ${C11} ${cunits}"
|
||||||
|
print "Elastic Constant C22 = ${C22} ${cunits}"
|
||||||
|
print "Elastic Constant C33 = ${C33} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C12 = ${C12} ${cunits}"
|
||||||
|
print "Elastic Constant C13 = ${C13} ${cunits}"
|
||||||
|
print "Elastic Constant C23 = ${C23} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C44 = ${C44} ${cunits}"
|
||||||
|
print "Elastic Constant C55 = ${C55} ${cunits}"
|
||||||
|
print "Elastic Constant C66 = ${C66} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C14 = ${C14} ${cunits}"
|
||||||
|
print "Elastic Constant C15 = ${C15} ${cunits}"
|
||||||
|
print "Elastic Constant C16 = ${C16} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C24 = ${C24} ${cunits}"
|
||||||
|
print "Elastic Constant C25 = ${C25} ${cunits}"
|
||||||
|
print "Elastic Constant C26 = ${C26} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C34 = ${C34} ${cunits}"
|
||||||
|
print "Elastic Constant C35 = ${C35} ${cunits}"
|
||||||
|
print "Elastic Constant C36 = ${C36} ${cunits}"
|
||||||
|
|
||||||
|
print "Elastic Constant C45 = ${C45} ${cunits}"
|
||||||
|
print "Elastic Constant C46 = ${C46} ${cunits}"
|
||||||
|
print "Elastic Constant C56 = ${C56} ${cunits}"
|
||||||
|
|
||||||
|
print "========================================="
|
||||||
|
print "Average properties for a cubic crystal"
|
||||||
|
print "========================================="
|
||||||
|
|
||||||
|
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||||
|
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||||
|
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||||
|
print "Poisson Ratio = ${poissonratio}"
|
||||||
|
|
||||||
|
# summarize sampling protocol
|
||||||
|
|
||||||
|
variable tmp equal atoms
|
||||||
|
print "Number of atoms = ${tmp}"
|
||||||
|
print "Stress sampling interval = ${nevery}"
|
||||||
|
variable tmp equal ${nrun}/${nevery}
|
||||||
|
print "Stress sample count = ${tmp}"
|
||||||
|
print "Born sampling interval = ${neveryborn}"
|
||||||
|
variable tmp equal ${nrun}/${neveryborn}
|
||||||
|
print "Born sample count = ${tmp}"
|
||||||
25
examples/ELASTIC_T/BORN_MATRIX/Silicon/in.elastic
Normal file
25
examples/ELASTIC_T/BORN_MATRIX/Silicon/in.elastic
Normal file
@ -0,0 +1,25 @@
|
|||||||
|
# Compute elastic constant tensor for a crystal at finite temperature
|
||||||
|
# These settings replicate the 1477~K benchmark of
|
||||||
|
# Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
|
||||||
|
# Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||||
|
|
||||||
|
# here: Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||||
|
|
||||||
|
include init.in
|
||||||
|
|
||||||
|
# Compute initial state
|
||||||
|
|
||||||
|
include potential.in
|
||||||
|
thermo_style custom step temp pe press density
|
||||||
|
run ${nequil}
|
||||||
|
|
||||||
|
# Run dynamics
|
||||||
|
|
||||||
|
include potential.in
|
||||||
|
include output.in
|
||||||
|
|
||||||
|
run ${nrun}
|
||||||
|
|
||||||
|
# Output final values
|
||||||
|
|
||||||
|
include final_output.in
|
||||||
59
examples/ELASTIC_T/BORN_MATRIX/Silicon/init.in
Normal file
59
examples/ELASTIC_T/BORN_MATRIX/Silicon/init.in
Normal file
@ -0,0 +1,59 @@
|
|||||||
|
# NOTE: This script can be modified for different atomic structures,
|
||||||
|
# units, etc. See in.elastic for more info.
|
||||||
|
#
|
||||||
|
|
||||||
|
# Define MD parameters
|
||||||
|
# These can be modified by the user
|
||||||
|
# These settings replicate the 1477~K benchmark of
|
||||||
|
# Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
|
||||||
|
# Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||||
|
|
||||||
|
# select temperature and pressure (lattice constant)
|
||||||
|
|
||||||
|
variable temp index 1477.0 # temperature of initial sample
|
||||||
|
variable a index 5.457 # lattice constant
|
||||||
|
|
||||||
|
# select sampling parameters, important for speed/convergence
|
||||||
|
|
||||||
|
variable nthermo index 1500 # interval for thermo output
|
||||||
|
variable nevery index 10 # stress sampling interval
|
||||||
|
variable neveryborn index 100 # Born sampling interval
|
||||||
|
variable timestep index 0.000766 # timestep
|
||||||
|
variable nlat index 3 # number of lattice unit cells
|
||||||
|
|
||||||
|
# other settings
|
||||||
|
|
||||||
|
variable mass1 index 28.06 # mass
|
||||||
|
variable tdamp index 0.01 # time constant for thermostat
|
||||||
|
variable seed index 123457 # seed for thermostat
|
||||||
|
variable thermostat index 1 # 0 if NVE, 1 if NVT
|
||||||
|
variable delta index 1.0e-6 # Born numdiff strain magnitude
|
||||||
|
|
||||||
|
# hard-coded rules-of-thumb for run length, etc.
|
||||||
|
|
||||||
|
variable nfreq equal ${nthermo} # interval for averaging output
|
||||||
|
variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
|
||||||
|
variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
|
||||||
|
variable nequil equal 10*${nthermo} # length of equilibration run
|
||||||
|
variable nrun equal 100*${nthermo} # length of equilibrated run
|
||||||
|
|
||||||
|
# generate the box and atom positions using a diamond lattice
|
||||||
|
|
||||||
|
units metal
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
# this generates a standard 8-atom cubic cell
|
||||||
|
|
||||||
|
lattice diamond $a
|
||||||
|
region box prism 0 1 0 1 0 1 0 0 0
|
||||||
|
|
||||||
|
# this generates a 2-atom triclinic cell
|
||||||
|
#include tri.in
|
||||||
|
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass 1 ${mass1}
|
||||||
|
replicate ${nlat} ${nlat} ${nlat}
|
||||||
|
velocity all create ${temp} 87287
|
||||||
|
|
||||||
140
examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in
Normal file
140
examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in
Normal file
@ -0,0 +1,140 @@
|
|||||||
|
# Setup output
|
||||||
|
|
||||||
|
# Stress fluctuation term F
|
||||||
|
|
||||||
|
compute stress all pressure thermo_temp
|
||||||
|
variable s1 equal c_stress[1]
|
||||||
|
variable s2 equal c_stress[2]
|
||||||
|
variable s3 equal c_stress[3]
|
||||||
|
variable s4 equal c_stress[6]
|
||||||
|
variable s5 equal c_stress[5]
|
||||||
|
variable s6 equal c_stress[4]
|
||||||
|
|
||||||
|
variable s11 equal v_s1*v_s1
|
||||||
|
variable s22 equal v_s2*v_s2
|
||||||
|
variable s33 equal v_s3*v_s3
|
||||||
|
variable s44 equal v_s4*v_s4
|
||||||
|
variable s55 equal v_s5*v_s5
|
||||||
|
variable s66 equal v_s6*v_s6
|
||||||
|
variable s33 equal v_s3*v_s3
|
||||||
|
variable s12 equal v_s1*v_s2
|
||||||
|
variable s13 equal v_s1*v_s3
|
||||||
|
variable s14 equal v_s1*v_s4
|
||||||
|
variable s15 equal v_s1*v_s5
|
||||||
|
variable s16 equal v_s1*v_s6
|
||||||
|
variable s23 equal v_s2*v_s3
|
||||||
|
variable s24 equal v_s2*v_s4
|
||||||
|
variable s25 equal v_s2*v_s5
|
||||||
|
variable s26 equal v_s2*v_s6
|
||||||
|
variable s34 equal v_s3*v_s4
|
||||||
|
variable s35 equal v_s3*v_s5
|
||||||
|
variable s36 equal v_s3*v_s6
|
||||||
|
variable s45 equal v_s4*v_s5
|
||||||
|
variable s46 equal v_s4*v_s6
|
||||||
|
variable s56 equal v_s5*v_s6
|
||||||
|
|
||||||
|
variable mytemp equal temp
|
||||||
|
variable mypress equal press
|
||||||
|
variable mype equal pe/atoms
|
||||||
|
fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
|
||||||
|
fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
|
||||||
|
fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
|
||||||
|
fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||||
|
fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} &
|
||||||
|
v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 &
|
||||||
|
v_s12 v_s13 v_s14 v_s15 v_s16 &
|
||||||
|
v_s23 v_s24 v_s25 v_s26 &
|
||||||
|
v_s34 v_s35 v_s36 &
|
||||||
|
v_s45 v_s46 &
|
||||||
|
v_s56 &
|
||||||
|
ave running
|
||||||
|
|
||||||
|
# bar to GPa
|
||||||
|
variable pconv equal 1.0e5/1.0e9
|
||||||
|
variable cunits index GPa
|
||||||
|
# metal unit constants from LAMMPS
|
||||||
|
# force->nktv2p = 1.6021765e6;
|
||||||
|
# force->boltz = 8.617343e-5;
|
||||||
|
variable boltz equal 8.617343e-5
|
||||||
|
variable nktv2p equal 1.6021765e6
|
||||||
|
variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
|
||||||
|
variable ffac equal ${pconv}*${vkt}
|
||||||
|
|
||||||
|
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
|
||||||
|
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
|
||||||
|
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
|
||||||
|
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
|
||||||
|
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
|
||||||
|
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
|
||||||
|
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
|
||||||
|
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
|
||||||
|
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
|
||||||
|
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
|
||||||
|
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
|
||||||
|
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
|
||||||
|
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
|
||||||
|
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
|
||||||
|
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
|
||||||
|
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
|
||||||
|
|
||||||
|
# Born term
|
||||||
|
|
||||||
|
compute virial all pressure NULL virial
|
||||||
|
compute born all born/matrix numdiff ${delta} virial
|
||||||
|
fix avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||||
|
|
||||||
|
variable bfac equal ${pconv}*${nktv2p}/vol
|
||||||
|
variable B vector f_avborn*${bfac}
|
||||||
|
|
||||||
|
# Kinetic term
|
||||||
|
|
||||||
|
variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||||
|
variable K11 equal 4.0*${kfac}
|
||||||
|
variable K22 equal 4.0*${kfac}
|
||||||
|
variable K33 equal 4.0*${kfac}
|
||||||
|
variable K44 equal 2.0*${kfac}
|
||||||
|
variable K55 equal 2.0*${kfac}
|
||||||
|
variable K66 equal 2.0*${kfac}
|
||||||
|
|
||||||
|
# Add F, K, and B together
|
||||||
|
|
||||||
|
variable C11 equal v_F11+v_B[1]+v_K11
|
||||||
|
variable C22 equal v_F22+v_B[2]+v_K22
|
||||||
|
variable C33 equal v_F33+v_B[3]+v_K33
|
||||||
|
variable C44 equal v_F44+v_B[4]+v_K44
|
||||||
|
variable C55 equal v_F55+v_B[5]+v_K55
|
||||||
|
variable C66 equal v_F66+v_B[6]+v_K66
|
||||||
|
|
||||||
|
variable C12 equal v_F12+v_B[7]
|
||||||
|
variable C13 equal v_F13+v_B[8]
|
||||||
|
variable C14 equal v_F14+v_B[9]
|
||||||
|
variable C15 equal v_F15+v_B[10]
|
||||||
|
variable C16 equal v_F16+v_B[11]
|
||||||
|
|
||||||
|
variable C23 equal v_F23+v_B[12]
|
||||||
|
variable C24 equal v_F24+v_B[13]
|
||||||
|
variable C25 equal v_F25+v_B[14]
|
||||||
|
variable C26 equal v_F26+v_B[15]
|
||||||
|
|
||||||
|
variable C34 equal v_F34+v_B[16]
|
||||||
|
variable C35 equal v_F35+v_B[17]
|
||||||
|
variable C36 equal v_F36+v_B[18]
|
||||||
|
|
||||||
|
variable C45 equal v_F45+v_B[19]
|
||||||
|
variable C46 equal v_F46+v_B[20]
|
||||||
|
|
||||||
|
variable C56 equal v_F56+v_B[21]
|
||||||
|
|
||||||
|
thermo ${nthermo}
|
||||||
|
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[1] v_B[2] v_B[3] v_B[4] v_B[5] v_B[6] v_B[7] v_B[8] v_B[12]
|
||||||
|
thermo_modify norm no
|
||||||
21
examples/ELASTIC_T/BORN_MATRIX/Silicon/potential.in
Normal file
21
examples/ELASTIC_T/BORN_MATRIX/Silicon/potential.in
Normal file
@ -0,0 +1,21 @@
|
|||||||
|
# NOTE: This script can be modified for different pair styles
|
||||||
|
# See in.elastic for more info.
|
||||||
|
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# Choose potential
|
||||||
|
pair_style sw
|
||||||
|
pair_coeff * * Si.sw Si
|
||||||
|
|
||||||
|
# Setup neighbor style
|
||||||
|
neighbor 1.0 nsq
|
||||||
|
neigh_modify once no every 1 delay 0 check yes
|
||||||
|
|
||||||
|
# Setup MD
|
||||||
|
|
||||||
|
timestep ${timestep}
|
||||||
|
fix 4 all nve
|
||||||
|
if "${thermostat} == 1" then &
|
||||||
|
"fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||||
|
|
||||||
|
|
||||||
26
examples/ELASTIC_T/BORN_MATRIX/Silicon/tri.in
Normal file
26
examples/ELASTIC_T/BORN_MATRIX/Silicon/tri.in
Normal file
@ -0,0 +1,26 @@
|
|||||||
|
# this generates a 2-atom triclinic cell
|
||||||
|
# due to rotation on to x-axis,
|
||||||
|
# elastic constant analysis is not working yet
|
||||||
|
|
||||||
|
# unit lattice vectors are
|
||||||
|
# a1 = (1 0 0)
|
||||||
|
# a2 = (1/2 sqrt3/2 0)
|
||||||
|
# a3 = (1/2 1/(2sqrt3) sqrt2/sqrt3)
|
||||||
|
|
||||||
|
variable a1x equal 1
|
||||||
|
variable a2x equal 1/2
|
||||||
|
variable a2y equal sqrt(3)/2
|
||||||
|
variable a3x equal 1/2
|
||||||
|
variable a3y equal 1/(2*sqrt(3))
|
||||||
|
variable a3z equal sqrt(2/3)
|
||||||
|
variable l equal $a/sqrt(2)
|
||||||
|
|
||||||
|
lattice custom ${l} &
|
||||||
|
a1 ${a1x} 0 0 &
|
||||||
|
a2 ${a2x} ${a2y} 0.0 &
|
||||||
|
a3 ${a3x} ${a3y} ${a3z} &
|
||||||
|
basis 0 0 0 &
|
||||||
|
basis 0.25 0.25 0.25 &
|
||||||
|
spacing 1 1 1
|
||||||
|
|
||||||
|
region box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||||
1
examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw
Symbolic link
1
examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw
Symbolic link
@ -0,0 +1 @@
|
|||||||
|
../../../../potentials/Si.sw
|
||||||
@ -2,7 +2,7 @@
|
|||||||
# See in.elastic for more info.
|
# See in.elastic for more info.
|
||||||
|
|
||||||
# we must undefine any fix ave/* fix before using reset_timestep
|
# we must undefine any fix ave/* fix before using reset_timestep
|
||||||
if "$(is_defined(fix,avp)" then "unfix avp"
|
if "$(is_defined(fix,avp))" then "unfix avp"
|
||||||
reset_timestep 0
|
reset_timestep 0
|
||||||
|
|
||||||
# Choose potential
|
# Choose potential
|
||||||
@ -1,18 +0,0 @@
|
|||||||
# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
|
|
||||||
# Stillinger-Weber parameters for various elements and mixtures
|
|
||||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
|
||||||
# these entries are in LAMMPS "metal" units:
|
|
||||||
# epsilon = eV; sigma = Angstroms
|
|
||||||
# other quantities are unitless
|
|
||||||
|
|
||||||
# format of a single entry (one or more lines):
|
|
||||||
# element 1, element 2, element 3,
|
|
||||||
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
|
|
||||||
|
|
||||||
# Here are the original parameters in metal units, for Silicon from:
|
|
||||||
#
|
|
||||||
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
|
|
||||||
#
|
|
||||||
|
|
||||||
Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
|
|
||||||
7.049556277 0.6022245584 4.0 0.0 0.0
|
|
||||||
@ -94,7 +94,7 @@ msst: MSST shock dynamics
|
|||||||
nb3b: use of nonbonded 3-body harmonic pair style
|
nb3b: use of nonbonded 3-body harmonic pair style
|
||||||
neb: nudged elastic band (NEB) calculation for barrier finding
|
neb: nudged elastic band (NEB) calculation for barrier finding
|
||||||
nemd: non-equilibrium MD of 2d sheared system
|
nemd: non-equilibrium MD of 2d sheared system
|
||||||
numdiff: numerical difference computation of forces and virial
|
numdiff: numerical difference computation of forces, virial, and Born matrix
|
||||||
obstacle: flow around two voids in a 2d channel
|
obstacle: flow around two voids in a 2d channel
|
||||||
peptide: dynamics of a small solvated peptide chain (5-mer)
|
peptide: dynamics of a small solvated peptide chain (5-mer)
|
||||||
peri: Peridynamic model of cylinder impacted by indenter
|
peri: Peridynamic model of cylinder impacted by indenter
|
||||||
@ -153,12 +153,19 @@ either by itself or in tandem with another code or library. See the
|
|||||||
COUPLE/README file to get started.
|
COUPLE/README file to get started.
|
||||||
|
|
||||||
The ELASTIC directory has an example script for computing elastic
|
The ELASTIC directory has an example script for computing elastic
|
||||||
constants at zero temperature, using an Si example. See the
|
stiffness tensor (elastic constants)
|
||||||
|
at zero temperature, using an Si example. See the
|
||||||
ELASTIC/in.elastic file for more info.
|
ELASTIC/in.elastic file for more info.
|
||||||
|
|
||||||
The ELASTIC_T directory has an example script for computing elastic
|
The ELASTIC_T directory has example scripts for the computing elastic
|
||||||
constants at finite temperature, using an Si example. See the
|
stiffness tensor at finite temperature. Two different methods are
|
||||||
ELASTIC_T/in.elastic file for more info.
|
demonstrated. DEFORMATION estimates the change in the average
|
||||||
|
stress tensor between multiple simulations
|
||||||
|
in which small finite deformations are made to the simulation cell.
|
||||||
|
BORN_MATRIX runs a single simulation in which the Born matrix and stress
|
||||||
|
fluctuations are averaged. The second method
|
||||||
|
is newer in LAMMPS and is generally more efficient and
|
||||||
|
more reliable.
|
||||||
|
|
||||||
The HEAT directory has example scripts for heat exchange algorithms
|
The HEAT directory has example scripts for heat exchange algorithms
|
||||||
(e.g. used for establishing a thermal gradient), using two different
|
(e.g. used for establishing a thermal gradient), using two different
|
||||||
|
|||||||
@ -1,8 +1,11 @@
|
|||||||
# LAMMPS FIX NUMDIFF EXAMPLE
|
# LAMMPS NUMDIFF EXAMPLES FOR FORCES, VIRIAL, and BORN MATRIX
|
||||||
|
|
||||||
## Numerical Difference Fix
|
## Numerical Difference Fixes and Computes
|
||||||
|
|
||||||
This directory contains the ingredients to run an NVE simulation using the numerical difference fix and calculate error in forces.
|
This directory contains the input script for an NVE simulation with
|
||||||
|
fix numdiff, fix numdiff/virial, and compute born/matrix numdiff.
|
||||||
|
In each cases, results are compared to exact analytic expressions
|
||||||
|
and the small relative differences are reported.
|
||||||
|
|
||||||
Example:
|
Example:
|
||||||
```
|
```
|
||||||
@ -10,4 +13,4 @@ NP=4 #number of processors
|
|||||||
mpirun -np $NP lmp_mpi -in.numdiff
|
mpirun -np $NP lmp_mpi -in.numdiff
|
||||||
```
|
```
|
||||||
|
|
||||||
## Required LAMMPS packages: MOLECULE package
|
## Required LAMMPS packages: EXTRA-FIX, EXTRA-COMPUTE
|
||||||
|
|||||||
@ -1,5 +1,5 @@
|
|||||||
# Numerical difference calculation
|
# Numerical difference calculation
|
||||||
# of error in forces and virial stress
|
# of error in forces, virial stress, and Born matrix
|
||||||
|
|
||||||
# adjustable parameters
|
# adjustable parameters
|
||||||
|
|
||||||
@ -8,8 +8,10 @@ variable nthermo index 10 # thermo output interval
|
|||||||
variable ndump index 500 # dump output interval
|
variable ndump index 500 # dump output interval
|
||||||
variable nlat index 3 # size of box
|
variable nlat index 3 # size of box
|
||||||
variable fdelta index 1.0e-4 # displacement size
|
variable fdelta index 1.0e-4 # displacement size
|
||||||
variable vdelta index 1.0e-6 # strain size
|
variable vdelta index 1.0e-6 # strain size for numdiff/virial
|
||||||
|
variable bdelta index 1.0e-8 # strain size for numdiff Born matrix
|
||||||
variable temp index 10.0 # temperature
|
variable temp index 10.0 # temperature
|
||||||
|
variable nugget equal 1.0e-6 # regularization for relerr
|
||||||
|
|
||||||
units metal
|
units metal
|
||||||
atom_style atomic
|
atom_style atomic
|
||||||
@ -23,8 +25,8 @@ mass 1 39.903
|
|||||||
|
|
||||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||||
|
|
||||||
pair_style lj/cubic
|
pair_style lj/cut 5.0
|
||||||
pair_coeff * * 0.0102701 3.42
|
pair_coeff 1 1 0.0102701 3.42
|
||||||
|
|
||||||
neighbor 0.0 bin
|
neighbor 0.0 bin
|
||||||
neigh_modify every 1 delay 0 check no
|
neigh_modify every 1 delay 0 check no
|
||||||
@ -42,7 +44,7 @@ variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
|||||||
compute faverrsq all reduce ave v_ferrsq
|
compute faverrsq all reduce ave v_ferrsq
|
||||||
variable fsq atom fx^2+fy^2+fz^2
|
variable fsq atom fx^2+fy^2+fz^2
|
||||||
compute favsq all reduce ave v_fsq
|
compute favsq all reduce ave v_fsq
|
||||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget}))
|
||||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||||
|
|
||||||
# define numerical virial stress tensor calculation
|
# define numerical virial stress tensor calculation
|
||||||
@ -67,8 +69,59 @@ variable vsq equal "c_myvirial[1]^2 + &
|
|||||||
c_myvirial[4]^2 + &
|
c_myvirial[4]^2 + &
|
||||||
c_myvirial[5]^2 + &
|
c_myvirial[5]^2 + &
|
||||||
c_myvirial[6]^2"
|
c_myvirial[6]^2"
|
||||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget}))
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
# define numerical Born matrix calculation
|
||||||
|
|
||||||
|
compute bornnum all born/matrix numdiff ${bdelta} myvirial
|
||||||
|
compute born all born/matrix
|
||||||
|
variable berr vector c_bornnum-c_born
|
||||||
|
variable berrsq equal "v_berr[1]^2 + &
|
||||||
|
v_berr[2]^2 + &
|
||||||
|
v_berr[3]^2 + &
|
||||||
|
v_berr[4]^2 + &
|
||||||
|
v_berr[5]^2 + &
|
||||||
|
v_berr[6]^2 + &
|
||||||
|
v_berr[7]^2 + &
|
||||||
|
v_berr[8]^2 + &
|
||||||
|
v_berr[9]^2 + &
|
||||||
|
v_berr[10]^2 + &
|
||||||
|
v_berr[11]^2 + &
|
||||||
|
v_berr[12]^2 + &
|
||||||
|
v_berr[13]^2 + &
|
||||||
|
v_berr[14]^2 + &
|
||||||
|
v_berr[15]^2 + &
|
||||||
|
v_berr[16]^2 + &
|
||||||
|
v_berr[17]^2 + &
|
||||||
|
v_berr[18]^2 + &
|
||||||
|
v_berr[19]^2 + &
|
||||||
|
v_berr[20]^2 + &
|
||||||
|
v_berr[21]^2"
|
||||||
|
|
||||||
|
variable bsq equal "c_born[1]^2 + &
|
||||||
|
c_born[2]^2 + &
|
||||||
|
c_born[3]^2 + &
|
||||||
|
c_born[4]^2 + &
|
||||||
|
c_born[5]^2 + &
|
||||||
|
c_born[6]^2 + &
|
||||||
|
c_born[7]^2 + &
|
||||||
|
c_born[8]^2 + &
|
||||||
|
c_born[9]^2 + &
|
||||||
|
c_born[10]^2 + &
|
||||||
|
c_born[11]^2 + &
|
||||||
|
c_born[12]^2 + &
|
||||||
|
c_born[13]^2 + &
|
||||||
|
c_born[14]^2 + &
|
||||||
|
c_born[15]^2 + &
|
||||||
|
c_born[16]^2 + &
|
||||||
|
c_born[17]^2 + &
|
||||||
|
c_born[18]^2 + &
|
||||||
|
c_born[19]^2 + &
|
||||||
|
c_born[20]^2 + &
|
||||||
|
c_born[21]^2"
|
||||||
|
|
||||||
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget}))
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr
|
||||||
thermo ${nthermo}
|
thermo ${nthermo}
|
||||||
run ${nsteps}
|
run ${nsteps}
|
||||||
|
|||||||
197
examples/numdiff/log.19Feb2022.log.numdiff.g++.1
Normal file
197
examples/numdiff/log.19Feb2022.log.numdiff.g++.1
Normal file
@ -0,0 +1,197 @@
|
|||||||
|
LAMMPS (17 Feb 2022)
|
||||||
|
# Numerical difference calculation
|
||||||
|
# of error in forces, virial stress, and Born matrix
|
||||||
|
|
||||||
|
# adjustable parameters
|
||||||
|
|
||||||
|
variable nsteps index 500 # length of run
|
||||||
|
variable nthermo index 10 # thermo output interval
|
||||||
|
variable ndump index 500 # dump output interval
|
||||||
|
variable nlat index 3 # size of box
|
||||||
|
variable fdelta index 1.0e-4 # displacement size
|
||||||
|
variable vdelta index 1.0e-6 # strain size for numdiff/virial
|
||||||
|
variable bdelta index 1.0e-8 # strain size for numdiff Born matrix
|
||||||
|
variable temp index 10.0 # temperature
|
||||||
|
variable nugget equal 1.0e-6 # regularization for relerr
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
atom_modify map yes
|
||||||
|
lattice fcc 5.358000
|
||||||
|
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
||||||
|
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||||
|
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||||
|
region box block 0 3 0 3 0 ${nlat}
|
||||||
|
region box block 0 3 0 3 0 3
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 108 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
mass 1 39.903
|
||||||
|
|
||||||
|
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||||
|
velocity all create 10.0 2357 mom yes dist gaussian
|
||||||
|
|
||||||
|
pair_style lj/cut 5.0
|
||||||
|
pair_coeff 1 1 0.0102701 3.42
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check no
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
fix nve all nve
|
||||||
|
|
||||||
|
# define numerical force calculation
|
||||||
|
|
||||||
|
fix numforce all numdiff ${nthermo} ${fdelta}
|
||||||
|
fix numforce all numdiff 10 ${fdelta}
|
||||||
|
fix numforce all numdiff 10 1.0e-4
|
||||||
|
variable ferrx atom f_numforce[1]-fx
|
||||||
|
variable ferry atom f_numforce[2]-fy
|
||||||
|
variable ferrz atom f_numforce[3]-fz
|
||||||
|
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
||||||
|
compute faverrsq all reduce ave v_ferrsq
|
||||||
|
variable fsq atom fx^2+fy^2+fz^2
|
||||||
|
compute favsq all reduce ave v_fsq
|
||||||
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget}))
|
||||||
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+1e-06))
|
||||||
|
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||||
|
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
||||||
|
|
||||||
|
# define numerical virial stress tensor calculation
|
||||||
|
|
||||||
|
compute myvirial all pressure NULL virial
|
||||||
|
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
||||||
|
fix numvirial all numdiff/virial 10 ${vdelta}
|
||||||
|
fix numvirial all numdiff/virial 10 1.0e-6
|
||||||
|
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
||||||
|
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
||||||
|
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
||||||
|
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
||||||
|
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
||||||
|
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
||||||
|
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
||||||
|
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
||||||
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget}))
|
||||||
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+1e-06))
|
||||||
|
|
||||||
|
# define numerical Born matrix calculation
|
||||||
|
|
||||||
|
compute bornnum all born/matrix numdiff ${bdelta} myvirial
|
||||||
|
compute bornnum all born/matrix numdiff 1.0e-8 myvirial
|
||||||
|
compute born all born/matrix
|
||||||
|
variable berr vector c_bornnum-c_born
|
||||||
|
variable berrsq equal "v_berr[1]^2 + v_berr[2]^2 + v_berr[3]^2 + v_berr[4]^2 + v_berr[5]^2 + v_berr[6]^2 + v_berr[7]^2 + v_berr[8]^2 + v_berr[9]^2 + v_berr[10]^2 + v_berr[11]^2 + v_berr[12]^2 + v_berr[13]^2 + v_berr[14]^2 + v_berr[15]^2 + v_berr[16]^2 + v_berr[17]^2 + v_berr[18]^2 + v_berr[19]^2 + v_berr[20]^2 + v_berr[21]^2"
|
||||||
|
|
||||||
|
variable bsq equal "c_born[1]^2 + c_born[2]^2 + c_born[3]^2 + c_born[4]^2 + c_born[5]^2 + c_born[6]^2 + c_born[7]^2 + c_born[8]^2 + c_born[9]^2 + c_born[10]^2 + c_born[11]^2 + c_born[12]^2 + c_born[13]^2 + c_born[14]^2 + c_born[15]^2 + c_born[16]^2 + c_born[17]^2 + c_born[18]^2 + c_born[19]^2 + c_born[20]^2 + c_born[21]^2"
|
||||||
|
|
||||||
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget}))
|
||||||
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+1e-06))
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr
|
||||||
|
thermo ${nthermo}
|
||||||
|
thermo 10
|
||||||
|
run ${nsteps}
|
||||||
|
run 500
|
||||||
|
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5
|
||||||
|
ghost atom cutoff = 5
|
||||||
|
binsize = 2.5, bins = 7 7 7
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) compute born/matrix, occasional, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.823 | 6.823 | 6.823 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr
|
||||||
|
0 10 -6.6101864 -6.471878 947.70558 5.7012262e-09 1.4849734e-08 9.036398e-09
|
||||||
|
10 9.9357441 -6.6092976 -6.471878 949.3486 1.3828998e-08 1.9248385e-09 4.0233493e-09
|
||||||
|
20 9.7444561 -6.6066519 -6.4718779 954.23637 1.385204e-08 1.7476399e-09 4.0061081e-09
|
||||||
|
30 9.4311148 -6.6023181 -6.4718779 962.23331 1.4147226e-08 1.7647816e-09 3.3866543e-09
|
||||||
|
40 9.0043293 -6.5964152 -6.4718778 973.10762 1.4128155e-08 1.6390138e-09 3.2652821e-09
|
||||||
|
50 8.4762135 -6.5891108 -6.4718777 986.53572 1.4168048e-08 2.3910821e-09 4.7266627e-09
|
||||||
|
60 7.8621735 -6.5806179 -6.4718775 1002.1092 1.411958e-08 2.0683414e-09 2.6951001e-09
|
||||||
|
70 7.1805874 -6.5711908 -6.4718773 1019.3448 1.4139911e-08 1.6084571e-09 3.1477301e-09
|
||||||
|
80 6.4523557 -6.5611186 -6.4718771 1037.6974 1.4105096e-08 1.9929271e-09 3.4733802e-09
|
||||||
|
90 5.7003071 -6.5507169 -6.4718769 1056.5767 1.4084183e-08 1.750579e-09 4.310104e-09
|
||||||
|
100 4.9484503 -6.5403179 -6.4718767 1075.3674 1.4063796e-08 1.0250271e-09 2.9213594e-09
|
||||||
|
110 4.221081 -6.5302576 -6.4718765 1093.4526 1.400901e-08 1.389277e-09 4.3909721e-09
|
||||||
|
120 3.5417733 -6.520862 -6.4718763 1110.2388 1.4038158e-08 8.6231891e-10 2.5890696e-09
|
||||||
|
130 2.9323072 -6.5124324 -6.4718762 1125.183 1.4048645e-08 7.0840985e-10 3.388192e-09
|
||||||
|
140 2.411607 -6.5052306 -6.471876 1137.8182 1.3968429e-08 1.8508015e-09 3.2976031e-09
|
||||||
|
150 1.9947801 -6.4994654 -6.4718759 1147.7764 1.395965e-08 1.9484728e-09 4.2924605e-09
|
||||||
|
160 1.6923481 -6.4952825 -6.4718759 1154.8063 1.3948606e-08 1.5275137e-09 4.0204309e-09
|
||||||
|
170 1.5097515 -6.492757 -6.4718759 1158.7853 1.3845523e-08 1.5455e-09 4.8781309e-09
|
||||||
|
180 1.4471795 -6.4918916 -6.4718759 1159.7221 1.3788451e-08 1.578099e-09 3.0795316e-09
|
||||||
|
190 1.4997431 -6.4926187 -6.471876 1157.7529 1.374841e-08 2.142073e-09 2.4376961e-09
|
||||||
|
200 1.6579637 -6.4948072 -6.4718761 1153.1286 1.3674788e-08 2.111894e-09 3.7055708e-09
|
||||||
|
210 1.908522 -6.4982727 -6.4718763 1146.1965 1.3639408e-08 1.2386489e-09 3.160881e-09
|
||||||
|
220 2.23518 -6.5027908 -6.4718764 1137.3775 1.3524209e-08 1.7016573e-09 3.6982265e-09
|
||||||
|
230 2.6197892 -6.5081105 -6.4718766 1127.1415 1.3344007e-08 1.5843477e-09 3.7272821e-09
|
||||||
|
240 3.043298 -6.5139681 -6.4718768 1115.9815 1.3245227e-08 1.5502368e-09 3.898015e-09
|
||||||
|
250 3.4866901 -6.5201007 -6.4718769 1104.3906 1.3080142e-08 1.369987e-09 4.9133863e-09
|
||||||
|
260 3.9318061 -6.5262572 -6.4718771 1092.84 1.2885339e-08 1.0743728e-09 5.7271364e-09
|
||||||
|
270 4.3620216 -6.5322076 -6.4718772 1081.7617 1.2705966e-08 1.3618619e-09 2.3225062e-09
|
||||||
|
280 4.7627723 -6.5377504 -6.4718773 1071.5341 1.2480463e-08 1.4346869e-09 3.281167e-09
|
||||||
|
290 5.1219322 -6.542718 -6.4718774 1062.4716 1.2434727e-08 2.1935942e-09 2.8198924e-09
|
||||||
|
300 5.4300557 -6.5469796 -6.4718774 1054.8177 1.2321314e-08 8.2365886e-10 3.2731015e-09
|
||||||
|
310 5.6804997 -6.5504435 -6.4718774 1048.7409 1.2300884e-08 1.4855741e-09 4.1031988e-09
|
||||||
|
320 5.8694423 -6.5530567 -6.4718774 1044.3341 1.2483087e-08 1.8711589e-09 3.9368436e-09
|
||||||
|
330 5.9958115 -6.5548045 -6.4718774 1041.6165 1.2627617e-08 1.9256986e-09 4.3283764e-09
|
||||||
|
340 6.0611353 -6.555708 -6.4718774 1040.5369 1.2935701e-08 1.6609255e-09 3.8728039e-09
|
||||||
|
350 6.0693222 -6.5558211 -6.4718773 1040.9803 1.3218179e-08 1.985355e-09 2.618577e-09
|
||||||
|
360 6.0263776 -6.5552271 -6.4718773 1042.7755 1.3471701e-08 1.5125203e-09 2.936238e-09
|
||||||
|
370 5.9400629 -6.5540332 -6.4718772 1045.7049 1.3676495e-08 1.7364093e-09 2.9097362e-09
|
||||||
|
380 5.8195019 -6.5523657 -6.4718771 1049.515 1.3859995e-08 1.6834835e-09 2.7416302e-09
|
||||||
|
390 5.6747442 -6.5503635 -6.471877 1053.9288 1.3987553e-08 1.7893896e-09 2.8552537e-09
|
||||||
|
400 5.5162948 -6.5481719 -6.4718769 1058.6583 1.4091878e-08 1.4468098e-09 3.2733654e-09
|
||||||
|
410 5.3546269 -6.5459358 -6.4718768 1063.4182 1.4188438e-08 1.7231047e-09 3.3165187e-09
|
||||||
|
420 5.1996958 -6.5437929 -6.4718768 1067.9384 1.4205207e-08 1.3551982e-09 3.8687611e-09
|
||||||
|
430 5.0604771 -6.5418673 -6.4718767 1071.9767 1.4267199e-08 1.361845e-09 3.1210672e-09
|
||||||
|
440 4.9445529 -6.5402639 -6.4718766 1075.3292 1.4253464e-08 1.3945282e-09 2.6483572e-09
|
||||||
|
450 4.8577717 -6.5390637 -6.4718766 1077.8394 1.4240998e-08 1.8767323e-09 3.2040422e-09
|
||||||
|
460 4.8040023 -6.53832 -6.4718766 1079.4048 1.4242259e-08 1.4785379e-09 3.4402279e-09
|
||||||
|
470 4.7849977 -6.5380571 -6.4718766 1079.9795 1.4227939e-08 1.8623848e-09 4.3634918e-09
|
||||||
|
480 4.8003794 -6.5382699 -6.4718766 1079.5756 1.4215836e-08 1.2821795e-09 2.6846581e-09
|
||||||
|
490 4.8477405 -6.538925 -6.4718767 1078.2596 1.4186541e-08 2.47604e-09 3.2044632e-09
|
||||||
|
500 4.9228588 -6.539964 -6.4718767 1076.1469 1.4099819e-08 1.6653302e-09 3.267113e-09
|
||||||
|
Loop time of 0.458483 on 1 procs for 500 steps with 108 atoms
|
||||||
|
|
||||||
|
Performance: 94.224 ns/day, 0.255 hours/ns, 1090.552 timesteps/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0042278 | 0.0042278 | 0.0042278 | 0.0 | 0.92
|
||||||
|
Neigh | 0.02481 | 0.02481 | 0.02481 | 0.0 | 5.41
|
||||||
|
Comm | 0.002944 | 0.002944 | 0.002944 | 0.0 | 0.64
|
||||||
|
Output | 0.014731 | 0.014731 | 0.014731 | 0.0 | 3.21
|
||||||
|
Modify | 0.41122 | 0.41122 | 0.41122 | 0.0 | 89.69
|
||||||
|
Other | | 0.0005545 | | | 0.12
|
||||||
|
|
||||||
|
Nlocal: 108 ave 108 max 108 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 256 ave 256 max 256 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 648 ave 648 max 648 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 648
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 500
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:00
|
||||||
197
examples/numdiff/log.19Feb2022.log.numdiff.g++.4
Normal file
197
examples/numdiff/log.19Feb2022.log.numdiff.g++.4
Normal file
@ -0,0 +1,197 @@
|
|||||||
|
LAMMPS (17 Feb 2022)
|
||||||
|
# Numerical difference calculation
|
||||||
|
# of error in forces, virial stress, and Born matrix
|
||||||
|
|
||||||
|
# adjustable parameters
|
||||||
|
|
||||||
|
variable nsteps index 500 # length of run
|
||||||
|
variable nthermo index 10 # thermo output interval
|
||||||
|
variable ndump index 500 # dump output interval
|
||||||
|
variable nlat index 3 # size of box
|
||||||
|
variable fdelta index 1.0e-4 # displacement size
|
||||||
|
variable vdelta index 1.0e-6 # strain size for numdiff/virial
|
||||||
|
variable bdelta index 1.0e-8 # strain size for numdiff Born matrix
|
||||||
|
variable temp index 10.0 # temperature
|
||||||
|
variable nugget equal 1.0e-6 # regularization for relerr
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
atom_modify map yes
|
||||||
|
lattice fcc 5.358000
|
||||||
|
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
||||||
|
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||||
|
region box block 0 3 0 ${nlat} 0 ${nlat}
|
||||||
|
region box block 0 3 0 3 0 ${nlat}
|
||||||
|
region box block 0 3 0 3 0 3
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 108 atoms
|
||||||
|
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
mass 1 39.903
|
||||||
|
|
||||||
|
velocity all create ${temp} 2357 mom yes dist gaussian
|
||||||
|
velocity all create 10.0 2357 mom yes dist gaussian
|
||||||
|
|
||||||
|
pair_style lj/cut 5.0
|
||||||
|
pair_coeff 1 1 0.0102701 3.42
|
||||||
|
|
||||||
|
neighbor 0.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check no
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
fix nve all nve
|
||||||
|
|
||||||
|
# define numerical force calculation
|
||||||
|
|
||||||
|
fix numforce all numdiff ${nthermo} ${fdelta}
|
||||||
|
fix numforce all numdiff 10 ${fdelta}
|
||||||
|
fix numforce all numdiff 10 1.0e-4
|
||||||
|
variable ferrx atom f_numforce[1]-fx
|
||||||
|
variable ferry atom f_numforce[2]-fy
|
||||||
|
variable ferrz atom f_numforce[3]-fz
|
||||||
|
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
||||||
|
compute faverrsq all reduce ave v_ferrsq
|
||||||
|
variable fsq atom fx^2+fy^2+fz^2
|
||||||
|
compute favsq all reduce ave v_fsq
|
||||||
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget}))
|
||||||
|
variable frelerr equal sqrt(c_faverrsq/(c_favsq+1e-06))
|
||||||
|
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
||||||
|
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
||||||
|
|
||||||
|
# define numerical virial stress tensor calculation
|
||||||
|
|
||||||
|
compute myvirial all pressure NULL virial
|
||||||
|
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
||||||
|
fix numvirial all numdiff/virial 10 ${vdelta}
|
||||||
|
fix numvirial all numdiff/virial 10 1.0e-6
|
||||||
|
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
||||||
|
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
||||||
|
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
||||||
|
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
||||||
|
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
||||||
|
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
||||||
|
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
||||||
|
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
||||||
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget}))
|
||||||
|
variable vrelerr equal sqrt(v_verrsq/(v_vsq+1e-06))
|
||||||
|
|
||||||
|
# define numerical Born matrix calculation
|
||||||
|
|
||||||
|
compute bornnum all born/matrix numdiff ${bdelta} myvirial
|
||||||
|
compute bornnum all born/matrix numdiff 1.0e-8 myvirial
|
||||||
|
compute born all born/matrix
|
||||||
|
variable berr vector c_bornnum-c_born
|
||||||
|
variable berrsq equal "v_berr[1]^2 + v_berr[2]^2 + v_berr[3]^2 + v_berr[4]^2 + v_berr[5]^2 + v_berr[6]^2 + v_berr[7]^2 + v_berr[8]^2 + v_berr[9]^2 + v_berr[10]^2 + v_berr[11]^2 + v_berr[12]^2 + v_berr[13]^2 + v_berr[14]^2 + v_berr[15]^2 + v_berr[16]^2 + v_berr[17]^2 + v_berr[18]^2 + v_berr[19]^2 + v_berr[20]^2 + v_berr[21]^2"
|
||||||
|
|
||||||
|
variable bsq equal "c_born[1]^2 + c_born[2]^2 + c_born[3]^2 + c_born[4]^2 + c_born[5]^2 + c_born[6]^2 + c_born[7]^2 + c_born[8]^2 + c_born[9]^2 + c_born[10]^2 + c_born[11]^2 + c_born[12]^2 + c_born[13]^2 + c_born[14]^2 + c_born[15]^2 + c_born[16]^2 + c_born[17]^2 + c_born[18]^2 + c_born[19]^2 + c_born[20]^2 + c_born[21]^2"
|
||||||
|
|
||||||
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget}))
|
||||||
|
variable brelerr equal sqrt(v_berrsq/(v_bsq+1e-06))
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr
|
||||||
|
thermo ${nthermo}
|
||||||
|
thermo 10
|
||||||
|
run ${nsteps}
|
||||||
|
run 500
|
||||||
|
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check no
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 5
|
||||||
|
ghost atom cutoff = 5
|
||||||
|
binsize = 2.5, bins = 7 7 7
|
||||||
|
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
(2) compute born/matrix, occasional, copy from (1)
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: copy
|
||||||
|
stencil: none
|
||||||
|
bin: none
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr
|
||||||
|
0 10 -6.6101864 -6.471878 947.70558 1.9110624e-09 9.4407596e-10 3.1867416e-09
|
||||||
|
10 9.9369961 -6.6093149 -6.471878 949.31222 1.3055176e-08 4.996456e-10 2.7421655e-09
|
||||||
|
20 9.7500224 -6.6067289 -6.4718779 954.07898 1.3721178e-08 5.6039795e-10 2.3689718e-09
|
||||||
|
30 9.4448115 -6.6025075 -6.4718779 961.85502 1.3813156e-08 6.8451692e-10 1.9844663e-09
|
||||||
|
40 9.0305392 -6.5967776 -6.4718777 972.39819 1.3961749e-08 3.1134064e-10 1.7915052e-09
|
||||||
|
50 8.5196068 -6.5897109 -6.4718776 985.38158 1.3996941e-08 7.0149406e-10 2.002272e-09
|
||||||
|
60 7.9273388 -6.5815192 -6.4718775 1000.4024 1.4000005e-08 3.5766629e-10 2.4944703e-09
|
||||||
|
70 7.2715879 -6.5724494 -6.4718773 1016.9932 1.3996503e-08 6.2731503e-10 1.7010533e-09
|
||||||
|
80 6.5722375 -6.5627766 -6.4718771 1034.6361 1.3973603e-08 3.1142917e-10 2.808524e-09
|
||||||
|
90 5.8505991 -6.5527956 -6.4718769 1052.7794 1.3983301e-08 3.9931135e-10 2.6118214e-09
|
||||||
|
100 5.128708 -6.542811 -6.4718767 1070.8561 1.395586e-08 2.3152413e-10 2.8742755e-09
|
||||||
|
110 4.4285344 -6.5331269 -6.4718766 1088.305 1.3938374e-08 4.2173005e-10 2.3059886e-09
|
||||||
|
120 3.7711361 -6.5240343 -6.4718764 1104.5919 1.3915264e-08 2.5458038e-10 1.4864012e-09
|
||||||
|
130 3.1757964 -6.5158002 -6.4718762 1119.2319 1.3858843e-08 5.7490448e-10 2.6191823e-09
|
||||||
|
140 2.6591997 -6.5086551 -6.4718761 1131.8095 1.3814891e-08 3.5434633e-10 2.2009364e-09
|
||||||
|
150 2.2347034 -6.5027839 -6.471876 1141.9961 1.3781115e-08 5.0639594e-10 2.9032558e-09
|
||||||
|
160 1.9117661 -6.4983173 -6.471876 1149.564 1.3734288e-08 3.1954962e-10 2.6097446e-09
|
||||||
|
170 1.6955808 -6.4953273 -6.471876 1154.3946 1.3682252e-08 3.5426781e-10 2.9605676e-09
|
||||||
|
180 1.586949 -6.4938249 -6.471876 1156.4812 1.363e-08 4.0804881e-10 2.1707904e-09
|
||||||
|
190 1.5824056 -6.4937621 -6.4718761 1155.925 1.3532637e-08 4.0767685e-10 3.0091462e-09
|
||||||
|
200 1.6745831 -6.4950371 -6.4718762 1152.926 1.3455927e-08 2.953369e-10 2.5029298e-09
|
||||||
|
210 1.8527803 -6.4975018 -6.4718763 1147.7684 1.335224e-08 3.5042319e-10 3.0550064e-09
|
||||||
|
220 2.1036825 -6.5009721 -6.4718764 1140.8026 1.3239176e-08 3.5988448e-10 2.6852683e-09
|
||||||
|
230 2.4121721 -6.5052389 -6.4718766 1132.4243 1.3090019e-08 3.5004036e-10 2.8838602e-09
|
||||||
|
240 2.7621668 -6.5100798 -6.4718767 1123.0538 1.2946525e-08 4.1216361e-10 2.1105916e-09
|
||||||
|
250 3.1374274 -6.5152701 -6.4718768 1113.1152 1.277789e-08 5.9848318e-10 2.3087106e-09
|
||||||
|
260 3.5222906 -6.5205932 -6.471877 1103.0171 1.2591089e-08 2.0080182e-10 1.6969069e-09
|
||||||
|
270 3.9022942 -6.5258491 -6.4718771 1093.1369 1.2432232e-08 4.2494727e-10 1.7375594e-09
|
||||||
|
280 4.2646753 -6.5308612 -6.4718772 1083.8072 1.2268238e-08 6.1239266e-10 1.7005135e-09
|
||||||
|
290 4.598736 -6.5354816 -6.4718772 1075.306 1.2181179e-08 4.9338341e-10 2.1326848e-09
|
||||||
|
300 4.896078 -6.5395941 -6.4718773 1067.85 1.2098274e-08 3.4564838e-10 2.4199891e-09
|
||||||
|
310 5.150715 -6.543116 -6.4718773 1061.5918 1.2184958e-08 4.2383299e-10 2.2243759e-09
|
||||||
|
320 5.3590742 -6.5459978 -6.4718773 1056.6189 1.2312948e-08 3.5194185e-10 1.3856935e-09
|
||||||
|
330 5.5199009 -6.5482222 -6.4718773 1052.9565 1.2573918e-08 4.2401322e-10 2.9882e-09
|
||||||
|
340 5.6340787 -6.5498013 -6.4718773 1050.5719 1.2821551e-08 5.8802825e-10 2.7333289e-09
|
||||||
|
350 5.7043792 -6.5507736 -6.4718772 1049.3813 1.3067314e-08 4.0014945e-10 2.3564728e-09
|
||||||
|
360 5.7351548 -6.5511992 -6.4718772 1049.2581 1.331283e-08 4.1684815e-10 1.735621e-09
|
||||||
|
370 5.7319891 -6.5511553 -6.4718771 1050.042 1.354018e-08 3.8495426e-10 2.4460056e-09
|
||||||
|
380 5.7013193 -6.5507311 -6.4718771 1051.5496 1.3734888e-08 3.5333605e-10 2.5174342e-09
|
||||||
|
390 5.6500487 -6.5500219 -6.471877 1053.5847 1.3892287e-08 3.8154957e-10 1.77358e-09
|
||||||
|
400 5.5851679 -6.5491245 -6.471877 1055.9489 1.3988171e-08 5.8769536e-10 1.9262201e-09
|
||||||
|
410 5.5134009 -6.5481319 -6.4718769 1058.4508 1.4088779e-08 3.6754739e-10 2.7586362e-09
|
||||||
|
420 5.4408957 -6.547129 -6.4718769 1060.9152 1.4139924e-08 4.9030281e-10 3.2871245e-09
|
||||||
|
430 5.3729707 -6.5461895 -6.4718768 1063.1898 1.4173041e-08 5.2345074e-10 3.5995984e-09
|
||||||
|
440 5.3139284 -6.5453729 -6.4718768 1065.1506 1.4191516e-08 5.9481094e-10 2.5005297e-09
|
||||||
|
450 5.2669383 -6.5447229 -6.4718768 1066.7054 1.4168424e-08 3.0799668e-10 2.0864191e-09
|
||||||
|
460 5.2339881 -6.5442672 -6.4718768 1067.7958 1.4163444e-08 6.3927736e-10 2.2872669e-09
|
||||||
|
470 5.2158979 -6.544017 -6.4718768 1068.3968 1.413819e-08 5.5108262e-10 4.4334972e-09
|
||||||
|
480 5.2123873 -6.5439685 -6.4718768 1068.5155 1.4083227e-08 3.9249548e-10 2.5568235e-09
|
||||||
|
490 5.2221849 -6.544104 -6.4718768 1068.188 1.4035287e-08 2.1988631e-10 2.1264034e-09
|
||||||
|
500 5.2431716 -6.5443943 -6.4718768 1067.4759 1.3968666e-08 3.9100701e-10 3.290368e-09
|
||||||
|
Loop time of 0.170182 on 4 procs for 500 steps with 108 atoms
|
||||||
|
|
||||||
|
Performance: 253.846 ns/day, 0.095 hours/ns, 2938.035 timesteps/s
|
||||||
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.0012069 | 0.0012994 | 0.0013512 | 0.2 | 0.76
|
||||||
|
Neigh | 0.0048233 | 0.0050244 | 0.0053881 | 0.3 | 2.95
|
||||||
|
Comm | 0.0072462 | 0.0078013 | 0.008175 | 0.4 | 4.58
|
||||||
|
Output | 0.0080632 | 0.0081244 | 0.0082899 | 0.1 | 4.77
|
||||||
|
Modify | 0.1476 | 0.14764 | 0.14768 | 0.0 | 86.75
|
||||||
|
Other | | 0.0002961 | | | 0.17
|
||||||
|
|
||||||
|
Nlocal: 27 ave 31 max 24 min
|
||||||
|
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||||
|
Nghost: 135 ave 138 max 131 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||||
|
Neighs: 162 ave 191 max 148 min
|
||||||
|
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 648
|
||||||
|
Ave neighs/atom = 6
|
||||||
|
Neighbor list builds = 500
|
||||||
|
Dangerous builds not checked
|
||||||
|
Total wall time: 0:00:00
|
||||||
@ -1,175 +0,0 @@
|
|||||||
LAMMPS (7 Jan 2022)
|
|
||||||
# Numerical difference calculation
|
|
||||||
# of error in forces and virial stress
|
|
||||||
|
|
||||||
# adjustable parameters
|
|
||||||
|
|
||||||
variable nsteps index 500 # length of run
|
|
||||||
variable nthermo index 10 # thermo output interval
|
|
||||||
variable ndump index 500 # dump output interval
|
|
||||||
variable nlat index 3 # size of box
|
|
||||||
variable fdelta index 1.0e-4 # displacement size
|
|
||||||
variable vdelta index 1.0e-6 # strain size
|
|
||||||
variable temp index 10.0 # temperature
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
atom_modify map yes
|
|
||||||
lattice fcc 5.358000
|
|
||||||
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
|
||||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
|
||||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
|
||||||
region box block 0 3 0 3 0 ${nlat}
|
|
||||||
region box block 0 3 0 3 0 3
|
|
||||||
create_box 1 box
|
|
||||||
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 108 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
mass 1 39.903
|
|
||||||
|
|
||||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
|
||||||
velocity all create 10.0 2357 mom yes dist gaussian
|
|
||||||
|
|
||||||
pair_style lj/cubic
|
|
||||||
pair_coeff * * 0.0102701 3.42
|
|
||||||
|
|
||||||
neighbor 0.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check no
|
|
||||||
|
|
||||||
timestep 0.001
|
|
||||||
fix nve all nve
|
|
||||||
|
|
||||||
# define numerical force calculation
|
|
||||||
|
|
||||||
fix numforce all numdiff ${nthermo} ${fdelta}
|
|
||||||
fix numforce all numdiff 10 ${fdelta}
|
|
||||||
fix numforce all numdiff 10 1.0e-4
|
|
||||||
variable ferrx atom f_numforce[1]-fx
|
|
||||||
variable ferry atom f_numforce[2]-fy
|
|
||||||
variable ferrz atom f_numforce[3]-fz
|
|
||||||
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
|
||||||
compute faverrsq all reduce ave v_ferrsq
|
|
||||||
variable fsq atom fx^2+fy^2+fz^2
|
|
||||||
compute favsq all reduce ave v_fsq
|
|
||||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
|
||||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
|
||||||
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
|
||||||
|
|
||||||
# define numerical virial stress tensor calculation
|
|
||||||
|
|
||||||
compute myvirial all pressure NULL virial
|
|
||||||
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
|
||||||
fix numvirial all numdiff/virial 10 ${vdelta}
|
|
||||||
fix numvirial all numdiff/virial 10 1.0e-6
|
|
||||||
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
|
||||||
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
|
||||||
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
|
||||||
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
|
||||||
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
|
||||||
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
|
||||||
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
|
||||||
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
|
||||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
|
||||||
thermo ${nthermo}
|
|
||||||
thermo 10
|
|
||||||
run ${nsteps}
|
|
||||||
run 500
|
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check no
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5.9407173
|
|
||||||
ghost atom cutoff = 5.9407173
|
|
||||||
binsize = 2.9703587, bins = 6 6 6
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/cubic, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.083 | 6.083 | 6.083 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
|
|
||||||
0 10 -7.0259569 -6.8876486 28.564278 19203.344 1.5660292e-06
|
|
||||||
10 9.9376583 -7.0250947 -6.8876486 30.254762 1.5040965e-08 2.1991382e-07
|
|
||||||
20 9.7520139 -7.022527 -6.8876485 35.28505 1.4756358e-08 2.6265315e-06
|
|
||||||
30 9.4477557 -7.0183188 -6.8876485 43.519863 1.4688198e-08 2.6356166e-07
|
|
||||||
40 9.0330215 -7.0125826 -6.8876484 54.727797 1.4637921e-08 5.2292327e-08
|
|
||||||
50 8.5192918 -7.0054772 -6.8876483 68.585553 1.4587854e-08 7.1324716e-08
|
|
||||||
60 7.9212026 -6.997205 -6.8876481 84.684636 1.4525561e-08 3.1108149e-08
|
|
||||||
70 7.2562592 -6.9880081 -6.8876479 102.54088 1.450885e-08 3.2311094e-08
|
|
||||||
80 6.5444294 -6.9781627 -6.8876478 121.60715 1.4444738e-08 2.1776998e-08
|
|
||||||
90 5.8075961 -6.9679715 -6.8876476 141.2895 1.4493562e-08 2.0400898e-08
|
|
||||||
100 5.0688629 -6.957754 -6.8876474 160.9668 1.445455e-08 1.2636688e-08
|
|
||||||
110 4.3517145 -6.947835 -6.8876472 180.0135 1.4460371e-08 1.2528038e-08
|
|
||||||
120 3.6790589 -6.9385314 -6.887647 197.82486 1.4371757e-08 1.4489522e-08
|
|
||||||
130 3.0721984 -6.9301379 -6.8876468 213.84331 1.4364708e-08 1.2461922e-08
|
|
||||||
140 2.5497991 -6.9229125 -6.8876467 227.58429 1.4330926e-08 9.3913926e-09
|
|
||||||
150 2.1269443 -6.917064 -6.8876466 238.6596 1.4287002e-08 4.1510266e-09
|
|
||||||
160 1.8143642 -6.9127407 -6.8876465 246.79599 1.4282669e-08 7.7048281e-09
|
|
||||||
170 1.6179191 -6.9100237 -6.8876465 251.84748 1.42726e-08 1.2719973e-08
|
|
||||||
180 1.5383946 -6.9089239 -6.8876466 253.79991 1.4236534e-08 8.1200831e-09
|
|
||||||
190 1.5716287 -6.9093836 -6.8876467 252.76745 1.41706e-08 6.5670612e-09
|
|
||||||
200 1.7089493 -6.911283 -6.8876468 248.98142 1.4096463e-08 1.1685863e-08
|
|
||||||
210 1.9378716 -6.9144493 -6.8876469 242.77289 1.4008978e-08 1.1226902e-08
|
|
||||||
220 2.2429731 -6.9186692 -6.887647 234.55055 1.3886901e-08 9.9914102e-09
|
|
||||||
230 2.606862 -6.9237023 -6.8876472 224.77626 1.3864576e-08 1.1540228e-08
|
|
||||||
240 3.0111524 -6.9292941 -6.8876474 213.93996 1.3696314e-08 1.1697747e-08
|
|
||||||
250 3.4373794 -6.9351893 -6.8876475 202.53583 1.3626701e-08 1.0398197e-08
|
|
||||||
260 3.8678047 -6.9411426 -6.8876476 191.04084 1.3489489e-08 6.6603364e-09
|
|
||||||
270 4.2860853 -6.9469279 -6.8876478 179.89646 1.3312014e-08 1.1687917e-08
|
|
||||||
280 4.6777954 -6.9523457 -6.8876479 169.49404 1.3081144e-08 1.1336675e-08
|
|
||||||
290 5.030805 -6.9572282 -6.887648 160.16371 1.2947385e-08 1.7342825e-08
|
|
||||||
300 5.3355278 -6.9614428 -6.887648 152.16682 1.2893673e-08 1.7510534e-08
|
|
||||||
310 5.5850532 -6.964894 -6.887648 145.69148 1.2842022e-08 1.2782546e-08
|
|
||||||
320 5.7751794 -6.9675236 -6.8876481 140.85102 1.2903488e-08 1.5319437e-08
|
|
||||||
330 5.9043601 -6.9693103 -6.887648 137.68497 1.3076809e-08 1.1208999e-08
|
|
||||||
340 5.9735784 -6.9702676 -6.887648 136.16232 1.3296904e-08 1.891087e-08
|
|
||||||
350 5.9861549 -6.9704415 -6.887648 136.18679 1.3504051e-08 2.5783601e-08
|
|
||||||
360 5.947496 -6.9699067 -6.8876479 137.60397 1.3731112e-08 2.0556839e-08
|
|
||||||
370 5.8647874 -6.9687627 -6.8876478 140.2101 1.4009878e-08 2.1771736e-08
|
|
||||||
380 5.7466376 -6.9671285 -6.8876477 143.76234 1.4092054e-08 1.1085162e-08
|
|
||||||
390 5.6026773 -6.9651374 -6.8876477 147.99019 1.4282872e-08 2.0221602e-08
|
|
||||||
400 5.4431231 -6.9629305 -6.8876476 152.60787 1.4317739e-08 1.7076065e-08
|
|
||||||
410 5.2783192 -6.960651 -6.8876475 157.32722 1.4415075e-08 2.5031776e-08
|
|
||||||
420 5.1182723 -6.9584374 -6.8876474 161.87063 1.4441435e-08 2.2519289e-08
|
|
||||||
430 4.9722 -6.956417 -6.8876473 165.98344 1.4550624e-08 2.4512613e-08
|
|
||||||
440 4.8481153 -6.9547008 -6.8876473 169.44527 1.4544672e-08 1.4758301e-08
|
|
||||||
450 4.7524707 -6.9533779 -6.8876472 172.07964 1.4546492e-08 1.324687e-08
|
|
||||||
460 4.6898817 -6.9525122 -6.8876472 173.76132 1.4537475e-08 1.351367e-08
|
|
||||||
470 4.6629495 -6.9521397 -6.8876472 174.42109 1.4530458e-08 1.521106e-08
|
|
||||||
480 4.6721922 -6.9522675 -6.8876472 174.04742 1.4543785e-08 1.0905422e-08
|
|
||||||
490 4.7160887 -6.9528747 -6.8876473 172.68525 1.4545591e-08 2.0128525e-08
|
|
||||||
500 4.7912313 -6.953914 -6.8876473 170.43183 1.4438981e-08 1.6062775e-08
|
|
||||||
Loop time of 0.837333 on 1 procs for 500 steps with 108 atoms
|
|
||||||
|
|
||||||
Performance: 51.592 ns/day, 0.465 hours/ns, 597.134 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0097726 | 0.0097726 | 0.0097726 | 0.0 | 1.17
|
|
||||||
Neigh | 0.03095 | 0.03095 | 0.03095 | 0.0 | 3.70
|
|
||||||
Comm | 0.005564 | 0.005564 | 0.005564 | 0.0 | 0.66
|
|
||||||
Output | 0.0042451 | 0.0042451 | 0.0042451 | 0.0 | 0.51
|
|
||||||
Modify | 0.78618 | 0.78618 | 0.78618 | 0.0 | 93.89
|
|
||||||
Other | | 0.0006258 | | | 0.07
|
|
||||||
|
|
||||||
Nlocal: 108 ave 108 max 108 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 558 ave 558 max 558 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 972 ave 972 max 972 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 972
|
|
||||||
Ave neighs/atom = 9
|
|
||||||
Neighbor list builds = 500
|
|
||||||
Dangerous builds not checked
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,175 +0,0 @@
|
|||||||
LAMMPS (7 Jan 2022)
|
|
||||||
# Numerical difference calculation
|
|
||||||
# of error in forces and virial stress
|
|
||||||
|
|
||||||
# adjustable parameters
|
|
||||||
|
|
||||||
variable nsteps index 500 # length of run
|
|
||||||
variable nthermo index 10 # thermo output interval
|
|
||||||
variable ndump index 500 # dump output interval
|
|
||||||
variable nlat index 3 # size of box
|
|
||||||
variable fdelta index 1.0e-4 # displacement size
|
|
||||||
variable vdelta index 1.0e-6 # strain size
|
|
||||||
variable temp index 10.0 # temperature
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
atom_modify map yes
|
|
||||||
lattice fcc 5.358000
|
|
||||||
Lattice spacing in x,y,z = 5.358 5.358 5.358
|
|
||||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
|
||||||
region box block 0 3 0 ${nlat} 0 ${nlat}
|
|
||||||
region box block 0 3 0 3 0 ${nlat}
|
|
||||||
region box block 0 3 0 3 0 3
|
|
||||||
create_box 1 box
|
|
||||||
Created orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 box
|
|
||||||
Created 108 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (16.074 16.074 16.074)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
mass 1 39.903
|
|
||||||
|
|
||||||
velocity all create ${temp} 2357 mom yes dist gaussian
|
|
||||||
velocity all create 10.0 2357 mom yes dist gaussian
|
|
||||||
|
|
||||||
pair_style lj/cubic
|
|
||||||
pair_coeff * * 0.0102701 3.42
|
|
||||||
|
|
||||||
neighbor 0.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check no
|
|
||||||
|
|
||||||
timestep 0.001
|
|
||||||
fix nve all nve
|
|
||||||
|
|
||||||
# define numerical force calculation
|
|
||||||
|
|
||||||
fix numforce all numdiff ${nthermo} ${fdelta}
|
|
||||||
fix numforce all numdiff 10 ${fdelta}
|
|
||||||
fix numforce all numdiff 10 1.0e-4
|
|
||||||
variable ferrx atom f_numforce[1]-fx
|
|
||||||
variable ferry atom f_numforce[2]-fy
|
|
||||||
variable ferrz atom f_numforce[3]-fz
|
|
||||||
variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
|
|
||||||
compute faverrsq all reduce ave v_ferrsq
|
|
||||||
variable fsq atom fx^2+fy^2+fz^2
|
|
||||||
compute favsq all reduce ave v_fsq
|
|
||||||
variable frelerr equal sqrt(c_faverrsq/c_favsq)
|
|
||||||
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
|
|
||||||
dump errors all custom 500 force_error.dump v_ferrx v_ferry v_ferrz
|
|
||||||
|
|
||||||
# define numerical virial stress tensor calculation
|
|
||||||
|
|
||||||
compute myvirial all pressure NULL virial
|
|
||||||
fix numvirial all numdiff/virial ${nthermo} ${vdelta}
|
|
||||||
fix numvirial all numdiff/virial 10 ${vdelta}
|
|
||||||
fix numvirial all numdiff/virial 10 1.0e-6
|
|
||||||
variable errxx equal f_numvirial[1]-c_myvirial[1]
|
|
||||||
variable erryy equal f_numvirial[2]-c_myvirial[2]
|
|
||||||
variable errzz equal f_numvirial[3]-c_myvirial[3]
|
|
||||||
variable erryz equal f_numvirial[4]-c_myvirial[6]
|
|
||||||
variable errxz equal f_numvirial[5]-c_myvirial[5]
|
|
||||||
variable errxy equal f_numvirial[6]-c_myvirial[4]
|
|
||||||
variable verrsq equal "v_errxx^2 + v_erryy^2 + v_errzz^2 + v_erryz^2 + v_errxz^2 + v_errxy^2"
|
|
||||||
variable vsq equal "c_myvirial[1]^2 + c_myvirial[3]^2 + c_myvirial[3]^2 + c_myvirial[4]^2 + c_myvirial[5]^2 + c_myvirial[6]^2"
|
|
||||||
variable vrelerr equal sqrt(v_verrsq/v_vsq)
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
|
|
||||||
thermo ${nthermo}
|
|
||||||
thermo 10
|
|
||||||
run ${nsteps}
|
|
||||||
run 500
|
|
||||||
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check no
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 5.9407173
|
|
||||||
ghost atom cutoff = 5.9407173
|
|
||||||
binsize = 2.9703587, bins = 6 6 6
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/cubic, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.067 | 6.067 | 6.067 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press v_frelerr v_vrelerr
|
|
||||||
0 10 -7.0259569 -6.8876486 28.564278 10664.391 9.1481187e-08
|
|
||||||
10 9.9388179 -7.0251107 -6.8876486 30.21736 1.4771865e-08 1.3452512e-07
|
|
||||||
20 9.7572185 -7.022599 -6.8876485 35.123527 1.437525e-08 8.0966999e-07
|
|
||||||
30 9.4606673 -7.0184974 -6.8876484 43.132052 1.4375468e-08 1.990012e-08
|
|
||||||
40 9.0579092 -7.0129268 -6.8876483 54.000927 1.4350331e-08 1.7239028e-08
|
|
||||||
50 8.5607685 -7.0060508 -6.8876482 67.403151 1.4353284e-08 7.813181e-09
|
|
||||||
60 7.9838726 -6.9980717 -6.8876481 82.935358 1.4398078e-08 2.022316e-08
|
|
||||||
70 7.3442875 -6.9892255 -6.8876479 100.12892 1.434409e-08 7.5938179e-09
|
|
||||||
80 6.6610579 -6.9797757 -6.8876477 118.46358 1.4324787e-08 7.1972571e-09
|
|
||||||
90 5.9546462 -6.9700053 -6.8876476 137.38365 1.4322718e-08 4.3978378e-09
|
|
||||||
100 5.2462727 -6.9602077 -6.8876474 156.31651 1.4273172e-08 4.6728038e-09
|
|
||||||
110 4.5571706 -6.9506767 -6.8876472 174.69294 1.4266163e-08 3.522225e-09
|
|
||||||
120 3.9077807 -6.9416949 -6.887647 191.96859 1.42241e-08 3.5357511e-09
|
|
||||||
130 3.3169241 -6.9335227 -6.8876469 207.64566 1.4203813e-08 2.5182488e-09
|
|
||||||
140 2.8010028 -6.926387 -6.8876468 221.29333 1.4164215e-08 2.3112509e-09
|
|
||||||
150 2.3732854 -6.9204712 -6.8876467 232.5658 1.4134122e-08 1.9368963e-09
|
|
||||||
160 2.0433329 -6.9159076 -6.8876466 241.21647 1.4095473e-08 3.6806452e-09
|
|
||||||
170 1.8166184 -6.912772 -6.8876466 247.10715 1.4049531e-08 2.5319322e-09
|
|
||||||
180 1.6943727 -6.9110813 -6.8876467 250.21143 1.3997912e-08 1.952404e-09
|
|
||||||
190 1.6736731 -6.910795 -6.8876467 250.61203 1.3915487e-08 1.4271767e-09
|
|
||||||
200 1.7477659 -6.9118199 -6.8876468 248.49223 1.3850618e-08 2.4515718e-09
|
|
||||||
210 1.9065921 -6.9140167 -6.8876469 244.12226 1.3747916e-08 1.7957531e-09
|
|
||||||
220 2.1374676 -6.91721 -6.887647 237.84173 1.3674779e-08 2.6613511e-09
|
|
||||||
230 2.4258607 -6.9211989 -6.8876472 230.0395 1.3565712e-08 3.0777067e-09
|
|
||||||
240 2.7562034 -6.9257679 -6.8876473 221.13265 1.3440442e-08 1.7111501e-09
|
|
||||||
250 3.1126827 -6.9306984 -6.8876474 211.54566 1.3270914e-08 1.6690112e-09
|
|
||||||
260 3.4799641 -6.9357784 -6.8876476 201.69126 1.3105092e-08 2.1637558e-09
|
|
||||||
270 3.8438148 -6.9408108 -6.8876477 191.95361 1.2962846e-08 4.4613506e-09
|
|
||||||
280 4.191607 -6.9456212 -6.8876478 182.6745 1.2846383e-08 3.3730203e-09
|
|
||||||
290 4.5126922 -6.9500621 -6.8876478 174.14285 1.2710692e-08 2.2809889e-09
|
|
||||||
300 4.7986487 -6.9540172 -6.8876479 166.58747 1.2657778e-08 6.9880891e-09
|
|
||||||
310 5.0434083 -6.9574025 -6.8876479 160.17316 1.266381e-08 4.2486217e-09
|
|
||||||
320 5.243275 -6.9601668 -6.8876479 154.99974 1.279856e-08 5.1505673e-09
|
|
||||||
330 5.3968455 -6.9622908 -6.8876479 151.1038 1.2981831e-08 3.3339333e-09
|
|
||||||
340 5.5048468 -6.9637845 -6.8876479 148.46296 1.3159021e-08 1.7881393e-09
|
|
||||||
350 5.569902 -6.9646843 -6.8876479 147.00205 1.3439465e-08 5.6876219e-09
|
|
||||||
360 5.5962378 -6.9650485 -6.8876478 146.60113 1.3645943e-08 7.233847e-09
|
|
||||||
370 5.5893468 -6.9649531 -6.8876478 147.10471 1.3829581e-08 4.5514318e-09
|
|
||||||
380 5.5556199 -6.9644866 -6.8876477 148.33195 1.4005893e-08 4.2971846e-09
|
|
||||||
390 5.5019639 -6.9637444 -6.8876476 150.08725 1.4157454e-08 3.3564262e-09
|
|
||||||
400 5.4354239 -6.962824 -6.8876476 152.17073 1.4226422e-08 4.2393923e-09
|
|
||||||
410 5.3628267 -6.9618199 -6.8876475 154.38825 1.4302679e-08 3.8937698e-09
|
|
||||||
420 5.2904639 -6.960819 -6.8876475 156.56034 1.4381099e-08 4.315875e-09
|
|
||||||
430 5.2238282 -6.9598973 -6.8876474 158.52969 1.4426567e-08 4.2658185e-09
|
|
||||||
440 5.1674149 -6.9591171 -6.8876474 160.16704 1.4453381e-08 5.7055268e-09
|
|
||||||
450 5.1245913 -6.9585248 -6.8876474 161.37513 1.4449488e-08 4.4308801e-09
|
|
||||||
460 5.0975361 -6.9581506 -6.8876474 162.09077 1.4445596e-08 5.8269923e-09
|
|
||||||
470 5.0872416 -6.9580082 -6.8876474 162.28517 1.4444348e-08 4.8263194e-09
|
|
||||||
480 5.0935712 -6.9580957 -6.8876474 161.96268 1.4411666e-08 6.222228e-09
|
|
||||||
490 5.115362 -6.9583971 -6.8876474 161.15816 1.4369716e-08 3.3926077e-09
|
|
||||||
500 5.1505605 -6.958884 -6.8876474 159.9333 1.4288515e-08 3.8845251e-09
|
|
||||||
Loop time of 0.252598 on 4 procs for 500 steps with 108 atoms
|
|
||||||
|
|
||||||
Performance: 171.023 ns/day, 0.140 hours/ns, 1979.430 timesteps/s
|
|
||||||
99.8% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0021545 | 0.0022845 | 0.0023794 | 0.2 | 0.90
|
|
||||||
Neigh | 0.0063887 | 0.0067604 | 0.0069752 | 0.3 | 2.68
|
|
||||||
Comm | 0.01048 | 0.010916 | 0.011408 | 0.3 | 4.32
|
|
||||||
Output | 0.0026603 | 0.0027399 | 0.0029738 | 0.3 | 1.08
|
|
||||||
Modify | 0.2295 | 0.22952 | 0.22954 | 0.0 | 90.86
|
|
||||||
Other | | 0.0003814 | | | 0.15
|
|
||||||
|
|
||||||
Nlocal: 27 ave 29 max 25 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
|
||||||
Nghost: 325 ave 327 max 323 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
|
||||||
Neighs: 243 ave 273 max 228 min
|
|
||||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 972
|
|
||||||
Ave neighs/atom = 9
|
|
||||||
Neighbor list builds = 500
|
|
||||||
Dangerous builds not checked
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -453,6 +453,8 @@
|
|||||||
/compute_basal_atom.h
|
/compute_basal_atom.h
|
||||||
/compute_body_local.cpp
|
/compute_body_local.cpp
|
||||||
/compute_body_local.h
|
/compute_body_local.h
|
||||||
|
/compute_born_matrix.cpp
|
||||||
|
/compute_born_matrix.h
|
||||||
/compute_cnp_atom.cpp
|
/compute_cnp_atom.cpp
|
||||||
/compute_cnp_atom.h
|
/compute_cnp_atom.h
|
||||||
/compute_damage_atom.cpp
|
/compute_damage_atom.cpp
|
||||||
|
|||||||
1221
src/EXTRA-COMPUTE/compute_born_matrix.cpp
Normal file
1221
src/EXTRA-COMPUTE/compute_born_matrix.cpp
Normal file
File diff suppressed because it is too large
Load Diff
97
src/EXTRA-COMPUTE/compute_born_matrix.h
Normal file
97
src/EXTRA-COMPUTE/compute_born_matrix.h
Normal file
@ -0,0 +1,97 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://www.lammps.org/, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/*------------------------------------------------------------------------
|
||||||
|
Contributing Authors : Germain Clavier (TUe), Aidan Thompson (Sandia)
|
||||||
|
--------------------------------------------------------------------------*/
|
||||||
|
|
||||||
|
#ifdef COMPUTE_CLASS
|
||||||
|
// clang-format off
|
||||||
|
ComputeStyle(born/matrix,ComputeBornMatrix);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_COMPUTE_BORN_MATRIX_H
|
||||||
|
#define LMP_COMPUTE_BORN_MATRIX_H
|
||||||
|
|
||||||
|
#include "compute.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class ComputeBornMatrix : public Compute {
|
||||||
|
public:
|
||||||
|
ComputeBornMatrix(class LAMMPS *, int, char **);
|
||||||
|
~ComputeBornMatrix() override;
|
||||||
|
void init() override;
|
||||||
|
void init_list(int, class NeighList *) override;
|
||||||
|
void compute_vector() override;
|
||||||
|
double memory_usage() override;
|
||||||
|
|
||||||
|
private:
|
||||||
|
// Born matrix contributions
|
||||||
|
|
||||||
|
void compute_pairs(); // pair and manybody
|
||||||
|
void compute_bonds(); // bonds
|
||||||
|
void compute_angles(); // angles
|
||||||
|
void compute_dihedrals(); // dihedrals
|
||||||
|
void compute_numdiff(); // stress virial finite differences
|
||||||
|
void displace_atoms(int, int, double); // displace atoms
|
||||||
|
void force_clear(int); // zero out force array
|
||||||
|
void update_virial(); // recalculate the virial
|
||||||
|
void restore_atoms(int, int); // restore atom positions
|
||||||
|
void virial_addon(); // restore atom positions
|
||||||
|
void reallocate(); // grow the atom arrays
|
||||||
|
|
||||||
|
int me; // process rank
|
||||||
|
int nvalues; // length of elastic tensor
|
||||||
|
int numflag; // 1 if using finite differences
|
||||||
|
double numdelta; // size of finite strain
|
||||||
|
int maxatom; // allocated size of atom arrays
|
||||||
|
|
||||||
|
int pairflag, bondflag, angleflag;
|
||||||
|
int dihedflag, impflag, kspaceflag;
|
||||||
|
|
||||||
|
double *values_local, *values_global;
|
||||||
|
double pos, pos1, dt, nktv2p, ftm2v;
|
||||||
|
class NeighList *list;
|
||||||
|
|
||||||
|
char *id_virial; // name of virial compute
|
||||||
|
class Compute *compute_virial; // pointer to virial compute
|
||||||
|
|
||||||
|
static constexpr int NDIR_VIRIAL = 6; // dimension of virial and strain vectors
|
||||||
|
static constexpr int NXYZ_VIRIAL = 3; // number of Cartesian coordinates
|
||||||
|
int revalbe[NDIR_VIRIAL][NDIR_VIRIAL];
|
||||||
|
int virialVtoV[NDIR_VIRIAL];
|
||||||
|
double **temp_x; // original coords
|
||||||
|
double **temp_f; // original forces
|
||||||
|
double fixedpoint[NXYZ_VIRIAL]; // displacement field origin
|
||||||
|
int dirlist[NDIR_VIRIAL][2]; // strain cartesian indices
|
||||||
|
};
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: ... style does not support compute born/matrix
|
||||||
|
|
||||||
|
Some component of the force field (pair, bond, angle...) does not provide
|
||||||
|
a function to return the Born term contribution.
|
||||||
|
*/
|
||||||
@ -25,6 +25,7 @@
|
|||||||
#include "force.h"
|
#include "force.h"
|
||||||
#include "memory.h"
|
#include "memory.h"
|
||||||
#include "neighbor.h"
|
#include "neighbor.h"
|
||||||
|
#include "domain.h"
|
||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
|
|
||||||
@ -39,6 +40,7 @@ DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp)
|
|||||||
{
|
{
|
||||||
writedata = 1;
|
writedata = 1;
|
||||||
a = nullptr;
|
a = nullptr;
|
||||||
|
born_matrix_enable = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -336,3 +338,64 @@ void DihedralNHarmonic::write_data(FILE *fp)
|
|||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------*/
|
||||||
|
|
||||||
|
void DihedralNHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4,
|
||||||
|
double &dudih, double &du2dih) {
|
||||||
|
int i,type;
|
||||||
|
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||||
|
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||||
|
double c,s,kf;
|
||||||
|
|
||||||
|
int **dihedrallist = neighbor->dihedrallist;
|
||||||
|
double **x = atom->x;
|
||||||
|
|
||||||
|
int ndihedrallist = neighbor->ndihedrallist;
|
||||||
|
type = dihedrallist[nd][4];
|
||||||
|
|
||||||
|
vb1x = x[i1][0] - x[i2][0];
|
||||||
|
vb1y = x[i1][1] - x[i2][1];
|
||||||
|
vb1z = x[i1][2] - x[i2][2];
|
||||||
|
|
||||||
|
vb2x = x[i3][0] - x[i2][0];
|
||||||
|
vb2y = x[i3][1] - x[i2][1];
|
||||||
|
vb2z = x[i3][2] - x[i2][2];
|
||||||
|
|
||||||
|
vb2xm = -vb2x;
|
||||||
|
vb2ym = -vb2y;
|
||||||
|
vb2zm = -vb2z;
|
||||||
|
|
||||||
|
vb3x = x[i4][0] - x[i3][0];
|
||||||
|
vb3y = x[i4][1] - x[i3][1];
|
||||||
|
vb3z = x[i4][2] - x[i3][2];
|
||||||
|
|
||||||
|
// c,s calculation
|
||||||
|
|
||||||
|
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||||
|
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||||
|
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||||
|
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||||
|
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||||
|
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||||
|
|
||||||
|
rasq = ax*ax + ay*ay + az*az;
|
||||||
|
rbsq = bx*bx + by*by + bz*bz;
|
||||||
|
|
||||||
|
ra2inv = rb2inv = 0.0;
|
||||||
|
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||||
|
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||||
|
rabinv = sqrt(ra2inv*rb2inv);
|
||||||
|
|
||||||
|
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||||
|
|
||||||
|
dudih = 0.0;
|
||||||
|
du2dih = 0.0;
|
||||||
|
for (i = 1; i < nterms[type]; i++) {
|
||||||
|
dudih += this->a[type][i]*i*pow(c,i-1);
|
||||||
|
}
|
||||||
|
|
||||||
|
for (i = 2; i < nterms[type]; i++) {
|
||||||
|
du2dih += this->a[type][i]*i*(i-1)*pow(c, i-2);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|||||||
@ -33,6 +33,7 @@ class DihedralNHarmonic : public Dihedral {
|
|||||||
void write_restart(FILE *) override;
|
void write_restart(FILE *) override;
|
||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
void write_data(FILE *) override;
|
void write_data(FILE *) override;
|
||||||
|
void born_matrix(int /*dtype*/, int, int, int, int, double &, double &) override;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
int *nterms;
|
int *nterms;
|
||||||
|
|||||||
@ -29,7 +29,10 @@ using MathConst::MY_PI;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
AngleCosine::AngleCosine(LAMMPS *_lmp) : Angle(_lmp) {}
|
AngleCosine::AngleCosine(LAMMPS *_lmp) : Angle(_lmp)
|
||||||
|
{
|
||||||
|
born_matrix_enable = 1;
|
||||||
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -235,6 +238,14 @@ double AngleCosine::single(int type, int i1, int i2, int i3)
|
|||||||
return k[type] * (1.0 + c);
|
return k[type] * (1.0 + c);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void AngleCosine::born_matrix(int type, int i1, int i2, int i3, double &du, double &du2)
|
||||||
|
{
|
||||||
|
du2 = 0;
|
||||||
|
du = k[type];
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
return ptr to internal members upon request
|
return ptr to internal members upon request
|
||||||
------------------------------------------------------------------------ */
|
------------------------------------------------------------------------ */
|
||||||
|
|||||||
@ -35,6 +35,7 @@ class AngleCosine : public Angle {
|
|||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
void write_data(FILE *) override;
|
void write_data(FILE *) override;
|
||||||
double single(int, int, int, int) override;
|
double single(int, int, int, int) override;
|
||||||
|
void born_matrix(int type, int i1, int i2, int i3, double& du, double& du2) override;
|
||||||
void *extract(const char *, int &) override;
|
void *extract(const char *, int &) override;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|||||||
@ -38,6 +38,7 @@ AngleCosineSquared::AngleCosineSquared(LAMMPS *_lmp) : Angle(_lmp)
|
|||||||
{
|
{
|
||||||
k = nullptr;
|
k = nullptr;
|
||||||
theta0 = nullptr;
|
theta0 = nullptr;
|
||||||
|
born_matrix_enable = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -262,3 +263,32 @@ double AngleCosineSquared::single(int type, int i1, int i2, int i3)
|
|||||||
double tk = k[type] * dcostheta;
|
double tk = k[type] * dcostheta;
|
||||||
return tk * dcostheta;
|
return tk * dcostheta;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void AngleCosineSquared::born_matrix(int type, int i1, int i2, int i3, double& du, double& du2)
|
||||||
|
{
|
||||||
|
double **x = atom->x;
|
||||||
|
|
||||||
|
double delx1 = x[i1][0] - x[i2][0];
|
||||||
|
double dely1 = x[i1][1] - x[i2][1];
|
||||||
|
double delz1 = x[i1][2] - x[i2][2];
|
||||||
|
domain->minimum_image(delx1,dely1,delz1);
|
||||||
|
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
|
||||||
|
|
||||||
|
double delx2 = x[i3][0] - x[i2][0];
|
||||||
|
double dely2 = x[i3][1] - x[i2][1];
|
||||||
|
double delz2 = x[i3][2] - x[i2][2];
|
||||||
|
domain->minimum_image(delx2,dely2,delz2);
|
||||||
|
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
|
||||||
|
|
||||||
|
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
|
||||||
|
c /= r1*r2;
|
||||||
|
if (c > 1.0) c = 1.0;
|
||||||
|
if (c < -1.0) c = -1.0;
|
||||||
|
|
||||||
|
double dcostheta = c - cos(theta0[type]);
|
||||||
|
double tk = k[type] * dcostheta;
|
||||||
|
du2 = 2*k[type];
|
||||||
|
du = du2*dcostheta;
|
||||||
|
}
|
||||||
|
|||||||
@ -35,6 +35,7 @@ class AngleCosineSquared : public Angle {
|
|||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
void write_data(FILE *) override;
|
void write_data(FILE *) override;
|
||||||
double single(int, int, int, int) override;
|
double single(int, int, int, int) override;
|
||||||
|
void born_matrix(int type, int i1, int i2, int i3, double& du, double& du2) override;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
double *k, *theta0;
|
double *k, *theta0;
|
||||||
|
|||||||
@ -27,7 +27,10 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
BondHarmonic::BondHarmonic(LAMMPS *_lmp) : Bond(_lmp) {}
|
BondHarmonic::BondHarmonic(LAMMPS *_lmp) : Bond(_lmp)
|
||||||
|
{
|
||||||
|
born_matrix_enable = 1;
|
||||||
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -197,6 +200,20 @@ double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, double &
|
|||||||
return rk * dr;
|
return rk * dr;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void BondHarmonic::born_matrix(int type, double rsq, int /*i*/, int /*j*/,
|
||||||
|
double &du, double& du2)
|
||||||
|
{
|
||||||
|
double r = sqrt(rsq);
|
||||||
|
double dr = r - r0[type];
|
||||||
|
du2 = 0.0;
|
||||||
|
du = 0.0;
|
||||||
|
du2 = 2*k[type];
|
||||||
|
if (r > 0.0) du = du2*dr;
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
return ptr to internal members upon request
|
return ptr to internal members upon request
|
||||||
------------------------------------------------------------------------ */
|
------------------------------------------------------------------------ */
|
||||||
|
|||||||
@ -35,6 +35,7 @@ class BondHarmonic : public Bond {
|
|||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
void write_data(FILE *) override;
|
void write_data(FILE *) override;
|
||||||
double single(int, double, int, int, double &) override;
|
double single(int, double, int, int, double &) override;
|
||||||
|
void born_matrix(int, double, int, int, double &, double &) override;
|
||||||
void *extract(const char *, int &) override;
|
void *extract(const char *, int &) override;
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|||||||
@ -34,6 +34,7 @@ Angle::Angle(LAMMPS *_lmp) : Pointers(_lmp)
|
|||||||
|
|
||||||
allocated = 0;
|
allocated = 0;
|
||||||
suffix_flag = Suffix::NONE;
|
suffix_flag = Suffix::NONE;
|
||||||
|
born_matrix_enable = 0;
|
||||||
|
|
||||||
maxeatom = maxvatom = maxcvatom = 0;
|
maxeatom = maxvatom = maxcvatom = 0;
|
||||||
eatom = nullptr;
|
eatom = nullptr;
|
||||||
|
|||||||
@ -25,7 +25,8 @@ class Angle : protected Pointers {
|
|||||||
public:
|
public:
|
||||||
int allocated;
|
int allocated;
|
||||||
int *setflag;
|
int *setflag;
|
||||||
int writedata; // 1 if writes coeffs to data file
|
int writedata; // 1 if writes coeffs to data file
|
||||||
|
int born_matrix_enable;
|
||||||
double energy; // accumulated energies
|
double energy; // accumulated energies
|
||||||
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
||||||
double *eatom, **vatom; // accumulated per-atom energy/virial
|
double *eatom, **vatom; // accumulated per-atom energy/virial
|
||||||
@ -59,6 +60,12 @@ class Angle : protected Pointers {
|
|||||||
virtual void read_restart_settings(FILE *){};
|
virtual void read_restart_settings(FILE *){};
|
||||||
virtual void write_data(FILE *) {}
|
virtual void write_data(FILE *) {}
|
||||||
virtual double single(int, int, int, int) = 0;
|
virtual double single(int, int, int, int) = 0;
|
||||||
|
virtual void born_matrix(int /*atype*/, int /*at1*/, int /*at2*/, int /*at3*/, double &du,
|
||||||
|
double &du2)
|
||||||
|
{
|
||||||
|
du = 0.0;
|
||||||
|
du2 = 0.0;
|
||||||
|
}
|
||||||
virtual double memory_usage();
|
virtual double memory_usage();
|
||||||
virtual void *extract(const char *, int &) { return nullptr; }
|
virtual void *extract(const char *, int &) { return nullptr; }
|
||||||
void reinit();
|
void reinit();
|
||||||
|
|||||||
728
src/atom.cpp
728
src/atom.cpp
File diff suppressed because it is too large
Load Diff
@ -49,6 +49,7 @@ Bond::Bond(LAMMPS *_lmp) : Pointers(_lmp)
|
|||||||
|
|
||||||
allocated = 0;
|
allocated = 0;
|
||||||
suffix_flag = Suffix::NONE;
|
suffix_flag = Suffix::NONE;
|
||||||
|
born_matrix_enable = 0;
|
||||||
partial_flag = 0;
|
partial_flag = 0;
|
||||||
|
|
||||||
maxeatom = maxvatom = 0;
|
maxeatom = maxvatom = 0;
|
||||||
|
|||||||
@ -33,6 +33,8 @@ class Bond : protected Pointers {
|
|||||||
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
||||||
double *eatom, **vatom; // accumulated per-atom energy/virial
|
double *eatom, **vatom; // accumulated per-atom energy/virial
|
||||||
|
|
||||||
|
int born_matrix_enable;
|
||||||
|
|
||||||
int comm_forward; // size of forward communication (0 if none)
|
int comm_forward; // size of forward communication (0 if none)
|
||||||
int comm_reverse; // size of reverse communication (0 if none)
|
int comm_reverse; // size of reverse communication (0 if none)
|
||||||
int comm_reverse_off; // size of reverse comm even if newton off
|
int comm_reverse_off; // size of reverse comm even if newton off
|
||||||
@ -69,6 +71,13 @@ class Bond : protected Pointers {
|
|||||||
virtual int pack_reverse_comm(int, int, double *) { return 0; }
|
virtual int pack_reverse_comm(int, int, double *) { return 0; }
|
||||||
virtual void unpack_reverse_comm(int, int *, double *) {}
|
virtual void unpack_reverse_comm(int, int *, double *) {}
|
||||||
|
|
||||||
|
virtual void born_matrix(int /*btype*/, double /*rsq*/, int /*at1*/, int /*at2*/, double &du,
|
||||||
|
double &du2)
|
||||||
|
{
|
||||||
|
du = 0.0;
|
||||||
|
du2 = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
void write_file(int, char **);
|
void write_file(int, char **);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
|
|||||||
@ -108,7 +108,7 @@ class Compute : protected Pointers {
|
|||||||
Compute(class LAMMPS *, int, char **);
|
Compute(class LAMMPS *, int, char **);
|
||||||
~Compute() override;
|
~Compute() override;
|
||||||
void modify_params(int, char **);
|
void modify_params(int, char **);
|
||||||
void reset_extra_dof();
|
virtual void reset_extra_dof();
|
||||||
|
|
||||||
virtual void init() = 0;
|
virtual void init() = 0;
|
||||||
virtual void init_list(int, class NeighList *) {}
|
virtual void init_list(int, class NeighList *) {}
|
||||||
|
|||||||
@ -119,6 +119,9 @@ ComputeTempProfile::ComputeTempProfile(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
nbins = nbinx*nbiny*nbinz;
|
nbins = nbinx*nbiny*nbinz;
|
||||||
if (nbins <= 0) error->all(FLERR,"Illegal compute temp/profile command");
|
if (nbins <= 0) error->all(FLERR,"Illegal compute temp/profile command");
|
||||||
|
|
||||||
|
nstreaming = (xflag==0 ? 0 : 1) + (yflag==0 ? 0 : 1) + (zflag==0 ? 0 : 1);
|
||||||
|
reset_extra_dof();
|
||||||
|
|
||||||
memory->create(vbin,nbins,ncount,"temp/profile:vbin");
|
memory->create(vbin,nbins,ncount,"temp/profile:vbin");
|
||||||
memory->create(binave,nbins,ncount,"temp/profile:binave");
|
memory->create(binave,nbins,ncount,"temp/profile:binave");
|
||||||
|
|
||||||
@ -197,9 +200,10 @@ void ComputeTempProfile::dof_compute()
|
|||||||
natoms_temp = group->count(igroup);
|
natoms_temp = group->count(igroup);
|
||||||
dof = domain->dimension * natoms_temp;
|
dof = domain->dimension * natoms_temp;
|
||||||
|
|
||||||
// subtract additional d*Nbins DOF, as in Evans and Morriss paper
|
// subtract additional Nbins DOF for each adjusted direction,
|
||||||
|
// as in Evans and Morriss paper
|
||||||
|
|
||||||
dof -= extra_dof + fix_dof + domain->dimension*nbins;
|
dof -= extra_dof + fix_dof + nstreaming*nbins;
|
||||||
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
|
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
|
||||||
else tfactor = 0.0;
|
else tfactor = 0.0;
|
||||||
}
|
}
|
||||||
@ -334,14 +338,19 @@ void ComputeTempProfile::compute_array()
|
|||||||
|
|
||||||
MPI_Allreduce(tbin,tbinall,nbins,MPI_DOUBLE,MPI_SUM,world);
|
MPI_Allreduce(tbin,tbinall,nbins,MPI_DOUBLE,MPI_SUM,world);
|
||||||
|
|
||||||
int nper = domain->dimension;
|
double totcount = 0.0;
|
||||||
for (i = 0; i < nbins; i++) {
|
for (i = 0; i < nbins; i++) {
|
||||||
array[i][0] = binave[i][ncount-1];
|
array[i][0] = binave[i][ncount-1];
|
||||||
|
totcount += array[i][0];
|
||||||
|
}
|
||||||
|
double nper = domain->dimension - (extra_dof + fix_dof)/totcount;
|
||||||
|
double dofbin, tfactorbin;
|
||||||
|
for (i = 0; i < nbins; i++) {
|
||||||
if (array[i][0] > 0.0) {
|
if (array[i][0] > 0.0) {
|
||||||
dof = nper*array[i][0] - extra_dof;
|
dofbin = nper*array[i][0] - nstreaming;
|
||||||
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
|
if (dofbin > 0) tfactorbin = force->mvv2e / (dofbin * force->boltz);
|
||||||
else tfactor = 0.0;
|
else tfactorbin = 0.0;
|
||||||
array[i][1] = tfactor*tbinall[i];
|
array[i][1] = tfactorbin*tbinall[i];
|
||||||
} else array[i][1] = 0.0;
|
} else array[i][1] = 0.0;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -576,6 +585,12 @@ void ComputeTempProfile::bin_assign()
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void ComputeTempProfile::reset_extra_dof() {
|
||||||
|
extra_dof = domain->dimension - nstreaming;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
double ComputeTempProfile::memory_usage()
|
double ComputeTempProfile::memory_usage()
|
||||||
{
|
{
|
||||||
double bytes = (double)maxatom * sizeof(int);
|
double bytes = (double)maxatom * sizeof(int);
|
||||||
|
|||||||
@ -34,6 +34,7 @@ class ComputeTempProfile : public Compute {
|
|||||||
void compute_vector() override;
|
void compute_vector() override;
|
||||||
void compute_array() override;
|
void compute_array() override;
|
||||||
|
|
||||||
|
void reset_extra_dof() override;
|
||||||
void remove_bias(int, double *) override;
|
void remove_bias(int, double *) override;
|
||||||
void remove_bias_thr(int, double *, double *) override;
|
void remove_bias_thr(int, double *, double *) override;
|
||||||
void remove_bias_all() override;
|
void remove_bias_all() override;
|
||||||
@ -47,6 +48,7 @@ class ComputeTempProfile : public Compute {
|
|||||||
int nbinx, nbiny, nbinz, nbins;
|
int nbinx, nbiny, nbinz, nbins;
|
||||||
int ivx, ivy, ivz;
|
int ivx, ivy, ivz;
|
||||||
double tfactor;
|
double tfactor;
|
||||||
|
double nstreaming;
|
||||||
|
|
||||||
int box_change, triclinic;
|
int box_change, triclinic;
|
||||||
int *periodicity;
|
int *periodicity;
|
||||||
|
|||||||
@ -35,6 +35,7 @@ Dihedral::Dihedral(LAMMPS *_lmp) : Pointers(_lmp)
|
|||||||
|
|
||||||
allocated = 0;
|
allocated = 0;
|
||||||
suffix_flag = Suffix::NONE;
|
suffix_flag = Suffix::NONE;
|
||||||
|
born_matrix_enable = 0;
|
||||||
|
|
||||||
maxeatom = maxvatom = maxcvatom = 0;
|
maxeatom = maxvatom = maxcvatom = 0;
|
||||||
eatom = nullptr;
|
eatom = nullptr;
|
||||||
|
|||||||
@ -25,7 +25,8 @@ class Dihedral : protected Pointers {
|
|||||||
public:
|
public:
|
||||||
int allocated;
|
int allocated;
|
||||||
int *setflag;
|
int *setflag;
|
||||||
int writedata; // 1 if writes coeffs to data file
|
int writedata; // 1 if writes coeffs to data file
|
||||||
|
int born_matrix_enable;
|
||||||
double energy; // accumulated energy
|
double energy; // accumulated energy
|
||||||
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
||||||
double *eatom, **vatom; // accumulated per-atom energy/virial
|
double *eatom, **vatom; // accumulated per-atom energy/virial
|
||||||
@ -55,6 +56,12 @@ class Dihedral : protected Pointers {
|
|||||||
virtual void read_restart_settings(FILE *){};
|
virtual void read_restart_settings(FILE *){};
|
||||||
virtual void write_data(FILE *) {}
|
virtual void write_data(FILE *) {}
|
||||||
virtual double memory_usage();
|
virtual double memory_usage();
|
||||||
|
virtual void born_matrix(int /*dtype*/, int /*at1*/, int /*at2*/, int /*at3*/, int /*at4*/,
|
||||||
|
double &du, double &du2)
|
||||||
|
{
|
||||||
|
du = 0.0;
|
||||||
|
du2 = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
int suffix_flag; // suffix compatibility flag
|
int suffix_flag; // suffix compatibility flag
|
||||||
|
|||||||
@ -251,7 +251,7 @@ void FixBondHistory::post_neighbor()
|
|||||||
|
|
||||||
double FixBondHistory::memory_usage()
|
double FixBondHistory::memory_usage()
|
||||||
{
|
{
|
||||||
return maxbond * ndata * sizeof(double);
|
return (double) maxbond * ndata * sizeof(double);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -33,6 +33,7 @@ Improper::Improper(LAMMPS *_lmp) : Pointers(_lmp)
|
|||||||
|
|
||||||
allocated = 0;
|
allocated = 0;
|
||||||
suffix_flag = Suffix::NONE;
|
suffix_flag = Suffix::NONE;
|
||||||
|
born_matrix_enable = 0;
|
||||||
|
|
||||||
maxeatom = maxvatom = maxcvatom = 0;
|
maxeatom = maxvatom = maxcvatom = 0;
|
||||||
eatom = nullptr;
|
eatom = nullptr;
|
||||||
|
|||||||
@ -25,7 +25,8 @@ class Improper : protected Pointers {
|
|||||||
public:
|
public:
|
||||||
int allocated;
|
int allocated;
|
||||||
int *setflag;
|
int *setflag;
|
||||||
int writedata; // 1 if writes coeffs to data file
|
int writedata; // 1 if writes coeffs to data file
|
||||||
|
int born_matrix_enable;
|
||||||
double energy; // accumulated energies
|
double energy; // accumulated energies
|
||||||
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
double virial[6]; // accumulated virial: xx,yy,zz,xy,xz,yz
|
||||||
double *eatom, **vatom; // accumulated per-atom energy/virial
|
double *eatom, **vatom; // accumulated per-atom energy/virial
|
||||||
@ -55,6 +56,12 @@ class Improper : protected Pointers {
|
|||||||
virtual void read_restart_settings(FILE *){};
|
virtual void read_restart_settings(FILE *){};
|
||||||
virtual void write_data(FILE *) {}
|
virtual void write_data(FILE *) {}
|
||||||
virtual double memory_usage();
|
virtual double memory_usage();
|
||||||
|
virtual void born_matrix(int /*dtype*/, int /*at1*/, int /*at2*/, int /*at3*/, int /*at4*/,
|
||||||
|
double &du, double &du2)
|
||||||
|
{
|
||||||
|
du = 0.0;
|
||||||
|
du2 = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
int suffix_flag; // suffix compatibility flag
|
int suffix_flag; // suffix compatibility flag
|
||||||
|
|||||||
@ -58,6 +58,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
comm_forward = comm_reverse = comm_reverse_off = 0;
|
comm_forward = comm_reverse = comm_reverse_off = 0;
|
||||||
|
|
||||||
single_enable = 1;
|
single_enable = 1;
|
||||||
|
born_matrix_enable = 0;
|
||||||
single_hessian_enable = 0;
|
single_hessian_enable = 0;
|
||||||
restartinfo = 1;
|
restartinfo = 1;
|
||||||
respa_enable = 0;
|
respa_enable = 0;
|
||||||
|
|||||||
@ -52,6 +52,7 @@ class Pair : protected Pointers {
|
|||||||
int comm_reverse_off; // size of reverse comm even if newton off
|
int comm_reverse_off; // size of reverse comm even if newton off
|
||||||
|
|
||||||
int single_enable; // 1 if single() routine exists
|
int single_enable; // 1 if single() routine exists
|
||||||
|
int born_matrix_enable; // 1 if born_matrix() routine exists
|
||||||
int single_hessian_enable; // 1 if single_hessian() routine exists
|
int single_hessian_enable; // 1 if single_hessian() routine exists
|
||||||
int restartinfo; // 1 if pair style writes restart info
|
int restartinfo; // 1 if pair style writes restart info
|
||||||
int respa_enable; // 1 if inner/middle/outer rRESPA routines
|
int respa_enable; // 1 if inner/middle/outer rRESPA routines
|
||||||
@ -169,6 +170,12 @@ class Pair : protected Pointers {
|
|||||||
return 0.0;
|
return 0.0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
virtual void born_matrix(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, double /*rsq*/,
|
||||||
|
double /*factor_coul*/, double /*factor_lj*/, double &du, double &du2)
|
||||||
|
{
|
||||||
|
du = du2 = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
virtual void settings(int, char **) = 0;
|
virtual void settings(int, char **) = 0;
|
||||||
virtual void coeff(int, char **) = 0;
|
virtual void coeff(int, char **) = 0;
|
||||||
|
|
||||||
|
|||||||
@ -391,6 +391,7 @@ void PairHybrid::flags()
|
|||||||
// single_enable = 1 if all sub-styles are set
|
// single_enable = 1 if all sub-styles are set
|
||||||
// respa_enable = 1 if all sub-styles are set
|
// respa_enable = 1 if all sub-styles are set
|
||||||
// manybody_flag = 1 if any sub-style is set
|
// manybody_flag = 1 if any sub-style is set
|
||||||
|
// born_matrix_enable = 1 if all sub-styles are set
|
||||||
// no_virial_fdotr_compute = 1 if any sub-style is set
|
// no_virial_fdotr_compute = 1 if any sub-style is set
|
||||||
// ghostneigh = 1 if any sub-style is set
|
// ghostneigh = 1 if any sub-style is set
|
||||||
// ewaldflag, pppmflag, msmflag, dipoleflag, dispersionflag, tip4pflag = 1
|
// ewaldflag, pppmflag, msmflag, dipoleflag, dispersionflag, tip4pflag = 1
|
||||||
@ -401,11 +402,13 @@ void PairHybrid::flags()
|
|||||||
compute_flag = 0;
|
compute_flag = 0;
|
||||||
respa_enable = 0;
|
respa_enable = 0;
|
||||||
restartinfo = 0;
|
restartinfo = 0;
|
||||||
|
born_matrix_enable = 0;
|
||||||
|
|
||||||
for (m = 0; m < nstyles; m++) {
|
for (m = 0; m < nstyles; m++) {
|
||||||
if (styles[m]->single_enable) ++single_enable;
|
if (styles[m]->single_enable) ++single_enable;
|
||||||
if (styles[m]->respa_enable) ++respa_enable;
|
if (styles[m]->respa_enable) ++respa_enable;
|
||||||
if (styles[m]->restartinfo) ++restartinfo;
|
if (styles[m]->restartinfo) ++restartinfo;
|
||||||
|
if (styles[m]->born_matrix_enable) ++born_matrix_enable;
|
||||||
if (styles[m]->manybody_flag) manybody_flag = 1;
|
if (styles[m]->manybody_flag) manybody_flag = 1;
|
||||||
if (styles[m]->no_virial_fdotr_compute) no_virial_fdotr_compute = 1;
|
if (styles[m]->no_virial_fdotr_compute) no_virial_fdotr_compute = 1;
|
||||||
if (styles[m]->ghostneigh) ghostneigh = 1;
|
if (styles[m]->ghostneigh) ghostneigh = 1;
|
||||||
@ -422,6 +425,7 @@ void PairHybrid::flags()
|
|||||||
single_enable = (single_enable == nstyles) ? 1 : 0;
|
single_enable = (single_enable == nstyles) ? 1 : 0;
|
||||||
respa_enable = (respa_enable == nstyles) ? 1 : 0;
|
respa_enable = (respa_enable == nstyles) ? 1 : 0;
|
||||||
restartinfo = (restartinfo == nstyles) ? 1 : 0;
|
restartinfo = (restartinfo == nstyles) ? 1 : 0;
|
||||||
|
born_matrix_enable = (born_matrix_enable == nstyles) ? 1 : 0;
|
||||||
init_svector();
|
init_svector();
|
||||||
|
|
||||||
// set centroidstressflag for pair hybrid
|
// set centroidstressflag for pair hybrid
|
||||||
@ -867,6 +871,40 @@ double PairHybrid::single(int i, int j, int itype, int jtype,
|
|||||||
return esum;
|
return esum;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
call sub-style to compute born matrix interaction
|
||||||
|
error if sub-style does not support born_matrix call
|
||||||
|
since overlay could have multiple sub-styles, sum results explicitly
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairHybrid::born_matrix(int i, int j, int itype, int jtype, double rsq,
|
||||||
|
double factor_coul, double factor_lj,
|
||||||
|
double &dupair, double &du2pair)
|
||||||
|
{
|
||||||
|
if (nmap[itype][jtype] == 0)
|
||||||
|
error->one(FLERR,"Invoked pair born_matrix on pair style none");
|
||||||
|
|
||||||
|
double du, du2;
|
||||||
|
dupair = du2pair = 0.0;
|
||||||
|
|
||||||
|
for (int m = 0; m < nmap[itype][jtype]; m++) {
|
||||||
|
if (rsq < styles[map[itype][jtype][m]]->cutsq[itype][jtype]) {
|
||||||
|
if (styles[map[itype][jtype][m]]->born_matrix_enable == 0)
|
||||||
|
error->one(FLERR,"Pair hybrid sub-style does not support born_matrix call");
|
||||||
|
|
||||||
|
if ((special_lj[map[itype][jtype][m]] != nullptr) ||
|
||||||
|
(special_coul[map[itype][jtype][m]] != nullptr))
|
||||||
|
error->one(FLERR,"Pair hybrid born_matrix calls do not support"
|
||||||
|
" per sub-style special bond values");
|
||||||
|
|
||||||
|
du = du2 = 0.0;
|
||||||
|
styles[map[itype][jtype][m]]->born_matrix(i,j,itype,jtype,rsq,factor_coul,factor_lj,du,du2);
|
||||||
|
dupair += du;
|
||||||
|
du2pair += du2;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
copy Pair::svector data
|
copy Pair::svector data
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -49,6 +49,8 @@ class PairHybrid : public Pair {
|
|||||||
void write_restart(FILE *) override;
|
void write_restart(FILE *) override;
|
||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
double single(int, int, int, int, double, double, double, double &) override;
|
double single(int, int, int, int, double, double, double, double &) override;
|
||||||
|
void born_matrix(int, int, int, int, double, double, double, double &, double &) override;
|
||||||
|
|
||||||
void modify_params(int narg, char **arg) override;
|
void modify_params(int narg, char **arg) override;
|
||||||
double memory_usage() override;
|
double memory_usage() override;
|
||||||
|
|
||||||
|
|||||||
@ -413,7 +413,7 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq,
|
|||||||
(special_coul[map[itype][jtype][m]] != nullptr))
|
(special_coul[map[itype][jtype][m]] != nullptr))
|
||||||
error->one(FLERR, "Pair hybrid single() does not support per sub-style special_bond");
|
error->one(FLERR, "Pair hybrid single() does not support per sub-style special_bond");
|
||||||
|
|
||||||
scale = scaleval[map[itype][jtype][m]];
|
double scale = scaleval[map[itype][jtype][m]];
|
||||||
esum += scale * pstyle->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fone);
|
esum += scale * pstyle->single(i, j, itype, jtype, rsq, factor_coul, factor_lj, fone);
|
||||||
fforce += scale * fone;
|
fforce += scale * fone;
|
||||||
}
|
}
|
||||||
@ -423,6 +423,57 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq,
|
|||||||
return esum;
|
return esum;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
call sub-style to compute born matrix interaction
|
||||||
|
error if sub-style does not support born_matrix call
|
||||||
|
since overlay could have multiple sub-styles, sum results explicitly
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairHybridScaled::born_matrix(int i, int j, int itype, int jtype, double rsq,
|
||||||
|
double factor_coul, double factor_lj, double &dupair,
|
||||||
|
double &du2pair)
|
||||||
|
{
|
||||||
|
if (nmap[itype][jtype] == 0) error->one(FLERR, "Invoked pair born_matrix on pair style none");
|
||||||
|
|
||||||
|
// update scale values from variables where needed
|
||||||
|
|
||||||
|
const int nvars = scalevars.size();
|
||||||
|
if (nvars > 0) {
|
||||||
|
double *vals = new double[nvars];
|
||||||
|
for (int k = 0; k < nvars; ++k) {
|
||||||
|
int m = input->variable->find(scalevars[k].c_str());
|
||||||
|
if (m < 0)
|
||||||
|
error->all(FLERR, "Variable '{}' not found when updating scale factors", scalevars[k]);
|
||||||
|
vals[k] = input->variable->compute_equal(m);
|
||||||
|
}
|
||||||
|
for (int k = 0; k < nstyles; ++k) {
|
||||||
|
if (scaleidx[k] >= 0) scaleval[k] = vals[scaleidx[k]];
|
||||||
|
}
|
||||||
|
delete[] vals;
|
||||||
|
}
|
||||||
|
|
||||||
|
double du, du2, scale;
|
||||||
|
dupair = du2pair = scale = 0.0;
|
||||||
|
|
||||||
|
for (int m = 0; m < nmap[itype][jtype]; m++) {
|
||||||
|
auto pstyle = styles[map[itype][jtype][m]];
|
||||||
|
if (rsq < pstyle->cutsq[itype][jtype]) {
|
||||||
|
if (pstyle->born_matrix_enable == 0)
|
||||||
|
error->one(FLERR, "Pair hybrid sub-style does not support born_matrix call");
|
||||||
|
|
||||||
|
if ((special_lj[map[itype][jtype][m]] != nullptr) ||
|
||||||
|
(special_coul[map[itype][jtype][m]] != nullptr))
|
||||||
|
error->one(FLERR, "Pair hybrid born_matrix() does not support per sub-style special_bond");
|
||||||
|
|
||||||
|
du = du2 = 0.0;
|
||||||
|
scale = scaleval[map[itype][jtype][m]];
|
||||||
|
pstyle->born_matrix(i, j, itype, jtype, rsq, factor_coul, factor_lj, du, du2);
|
||||||
|
dupair += scale * du;
|
||||||
|
du2pair += scale * du2;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
set coeffs for one or more type pairs
|
set coeffs for one or more type pairs
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -38,6 +38,7 @@ class PairHybridScaled : public PairHybrid {
|
|||||||
void write_restart(FILE *) override;
|
void write_restart(FILE *) override;
|
||||||
void read_restart(FILE *) override;
|
void read_restart(FILE *) override;
|
||||||
double single(int, int, int, int, double, double, double, double &) override;
|
double single(int, int, int, int, double, double, double, double &) override;
|
||||||
|
void born_matrix(int, int, int, int, double, double, double, double &, double &) override;
|
||||||
|
|
||||||
void init_svector() override;
|
void init_svector() override;
|
||||||
void copy_svector(int, int) override;
|
void copy_svector(int, int) override;
|
||||||
|
|||||||
@ -39,6 +39,7 @@ using namespace MathConst;
|
|||||||
PairLJCut::PairLJCut(LAMMPS *lmp) : Pair(lmp)
|
PairLJCut::PairLJCut(LAMMPS *lmp) : Pair(lmp)
|
||||||
{
|
{
|
||||||
respa_enable = 1;
|
respa_enable = 1;
|
||||||
|
born_matrix_enable = 1;
|
||||||
writedata = 1;
|
writedata = 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -672,6 +673,28 @@ double PairLJCut::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCut::born_matrix(int /*i*/, int /*j*/, int itype, int jtype, double rsq,
|
||||||
|
double /*factor_coul*/, double factor_lj, double &dupair,
|
||||||
|
double &du2pair)
|
||||||
|
{
|
||||||
|
double rinv, r2inv, r6inv, du, du2;
|
||||||
|
|
||||||
|
r2inv = 1.0 / rsq;
|
||||||
|
rinv = sqrt(r2inv);
|
||||||
|
r6inv = r2inv * r2inv * r2inv;
|
||||||
|
|
||||||
|
// Reminder: lj1 = 48*e*s^12, lj2 = 24*e*s^6
|
||||||
|
// so dupair = -forcelj/r = -fforce*r (forcelj from single method)
|
||||||
|
|
||||||
|
du = r6inv * rinv * (lj2[itype][jtype] - lj1[itype][jtype] * r6inv);
|
||||||
|
du2 = r6inv * r2inv * (13 * lj1[itype][jtype] * r6inv - 7 * lj2[itype][jtype]);
|
||||||
|
|
||||||
|
dupair = factor_lj * du;
|
||||||
|
du2pair = factor_lj * du2;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void *PairLJCut::extract(const char *str, int &dim)
|
void *PairLJCut::extract(const char *str, int &dim)
|
||||||
{
|
{
|
||||||
dim = 2;
|
dim = 2;
|
||||||
|
|||||||
@ -40,6 +40,7 @@ class PairLJCut : public Pair {
|
|||||||
void write_data(FILE *) override;
|
void write_data(FILE *) override;
|
||||||
void write_data_all(FILE *) override;
|
void write_data_all(FILE *) override;
|
||||||
double single(int, int, int, int, double, double, double, double &) override;
|
double single(int, int, int, int, double, double, double, double &) override;
|
||||||
|
void born_matrix(int, int, int, int, double, double, double, double &, double &) override;
|
||||||
void *extract(const char *, int &) override;
|
void *extract(const char *, int &) override;
|
||||||
|
|
||||||
void compute_inner() override;
|
void compute_inner() override;
|
||||||
|
|||||||
@ -120,6 +120,12 @@ std::string utils::strfind(const std::string &text, const std::string &pattern)
|
|||||||
return "";
|
return "";
|
||||||
}
|
}
|
||||||
|
|
||||||
|
void utils::missing_cmd_args(const std::string &file, int line, const std::string &cmd,
|
||||||
|
Error *error)
|
||||||
|
{
|
||||||
|
if (error) error->all(file, line, "Illegal {} command: missing argument(s)", cmd);
|
||||||
|
}
|
||||||
|
|
||||||
/* specialization for the case of just a single string argument */
|
/* specialization for the case of just a single string argument */
|
||||||
|
|
||||||
void utils::logmesg(LAMMPS *lmp, const std::string &mesg)
|
void utils::logmesg(LAMMPS *lmp, const std::string &mesg)
|
||||||
@ -571,14 +577,14 @@ void utils::bounds(const char *file, int line, const std::string &str,
|
|||||||
error->all(file, line, fmt::format("Invalid range string: {}", str));
|
error->all(file, line, fmt::format("Invalid range string: {}", str));
|
||||||
|
|
||||||
if (nlo < nmin)
|
if (nlo < nmin)
|
||||||
error->all(file, line, fmt::format("Numeric index {} is out of bounds "
|
error->all(file, line, fmt::format("Numeric index {} is out of bounds ({}-{})",
|
||||||
"({}-{})", nlo, nmin, nmax));
|
nlo, nmin, nmax));
|
||||||
else if (nhi > nmax)
|
else if (nhi > nmax)
|
||||||
error->all(file, line, fmt::format("Numeric index {} is out of bounds "
|
error->all(file, line, fmt::format("Numeric index {} is out of bounds ({}-{})",
|
||||||
"({}-{})", nhi, nmin, nmax));
|
nhi, nmin, nmax));
|
||||||
else if (nlo > nhi)
|
else if (nlo > nhi)
|
||||||
error->all(file, line, fmt::format("Numeric index {} is out of bounds "
|
error->all(file, line, fmt::format("Numeric index {} is out of bounds ({}-{})",
|
||||||
"({}-{})", nlo, nmin, nhi));
|
nlo, nmin, nhi));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
12
src/utils.h
12
src/utils.h
@ -47,6 +47,18 @@ namespace utils {
|
|||||||
|
|
||||||
std::string strfind(const std::string &text, const std::string &pattern);
|
std::string strfind(const std::string &text, const std::string &pattern);
|
||||||
|
|
||||||
|
/*! Print error message about missing arguments for command
|
||||||
|
*
|
||||||
|
* This function simplifies the repetitive reporting missing arguments to a command.
|
||||||
|
*
|
||||||
|
* \param file name of source file for error message
|
||||||
|
* \param line line number in source file for error message
|
||||||
|
* \param cmd name of the failing command
|
||||||
|
* \param error pointer to Error class instance (for abort) or nullptr */
|
||||||
|
|
||||||
|
[[noreturn]] void missing_cmd_args(const std::string &file, int line, const std::string &cmd,
|
||||||
|
Error *error);
|
||||||
|
|
||||||
/* Internal function handling the argument list for logmesg(). */
|
/* Internal function handling the argument list for logmesg(). */
|
||||||
|
|
||||||
void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args);
|
void fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_args args);
|
||||||
|
|||||||
Reference in New Issue
Block a user