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Merge pull request #2796 from macstein/mliap_so3_ver2

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Add support for SO3 descriptor to MLIAP package
This commit is contained in:
Axel Kohlmeyer
2021-06-21 11:03:11 -04:00
committed by GitHub
parent 6a07942428 1bb9fb2819
commit f59273fb09
40 changed files with 3112 additions and 231 deletions
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225
doc/src/pair_mliap.rst
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@ -19,7 +19,7 @@ Syntax
style = *linear* or *quadratic* or *nn* or *mliappy*
filename = name of file containing model definitions
*descriptor* values = style filename
style = *sna*
style = *sna* or *so3*
filename = name of file containing descriptor definitions
Examples
@ -29,65 +29,70 @@ Examples
pair_style mliap model linear InP.mliap.model descriptor sna InP.mliap.descriptor
pair_style mliap model quadratic W.mliap.model descriptor sna W.mliap.descriptor
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
pair_coeff * * In P
Description
"""""""""""
Pair style *mliap* provides a general interface to families of
machine-learning interatomic potentials. It allows separate
definitions of the interatomic potential functional form (*model*)
and the geometric quantities that characterize the atomic positions
(*descriptor*). By defining *model* and *descriptor* separately,
it is possible to use many different models with a given descriptor,
or many different descriptors with a given model. The
pair style currently supports just one descriptor style, but it is
is straightforward to add new descriptor styles.
The SNAP descriptor style *sna* is the same as that used by :doc:`pair_style snap <pair_snap>`,
including the linear, quadratic, and chem variants.
The available models are *linear*, *quadratic*, *nn*, and *mliappy*.
The *mliappy* style can be used to couple python models,
e.g. PyTorch neural network energy models, and requires building
LAMMPS with the PYTHON package (see below).
In order to train a model, it is useful to know the gradient or derivative
of energy, force, and stress w.r.t. model parameters. This information
can be accessed using the related :doc:`compute mliap <compute_mliap>` command.
machine-learning interatomic potentials. It allows separate definitions
of the interatomic potential functional form (*model*) and the geometric
quantities that characterize the atomic positions (*descriptor*). By
defining *model* and *descriptor* separately, it is possible to use many
different models with a given descriptor, or many different descriptors
with a given model. The pair style currently supports only *sna* and *so3*
descriptor styles, but it is is straightforward to add new descriptor
styles.
The pair_style *mliap* command must be followed by two keywords
*model* and *descriptor* in either order. A single
*pair_coeff* command is also required. The first 2 arguments
must be \* \* so as to span all LAMMPS atom types.
This is followed by a list of N arguments
that specify the mapping of MLIAP
element names to LAMMPS atom types,
where N is the number of LAMMPS atom types.
The SNAP descriptor style *sna* is the same as that used by
:doc:`pair_style snap <pair_snap>`, including the linear, quadratic, and
chem variants. The available models are *linear*, *quadratic*, *nn*,
and *mliappy*. The *mliappy* style can be used to couple python models,
e.g. PyTorch neural network energy models, and requires building LAMMPS
with the PYTHON package (see below). In order to train a model, it is
useful to know the gradient or derivative of energy, force, and stress
w.r.t. model parameters. This information can be accessed using the
related :doc:`compute mliap <compute_mliap>` command.
The *model* keyword is followed by the model style. This is followed
by a single argument specifying the model filename containing the
parameters for a set of elements.
The model filename usually ends in the *.mliap.model* extension.
It may contain parameters for many elements. The only requirement is that it
contain at least those element names appearing in the
*pair_coeff* command.
The descriptor style *so3* is a descriptor that is derived from the
the smooth SO(3) power spectrum with the explicit inclusion of a radial
basis :ref:`(Bartok) <Bartok2013>` and :ref:`(Zagaceta) <Zagaceta2020>`.
The available models are *linear* and *nn*.
The top of the model file can contain any number of blank and comment lines (start with #),
but follows a strict format after that. The first non-blank non-comment
line must contain two integers:
The pair_style *mliap* command must be followed by two keywords *model*
and *descriptor* in either order. A single *pair_coeff* command is also
required. The first 2 arguments must be \* \* so as to span all LAMMPS
atom types. This is followed by a list of N arguments that specify the
mapping of MLIAP element names to LAMMPS atom types, where N is the
number of LAMMPS atom types.
The *model* keyword is followed by the model style. This is followed by
a single argument specifying the model filename containing the
parameters for a set of elements. The model filename usually ends in
the *.mliap.model* extension. It may contain parameters for many
elements. The only requirement is that it contain at least those element
names appearing in the *pair_coeff* command.
The top of the model file can contain any number of blank and comment
lines (start with #), but follows a strict format after that. The first
non-blank non-comment line must contain two integers:
* nelems = Number of elements
* nparams = Number of parameters
When the *model* keyword is *linear* or *quadratic*,
this is followed by one block for each of the *nelem* elements.
Each block consists of *nparams* parameters, one per line.
Note that this format is similar, but not identical to that used
for the :doc:`pair_style snap <pair_snap>` coefficient file.
Specifically, the line containing the element weight and radius is omitted,
since these are handled by the *descriptor*.
When the *model* keyword is *linear* or *quadratic*, this is followed by
one block for each of the *nelem* elements. Each block consists of
*nparams* parameters, one per line. Note that this format is similar,
but not identical to that used for the :doc:`pair_style snap
<pair_snap>` coefficient file. Specifically, the line containing the
element weight and radius is omitted, since these are handled by the
*descriptor*.
When the *model* keyword is *nn* (neural networks), the model file can contain
blank and comment lines (start with #) anywhere. The second non-blank non-comment
line must contain the string NET, followed by two integers:
When the *model* keyword is *nn* (neural networks), the model file can
contain blank and comment lines (start with #) anywhere. The second
non-blank non-comment line must contain the string NET, followed by two
integers:
* ndescriptors = Number of descriptors
* nlayers = Number of layers (including the hidden layers and the output layer)
@ -97,54 +102,71 @@ and followed by a sequence of a string and an integer for each layer:
* Activation function (linear, sigmoid, tanh or relu)
* nnodes = Number of nodes
This is followed by one block for each of the *nelem* elements. Each block consists
of *scale0* minimum value, *scale1* (maximum - minimum) value,
in order to normalize the descriptors, followed by *nparams* parameters,
including *bias* and *weights* of the model, starting with the first node of the first layer
and so on, with a maximum of 30 values per line.
This is followed by one block for each of the *nelem* elements. Each
block consists of *scale0* minimum value, *scale1* (maximum - minimum)
value, in order to normalize the descriptors, followed by *nparams*
parameters, including *bias* and *weights* of the model, starting with
the first node of the first layer and so on, with a maximum of 30 values
per line.
Notes on mliappy models:
When the *model* keyword is *mliappy*, the filename should end in '.pt',
'.pth' for pytorch models, or be a pickle file. To load a model from
memory (i.e. an existing python object), specify the filename as
"LATER", and then call `lammps.mliap.load_model(model)` from python
before using the pair style. When using lammps via the library mode, you will need to call
`lammps.mliappy.activate_mliappy(lmp)` on the active lammps object
before the pair style is defined. This call locates and loads the mliap-specific
python module that is built into lammps.
The detail of *nn* module implementation can be found at :ref:`(Yanxon) <Yanxon2020>`.
.. admonition:: Notes on mliappy models
When the *model* keyword is *mliappy*, the filename should end in '.pt',
'.pth' for pytorch models, or be a pickle file. To load a model from
memory (i.e. an existing python object), specify the filename as
"LATER", and then call `lammps.mliap.load_model(model)` from python
before using the pair style. When using lammps via the library mode, you
will need to call `lammps.mliappy.activate_mliappy(lmp)` on the active
lammps object before the pair style is defined. This call locates and
loads the mliap-specific python module that is built into lammps.
The *descriptor* keyword is followed by a descriptor style, and additional arguments.
Currently the only descriptor style is *sna*, indicating the bispectrum component
descriptors used by the Spectral Neighbor Analysis Potential (SNAP) potentials of
:doc:`pair_style snap <pair_snap>`.
A single additional argument specifies the descriptor filename
containing the parameters and setting used by the SNAP descriptor.
The descriptor filename usually ends in the *.mliap.descriptor* extension.
Currently two descriptor styles are available: *sna* and *so3*.
- *sna* indicates the bispectrum component descriptors used by the Spectral
Neighbor Analysis Potential (SNAP) potentials of :doc:`pair_style snap
<pair_snap>`. A single additional argument specifies the descriptor
filename containing the parameters and setting used by the SNAP
descriptor. The descriptor filename usually ends in the
*.mliap.descriptor* extension.
- *so3* indicated the power spectrum component descriptors. A single additional
argument specifies the descriptor filename containing the parameters and setting.
The SNAP descriptor file closely follows the format of the
:doc:`pair_style snap <pair_snap>` parameter file.
The file can contain blank and comment lines (start
with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . There are many optional keywords that are described
on the :doc:`pair_style snap <pair_snap>` doc page.
In addition, the SNAP descriptor file must contain
the *nelems*, *elems*, *radelems*, and *welems* keywords.
The *nelems* keyword specifies the number of elements
provided in the other three keywords.
The *elems* keyword is followed by a list of *nelems*
element names that must include the element
names appearing in the *pair_coeff* command,
but can contain other names too.
Similarly, the *radelems* and *welems* keywords are
followed by lists of *nelems* numbers giving the element radius
and element weight of each element. Obviously, the order
in which the elements are listed must be consistent for all
three keywords.
:doc:`pair_style snap <pair_snap>` parameter file. The file can contain
blank and comment lines (start with #) anywhere. Each non-blank
non-comment line must contain one keyword/value pair. The required
keywords are *rcutfac* and *twojmax*\ . There are many optional keywords
that are described on the :doc:`pair_style snap <pair_snap>` doc page.
In addition, the SNAP descriptor file must contain the *nelems*,
*elems*, *radelems*, and *welems* keywords. The *nelems* keyword
specifies the number of elements provided in the other three keywords.
The *elems* keyword is followed by a list of *nelems* element names that
must include the element names appearing in the *pair_coeff* command,
but can contain other names too. Similarly, the *radelems* and *welems*
keywords are followed by lists of *nelems* numbers giving the element
radius and element weight of each element. Obviously, the order in which
the elements are listed must be consistent for all three keywords.
The SO3 descriptor file is similar to the SNAP descriptor except that it
contains a few more arguments (e.g., *nmax* and *alpha*). The preparation
of SO3 descriptor and model files can be done with the
`*Pyxtal_FF*<https://github.com/qzhu2017/PyXtal_FF>`_ package.
See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
to specify the path for these *model* and *descriptor* files.
.. note::
To significantly reduce SO3 descriptor/force calculation time,
some properties are pre-computed and reused during the calculation.
These can consume a significant amount of RAM for simulations of
larger systems since their size depends on the total number of
neighbors per MPI process.
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -156,9 +178,10 @@ specify a pair_coeff command with I != J arguments for this style.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential files. Thus, you need
to re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
@ -169,11 +192,11 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
This pair style is part of the MLIAP package. It is only enabled if LAMMPS
was built with that package. In addition, building LAMMPS with the MLIAP package
requires building LAMMPS with the SNAP package.
The *mliappy* model requires building LAMMPS with the PYTHON package.
See the :doc:`Build package <Build_package>` doc page for more info.
This pair style is part of the MLIAP package. It is only enabled if
LAMMPS was built with that package. In addition, building LAMMPS with
the MLIAP package requires building LAMMPS with the SNAP package. The
*mliappy* model requires building LAMMPS with the PYTHON package. See
the :doc:`Build package <Build_package>` doc page for more info.
Related commands
@ -185,3 +208,19 @@ Default
"""""""
none
----------
.. _Bartok2013:
**(Bartok2013)** Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
.. _Zagaceta2020:
**(Zagaceta2020)** Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
.. _Yanxon2020:
**(Yanxon2020)** Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).

2
doc/src/pair_snap.rst
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@ -262,7 +262,7 @@ none
.. _Bartok20102:
**(Bartok2010)** Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok2010)** Bartok, Payne, Kondor, Csanyi, Phys Rev Lett, 104, 136403 (2010).
.. _Wood20182:

26
examples/mliap/Ni_Mo.data Normal file
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@ -0,0 +1,26 @@
NiMo.data (written by ASE)
10 atoms
2 atom types
0.0 5.7209004999999999 xlo xhi
0.0 5.7209004999999999 ylo yhi
0.0 3.5556619999999999 zlo zhi
Masses
1 95.96
2 58.6934
Atoms
1 1 0 0 0
2 1 2.86045025 2.86045025 1.7778309999999999
3 2 2.2921502965812497 4.5858137713447498 0
4 2 3.4287502034187498 1.13508672865525 0
5 2 1.72536352134475 0.56829995341874995 1.7778309999999999
6 2 3.9955369786552501 5.1526005465812501 1.7778309999999999
7 2 5.1526005465812501 1.72536352134475 1.7778309999999999
8 2 0.56829995341874995 3.9955369786552501 1.7778309999999999
9 2 4.5858137713447498 3.4287502034187498 0
10 2 1.13508672865525 2.2921502965812497 0

1
examples/mliap/Ni_Mo.mliap.descriptor Symbolic link
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@ -0,0 +1 @@
../../potentials/Ni_Mo.mliap.descriptor

1
examples/mliap/Ni_Mo.mliap.model Symbolic link
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@ -0,0 +1 @@
../../potentials/Ni_Mo.mliap.model

1
examples/mliap/Si.nn.mliap.descriptor Symbolic link
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@ -0,0 +1 @@
../../potentials/Si.nn.mliap.descriptor

1
examples/mliap/Si.nn.mliap.model Symbolic link
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@ -0,0 +1 @@
../../potentials/Si.nn.mliap.model

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examples/mliap/compute.quadratic.gg0.dat Normal file
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@ -0,0 +1,17 @@
# Time-averaged data for fix snap
# TimeStep Number-of-rows
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43]
0 13
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06

17
examples/mliap/compute.quadratic.gg1.dat Normal file
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@ -0,0 +1,17 @@
# Time-averaged data for fix snap
# TimeStep Number-of-rows
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13] c_snap[14] c_snap[15] c_snap[16] c_snap[17] c_snap[18] c_snap[19] c_snap[20] c_snap[21] c_snap[22] c_snap[23] c_snap[24] c_snap[25] c_snap[26] c_snap[27] c_snap[28] c_snap[29] c_snap[30] c_snap[31] c_snap[32] c_snap[33] c_snap[34] c_snap[35] c_snap[36] c_snap[37] c_snap[38] c_snap[39] c_snap[40] c_snap[41] c_snap[42] c_snap[43]
0 13
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 3.31573e+10 3.88807e+10 1.95617e+10 2.23819e+10 7.50718e+09 1.1398e+10 1.14692e+10 1.31227e+10 4.40152e+09 2.88519e+09 6.60228e+09 2.21449e+09 3.77706e+09 2.53375e+09 4.24928e+08 322.87
2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 0 -3.76889e+07 -5.33719e+07 -7.9033e+07 -3.95849e+07 -2.20973e+07 -4.24099e+07 -5.9058e+07 -2.74755e+07 -1.57438e+07 -4.1327e+07 -1.77189e+07 -2.66745e+07 -2.23073e+07 -4.48124e+06 -20.7188
3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 0 -2.3255e+08 -3.35235e+08 -5.0113e+08 -2.51613e+08 -1.36345e+08 -2.65149e+08 -3.72304e+08 -1.73849e+08 -9.88886e+07 -2.6097e+08 -1.12172e+08 -1.69137e+08 -1.41653e+08 -2.8484e+07 -106.829
4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 0 1.46568e+08 2.08973e+08 3.10574e+08 1.55696e+08 8.59341e+07 1.65757e+08 2.3156e+08 1.07878e+08 6.16434e+07 1.62145e+08 6.95847e+07 1.04822e+08 8.77079e+07 1.76257e+07 74.8128
5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 0 3.76889e+07 5.33719e+07 7.9033e+07 3.95849e+07 2.20973e+07 4.24099e+07 5.9058e+07 2.74755e+07 1.57438e+07 4.1327e+07 1.77189e+07 2.66745e+07 2.23073e+07 4.48124e+06 20.7188
6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 0 2.3255e+08 3.35235e+08 5.0113e+08 2.51613e+08 1.36345e+08 2.65149e+08 3.72304e+08 1.73849e+08 9.88886e+07 2.6097e+08 1.12172e+08 1.69137e+08 1.41653e+08 2.8484e+07 106.829
7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 0 -1.46568e+08 -2.08973e+08 -3.10574e+08 -1.55696e+08 -8.59341e+07 -1.65757e+08 -2.3156e+08 -1.07878e+08 -6.16434e+07 -1.62145e+08 -6.95847e+07 -1.04822e+08 -8.77079e+07 -1.76257e+07 -74.8128
8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 0 -6.70623e+10 -7.41396e+10 -9.24395e+10 -4.65087e+10 -3.93191e+10 -6.32509e+10 -7.68322e+10 -3.48602e+10 -2.18699e+10 -5.2291e+10 -2.21123e+10 -3.11993e+10 -2.61618e+10 -5.26504e+09 1.3152e+08
9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 0 -6.68105e+10 -7.36261e+10 -9.1545e+10 -4.60582e+10 -3.91714e+10 -6.28755e+10 -7.62227e+10 -3.45676e+10 -2.17185e+10 -5.18538e+10 -2.19213e+10 -3.08974e+10 -2.59085e+10 -5.21405e+09 1.2154e+08
10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 0 -6.69666e+10 -7.39444e+10 -9.20993e+10 -4.63376e+10 -3.9263e+10 -6.31081e+10 -7.66004e+10 -3.47491e+10 -2.18124e+10 -5.21248e+10 -2.20397e+10 -3.10845e+10 -2.60656e+10 -5.24568e+09 1.27407e+08
11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 0 -2.06474e+08 -3.3576e+08 -5.32545e+08 -2.70086e+08 -1.21057e+08 -2.57765e+08 -3.81922e+08 -1.81728e+08 -9.90436e+07 -2.70414e+08 -1.17681e+08 -1.7974e+08 -1.51444e+08 -3.05753e+07 -5.32884e+06
12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 0 -3.33961e+07 -5.43839e+07 -8.63107e+07 -4.37476e+07 -1.95804e+07 -4.17369e+07 -6.18761e+07 -2.94301e+07 -1.60423e+07 -4.38153e+07 -1.90614e+07 -2.91308e+07 -2.45361e+07 -4.95247e+06 -1.08912e+06
13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 0 5.30528e+07 8.63186e+07 1.36941e+08 6.94355e+07 3.11053e+07 6.62589e+07 9.81954e+07 4.67164e+07 2.54626e+07 6.95288e+07 3.02541e+07 4.6219e+07 3.89377e+07 7.86049e+06 1.50556e+06

17
examples/mliap/compute.snap.gg0.dat Normal file
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@ -0,0 +1,17 @@
# Time-averaged data for fix snap
# TimeStep Number-of-rows
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13]
0 13
1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87
2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188
3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829
4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128
5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188
6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829
7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128
8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08
9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08
10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08
11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06
12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06
13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06

17
examples/mliap/compute.snap.gg1.dat Normal file
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@ -0,0 +1,17 @@
# Time-averaged data for fix snap
# TimeStep Number-of-rows
# Row c_snap[1] c_snap[2] c_snap[3] c_snap[4] c_snap[5] c_snap[6] c_snap[7] c_snap[8] c_snap[9] c_snap[10] c_snap[11] c_snap[12] c_snap[13]
0 13
1 0 0 0 0 0 0 2 364183 213523 107428 122916 41227.5 322.87
2 0 0 0 0 0 0 0 0 -206.978 -293.105 -434.029 -217.39 -20.7188
3 0 0 0 0 0 0 0 0 -1277.1 -1841.02 -2752.08 -1381.8 -106.829
4 0 0 0 0 0 0 0 0 804.916 1147.62 1705.6 855.045 74.8128
5 0 0 0 0 0 0 0 0 206.978 293.105 434.029 217.39 20.7188
6 0 0 0 0 0 0 0 0 1277.1 1841.02 2752.08 1381.8 106.829
7 0 0 0 0 0 0 0 0 -804.916 -1147.62 -1705.6 -855.045 -74.8128
8 0 0 0 0 0 0 0 0 -368289 -407156 -507654 -255414 1.3152e+08
9 0 0 0 0 0 0 0 0 -366906 -404336 -502742 -252940 1.2154e+08
10 0 0 0 0 0 0 0 0 -367764 -406084 -505786 -254475 1.27407e+08
11 0 0 0 0 0 0 0 0 -1133.9 -1843.91 -2924.6 -1483.25 -5.32884e+06
12 0 0 0 0 0 0 0 0 -183.403 -298.662 -473.996 -240.251 -1.08912e+06
13 0 0 0 0 0 0 0 0 291.353 474.04 752.045 381.322 1.50556e+06

25
examples/mliap/in.mliap.so3.Ni_Mo Normal file
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@ -0,0 +1,25 @@
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic
read_data Ni_Mo.data
#change_box all x scale 0.9 y scale 0.9 z scale 0.9
pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor
pair_coeff * * Mo Ni
variable e equal pe
variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1
# dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 3

52
examples/mliap/in.mliap.so3.nn.Si Normal file
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@ -0,0 +1,52 @@
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
#read_data Si.data
lattice diamond 5.43
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 29.0
# temperature
variable t equal 500.
# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
pair_coeff * * Si Si
# Set-up output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create $t 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
run ${nsteps}

41
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.1 → examples/mliap/log.14Jun21.mliap.nn.Cu.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
LAMMPS (27 May 2021)
# Demonstrate MLIAP interface to SNAP nn Cu potential
# Initialize simulation
@ -93,30 +92,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 31.17 | 31.17 | 31.17 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
Loop time of 12.7584 on 1 procs for 100 steps with 256 atoms
10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826
20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872
30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006
40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801
50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019
60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144
70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871
80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364
90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222
100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923
Loop time of 4.77867 on 1 procs for 100 steps with 256 atoms
Performance: 0.339 ns/day, 70.880 hours/ns, 7.838 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.904 ns/day, 26.548 hours/ns, 20.926 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.755 | 12.755 | 12.755 | 0.0 | 99.97
Pair | 4.7771 | 4.7771 | 4.7771 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014069 | 0.0014069 | 0.0014069 | 0.0 | 0.01
Output | 0.00085897 | 0.00085897 | 0.00085897 | 0.0 | 0.01
Modify | 0.00075486 | 0.00075486 | 0.00075486 | 0.0 | 0.01
Other | | 0.0003242 | | | 0.00
Comm | 0.00052619 | 0.00052619 | 0.00052619 | 0.0 | 0.01
Output | 0.00054073 | 0.00054073 | 0.00054073 | 0.0 | 0.01
Modify | 0.00021744 | 0.00021744 | 0.00021744 | 0.0 | 0.00
Other | | 0.0002317 | | | 0.00
Nlocal: 256.000 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -131,4 +130,4 @@ Total # of neighbors = 19968
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:12
Total wall time: 0:00:04

41
examples/mliap/log.03Mar21.mliap.nn.Cu.g++.4 → examples/mliap/log.14Jun21.mliap.nn.Cu.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
LAMMPS (27 May 2021)
# Demonstrate MLIAP interface to SNAP nn Cu potential
# Initialize simulation
@ -93,30 +92,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 300 -4.0935581 -4.0935581 -4.0549315 -2916.7505 2916.7505
10 294.19698 -4.0927997 -4.0927997 -4.0549203 -2653.7504 2653.7504
20 277.15991 -4.0905816 -4.0905816 -4.0548958 -1875.7718 1875.7718
30 250.30462 -4.0870777 -4.0870777 -4.0548496 -618.45378 618.45378
40 215.94455 -4.0825861 -4.0825861 -4.0547821 1014.6151 -1014.6151
50 177.29307 -4.0775299 -4.0775299 -4.0547025 2846.7675 -2846.7675
60 138.26899 -4.072429 -4.072429 -4.0546261 4698.9654 -4698.9654
70 103.04321 -4.0678341 -4.0678341 -4.0545667 6401.8077 -6401.8077
80 75.426905 -4.0642423 -4.0642423 -4.0545307 7766.2217 -7766.2217
90 58.150738 -4.0620015 -4.0620015 -4.0545143 8668.0598 -8668.0598
100 52.301012 -4.0612408 -4.0612408 -4.0545067 9049.3141 -9049.3141
Loop time of 3.22769 on 4 procs for 100 steps with 256 atoms
10 294.11049 -4.0927998 -4.0927998 -4.0549315 -2654.7826 2654.7826
20 276.89115 -4.0905826 -4.0905826 -4.0549314 -1879.2872 1879.2872
30 249.71134 -4.0870829 -4.0870829 -4.0549312 -627.47006 627.47006
40 214.92415 -4.0826036 -4.0826036 -4.054931 995.44801 -995.44801
50 175.86879 -4.0775747 -4.0775747 -4.0549307 2811.6019 -2811.6019
60 136.62706 -4.0725218 -4.0725218 -4.0549303 4640.4144 -4640.4144
70 101.48566 -4.0679968 -4.0679968 -4.05493 6313.5871 -6313.5871
80 74.248664 -4.0644897 -4.0644897 -4.0549298 7644.1364 -7644.1364
90 57.500423 -4.0623332 -4.0623332 -4.0549297 8514.2222 -8514.2222
100 52.104609 -4.0616385 -4.0616385 -4.0549298 8870.8923 -8870.8923
Loop time of 1.25021 on 4 procs for 100 steps with 256 atoms
Performance: 1.338 ns/day, 17.932 hours/ns, 30.982 timesteps/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 3.455 ns/day, 6.946 hours/ns, 79.987 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.19 | 3.2037 | 3.2196 | 0.7 | 99.26
Pair | 1.2256 | 1.2347 | 1.2415 | 0.5 | 98.76
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0061415 | 0.022081 | 0.035855 | 8.9 | 0.68
Output | 0.00093221 | 0.00094824 | 0.00098861 | 0.0 | 0.03
Modify | 0.0002173 | 0.00022773 | 0.00024477 | 0.0 | 0.01
Other | | 0.0006805 | | | 0.02
Comm | 0.0074687 | 0.014311 | 0.023481 | 4.8 | 1.14
Output | 0.00060678 | 0.00062859 | 0.00066781 | 0.0 | 0.05
Modify | 8.7976e-05 | 9.7811e-05 | 0.00010943 | 0.0 | 0.01
Other | | 0.0004484 | | | 0.04
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -131,4 +130,4 @@ Total # of neighbors = 19968
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:01

21
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.1 → examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.1
View File

@ -1,5 +1,4 @@
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
LAMMPS (27 May 2021)
# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
@ -125,20 +124,20 @@ Step Temp E_pair c_energy TotEng Press v_press
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 3.05207 on 1 procs for 100 steps with 128 atoms
Loop time of 1.46158 on 1 procs for 100 steps with 128 atoms
Performance: 1.415 ns/day, 16.956 hours/ns, 32.765 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 2.956 ns/day, 8.120 hours/ns, 68.419 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0503 | 3.0503 | 3.0503 | 0.0 | 99.94
Pair | 1.4607 | 1.4607 | 1.4607 | 0.0 | 99.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00072395 | 0.00072395 | 0.00072395 | 0.0 | 0.02
Output | 0.00050893 | 0.00050893 | 0.00050893 | 0.0 | 0.02
Modify | 0.00037375 | 0.00037375 | 0.00037375 | 0.0 | 0.01
Other | | 0.0001878 | | | 0.01
Comm | 0.00028086 | 0.00028086 | 0.00028086 | 0.0 | 0.02
Output | 0.00035334 | 0.00035334 | 0.00035334 | 0.0 | 0.02
Modify | 0.00011992 | 0.00011992 | 0.00011992 | 0.0 | 0.01
Other | | 0.0001502 | | | 0.01
Nlocal: 128.000 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -154,4 +153,4 @@ Ave neighs/atom = 58.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:01

21
examples/mliap/log.03Mar21.mliap.nn.Ta06A.g++.4 → examples/mliap/log.14Jun21.mliap.nn.Ta06A.g++.4
View File

@ -1,5 +1,4 @@
LAMMPS (10 Feb 2021)
using 1 OpenMP thread(s) per MPI task
LAMMPS (27 May 2021)
# Demonstrate MLIAP interface to linear SNAP potential
# Initialize simulation
@ -32,7 +31,7 @@ Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (13.264000 13.264000
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 128 atoms
create_atoms CPU = 0.000 seconds
create_atoms CPU = 0.001 seconds
mass 1 180.88
@ -125,20 +124,20 @@ Step Temp E_pair c_energy TotEng Press v_press
80 124.79303 -11.829099 -11.829099 -11.813094 1947.0715 -1947.0715
90 97.448054 -11.825592 -11.825592 -11.813094 2231.9563 -2231.9563
100 74.035418 -11.822589 -11.822589 -11.813094 2515.8526 -2515.8526
Loop time of 0.858301 on 4 procs for 100 steps with 128 atoms
Loop time of 0.466162 on 4 procs for 100 steps with 128 atoms
Performance: 5.033 ns/day, 4.768 hours/ns, 116.509 timesteps/s
100.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 9.267 ns/day, 2.590 hours/ns, 214.518 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.75351 | 0.79999 | 0.85429 | 4.2 | 93.21
Pair | 0.36478 | 0.41101 | 0.45575 | 6.9 | 88.17
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0026857 | 0.057019 | 0.10354 | 15.8 | 6.64
Output | 0.00078796 | 0.00080864 | 0.00085671 | 0.0 | 0.09
Modify | 0.00011437 | 0.00012275 | 0.00013339 | 0.0 | 0.01
Other | | 0.0003564 | | | 0.04
Comm | 0.0095217 | 0.054209 | 0.10046 | 19.0 | 11.63
Output | 0.00042248 | 0.00045168 | 0.00051188 | 0.0 | 0.10
Modify | 5.4359e-05 | 6.0737e-05 | 6.5088e-05 | 0.0 | 0.01
Other | | 0.0004352 | | | 0.09
Nlocal: 32.0000 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0

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LAMMPS (27 May 2021)
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic
read_data Ni_Mo.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620)
1 by 1 by 1 MPI processor grid
reading atoms ...
10 atoms
read_data CPU = 0.000 seconds
#change_box all x scale 0.9 y scale 0.9 z scale 0.9
pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor
Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05
SO3 keyword rcutfac 4.1
SO3 keyword nmax 3
SO3 keyword lmax 2
SO3 keyword alpha 2.0
SO3 keyword nelems 2
SO3 keyword elems Mo
SO3 keyword radelems 0.5
SO3 keyword welems 42
pair_coeff * * Mo Ni
variable e equal pe
variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1
# dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 3
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.22 | 17.22 | 17.22 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.00634885 on 1 procs for 3 steps with 10 atoms
Performance: 40.826 ns/day, 0.588 hours/ns, 472.527 timesteps/s
78.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0063019 | 0.0063019 | 0.0063019 | 0.0 | 99.26
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.12
Output | 3.4094e-05 | 3.4094e-05 | 3.4094e-05 | 0.0 | 0.54
Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.03
Other | | 3.099e-06 | | | 0.05
Nlocal: 10.0000 ave 10 max 10 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 423.000 ave 423 max 423 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 780.000 ave 780 max 780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 780
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 May 2021)
# ---------- Initialize Simulation ---------------------
clear
units metal
dimension 3
boundary p p p
atom_style atomic
read_data Ni_Mo.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (5.7209005 5.7209005 3.5556620)
2 by 2 by 1 MPI processor grid
reading atoms ...
10 atoms
read_data CPU = 0.000 seconds
#change_box all x scale 0.9 y scale 0.9 z scale 0.9
pair_style mliap model linear Ni_Mo.mliap.model descriptor so3 Ni_Mo.mliap.descriptor
Reading potential file Ni_Mo.mliap.descriptor with DATE: 2014-09-05
SO3 keyword rcutfac 4.1
SO3 keyword nmax 3
SO3 keyword lmax 2
SO3 keyword alpha 2.0
SO3 keyword nelems 2
SO3 keyword elems Mo
SO3 keyword radelems 0.5
SO3 keyword welems 42
pair_coeff * * Mo Ni
variable e equal pe
variable N equal count(all)
thermo_style custom pe pxx pyy pzz pxy pxz pyz
thermo 1
# dump 1 all custom 1 dump.myforce.* id type fx fy fz
velocity all create 300.0 4928459 loop geom
fix 1 all nve
run 3
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.1
ghost atom cutoff = 6.1
binsize = 3.05, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.23 | 17.23 | 17.23 Mbytes
PotEng Pxx Pyy Pzz Pxy Pxz Pyz
-60.509577 -38.702887 -342.91582 1831.0743 -819.59439 427.87407 446.40498
-60.509344 -29.050171 -342.67124 1839.4215 -832.92479 439.72661 448.55829
-60.509056 -9.4119072 -335.83361 1856.2802 -846.04664 451.4663 450.35456
-60.508714 20.205972 -322.43019 1881.6 -858.97774 463.10122 451.79916
Loop time of 0.00191921 on 4 procs for 3 steps with 10 atoms
Performance: 135.056 ns/day, 0.178 hours/ns, 1563.143 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0012183 | 0.0015162 | 0.0018141 | 0.8 | 79.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 5.3883e-05 | 0.00035822 | 0.00065947 | 0.0 | 18.67
Output | 3.4094e-05 | 3.8326e-05 | 4.6492e-05 | 0.0 | 2.00
Modify | 9.5367e-07 | 1.1325e-06 | 1.4305e-06 | 0.0 | 0.06
Other | | 5.305e-06 | | | 0.28
Nlocal: 2.50000 ave 3 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 303.500 ave 304 max 303 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 195.000 ave 234 max 156 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 780
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (27 May 2021)
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
#read_data Si.data
lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 2 0 2 0 2
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 64 atoms
create_atoms CPU = 0.000 seconds
mass 1 29.0
# temperature
variable t equal 500.
# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
SO3 keyword rcutfac 5.0
SO3 keyword nmax 3
SO3 keyword lmax 4
SO3 keyword alpha 2.0
SO3 keyword nelems 1
SO3 keyword elems Si
SO3 keyword radelems 0.5
SO3 keyword welems 14
pair_coeff * * Si Si
# Set-up output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create $t 5287287 loop geom
velocity all create 500 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2
run ${nsteps}
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 3.39264 on 1 procs for 100 steps with 64 atoms
Performance: 1.273 ns/day, 18.848 hours/ns, 29.476 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.391 | 3.391 | 3.391 | 0.0 | 99.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00029302 | 0.00029302 | 0.00029302 | 0.0 | 0.01
Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.01
Modify | 0.00074792 | 0.00074792 | 0.00074792 | 0.0 | 0.02
Other | | 0.0002153 | | | 0.01
Nlocal: 64.0000 ave 64 max 64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 557.000 ave 557 max 557 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 2944.00 ave 2944 max 2944 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2944
Ave neighs/atom = 46.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (27 May 2021)
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0
# NOTE: These are not intended to represent real materials
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
#read_data Si.data
lattice diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region box block 0 2 0 2 0 2
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 64 atoms
create_atoms CPU = 0.000 seconds
mass 1 29.0
# temperature
variable t equal 500.
# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
SO3 keyword rcutfac 5.0
SO3 keyword nmax 3
SO3 keyword lmax 4
SO3 keyword alpha 2.0
SO3 keyword nelems 1
SO3 keyword elems Si
SO3 keyword radelems 0.5
SO3 keyword welems 14
pair_coeff * * Si Si
# Set-up output
compute eatom all pe/atom
compute energy all reduce sum c_eatom
compute satom all stress/atom NULL
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp epair c_energy etotal press v_press
thermo 10
thermo_modify norm yes
# Set up NVE run
timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes
# Run MD
velocity all create $t 5287287 loop geom
velocity all create 500 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2
run ${nsteps}
run 100
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6
ghost atom cutoff = 6
binsize = 3, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair mliap, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 298.2 | 298.2 | 298.2 Mbytes
Step Temp E_pair c_energy TotEng Press v_press
0 500 -3.8376374 -3.8376374 -3.7740172 -7295.2456 7295.2456
10 489.81 -3.8363423 -3.8363423 -3.7740187 -6964.5624 6964.5624
20 460.24523 -3.8325828 -3.8325828 -3.774021 -6014.7165 6014.7165
30 414.4367 -3.826752 -3.826752 -3.7740189 -4572.0641 4572.0641
40 358.34511 -3.8196022 -3.8196022 -3.7740062 -2849.9177 2849.9177
50 300.80447 -3.8122536 -3.8122536 -3.7739791 -1128.7008 1128.7008
60 251.6276 -3.8059543 -3.8059543 -3.7739371 306.20639 -306.20639
70 218.02888 -3.8016236 -3.8016236 -3.7738815 1253.4391 -1253.4391
80 201.70095 -3.7994767 -3.7994767 -3.7738122 1661.6675 -1661.6675
90 198.91416 -3.7990366 -3.7990366 -3.7737266 1628.78 -1628.78
100 203.36197 -3.799497 -3.799497 -3.7736212 1338.0458 -1338.0458
Loop time of 1.06231 on 4 procs for 100 steps with 64 atoms
Performance: 4.067 ns/day, 5.902 hours/ns, 94.135 timesteps/s
95.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.97395 | 1.0072 | 1.048 | 2.7 | 94.81
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.012069 | 0.052803 | 0.086037 | 12.0 | 4.97
Output | 0.00052595 | 0.0005523 | 0.00062776 | 0.0 | 0.05
Modify | 0.0014014 | 0.001442 | 0.0014772 | 0.1 | 0.14
Other | | 0.0003045 | | | 0.03
Nlocal: 16.0000 ave 16 max 16 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 349.000 ave 349 max 349 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 736.000 ave 736 max 736 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2944
Ave neighs/atom = 46.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

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# DATE: 2014-09-05 UNITS: metal CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014)
# LAMMPS SNAP parameters for Ta_Cand06A
# required
rcutfac 4.1
nmax 3
lmax 2
alpha 2.0
nelems 2
elems Mo Ni
radelems 0.5 0.5
welems 42 28

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# Polynomial Regression weights generated in PyXtal_FF
# total_species ncoefficient
2 19
-10.484582207168929
0.002181984336398585
0.00014278726759476177
-3.8073123887240994e-05
0.00942160245354996
-0.002953156990653782
0.0035289893532609155
0.010388199227015397
-0.007293285178559783
0.007778725702022789
0.02409088304815118
-0.006471686904018551
0.007708629032670791
0.05493502344189282
-0.037332449564392266
0.03526780681504278
0.07467315638703718
-0.040318596628773226
0.0422992011630305
-4.847096371333525
0.00026609729899863425
0.0006174790678830839
0.0011724604882377416
0.0007124714756813229
0.0008021747400134603
0.004032016341419122
0.00011594166533859027
-0.0007692676499943738
0.003157768943516899
0.0029578461448900376
0.004176054309089772
0.013203612422421204
0.003423023528944328
-0.0030482554314720275
0.021258801851889702
0.009238194498574716
-0.0031503286063986977
0.03174623113337486

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# Descriptor parameters generated in PyXtal_FF
# Required
rcutfac 5.0
nmax 3
lmax 4
alpha 2.0
# Elements
nelems 1
elems Si
radelems 0.5
welems 14

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# Neural networks weights generated in PyXtal_FF
# total_species nparams
1 785
# NET ndescriptors nlayers activation_func for layer 1, number of nodes for layer 1, ..., ..., ....,
NET 30 3 tanh 16 tanh 16 linear 1
# Scale0
882.1455698558184 0.0000000000000 0.0000000000000 5.8841777702371 5.7517799958383
-3238.9045671946642 -251.4215568867158 -178.2481266736228 -179.1034402268287 -221.9598950116207
90.0327111887464 0.0000000000000 0.0000000000000 1.0415952549641 2.1678474306880
-322.3587241302986 -75.7646415488627 -76.7145786721378 -129.0677794487796 -112.8987161484017
-245.1898929301280 -74.2072298868271 -80.7839875646899 -88.2638908840287 -72.5147728162335
0.0000000611830 0.0000000000000 0.0000000000000 0.8210754495092 0.8535996334201
# Scale1
5596.5949073820930 631.6650003257006 507.4436535576392 526.9938853932412 578.4408280351018
2946.1154148172673 387.1899445036270 289.3330986716401 400.3133327930956 344.7757780648306
1791.3334649717744 229.6824470442407 282.7126942391381 295.8232977577057 213.4074061628525
702.0628109646157 116.5739852500949 94.8723519732492 161.8196514838781 125.3225027894728
336.8056307932885 81.6558752026350 86.1654467256720 94.0311967431067 81.3402101281388
36.4668951370478 29.7270744697909 30.5640947358207 43.8634527339667 37.3463021205072
# Coefficients (Si)
0.3685385859286 -0.7362089264023 0.2715981065192 -0.1163322715384 0.3075404404972
-0.1610935909884 0.0015719318101 -0.5946522948990 -0.1053262271503 0.0880530740557
-0.1994084791015 0.5117820573250 -0.3213661835683 -0.0937083715377 -0.2683319723078
-0.2532296010987 -0.5584453847766 -0.1042993171458 0.1662189986326 0.1082297339321
0.4454372211944 0.7546740467117 -0.4766645580419 -0.6032704524575 -0.5618001207332
-0.3428319344940 0.0260954348575 -0.1489788544525 -0.1717162356069 -0.2914269918301
0.1840607080241 -0.0255899000658 1.0924323643612 0.4260148927592 0.1239175432774
-0.9116368030807 -1.2975392383857 0.2389860982057 0.5160804882868 0.1210706506477
-0.1473192701817 0.8192625410393 0.2152596573607 0.1358353711302 0.6717634613131
-0.2315709284550 0.1741413084117 -0.0099955470754 0.2616483846714 0.3912502053220
0.8749951208333 -0.0431582056181 0.0102692478410 0.1186685028545 0.1946870540726
0.4036277185047 0.5928075256653 -0.4496293441759 0.9264124791852 0.1716675841982
0.2708051872856 0.4463867931709 -0.4957162076397 -0.0746578010730 0.0073625462495
0.0092517223471 -0.0415038367188 0.0045399774768 -0.2776779881357 -0.3091863908603
-0.1016267540100 -0.0784091348819 -0.0203494059243 -0.2990856988363 0.2401024708934
0.0708936055962 0.1431336258523 0.1858443893117 -0.2816923101943 -0.2910022130389
-0.3135572060018 -0.1521378607704 -0.2453897063581 -0.2726430057341 -0.2421602698082
-0.3128029713546 -0.1827056998260 -0.3901520035262 -0.1324626884016 0.1607549950922
-0.1272025961543 -0.2662529289302 -0.2001902105085 1.3322746230916 -0.8843714935272
0.0610990084591 -0.2018171772711 -1.2055303456803 -0.2325866875488 0.1081275282523
-0.1491391559555 -0.5520812407412 -0.0640761380549 0.6765175020195 1.2206531572117
0.1078375642360 -0.1028473414486 0.6249292293014 -0.2018181367134 -0.4251848300159
0.0381912209677 -0.2839240973504 0.6938189551207 0.4475271058663 1.2439556871932
0.0958715552130 0.0848914643322 0.0359333433729 -0.1426658987523 0.3878612432265
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32
src/MLIAP/mliap_descriptor.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -18,14 +17,39 @@
#include "mliap_descriptor.h"
#include "memory.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPDescriptor::MLIAPDescriptor(LAMMPS *lmp) :
Pointers(lmp), ndescriptors(0), nelements(0), elements(nullptr), cutsq(nullptr),
radelem(nullptr), wjelem(nullptr)
{
cutmax = 0.0;
}
/* ---------------------------------------------------------------------- */
MLIAPDescriptor::MLIAPDescriptor(LAMMPS *lmp) : Pointers(lmp) {}
MLIAPDescriptor::~MLIAPDescriptor()
{
for (int i = 0; i < nelements; i++) delete[] elements[i];
delete[] elements;
memory->destroy(cutsq);
memory->destroy(radelem);
memory->destroy(wjelem);
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
memory usage
------------------------------------------------------------------------- */
MLIAPDescriptor::~MLIAPDescriptor() {}
double MLIAPDescriptor::memory_usage()
{
double bytes = (double)nelements*sizeof(double); // radelem
bytes += (double)nelements*sizeof(double); // welem
bytes += (double)nelements*nelements*sizeof(double); // cutsq
return bytes;
}

6
src/MLIAP/mliap_descriptor.h
View File

@ -21,19 +21,21 @@ namespace LAMMPS_NS {
class MLIAPDescriptor : protected Pointers {
public:
MLIAPDescriptor(LAMMPS *);
~MLIAPDescriptor();
virtual ~MLIAPDescriptor();
virtual void compute_descriptors(class MLIAPData *) = 0;
virtual void compute_forces(class MLIAPData *) = 0;
virtual void compute_force_gradients(class MLIAPData *) = 0;
virtual void compute_descriptor_gradients(class MLIAPData *) = 0;
virtual void init() = 0;
virtual double memory_usage() = 0;
virtual double memory_usage();
int ndescriptors; // number of descriptors
int nelements; // # of unique elements
char **elements; // names of unique elements
double **cutsq; // nelem x nelem rcutsq values
double cutmax; // maximum cutoff needed
double *radelem; // element radii
double *wjelem; // elements weights
protected:
};

29
src/MLIAP/mliap_descriptor_snap.cpp
View File

@ -39,8 +39,6 @@ using namespace LAMMPS_NS;
MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
MLIAPDescriptor(lmp)
{
nelements = 0;
elements = nullptr;
radelem = nullptr;
wjelem = nullptr;
snaptr = nullptr;
@ -51,25 +49,15 @@ MLIAPDescriptorSNAP::MLIAPDescriptorSNAP(LAMMPS *lmp, char *paramfilename):
chemflag, bnormflag, wselfallflag, nelements);
ndescriptors = snaptr->ncoeff;
}
/* ---------------------------------------------------------------------- */
MLIAPDescriptorSNAP::~MLIAPDescriptorSNAP()
{
if (nelements) {
for (int i = 0; i < nelements; i++)
delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
}
memory->destroy(radelem);
memory->destroy(wjelem);
delete snaptr;
}
/* ----------------------------------------------------------------------
@ -374,6 +362,12 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
bnormflag = 0;
wselfallflag = 0;
for (int i = 0; i < nelements; i++) delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
// open SNAP parameter file on proc 0
FILE *fpparam;
@ -510,13 +504,8 @@ void MLIAPDescriptorSNAP::read_paramfile(char *paramfilename)
double MLIAPDescriptorSNAP::memory_usage()
{
double bytes = 0;
bytes += (double)nelements*sizeof(double); // radelem
bytes += (double)nelements*sizeof(double); // welem
bytes += (double)nelements*nelements*sizeof(int); // cutsq
double bytes = MLIAPDescriptor::memory_usage();
bytes += snaptr->memory_usage(); // SNA object
return bytes;
}

4
src/MLIAP/mliap_descriptor_snap.h
View File

@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class MLIAPDescriptorSNAP : public MLIAPDescriptor {
public:
MLIAPDescriptorSNAP(LAMMPS *, char *);
~MLIAPDescriptorSNAP();
virtual ~MLIAPDescriptorSNAP();
virtual void compute_descriptors(class MLIAPData *);
virtual void compute_forces(class MLIAPData *);
virtual void compute_force_gradients(class MLIAPData *);
@ -37,8 +37,6 @@ class MLIAPDescriptorSNAP : public MLIAPDescriptor {
inline int equal(double *x, double *y);
inline double dist2(double *x, double *y);
double *radelem; // element radii
double *wjelem; // elements weights
int twojmax, switchflag, bzeroflag;
int chemflag, bnormflag, wselfallflag;
double rfac0, rmin0;

281
src/MLIAP/mliap_descriptor_so3.cpp Normal file
View File

@ -0,0 +1,281 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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: Byungkyun Kang (University of Nevada, Las Vegas)
------------------------------------------------------------------------- */
#include "mliap_descriptor_so3.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "memory.h"
#include "mliap_data.h"
#include "mliap_so3.h"
#include "pair_mliap.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define MAXWORD 3
/* ---------------------------------------------------------------------- */
MLIAPDescriptorSO3::MLIAPDescriptorSO3(LAMMPS *lmp, char *paramfilename) : MLIAPDescriptor(lmp)
{
radelem = nullptr;
wjelem = nullptr;
so3ptr = nullptr;
read_paramfile(paramfilename);
so3ptr = new MLIAP_SO3(lmp, rcutfac, lmax, nmax, alpha);
ndescriptors = so3ptr->ncoeff;
}
/* ---------------------------------------------------------------------- */
MLIAPDescriptorSO3::~MLIAPDescriptorSO3()
{
memory->destroy(radelem);
memory->destroy(wjelem);
delete so3ptr;
}
/* ---------------------------------------------------------------------- */
void MLIAPDescriptorSO3::read_paramfile(char *paramfilename)
{
int rcutfacflag = 0;
int nelementsflag = 0;
int elementsflag = 0;
int radelemflag = 0;
int wjelemflag = 0;
int nmaxflag = 0;
int lmaxflag = 0;
int alphaflag = 0;
// set defaults for optional keywords
rfac0 = 0.99363;
rmin0 = 0.0;
for (int i = 0; i < nelements; i++) delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(cutsq);
// open SO3 parameter file on proc 0
FILE *fpparam;
if (comm->me == 0) {
fpparam = utils::open_potential(paramfilename, lmp, nullptr);
if (fpparam == nullptr)
error->one(FLERR, "Cannot open SO3 parameter file {}: {}", paramfilename,
utils::getsyserror());
}
char line[MAXLINE], *ptr;
int eof = 0;
int n, nwords;
while (1) {
if (comm->me == 0) {
ptr = utils::fgets_trunc(line, MAXLINE, fpparam);
if (ptr == nullptr) {
eof = 1;
fclose(fpparam);
} else
n = strlen(line) + 1;
}
MPI_Bcast(&eof, 1, MPI_INT, 0, world);
if (eof) break;
MPI_Bcast(&n, 1, MPI_INT, 0, world);
MPI_Bcast(line, n, MPI_CHAR, 0, world);
// strip comment, skip line if blank
if ((ptr = strchr(line, '#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
// words = ptrs to all words in line
// strip single and double quotes from words
Tokenizer p(line, "' \t\n\r\f");
std::string skeywd = p.next();
std::string skeyval = p.next();
if (comm->me == 0) { utils::logmesg(lmp, "SO3 keyword {} {} \n", skeywd, skeyval); }
// check for keywords with one value per element
if (strcmp(skeywd.c_str(), "elems") == 0 || strcmp(skeywd.c_str(), "radelems") == 0 ||
strcmp(skeywd.c_str(), "welems") == 0) {
if (nelementsflag == 0 || nwords != nelements + 1)
error->all(FLERR, "Incorrect SO3 parameter file");
if (strcmp(skeywd.c_str(), "elems") == 0) {
for (int ielem = 0; ielem < nelements; ielem++) {
elements[ielem] = utils::strdup(skeyval);
if (ielem < nelements - 1) skeyval = p.next();
}
elementsflag = 1;
} else if (strcmp(skeywd.c_str(), "radelems") == 0) {
for (int ielem = 0; ielem < nelements; ielem++) {
radelem[ielem] = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
if (ielem < nelements - 1) skeyval = p.next();
}
radelemflag = 1;
} else if (strcmp(skeywd.c_str(), "welems") == 0) {
for (int ielem = 0; ielem < nelements; ielem++) {
wjelem[ielem] = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
if (ielem < nelements - 1) skeyval = p.next();
}
wjelemflag = 1;
}
} else {
// all other keywords take one value
if (nwords != 2) error->all(FLERR, "Incorrect SO3 parameter file");
if (strcmp(skeywd.c_str(), "nelems") == 0) {
nelements = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
elements = new char *[nelements];
memory->create(radelem, nelements, "mliap_so3_descriptor:radelem");
memory->create(wjelem, nelements, "mliap_so3_descriptor:wjelem");
nelementsflag = 1;
} else if (strcmp(skeywd.c_str(), "rcutfac") == 0) {
rcutfac = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
rcutfacflag = 1;
} else if (strcmp(skeywd.c_str(), "nmax") == 0) {
nmax = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
nmaxflag = 1;
} else if (strcmp(skeywd.c_str(), "lmax") == 0) {
lmax = utils::inumeric(FLERR, skeyval.c_str(), false, lmp);
lmaxflag = 1;
} else if (strcmp(skeywd.c_str(), "alpha") == 0) {
alpha = utils::numeric(FLERR, skeyval.c_str(), false, lmp);
alphaflag = 1;
} else
error->all(FLERR, "Incorrect SO3 parameter file");
}
}
if (!rcutfacflag || !nelementsflag || !elementsflag || !radelemflag || !wjelemflag || !nmaxflag ||
!lmaxflag || !alphaflag)
error->all(FLERR, "Incorrect SO3 parameter file");
// construct cutsq
double cut;
cutmax = 0.0;
memory->create(cutsq, nelements, nelements, "mliap/descriptor/so3:cutsq");
for (int ielem = 0; ielem < nelements; ielem++) {
cut = 2.0 * radelem[ielem] * rcutfac;
if (cut > cutmax) cutmax = cut;
cutsq[ielem][ielem] = cut * cut;
for (int jelem = ielem + 1; jelem < nelements; jelem++) {
cut = (radelem[ielem] + radelem[jelem]) * rcutfac;
cutsq[ielem][jelem] = cutsq[jelem][ielem] = cut * cut;
}
}
}
/* ---------------------------------------------------------------------- */
void MLIAPDescriptorSO3::compute_descriptors(class MLIAPData *data)
{
so3ptr->spectrum(data->nlistatoms, data->numneighs, data->jelems, wjelem, data->rij, nmax, lmax,
rcutfac, alpha, data->ndescriptors);
for (int ii = 0; ii < data->nlistatoms; ii++) {
for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++)
data->descriptors[ii][icoeff] = so3ptr->m_plist_r[ii * (data->ndescriptors) + icoeff];
}
}
/* ---------------------------------------------------------------------- */
void MLIAPDescriptorSO3::compute_forces(class MLIAPData *data)
{
int npairs = 0;
for (int ii = 0; ii < data->nlistatoms; ii++) npairs += data->numneighs[ii];
so3ptr->spectrum_dxdr(data->nlistatoms, data->numneighs, data->jelems, wjelem, data->rij, nmax,
lmax, rcutfac, alpha, npairs, data->ndescriptors);
double fij[3];
double **f = atom->f;
int ij = 0;
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
// insure rij, inside, wj, and rcutij are of size jnum
const int jnum = data->numneighs[ii];
for (int jj = 0; jj < jnum; jj++) {
int j = data->jatoms[ij];
for (int ir = 0; ir < 3; ir++) {
fij[ir] = 0.0;
for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++)
fij[ir] += data->betas[ii][icoeff] *
so3ptr->m_dplist_r[(ij * (data->ndescriptors) + icoeff) * 3 + ir];
}
f[i][0] += fij[0];
f[i][1] += fij[1];
f[i][2] += fij[2];
f[j][0] -= fij[0];
f[j][1] -= fij[1];
f[j][2] -= fij[2];
// add in global and per-atom virial contributions
// this is optional and has no effect on force calculation
if (data->vflag) data->pairmliap->v_tally(i, j, fij, data->rij[ij]);
ij++;
}
}
}
/* ---------------------------------------------------------------------- */
void MLIAPDescriptorSO3::init()
{
so3ptr->init();
}
/* ---------------------------------------------------------------------- */
double MLIAPDescriptorSO3::memory_usage()
{
double bytes = MLIAPDescriptor::memory_usage();
bytes += so3ptr->memory_usage();
return bytes;
}

51
src/MLIAP/mliap_descriptor_so3.h Normal file
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@ -0,0 +1,51 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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.
------------------------------------------------------------------------- */
#ifndef LMP_MLIAP_DESCRIPTOR_SO3_H
#define LMP_MLIAP_DESCRIPTOR_SO3_H
#include "mliap_descriptor.h"
namespace LAMMPS_NS {
class MLIAPDescriptorSO3 : public MLIAPDescriptor {
public:
MLIAPDescriptorSO3(LAMMPS *, char *);
virtual ~MLIAPDescriptorSO3();
virtual void compute_descriptors(class MLIAPData *);
virtual void compute_forces(class MLIAPData *);
virtual void compute_force_gradients(class MLIAPData *){};
virtual void compute_descriptor_gradients(class MLIAPData *){};
virtual void init();
virtual double memory_usage();
double rcutfac;
protected:
class MLIAP_SO3 *so3ptr;
void read_paramfile(char *);
inline int equal(double *x, double *y);
inline double dist2(double *x, double *y);
int nmax, lmax;
double alpha;
int twojmax, switchflag, bzeroflag;
int chemflag, bnormflag, wselfallflag;
double rfac0, rmin0;
};
} // namespace LAMMPS_NS
#endif

12
src/MLIAP/mliap_model.cpp
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@ -32,7 +32,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
MLIAPModel::MLIAPModel(LAMMPS *lmp, char *) : Pointers(lmp)
MLIAPModel::MLIAPModel(LAMMPS *lmp, char *) : Pointers(lmp), coeffelem(nullptr)
{
nparams = 0;
nelements = 0;
@ -44,6 +44,7 @@ MLIAPModel::MLIAPModel(LAMMPS *lmp, char *) : Pointers(lmp)
MLIAPModel::~MLIAPModel()
{
memory->destroy(coeffelem);
}
/* ----------------------------------------------------------------------
@ -77,19 +78,11 @@ void MLIAPModel::set_ndescriptors(int ndescriptors_in)
MLIAPModelSimple::MLIAPModelSimple(LAMMPS *lmp, char *coefffilename) : MLIAPModel(lmp, coefffilename)
{
coeffelem = nullptr;
if (coefffilename) read_coeffs(coefffilename);
}
/* ---------------------------------------------------------------------- */
MLIAPModelSimple::~MLIAPModelSimple()
{
memory->destroy(coeffelem);
}
/* ---------------------------------------------------------------------- */
void MLIAPModelSimple::read_coeffs(char *coefffilename)
{
@ -143,6 +136,7 @@ void MLIAPModelSimple::read_coeffs(char *coefffilename)
// set up coeff lists
memory->destroy(coeffelem);
memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem");
// Loop over nelements blocks in the coefficient file

6
src/MLIAP/mliap_model.h
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@ -21,7 +21,7 @@ namespace LAMMPS_NS {
class MLIAPModel : protected Pointers {
public:
MLIAPModel(LAMMPS *, char *);
~MLIAPModel();
virtual ~MLIAPModel();
void set_ndescriptors(int);
void set_nelements(int);
virtual int get_nparams() = 0;
@ -35,6 +35,7 @@ class MLIAPModel : protected Pointers {
int nonlinearflag; // 1 if gradient() requires descriptors
int ndescriptors; // number of descriptors
int nparams; // number of parameters per element
double **coeffelem; // element coefficients
protected:
virtual void read_coeffs(char *) = 0;
@ -43,11 +44,10 @@ class MLIAPModel : protected Pointers {
class MLIAPModelSimple : public MLIAPModel {
public:
MLIAPModelSimple(LAMMPS *, char *);
~MLIAPModelSimple();
~MLIAPModelSimple(){};
virtual double memory_usage();
protected:
double **coeffelem; // element coefficients
virtual void read_coeffs(char *);
};

10
src/MLIAP/mliap_model_nn.cpp
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@ -36,18 +36,17 @@ using namespace LAMMPS_NS;
MLIAPModelNN::MLIAPModelNN(LAMMPS* lmp, char* coefffilename) :
MLIAPModel(lmp, coefffilename)
{
coeffelem = nullptr;
nnodes = nullptr;
activation = nullptr;
scale = nullptr;
if (coefffilename) read_coeffs(coefffilename);
nonlinearflag = 1;
}
/* ---------------------------------------------------------------------- */
MLIAPModelNN::~MLIAPModelNN()
{
memory->destroy(coeffelem);
memory->destroy(nnodes);
memory->destroy(activation);
memory->destroy(scale);
@ -118,6 +117,7 @@ void MLIAPModelNN::read_coeffs(char *coefffilename)
// set up coeff lists
memory->destroy(coeffelem);
memory->create(coeffelem,nelements,nparams,"mliap_snap_model:coeffelem");
int stats = 0;
@ -352,9 +352,9 @@ void MLIAPModelNN::compute_gradients(MLIAPData* data)
// Deleting the variables
for (int n=0; n<nl; n++) {
delete nodes[n];
delete dnodes[n];
delete bnodes[n];
delete[] nodes[n];
delete[] dnodes[n];
delete[] bnodes[n];
}
delete[] nodes;

1
src/MLIAP/mliap_model_nn.h
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@ -35,7 +35,6 @@ class MLIAPModelNN : public MLIAPModel {
int *activation; // activation functions
int *nnodes; // number of nodes per layer
double ***scale; // element scale values
double **coeffelem; // element coefficients
virtual void read_coeffs(char *);
inline double sigm(double x, double &deriv)

1243
src/MLIAP/mliap_so3.cpp Normal file
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File diff suppressed because it is too large Load Diff

89
src/MLIAP/mliap_so3.h Normal file
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@ -0,0 +1,89 @@
#ifndef LMP_MLIAP_SO3_H
#define LMP_MLIAP_SO3_H
#include "pointers.h"
namespace LAMMPS_NS {
class MLIAP_SO3 : protected Pointers {
public:
MLIAP_SO3(LAMMPS *, double vrcut, int vlmax, int vnmax, double valpha);
MLIAP_SO3(LAMMPS *lmp) : Pointers(lmp){};
~MLIAP_SO3();
void init();
double memory_usage();
int ncoeff;
double *m_plist_r;
double *m_dplist_r;
private:
double alloc_init, alloc_arrays;
int *m_ellpl1, *m_ellm1;
double *m_pfac;
int m_pfac_l1, m_pfac_l2;
double *m_dfac0, *m_dfac1, *m_dfac2, *m_dfac3, *m_dfac4, *m_dfac5;
int m_dfac_l1, m_dfac_l2;
double m_rcut, m_alpha;
int m_lmax, m_nmax, m_Nmax, m_ldim;
double *m_g_array, *m_w, *m_rootpq;
int *m_idxu_block, *m_idxylm;
int m_idxu_count, m_idxy_count;
int m_numYlms;
double *m_clisttot_r, *m_clisttot_i;
double *m_rip_array, *m_rip_darray;
double *m_sbes_array, *m_sbes_darray;
int m_init_arrays;
double *m_plist_i;
double *m_clist_r, *m_clist_i;
double *m_ulist_r, *m_ulist_i;
double *m_Ylms_r, *m_Ylms_i, *m_dYlm_r, *m_dYlm_i;
double *m_dplist_i, *m_dclist_r, *m_dclist_i, *m_tempdp_r;
public:
void spectrum(int nlocal, int *numneighs, int *jelems, double *wjelem, double **rij, int nmax,
int lmax, double rcut, double alpha, int ncoefs);
void spectrum_dxdr(int nlocal, int *numneighs, int *jelems, double *wjelem, double **rij,
int nmax, int lmax, double rcut, double alpha, int npairs, int ncoefs);
private:
double Cosine(double Rij, double Rc);
double CosinePrime(double Rij, double Rc);
double compute_sfac(double r, double rcut);
double compute_dsfac(double r, double rcut);
void get_sbes_array(int nlocal, int *numneighs, double **rij, int lmax, double rcut,
double alpha);
void get_rip_array(int nlocal, int *numneighs, double **rij, int nmax, int lmax, double alpha);
void init_arrays(int nlocal, int ncoefs);
void init_garray(int nmax, int lmax, double rcut, double alpha, double *w, int lw1,
double *g_array, int lg2);
void compute_uarray_recursive(double x, double y, double z, double r, int twol, double *ulist_r,
double *ulist_i, int *idxu_block, double *rootpqarray);
void compute_ncoeff();
int get_sum(int istart, int iend, int id, int imult);
void compute_dpidrj(int nmax, int lmax, double *clisttot_r, double *clisttot_i, int lctot2,
double *dclist_r, double *dclist_i, int ldcli2, int ldcli3, double *dplist_r,
int dpli2);
double compute_g(double r, int n, int nmax, double rcut, double *w, int lw1);
double phi(double r, int alpha, double rcut);
void compute_pi(int nmax, int lmax, double *clisttot_r, double *clisttot_i, int lcl2,
double *plist_r, double *plist_i, int lpl2, int indpl);
void compute_W(int nmax, double *arr);
};
} // namespace LAMMPS_NS
#endif

167
src/MLIAP/mliap_so3_math.h Normal file
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@ -0,0 +1,167 @@
/*
* MLIAP_SO3_math.h
*
* Created on: Apr 12, 2021
* Author: macstein
*/
#ifndef LMP_MLIAP_SO3_MATH_H
#define LMP_MLIAP_SO3_MATH_H
#include "math_eigen_impl.h"
namespace SO3Math {
int jacobin(int n, double const *const *mat, double *eval, double **evec);
int invert_matrix(int n, double *A, double *Ainv);
int LUPdecompose(int n, double dtol, double *A, int *P);
void LUPSolve(int n, double *A, double *B, int *P);
} // namespace SO3Math
using namespace MathEigen;
typedef Jacobi<double, double *, double **, double const *const *> Jacobi_v2;
int SO3Math::jacobin(int n, double const *const *mat, double *eval, double **evec)
{
int i, j;
double **mat_cpy;
mat_cpy = new double *[n];
for (int iy = 0; iy < n; iy++) mat_cpy[iy] = new double[n];
for (i = 0; i < n; i++)
for (j = 0; j < n; j++) mat_cpy[i][j] = mat[i][j];
double *M[n];
for (i = 0; i < n; i++) M[i] = &(mat_cpy[i][0]);
int midx[n];
Jacobi_v2 ecalcn(n, M, midx);
int ierror = ecalcn.Diagonalize(mat, eval, evec, Jacobi_v2::SORT_DECREASING_EVALS);
for (int i = 0; i < n; i++)
for (int j = i + 1; j < n; j++) std::swap(evec[i][j], evec[j][i]);
for (int iy = 0; iy < n; iy++) delete[] mat_cpy[iy];
delete[] mat_cpy;
return ierror;
}
int SO3Math::invert_matrix(int n, double *A, double *Ainv)
{
int i, j;
double dtol = 1.e-30;
int *P;
double *b, *Atemp;
P = new int[n];
b = new double[n];
Atemp = new double[n * n];
for (i = 0; i < n * n; i++) Atemp[i] = A[i];
if (LUPdecompose(n, dtol, Atemp, P) != 0) return 1;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) b[j] = 0.0;
b[i] = 1.0;
LUPSolve(n, Atemp, b, P);
for (j = 0; j < n; j++) Ainv[j * n + i] = b[j];
}
delete[] P;
delete[] b;
delete[] Atemp;
return 0;
}
int SO3Math::LUPdecompose(int n, double dtol, double *A, int *P)
{
int i, j, k, maxi;
double maxA, Atemp;
double *normi;
maxi = 0;
normi = new double[n];
for (i = 0; i < n; i++) {
maxA = 0.0;
for (j = 0; j < n; j++) {
Atemp = fabs(A[i * n + j]);
if (Atemp > maxA) maxA = Atemp;
}
if (maxA < dtol) return 1;
normi[i] = 1.0 / maxA;
}
for (j = 0; j < n; j++) {
for (i = 0; i < j; i++)
for (k = 0; k < i; k++) A[i * n + j] -= A[i * n + k] * A[k * n + j];
maxA = 0.0;
for (i = j; i < n; i++) {
for (k = 0; k < j; k++) A[i * n + j] -= A[i * n + k] * A[k * n + j];
Atemp = fabs(A[i * n + j]) * normi[i];
if (Atemp >= maxA) {
maxA = Atemp;
maxi = i;
}
}
if (maxi != j) {
if ((j == (n - 2)) && (A[j * n + j + 1] == 0.0))
maxi = j;
else {
for (k = 0; k < n; k++) {
Atemp = A[j * n + k];
A[j * n + k] = A[maxi * n + k];
A[maxi * n + k] = Atemp;
}
normi[maxi] = normi[j];
}
}
P[j] = maxi;
if (A[j * n + j] == 0.0) A[j * n + j] = dtol;
if (j != (n - 1)) {
Atemp = 1.0 / A[j * n + j];
for (i = (j + 1); i < n; i++) A[i * n + j] *= Atemp;
}
}
delete[] normi;
return 0;
}
void SO3Math::LUPSolve(int n, double *A, double *B, int *P)
{
int i, j;
double dtemp;
for (i = 0; i < n; i++) {
dtemp = B[P[i]];
B[P[i]] = B[i];
for (j = (i - 1); j >= 0; j--) dtemp -= A[i * n + j] * B[j];
B[i] = dtemp;
}
for (i = (n - 1); i >= 0; i--) {
for (j = (i + 1); j < n; j++) B[i] -= A[i * n + j] * B[j];
B[i] /= A[i * n + i];
}
}
#endif /* LMP_MLIAP_SO3_MATH_H_ */

51
src/MLIAP/pair_mliap.cpp
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@ -19,10 +19,11 @@
#include "pair_mliap.h"
#include "mliap_data.h"
#include "mliap_model_linear.h"
#include "mliap_model_quadratic.h"
#include "mliap_model_nn.h"
#include "mliap_descriptor_snap.h"
#include "mliap_descriptor_so3.h"
#include "mliap_model_linear.h"
#include "mliap_model_nn.h"
#include "mliap_model_quadratic.h"
#ifdef MLIAP_PYTHON
#include "mliap_model_python.h"
#endif
@ -41,7 +42,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairMLIAP::PairMLIAP(LAMMPS *lmp) : Pair(lmp)
PairMLIAP::PairMLIAP(LAMMPS *lmp) :
Pair(lmp), map(nullptr), model(nullptr), descriptor(nullptr), data(nullptr)
{
single_enable = 0;
restartinfo = 0;
@ -65,7 +67,6 @@ PairMLIAP::~PairMLIAP()
memory->destroy(cutsq);
memory->destroy(map);
}
}
/* ----------------------------------------------------------------------
@ -77,27 +78,22 @@ void PairMLIAP::compute(int eflag, int vflag)
// consistency checks
if (data->ndescriptors != model->ndescriptors) {
error->all(FLERR,"Incompatible model and descriptor descriptor count");
};
if (data->ndescriptors != model->ndescriptors)
error->all(FLERR, "Incompatible model and descriptor descriptor count");
if (data->nelements != model->nelements) {
error->all(FLERR,"Incompatible model and descriptor element count");
};
ev_init(eflag,vflag);
if (data->nelements != model->nelements)
error->all(FLERR, "Incompatible model and descriptor element count");
ev_init(eflag, vflag);
data->generate_neighdata(list, eflag, vflag);
// compute descriptors, if needed
if (model->nonlinearflag || eflag)
descriptor->compute_descriptors(data);
if (model->nonlinearflag || eflag) descriptor->compute_descriptors(data);
// compute E_i and beta_i = dE_i/dB_i for all i in list
model->compute_gradients(data);
e_tally(data);
// calculate force contributions beta_i*dB_i/dR_j
@ -129,7 +125,6 @@ void PairMLIAP::allocate()
void PairMLIAP::settings(int narg, char ** arg)
{
if (narg < 4)
error->all(FLERR,"Illegal pair_style command");
@ -137,6 +132,8 @@ void PairMLIAP::settings(int narg, char ** arg)
int modelflag = 0;
int descriptorflag = 0;
delete model;
delete descriptor;
// process keywords
@ -159,9 +156,9 @@ void PairMLIAP::settings(int narg, char ** arg)
iarg += 3;
#ifdef MLIAP_PYTHON
} else if (strcmp(arg[iarg+1],"mliappy") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
model = new MLIAPModelPython(lmp,arg[iarg+2]);
iarg += 3;
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
model = new MLIAPModelPython(lmp,arg[iarg+2]);
iarg += 3;
#endif
} else error->all(FLERR,"Illegal pair_style mliap command");
modelflag = 1;
@ -171,6 +168,11 @@ void PairMLIAP::settings(int narg, char ** arg)
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
descriptor = new MLIAPDescriptorSNAP(lmp,arg[iarg+2]);
iarg += 3;
} else if (strcmp(arg[iarg+1],"so3") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
descriptor = new MLIAPDescriptorSO3(lmp,arg[iarg+2]);
iarg += 3;
} else error->all(FLERR,"Illegal pair_style mliap command");
descriptorflag = 1;
} else
@ -241,10 +243,9 @@ void PairMLIAP::coeff(int narg, char **arg)
model->init();
descriptor->init();
int gradgradflag = -1;
delete data;
data = new MLIAPData(lmp, gradgradflag, map, model, descriptor, this);
data->init();
}
/* ----------------------------------------------------------------------
@ -255,10 +256,8 @@ void PairMLIAP::e_tally(MLIAPData* data)
{
if (eflag_global) eng_vdwl += data->energy;
if (eflag_atom)
for (int ii = 0; ii < data->nlistatoms; ii++) {
const int i = data->iatoms[ii];
eatom[i] += data->eatoms[ii];
}
for (int ii = 0; ii < data->nlistatoms; ii++)
eatom[data->iatoms[ii]] += data->eatoms[ii];
}
/* ----------------------------------------------------------------------

156
unittest/force-styles/tests/manybody-pair-mliap_so3.yaml Normal file
View File

@ -0,0 +1,156 @@
---
lammps_version: 27 May 2021
date_generated: Sun Jun 13 17:44:07 2021
epsilon: 5e-13
skip_tests:
prerequisites: ! |
pair mliap
pre_commands: ! |
variable newton_pair delete
variable newton_pair index on
post_commands: ! ""
input_file: in.manybody
pair_style: mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
pair_coeff: ! |
* * Si Si Si Si Si Si Si Si
extract: ! ""
natoms: 64
init_vdwl: -242.08541438097282
init_coul: 0
init_stress: ! |2-
3.5856243389095512e+00 4.3178319509851431e+00 5.1450742391421338e+00 -2.3382445177587403e+00 6.3444541794487845e+00 9.1752299438021412e-01
init_forces: ! |2
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2 -3.4055902237163499e-01 -3.3463048947437657e-01 -2.0463281550586621e-01
3 1.0965493482185078e-01 1.1852119996899939e-02 -6.8690216469585785e-02
4 -4.2917681710400246e-01 5.8785334295730940e-01 2.6944024734509658e-01
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7 -1.6648111143006419e-01 -2.1580818190690107e-01 4.5962059999665661e-01
8 5.1793872208577641e-03 9.8258205721181310e-02 -2.1237239804032296e-01
9 -2.2695156450444193e-01 -3.0886720222241792e-01 -3.3982471524904129e-01
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23 3.8898630617701757e-01 4.6455023282884689e-01 3.3423521635638376e-01
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51 -5.9079732678911834e-01 5.4485696856005095e-01 6.8471642407028899e-01
52 1.2500943393870998e+00 -1.2483610604845263e+00 1.3764499435893642e+00
53 7.5044082180665861e-01 7.1006339405720620e-01 6.8752933088770685e-01
54 5.7790768581732632e-01 -6.0482253610873882e-01 -5.7995317962912973e-01
55 4.4776151869164765e-01 -5.9219393004341692e-01 -6.9398818388834249e-01
56 -7.4276087479339600e-02 3.8502591921562142e-02 -3.1482369726424059e-01
57 -4.9028410280524036e-02 -5.8115359646338252e-02 -2.6774949685019013e-02
58 3.7437462851140180e-01 -2.3858950328415252e-01 2.7176318794239890e-01
59 7.5049664891509604e-01 6.0003203348980849e-01 -6.0606097897888678e-01
60 -7.8027828178258207e-01 -1.0282777251742856e+00 -7.6957323203237027e-01
61 -2.0704735890388715e-01 2.1426153130500308e-01 -1.7757121507272916e-01
62 -4.9195674075326684e-01 5.5632927867395221e-01 -4.8501482619942371e-01
63 4.0392077364288381e-01 -6.5683525718558333e-01 -3.5450072515244213e-01
64 8.3136790206790612e-01 8.4030959270424599e-01 9.6744125066169429e-01
run_vdwl: -242.07509367477505
run_coul: 0
run_stress: ! |2-
3.6067334447532695e+00 4.3471333638967478e+00 5.1979080340147519e+00 -2.2917015647694656e+00 6.3545457412614894e+00 1.0105656026958723e+00
run_forces: ! |2
1 -3.2099025878012155e-01 5.6621647667818076e-01 3.5950167010603051e-01
2 -3.4509776918969848e-01 -3.3867254821455528e-01 -2.0920538372184505e-01
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8 2.4173198798722703e-03 9.8119054544594395e-02 -2.1160344210292820e-01
9 -2.3309913937974988e-01 -3.1480594421707164e-01 -3.4564398106874977e-01
10 -5.4522048631510535e-02 -2.6706654804162977e-01 -4.5324758936337878e-01
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...