documentation and examples
This commit is contained in:
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@ -108,6 +108,10 @@ KOKKOS, o = OPENMP, t = OPT.
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* :doc:`pe/mol/tally <compute_tally>`
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* :doc:`pe/tally <compute_tally>`
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* :doc:`plasticity/atom <compute_plasticity_atom>`
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* :doc:`pod/atom <compute_pod_atom>`
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* :doc:`podd/atom <compute_pod_atom>`
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* :doc:`pod/ldd <compute_pod_atom>`
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* :doc:`pod/gdd <compute_pod_atom>`
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* :doc:`pressure <compute_pressure>`
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* :doc:`pressure/alchemy <compute_pressure_alchemy>`
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* :doc:`pressure/uef <compute_pressure_uef>`
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@ -272,6 +272,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
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* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
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* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
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* :doc:`pod/atom <compute_pod_atom>` - POD descriptors for each atom
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* :doc:`podd/atom <compute_pod_atom>` - derivative of POD descriptors for each atom
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* :doc:`pod/ldd <compute_pod_atom>` - local POD descriptors and their derivatives
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* :doc:`pod/gdd <compute_pod_atom>` - global POD descriptors and their derivatives
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* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
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* :doc:`pressure/alchemy <compute_pressure_alchemy>` - mixed system total pressure and pressure tensor for :doc:`fix alchemy <fix_alchemy>` runs
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* :doc:`pressure/uef <compute_pressure_uef>` - pressure tensor in the reference frame of an applied flow field
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127
doc/src/compute_pod_atom.rst
Normal file
127
doc/src/compute_pod_atom.rst
Normal file
@ -0,0 +1,127 @@
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.. index:: compute pod/atom
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.. index:: compute podd/atom
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.. index:: compute pod/ldd
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.. index:: compute pod/gdd
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compute pod/atom command
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========================
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compute podd/atom command
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=========================
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compute pod/ldd command
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=======================
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compute pod/gdd command
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=======================
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Syntax
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""""""
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.. code-block:: LAMMPS
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compute ID group-ID pod/atom param.pod projection_matrix.pod centroids.pod
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compute ID group-ID podd/atom param.pod projection_matrix.pod centroids.pod
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compute ID group-ID pod/ldd param.pod projection_matrix.pod centroids.pod
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compute ID group-ID pod/gdd param.pod projection_matrix.pod centroids.pod
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* pod/atom = style name of this compute command
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* param.pod = the parameter file specifies parameters of the POD descriptors
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* projection_matrix.pod = the projection matrix file
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* centroids.pod = the centroid file
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute d all pod/atom Ta_param.pod
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compute dd all podd/atom Ta_param.pod
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compute ldd all pod/ldd Ta_param.pod
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compute gdd all podd/gdd Ta_param.pod
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compute d all pod/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
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compute dd all podd/atom Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
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compute ldd all pod/ldd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
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compute gdd all podd/gdd Ta_param.pod Ta_projection_matrix.pod Ta_centroids.pod
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Description
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"""""""""""
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Define a computation that calculates a set of quantities related to the
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POD descriptors of the atoms in a group. These computes are used
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primarily for calculating the dependence of energy and force components
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on the linear coefficients in the :doc:`pod pair_style
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<pair_pod>`, which is useful when training a POD potential to match
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target data. POD descriptors of an atom are characterized by the
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radial and angular distribution of neighbor atoms. The detailed
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mathematical definition is given in the papers by :ref:`(Nguyen and Rohskopf) <Nguyen20222>`,
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:ref:`(Nguyen2023) <Nguyen20232>`, :ref:`(Nguyen2024) <Nguyen20242>`, and :ref:`(Nguyen and Sema) <Nguyen20243>`.
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Compute *pod/atom* calculates the per-atom POD descriptors.
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Compute *podd/atom* calculates derivatives of the per-atom POD descriptors with respect to atom positions.
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Compute *pod/ldd* calculates the per-atom POD descriptors and their derivatives with respect to atom positions.
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Compute *pod/gdd* calculates the global POD descriptors and their derivatives with respect to atom positions.
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Examples how to use Compute POD commands are found in the directory lammps/examples/PACKAGES/pod.
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----------
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Output info
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"""""""""""
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Compute *pod/atom* produces an 2D array of size :math:`N \times M`, where :math:`N` is the number of atoms
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and :math:`M` is the number of descriptors. Each column corresponds to a particular POD descriptor.
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Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3 N)`. Each column
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corresponds to a particular derivative of a POD descriptor.
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Compute *pod/ldd* produces an 2D array of size :math:`(1 + 3N) \times (M * N)`.
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The first row contains the per-atom descriptors, and the last 3N rows contain the derivatives
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of the per-atom descriptors with respect to atom positions.
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Compute *pod/gdd* produces an 2D array of size :math:`(1 + 3N) \times (M)`.
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The first row contains the global descriptors, and the last 3N rows contain the derivatives
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of the global descriptors with respect to atom positions.
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Restrictions
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""""""""""""
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These computes are part of the ML-POD package. They are only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`fitpod <fitpod_command>`,
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:doc:`pair_style pod <pair_pod>`
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Default
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"""""""
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none
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----------
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.. _Nguyen20222:
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**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
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.. _Nguyen20232:
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**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
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.. _Nguyen20242:
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**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
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.. _Nguyen20243:
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**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
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@ -8,11 +8,14 @@ Syntax
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.. code-block:: LAMMPS
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fitpod Ta_param.pod Ta_data.pod
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fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
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* fitpod = style name of this command
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* Ta_param.pod = an input file that describes proper orthogonal descriptors (PODs)
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* Ta_data.pod = an input file that specifies DFT data used to fit a POD potential
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* Ta_coefficients.pod (optional) = an input file that specifies trainable coefficients of a POD potential
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* Ta_projection_matrix.pod (optional) = an input file that specifies a projection matrix for dimensionlity reduction via principal component analysis
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* Ta_centroids.pod (optional) = an input file that specifies centroids of clusters computed using k-means algorithm
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Examples
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""""""""
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@ -20,20 +23,23 @@ Examples
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.. code-block:: LAMMPS
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fitpod Ta_param.pod Ta_data.pod
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fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
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fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
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Description
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"""""""""""
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.. versionadded:: 22Dec2022
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Fit a machine-learning interatomic potential (ML-IAP) based on proper
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orthogonal descriptors (POD). Two input files are required for this
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command. The first input file describes a POD potential parameter
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settings, while the second input file specifies the DFT data used for
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the fitting procedure.
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orthogonal descriptors (POD); please see :ref:`(Nguyen and Rohskopf) <Nguyen20222>`,
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:ref:`(Nguyen2023) <Nguyen20232>`, :ref:`(Nguyen2024) <Nguyen20242>`, and :ref:`(Nguyen and Sema) <Nguyen20243>` for details.
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The fitted POD potential can be used to run MD simulations via :doc:`pair_style pod <pair_pod>`.
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The table below has one-line descriptions of all the keywords that can
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be used in the first input file (i.e. ``Ta_param.pod`` in the example
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above):
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Two input files are required for this command. The first input file describes a POD potential parameter
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settings, while the second input file specifies the DFT data used for
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the fitting procedure. All keywords except *species* have default values. If a keyword is not
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set in the input file, its default value is used. The table below has one-line descriptions of all the keywords that can
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be used in the first input file (i.e. ``Ta_param.pod``)
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.. list-table::
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:header-rows: 1
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@ -52,7 +58,7 @@ above):
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- INT
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- three integer constants specify boundary conditions
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* - rin
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- 1.0
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- 0.5
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- REAL
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- a real number specifies the inner cut-off radius
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* - rcut
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@ -60,47 +66,74 @@ above):
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- REAL
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- a real number specifies the outer cut-off radius
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* - bessel_polynomial_degree
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- 3
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- 4
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- INT
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- the maximum degree of Bessel polynomials
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* - inverse_polynomial_degree
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- 6
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- 8
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- INT
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- the maximum degree of inverse radial basis functions
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* - number_of_environment_clusters
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- 1
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- INT
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- the number of clusters for environment-adaptive potentials
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* - number_of_principal_components
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- 2
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- INT
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- the number of principal components for dimensionality reduction
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* - onebody
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- 1
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- BOOL
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- turns on/off one-body potential
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* - twobody_number_radial_basis_functions
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- 6
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- 8
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- INT
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- number of radial basis functions for two-body potential
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* - threebody_number_radial_basis_functions
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- 5
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- 6
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- INT
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- number of radial basis functions for three-body potential
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* - threebody_number_angular_basis_functions
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* - threebody_angular_degree
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- 5
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- INT
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- number of angular basis functions for three-body potential
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* - fourbody_snap_twojmax
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- angular degree for three-body potential
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* - fourbody_number_radial_basis_functions
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- 4
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- INT
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- number of radial basis functions for four-body potential
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* - fourbody_angular_degree
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- 3
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- INT
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- angular degree for four-body potential
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* - fivebody_number_radial_basis_functions
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- 0
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- INT
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- band limit for SNAP bispectrum components (0,2,4,6,8... allowed)
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* - fourbody_snap_chemflag
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- number of radial basis functions for five-body potential
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* - fivebody_angular_degree
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- 0
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- BOOL
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- turns on/off the explicit multi-element variant of the SNAP bispectrum components
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* - quadratic_pod_potential
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- INT
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- angular degree for five-body potential
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* - sixbody_number_radial_basis_functions
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- 0
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- BOOL
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- turns on/off quadratic POD potential
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- INT
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- number of radial basis functions for six-body potential
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* - sixbody_angular_degree
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- 0
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- INT
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- angular degree for six-body potential
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* - sevenbody_number_radial_basis_functions
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- 0
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- INT
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- number of radial basis functions for seven-body potential
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* - sevenbody_angular_degree
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- 0
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- INT
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- angular degree for seven-body potential
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All keywords except *species* have default values. If a keyword is not
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set in the input file, its default value is used. The next table
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describes all keywords that can be used in the second input file
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Note that both the number of radial basis functions and angular degree must decrease as the body order increases. The next table describes all keywords that can be used in the second input file
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(i.e. ``Ta_data.pod`` in the example above):
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.. list-table::
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:header-rows: 1
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:widths: auto
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@ -125,6 +158,10 @@ describes all keywords that can be used in the second input file
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- ""
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- STRING
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- specifies the path to test data files in double quotes
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* - path_to_environment_configuration_set
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- ""
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- STRING
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- specifies the path to environment configuration files in double quotes
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* - fraction_training_data_set
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- 1.0
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- REAL
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@ -133,6 +170,14 @@ describes all keywords that can be used in the second input file
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- 0
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- BOOL
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- turns on/off randomization of the training set
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* - fraction_test_data_set
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- 1.0
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- REAL
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- a real number (<= 1.0) specifies the fraction of the test set used to validate POD
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* - randomize_test_data_set
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- 0
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- BOOL
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- turns on/off randomization of the test set
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* - fitting_weight_energy
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- 100.0
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- REAL
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@ -161,6 +206,10 @@ describes all keywords that can be used in the second input file
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- 8
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- INT
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- number of digits after the decimal points for numbers in the coefficient file
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* - group_weights
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- global
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- STRING
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- ``table`` uses group weights defined for each group named by filename
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All keywords except *path_to_training_data_set* have default values. If
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a keyword is not set in the input file, its default value is used. After
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@ -171,15 +220,46 @@ successful training, a number of output files are produced, if enabled:
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* ``<basename>_test_errors.pod`` reports errors for the test data set
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* ``<basename>_test_analysis.pod`` reports detailed errors for all test configurations
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* ``<basename>_coefficients.pod`` contains the coefficients of the POD potential
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* ``<basename>_projection_matrix.pod`` contains the projection matrix from the principal component analysis
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* ``<basename>_centroids.pod`` contains the centroids of the atom clusters
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|
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After training the POD potential, ``Ta_param.pod`` and ``<basename>_coefficients.pod``
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are the two files needed to use the POD potential in LAMMPS. See
|
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:doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
|
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are the two files needed to use the POD potential in LAMMPS.
|
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If the number of environment clusters is greater than 1, then
|
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``<basename>_projection_matrix.pod`` and ``<basename>_centroids.pod`` are also needed.
|
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See :doc:`pair_style pod <pair_pod>` for using the POD potential. Examples
|
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about training and using POD potentials are found in the directory
|
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lammps/examples/PACKAGES/pod.
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lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
|
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|
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Parameterized Potential Energy Surface
|
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""""""""""""""""""""""""""""""""""""""
|
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Loss Function Group Weights
|
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^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
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|
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The ``group_weights`` keyword in the ``data.pod`` file is responsible for weighting certain groups
|
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of configurations in the loss function. For example:
|
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|
||||
.. code-block:: LAMMPS
|
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|
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group_weights table
|
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Displaced_A15 100.0 1.0
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Displaced_BCC 100.0 1.0
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Displaced_FCC 100.0 1.0
|
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Elastic_BCC 100.0 1.0
|
||||
Elastic_FCC 100.0 1.0
|
||||
GSF_110 100.0 1.0
|
||||
GSF_112 100.0 1.0
|
||||
Liquid 100.0 1.0
|
||||
Surface 100.0 1.0
|
||||
Volume_A15 100.0 1.0
|
||||
Volume_BCC 100.0 1.0
|
||||
Volume_FCC 100.0 1.0
|
||||
|
||||
This will apply an energy weight of ``100.0`` and a force weight of ``1.0`` for all groups in the
|
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``Ta`` example. The groups are named by their respecive filename. If certain groups are left out of
|
||||
this table, then the globally defined weights from the ``fitting_weight_energy`` and
|
||||
``fitting_weight_force`` keywords will be used.
|
||||
|
||||
POD Potential
|
||||
"""""""""""""
|
||||
|
||||
We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
|
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unique elements. We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
|
||||
@ -187,495 +267,35 @@ position vector and type of an atom *n* in the system,
|
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respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
|
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\}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
|
||||
\boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
|
||||
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The potential energy surface
|
||||
(PES) of the system can be expressed as a many-body expansion of the
|
||||
form
|
||||
Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the
|
||||
POD potential is expressed as :math:`E(\boldsymbol R, \boldsymbol Z) =
|
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\sum_{i=1}^N E_i(\boldsymbol R_i, \boldsymbol Z_i)`, where
|
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|
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.. math::
|
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|
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E(\boldsymbol R, \boldsymbol Z, \boldsymbol{\eta}, \boldsymbol{\mu}) \ = \ & \sum_{i} V^{(1)}(\boldsymbol r_i, Z_i, \boldsymbol \mu^{(1)} ) + \frac12 \sum_{i,j} V^{(2)}(\boldsymbol r_i, \boldsymbol r_j, Z_i, Z_j, \boldsymbol \eta, \boldsymbol \mu^{(2)}) \\
|
||||
& + \frac16 \sum_{i,j,k} V^{(3)}(\boldsymbol r_i, \boldsymbol r_j, \boldsymbol r_k, Z_i, Z_j, Z_k, \boldsymbol \eta, \boldsymbol \mu^{(3)}) + \ldots
|
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E_i(\boldsymbol R_i, \boldsymbol Z_i) \ = \ \sum_{m=1}^M c_m \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)
|
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|
||||
where :math:`V^{(1)}` is the one-body potential often used for
|
||||
representing external field or energy of isolated elements, and the
|
||||
higher-body potentials :math:`V^{(2)}, V^{(3)}, \ldots` are symmetric,
|
||||
uniquely defined, and zero if two or more indices take identical values.
|
||||
The superscript on each potential denotes its body order. Each *q*-body
|
||||
potential :math:`V^{(q)}` depends on :math:`\boldsymbol \mu^{(q)}` which
|
||||
are sets of parameters to fit the PES. Note that :math:`\boldsymbol \mu`
|
||||
is a collection of all potential parameters :math:`\boldsymbol
|
||||
\mu^{(1)}`, :math:`\boldsymbol \mu^{(2)}`, :math:`\boldsymbol
|
||||
\mu^{(3)}`, etc, and that :math:`\boldsymbol \eta` is a set of
|
||||
hyper-parameters such as inner cut-off radius :math:`r_{\rm in}` and
|
||||
outer cut-off radius :math:`r_{\rm cut}`.
|
||||
|
||||
Interatomic potentials rely on parameters to learn relationship between
|
||||
atomic environments and interactions. Since interatomic potentials are
|
||||
approximations by nature, their parameters need to be set to some
|
||||
reference values or fitted against data by necessity. Typically,
|
||||
potential fitting finds optimal parameters, :math:`\boldsymbol \mu^*`,
|
||||
to minimize a certain loss function of the predicted quantities and
|
||||
data. Since the fitted potential depends on the data set used to fit it,
|
||||
different data sets will yield different optimal parameters and thus
|
||||
different fitted potentials. When fitting the same functional form on
|
||||
*Q* different data sets, we would obtain *Q* different optimized
|
||||
potentials, :math:`E(\boldsymbol R,\boldsymbol Z, \boldsymbol \eta,
|
||||
\boldsymbol \mu_q^*), 1 \le q \le Q`. Consequently, there exist many
|
||||
different sets of optimized parameters for empirical interatomic
|
||||
potentials.
|
||||
|
||||
Instead of optimizing the potential parameters, inspired by the reduced
|
||||
basis method :ref:`(Grepl) <Grepl20072>` for parameterized partial
|
||||
differential equations, we view the parameterized PES as a parametric
|
||||
manifold of potential energies
|
||||
|
||||
.. math::
|
||||
|
||||
\mathcal{M} = \{E(\boldsymbol R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu) \ | \ \boldsymbol \mu \in \Omega^{\boldsymbol \mu} \}
|
||||
|
||||
where :math:`\Omega^{\boldsymbol \mu}` is a parameter domain in which
|
||||
:math:`\boldsymbol \mu` resides. The parametric manifold
|
||||
:math:`\mathcal{M}` contains potential energy surfaces for all values of
|
||||
:math:`\boldsymbol \mu \in \Omega^{\boldsymbol \mu}`. Therefore, the
|
||||
parametric manifold yields a much richer and more transferable atomic
|
||||
representation than any particular individual PES :math:`E(\boldsymbol
|
||||
R, \boldsymbol Z, \boldsymbol \eta, \boldsymbol \mu^*)`.
|
||||
|
||||
We propose specific forms of the parameterized potentials for one-body,
|
||||
two-body, and three-body interactions. We apply the Karhunen-Loeve
|
||||
expansion to snapshots of the parameterized potentials to obtain sets of
|
||||
orthogonal basis functions. These basis functions are aggregated
|
||||
according to the chemical elements of atoms, thus leading to
|
||||
multi-element proper orthogonal descriptors.
|
||||
|
||||
Proper Orthogonal Descriptors
|
||||
"""""""""""""""""""""""""""""
|
||||
|
||||
Proper orthogonal descriptors are finger prints characterizing the
|
||||
radial and angular distribution of a system of atoms. The detailed
|
||||
mathematical definition is given in the paper by Nguyen and Rohskopf
|
||||
:ref:`(Nguyen) <Nguyen20222>`.
|
||||
|
||||
The descriptors for the one-body interaction are used to capture energy
|
||||
of isolated elements and defined as follows
|
||||
|
||||
.. math::
|
||||
|
||||
D_{ip}^{(1)} = \left\{
|
||||
\begin{array}{ll}
|
||||
1, & \mbox{if } Z_i = p \\
|
||||
0, & \mbox{if } Z_i \neq p
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
for :math:`1 \le i \le N, 1 \le p \le N_{\rm e}`. The number of one-body
|
||||
descriptors per atom is equal to the number of elements. The one-body
|
||||
descriptors are independent of atom positions, but dependent on atom
|
||||
types. The one-body descriptors are active only when the keyword
|
||||
*onebody* is set to 1.
|
||||
|
||||
We adopt the usual assumption that the direct interaction between two
|
||||
atoms vanishes smoothly when their distance is greater than the outer
|
||||
cutoff distance :math:`r_{\rm cut}`. Furthermore, we assume that two
|
||||
atoms can not get closer than the inner cutoff distance :math:`r_{\rm
|
||||
in}` due to the Pauli repulsion principle. Let :math:`r \in (r_{\rm in},
|
||||
r_{\rm cut})`, we introduce the following parameterized radial functions
|
||||
|
||||
.. math::
|
||||
|
||||
\phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) = \frac{\sin (\alpha \pi x) }{r - r_{\rm in}}, \qquad \varphi(r, \gamma) = \frac{1}{r^\gamma} ,
|
||||
|
||||
where the scaled distance function :math:`x` is defined below to enrich the two-body manifold
|
||||
|
||||
.. math::
|
||||
|
||||
x(r, r_{\rm in}, r_{\rm cut}, \beta) = \frac{e^{-\beta(r - r_{\rm in})/(r_{\rm cut} - r_{\rm in})} - 1}{e^{-\beta} - 1} .
|
||||
|
||||
We introduce the following function as a convex combination of the two functions
|
||||
|
||||
.. math::
|
||||
|
||||
\psi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta, \gamma, \kappa) = \kappa \phi(r, r_{\rm in}, r_{\rm cut}, \alpha, \beta) + (1- \kappa) \varphi(r, \gamma) .
|
||||
|
||||
We see that :math:`\psi` is a function of distance :math:`r`, cut-off
|
||||
distances :math:`r_{\rm in}` and :math:`r_{\rm cut}`, and parameters
|
||||
:math:`\alpha, \beta, \gamma, \kappa`. Together these parameters allow
|
||||
the function :math:`\psi` to characterize a diverse spectrum of two-body
|
||||
interactions within the cut-off interval :math:`(r_{\rm in}, r_{\rm
|
||||
cut})`.
|
||||
|
||||
Next, we introduce the following parameterized potential
|
||||
|
||||
.. math::
|
||||
|
||||
W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}) = f_{\rm c}(r_{ij}, \boldsymbol \eta) \psi(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)})
|
||||
|
||||
where :math:`\eta_1 = r_{\rm in}, \eta_2 = r_{\rm cut}, \mu_1^{(2)} =
|
||||
\alpha, \mu_2^{(2)} = \beta, \mu_3^{(2)} = \gamma`, and
|
||||
:math:`\mu_4^{(2)} = \kappa`. Here the cut-off function :math:`f_{\rm
|
||||
c}(r_{ij}, \boldsymbol \eta)` proposed in [refs] is used to ensure the
|
||||
smooth vanishing of the potential and its derivative for :math:`r_{ij}
|
||||
\ge r_{\rm cut}`:
|
||||
|
||||
.. math::
|
||||
|
||||
f_{\rm c}(r_{ij}, r_{\rm in}, r_{\rm cut}) = \exp \left(1 -\frac{1}{\sqrt{\left(1 - \frac{(r-r_{\rm in})^3}{(r_{\rm cut} - r_{\rm in})^3} \right)^2 + 10^{-6}}} \right)
|
||||
|
||||
Based on the parameterized potential, we form a set of snapshots as
|
||||
follows. We assume that we are given :math:`N_{\rm s}` parameter tuples
|
||||
:math:`\boldsymbol \mu^{(2)}_\ell, 1 \le \ell \le N_{\rm s}`. We
|
||||
introduce the following set of snapshots on :math:`(r_{\rm in}, r_{\rm
|
||||
cut})`:
|
||||
|
||||
.. math::
|
||||
|
||||
\xi_\ell(r_{ij}, \boldsymbol \eta) = W^{(2)}(r_{ij}, \boldsymbol \eta, \boldsymbol \mu^{(2)}_\ell), \quad \ell = 1, \ldots, N_{\rm s} .
|
||||
|
||||
To ensure adequate sampling of the PES for different parameters, we
|
||||
choose :math:`N_{\rm s}` parameter points :math:`\boldsymbol
|
||||
\mu^{(2)}_\ell = (\alpha_\ell, \beta_\ell, \gamma_\ell, \kappa_\ell), 1
|
||||
\le \ell \le N_{\rm s}` as follows. The parameters :math:`\alpha \in [1,
|
||||
N_\alpha]` and :math:`\gamma \in [1, N_\gamma]` are integers, where
|
||||
:math:`N_\alpha` and :math:`N_\gamma` are the highest degrees for
|
||||
:math:`\alpha` and :math:`\gamma`, respectively. We next choose
|
||||
:math:`N_\beta` different values of :math:`\beta` in the interval
|
||||
:math:`[\beta_{\min}, \beta_{\max}]`, where :math:`\beta_{\min} = 0` and
|
||||
:math:`\beta_{\max} = 4`. The parameter :math:`\kappa` can be set either
|
||||
0 or 1. Hence, the total number of parameter points is :math:`N_{\rm s}
|
||||
= N_\alpha N_\beta + N_\gamma`. Although :math:`N_\alpha, N_\beta,
|
||||
N_\gamma` can be chosen conservatively large, we find that
|
||||
:math:`N_\alpha = 6, N_\beta = 3, N_\gamma = 8` are adequate for most
|
||||
problems. Note that :math:`N_\alpha` and :math:`N_\gamma` correspond to
|
||||
*bessel_polynomial_degree* and *inverse_polynomial_degree*,
|
||||
respectively.
|
||||
|
||||
We employ the Karhunen-Loeve (KL) expansion to generate an orthogonal
|
||||
basis set which is known to be optimal for representation of the
|
||||
snapshot family :math:`\{\xi_\ell\}_{\ell=1}^{N_{\rm s}}`. The two-body
|
||||
orthogonal basis functions are computed as follows
|
||||
|
||||
.. math::
|
||||
|
||||
U^{(2)}_m(r_{ij}, \boldsymbol \eta) = \sum_{\ell = 1}^{N_{\rm s}} A_{\ell m}(\boldsymbol \eta) \, \xi_\ell(r_{ij}, \boldsymbol \eta), \qquad m = 1, \ldots, N_{\rm 2b} ,
|
||||
|
||||
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{N_{\rm s} \times
|
||||
N_{\rm s}}` consists of eigenvectors of the eigenvalue problem
|
||||
|
||||
.. math::
|
||||
|
||||
\boldsymbol C \boldsymbol a = \lambda \boldsymbol a
|
||||
|
||||
with the entries of :math:`\boldsymbol C \in \mathbb{R}^{N_{\rm s} \times N_{\rm s}}` being given by
|
||||
|
||||
.. math::
|
||||
|
||||
C_{ij} = \frac{1}{N_{\rm s}} \int_{r_{\rm in}}^{r_{\rm cut}} \xi_i(x, \boldsymbol \eta) \xi_j(x, \boldsymbol \eta) dx, \quad 1 \le i, j \le N_{\rm s}
|
||||
|
||||
Note that the eigenvalues :math:`\lambda_\ell, 1 \le \ell \le N_{\rm
|
||||
s}`, are ordered such that :math:`\lambda_1 \ge \lambda_2 \ge \ldots \ge
|
||||
\lambda_{N_{\rm s}}`, and that the matrix :math:`\boldsymbol A` is
|
||||
pe-computed and stored for any given :math:`\boldsymbol \eta`. Owing to
|
||||
the rapid convergence of the KL expansion, only a small number of
|
||||
orthogonal basis functions is needed to obtain accurate
|
||||
approximation. The value of :math:`N_{\rm 2b}` corresponds to
|
||||
*twobody_number_radial_basis_functions*.
|
||||
|
||||
The two-body proper orthogonal descriptors at each atom *i* are computed
|
||||
by summing the orthogonal basis functions over the neighbors of atom *i*
|
||||
and numerating on the atom types as follows
|
||||
|
||||
.. math::
|
||||
|
||||
D^{(2)}_{im l(p, q) }(\boldsymbol \eta) = \left\{
|
||||
\begin{array}{ll}
|
||||
\displaystyle \sum_{\{j | Z_j = q\}} U^{(2)}_m(r_{ij}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
|
||||
0, & \mbox{if } Z_i \neq p
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
for :math:`1 \le i \le N, 1 \le m \le N_{\rm 2b}, 1 \le q, p \le N_{\rm
|
||||
e}`. Here :math:`l(p,q)` is a symmetric index mapping such that
|
||||
|
||||
.. math::
|
||||
|
||||
l(p,q) = \left\{
|
||||
\begin{array}{ll}
|
||||
q + (p-1) N_{\rm e} - p(p-1)/2, & \mbox{if } q \ge p \\
|
||||
p + (q-1) N_{\rm e} - q(q-1)/2, & \mbox{if } q < p .
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
The number of two-body descriptors per atom is thus :math:`N_{\rm 2b}
|
||||
N_{\rm e}(N_{\rm e}+1)/2`.
|
||||
|
||||
It is important to note that the orthogonal basis functions do not
|
||||
depend on the atomic numbers :math:`Z_i` and :math:`Z_j`. Therefore, the
|
||||
cost of evaluating the basis functions and their derivatives with
|
||||
respect to :math:`r_{ij}` is independent of the number of elements
|
||||
:math:`N_{\rm e}`. Consequently, even though the two-body proper
|
||||
orthogonal descriptors depend on :math:`\boldsymbol Z`, their
|
||||
computational complexity is independent of :math:`N_{\rm e}`.
|
||||
|
||||
In order to provide proper orthogonal descriptors for three-body
|
||||
interactions, we need to introduce a three-body parameterized
|
||||
potential. In particular, the three-body potential is defined as a
|
||||
product of radial and angular functions as follows
|
||||
|
||||
.. math::
|
||||
|
||||
W^{(3)}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta, \boldsymbol \mu^{(3)}) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}) \\
|
||||
\psi(r_{ik}, r_{\rm min}, r_{\rm max}, \alpha, \beta, \gamma, \kappa) f_{\rm c}(r_{ik}, r_{\rm min}, r_{\rm max}) \\
|
||||
\cos (\sigma \theta_{ijk} + \zeta)
|
||||
|
||||
where :math:`\sigma` is the periodic multiplicity, :math:`\zeta` is the
|
||||
equilibrium angle, :math:`\boldsymbol \mu^{(3)} = (\alpha, \beta,
|
||||
\gamma, \kappa, \sigma, \zeta)`. The three-body potential provides an
|
||||
angular fingerprint of the atomic environment through the bond angles
|
||||
:math:`\theta_{ijk}` formed with each pair of neighbors :math:`j` and
|
||||
:math:`k`. Compared to the two-body potential, the three-body potential
|
||||
has two extra parameters :math:`(\sigma, \zeta)` associated with the
|
||||
angular component.
|
||||
|
||||
Let :math:`\boldsymbol \varrho = (\alpha, \beta, \gamma, \kappa)`. We
|
||||
assume that we are given :math:`L_{\rm r}` parameter tuples
|
||||
:math:`\boldsymbol \varrho_\ell, 1 \le \ell \le L_{\rm r}`. We
|
||||
introduce the following set of snapshots on :math:`(r_{\min},
|
||||
r_{\max})`:
|
||||
|
||||
.. math::
|
||||
|
||||
\zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ) = \psi(r_{ij}, r_{\rm min}, r_{\rm max}, \boldsymbol \varrho_\ell) f_{\rm c}(r_{ij}, r_{\rm min}, r_{\rm max}), \quad 1 \le \ell \le L_{\rm r} .
|
||||
|
||||
We apply the Karhunen-Loeve (KL) expansion to this set of snapshots to
|
||||
obtain orthogonal basis functions as follows
|
||||
|
||||
.. math::
|
||||
|
||||
U^{r}_m(r_{ij}, r_{\rm min}, r_{\rm max} ) = \sum_{\ell = 1}^{L_{\rm r}} A_{\ell m} \, \zeta_\ell(r_{ij}, r_{\rm min}, r_{\rm max} ), \qquad m = 1, \ldots, N_{\rm r} ,
|
||||
|
||||
where the matrix :math:`\boldsymbol A \in \mathbb{R}^{L_{\rm r} \times L_{\rm r}}` consists
|
||||
of eigenvectors of the eigenvalue problem. For the parameterized angular function,
|
||||
we consider angular basis functions
|
||||
|
||||
.. math::
|
||||
|
||||
U^{a}_n(\theta_{ijk}) = \cos ((n-1) \theta_{ijk}), \qquad n = 1,\ldots, N_{\rm a},
|
||||
|
||||
where :math:`N_{\rm a}` is the number of angular basis functions. The orthogonal
|
||||
basis functions for the parameterized potential are computed as follows
|
||||
|
||||
.. math::
|
||||
|
||||
U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta) = U^{r}_m(r_{ij}, \boldsymbol \eta) U^{r}_m(r_{ik}, \boldsymbol \eta) U^{a}_n(\theta_{ijk}),
|
||||
|
||||
for :math:`1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}`. The number of three-body
|
||||
orthogonal basis functions is equal to :math:`N_{\rm 3b} = N_{\rm r} N_{\rm a}` and
|
||||
independent of the number of elements. The value of :math:`N_{\rm r}` corresponds to
|
||||
*threebody_number_radial_basis_functions*, while that of :math:`N_{\rm a}` to
|
||||
*threebody_number_angular_basis_functions*.
|
||||
|
||||
The three-body proper orthogonal descriptors at each atom *i*
|
||||
are obtained by summing over the neighbors *j* and *k* of atom *i* as
|
||||
|
||||
.. math::
|
||||
|
||||
D^{(3)}_{imn \ell(p, q, s)}(\boldsymbol \eta) = \left\{
|
||||
\begin{array}{ll}
|
||||
\displaystyle \sum_{\{j | Z_j = q\}} \sum_{\{k | Z_k = s\}} U^{(3)}_{mn}(r_{ij}, r_{ik}, \theta_{ijk}, \boldsymbol \eta), & \mbox{if } Z_i = p \\
|
||||
0, & \mbox{if } Z_i \neq p
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
for :math:`1 \le i \le N, 1 \le m \le N_{\rm r}, 1 \le n \le N_{\rm a}, 1 \le q, p, s \le N_{\rm e}`,
|
||||
where
|
||||
|
||||
.. math::
|
||||
|
||||
\ell(p,q,s) = \left\{
|
||||
\begin{array}{ll}
|
||||
s + (q-1) N_{\rm e} - q(q-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2 , & \mbox{if } s \ge q \\
|
||||
q + (s-1) N_{\rm e} - s(s-1)/2 + (p-1)N_{\rm e}(1+N_{\rm e})/2, & \mbox{if } s < q .
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
The number of three-body descriptors per atom is thus :math:`N_{\rm 3b} N_{\rm e}^2(N_{\rm e}+1)/2`.
|
||||
While the number of three-body PODs is cubic function of the number of elements,
|
||||
the computational complexity of the three-body PODs is independent of the number of elements.
|
||||
|
||||
Four-Body SNAP Descriptors
|
||||
""""""""""""""""""""""""""
|
||||
|
||||
In addition to the proper orthogonal descriptors described above, we also employ
|
||||
the spectral neighbor analysis potential (SNAP) descriptors. SNAP uses bispectrum components
|
||||
to characterize the local neighborhood of each atom in a very general way. The mathematical definition
|
||||
of the bispectrum calculation and its derivatives w.r.t. atom positions is described in
|
||||
:doc:`compute snap <compute_sna_atom>`. In SNAP, the
|
||||
total energy is decomposed into a sum over atom energies. The energy of
|
||||
atom *i* is expressed as a weighted sum over bispectrum components.
|
||||
|
||||
.. math::
|
||||
|
||||
E_i^{\rm SNAP} = \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}
|
||||
|
||||
|
||||
where the SNAP descriptors are related to the bispectrum components by
|
||||
|
||||
.. math::
|
||||
|
||||
D^{(4)}_{ikp} = \left\{
|
||||
\begin{array}{ll}
|
||||
\displaystyle B_{ik}, & \mbox{if } Z_i = p \\
|
||||
0, & \mbox{if } Z_i \neq p
|
||||
\end{array}
|
||||
\right.
|
||||
|
||||
Here :math:`B_{ik}` is the *k*\ -th bispectrum component of atom *i*. The number of
|
||||
bispectrum components :math:`N_{\rm 4b}` depends on the value of *fourbody_snap_twojmax* :math:`= 2 J_{\rm max}`
|
||||
and *fourbody_snap_chemflag*. If *fourbody_snap_chemflag* = 0
|
||||
then :math:`N_{\rm 4b} = (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
|
||||
If *fourbody_snap_chemflag* = 1 then :math:`N_{\rm 4b} = N_{\rm e}^3 (J_{\rm max}+1)(J_{\rm max}+2)(J_{\rm max}+1.5)/3`.
|
||||
The bispectrum calculation is described in more detail in :doc:`compute sna/atom <compute_sna_atom>`.
|
||||
|
||||
Linear Proper Orthogonal Descriptor Potentials
|
||||
""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
The proper orthogonal descriptors and SNAP descriptors are used to define the atomic energies
|
||||
in the following expansion
|
||||
|
||||
.. math::
|
||||
|
||||
E_{i}(\boldsymbol \eta) = \sum_{p=1}^{N_{\rm e}} c^{(1)}_p D^{(1)}_{ip} + \sum_{m=1}^{N_{\rm 2b}} \sum_{l=1}^{N_{\rm e}(N_{\rm e}+1)/2} c^{(2)}_{ml} D^{(2)}_{iml}(\boldsymbol \eta) + \sum_{m=1}^{N_{\rm r}} \sum_{n=1}^{N_{\rm a}} \sum_{\ell=1}^{N_{\rm e}^2(N_{\rm e}+1)/2} c^{(3)}_{mn\ell} D^{(3)}_{imn\ell}(\boldsymbol \eta) + \sum_{k=1}^{N_{\rm 4b}} \sum_{p=1}^{N_{\rm e}} c_{kp}^{(4)} D_{ikp}^{(4)}(\boldsymbol \eta),
|
||||
|
||||
where :math:`D^{(1)}_{ip}, D^{(2)}_{iml}, D^{(3)}_{imn\ell}, D^{(4)}_{ikp}` are the one-body, two-body, three-body, four-body descriptors,
|
||||
respectively, and :math:`c^{(1)}_p, c^{(2)}_{ml}, c^{(3)}_{mn\ell}, c^{(4)}_{kp}` are their respective expansion
|
||||
coefficients. In a more compact notation that implies summation over descriptor indices
|
||||
the atomic energies can be written as
|
||||
|
||||
.. math::
|
||||
|
||||
E_i(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m D^{(1)}_{im} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_k D^{(2)}_{im} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m D^{(3)}_{im} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m D^{(4)}_{im}
|
||||
|
||||
where :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2`,
|
||||
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2`, and
|
||||
:math:`N_{\rm d}^{(4)} = N_{\rm 4b} N_{\rm e}` are
|
||||
the number of two-body, three-body, and four-body descriptors, respectively.
|
||||
|
||||
The potential energy is then obtained by summing local atomic energies :math:`E_i`
|
||||
for all atoms :math:`i` in the system
|
||||
|
||||
.. math::
|
||||
|
||||
E(\boldsymbol \eta) = \sum_{i}^N E_{i}(\boldsymbol \eta)
|
||||
|
||||
Because the descriptors are one-body, two-body, and three-body terms,
|
||||
the resulting POD potential is a three-body PES. We can express the potential
|
||||
energy as a linear combination of the global descriptors as follows
|
||||
|
||||
.. math::
|
||||
|
||||
E(\boldsymbol \eta) = \sum_{m=1}^{N_{\rm e}} c^{(1)}_m d^{(1)}_{m} + \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m d^{(2)}_{m} + \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m d^{(3)}_{m} + \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m d^{(4)}_{m}
|
||||
|
||||
where the global descriptors are given by
|
||||
|
||||
.. math::
|
||||
|
||||
d_{m}^{(1)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(1)}(\boldsymbol \eta), \quad d_{m}^{(2)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(2)}(\boldsymbol \eta), \quad d_{m}^{(3)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(3)}(\boldsymbol \eta), \quad d_{m}^{(4)}(\boldsymbol \eta) = \sum_{i=1}^N D_{im}^{(4)}(\boldsymbol \eta)
|
||||
|
||||
Hence, we obtain the atomic forces as
|
||||
|
||||
.. math::
|
||||
|
||||
\boldsymbol F = -\nabla E(\boldsymbol \eta) = - \sum_{m=1}^{N_{\rm d}^{(2)}} c^{(2)}_m \nabla d_m^{(2)} - \sum_{m=1}^{N_{\rm d}^{(3)}} c^{(3)}_m \nabla d_m^{(3)} - \sum_{m=1}^{N_{\rm d}^{(4)}} c^{(4)}_m \nabla d_m^{(4)}
|
||||
|
||||
where :math:`\nabla d_m^{(2)}`, :math:`\nabla d_m^{(3)}` and :math:`\nabla d_m^{(4)}` are derivatives of the two-body
|
||||
three-body, and four-body global descriptors with respect to atom positions, respectively.
|
||||
Note that since the first-body global descriptors are constant, their derivatives are zero.
|
||||
|
||||
Quadratic Proper Orthogonal Descriptor Potentials
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
We recall two-body PODs :math:`D^{(2)}_{ik}, 1 \le k \le N_{\rm d}^{(2)}`,
|
||||
and three-body PODs :math:`D^{(3)}_{im}, 1 \le m \le N_{\rm d}^{(3)}`,
|
||||
with :math:`N_{\rm d}^{(2)} = N_{\rm 2b} N_{\rm e} (N_{\rm e}+1)/2` and
|
||||
:math:`N_{\rm d}^{(3)} = N_{\rm 3b} N_{\rm e}^2 (N_{\rm e}+1)/2` being
|
||||
the number of descriptors per atom for the two-body PODs and three-body PODs,
|
||||
respectively. We employ them to define a new set of atomic descriptors as follows
|
||||
|
||||
.. math::
|
||||
|
||||
D^{(2*3)}_{ikm} = \frac{1}{2N}\left( D^{(2)}_{ik} \sum_{j=1}^N D^{(3)}_{jm} + D^{(3)}_{im} \sum_{j=1}^N D^{(2)}_{jk} \right)
|
||||
|
||||
for :math:`1 \le i \le N, 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`.
|
||||
The new descriptors are four-body because they involve central atom :math:`i` together
|
||||
with three neighbors :math:`j, k` and :math:`l`. The total number of new descriptors per atom is equal to
|
||||
|
||||
.. math::
|
||||
|
||||
N_{\rm d}^{(2*3)} = N_{\rm d}^{(2)} * N_{\rm d}^{(3)} = N_{\rm 2b} N_{\rm 3b} N_{\rm e}^3 (N_{\rm e}+1)^2/4 .
|
||||
|
||||
The new global descriptors are calculated as
|
||||
|
||||
.. math::
|
||||
|
||||
d^{(2*3)}_{km} = \sum_{i=1}^N D^{(2*3)}_{ikm} = \left( \sum_{i=1}^N D^{(2)}_{ik} \right) \left( \sum_{i=1}^N D^{(3)}_{im} \right) = d^{(2)}_{k} d^{(3)}_m,
|
||||
|
||||
for :math:`1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)}`. Hence, the gradient
|
||||
of the new global descriptors with respect to atom positions is calculated as
|
||||
|
||||
.. math::
|
||||
|
||||
\nabla d^{(2*3)}_{km} = d^{(3)}_m \nabla d^{(2)}_{k} + d^{(2)}_{k} \nabla d^{(3)}_m, \quad 1 \le k \le N_{\rm d}^{(2)}, 1 \le m \le N_{\rm d}^{(3)} .
|
||||
|
||||
The quadratic POD potential is defined as a linear combination of the
|
||||
original and new global descriptors as follows
|
||||
|
||||
.. math::
|
||||
|
||||
E^{(2*3)} = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d^{(2*3)}_{km} .
|
||||
|
||||
It thus follows that
|
||||
|
||||
.. math::
|
||||
|
||||
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \left( \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)} \right) d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} \left( \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)} \right) d_m^{(3)} ,
|
||||
|
||||
which is simplified to
|
||||
|
||||
.. math::
|
||||
|
||||
E^{(2*3)} = 0.5 \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b_k^{(2)} d_k^{(2)} + 0.5 \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b_m^{(3)} d_m^{(3)}
|
||||
|
||||
where
|
||||
|
||||
.. math::
|
||||
|
||||
b_k^{(2)} & = \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} d_m^{(3)}, \quad k = 1,\ldots, N_{\rm 2d}^{(2*3)}, \\
|
||||
b_m^{(3)} & = \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} c^{(2*3)}_{km} d_k^{(2)}, \quad m = 1,\ldots, N_{\rm 3d}^{(2*3)} .
|
||||
|
||||
The quadratic POD potential results in the following atomic forces
|
||||
|
||||
.. math::
|
||||
|
||||
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} c^{(2*3)}_{km} \nabla d^{(2*3)}_{km} .
|
||||
|
||||
It can be shown that
|
||||
|
||||
.. math::
|
||||
|
||||
\boldsymbol F^{(2*3)} = - \sum_{k=1}^{N_{\rm 2d}^{(2*3)}} b^{(2)}_k \nabla d_k^{(2)} - \sum_{m=1}^{N_{\rm 3d}^{(2*3)}} b^{(3)}_m \nabla d_m^{(3)} .
|
||||
|
||||
The calculation of the atomic forces for the quadratic POD potential
|
||||
only requires the extra calculation of :math:`b_k^{(2)}` and :math:`b_m^{(3)}` which can be negligible.
|
||||
As a result, the quadratic POD potential does not increase the computational complexity.
|
||||
Here :math:`c_m` are trainable coefficients and :math:`\mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)`
|
||||
are per-atom POD descriptors. Summing the per-atom descriptors over :math:`i` yields the
|
||||
global descriptors :math:`d_m(\boldsymbol R, \boldsymbol Z) = \sum_{i=1}^N \mathcal{D}_{im}(\boldsymbol R_i, \boldsymbol Z_i)`.
|
||||
It thus follows that :math:`E(\boldsymbol R, \boldsymbol Z) =
|
||||
\sum_{m=1}^M c_m d_m(\boldsymbol R, \boldsymbol Z)`.
|
||||
|
||||
The per-atom POD descriptors include one, two, three, four, five, six, and seven-body
|
||||
descriptors, which can be specified in the first input file. Furthermore, the per-atom POD descriptors
|
||||
also depend on the number of environment clusters speciefied in the first input file.
|
||||
Please see :ref:`(Nguyen2024) <Nguyen20242>` and :ref:`(Nguyen and Sema) <Nguyen20243>` for the detailed description of the per-atom POD descriptors.
|
||||
|
||||
Training
|
||||
""""""""
|
||||
|
||||
POD potentials are trained using the least-squares regression against
|
||||
POD potential is trained using the least-squares regression against
|
||||
density functional theory (DFT) data. Let :math:`J` be the number of
|
||||
training configurations, with :math:`N_j` being the number of atoms in
|
||||
the j-th configuration. Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
|
||||
the j-th configuration. The training configurations are extracted from
|
||||
the extended XYZ files located in a directory (i.e., path_to_training_data_set
|
||||
in the second input file). Let :math:`\{E^{\star}_j\}_{j=1}^{J}` and
|
||||
:math:`\{\boldsymbol F^{\star}_j\}_{j=1}^{J}` be the DFT energies and
|
||||
forces for :math:`J` configurations. Next, we calculate the global
|
||||
descriptors and their derivatives for all training configurations. Let
|
||||
@ -694,7 +314,7 @@ found by solving the following least-squares problem
|
||||
|
||||
.. math::
|
||||
|
||||
{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A(\boldsymbol \eta) \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B(\boldsymbol \eta) \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
|
||||
{\min}_{\boldsymbol c \in \mathbb{R}^{M}} \ w_E \|\boldsymbol A \boldsymbol c - \bar{\boldsymbol E}^{\star} \|^2 + w_F \|\boldsymbol B \boldsymbol c + \boldsymbol F^{\star} \|^2 + w_R \|\boldsymbol c \|^2,
|
||||
|
||||
where :math:`w_E` and :math:`w_F` are weights for the energy
|
||||
(*fitting_weight_energy*) and force (*fitting_weight_force*),
|
||||
@ -704,18 +324,25 @@ E^{\star}_j/N_j` and :math:`\boldsymbol F^{\star}` is a vector of
|
||||
:math:`\mathcal{N}` entries obtained by stacking :math:`\{\boldsymbol
|
||||
F^{\star}_j\}_{j=1}^{J}` from top to bottom.
|
||||
|
||||
The training procedure is the same for both the linear and quadratic POD
|
||||
potentials. However, since the quadratic POD potential has a
|
||||
significantly larger number of the global descriptors, it is more
|
||||
expensive to train the linear POD potential. This is because the
|
||||
training of the quadratic POD potential still requires us to calculate
|
||||
and store the quadratic global descriptors and their
|
||||
gradient. Furthermore, the quadratic POD potential may require more
|
||||
training data in order to prevent over-fitting. In order to reduce the
|
||||
computational cost of fitting the quadratic POD potential and avoid
|
||||
over-fitting, we can use subsets of two-body and three-body PODs for
|
||||
constructing the new descriptors.
|
||||
Validation
|
||||
""""""""""
|
||||
|
||||
POD potential can be validated on a test dataset in a directory specified
|
||||
by setting path_to_test_data_set in the second input file. It is possible to
|
||||
validate the POD potential after the training is complete. This is done by
|
||||
providing the coefficient file as an input to :doc:`fitpod <fitpod_command>`,
|
||||
for example,
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod
|
||||
|
||||
However, if the number of clusters is greater than 1, then both the projection matrix and the centroids
|
||||
must also be provided
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
fitpod Ta_param.pod Ta_data.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
@ -727,7 +354,11 @@ LAMMPS was built with that package. See the :doc:`Build package
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style pod <pair_pod>`
|
||||
:doc:`pair_style pod <pair_pod>`,
|
||||
:doc:`compute pod/atom <compute_pod_atom>`,
|
||||
:doc:`compute podd/atom <compute_pod_atom>`,
|
||||
:doc:`compute pod/ldd <compute_pod_atom>`,
|
||||
:doc:`compute pod/gdd <compute_pod_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -736,10 +367,20 @@ The keyword defaults are also given in the description of the input files.
|
||||
|
||||
----------
|
||||
|
||||
.. _Grepl20072:
|
||||
|
||||
**(Grepl)** Grepl, Maday, Nguyen, and Patera, ESAIM: Mathematical Modelling and Numerical Analysis 41(3), 575-605, (2007).
|
||||
|
||||
.. _Nguyen20222:
|
||||
|
||||
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).
|
||||
**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
|
||||
|
||||
.. _Nguyen20232:
|
||||
|
||||
**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
|
||||
|
||||
.. _Nguyen20242:
|
||||
|
||||
**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
|
||||
|
||||
.. _Nguyen20243:
|
||||
|
||||
**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
|
||||
|
||||
|
||||
|
||||
@ -3,6 +3,8 @@
|
||||
pair_style pod command
|
||||
========================
|
||||
|
||||
Accelerator Variants: *pod/kk*
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
@ -16,7 +18,7 @@ Examples
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod Ta
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
@ -24,12 +26,18 @@ Description
|
||||
.. versionadded:: 22Dec2022
|
||||
|
||||
Pair style *pod* defines the proper orthogonal descriptor (POD)
|
||||
potential :ref:`(Nguyen) <Nguyen20221>`. The mathematical definition of
|
||||
the POD potential is described from :doc:`fitpod <fitpod_command>`, which is
|
||||
used to fit the POD potential to *ab initio* energy and force data.
|
||||
potential :ref:`(Nguyen and Rohskopf) <Nguyen20222>`,
|
||||
:ref:`(Nguyen2023) <Nguyen20232>`, :ref:`(Nguyen2024) <Nguyen20242>`, and :ref:`(Nguyen and Sema) <Nguyen20243>`.
|
||||
The :doc:`fitpod <fitpod_command>` is used to fit the POD potential.
|
||||
|
||||
Only a single pair_coeff command is used with the *pod* style which
|
||||
specifies a POD parameter file followed by a coefficient file.
|
||||
specifies a POD parameter file followed by a coefficient file,
|
||||
a projection matrix file, and a centroid file.
|
||||
|
||||
The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
|
||||
(start with #) anywhere. Each non-blank non-comment line must contain
|
||||
one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
|
||||
of all the keywords that can be assigned in the parameter file.
|
||||
|
||||
The coefficient file (``Ta_coefficients.pod``) contains coefficients for the
|
||||
POD potential. The top of the coefficient file can contain any number of
|
||||
@ -42,10 +50,27 @@ This is followed by *ncoeff* coefficients, one per line. The coefficient
|
||||
file is generated after training the POD potential using :doc:`fitpod
|
||||
<fitpod_command>`.
|
||||
|
||||
The POD parameter file (``Ta_param.pod``) can contain blank and comment lines
|
||||
(start with #) anywhere. Each non-blank non-comment line must contain
|
||||
one keyword/value pair. See :doc:`fitpod <fitpod_command>` for the description
|
||||
of all the keywords that can be assigned in the parameter file.
|
||||
The projection matrix file (``Ta_projection_matrix.pod``) contains a matrix of the
|
||||
principal component analysis. This matrix is used to project the per-atom descriptors
|
||||
onto a low-dimensional descriptor space. The top of the projection matrix 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:
|
||||
|
||||
* projection_matrix: *nentry*
|
||||
|
||||
This is followed by *nentry* entries, one per line. The projection matrix
|
||||
file is generated by using :doc:`fitpod <fitpod_command>` when the number of environment clusters is greater than 1.
|
||||
|
||||
The centroid matrix file (``Ta_centroids.pod``) contains centroids of the atom clusters
|
||||
computed by applying the k-means algorithm to the low-dimensional descriptor space.
|
||||
The top of the centroid 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:
|
||||
|
||||
* centroids: *nentry*
|
||||
|
||||
This is followed by *nentry* entries, one per line. The centroid
|
||||
file is generated by using :doc:`fitpod
|
||||
<fitpod_command>` when the number of environment clusters is greater than 1.
|
||||
|
||||
As an example, if a LAMMPS indium phosphide simulation has 4 atoms
|
||||
types, with the first two being indium and the third and fourth being
|
||||
@ -53,7 +78,7 @@ phophorous, the pair_coeff command would look like this:
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff * * pod InP_param.pod InP_coefficients.pod In In P P
|
||||
pair_coeff * * pod InP_param.pod InP_coefficients.pod "" "" In In P P
|
||||
|
||||
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
|
||||
The two filenames are for the parameter and coefficient files, respectively.
|
||||
@ -61,13 +86,47 @@ The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the
|
||||
POD 'In' element. The two trailing 'P' arguments map LAMMPS atom types
|
||||
3 and 4 to the POD 'P' element.
|
||||
|
||||
If the number of environment clusters is greater than 1, then both the projection matrix and the centroids
|
||||
must also be provided
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_coeff * * pod InP_param.pod InP_coefficients.pod InP_projection_matrix.pod InP_centroids.pod In In P P
|
||||
|
||||
|
||||
If a POD mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a *pod* potential is used as part of
|
||||
the *hybrid* pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
|
||||
Examples about training and using POD potentials are found in the
|
||||
directory lammps/examples/PACKAGES/pod.
|
||||
directory lammps/examples/PACKAGES/pod and the Github repo https://github.com/cesmix-mit/pod-examples.
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
For atom type pairs I,J and I != J, where types I and J correspond to
|
||||
two different element types, mixing is performed by LAMMPS with
|
||||
user-specifiable parameters as described above. You never need to
|
||||
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 can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
*inner*, *middle*, *outer* keywords.
|
||||
|
||||
----------
|
||||
|
||||
.. include:: accel_styles.rst
|
||||
|
||||
----------
|
||||
|
||||
@ -78,12 +137,14 @@ This style is part of the ML-POD package. It is only enabled if LAMMPS
|
||||
was built with that package. See the :doc:`Build package
|
||||
<Build_package>` page for more info.
|
||||
|
||||
This pair style does not compute per-atom energies and per-atom stresses.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fitpod <fitpod_command>`,
|
||||
:doc:`compute pod/atom <compute_pod_atom>`,
|
||||
:doc:`compute podd/atom <compute_pod_atom>`,
|
||||
:doc:`compute pod/ldd <compute_pod_atom>`,
|
||||
:doc:`compute pod/gdd <compute_pod_atom>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
@ -92,6 +153,20 @@ none
|
||||
|
||||
----------
|
||||
|
||||
.. _Nguyen20221:
|
||||
.. _Nguyen20222:
|
||||
|
||||
**(Nguyen and Rohskopf)** Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
|
||||
|
||||
.. _Nguyen20232:
|
||||
|
||||
**(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
|
||||
|
||||
.. _Nguyen20242:
|
||||
|
||||
**(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
|
||||
|
||||
.. _Nguyen20243:
|
||||
|
||||
**(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
|
||||
|
||||
|
||||
**(Nguyen)** Nguyen and Rohskopf, arXiv preprint arXiv:2209.02362 (2022).
|
||||
|
||||
9
examples/PACKAGES/pod/InP/InP_centroids.pod
Normal file
9
examples/PACKAGES/pod/InP/InP_centroids.pod
Normal file
@ -0,0 +1,9 @@
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607
examples/PACKAGES/pod/InP/InP_coefficients.pod
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607
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8.819992
|
||||
-11.235022
|
||||
0.504319
|
||||
-0.541901
|
||||
-2.140775
|
||||
0.123051
|
||||
1534.572721
|
||||
546.439498
|
||||
-1444.424864
|
||||
-5459.323939
|
||||
-52.454952
|
||||
2.219270
|
||||
76.918333
|
||||
88.002989
|
||||
-6.500313
|
||||
1.773176
|
||||
11.330731
|
||||
-0.328410
|
||||
0.823224
|
||||
-1.019337
|
||||
-1.133545
|
||||
-0.208611
|
||||
2501.324907
|
||||
3545.715003
|
||||
-4608.490130
|
||||
2923.155708
|
||||
-37.981021
|
||||
-49.641959
|
||||
89.134040
|
||||
-32.647515
|
||||
0.496357
|
||||
1.676540
|
||||
2.419208
|
||||
3.122471
|
||||
-0.954858
|
||||
-0.733537
|
||||
0.793281
|
||||
-1.504076
|
||||
-2701.690060
|
||||
-2248.982987
|
||||
5969.829579
|
||||
-1168.494290
|
||||
63.809510
|
||||
21.732591
|
||||
-123.940207
|
||||
25.411604
|
||||
4.532029
|
||||
-3.357758
|
||||
-5.109263
|
||||
0.202613
|
||||
-0.339567
|
||||
0.932445
|
||||
-0.052674
|
||||
-0.099175
|
||||
@ -1,20 +1,21 @@
|
||||
file_format extxyz
|
||||
file_extension xyz
|
||||
|
||||
path_to_training_data_set "../Ta/XYZ"
|
||||
path_to_test_data_set "../Ta/XYZ"
|
||||
path_to_training_data_set "XYZ"
|
||||
path_to_test_data_set "XYZ"
|
||||
path_to_environment_configuration_set "XYZ"
|
||||
|
||||
fitting_weight_energy 100.0
|
||||
fitting_weight_force 1.0
|
||||
fitting_regularization_parameter 1e-10
|
||||
fitting_regularization_parameter 1e-12
|
||||
|
||||
error_analysis_for_training_data_set 1
|
||||
error_analysis_for_test_data_set 0
|
||||
|
||||
# Add the following basename to the name of output files
|
||||
basename_for_output_files Ta
|
||||
basename_for_output_files InP
|
||||
|
||||
# number of digits after the decimal point for pod coefficients
|
||||
precision_for_pod_coefficients 5
|
||||
precision_for_pod_coefficients 6
|
||||
|
||||
|
||||
1
examples/PACKAGES/pod/InP/InP_fit.pod
Normal file
1
examples/PACKAGES/pod/InP/InP_fit.pod
Normal file
@ -0,0 +1 @@
|
||||
fitpod InP_param.pod InP_data.pod
|
||||
@ -1,13 +1,13 @@
|
||||
# Demonstrate POD Ta potential
|
||||
# Demonstrate POD potential for InP
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
variable a equal 5.83
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
@ -15,17 +15,17 @@ variable nz equal ${nrep}
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice diamond $a
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 180.88
|
||||
create_box 2 box
|
||||
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
|
||||
|
||||
mass 1 114.76
|
||||
mass 2 30.98
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
|
||||
pair_coeff * * InP_param.pod InP_coefficients.pod InP_projection_matrix.pod InP_centroids.pod In P
|
||||
|
||||
# Setup output
|
||||
|
||||
@ -44,4 +44,3 @@ velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
48
examples/PACKAGES/pod/InP/InP_param.pod
Normal file
48
examples/PACKAGES/pod/InP/InP_param.pod
Normal file
@ -0,0 +1,48 @@
|
||||
# chemical element symbols
|
||||
species In P
|
||||
|
||||
# periodic boundary conditions
|
||||
pbc 1 1 1
|
||||
|
||||
# inner cut-off radius
|
||||
rin 0.8
|
||||
|
||||
# outer cut-off radius
|
||||
rcut 5.0
|
||||
|
||||
# use only for enviroment-adaptive potentials
|
||||
number_of_environment_clusters 2
|
||||
|
||||
# principal_components of local descriptors
|
||||
number_of_principal_components 2
|
||||
|
||||
# polynomial degrees for radial basis functions
|
||||
bessel_polynomial_degree 4
|
||||
inverse_polynomial_degree 8
|
||||
|
||||
# one-body potential
|
||||
onebody 1
|
||||
|
||||
# two-body linear POD potential
|
||||
twobody_number_radial_basis_functions 6
|
||||
|
||||
# three-body linear POD potential
|
||||
threebody_number_radial_basis_functions 5
|
||||
threebody_angular_degree 4
|
||||
|
||||
# four-body linear POD potential
|
||||
fourbody_number_radial_basis_functions 4
|
||||
fourbody_angular_degree 2
|
||||
|
||||
# five-body linear POD potential
|
||||
fivebody_number_radial_basis_functions 0
|
||||
fivebody_angular_degree 0
|
||||
|
||||
# six-body linear POD potential
|
||||
sixbody_number_radial_basis_functions 0
|
||||
sixbody_angular_degree 0
|
||||
|
||||
# seven-body linear POD potential
|
||||
sevenbody_number_radial_basis_functions 0
|
||||
sevenbody_angular_degree 0
|
||||
|
||||
605
examples/PACKAGES/pod/InP/InP_projection_matrix.pod
Normal file
605
examples/PACKAGES/pod/InP/InP_projection_matrix.pod
Normal file
@ -0,0 +1,605 @@
|
||||
projection_matrix: 604
|
||||
-0.004243814352167
|
||||
-0.000448397839713
|
||||
-0.016983432235848
|
||||
-0.001966255722913
|
||||
0.029010522561179
|
||||
0.003762443132787
|
||||
0.039911387659253
|
||||
0.005314048931287
|
||||
0.062720732404074
|
||||
0.003974941916687
|
||||
0.149105158115930
|
||||
-0.006385178431929
|
||||
-0.012144265525053
|
||||
0.000691773161962
|
||||
-0.048756265240017
|
||||
0.003162850333944
|
||||
0.088936305131128
|
||||
-0.007476564488709
|
||||
0.097191101104149
|
||||
-0.012420842104229
|
||||
0.049530921529631
|
||||
-0.007497348608745
|
||||
-0.061866651906812
|
||||
0.019069047297503
|
||||
-0.000492419081414
|
||||
-0.000293862032664
|
||||
-0.000002635581044
|
||||
-0.000003065342642
|
||||
-0.000168331478341
|
||||
-0.000105808377301
|
||||
-0.000004173787128
|
||||
-0.000018813205626
|
||||
-0.000108880499290
|
||||
-0.000076115651045
|
||||
-0.007951266916205
|
||||
-0.005095861985029
|
||||
-0.000044609617755
|
||||
-0.000050327409131
|
||||
-0.002723300141994
|
||||
-0.001834663825885
|
||||
-0.000070415842279
|
||||
-0.000310522263376
|
||||
-0.001765120688164
|
||||
-0.001315649797538
|
||||
-0.023386281521888
|
||||
-0.016474739963351
|
||||
-0.000147608215330
|
||||
-0.000179462143587
|
||||
-0.008051097347282
|
||||
-0.005979346101489
|
||||
-0.000236412343751
|
||||
-0.001069954403330
|
||||
-0.005246794465748
|
||||
-0.004319468842899
|
||||
-0.044836507594739
|
||||
-0.032241019339557
|
||||
-0.000254445061629
|
||||
-0.000246893489913
|
||||
-0.015410082140288
|
||||
-0.011595307648319
|
||||
-0.000391867170232
|
||||
-0.001493048009616
|
||||
-0.010023404295316
|
||||
-0.008215226532129
|
||||
-0.107847451495494
|
||||
-0.049206897409385
|
||||
-0.000392461393943
|
||||
-0.000124685472075
|
||||
-0.036393564644511
|
||||
-0.017006992346809
|
||||
-0.000459511508882
|
||||
-0.000666682587776
|
||||
-0.023190595633852
|
||||
-0.011435928903553
|
||||
-0.001341168054356
|
||||
-0.000281383852822
|
||||
0.000003694560286
|
||||
0.000003287833275
|
||||
-0.000446021587457
|
||||
-0.000093772897761
|
||||
0.000001366336946
|
||||
0.000000027954934
|
||||
-0.000290967051453
|
||||
-0.000049203783622
|
||||
-0.021518914070270
|
||||
-0.004460723381491
|
||||
0.000061825830435
|
||||
0.000052639132893
|
||||
-0.007153233284514
|
||||
-0.001481563630289
|
||||
0.000023344261861
|
||||
-0.000000339443387
|
||||
-0.004665571294319
|
||||
-0.000772955013055
|
||||
-0.066587276364908
|
||||
-0.011665225758550
|
||||
0.000203643521773
|
||||
0.000183330009709
|
||||
-0.022114086481450
|
||||
-0.003833740586571
|
||||
0.000074842179097
|
||||
0.000001292689915
|
||||
-0.014431221162836
|
||||
-0.001915929630527
|
||||
-0.098375048130725
|
||||
-0.008053805924953
|
||||
0.000322027105115
|
||||
0.000203332502638
|
||||
-0.032572603420125
|
||||
-0.002412861885039
|
||||
0.000137395632220
|
||||
-0.000024561841338
|
||||
-0.021299177220420
|
||||
-0.000836965788501
|
||||
-0.077623486339473
|
||||
0.002278581077192
|
||||
0.000322312533464
|
||||
-0.000058415175290
|
||||
-0.025601721505924
|
||||
0.001125685127836
|
||||
0.000201022951052
|
||||
-0.000092745232701
|
||||
-0.016728404128161
|
||||
0.001243816573311
|
||||
-0.003805362289692
|
||||
-0.000202499178320
|
||||
-0.000021541514327
|
||||
-0.000031293333450
|
||||
-0.001280735995282
|
||||
-0.000077837017648
|
||||
-0.000799104770912
|
||||
0.000049892170553
|
||||
-0.000990678233878
|
||||
-0.000057972933150
|
||||
-0.061167917475045
|
||||
-0.001670533450180
|
||||
-0.000313471258490
|
||||
-0.000408760242699
|
||||
-0.020575877527556
|
||||
-0.000694072585444
|
||||
-0.012850521006094
|
||||
0.001086502812555
|
||||
-0.015907657538993
|
||||
-0.000485067914821
|
||||
-0.202534794887672
|
||||
0.006078023099047
|
||||
-0.000840799345901
|
||||
-0.000854656703289
|
||||
-0.068076832515629
|
||||
0.001699727176750
|
||||
-0.042729778249634
|
||||
0.005347374162475
|
||||
-0.052627119107608
|
||||
0.001460759058382
|
||||
-0.241127224303136
|
||||
0.032984103283574
|
||||
-0.000897811435368
|
||||
-0.000113825913441
|
||||
-0.081050853500115
|
||||
0.010766585150484
|
||||
-0.050966880119687
|
||||
0.010312462105552
|
||||
-0.062497571207214
|
||||
0.008679133850273
|
||||
-0.063681436296054
|
||||
0.011767279839477
|
||||
-0.001559125583916
|
||||
-0.001501080151139
|
||||
-0.022088293229762
|
||||
0.003004703660736
|
||||
-0.014068818756900
|
||||
0.000646687827478
|
||||
-0.017160642621993
|
||||
0.001780114246086
|
||||
-0.000068041068811
|
||||
-0.000114301484463
|
||||
-0.000000367291189
|
||||
-0.000000692692885
|
||||
-0.000023270053209
|
||||
-0.000039357456980
|
||||
-0.000000158370961
|
||||
-0.000000247503787
|
||||
-0.004530069319205
|
||||
-0.008098866063646
|
||||
-0.000024941600163
|
||||
-0.000045651426116
|
||||
-0.001551774477182
|
||||
-0.002787523492629
|
||||
-0.000010819192006
|
||||
-0.000016408970965
|
||||
0.023461418895442
|
||||
0.046121961672639
|
||||
0.000148796976912
|
||||
0.000283887511935
|
||||
0.008085150870850
|
||||
0.015939558405832
|
||||
0.000067535669401
|
||||
0.000104875068210
|
||||
0.065033210746072
|
||||
0.127078014374112
|
||||
0.000324152570957
|
||||
0.000497651079924
|
||||
0.022320143677641
|
||||
0.043627492907257
|
||||
0.000140916588128
|
||||
0.000184923898247
|
||||
-0.000167561718265
|
||||
-0.000142419756156
|
||||
-0.000000692502412
|
||||
-0.000000501670729
|
||||
-0.000057155487514
|
||||
-0.000049831024729
|
||||
0.000000207997493
|
||||
0.000000273762495
|
||||
-0.010845106252368
|
||||
-0.009520281495239
|
||||
-0.000047292171440
|
||||
-0.000033261906929
|
||||
-0.003703412100727
|
||||
-0.003332451408544
|
||||
0.000013930274327
|
||||
0.000017913623855
|
||||
0.056946149585956
|
||||
0.047765886762146
|
||||
0.000281576513299
|
||||
0.000225307551103
|
||||
0.019492513980010
|
||||
0.016838974330287
|
||||
-0.000084054059133
|
||||
-0.000112926845235
|
||||
0.112453156055799
|
||||
0.074225697560025
|
||||
0.000563813636938
|
||||
0.000339274035506
|
||||
0.038295019215198
|
||||
0.026034893927783
|
||||
-0.000155952002882
|
||||
-0.000169037255371
|
||||
-0.000444601427715
|
||||
-0.000229035159636
|
||||
0.000001001161119
|
||||
0.000000518684452
|
||||
-0.000148074552704
|
||||
-0.000076759590976
|
||||
-0.000000627425698
|
||||
-0.000000824370190
|
||||
-0.028440347773717
|
||||
-0.013685567792505
|
||||
0.000067778049176
|
||||
0.000032758466350
|
||||
-0.009466552819189
|
||||
-0.004578819227112
|
||||
-0.000038685102217
|
||||
-0.000046759090854
|
||||
0.157389361507046
|
||||
0.056878643804038
|
||||
-0.000405025462965
|
||||
-0.000213671493662
|
||||
0.052324137472395
|
||||
0.018933274335553
|
||||
0.000203147566276
|
||||
0.000218299918859
|
||||
0.245967893998624
|
||||
0.024575433341962
|
||||
-0.000754452416584
|
||||
-0.000209604853992
|
||||
0.081544840674947
|
||||
0.007743464161359
|
||||
0.000349367419741
|
||||
0.000209064852207
|
||||
-0.001230136588862
|
||||
-0.000337531532999
|
||||
-0.000007137707136
|
||||
-0.000010431721982
|
||||
-0.000413846800457
|
||||
-0.000115463923562
|
||||
-0.000002766814333
|
||||
-0.000004181778913
|
||||
-0.078699017434422
|
||||
-0.016465828563563
|
||||
-0.000400632373361
|
||||
-0.000507567012697
|
||||
-0.026460121750950
|
||||
-0.005630473407170
|
||||
-0.000151421376173
|
||||
-0.000195447572282
|
||||
0.468155853700693
|
||||
0.034823482766763
|
||||
0.001805690344462
|
||||
0.001521766130495
|
||||
0.157268809833729
|
||||
0.012079599694503
|
||||
0.000653304625520
|
||||
0.000522483743620
|
||||
0.602381431761162
|
||||
-0.079991950959401
|
||||
0.002295801196837
|
||||
-0.000242138286832
|
||||
0.202444343814270
|
||||
-0.026482064831284
|
||||
0.000861364047583
|
||||
-0.000238214039069
|
||||
-0.012226896113148
|
||||
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||||
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||||
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|
||||
1932
examples/PACKAGES/pod/InP/InP_training_analysis.pod
Normal file
1932
examples/PACKAGES/pod/InP/InP_training_analysis.pod
Normal file
File diff suppressed because it is too large
Load Diff
27
examples/PACKAGES/pod/InP/InP_training_errors.pod
Normal file
27
examples/PACKAGES/pod/InP/InP_training_errors.pod
Normal file
@ -0,0 +1,27 @@
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
--------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
--------------------------------------------------------------------------------------------
|
||||
Bulk.xyz 1 8 0.000389 0.000389 0.000000 0.000000
|
||||
EOS.xyz 268 2080 0.000423 0.000810 0.000553 0.007988
|
||||
Shear.xyz 346 2768 0.000150 0.000264 0.002567 0.004527
|
||||
Strain.xyz 163 1304 0.000770 0.000979 0.000020 0.000031
|
||||
aIn.xyz 54 11664 0.000246 0.000309 0.005992 0.011748
|
||||
aP.xyz 21 4536 0.000664 0.000669 0.010923 0.029263
|
||||
aa.xyz 20 4320 0.000836 0.000836 0.010665 0.016490
|
||||
iIn.xyz 41 8897 0.000679 0.000706 0.009217 0.015986
|
||||
iP.xyz 100 21700 0.000571 0.000636 0.006515 0.010972
|
||||
s_aIn.xyz 121 7744 0.000268 0.000297 0.007737 0.013057
|
||||
s_aP.xyz 72 4608 0.000450 0.000557 0.023867 0.034977
|
||||
s_aa.xyz 18 1152 0.000208 0.000211 0.018859 0.026432
|
||||
s_iIn.xyz 144 9360 0.000530 0.000656 0.021601 0.029989
|
||||
s_iP.xyz 337 21905 0.000353 0.000457 0.016457 0.023761
|
||||
s_vIn.xyz 17 1071 0.001193 0.001209 0.015590 0.025467
|
||||
s_vP.xyz 77 4851 0.000216 0.000246 0.012823 0.019041
|
||||
s_vv.xyz 65 4030 0.000798 0.001021 0.025625 0.034398
|
||||
vP.xyz 10 2150 0.000123 0.000123 0.003821 0.006631
|
||||
vv.xyz 19 4066 0.000459 0.000487 0.014390 0.020840
|
||||
--------------------------------------------------------------------------------------------
|
||||
All files 1894 118214 0.000413 0.000614 0.011846 0.020437
|
||||
--------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
16
examples/PACKAGES/pod/InP/README.md
Normal file
16
examples/PACKAGES/pod/InP/README.md
Normal file
@ -0,0 +1,16 @@
|
||||
### POD example for InP
|
||||
|
||||
We will fit a potential to the `InP` training data in the `XYZ` directory, which houses `.xyz` files
|
||||
|
||||
Please download the training data from [the repo](https://github.com/cesmix-mit/pod-examples/tree/main/JCP2023_InP/XYZ)
|
||||
|
||||
Fit POD with
|
||||
|
||||
lmp -in InP_fit.pod
|
||||
|
||||
This creates `InP_coefficients.pod` for the linear model, which we can use to run MD with
|
||||
|
||||
lmp -in InP_mdrun.pod
|
||||
|
||||
|
||||
|
||||
10
examples/PACKAGES/pod/InP/XYZ/Bulk.xyz
Normal file
10
examples/PACKAGES/pod/InP/XYZ/Bulk.xyz
Normal file
@ -0,0 +1,10 @@
|
||||
8
|
||||
Lattice="5.83 0.0 0.0 0.0 5.83 0.0 0.0 0.0 5.83" Properties=species:S:1:pos:R:3:forces:R:3 energy=-38.72767843 stress="-0.49498 0.0 0.0 0.0 -0.49498 -0.0 0.0 -0.0 -0.49498" pbc="T T T"
|
||||
In 0.0 0.0 0.0 -0.0 -0.0 -0.0
|
||||
In 2.915 0.0 2.915 -0.0 -0.0 0.0
|
||||
In 0.0 2.915 2.915 -0.0 0.0 -0.0
|
||||
In 2.915 2.915 0.0 -0.0 0.0 0.0
|
||||
P 1.4575 1.4575 4.3725 0.0 -0.0 -0.0
|
||||
P 4.3725 1.4575 1.4575 0.0 0.0 0.0
|
||||
P 1.4575 4.3725 1.4575 0.0 -0.0 0.0
|
||||
P 4.3725 4.3725 4.3725 0.0 -0.0 -0.0
|
||||
2616
examples/PACKAGES/pod/InP/XYZ/EOS.xyz
Normal file
2616
examples/PACKAGES/pod/InP/XYZ/EOS.xyz
Normal file
File diff suppressed because it is too large
Load Diff
3460
examples/PACKAGES/pod/InP/XYZ/Shear.xyz
Normal file
3460
examples/PACKAGES/pod/InP/XYZ/Shear.xyz
Normal file
File diff suppressed because it is too large
Load Diff
1630
examples/PACKAGES/pod/InP/XYZ/Strain.xyz
Normal file
1630
examples/PACKAGES/pod/InP/XYZ/Strain.xyz
Normal file
File diff suppressed because it is too large
Load Diff
11772
examples/PACKAGES/pod/InP/XYZ/aIn.xyz
Normal file
11772
examples/PACKAGES/pod/InP/XYZ/aIn.xyz
Normal file
File diff suppressed because it is too large
Load Diff
4578
examples/PACKAGES/pod/InP/XYZ/aP.xyz
Normal file
4578
examples/PACKAGES/pod/InP/XYZ/aP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
4360
examples/PACKAGES/pod/InP/XYZ/aa.xyz
Normal file
4360
examples/PACKAGES/pod/InP/XYZ/aa.xyz
Normal file
File diff suppressed because it is too large
Load Diff
8979
examples/PACKAGES/pod/InP/XYZ/iIn.xyz
Normal file
8979
examples/PACKAGES/pod/InP/XYZ/iIn.xyz
Normal file
File diff suppressed because it is too large
Load Diff
21900
examples/PACKAGES/pod/InP/XYZ/iP.xyz
Normal file
21900
examples/PACKAGES/pod/InP/XYZ/iP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
7986
examples/PACKAGES/pod/InP/XYZ/s_aIn.xyz
Normal file
7986
examples/PACKAGES/pod/InP/XYZ/s_aIn.xyz
Normal file
File diff suppressed because it is too large
Load Diff
4752
examples/PACKAGES/pod/InP/XYZ/s_aP.xyz
Normal file
4752
examples/PACKAGES/pod/InP/XYZ/s_aP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
1188
examples/PACKAGES/pod/InP/XYZ/s_aa.xyz
Normal file
1188
examples/PACKAGES/pod/InP/XYZ/s_aa.xyz
Normal file
File diff suppressed because it is too large
Load Diff
9648
examples/PACKAGES/pod/InP/XYZ/s_iIn.xyz
Normal file
9648
examples/PACKAGES/pod/InP/XYZ/s_iIn.xyz
Normal file
File diff suppressed because it is too large
Load Diff
22579
examples/PACKAGES/pod/InP/XYZ/s_iP.xyz
Normal file
22579
examples/PACKAGES/pod/InP/XYZ/s_iP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
1105
examples/PACKAGES/pod/InP/XYZ/s_vIn.xyz
Normal file
1105
examples/PACKAGES/pod/InP/XYZ/s_vIn.xyz
Normal file
File diff suppressed because it is too large
Load Diff
5005
examples/PACKAGES/pod/InP/XYZ/s_vP.xyz
Normal file
5005
examples/PACKAGES/pod/InP/XYZ/s_vP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
4160
examples/PACKAGES/pod/InP/XYZ/s_vv.xyz
Normal file
4160
examples/PACKAGES/pod/InP/XYZ/s_vv.xyz
Normal file
File diff suppressed because it is too large
Load Diff
2170
examples/PACKAGES/pod/InP/XYZ/vP.xyz
Normal file
2170
examples/PACKAGES/pod/InP/XYZ/vP.xyz
Normal file
File diff suppressed because it is too large
Load Diff
4104
examples/PACKAGES/pod/InP/XYZ/vv.xyz
Normal file
4104
examples/PACKAGES/pod/InP/XYZ/vv.xyz
Normal file
File diff suppressed because it is too large
Load Diff
@ -3,19 +3,36 @@
|
||||
Go to `lammps` directory and build with the POD package:
|
||||
|
||||
cd path/to/lammps
|
||||
mkdir build-pod
|
||||
cd build-pod
|
||||
mkdir build
|
||||
cd build
|
||||
cmake -C ../cmake/presets/basic.cmake -D PKG_ML-POD=on ../cmake
|
||||
cmake --build .
|
||||
|
||||
### Fit a POD potential for tantalum
|
||||
### Compile LAMMPS/POD with Kokkos
|
||||
|
||||
cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake -D PKG_ML-POD=on ../cmake
|
||||
|
||||
### Fit a POD potential for Tantalum
|
||||
|
||||
Go to `lammps/examples/PACKAGES/pod/Ta` directory and run
|
||||
|
||||
lmp -in in.podfit
|
||||
lmp -in Ta_fit.pod
|
||||
|
||||
See the README in `lammps/examples/PACKAGES/pod/Ta` for instructions on how to run MD with the potential.
|
||||
This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with
|
||||
|
||||
lmp -in Ta_mdrun.pod
|
||||
|
||||
### Fit a POD potential for Indium Phosphide
|
||||
|
||||
Go to `lammps/examples/PACKAGES/pod/InP` directory and run
|
||||
|
||||
lmp -in InP_fit.pod
|
||||
|
||||
This creates `InP_coefficients.pod` for the linear model, which we can use to run MD with
|
||||
|
||||
lmp -in InP_mdrun.pod
|
||||
|
||||
### Examples for other materials
|
||||
|
||||
See [https://github.com/cesmix-mit/pod-examples](https://github.com/cesmix-mit/pod-examples)
|
||||
|
||||
|
||||
@ -5,11 +5,11 @@ of the training data taken from [the FitSNAP repo](https://github.com/FitSNAP/Fi
|
||||
|
||||
Fit POD with
|
||||
|
||||
lmp -in in.fitpod
|
||||
lmp -in Ta_fit.pod
|
||||
|
||||
This creates `Ta_coefficients.pod` for the linear model, which we can use to run MD with
|
||||
|
||||
lmp -in in.pod
|
||||
lmp -in Ta_mdrun.pod
|
||||
|
||||
|
||||
|
||||
|
||||
5
examples/PACKAGES/pod/Ta/Ta_centroids.pod
Normal file
5
examples/PACKAGES/pod/Ta/Ta_centroids.pod
Normal file
@ -0,0 +1,5 @@
|
||||
centroids: 4
|
||||
709.809117183618014
|
||||
-87.224242759325506
|
||||
290.052334466774596
|
||||
-48.651919394376264
|
||||
@ -1 +0,0 @@
|
||||
../../../../potentials/Ta_coeff.pod
|
||||
@ -1,33 +1,124 @@
|
||||
POD_coefficients: 32
|
||||
-4.44242
|
||||
4.10219
|
||||
2.36987
|
||||
3.92184
|
||||
-0.83796
|
||||
-0.79457
|
||||
-0.26230
|
||||
-21.24294
|
||||
-15.38460
|
||||
-38.44056
|
||||
8.29872
|
||||
-42.54514
|
||||
2.79976
|
||||
3.76109
|
||||
5.23499
|
||||
0.04878
|
||||
2.96006
|
||||
0.09101
|
||||
-0.19257
|
||||
-0.24326
|
||||
-0.16735
|
||||
0.53738
|
||||
0.02236
|
||||
-0.00154
|
||||
0.02488
|
||||
-0.00565
|
||||
0.07672
|
||||
-0.05894
|
||||
-0.05604
|
||||
-0.12664
|
||||
0.11723
|
||||
0.00262
|
||||
POD_coefficients: 123
|
||||
-3.458751
|
||||
143.517314
|
||||
-91.271784
|
||||
-21.429012
|
||||
2.598161
|
||||
1.030864
|
||||
1.223820
|
||||
-121.482397
|
||||
392.117907
|
||||
543.953048
|
||||
-816.616650
|
||||
-578.399889
|
||||
22.163370
|
||||
-43.385671
|
||||
-67.217034
|
||||
138.186103
|
||||
93.209528
|
||||
-2.637263
|
||||
3.772121
|
||||
2.911027
|
||||
-18.110203
|
||||
-9.463577
|
||||
-1.510057
|
||||
0.340007
|
||||
4.003655
|
||||
0.310931
|
||||
-0.153950
|
||||
0.030718
|
||||
-0.035877
|
||||
-0.106800
|
||||
0.019145
|
||||
0.071654
|
||||
-11.414721
|
||||
71.041854
|
||||
-12.721979
|
||||
-290.927292
|
||||
682.437227
|
||||
-714.053484
|
||||
118.446067
|
||||
-0.226263
|
||||
-6.276665
|
||||
-1.109522
|
||||
13.899872
|
||||
-34.851630
|
||||
30.942571
|
||||
-6.503493
|
||||
0.097540
|
||||
-0.129073
|
||||
-0.940310
|
||||
0.470152
|
||||
-2.447252
|
||||
1.473115
|
||||
0.325069
|
||||
0.319285
|
||||
0.009253
|
||||
-1.136040
|
||||
-0.163554
|
||||
-0.100805
|
||||
0.156693
|
||||
0.641712
|
||||
1.768564
|
||||
0.313210
|
||||
-151.538292
|
||||
83.512311
|
||||
20.267898
|
||||
-2.719152
|
||||
0.126556
|
||||
0.399734
|
||||
59.540773
|
||||
-163.812047
|
||||
309.808672
|
||||
407.033341
|
||||
-154.465736
|
||||
-16.567161
|
||||
15.092770
|
||||
-42.626942
|
||||
-41.549925
|
||||
25.919013
|
||||
3.778613
|
||||
0.438276
|
||||
0.770035
|
||||
-0.316432
|
||||
-2.478113
|
||||
0.706317
|
||||
0.306337
|
||||
0.000070
|
||||
0.024458
|
||||
-0.469368
|
||||
-0.000600
|
||||
-0.024069
|
||||
-0.032836
|
||||
0.020040
|
||||
-0.033612
|
||||
-12.034484
|
||||
35.342518
|
||||
24.023859
|
||||
492.717052
|
||||
-329.723884
|
||||
-343.939088
|
||||
-138.877619
|
||||
1.371539
|
||||
3.556454
|
||||
0.531160
|
||||
-25.622499
|
||||
12.115168
|
||||
11.612835
|
||||
4.687699
|
||||
0.173446
|
||||
0.742106
|
||||
0.198527
|
||||
-1.299577
|
||||
0.087882
|
||||
-0.017498
|
||||
-0.376770
|
||||
-0.068883
|
||||
0.002445
|
||||
0.142343
|
||||
-0.000518
|
||||
-0.046867
|
||||
-0.075770
|
||||
-0.123717
|
||||
-0.518992
|
||||
-0.384554
|
||||
|
||||
41
examples/PACKAGES/pod/Ta/Ta_compute.pod
Normal file
41
examples/PACKAGES/pod/Ta/Ta_compute.pod
Normal file
@ -0,0 +1,41 @@
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
||||
variable nsteps index 0
|
||||
variable nrep equal 1
|
||||
variable a equal 2.0
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
variable nz equal ${nrep}
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
create_box 2 box
|
||||
create_atoms 2 box
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up dummy potential to satisfy cutoff
|
||||
variable rcutfac equal 6.0
|
||||
pair_style zero ${rcutfac}
|
||||
pair_coeff * *
|
||||
|
||||
# calculate global POD descriptors and their derivatives
|
||||
compute gdd all pod/gdd Ta_param.pod "" "" C C
|
||||
fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector
|
||||
|
||||
# calculate per-atom POD descriptors and their derivatives
|
||||
compute ldd all pod/ldd Ta_param.pod "" "" C C
|
||||
fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector
|
||||
|
||||
|
||||
@ -3,10 +3,11 @@ file_extension xyz
|
||||
|
||||
path_to_training_data_set "XYZ"
|
||||
path_to_test_data_set "XYZ"
|
||||
path_to_environment_configuration_set "XYZ"
|
||||
|
||||
fitting_weight_energy 100.0
|
||||
fitting_weight_force 1.0
|
||||
fitting_regularization_parameter 1e-10
|
||||
fitting_regularization_parameter 1e-12
|
||||
|
||||
error_analysis_for_training_data_set 1
|
||||
error_analysis_for_test_data_set 0
|
||||
@ -15,6 +16,5 @@ error_analysis_for_test_data_set 0
|
||||
basename_for_output_files Ta
|
||||
|
||||
# number of digits after the decimal point for pod coefficients
|
||||
precision_for_pod_coefficients 5
|
||||
|
||||
precision_for_pod_coefficients 6
|
||||
|
||||
|
||||
1
examples/PACKAGES/pod/Ta/Ta_fit.pod
Normal file
1
examples/PACKAGES/pod/Ta/Ta_fit.pod
Normal file
@ -0,0 +1 @@
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
@ -1,13 +1,13 @@
|
||||
# Demonstrate POD Ta potential
|
||||
# Demonstrate POD potential for InP
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
variable a equal 3.816
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
# generate the box and atom positions using a FCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable ny equal ${nrep}
|
||||
@ -22,10 +22,9 @@ create_atoms 1 box
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coeff.pod Ta
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta_projection_matrix.pod Ta_centroids.pod Ta
|
||||
|
||||
# Setup output
|
||||
|
||||
@ -44,4 +43,3 @@ velocity all create 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
run ${nsteps}
|
||||
|
||||
|
||||
@ -1,4 +1,3 @@
|
||||
# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362
|
||||
# chemical element symbols
|
||||
species Ta
|
||||
|
||||
@ -11,22 +10,37 @@ rin 1.0
|
||||
# outer cut-off radius
|
||||
rcut 5.0
|
||||
|
||||
# polynomial degrees for radial basis functions
|
||||
bessel_polynomial_degree 3
|
||||
inverse_polynomial_degree 6
|
||||
# use only for enviroment-adaptive potentials
|
||||
number_of_environment_clusters 2
|
||||
|
||||
# one-body potential
|
||||
onebody 1
|
||||
# principal_components of local descriptors
|
||||
number_of_principal_components 2
|
||||
|
||||
# polynomial degrees for radial basis functions
|
||||
bessel_polynomial_degree 4
|
||||
inverse_polynomial_degree 8
|
||||
|
||||
# two-body linear POD potential
|
||||
twobody_number_radial_basis_functions 6
|
||||
|
||||
# three-body linear POD potential
|
||||
threebody_number_radial_basis_functions 5
|
||||
threebody_number_angular_basis_functions 5
|
||||
threebody_angular_degree 4
|
||||
|
||||
# four-body linear POD potential
|
||||
fourbody_number_radial_basis_functions 4
|
||||
fourbody_angular_degree 3
|
||||
|
||||
# five-body linear POD potential
|
||||
fivebody_number_radial_basis_functions 2
|
||||
fivebody_angular_degree 0
|
||||
|
||||
# six-body linear POD potential
|
||||
sixbody_number_radial_basis_functions 0
|
||||
sixbody_angular_degree 0
|
||||
|
||||
# seven-body linear POD potential
|
||||
sevenbody_number_radial_basis_functions 0
|
||||
sevenbody_angular_degree 0
|
||||
|
||||
# four-body linear SNAP potential
|
||||
fourbody_snap_twojmax 0
|
||||
|
||||
# quadratic POD potential
|
||||
quadratic_pod_potential 0
|
||||
|
||||
123
examples/PACKAGES/pod/Ta/Ta_projection_matrix.pod
Normal file
123
examples/PACKAGES/pod/Ta/Ta_projection_matrix.pod
Normal file
@ -0,0 +1,123 @@
|
||||
projection_matrix: 122
|
||||
0.001542180493544
|
||||
-0.000208856257237
|
||||
0.004696325552750
|
||||
-0.000799660184854
|
||||
-0.008000933039354
|
||||
0.001989066009842
|
||||
0.010419332874197
|
||||
-0.004225089382829
|
||||
-0.007707874791396
|
||||
0.002363181997412
|
||||
0.000252747866160
|
||||
0.001096501878869
|
||||
0.002521274077638
|
||||
0.001255396173484
|
||||
0.000003198549918
|
||||
-0.000001703803015
|
||||
0.000842660980413
|
||||
0.000418209680165
|
||||
0.000003061593770
|
||||
-0.000001369337964
|
||||
0.000513414778155
|
||||
0.000251234560810
|
||||
0.022147135061506
|
||||
0.008240622324666
|
||||
0.000028539708383
|
||||
-0.000015268759157
|
||||
0.007398308113533
|
||||
0.002742126611657
|
||||
0.000026507655563
|
||||
-0.000012826875616
|
||||
0.004500875045773
|
||||
0.001633854036062
|
||||
0.057992487693725
|
||||
0.004399845607684
|
||||
0.000087830232758
|
||||
-0.000047234108179
|
||||
0.019371949049613
|
||||
0.001446775035292
|
||||
0.000080198873386
|
||||
-0.000042979676692
|
||||
0.011803130149159
|
||||
0.000782571344815
|
||||
0.088729781220177
|
||||
-0.033994314705254
|
||||
0.000137177658945
|
||||
-0.000074274009518
|
||||
0.029695365361865
|
||||
-0.011332825206724
|
||||
0.000122060283043
|
||||
-0.000052535526824
|
||||
0.018045534605097
|
||||
-0.006782004476568
|
||||
0.055582489447206
|
||||
0.003772200119617
|
||||
0.000646578781880
|
||||
-0.000349051715974
|
||||
0.019370224642909
|
||||
0.000987429380699
|
||||
0.000694664152378
|
||||
-0.000356051148475
|
||||
0.013204007612778
|
||||
0.000033323607623
|
||||
0.006287016338539
|
||||
0.008111146381732
|
||||
0.000002906927243
|
||||
-0.000001544021580
|
||||
0.002099132506148
|
||||
0.002704732877153
|
||||
0.000000855105209
|
||||
-0.000000451274047
|
||||
0.000003248293518
|
||||
-0.000000929359692
|
||||
0.000000915975684
|
||||
-0.000000484424474
|
||||
0.000702049548752
|
||||
0.000902292714257
|
||||
0.147508875358135
|
||||
0.163338726563794
|
||||
0.000079212466319
|
||||
-0.000042330325042
|
||||
0.049232381316120
|
||||
0.054445792877955
|
||||
0.000022808960908
|
||||
-0.000012120255771
|
||||
0.000081934712487
|
||||
-0.000032032552482
|
||||
0.000024654547920
|
||||
-0.000013125789535
|
||||
0.016452677208933
|
||||
0.018148728886563
|
||||
-0.497044625586336
|
||||
-0.272420381812816
|
||||
-0.000429694480500
|
||||
0.000231265224342
|
||||
-0.165915482385230
|
||||
-0.090716849839959
|
||||
-0.000122170385668
|
||||
0.000065489737996
|
||||
-0.000412160028824
|
||||
0.000219466272503
|
||||
-0.000132569576157
|
||||
0.000071150412013
|
||||
-0.055459064271160
|
||||
-0.030179801055923
|
||||
0.759425661897290
|
||||
-0.272348251690369
|
||||
0.000902102714429
|
||||
-0.000491276831878
|
||||
0.254142401970119
|
||||
-0.090716899722035
|
||||
0.000236933162140
|
||||
-0.000128609542277
|
||||
0.000862208110144
|
||||
-0.000338899866819
|
||||
0.000269952453949
|
||||
-0.000146573630517
|
||||
0.085350180561593
|
||||
-0.030206193610594
|
||||
0.022754383713675
|
||||
0.041585035581713
|
||||
0.176911302470102
|
||||
0.311330589561799
|
||||
@ -1,387 +1,387 @@
|
||||
# Displaced_A15.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
1 64 -753.4412087 -754.220443 0.01217553565 7.734608752 8.398670477 0.1147177501
|
||||
2 64 -752.99206 -753.865255 0.01364367179 8.845831302 9.134430545 0.128875643
|
||||
3 64 -753.3230789 -754.0221 0.01092220404 8.320493902 9.017261102 0.1155421197
|
||||
4 64 -753.5972757 -754.279613 0.01066151964 7.709417684 8.381725092 0.1058659753
|
||||
5 64 -753.0554721 -753.777209 0.01127713895 8.89827564 9.478314477 0.1191609049
|
||||
6 64 -753.3515905 -754.048643 0.01089144564 7.808950564 8.465317938 0.1128142237
|
||||
7 64 -753.6515992 -754.317603 0.01040630929 7.441773668 8.127690491 0.1024025645
|
||||
8 64 -753.3305668 -753.969161 0.009978033993 8.524333384 9.425464952 0.1066300011
|
||||
9 64 -753.3982699 -754.141988 0.01162059588 8.165654685 8.821346913 0.1141641875
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
1 64 1191.016129 -754.1682516 -754.220443 0.0008154906292 7.919490785 8.398670477 0.08810178896
|
||||
2 64 1191.016129 -753.7452225 -753.865255 0.001875507408 8.852132827 9.134430545 0.1067448574
|
||||
3 64 1191.016129 -754.0260592 -754.0221 6.186227706e-05 8.490551138 9.017261102 0.08447948567
|
||||
4 64 1191.016129 -754.2843686 -754.279613 7.430701858e-05 7.91771607 8.381725092 0.07854931923
|
||||
5 64 1191.016129 -753.7095712 -753.777209 0.001056841022 9.172667767 9.478314477 0.09663340422
|
||||
6 64 1191.016129 -754.0109108 -754.048643 0.0005895648737 8.020321096 8.465317938 0.08284023414
|
||||
7 64 1191.016129 -754.3005839 -754.317603 0.0002659236712 7.721711454 8.127690491 0.07190121013
|
||||
8 64 1191.016129 -753.998336 -753.969161 0.0004558598185 8.921319313 9.425464952 0.07820416531
|
||||
9 64 1191.016129 -754.0850646 -754.141988 0.0008894286853 8.419196061 8.821346913 0.07891515228
|
||||
# Displaced_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
10 54 -631.72742 -631.019667 0.01310653789 15.42892812 16.625876 0.264811012
|
||||
11 54 -632.2725892 -631.719595 0.01024063328 14.51788198 15.58666626 0.2236637006
|
||||
12 54 -631.9431698 -631.386255 0.01031323642 15.21539049 15.92378883 0.2259171686
|
||||
13 54 -633.0728554 -632.575826 0.00920424781 13.38472946 14.55977162 0.2050161952
|
||||
14 54 -630.8933737 -630.450212 0.008206698429 16.5539163 16.96340726 0.2366453149
|
||||
15 54 -632.0739208 -631.669379 0.007491515672 15.23887638 16.05757315 0.2280333831
|
||||
16 54 -632.8030856 -632.431277 0.006885343815 14.21127984 14.69810718 0.2026063598
|
||||
17 54 -631.6814096 -630.960068 0.01335817778 14.70924474 15.99073148 0.2283605143
|
||||
18 54 -625.0410285 -623.378198 0.03079315656 23.39224423 24.67640432 0.3504654115
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
10 54 988.0479474 -630.8399816 -631.019667 0.003327508019 16.22983721 16.625876 0.1166841192
|
||||
11 54 988.0479474 -631.4883273 -631.719595 0.004282735705 15.47601559 15.58666626 0.1278852166
|
||||
12 54 988.0479474 -631.116453 -631.386255 0.004996333465 15.69725796 15.92378883 0.110159896
|
||||
13 54 988.0479474 -632.3673226 -632.575826 0.003861174511 14.23453548 14.55977162 0.1023769321
|
||||
14 54 988.0479474 -630.1154351 -630.450212 0.006199572532 16.94758688 16.96340726 0.1329301552
|
||||
15 54 988.0479474 -631.4787272 -631.669379 0.003530589718 15.7441935 16.05757315 0.1185424897
|
||||
16 54 988.0479474 -632.0889957 -632.431277 0.006338542749 14.7912999 14.69810718 0.11762314
|
||||
17 54 988.0479474 -630.7359558 -630.960068 0.004150225827 15.93379899 15.99073148 0.1231460258
|
||||
18 54 988.0479474 -623.4254021 -623.378198 0.0008741501167 24.46891061 24.67640432 0.178545932
|
||||
# Displaced_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
19 48 -555.9696753 -555.899463 0.001462755232 6.079460735 6.084617063 0.07083484607
|
||||
20 48 -555.9506355 -555.922478 0.0005866147697 6.28112122 6.297071211 0.09285822038
|
||||
21 48 -555.8344979 -555.800269 0.000713101184 6.153574445 6.021098636 0.08137696888
|
||||
22 48 -556.2639568 -556.196151 0.00141262046 5.066504178 5.127955094 0.08649299664
|
||||
23 48 -555.6269121 -555.488929 0.002874647697 6.848109843 7.050223459 0.08116202322
|
||||
24 48 -556.1089332 -556.027926 0.001687649405 5.662035842 5.611881174 0.07953916326
|
||||
25 48 -556.0580873 -555.968399 0.001868505799 5.879931332 5.979217189 0.07470196865
|
||||
26 48 -556.0083267 -556.047132 0.0008084440258 5.752828608 5.544452585 0.08224848502
|
||||
27 48 -555.82441 -555.747848 0.001595040721 6.367423657 6.47892568 0.09497869851
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
19 48 889.0559462 -556.0313767 -555.899463 0.002748202591 5.334490918 6.084617063 0.06286544063
|
||||
20 48 889.0559462 -556.0166472 -555.922478 0.001961859026 5.527819703 6.297071211 0.0708870867
|
||||
21 48 889.0559462 -555.9020504 -555.800269 0.00212044539 5.414809754 6.021098636 0.06270071892
|
||||
22 48 889.0559462 -556.2733994 -556.196151 0.001609341215 4.489992695 5.127955094 0.06153241625
|
||||
23 48 889.0559462 -555.6596151 -555.488929 0.003555960858 6.198596889 7.050223459 0.08173118183
|
||||
24 48 889.0559462 -556.1062392 -556.027926 0.00163152465 5.099746665 5.611881174 0.05978904464
|
||||
25 48 889.0559462 -556.0904298 -555.968399 0.002542307703 5.19960613 5.979217189 0.0701868467
|
||||
26 48 889.0559462 -556.1021813 -556.047132 0.001146860621 4.946085311 5.544452585 0.06086253467
|
||||
27 48 889.0559462 -555.8602469 -555.747848 0.00234164434 5.785466186 6.47892568 0.07657994242
|
||||
# Elastic_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
28 2 -23.68353253 -23.689367 0.002917237243 0.0006486347527 0.0006222748589 7.696560647e-06
|
||||
29 2 -23.68281295 -23.689888 0.003537526523 0.0006442481331 0.0006166052222 7.353613433e-06
|
||||
30 2 -23.68293438 -23.689996 0.00353080996 0.0009115876426 0.0008810425642 1.183334558e-05
|
||||
31 2 -23.68108003 -23.690957 0.004938485589 1.044193543e-06 0 4.166082999e-07
|
||||
32 2 -23.67919793 -23.690521 0.005661535829 0.0006261455712 0.0005982273815 7.573309962e-06
|
||||
33 2 -23.67785535 -23.69038 0.006262326378 0.0006219476538 0.0005925723585 8.098703345e-06
|
||||
34 2 -23.68415292 -23.689202 0.00252453823 0.0006520193214 0.0006279363025 7.128171197e-06
|
||||
35 2 -23.68169552 -23.690482 0.004393238412 0.0009021557258 0.0008640138888 1.329061297e-05
|
||||
36 2 -23.68301023 -23.689902 0.003445886213 0.0006432418939 0.0006152154094 8.589463686e-06
|
||||
37 2 -23.68063814 -23.690563 0.004962429905 0.0006318669831 0.0006038725031 7.463726891e-06
|
||||
38 2 -23.68337588 -23.690207 0.003415557958 0.001118071502 0.00107369735 1.811741272e-05
|
||||
39 2 -23.68369233 -23.689285 0.00279633424 0.0009215683923 0.000890013483 1.127366011e-05
|
||||
40 2 -23.68344234 -23.689768 0.003162828655 0.001120158205 0.001080249045 1.630224161e-05
|
||||
41 2 -23.68224173 -23.68968 0.003719136062 0.0009070521506 0.0008680034562 1.339908745e-05
|
||||
42 2 -23.68259685 -23.690074 0.003738573623 0.00143649564 0.001373818765 2.432187597e-05
|
||||
43 2 -23.68469428 -23.688108 0.001706858485 0.0006587619148 0.0006336134468 7.932733888e-06
|
||||
44 2 -23.68405177 -23.689241 0.002594615211 0.0009223784492 0.0008880101351 1.189350098e-05
|
||||
45 2 -23.68384626 -23.68952 0.002836868987 0.0009181252225 0.0008860011287 1.116431522e-05
|
||||
46 2 -23.68524763 -23.686278 0.0005151850613 0.0006668258323 0.0006406777661 8.58562287e-06
|
||||
47 2 -23.67629396 -23.690097 0.006901518594 0.0008737523828 0.0008410160522 1.125104926e-05
|
||||
48 2 -23.67835169 -23.690811 0.006229654604 0.0008814028122 0.0008500070588 1.103963422e-05
|
||||
49 2 -23.67981574 -23.690266 0.005225130991 0.001091936388 0.001044322747 1.944706281e-05
|
||||
50 2 -23.68209703 -23.690597 0.004249983197 0.001105769275 0.001050833003 2.242828165e-05
|
||||
51 2 -23.68050418 -23.690673 0.005084408246 0.000631172526 0.0006038907186 7.85857762e-06
|
||||
52 2 -23.68185505 -23.690551 0.00434797299 0.0009022813915 0.0008590064028 1.486707593e-05
|
||||
53 2 -23.68191508 -23.690693 0.004388958442 0.0009013677777 0.0008590110593 1.516503239e-05
|
||||
54 2 -23.68097184 -23.69021 0.004619081961 0.0009000307855 0.0008730051546 9.670733045e-06
|
||||
55 2 -23.68426495 -23.688943 0.002339025274 0.0009232115961 0.0008800306813 1.619629586e-05
|
||||
56 2 -23.67842316 -23.690136 0.005856419419 0.0006239138245 0.000593996633 8.394193459e-06
|
||||
57 2 -23.6849427 -23.687444 0.001250651312 0.0009347957747 0.000903059245 1.290489522e-05
|
||||
58 2 -23.6836322 -23.689801 0.003084401813 0.0009160470298 0.0008740011442 1.424271291e-05
|
||||
59 2 -23.6814842 -23.690408 0.00446190038 8.690218902e-07 0 3.245696976e-07
|
||||
60 2 -23.68115817 -23.690362 0.004601914896 0.0006345480975 0.0006067503605 9.377221838e-06
|
||||
61 2 -23.67229452 -23.688881 0.008293240443 0.0008566684404 0.0008250054545 1.108928728e-05
|
||||
62 2 -23.6791352 -23.690515 0.005689901939 0.001534883496 0.001475779794 2.124695951e-05
|
||||
63 2 -23.67786743 -23.690551 0.006341785918 0.0006228264143 0.0005996599036 7.295416678e-06
|
||||
64 2 -23.68316372 -23.689487 0.003161641446 0.0006469755816 0.0006194384554 7.530154689e-06
|
||||
65 2 -23.6834063 -23.68986 0.003226849907 0.0009142334935 0.0008860124153 1.052672488e-05
|
||||
66 2 -23.68377813 -23.689288 0.002754934411 0.00145229412 0.001396479144 1.702826801e-05
|
||||
67 2 -23.67700773 -23.690457 0.006724637324 0.0006187196638 0.0005939831647 7.080762895e-06
|
||||
68 2 -23.67552804 -23.689792 0.007131981721 0.0008698720997 0.0008340587509 1.418233126e-05
|
||||
69 2 -23.67583966 -23.690006 0.007083167888 0.0006146073806 0.0005897694465 8.07065747e-06
|
||||
70 2 -23.6777397 -23.690571 0.006415648131 0.0006207500925 0.0005939781141 7.401996527e-06
|
||||
71 2 -23.68270064 -23.690213 0.003756180649 0.001112284016 0.001084315452 1.142137177e-05
|
||||
72 2 -23.67870666 -23.690617 0.005955171449 0.0006250314539 0.0006024682564 6.623275772e-06
|
||||
73 2 -23.68231586 -23.689761 0.00372256923 0.0009095463313 0.0008790688255 1.222939687e-05
|
||||
74 2 -23.67673328 -23.69027 0.006768359835 7.188704983e-07 0 2.129270726e-07
|
||||
75 2 -23.68164707 -23.690599 0.004475963334 0.0006376044826 0.0006137752031 6.574310078e-06
|
||||
76 2 -23.67997815 -23.69061 0.00531592353 9.698202031e-07 0 3.95870452e-07
|
||||
77 2 -23.68008634 -23.690603 0.005258328411 0.0008923489326 0.0008590331775 1.256831367e-05
|
||||
78 2 -23.68488966 -23.687908 0.001509170978 0.0009340324028 0.0009010105438 1.204104822e-05
|
||||
79 2 -23.6795094 -23.690688 0.005589299031 0.0008890828456 0.0008470064935 1.419626566e-05
|
||||
80 2 -23.68316126 -23.689988 0.003413372454 0.0006451612224 0.0006194465272 7.422528505e-06
|
||||
81 2 -23.68321956 -23.689613 0.003196718897 0.000912899593 0.0008740732235 1.539555522e-05
|
||||
82 2 -23.68181374 -23.690678 0.004432127652 0.0006373963006 0.0006123757017 7.454253265e-06
|
||||
83 2 -23.68196226 -23.69017 0.004103870298 0.0009041773842 0.0008750051428 9.854119736e-06
|
||||
84 2 -23.68483517 -23.687892 0.001528413806 0.001142179928 0.001112070142 1.229243027e-05
|
||||
85 2 -23.68271169 -23.690132 0.003710155487 0.0009085291666 0.000868018433 1.49999647e-05
|
||||
86 2 -23.68018066 -23.690843 0.005331170668 0.0006305009468 0.0006081134763 5.90881572e-06
|
||||
87 2 -23.67957976 -23.690598 0.005509118787 0.001259431767 0.001217674833 1.243374729e-05
|
||||
88 2 -23.67869549 -23.690656 0.005980257091 0.0006251939788 0.0006024765556 7.13023928e-06
|
||||
89 2 -23.67884961 -23.690254 0.005702197143 0.001084797449 0.001043496047 1.68662339e-05
|
||||
90 2 -23.67961701 -23.690694 0.005538492834 0.0006273834422 0.0006010740387 8.134278748e-06
|
||||
91 2 -23.68202458 -23.690097 0.004036211359 0.0009041492449 0.0008730234819 1.169617364e-05
|
||||
92 2 -23.68476212 -23.688402 0.001819942156 0.0006575509652 0.000632180354 7.7469499e-06
|
||||
93 2 -23.68425036 -23.688669 0.002209320265 0.001133553123 0.001092474256 1.677033392e-05
|
||||
94 2 -23.68017683 -23.690538 0.005180583191 0.0008923392716 0.0008610145179 1.053989885e-05
|
||||
95 2 -23.68290142 -23.689722 0.003410287964 0.0006465597037 0.0006251287867 7.275875006e-06
|
||||
96 2 -23.6789537 -23.690581 0.005813649829 7.452601432e-07 0 2.355432868e-07
|
||||
97 2 -23.6840847 -23.688755 0.002335150427 0.0006519723076 0.0006251143895 8.25078808e-06
|
||||
98 2 -23.67367881 -23.689312 0.007816596299 0.0008618264365 0.0008290597083 1.323477647e-05
|
||||
99 2 -23.68489152 -23.687388 0.001248238956 0.001145929445 0.001120237475 1.049029355e-05
|
||||
100 2 -23.68174648 -23.690664 0.004458761579 0.0006367386055 0.0006109402589 6.270984336e-06
|
||||
101 2 -23.67450636 -23.68941 0.007451817634 0.0006119997091 0.0005883553348 7.715800125e-06
|
||||
102 2 -23.68321442 -23.690035 0.003410290658 0.0009128748923 0.0008810062429 1.106310227e-05
|
||||
103 2 -23.67584952 -23.690015 0.007082738579 0.0008706222251 0.0008450195264 9.898495893e-06
|
||||
104 2 -23.67856154 -23.690752 0.006095232174 0.0006245583967 0.0005996415596 7.033875201e-06
|
||||
105 2 -23.68297614 -23.689825 0.00342442945 0.0009134966073 0.0008800215906 1.147892484e-05
|
||||
106 2 -23.67876135 -23.690562 0.00590032283 0.0008849512172 0.0008560011682 1.005528708e-05
|
||||
107 2 -23.67874342 -23.690622 0.005939288687 0.0008835043772 0.0008390017878 1.530603189e-05
|
||||
108 2 -23.6843441 -23.688764 0.002209950672 0.0009250850126 0.0008910185183 1.254407066e-05
|
||||
109 2 -23.68340608 -23.690011 0.003302460748 0.0006464901241 0.0006194287691 7.216590251e-06
|
||||
110 2 -23.68476306 -23.687696 0.001466471271 0.001143422035 0.001087589996 2.279977174e-05
|
||||
111 2 -23.67977853 -23.691019 0.005620235289 0.000888876189 0.0008540035129 1.1779733e-05
|
||||
112 2 -23.68440001 -23.689025 0.002312496017 6.723949094e-07 0 2.648676661e-07
|
||||
113 2 -23.68208689 -23.689952 0.003932553163 7.386833996e-07 0 2.88150653e-07
|
||||
114 2 -23.67935439 -23.69061 0.005627806504 0.0008872685213 0.0008580011655 1.019979918e-05
|
||||
115 2 -23.68099138 -23.690595 0.004801812376 0.0008956193373 0.0008680069124 9.843191998e-06
|
||||
116 2 -23.67743565 -23.690231 0.006397673953 0.0006194343635 0.0005925892338 8.542917156e-06
|
||||
117 2 -23.67809541 -23.690469 0.006186797077 0.0008802359765 0.0008500294113 1.182654414e-05
|
||||
118 2 -23.68279142 -23.690482 0.003845288647 0.0009078436148 0.0008740102974 1.225600095e-05
|
||||
119 2 -23.67443144 -23.689613 0.007590778783 0.0008650318724 0.0008320192305 1.23538989e-05
|
||||
120 2 -23.68501591 -23.687426 0.001205043669 0.001145633567 0.00109577735 2.03694619e-05
|
||||
121 2 -23.68302307 -23.689562 0.003269464306 0.0006474095532 0.0006265237426 6.532536015e-06
|
||||
122 2 -23.68134549 -23.6904 0.004527256823 4.272990756e-07 0 1.732352808e-07
|
||||
123 2 -23.67843015 -23.690561 0.006065426647 0.0006235069318 0.0005982273815 6.816496585e-06
|
||||
124 2 -23.67292129 -23.689107 0.00809285397 0.0008589766346 0.0008180073349 1.439377155e-05
|
||||
125 2 -23.68123551 -23.690145 0.004454742608 0.0009009679944 0.0008740766557 1.132072203e-05
|
||||
126 2 -23.67777646 -23.690482 0.006352769316 0.0006215821083 0.0005939983165 8.362048689e-06
|
||||
127 2 -23.68318209 -23.689864 0.003340952886 0.0009142894487 0.0008860124153 1.044271435e-05
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
28 2 36.40799882 -23.68935266 -23.689367 7.168878343e-06 0.0005791393721 0.0006222748589 1.138033336e-05
|
||||
29 2 36.47727251 -23.69008875 -23.689888 0.0001003744201 0.0005692888887 0.0006166052222 1.209099821e-05
|
||||
30 2 36.47184897 -23.69016231 -23.689996 8.315556576e-05 0.0008112528739 0.0008810425642 2.394960977e-05
|
||||
31 2 36.62078348 -23.69160407 -23.690957 0.000323533345 9.040964751e-07 0 3.61961102e-07
|
||||
32 2 36.71197042 -23.69140398 -23.690521 0.0004414901764 0.0005342435063 0.0005982273815 1.577939361e-05
|
||||
33 2 36.77593928 -23.69138786 -23.69038 0.0005039275652 0.0005256100245 0.0005925723585 1.639144212e-05
|
||||
34 2 36.36547558 -23.6891719 -23.689202 1.504977335e-05 0.0005854132108 0.0006279363025 1.105961928e-05
|
||||
35 2 36.55974375 -23.69077024 -23.690482 0.0001441191505 0.000785315619 0.0008640138888 2.690934271e-05
|
||||
36 2 36.46414346 -23.69006247 -23.689902 8.02333664e-05 0.0005704101966 0.0006152154094 1.128520382e-05
|
||||
37 2 36.63368821 -23.69122878 -23.690563 0.0003328883811 0.0005455798024 0.0006038725031 1.380300235e-05
|
||||
38 2 36.45345189 -23.69036073 -23.690207 7.686648819e-05 0.0009894531016 0.00107369735 3.439226062e-05
|
||||
39 2 36.38484847 -23.68906335 -23.689285 0.0001108265837 0.0008276347239 0.000890013483 2.088438849e-05
|
||||
40 2 36.43347895 -23.68988438 -23.689768 5.818840896e-05 0.0009995854025 0.001080249045 3.293612314e-05
|
||||
41 2 36.50220719 -23.68988232 -23.68968 0.0001011615443 0.0007987715043 0.0008680034562 2.313480832e-05
|
||||
42 2 36.50719109 -23.69053288 -23.690074 0.0002294400544 0.001251664877 0.001373818765 4.011697596e-05
|
||||
43 2 36.28428565 -23.68794175 -23.688108 8.312420486e-05 0.0005986598004 0.0006336134468 9.281418142e-06
|
||||
44 2 36.3642236 -23.68905824 -23.689241 9.137877745e-05 0.0008315296326 0.0008880101351 1.887559387e-05
|
||||
45 2 36.40397469 -23.6896771 -23.68952 7.855223182e-05 0.0008258146364 0.0008860011287 2.017391988e-05
|
||||
46 2 36.15958616 -23.68590073 -23.686278 0.0001886370327 0.0006180554093 0.0006406777661 6.371396288e-06
|
||||
47 2 36.85012426 -23.69138986 -23.690097 0.0006464306412 0.0007342833303 0.0008410160522 3.561603494e-05
|
||||
48 2 36.76983294 -23.69198259 -23.690811 0.0005857945291 0.0007464868323 0.0008500070588 3.511590557e-05
|
||||
49 2 36.6630398 -23.69086423 -23.690266 0.0002991144941 0.0009288191325 0.001044322747 4.716382166e-05
|
||||
50 2 36.55357619 -23.69114266 -23.690597 0.0002728285897 0.000947778398 0.001050833003 4.207140425e-05
|
||||
51 2 36.65271066 -23.6915591 -23.690673 0.0004430516186 0.0005428776099 0.0006038907186 1.5218953e-05
|
||||
52 2 36.56222224 -23.69102891 -23.690551 0.0002389561584 0.000774875739 0.0008590064028 2.807921491e-05
|
||||
53 2 36.56679849 -23.69125002 -23.690693 0.0002785122603 0.0007753680903 0.0008590110593 2.815176061e-05
|
||||
54 2 36.59811665 -23.69068638 -23.69021 0.0002381891663 0.0007872682781 0.0008730051546 2.881955833e-05
|
||||
55 2 36.34900278 -23.68891574 -23.688943 1.362937502e-05 0.0008217831306 0.0008800306813 1.999409296e-05
|
||||
56 2 36.74034826 -23.69102993 -23.690136 0.0004469651652 0.0005307627739 0.000593996633 1.539088404e-05
|
||||
57 2 36.23610366 -23.68719357 -23.687444 0.0001252143692 0.0008622586338 0.000903059245 1.443948881e-05
|
||||
58 2 36.42259639 -23.68989382 -23.689801 4.640869711e-05 0.0008087918589 0.0008740011442 2.189207715e-05
|
||||
59 2 36.58194 -23.69097596 -23.690408 0.0002839823985 7.503746911e-07 0 2.799462454e-07
|
||||
60 2 36.59950783 -23.69098576 -23.690362 0.0003118823536 0.0005510011177 0.0006067503605 1.416397447e-05
|
||||
61 2 37.02589653 -23.69111966 -23.688881 0.001119329578 0.0006961173491 0.0008250054545 4.351784868e-05
|
||||
62 2 36.71189602 -23.69134752 -23.690515 0.0004162589173 0.001315448514 0.001475779794 6.296219244e-05
|
||||
63 2 36.78962367 -23.69180758 -23.690551 0.0006282890858 0.0005220927343 0.0005996599036 1.892223646e-05
|
||||
64 2 36.42642467 -23.68934442 -23.689487 7.129175935e-05 0.0005765059038 0.0006194384554 1.094283074e-05
|
||||
65 2 36.4423543 -23.69005198 -23.68986 9.598791646e-05 0.000820969408 0.0008860124153 2.187377734e-05
|
||||
66 2 36.39164409 -23.68928219 -23.689288 2.904742527e-06 0.001307397774 0.001396479144 2.84876039e-05
|
||||
67 2 36.83059874 -23.69184515 -23.690457 0.000694074458 0.0005166191319 0.0005939831647 1.910283849e-05
|
||||
68 2 36.8936692 -23.69152139 -23.689792 0.0008646931008 0.0007132722872 0.0008340587509 4.148921608e-05
|
||||
69 2 36.88495742 -23.69173908 -23.690006 0.0008665403088 0.000509225614 0.0005897694465 2.014031352e-05
|
||||
70 2 36.7928657 -23.6917618 -23.690571 0.0005954020471 0.000522233072 0.0005939781141 1.784694395e-05
|
||||
71 2 36.50844234 -23.69071409 -23.690213 0.0002505425174 0.00100006479 0.001084315452 3.439557116e-05
|
||||
72 2 36.74419477 -23.69167054 -23.690617 0.0005267677139 0.000527967872 0.0006024682564 1.799094801e-05
|
||||
73 2 36.49448266 -23.68984535 -23.689761 4.217684065e-05 0.0008081184665 0.0008790688255 2.433887648e-05
|
||||
74 2 36.83933705 -23.6916744 -23.69027 0.000702200495 6.051709007e-07 0 1.805959656e-07
|
||||
75 2 36.5709148 -23.69100516 -23.690599 0.0002030805029 0.0005539188049 0.0006137752031 1.42836673e-05
|
||||
76 2 36.67683082 -23.69149029 -23.69061 0.000440147338 8.19405771e-07 0 3.344275146e-07
|
||||
77 2 36.66115635 -23.69126428 -23.690603 0.0003306377446 0.0007644159139 0.0008590331775 3.182906898e-05
|
||||
78 2 36.25583797 -23.68760523 -23.687908 0.0001513865646 0.0008610549997 0.0009010105438 1.375539981e-05
|
||||
79 2 36.69315685 -23.69139673 -23.690688 0.0003543635076 0.0007539943095 0.0008470064935 3.150219089e-05
|
||||
80 2 36.46769977 -23.6903207 -23.689988 0.000166349129 0.00057046285 0.0006194465272 1.26899955e-05
|
||||
81 2 36.44434113 -23.68978845 -23.689613 8.772639065e-05 0.0008085000342 0.0008740732235 2.312629629e-05
|
||||
82 2 36.57453003 -23.69129515 -23.690678 0.0003085738172 0.0005540403669 0.0006123757017 1.45763918e-05
|
||||
83 2 36.54218785 -23.69059495 -23.69017 0.0002124774731 0.0007942599876 0.0008750051428 2.703366464e-05
|
||||
84 2 36.26350252 -23.68768016 -23.687892 0.0001059218404 0.001061457684 0.001112070142 2.066296054e-05
|
||||
85 2 36.49725495 -23.69047056 -23.690132 0.0001692803297 0.0007883161501 0.000868018433 2.691803767e-05
|
||||
86 2 36.66468316 -23.6915479 -23.690843 0.0003524495313 0.000539317225 0.0006081134763 1.667404934e-05
|
||||
87 2 36.69098146 -23.69138084 -23.690598 0.000391422181 0.001071567167 0.001217674833 3.643886126e-05
|
||||
88 2 36.7498524 -23.69180651 -23.690656 0.0005752547833 0.000527789675 0.0006024765556 1.838025723e-05
|
||||
89 2 36.72620595 -23.69122523 -23.690254 0.0004856160023 0.0009222234957 0.001043496047 4.953854452e-05
|
||||
90 2 36.7046344 -23.6917684 -23.690694 0.0005371985736 0.0005348454927 0.0006010740387 1.632563006e-05
|
||||
91 2 36.53215524 -23.69041038 -23.690097 0.0001566896488 0.000800819059 0.0008730234819 2.45509438e-05
|
||||
92 2 36.28988463 -23.68821971 -23.688402 9.114491667e-05 0.0005973853662 0.000632180354 8.798849334e-06
|
||||
93 2 36.330155 -23.68847499 -23.688669 9.700375974e-05 0.001027728106 0.001092474256 2.64442799e-05
|
||||
94 2 36.65451876 -23.69119399 -23.690538 0.0003279952785 0.0007669956996 0.0008610145179 3.135704811e-05
|
||||
95 2 36.46623662 -23.68991417 -23.689722 9.608645468e-05 0.0005705574359 0.0006251287867 1.358621926e-05
|
||||
96 2 36.73431174 -23.69168283 -23.690581 0.0005509134731 6.323934582e-07 0 2.001035598e-07
|
||||
97 2 36.34544239 -23.68858786 -23.688755 8.356963063e-05 0.0005883578628 0.0006251143895 9.471043776e-06
|
||||
98 2 36.9736935 -23.69138149 -23.689312 0.001034745771 0.0007066329298 0.0008290597083 4.178668599e-05
|
||||
99 2 36.24487417 -23.68726723 -23.687388 6.038705592e-05 0.001077440761 0.001120237475 1.747047954e-05
|
||||
100 2 36.57555586 -23.6912365 -23.690664 0.0002862502209 0.0005537425337 0.0006109402589 1.351319675e-05
|
||||
101 2 36.94151938 -23.69144967 -23.68941 0.001019837037 0.0005014347711 0.0005883553348 2.19408087e-05
|
||||
102 2 36.45547212 -23.69016301 -23.690035 6.400448387e-05 0.0008123923223 0.0008810062429 2.292847926e-05
|
||||
103 2 36.88496132 -23.69174097 -23.690015 0.000862985398 0.0007314433439 0.0008450195264 3.85750332e-05
|
||||
104 2 36.76103389 -23.69196872 -23.690752 0.0006083582391 0.0005266702015 0.0005996415596 1.789867459e-05
|
||||
105 2 36.45404349 -23.68980079 -23.689825 1.21041937e-05 0.0008098693325 0.0008800215906 2.356465165e-05
|
||||
106 2 36.74654739 -23.69176252 -23.690562 0.000600262294 0.0007547288177 0.0008560011682 3.382741999e-05
|
||||
107 2 36.74084732 -23.69164858 -23.690622 0.0005132916917 0.0007385047205 0.0008390017878 3.356835921e-05
|
||||
108 2 36.33025646 -23.68859242 -23.688764 8.578967698e-05 0.0008410207787 0.0008910185183 1.741451416e-05
|
||||
109 2 36.44122368 -23.69008798 -23.690011 3.848968077e-05 0.0005740036813 0.0006194287691 1.080005975e-05
|
||||
110 2 36.25348342 -23.68736362 -23.687696 0.0001661898332 0.001028336192 0.001087589996 2.41866647e-05
|
||||
111 2 36.69693588 -23.69191585 -23.691019 0.0004484248955 0.000759489717 0.0008540035129 3.186170711e-05
|
||||
112 2 36.3425194 -23.6889708 -23.689025 2.710120089e-05 6.079196827e-07 0 2.40092126e-07
|
||||
113 2 36.51656499 -23.69011781 -23.689952 8.290515026e-05 6.429861508e-07 0 2.522927625e-07
|
||||
114 2 36.71447816 -23.69168287 -23.69061 0.0005364328485 0.000759516095 0.0008580011655 3.305137668e-05
|
||||
115 2 36.62519495 -23.69145964 -23.690595 0.0004323194208 0.0007842976319 0.0008680069124 2.798414195e-05
|
||||
116 2 36.80154127 -23.69148354 -23.690231 0.0006262693175 0.0005212060476 0.0005925892338 1.729202306e-05
|
||||
117 2 36.77742539 -23.69172415 -23.690469 0.0006275768016 0.0007498307724 0.0008500294113 3.399854028e-05
|
||||
118 2 36.50183296 -23.69078621 -23.690482 0.0001521064099 0.0008017684479 0.0008740102974 2.43097787e-05
|
||||
119 2 36.93568763 -23.6913497 -23.689613 0.0008683490451 0.0007051115849 0.0008320192305 4.273163835e-05
|
||||
120 2 36.23289183 -23.68720637 -23.687426 0.0001098147166 0.001039370507 0.00109577735 2.30331168e-05
|
||||
121 2 36.44295904 -23.68953345 -23.689562 1.427314325e-05 0.0005729756495 0.0006265237426 1.317934246e-05
|
||||
122 2 36.59751671 -23.69116473 -23.6904 0.0003823650158 3.485529149e-07 0 1.415027615e-07
|
||||
123 2 36.76766724 -23.69189304 -23.690561 0.0006660198407 0.0005259591667 0.0005982273815 1.816463799e-05
|
||||
124 2 37.00025894 -23.69119787 -23.689107 0.001045433278 0.0006882515391 0.0008180073349 4.353839847e-05
|
||||
125 2 36.58722353 -23.6907127 -23.690145 0.0002838477051 0.0007944798089 0.0008740766557 2.746296994e-05
|
||||
126 2 36.79405605 -23.69178802 -23.690482 0.0006530116164 0.0005229308774 0.0005939983165 1.716633259e-05
|
||||
127 2 36.45320348 -23.69001701 -23.689864 7.650692467e-05 0.0008191998865 0.0008860124153 2.27311373e-05
|
||||
# Elastic_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
128 4 -46.449456 -46.437936 0.002880000611 0.0007088173441 0.001265949446 0.0001573706237
|
||||
129 4 -46.45317307 -46.438504 0.003667267825 0.0007210982328 0.001492549497 0.0002032393675
|
||||
130 4 -46.44686167 -46.436378 0.002620918523 0.0004870837365 0.000810592376 0.0001107544174
|
||||
131 4 -46.45357979 -46.441551 0.003007196305 0.0008634182131 0.001283675193 0.0001231453909
|
||||
132 4 -46.42409677 -46.416957 0.001784942313 0.0007481922079 0.001186145859 0.0001205918882
|
||||
133 4 -46.45078882 -46.440495 0.002573455911 0.0007289008721 0.001212440514 0.0001119490174
|
||||
134 4 -46.4501363 -46.437972 0.003041076136 0.001116532125 0.002358226452 0.0003166808771
|
||||
135 4 -46.46241981 -46.44586 0.004139951294 0.001077737689 0.002033949852 0.0002702964015
|
||||
136 4 -46.44743429 -46.435744 0.002922571394 0.0008383971706 0.001690849491 0.0002711013554
|
||||
137 4 -46.45237555 -46.438209 0.003541637787 0.0007039962535 0.001160049999 0.0001096430557
|
||||
138 4 -46.43645451 -46.42629 0.002541127472 0.0004839683449 0.0005297018029 1.480491546e-05
|
||||
139 4 -46.45466199 -46.443301 0.002840247268 0.0008590849412 0.001818421568 0.0002395191538
|
||||
140 4 -46.4513559 -46.439002 0.003088474484 0.000980675092 0.001416973535 0.0001142710898
|
||||
141 4 -46.44224357 -46.432438 0.00245139227 0.0008958100898 0.001010469198 5.862303988e-05
|
||||
142 4 -46.41846428 -46.412654 0.001452568802 0.001104791425 0.001801959766 0.0001900084105
|
||||
143 4 -46.45594552 -46.443231 0.003178629143 0.0006959928784 0.001691590967 0.0002104366356
|
||||
144 4 -46.44141177 -46.431513 0.00247469212 0.001149659372 0.001680544852 0.0001329997121
|
||||
145 4 -46.44458344 -46.435608 0.00224385943 0.000711021509 0.0009593039143 5.831382606e-05
|
||||
146 4 -46.45129649 -46.437689 0.003401871689 0.0007271142738 0.001217708504 0.0001414871092
|
||||
147 4 -46.43755262 -46.428447 0.002276404472 0.0008708378565 0.002060081552 0.0003082033743
|
||||
148 4 -46.44295113 -46.432255 0.00267403188 0.0005315813764 0.0006274201144 5.596270268e-05
|
||||
149 4 -46.45482154 -46.442315 0.003126635324 0.0008653689406 0.002424436842 0.0004107290683
|
||||
150 4 -46.44918467 -46.436613 0.003142918309 0.0004839663128 0.0005321240457 3.890880543e-05
|
||||
151 4 -46.44094809 -46.430825 0.002530772174 0.0007559646277 0.001399987143 0.0001669802678
|
||||
152 4 -46.44335614 -46.43312 0.002559035587 0.0004859700309 0.0007272771136 6.315695513e-05
|
||||
153 4 -46.44518607 -46.434347 0.002709767129 0.0007148497795 0.001284451634 0.0001580665901
|
||||
154 4 -46.43969219 -46.430573 0.002279798333 0.00072875179 0.001315746176 0.000142372977
|
||||
155 4 -46.46201856 -46.445665 0.004088390852 0.0008369246217 0.00180789159 0.0002715757049
|
||||
156 4 -46.44738266 -46.435898 0.002871166201 0.0007118215897 0.001869300939 0.0002650888178
|
||||
157 4 -46.45279209 -46.442107 0.002671271631 0.0005099355574 0.0006020930161 3.155335447e-05
|
||||
158 4 -46.44687446 -46.434432 0.003110615714 0.0008364031703 0.001092982159 9.484366005e-05
|
||||
159 4 -46.45033825 -46.436308 0.003507562522 0.0009954281391 0.001839150891 0.0002479613631
|
||||
160 4 -46.43248168 -46.423938 0.002135919949 0.0007772193879 0.001463463016 0.0001986681069
|
||||
161 4 -46.43702199 -46.428115 0.002226747981 0.0005418219957 0.0008584497656 9.283863381e-05
|
||||
162 4 -46.43553597 -46.4269 0.002158992752 0.001008467413 0.001845719914 0.00024455962
|
||||
163 4 -46.43191737 -46.421142 0.00269384137 0.0009169914298 0.001309150106 9.335100097e-05
|
||||
164 4 -46.44107961 -46.432233 0.002211651338 0.0006944670911 0.0007253109678 2.446203898e-05
|
||||
165 4 -46.44097784 -46.429408 0.002892459649 0.0007189999753 0.001068327665 9.331287519e-05
|
||||
166 4 -46.45970672 -46.445145 0.003640430606 0.0008323398895 0.001776038288 0.000241778013
|
||||
167 4 -46.44583143 -46.435868 0.002490857628 0.001007239475 0.002376074704 0.0003893124404
|
||||
168 4 -46.4515773 -46.439663 0.002978574612 0.0004764710524 0.001119403413 0.0001156692402
|
||||
169 4 -46.43612447 -46.428287 0.00195936642 0.001036891264 0.001277000392 6.942055774e-05
|
||||
170 4 -46.4323966 -46.424584 0.001953149801 0.0005497544117 0.0008032957114 5.852281957e-05
|
||||
171 4 -46.41884421 -46.413045 0.001449803236 0.0009011718881 0.001248322074 7.333380516e-05
|
||||
172 4 -46.44596985 -46.436994 0.002243961387 0.0008480487041 0.001331939188 0.0001689650386
|
||||
173 4 -46.45736434 -46.443604 0.003440085706 0.0007046835731 0.001177046303 0.000122309487
|
||||
174 4 -46.4531541 -46.439718 0.003359024693 6.718665563e-07 0 1.784212677e-07
|
||||
175 4 -46.44922127 -46.435527 0.003423566396 0.0008698447035 0.0009338393866 5.635428662e-05
|
||||
176 4 -46.44518705 -46.434787 0.002600012526 0.0008890985417 0.00117329195 6.906839261e-05
|
||||
177 4 -46.44789017 -46.434929 0.00324029173 0.001006522874 0.001349491756 8.807224523e-05
|
||||
178 4 -46.43673847 -46.426499 0.002559868692 0.0009134543992 0.001248937949 9.133606536e-05
|
||||
179 4 -46.44932495 -46.437025 0.003074986544 0.0006805240432 0.000938418883 7.446008431e-05
|
||||
180 4 -46.43885209 -46.428937 0.002478772296 0.0009031344997 0.001286352984 0.0001081690229
|
||||
181 4 -46.45413306 -46.442516 0.002904263993 0.000506604563 0.00094855469 0.0001414866709
|
||||
182 4 -46.44060244 -46.428736 0.002966609134 0.0007579010233 0.001424321593 0.0001681832084
|
||||
183 4 -46.44430426 -46.433359 0.002736316202 0.0008950557387 0.001276381604 0.0001027241271
|
||||
184 4 -46.45260002 -46.438799 0.00345025532 0.0006868717473 0.0008186940821 3.675916237e-05
|
||||
185 4 -46.45478935 -46.441993 0.003199088629 0.000703010985 0.001887735151 0.0002666518851
|
||||
186 4 -46.44949137 -46.439033 0.002614591408 0.0006795560995 0.000821568013 5.214373405e-05
|
||||
187 4 -46.44856954 -46.436967 0.002900635979 0.000860448627 0.001482323514 0.0001802503616
|
||||
188 4 -46.43759968 -46.427245 0.00258867094 0.0008795521813 0.001293885621 0.0001012099865
|
||||
189 4 -46.45133388 -46.438046 0.003321969731 0.0009940752633 0.001627288542 0.000174152867
|
||||
190 4 -46.42813695 -46.420083 0.002013486722 0.001161998446 0.002395244873 0.0003650969018
|
||||
191 4 -46.46060362 -46.445247 0.003839154837 0.0006909751141 0.001219330964 0.0001271217748
|
||||
192 4 -46.45903895 -46.446044 0.003248736964 0.0006847065621 0.001305329077 0.0001398957152
|
||||
193 4 -46.44724817 -46.434472 0.003194042613 0.0007061519125 0.0008323340675 6.681050285e-05
|
||||
194 4 -46.45649776 -46.44458 0.002979439009 0.0004998748498 0.0009744208536 8.547729233e-05
|
||||
195 4 -46.45403889 -46.441776 0.003065721535 0.0008652918641 0.001339231869 0.0001389938291
|
||||
196 4 -46.44933689 -46.436389 0.003236972034 0.001007551549 0.001786741168 0.0002029508895
|
||||
197 4 -46.459873 -46.446416 0.00336425035 0.0004914989987 0.0006588778339 6.549510811e-05
|
||||
198 4 -46.46569473 -46.449806 0.003972183676 0.000943305002 0.002135055034 0.0003137851731
|
||||
199 4 -46.43467991 -46.427189 0.00187272638 0.0007726175275 0.001050788276 7.135568315e-05
|
||||
200 4 -46.43621938 -46.427857 0.002090594118 0.0007686546978 0.001487666629 0.0001823668299
|
||||
201 4 -46.45576365 -46.44004 0.003930912967 0.0005030079851 0.000757202747 5.770676907e-05
|
||||
202 4 -46.4483913 -46.437214 0.002794325435 0.0007102028538 0.001505586265 0.000179529909
|
||||
203 4 -46.43168209 -46.422628 0.002263521917 0.0007374332623 0.001601713458 0.0002609325883
|
||||
204 4 -46.45732644 -46.443535 0.00344786022 0.0009811025521 0.001590304373 0.0001690672254
|
||||
205 4 -46.45144079 -46.439922 0.002879696366 0.0008698700101 0.001530493385 0.0001528171002
|
||||
206 4 -46.44960522 -46.437675 0.002982555611 0.00112440729 0.002440246094 0.0004061057502
|
||||
207 4 -46.45839808 -46.445558 0.003210018941 0.0006780842253 0.00113392416 0.0001196075532
|
||||
208 4 -46.45130112 -46.439106 0.003048781046 0.0009934671927 0.001830731002 0.000245168776
|
||||
209 4 -46.45826105 -46.443073 0.003797013279 0.0004759445984 0.0005766870902 2.863834812e-05
|
||||
210 4 -46.4536082 -46.4397 0.003477049491 0.0006982622456 0.001204174406 0.0001154782847
|
||||
211 4 -46.44819434 -46.436374 0.002955085327 0.0007363684621 0.001461656594 0.0002277550157
|
||||
212 4 -46.43668282 -46.426557 0.00253145389 0.0007326220467 0.001359624213 0.0001251472548
|
||||
213 4 -46.44485583 -46.434009 0.002711707903 0.000870647096 0.001391131194 0.0001541542453
|
||||
214 4 -46.44732696 -46.436262 0.002766239028 0.001116549362 0.002503347159 0.0003211377445
|
||||
215 4 -46.44414241 -46.434505 0.002409352177 0.0008685662223 0.001041637173 4.942106462e-05
|
||||
216 4 -46.45095913 -46.438768 0.003047783488 0.0008482298138 0.001098285027 8.657909629e-05
|
||||
217 4 -46.45111242 -46.440254 0.002714605501 0.0004892442432 0.0006069892915 5.824568303e-05
|
||||
218 4 -46.43463407 -46.42286 0.002943517186 0.0004976409931 0.0007365242698 7.564906264e-05
|
||||
219 4 -46.42611144 -46.418078 0.002008360417 0.001053243552 0.002028412187 0.0002473380313
|
||||
220 4 -46.45344976 -46.440513 0.003234189608 0.0007024129954 0.001158189967 0.0001371889048
|
||||
221 4 -46.41584187 -46.409824 0.001504467167 0.0007558580012 0.001759573812 0.0002386003087
|
||||
222 4 -46.45494987 -46.440329 0.003655216631 0.0005034620022 0.0009534044263 0.0001064495091
|
||||
223 4 -46.45000759 -46.43773 0.003069396495 0.0006831478015 0.000926180328 7.390298375e-05
|
||||
224 4 -46.42538863 -46.416525 0.002215907169 0.0005605993692 0.0007573664899 5.946405938e-05
|
||||
225 4 -46.45386072 -46.440293 0.003391930454 0.0006980795454 0.0007725386722 1.86450807e-05
|
||||
226 4 -46.4527969 -46.43839 0.003601726069 0.0005103417187 0.0005612022808 1.656002337e-05
|
||||
227 4 -46.45374294 -46.438916 0.00370673382 0.0006956794369 0.001650878554 0.0002154167998
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
128 4 74.14589882 -46.4365399 -46.437936 0.0003490253695 0.0006778763562 0.001265949446 0.0001709209414
|
||||
129 4 74.26852111 -46.43873511 -46.438504 5.777717929e-05 0.0007503851359 0.001492549497 0.0001964708888
|
||||
130 4 74.05957274 -46.43494258 -46.436378 0.0003588561295 0.0004091403196 0.000810592376 0.0001235186477
|
||||
131 4 74.30647158 -46.43878572 -46.441551 0.0006913207875 0.0008401870557 0.001283675193 0.000117670841
|
||||
132 4 73.40902276 -46.41981732 -46.416957 0.0007150811941 0.0007698794521 0.001186145859 0.0001183848728
|
||||
133 4 74.1804881 -46.43741714 -46.440495 0.0007694653618 0.000764535615 0.001212440514 0.0001037058436
|
||||
134 4 74.17596744 -46.43686048 -46.437972 0.0002778801153 0.001042376421 0.002358226452 0.0003211452935
|
||||
135 4 74.73528136 -46.44278872 -46.44586 0.0007678201944 0.0009464853028 0.002033949852 0.0002884495696
|
||||
136 4 74.0787509 -46.435261 -46.435744 0.000120750513 0.000701047998 0.001690849491 0.0002978199749
|
||||
137 4 74.24609528 -46.43826893 -46.438209 1.498150614e-05 0.0006653291189 0.001160049999 0.0001204040155
|
||||
138 4 73.73005434 -46.42836535 -46.42629 0.0005188370146 0.0004160879166 0.0005297018029 2.593986809e-05
|
||||
139 4 74.33993289 -46.43949676 -46.443301 0.0009510596674 0.0008343735689 0.001818421568 0.0002340478921
|
||||
140 4 74.20715045 -46.43767989 -46.439002 0.0003305284497 0.0008756041332 0.001416973535 0.000138076772
|
||||
141 4 73.89686848 -46.43217385 -46.432438 6.603760684e-05 0.0009098901281 0.001010469198 5.849923828e-05
|
||||
142 4 73.27773838 -46.41574396 -46.412654 0.0007724896281 0.001208930824 0.001801959766 0.000163826793
|
||||
143 4 74.40027968 -46.44010931 -46.443231 0.0007804219166 0.0006479839207 0.001691590967 0.0002097109297
|
||||
144 4 73.86123747 -46.43173129 -46.431513 5.457318322e-05 0.001155222461 0.001680544852 0.0001244918437
|
||||
145 4 73.96908649 -46.43368132 -46.435608 0.0004816703497 0.0006901785796 0.0009593039143 6.512547442e-05
|
||||
146 4 74.18717232 -46.43781824 -46.437689 3.231087952e-05 0.0007610880958 0.001217708504 0.0001332916958
|
||||
147 4 73.76897316 -46.42901321 -46.428447 0.0001415522382 0.0008290742779 0.002060081552 0.0003002656668
|
||||
148 4 73.9161373 -46.4326492 -46.432255 9.855071193e-05 0.0005720819518 0.0006274201144 5.005366155e-05
|
||||
149 4 74.36502962 -46.43936432 -46.442315 0.0007376709082 0.0008396652585 0.002424436842 0.0004197689306
|
||||
150 4 74.11860796 -46.43651236 -46.436613 2.516036845e-05 0.0004027445072 0.0005321240457 5.236241076e-05
|
||||
151 4 73.86741001 -46.4312477 -46.430825 0.0001056748319 0.0008169191308 0.001399987143 0.0001527015481
|
||||
152 4 73.94132612 -46.43279504 -46.43312 8.124081023e-05 0.0004118950513 0.0007272771136 7.568884217e-05
|
||||
153 4 73.9811119 -46.43412245 -46.434347 5.613857813e-05 0.0006934815469 0.001284451634 0.0001648706819
|
||||
154 4 73.82698041 -46.43048826 -46.430573 2.118574418e-05 0.000721304342 0.001315746176 0.0001459557407
|
||||
155 4 74.70690467 -46.44272265 -46.445665 0.0007355887337 0.000830867335 0.00180789159 0.0002733307738
|
||||
156 4 74.08446722 -46.43517655 -46.435898 0.0001803627697 0.0006852180888 0.001869300939 0.0002597665795
|
||||
157 4 74.25274774 -46.43856918 -46.442107 0.0008844553139 0.0005306212583 0.0006020930161 2.766150774e-05
|
||||
158 4 74.05043726 -46.43504857 -46.434432 0.000154143348 0.0006999023626 0.001092982159 0.0001210519797
|
||||
159 4 74.16653794 -46.43714625 -46.436308 0.0002095629376 0.0009493605386 0.001839150891 0.0002529617689
|
||||
160 4 73.62293094 -46.42564869 -46.423938 0.0004276731361 0.0008587655751 0.001463463016 0.0001897804852
|
||||
161 4 73.74948122 -46.42870613 -46.428115 0.0001477819203 0.0005931538283 0.0008584497656 8.420193161e-05
|
||||
162 4 73.70731572 -46.42771872 -46.4269 0.0002046807972 0.0009469014219 0.001845719914 0.0002469260205
|
||||
163 4 73.59054722 -46.42543123 -46.421142 0.001072308169 0.0009620052068 0.001309150106 8.335904249e-05
|
||||
164 4 73.85798892 -46.43145704 -46.432233 0.0001939901566 0.0005947623483 0.0007253109678 3.2683905e-05
|
||||
165 4 73.86179419 -46.43130921 -46.429408 0.0004753021396 0.0007089743889 0.001068327665 9.801988386e-05
|
||||
166 4 74.58468636 -46.44179134 -46.445145 0.0008384160469 0.000727599272 0.001776038288 0.0002575365623
|
||||
167 4 74.02247797 -46.43433934 -46.435868 0.0003821644998 0.0009755195886 0.002376074704 0.0003777681492
|
||||
168 4 74.20501804 -46.43791767 -46.439663 0.0004363336496 0.0003915596944 0.001119403413 0.0001295508544
|
||||
169 4 73.72492498 -46.42809459 -46.428287 4.810140297e-05 0.001036303887 0.001277000392 6.284262343e-05
|
||||
170 4 73.62492908 -46.42556003 -46.424584 0.0002440066181 0.0006080896398 0.0008032957114 4.880135206e-05
|
||||
171 4 73.28647 -46.41601594 -46.413045 0.0007427346831 0.0008994327002 0.001248322074 8.558617494e-05
|
||||
172 4 74.01119894 -46.43455295 -46.436994 0.0006102631177 0.0007175320236 0.001331939188 0.000194044023
|
||||
173 4 74.45838911 -46.44083906 -46.443604 0.0006912359075 0.0007179005695 0.001177046303 0.0001204148769
|
||||
174 4 74.29439096 -46.43851563 -46.439718 0.0003005917742 6.779735709e-07 0 1.850840692e-07
|
||||
175 4 74.12581885 -46.43647031 -46.435527 0.0002358272884 0.0008623111483 0.0009338393866 6.110995551e-05
|
||||
176 4 73.97170625 -46.43419386 -46.434787 0.0001482856379 0.0008964684767 0.00117329195 5.683970236e-05
|
||||
177 4 74.0799757 -46.43566421 -46.434929 0.000183801417 0.0009666850325 0.001349491756 9.790390672e-05
|
||||
178 4 73.74433679 -46.42848689 -46.426499 0.0004969718736 0.0009439910982 0.001248937949 8.270872203e-05
|
||||
179 4 74.14770713 -46.43636452 -46.437025 0.0001651198263 0.0005651173523 0.000938418883 8.800287474e-05
|
||||
180 4 73.80957625 -46.42984517 -46.428937 0.00022704173 0.0009257049352 0.001286352984 9.212521395e-05
|
||||
181 4 74.32407369 -46.43913513 -46.442516 0.0008452171781 0.0005247762839 0.00094855469 0.000138510299
|
||||
182 4 73.84764949 -46.43111652 -46.428736 0.0005951290806 0.0008203602845 0.001424321593 0.0001535150579
|
||||
183 4 73.97111028 -46.43336044 -46.433359 3.606158838e-07 0.0009045821114 0.001276381604 8.957409536e-05
|
||||
184 4 74.25298337 -46.43837828 -46.438799 0.0001051803124 0.0005671501776 0.0008186940821 5.9584468e-05
|
||||
185 4 74.36513571 -46.43933069 -46.441993 0.000665578083 0.000659139815 0.001887735151 0.0002779916191
|
||||
186 4 74.14572274 -46.43655347 -46.439033 0.0006198812681 0.0005643310555 0.000821568013 6.539805158e-05
|
||||
187 4 74.11964094 -46.43596676 -46.436967 0.0002500605132 0.0007922560128 0.001482323514 0.0001890636838
|
||||
188 4 73.76706483 -46.42906594 -46.427245 0.0004552360994 0.0008420124691 0.001293885621 0.000123769258
|
||||
189 4 74.21830016 -46.43757193 -46.438046 0.0001185169019 0.0009431935765 0.001627288542 0.000180451532
|
||||
190 4 73.51075683 -46.42264908 -46.420083 0.0006415203479 0.0011581645 0.002395244873 0.0003416944607
|
||||
191 4 74.62704502 -46.44219675 -46.445247 0.0007625624466 0.0006922298428 0.001219330964 0.0001267062759
|
||||
192 4 74.54172989 -46.44157042 -46.446044 0.001118394681 0.0006279207868 0.001305329077 0.0001545426103
|
||||
193 4 74.05152275 -46.43533022 -46.434472 0.0002145548979 0.0006783459137 0.0008323340675 4.815802863e-05
|
||||
194 4 74.415732 -46.44043452 -46.44458 0.001036371024 0.0005115810797 0.0009744208536 8.368157786e-05
|
||||
195 4 74.3298536 -46.43901696 -46.441776 0.0006897594475 0.0008419729125 0.001339231869 0.0001331126632
|
||||
196 4 74.14951222 -46.43635108 -46.436389 9.479448964e-06 0.0009656745203 0.001786741168 0.0002070075846
|
||||
197 4 74.58621137 -46.44192833 -46.446416 0.001121916267 0.0004949274321 0.0006588778339 6.47201301e-05
|
||||
198 4 74.93791818 -46.44387394 -46.449806 0.001483014862 0.0008253040951 0.002135055034 0.0003190372343
|
||||
199 4 73.6789527 -46.42716959 -46.427189 4.852790987e-06 0.0008507065458 0.001050788276 5.271232915e-05
|
||||
200 4 73.72666848 -46.42818016 -46.427857 8.078959573e-05 0.0008427653602 0.001487666629 0.0001650754909
|
||||
201 4 74.38554824 -46.44003106 -46.44004 2.235981732e-06 0.0005169540114 0.000757202747 5.589412725e-05
|
||||
202 4 74.09024992 -46.43604701 -46.437214 0.0002917470364 0.0006844855267 0.001505586265 0.0001737573979
|
||||
203 4 73.60013606 -46.42513223 -46.422628 0.0006260572254 0.0007443584872 0.001601713458 0.0002614387902
|
||||
204 4 74.47827164 -46.44057644 -46.443535 0.0007396409936 0.0009060249865 0.001590304373 0.0001810833299
|
||||
205 4 74.22558703 -46.43761918 -46.439922 0.0005757039773 0.0008549412332 0.001530493385 0.000154153517
|
||||
206 4 74.15291432 -46.43659149 -46.437675 0.0002708783628 0.001097827078 0.002440246094 0.0003926910439
|
||||
207 4 74.50981896 -46.44129461 -46.445558 0.001065846715 0.0006199615106 0.00113392416 0.0001347351709
|
||||
208 4 74.19814905 -46.43773076 -46.439106 0.0003438089032 0.0009450786461 0.001830731002 0.0002506276284
|
||||
209 4 74.51720313 -46.44107696 -46.443073 0.0004990097956 0.0003821944024 0.0005766870902 4.411462742e-05
|
||||
210 4 74.29924604 -46.4388913 -46.4397 0.0002021743594 0.000655919615 0.001204174406 0.0001271596208
|
||||
211 4 74.09425795 -46.43581832 -46.436374 0.0001389197185 0.0007783350169 0.001461656594 0.0002175981817
|
||||
212 4 73.73717548 -46.42852468 -46.426557 0.0004919190242 0.000731069721 0.001359624213 0.0001162614315
|
||||
213 4 73.99983876 -46.43362615 -46.434009 9.571351696e-05 0.0008142607396 0.001391131194 0.0001606369741
|
||||
214 4 74.07916779 -46.435195 -46.436262 0.000266750348 0.001049754613 0.002503347159 0.0003291171292
|
||||
215 4 73.94744484 -46.43344752 -46.434505 0.0002643689953 0.0008131240824 0.001041637173 6.793294444e-05
|
||||
216 4 74.2021224 -46.43735216 -46.438768 0.0003539605952 0.0007712639686 0.001098285027 9.728403498e-05
|
||||
217 4 74.20389194 -46.43749365 -46.440254 0.0006900865379 0.0004068582767 0.0006069892915 7.165751162e-05
|
||||
218 4 73.66782167 -46.42720704 -46.42286 0.001086758928 0.0004342488188 0.0007365242698 8.630537062e-05
|
||||
219 4 73.46349993 -46.42118113 -46.418078 0.0007757822236 0.001078687661 0.002028412187 0.0002554635547
|
||||
220 4 74.30307454 -46.43870444 -46.440513 0.0004521389732 0.0006607605594 0.001158189967 0.0001481729511
|
||||
221 4 73.21819832 -46.41381896 -46.409824 0.000998741091 0.0007907537894 0.001759573812 0.0002332345195
|
||||
222 4 74.35772636 -46.43958444 -46.440329 0.0001861393873 0.0005177035013 0.0009534044263 0.0001042756811
|
||||
223 4 74.17615527 -46.43673902 -46.43773 0.0002477446805 0.0005662970434 0.000926180328 8.78045986e-05
|
||||
224 4 73.43860935 -46.42072648 -46.416525 0.00105037112 0.0006307891456 0.0007573664899 4.810902154e-05
|
||||
225 4 74.31356506 -46.43899519 -46.440293 0.000324453316 0.0006547395537 0.0007725386722 2.822832849e-05
|
||||
226 4 74.25452523 -46.43854503 -46.43839 3.875707844e-05 0.0005304363564 0.0005612022808 1.336940357e-05
|
||||
227 4 74.27331932 -46.43923882 -46.438916 8.070513634e-05 0.0006578017222 0.001650878554 0.0002261574901
|
||||
# GSF_110.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
228 24 -278.7403996 -279.068761 0.01368172569 2.282668754 1.756353161 0.0474563559
|
||||
229 24 -279.902595 -279.784296 0.004929123882 0.9479314831 0.9057668891 0.02403120774
|
||||
230 24 -279.9942014 -279.901657 0.003856015841 0.2795933118 0.001565946359 0.01120665859
|
||||
231 24 -279.6335344 -279.584238 0.002054016531 1.573004204 1.035572248 0.05514377891
|
||||
232 24 -279.9025974 -279.784283 0.004929767703 0.947921084 0.9056396189 0.02406018404
|
||||
233 24 -279.1817177 -279.302158 0.005018345952 2.388096516 1.771965137 0.06275542538
|
||||
234 24 -279.5900705 -279.55564 0.001434605813 1.950503627 1.405626506 0.05370441115
|
||||
235 24 -279.0106063 -279.246939 0.00984719392 1.577003357 0.4813964151 0.08190583543
|
||||
236 24 -279.1817217 -279.302157 0.005018138375 2.388094324 1.771953347 0.06275588675
|
||||
237 24 -279.0107548 -279.246935 0.009840841347 1.576191869 0.4809484798 0.0819682416
|
||||
238 24 -279.9941671 -279.896025 0.004089255845 0.2809227604 0.01060549839 0.01118927817
|
||||
239 24 -279.6337951 -279.584237 0.002064919631 1.571895405 1.035836121 0.05510997377
|
||||
240 24 -278.8616595 -279.124427 0.0109486445 2.383512182 1.809545887 0.06232801199
|
||||
241 24 -279.2927133 -279.379366 0.003610531084 1.779238829 0.8982692706 0.07658702105
|
||||
242 24 -279.292656 -279.37937 0.003613082676 1.779203263 0.898081355 0.0765940488
|
||||
243 24 -278.8616573 -279.124427 0.01094873842 2.383511745 1.809523374 0.06232387507
|
||||
244 24 -279.9942014 -279.901657 0.003856015842 0.27959331 0.001570374478 0.01120603916
|
||||
245 24 -279.9072278 -279.79264 0.004774491325 0.8361247356 0.8392614852 0.02418251879
|
||||
246 24 -279.9941671 -279.896025 0.004089255843 0.2809227622 0.01060243293 0.01118973247
|
||||
247 24 -278.8973689 -279.206496 0.01288029691 1.390234609 0.005326518563 0.06648378416
|
||||
248 24 -279.590075 -279.55564 0.001434791018 1.950495712 1.4056319 0.05370353355
|
||||
249 24 -279.9072386 -279.79264 0.004774943229 0.8361385582 0.8392625708 0.02418484015
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
228 24 828.0362386 -278.8744577 -279.068761 0.008095970394 1.792731399 1.756353161 0.02034519972
|
||||
229 24 828.0362386 -279.8341084 -279.784296 0.002075517181 0.8648652932 0.9057668891 0.02551209867
|
||||
230 24 828.0362386 -279.9471394 -279.901657 0.001895100141 0.2564159584 0.001565946359 0.01064317525
|
||||
231 24 828.0362386 -279.6038327 -279.584238 0.0008164477458 1.049688296 1.035572248 0.03140137354
|
||||
232 24 828.0362386 -279.8341112 -279.784283 0.0020761763 0.8648598446 0.9056396189 0.02548378256
|
||||
233 24 828.0362386 -279.2648636 -279.302158 0.001553934622 1.915234303 1.771965137 0.0335979663
|
||||
234 24 828.0362386 -279.5694974 -279.55564 0.0005773927058 1.494983873 1.405626506 0.03580097866
|
||||
235 24 828.0362386 -279.1248712 -279.246939 0.005086159625 0.8364348174 0.4813964151 0.03952452096
|
||||
236 24 828.0362386 -279.2648669 -279.302157 0.001553753169 1.915236066 1.771953347 0.03359724569
|
||||
237 24 828.0362386 -279.1248615 -279.246935 0.005086395101 0.8359140271 0.4809484798 0.03945540619
|
||||
238 24 828.0362386 -279.947118 -279.896025 0.002128876838 0.2568271768 0.01060549839 0.01065119629
|
||||
239 24 828.0362386 -279.6036393 -279.584237 0.0008084312244 1.050432188 1.035836121 0.03142155668
|
||||
240 24 828.0362386 -278.9895496 -279.124427 0.005619891669 1.979936932 1.809545887 0.03605678241
|
||||
241 24 828.0362386 -279.3529271 -279.379366 0.001101619485 1.011781603 0.8982692706 0.03183638336
|
||||
242 24 828.0362386 -279.3529768 -279.37937 0.001099717196 1.011818683 0.898081355 0.03184392828
|
||||
243 24 828.0362386 -278.9895472 -279.124427 0.005619991364 1.979929186 1.809523374 0.03605792049
|
||||
244 24 828.0362386 -279.9471394 -279.901657 0.001895100142 0.2564159597 0.001570374478 0.01064089767
|
||||
245 24 828.0362386 -279.8381145 -279.79264 0.001894771958 0.7778094796 0.8392614852 0.02471034365
|
||||
246 24 828.0362386 -279.947118 -279.896025 0.002128876838 0.2568271754 0.01060243293 0.01065141858
|
||||
247 24 828.0362386 -279.016042 -279.206496 0.007935581546 0.4147822746 0.005326518563 0.02428272824
|
||||
248 24 828.0362386 -279.5695012 -279.55564 0.0005775513257 1.494983584 1.4056319 0.03580061053
|
||||
249 24 828.0362386 -279.838114 -279.79264 0.001894750832 0.7777710799 0.8392625708 0.02470477679
|
||||
# GSF_112.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
250 30 -345.1428414 -345.175835 0.001099787279 2.717783384 1.057395322 0.1393371019
|
||||
251 30 -346.8213325 -346.361714 0.01532061701 1.6320981 1.220284939 0.1010819808
|
||||
252 30 -346.3061373 -345.795524 0.01702044399 2.435031121 2.112860875 0.1171529224
|
||||
253 30 -344.8834516 -345.164602 0.009371679668 3.314987489 1.765832199 0.1576958872
|
||||
254 30 -346.9668291 -346.593523 0.01244353764 1.327935537 0.01148867129 0.08670065177
|
||||
255 30 -346.7938009 -346.396186 0.01325383111 1.743989434 0.9954683928 0.09783463277
|
||||
256 30 -345.0939055 -345.319406 0.007516682784 3.756566851 1.772040852 0.1806000978
|
||||
257 30 -345.6468551 -345.594794 0.001735368441 3.432645857 1.516014157 0.1670589876
|
||||
258 30 -346.2843474 -345.98566 0.00995624537 2.709563559 1.406252265 0.1356658489
|
||||
259 30 -345.7058793 -345.383994 0.01072951129 2.464665654 0.963574308 0.13389942
|
||||
260 30 -346.9664564 -346.582564 0.01279641284 1.32870642 0.0126740587 0.08670344939
|
||||
261 30 -345.3305431 -345.452139 0.004053195139 4.515828739 2.787719406 0.1519418929
|
||||
262 30 -346.966836 -346.593523 0.01244376534 1.327919807 0.01148834 0.08669988209
|
||||
263 30 -345.5935851 -345.281949 0.01038786965 2.922665543 1.873142686 0.1300383724
|
||||
264 30 -346.157169 -345.928661 0.007616932828 3.42803556 2.100874472 0.1330089569
|
||||
265 30 -344.6836135 -345.111657 0.01426811685 4.87813643 3.358068319 0.1517605656
|
||||
266 30 -346.8140968 -346.367123 0.01489912587 1.700448289 1.335797131 0.1014030448
|
||||
267 30 -346.9664062 -346.582565 0.0127947081 1.328695393 0.01254743735 0.08670444025
|
||||
268 30 -344.5284456 -344.91356 0.012837147 4.30679737 3.441834403 0.1293440404
|
||||
269 30 -346.3471173 -345.836703 0.01701381162 2.177883948 1.608769148 0.1178087924
|
||||
270 30 -344.9135302 -344.984307 0.002359225816 3.517317775 2.542628782 0.122092966
|
||||
271 30 -346.7846048 -346.393931 0.01302245877 1.941770224 1.211680725 0.09898842713
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
250 30 1075.650827 -345.0647258 -345.175835 0.003703640414 1.586006481 1.057395322 0.05239033232
|
||||
251 30 1075.650827 -346.4849408 -346.361714 0.004107558741 1.165792778 1.220284939 0.03940362221
|
||||
252 30 1075.650827 -345.9422323 -345.795524 0.004890275184 1.983945193 2.112860875 0.04774840228
|
||||
253 30 1075.650827 -344.890629 -345.164602 0.009132432709 1.959583829 1.765832199 0.04056148276
|
||||
254 30 1075.650827 -346.7012878 -346.593523 0.003592158718 0.4521893568 0.01148867129 0.03439985674
|
||||
255 30 1075.650827 -346.4872974 -346.396186 0.003037046146 1.222595835 0.9954683928 0.04286920279
|
||||
256 30 1075.650827 -345.1409912 -345.319406 0.005947159813 2.34345757 1.772040852 0.05459562504
|
||||
257 30 1075.650827 -345.5971874 -345.594794 7.978031452e-05 1.888464582 1.516014157 0.04776915006
|
||||
258 30 1075.650827 -346.0478761 -345.98566 0.002073871543 1.599970328 1.406252265 0.04517962817
|
||||
259 30 1075.650827 -345.4980112 -345.383994 0.00380057209 1.447900201 0.963574308 0.05226663105
|
||||
260 30 1075.650827 -346.701404 -346.582564 0.003961332349 0.452384513 0.0126740587 0.03442356549
|
||||
261 30 1075.650827 -345.3766652 -345.452139 0.002515794904 3.404804954 2.787719406 0.06209597773
|
||||
262 30 1075.650827 -346.7012889 -346.593523 0.003592196349 0.4521736146 0.01148834 0.03439745624
|
||||
263 30 1075.650827 -345.3367107 -345.281949 0.001825390615 2.32593477 1.873142686 0.05341247827
|
||||
264 30 1075.650827 -345.9644944 -345.928661 0.001194445717 2.440564868 2.100874472 0.05014616499
|
||||
265 30 1075.650827 -344.840756 -345.111657 0.009030032193 3.798622074 3.358068319 0.06786449722
|
||||
266 30 1075.650827 -346.4755376 -346.367123 0.003613819676 1.273531547 1.335797131 0.04052248443
|
||||
267 30 1075.650827 -346.7014359 -346.582565 0.003962362405 0.4519007788 0.01254743735 0.03441404169
|
||||
268 30 1075.650827 -344.6023278 -344.91356 0.01037440504 3.254996067 3.441834403 0.06094209056
|
||||
269 30 1075.650827 -346.0120092 -345.836703 0.005843540802 1.521838087 1.608769148 0.04827896456
|
||||
270 30 1075.650827 -344.8059172 -344.984307 0.005946327113 2.715683999 2.542628782 0.05162076211
|
||||
271 30 1075.650827 -346.4781805 -346.393931 0.00280831806 1.404594385 1.211680725 0.04450161425
|
||||
# Liquid.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
272 100 -1104.74829 -1105.601723 0.008534329546 31.13590643 31.39853886 0.5826598142
|
||||
273 100 -1099.007356 -1099.673012 0.006656557481 34.30763539 32.03167218 0.6355970492
|
||||
274 100 -1123.744375 -1121.31506 0.0242931528 23.69463257 20.81076453 0.4843518851
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
272 100 2002.996789 -1105.422245 -1105.601723 0.001794779756 30.76677076 31.39853886 0.2594845644
|
||||
273 100 2002.996789 -1099.821985 -1099.673012 0.001489725357 32.73534296 32.03167218 0.2526485766
|
||||
274 100 2002.996789 -1121.782711 -1121.31506 0.004676506693 20.46627972 20.81076453 0.2371789145
|
||||
# Surface.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
275 24 -279.9941674 -279.911828 0.003430809358 0.2809230274 0.002753093533 0.01155715982
|
||||
276 48 -551.0953781 -555.359452 0.08883487284 6.541312712 0.003020630398 0.1949601982
|
||||
277 40 -458.209131 -459.216162 0.02517577443 5.605061426 5.0461364 0.1098503638
|
||||
278 40 -459.8554229 -461.144076 0.03221632783 2.691145822 0.005582740008 0.0817493
|
||||
279 24 -279.8970746 -279.635146 0.01091369091 1.238573481 1.288799837 0.008644383713
|
||||
280 30 -346.9668295 -346.592525 0.01247681774 1.32793475 0.008446203407 0.08664452133
|
||||
281 30 -345.8871537 -345.744506 0.004754921864 3.992236552 3.124961367 0.08594721633
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
275 24 828.0362197 -279.9471179 -279.911828 0.001470413716 0.2568272078 0.002753093533 0.01085457857
|
||||
276 48 1756.536679 -554.9667185 -555.359452 0.008181947822 1.677149694 0.003020630398 0.06123954391
|
||||
277 40 1394.433693 -459.229835 -459.216162 0.000341824346 5.783414252 5.0461364 0.05348699588
|
||||
278 40 1394.433693 -461.3066626 -461.144076 0.004064664216 1.421939239 0.005582740008 0.06498907706
|
||||
279 24 828.0362197 -279.8476866 -279.635146 0.008855859231 1.285306001 1.288799837 0.01329697146
|
||||
280 30 1075.65076 -346.7012879 -346.592525 0.00362543101 0.4521898058 0.008446203407 0.03427440307
|
||||
281 30 1075.65076 -345.9867955 -345.744506 0.008076316241 3.358838262 3.124961367 0.04271128099
|
||||
# Volume_A15.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
282 8 -66.46788051 -66.990732 0.06535643627 8.928342366e-15 0 1.501728429e-15
|
||||
283 8 -72.67646146 -72.957807 0.03516819273 3.04869178e-14 0 5.1001593e-15
|
||||
284 8 -94.20621366 -94.145745 0.00755858243 1.880283026e-14 0 2.444387059e-15
|
||||
285 8 -94.43981933 -94.554682 0.01435783313 5.684495802e-15 0 8.992080697e-16
|
||||
286 8 -79.39814886 -79.438363 0.005026767696 1.186991025e-14 0 1.998979685e-15
|
||||
287 8 -69.38946962 -69.627817 0.02979342197 5.582708452e-15 0 9.058870552e-16
|
||||
288 8 -83.05531805 -82.604907 0.05630138147 5.067400154e-15 0 8.060681752e-16
|
||||
289 8 14.36690687 14.89048 0.0654466408 7.096605716e-14 0 9.778491674e-15
|
||||
290 8 -94.13472519 -94.367599 0.02910922586 1.767991013e-14 0 2.1395518e-15
|
||||
291 8 -89.38757156 -89.248227 0.01741807051 8.884610804e-15 0 1.30769238e-15
|
||||
292 8 -87.49741165 -87.211997 0.03567683079 8.006170389e-15 0 1.152290069e-15
|
||||
293 8 -93.42285179 -93.66897 0.03076477666 2.280172604e-15 0 3.891032311e-16
|
||||
294 8 -8.05187323 -7.989166 0.007838403785 7.482512497e-14 0 1.195728177e-14
|
||||
295 8 -85.3779751 -84.982834 0.04939263793 3.220622406e-15 0 4.863008144e-16
|
||||
296 8 -92.37490481 -92.536373 0.0201835236 1.673164165e-14 0 2.290124109e-15
|
||||
297 8 -26.56925158 -26.77612 0.02585855302 4.751528484e-14 0 7.423756449e-15
|
||||
298 8 -77.90929192 -77.544107 0.04564811452 4.617032687e-15 0 7.294873617e-16
|
||||
299 8 -80.55632181 -80.114217 0.05526310126 8.324980615e-15 0 1.201946528e-15
|
||||
300 8 -41.83202596 -42.143041 0.03887688062 3.384606082e-14 0 5.356279237e-15
|
||||
301 8 -91.02235339 -91.040671 0.002289700675 3.337550263e-15 0 5.490399801e-16
|
||||
302 8 -84.76781055 -84.499231 0.03357244376 3.246108052e-14 0 5.927694678e-15
|
||||
303 8 -60.71236154 -61.825173 0.1391014324 7.918599116e-15 0 1.30776466e-15
|
||||
304 8 -91.5794594 -91.156873 0.05282330009 3.642169681e-15 0 5.988997276e-16
|
||||
305 8 -54.28408457 -54.658744 0.04683242815 8.878350559e-14 0 1.511496461e-14
|
||||
306 8 -72.29317827 -72.277255 0.00199040924 2.467731222e-15 0 3.339523392e-16
|
||||
307 8 -75.14428628 -74.923334 0.02761903549 3.575872549e-15 0 5.510457542e-16
|
||||
308 8 -64.41647714 -64.798066 0.04769860741 1.525236831e-14 0 2.48556962e-15
|
||||
309 8 -93.29905733 -93.048342 0.03133941583 1.463792794e-14 0 2.408158856e-15
|
||||
310 8 -63.56375833 -64.38702 0.1029077093 2.897725758e-15 0 5.108399236e-16
|
||||
311 8 -88.81067445 -88.352871 0.05722543104 1.077500255e-14 0 1.707889472e-15
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
282 8 300.763 -67.01499491 -66.990732 0.003032863805 2.819700804e-14 0 4.921664315e-15
|
||||
283 8 97.336 -72.94232248 -72.957807 0.001935564941 3.383618726e-13 0 5.770138509e-14
|
||||
284 8 140.608 -94.18596485 -94.145745 0.005027481108 1.673821301e-13 0 2.925657833e-14
|
||||
285 8 148.877 -94.53758278 -94.554682 0.002137402752 2.850464593e-13 0 4.395447757e-14
|
||||
286 8 103.823 -79.36181765 -79.438363 0.009568168595 5.081629339e-13 0 6.957737592e-14
|
||||
287 8 287.496 -69.65695316 -69.627817 0.003642019814 3.585604755e-14 0 5.290180287e-15
|
||||
288 8 226.981 -82.57427967 -82.604907 0.003828416669 1.966569779e-14 0 3.055925575e-15
|
||||
289 8 64 14.91256765 14.89048 0.002760956607 1.268231782e-12 0 2.10661436e-13
|
||||
290 8 157.464 -94.30550126 -94.367599 0.00776221701 1.540418791e-13 0 2.429657954e-14
|
||||
291 8 195.112 -89.23482811 -89.248227 0.0016748608 3.497628958e-14 0 5.329927218e-15
|
||||
292 8 205.379 -87.1807549 -87.211997 0.003905261945 5.301165114e-14 0 8.25442139e-15
|
||||
293 8 166.375 -93.62647682 -93.66897 0.005311647976 1.601228328e-13 0 2.457003528e-14
|
||||
294 8 68.921 -8.062522011 -7.989166 0.009169501377 1.188384306e-12 0 1.962818845e-13
|
||||
295 8 216 -84.94655909 -84.982834 0.004534364367 1.973301171e-14 0 3.372873794e-15
|
||||
296 8 175.616 -92.5372774 -92.536373 0.0001130505542 1.082474676e-13 0 1.921252033e-14
|
||||
297 8 74.088 -26.71265433 -26.77612 0.007933208567 8.406758251e-13 0 1.23413094e-13
|
||||
298 8 250.047 -77.54300262 -77.544107 0.0001380478314 1.348343483e-14 0 1.739921762e-15
|
||||
299 8 238.328 -80.09696776 -80.114217 0.002156154988 2.985887014e-14 0 4.527486547e-15
|
||||
300 8 79.507 -42.10923352 -42.143041 0.004225934936 8.873294965e-13 0 1.304279839e-13
|
||||
301 8 185.193 -91.0484765 -91.040671 0.0009756871529 6.885228576e-14 0 1.154018536e-14
|
||||
302 8 110.592 -84.43529582 -84.499231 0.00799189727 3.195082704e-13 0 5.215998491e-14
|
||||
303 8 328.509 -61.77548856 -61.825173 0.006210554434 5.878540336e-14 0 8.695752295e-15
|
||||
304 8 125 -91.2249009 -91.156873 0.008503487686 2.626710929e-13 0 4.315195657e-14
|
||||
305 8 85.184 -54.71048614 -54.658744 0.006467767575 8.711801201e-13 0 1.458244697e-13
|
||||
306 8 274.625 -72.30263169 -72.277255 0.003172086572 1.532270828e-14 0 2.50834567e-15
|
||||
307 8 262.144 -74.93752725 -74.923334 0.001774156745 1.798582636e-14 0 2.843399878e-15
|
||||
308 8 91.125 -64.85266735 -64.798066 0.006825168142 5.038123694e-13 0 8.438668035e-14
|
||||
309 8 132.651 -93.13139176 -93.048342 0.01038121988 1.905847288e-13 0 3.119837139e-14
|
||||
310 8 314.432 -64.38640208 -64.38702 7.724055098e-05 2.424463435e-14 0 3.900193137e-15
|
||||
311 8 117.649 -88.3636073 -88.352871 0.001342037913 3.929722609e-13 0 6.544191929e-14
|
||||
# Volume_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
312 2 -16.38936242 -16.763625 0.1871312901 5.164700352e-16 0 1.827242061e-16
|
||||
313 2 16.19675433 16.314145 0.05869533666 6.530646709e-14 0 1.921032777e-14
|
||||
314 2 -21.24238574 -21.209071 0.01665736942 1.908874745e-15 0 7.170229344e-16
|
||||
315 2 -15.80560502 -15.780524 0.01254051029 3.122816732e-14 0 1.231252513e-14
|
||||
316 2 -19.05526774 -19.002205 0.02653137194 7.555287577e-15 0 2.037557095e-15
|
||||
317 2 -22.67434567 -22.620568 0.02688883674 1.349360652e-15 0 4.857225733e-16
|
||||
318 2 4.04311049 4.096885 0.02688725502 1.772872048e-14 0 6.601201067e-15
|
||||
319 2 56.2105911 56.26276 0.02608445186 1.377801077e-13 0 4.795418557e-14
|
||||
320 2 -22.55797904 -22.585113 0.01356697915 3.380715703e-15 0 1.276756478e-15
|
||||
321 2 -21.75972417 -21.795501 0.0178884163 1.168374574e-15 0 4.533410684e-16
|
||||
322 2 33.30678917 33.110078 0.09835558332 3.387360342e-14 0 9.173217741e-15
|
||||
323 2 -20.82125169 -20.885998 0.0323731563 9.918492908e-16 0 3.654484123e-16
|
||||
324 2 -23.55239721 -23.601336 0.02446939304 2.356479148e-15 0 7.090682208e-16
|
||||
325 2 -23.17147126 -23.207313 0.01792086946 1.448170847e-15 0 4.901445524e-16
|
||||
326 2 -19.78146338 -19.898089 0.05831281177 7.349099448e-15 0 2.984880861e-15
|
||||
327 2 -23.45038238 -23.405474 0.02245418985 2.124472575e-15 0 7.6356745e-16
|
||||
328 2 -4.653232293 -4.781324 0.06404585371 1.121589994e-14 0 3.980033895e-15
|
||||
329 2 -18.67517238 -18.864936 0.09488180756 4.972820174e-16 0 1.896631e-16
|
||||
330 2 -17.53439276 -17.813086 0.1393466189 8.350923499e-16 0 3.215020842e-16
|
||||
331 2 -11.04889659 -11.197201 0.07415220345 1.822150476e-14 0 6.092637968e-15
|
||||
332 2 -23.68489671 -23.696705 0.00590414498 1.240124986e-15 0 4.153217122e-16
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
312 2 74.088 -16.7332092 -16.763625 0.01520790164 7.099353229e-15 0 2.349972069e-15
|
||||
313 2 13.824 16.32535559 16.314145 0.005605295497 7.206477408e-13 0 2.189359805e-13
|
||||
314 2 27 -21.19450038 -21.209071 0.007285308619 8.524690845e-14 0 2.845872055e-14
|
||||
315 2 21.952 -15.79855366 -15.780524 0.009014829387 3.274910445e-13 0 1.205921936e-13
|
||||
316 2 24.389 -18.99894319 -19.002205 0.001630906437 5.65983876e-14 0 1.916710425e-14
|
||||
317 2 29.791 -22.63208654 -22.620568 0.005759269528 1.223367794e-13 0 3.321417215e-14
|
||||
318 2 15.625 4.078068596 4.096885 0.009408202093 3.980569958e-13 0 1.17267307e-13
|
||||
319 2 10.648 56.26309693 56.26276 0.0001684651718 1.290113748e-12 0 4.90646875e-13
|
||||
320 2 46.656 -22.58881547 -22.585113 0.001851235758 1.064824852e-13 0 4.281760132e-14
|
||||
321 2 50.653 -21.79068496 -21.795501 0.002408021354 7.022325188e-15 0 2.34072021e-15
|
||||
322 2 12.167 33.10655801 33.110078 0.001759994898 2.449948043e-13 0 6.483702464e-14
|
||||
323 2 54.872 -20.88036974 -20.885998 0.002814127848 6.466751305e-15 0 2.081668171e-15
|
||||
324 2 39.304 -23.59816272 -23.601336 0.001586639096 4.922784477e-14 0 1.894780629e-14
|
||||
325 2 42.875 -23.20710182 -23.207313 0.000105591261 1.230696119e-14 0 4.736951572e-15
|
||||
326 2 59.319 -19.89998094 -19.898089 0.0009459702552 2.180966656e-14 0 7.799316748e-15
|
||||
327 2 32.768 -23.4054617 -23.405474 6.148751057e-06 6.022627344e-14 0 2.364775042e-14
|
||||
328 2 17.576 -4.770344063 -4.781324 0.005489968594 5.096189894e-13 0 1.534420739e-13
|
||||
329 2 64 -18.87268499 -18.864936 0.00387449444 4.392402055e-15 0 1.415534356e-15
|
||||
330 2 68.921 -17.81340415 -17.813086 0.0001590760504 4.528839094e-15 0 1.480297366e-15
|
||||
331 2 19.683 -11.18640356 -11.197201 0.005398721194 2.008837354e-13 0 6.569744748e-14
|
||||
332 2 35.937 -23.68093667 -23.696705 0.007884165212 7.912770211e-14 0 2.84170835e-14
|
||||
# Volume_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
333 4 -19.13390887 -19.075994 0.01447871809 1.022152812e-14 0 2.293587909e-15
|
||||
334 4 -35.26038882 -34.873619 0.0966924543 1.299038035e-15 0 3.09937261e-16
|
||||
335 4 -43.93272346 -43.950003 0.004319884816 1.839067075e-15 0 3.483902981e-16
|
||||
336 4 -41.03733831 -40.991909 0.01135732773 4.481141716e-15 0 9.930207698e-16
|
||||
337 4 -43.4228254 -43.453929 0.007775899668 3.563251054e-14 0 1.025252039e-14
|
||||
338 4 -42.67289278 -42.686077 0.003296053998 3.08362874e-15 0 8.245357522e-16
|
||||
339 4 -33.58842759 -33.224653 0.09094364633 7.806891681e-16 0 2.054201716e-16
|
||||
340 4 -27.01189372 -26.862709 0.03729618105 6.429823751e-15 0 1.469359846e-15
|
||||
341 4 -25.59030438 -25.519883 0.01760534598 1.262126674e-15 0 3.031429274e-16
|
||||
342 4 3.441093749 3.463071 0.005494312714 2.222300041e-14 0 5.686075706e-15
|
||||
343 4 -31.9073245 -31.59595 0.07784362479 8.772505365e-16 0 2.178523565e-16
|
||||
344 4 -45.06068744 -45.100466 0.009944641012 2.844345405e-15 0 6.141228113e-16
|
||||
345 4 -46.03981427 -46.052258 0.0031109323 3.085311895e-15 0 7.534482297e-16
|
||||
346 4 -30.24326213 -30.001189 0.06051828302 1.033301257e-15 0 2.648344507e-16
|
||||
347 4 -22.957351 -22.8504 0.02673775024 1.649470508e-15 0 4.625206468e-16
|
||||
348 4 -9.130654755 -9.164691 0.008509061334 1.441769296e-14 0 2.967949237e-15
|
||||
349 4 -24.21746226 -24.150343 0.01677981454 9.080179666e-16 0 2.344767898e-16
|
||||
350 4 -46.44761241 -46.426795 0.005204351765 1.356833237e-15 0 3.249715312e-16
|
||||
351 4 -28.62111495 -28.451145 0.04249248833 8.73448718e-15 0 2.511662753e-15
|
||||
352 4 40.31615798 40.341566 0.006352005142 4.072809775e-14 0 8.11641299e-15
|
||||
353 4 19.51151427 19.617912 0.02659943252 2.395447746e-14 0 5.536534686e-15
|
||||
354 4 -27.06356399 -26.954384 0.02729499736 7.989451601e-16 0 1.662443331e-16
|
||||
355 4 -46.3678929 -46.323696 0.01104922394 3.225354336e-15 0 8.604228441e-16
|
||||
356 4 -45.87221055 -45.828947 0.01081588677 3.654195723e-15 0 9.691321819e-16
|
||||
357 4 -38.47076405 -38.16029 0.0776185126 1.743572283e-15 0 4.628820475e-16
|
||||
358 4 -33.06813795 -32.919741 0.03709923634 1.476523661e-14 0 4.182418301e-15
|
||||
359 4 -41.34431995 -41.272675 0.01791123821 3.354385367e-15 0 9.014870014e-16
|
||||
360 4 -39.95757678 -39.753322 0.05106369446 1.803308855e-15 0 4.257287097e-16
|
||||
361 4 -37.66252943 -37.547435 0.02877360828 4.901403086e-15 0 1.0480621e-15
|
||||
362 4 -36.89659259 -36.52595 0.09266064636 2.659569984e-15 0 6.744460314e-16
|
||||
363 4 -45.03250721 -45.016087 0.004105053075 1.580168365e-15 0 3.385601984e-16
|
||||
config # atoms volume energy DFT energy energy error force DFT force force error
|
||||
333 4 39.304 -19.06659267 -19.075994 0.002350333282 2.242940035e-13 0 5.36098943e-14
|
||||
334 4 140.608 -34.89905306 -34.873619 0.00635851401 1.010642247e-16 0 1.457893663e-17
|
||||
335 4 97.336 -43.96877955 -43.950003 0.004694138574 2.126246105e-14 0 5.054185566e-15
|
||||
336 4 54.872 -40.97274776 -40.991909 0.004790309081 1.185535763e-13 0 2.872376816e-14
|
||||
337 4 59.319 -43.42171543 -43.453929 0.008053391272 2.296458862e-13 0 6.082426591e-14
|
||||
338 4 103.823 -42.6597099 -42.686077 0.00659177457 1.126693835e-14 0 2.539877025e-15
|
||||
339 4 148.877 -33.23590559 -33.224653 0.002813146279 9.862084554e-17 0 1.423248321e-17
|
||||
340 4 42.875 -26.8470965 -26.862709 0.003903124023 1.228252896e-13 0 3.072946989e-14
|
||||
341 4 195.112 -25.53507107 -25.519883 0.003797016254 2.40907116e-17 0 2.83911759e-18
|
||||
342 4 32.768 3.473579709 3.463071 0.002627177357 3.931265555e-13 0 9.112155475e-14
|
||||
343 4 157.464 -31.59263229 -31.59595 0.0008294271493 2.267291431e-16 0 4.493514618e-17
|
||||
344 4 64 -45.11218345 -45.100466 0.002929361892 8.744726802e-14 0 1.918622277e-14
|
||||
345 4 68.921 -46.08241156 -46.052258 0.007538389436 3.520769013e-14 0 7.745262722e-15
|
||||
346 4 166.375 -29.98928023 -30.001189 0.002977192407 1.872398106e-17 0 2.20664233e-18
|
||||
347 4 216 -22.83820871 -22.8504 0.003047821897 2.702568737e-16 0 5.516376578e-17
|
||||
348 4 35.937 -9.176834259 -9.164691 0.003035814748 4.157079809e-13 0 9.613143614e-14
|
||||
349 4 205.379 -24.16849395 -24.150343 0.004537736731 2.7878918e-16 0 5.687491188e-17
|
||||
350 4 74.088 -46.43538667 -46.426795 0.00214791762 2.95902722e-14 0 6.469467415e-15
|
||||
351 4 175.616 -28.44095349 -28.451145 0.002547877441 7.659143271e-14 0 2.209485934e-14
|
||||
352 4 27 40.34562349 40.341566 0.001014373394 8.677203983e-13 0 2.146350834e-13
|
||||
353 4 29.791 19.60939801 19.617912 0.00212849842 2.92456555e-13 0 7.553779404e-14
|
||||
354 4 185.193 -26.95615297 -26.954384 0.0004422422046 2.650218936e-16 0 5.405833732e-17
|
||||
355 4 79.507 -46.31606323 -46.323696 0.001908191306 3.148631685e-14 0 7.773046049e-15
|
||||
356 4 85.184 -45.85584792 -45.828947 0.006725230708 1.015713192e-13 0 2.73791593e-14
|
||||
357 4 125 -38.18682329 -38.16029 0.006633321989 7.658848958e-15 0 1.812986134e-15
|
||||
358 4 46.656 -32.94315868 -32.919741 0.005854420743 2.730870501e-13 0 6.625169163e-14
|
||||
359 4 110.592 -41.24029859 -41.272675 0.008094103234 4.187006838e-14 0 1.139506022e-14
|
||||
360 4 117.649 -39.7548132 -39.753322 0.0003727992516 9.870333772e-15 0 2.279709731e-15
|
||||
361 4 50.653 -37.57897366 -37.547435 0.007884665601 1.384184361e-13 0 3.493877641e-14
|
||||
362 4 132.651 -36.5583082 -36.52595 0.008089548856 2.885226053e-16 0 5.871940193e-17
|
||||
363 4 91.125 -45.06584934 -45.016087 0.01244058561 1.491422927e-14 0 3.528053257e-15
|
||||
|
||||
@ -2,19 +2,19 @@
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650
|
||||
Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191
|
||||
Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800
|
||||
Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013
|
||||
Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207
|
||||
GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819
|
||||
GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090
|
||||
Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847
|
||||
Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623
|
||||
Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000
|
||||
Displaced_A15.xyz 9 576 0.000676 0.000864 0.085152 0.106723
|
||||
Displaced_BCC.xyz 9 486 0.004173 0.004452 0.125322 0.159417
|
||||
Displaced_FCC.xyz 9 432 0.002184 0.002287 0.067459 0.085235
|
||||
Elastic_BCC.xyz 100 200 0.000328 0.000428 0.000022 0.000031
|
||||
Elastic_FCC.xyz 100 400 0.000428 0.000545 0.000148 0.000209
|
||||
GSF_110.xyz 22 528 0.002796 0.003597 0.027455 0.046689
|
||||
GSF_112.xyz 22 660 0.004320 0.004996 0.047264 0.074519
|
||||
Liquid.xyz 3 300 0.002654 0.003017 0.249771 0.315210
|
||||
Surface.xyz 7 236 0.004945 0.005886 0.044779 0.100990
|
||||
Volume_A15.xyz 30 240 0.004419 0.005334 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.004208 0.005697 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.004424 0.005236 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.012917 0.025797 0.122473 0.260052
|
||||
All files 363 4224 0.001918 0.003222 0.064003 0.118266
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
|
||||
@ -1,5 +0,0 @@
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
|
||||
@ -1,114 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 0
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 0
|
||||
total number of descriptors for all potentials: 32
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
**************** Begin of Data File ****************
|
||||
file format: extxyz
|
||||
file extension: xyz
|
||||
path to training data set: XYZ
|
||||
path to test data set: XYZ
|
||||
training fraction: 1
|
||||
test fraction: 1
|
||||
randomize training data set: 1
|
||||
randomize test data set: 1
|
||||
error analysis for training data set: 1
|
||||
error analysis for test data set: 0
|
||||
energy/force calculation for training data set: 0
|
||||
energy/force calculation for test data set: 0
|
||||
fitting weight for energy: 100
|
||||
fitting weight for force: 1
|
||||
fitting weight for stress: 0
|
||||
fitting regularization parameter: 1e-10
|
||||
**************** End of Data File ****************
|
||||
**************** Begin of Training Data Set ****************
|
||||
---------------------------------------------------------------
|
||||
data file | number of configurations | number of atoms
|
||||
---------------------------------------------------------------
|
||||
Displaced_A15.xyz | 9 | 576
|
||||
Displaced_BCC.xyz | 9 | 486
|
||||
Displaced_FCC.xyz | 9 | 432
|
||||
Elastic_BCC.xyz | 100 | 200
|
||||
Elastic_FCC.xyz | 100 | 400
|
||||
GSF_110.xyz | 22 | 528
|
||||
GSF_112.xyz | 22 | 660
|
||||
Liquid.xyz | 3 | 300
|
||||
Surface.xyz | 7 | 236
|
||||
Volume_A15.xyz | 30 | 240
|
||||
Volume_BCC.xyz | 21 | 42
|
||||
Volume_FCC.xyz | 31 | 124
|
||||
---------------------------------------------------------------
|
||||
number of files: 12
|
||||
number of configurations in all files: 363
|
||||
number of atoms in all files: 4224
|
||||
minimum number of atoms: 2
|
||||
maximum number of atoms: 100
|
||||
**************** End of Training Data Set ****************
|
||||
**************** Begin of Memory Allocation ****************
|
||||
maximum number of atoms in periodic domain: 100
|
||||
maximum number of atoms in extended domain: 2700
|
||||
maximum number of neighbors in extended domain: 270000
|
||||
size of double memory: 223201
|
||||
size of int memory: 14709
|
||||
size of descriptor matrix: 32 x 32
|
||||
**************** End of Memory Allocation ****************
|
||||
**************** Begin of Least-Squares Fitting ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Least-Squares Fitting ****************
|
||||
**************** Begin of Error Calculation ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Error Calculation ****************
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650
|
||||
Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191
|
||||
Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800
|
||||
Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013
|
||||
Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207
|
||||
GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819
|
||||
GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090
|
||||
Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847
|
||||
Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623
|
||||
Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.012917 0.025797 0.122473 0.260052
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,114 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 0
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 0
|
||||
total number of descriptors for all potentials: 32
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
**************** Begin of Data File ****************
|
||||
file format: extxyz
|
||||
file extension: xyz
|
||||
path to training data set: XYZ
|
||||
path to test data set: XYZ
|
||||
training fraction: 1
|
||||
test fraction: 1
|
||||
randomize training data set: 1
|
||||
randomize test data set: 1
|
||||
error analysis for training data set: 1
|
||||
error analysis for test data set: 0
|
||||
energy/force calculation for training data set: 0
|
||||
energy/force calculation for test data set: 0
|
||||
fitting weight for energy: 100
|
||||
fitting weight for force: 1
|
||||
fitting weight for stress: 0
|
||||
fitting regularization parameter: 1e-10
|
||||
**************** End of Data File ****************
|
||||
**************** Begin of Training Data Set ****************
|
||||
---------------------------------------------------------------
|
||||
data file | number of configurations | number of atoms
|
||||
---------------------------------------------------------------
|
||||
Displaced_A15.xyz | 9 | 576
|
||||
Displaced_BCC.xyz | 9 | 486
|
||||
Displaced_FCC.xyz | 9 | 432
|
||||
Elastic_BCC.xyz | 100 | 200
|
||||
Elastic_FCC.xyz | 100 | 400
|
||||
GSF_110.xyz | 22 | 528
|
||||
GSF_112.xyz | 22 | 660
|
||||
Liquid.xyz | 3 | 300
|
||||
Surface.xyz | 7 | 236
|
||||
Volume_A15.xyz | 30 | 240
|
||||
Volume_BCC.xyz | 21 | 42
|
||||
Volume_FCC.xyz | 31 | 124
|
||||
---------------------------------------------------------------
|
||||
number of files: 12
|
||||
number of configurations in all files: 363
|
||||
number of atoms in all files: 4224
|
||||
minimum number of atoms: 2
|
||||
maximum number of atoms: 100
|
||||
**************** End of Training Data Set ****************
|
||||
**************** Begin of Memory Allocation ****************
|
||||
maximum number of atoms in periodic domain: 100
|
||||
maximum number of atoms in extended domain: 2700
|
||||
maximum number of neighbors in extended domain: 270000
|
||||
size of double memory: 223201
|
||||
size of int memory: 14709
|
||||
size of descriptor matrix: 32 x 32
|
||||
**************** End of Memory Allocation ****************
|
||||
**************** Begin of Least-Squares Fitting ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Least-Squares Fitting ****************
|
||||
**************** Begin of Error Calculation ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Error Calculation ****************
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.011286 0.011334 0.113353 0.141650
|
||||
Displaced_BCC.xyz 9 486 0.012178 0.014005 0.240613 0.312191
|
||||
Displaced_FCC.xyz 9 432 0.001445 0.001591 0.082688 0.103800
|
||||
Elastic_BCC.xyz 100 200 0.004452 0.004783 0.000010 0.000013
|
||||
Elastic_FCC.xyz 100 400 0.002865 0.002923 0.000146 0.000207
|
||||
GSF_110.xyz 22 528 0.005804 0.006853 0.047276 0.097819
|
||||
GSF_112.xyz 22 660 0.010588 0.011555 0.123342 0.191090
|
||||
Liquid.xyz 3 300 0.013161 0.015355 0.567536 0.757847
|
||||
Surface.xyz 7 236 0.025400 0.037555 0.096121 0.295623
|
||||
Volume_A15.xyz 30 240 0.039281 0.048678 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.049766 0.067554 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.030056 0.041738 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.012917 0.025797 0.122473 0.260052
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate POD Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coeff.pod Ta
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 0
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 0
|
||||
total number of descriptors for all potentials: 32
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
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 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
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 = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.841512 0 -11.803037 -15933.622
|
||||
10 296.91721 -11.841117 0 -11.803037 -15691.904
|
||||
20 287.83555 -11.839952 0 -11.803037 -14982.977
|
||||
30 273.25574 -11.838082 0 -11.803037 -13853.44
|
||||
40 253.98821 -11.835611 0 -11.803037 -12375.459
|
||||
50 231.10664 -11.832676 0 -11.803037 -10639.774
|
||||
60 205.8844 -11.829441 0 -11.803037 -8747.2222
|
||||
70 179.71599 -11.826085 0 -11.803037 -6799.8371
|
||||
80 154.02711 -11.822791 0 -11.803037 -4892.7805
|
||||
90 130.17821 -11.819732 0 -11.803036 -3108.1226
|
||||
100 109.36842 -11.817063 0 -11.803036 -1510.9592
|
||||
Loop time of 1.51641 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.849 ns/day, 8.425 hours/ns, 65.945 timesteps/s, 8.441 katom-step/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5158 | 1.5158 | 1.5158 | 0.0 | 99.96
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00023616 | 0.00023616 | 0.00023616 | 0.0 | 0.02
|
||||
Output | 0.00010779 | 0.00010779 | 0.00010779 | 0.0 | 0.01
|
||||
Modify | 9.7284e-05 | 9.7284e-05 | 9.7284e-05 | 0.0 | 0.01
|
||||
Other | | 0.0001254 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate POD Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coeff.pod Ta
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 0
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 0
|
||||
total number of descriptors for all potentials: 32
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
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 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
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 = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.841512 0 -11.803037 -15933.622
|
||||
10 296.91721 -11.841117 0 -11.803037 -15691.904
|
||||
20 287.83555 -11.839952 0 -11.803037 -14982.977
|
||||
30 273.25574 -11.838082 0 -11.803037 -13853.44
|
||||
40 253.98821 -11.835611 0 -11.803037 -12375.459
|
||||
50 231.10664 -11.832676 0 -11.803037 -10639.774
|
||||
60 205.8844 -11.829441 0 -11.803037 -8747.2222
|
||||
70 179.71599 -11.826085 0 -11.803037 -6799.8371
|
||||
80 154.02711 -11.822791 0 -11.803037 -4892.7805
|
||||
90 130.17821 -11.819732 0 -11.803036 -3108.1226
|
||||
100 109.36842 -11.817063 0 -11.803036 -1510.9592
|
||||
Loop time of 0.437423 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 9.876 ns/day, 2.430 hours/ns, 228.612 timesteps/s, 29.262 katom-step/s
|
||||
98.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41133 | 0.41882 | 0.42464 | 0.7 | 95.75
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.011279 | 0.017302 | 0.024975 | 3.7 | 3.96
|
||||
Output | 0.00012956 | 0.00029493 | 0.00077991 | 0.0 | 0.07
|
||||
Modify | 4.2093e-05 | 4.7838e-05 | 5.3039e-05 | 0.0 | 0.01
|
||||
Other | | 0.0009598 | | | 0.22
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 431 ave 431 max 431 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1856 ave 1856 max 1856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
3
examples/PACKAGES/pod/Ta/pod.gdd.dat
Normal file
3
examples/PACKAGES/pod/Ta/pod.gdd.dat
Normal file
@ -0,0 +1,3 @@
|
||||
# Time-averaged data for fix gdd
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_gdd[1] c_gdd[2] c_gdd[3] c_gdd[4] c_gdd[5] c_gdd[6] c_gdd[7] c_gdd[8] c_gdd[9] c_gdd[10] c_gdd[11] c_gdd[12] c_gdd[13] c_gdd[14] c_gdd[15] c_gdd[16] c_gdd[17] c_gdd[18] c_gdd[19] c_gdd[20] c_gdd[21] c_gdd[22] c_gdd[23] c_gdd[24] c_gdd[25] c_gdd[26] c_gdd[27] c_gdd[28] c_gdd[29] c_gdd[30] c_gdd[31] c_gdd[32] c_gdd[33] c_gdd[34] c_gdd[35] c_gdd[36] c_gdd[37] c_gdd[38] c_gdd[39] c_gdd[40] c_gdd[41] c_gdd[42] c_gdd[43] c_gdd[44] c_gdd[45] c_gdd[46] c_gdd[47] c_gdd[48] c_gdd[49] c_gdd[50] c_gdd[51] c_gdd[52] c_gdd[53] c_gdd[54] c_gdd[55] c_gdd[56] c_gdd[57] c_gdd[58] c_gdd[59] c_gdd[60] c_gdd[61] c_gdd[62] c_gdd[63] c_gdd[64] c_gdd[65] c_gdd[66] c_gdd[67] c_gdd[68] c_gdd[69] c_gdd[70] c_gdd[71] c_gdd[72] c_gdd[73] c_gdd[74] c_gdd[75] c_gdd[76] c_gdd[77] c_gdd[78] c_gdd[79] c_gdd[80] c_gdd[81] c_gdd[82] c_gdd[83] c_gdd[84] c_gdd[85] c_gdd[86] c_gdd[87] c_gdd[88] c_gdd[89] c_gdd[90] c_gdd[91] c_gdd[92] c_gdd[93] c_gdd[94] c_gdd[95] c_gdd[96] c_gdd[97] c_gdd[98] c_gdd[99] c_gdd[100] c_gdd[101] c_gdd[102] c_gdd[103] c_gdd[104] c_gdd[105] c_gdd[106] c_gdd[107] c_gdd[108] c_gdd[109] c_gdd[110] c_gdd[111] c_gdd[112] c_gdd[113] c_gdd[114] c_gdd[115] c_gdd[116] c_gdd[117] c_gdd[118] c_gdd[119] c_gdd[120] c_gdd[121] c_gdd[122] c_gdd[123]
|
||||
3
examples/PACKAGES/pod/Ta/pod.ldd.dat
Normal file
3
examples/PACKAGES/pod/Ta/pod.ldd.dat
Normal file
@ -0,0 +1,3 @@
|
||||
# Time-averaged data for fix ldd
|
||||
# TimeStep Number-of-rows
|
||||
# Row c_ldd[1] c_ldd[2] c_ldd[3] c_ldd[4] c_ldd[5] c_ldd[6] c_ldd[7] c_ldd[8] c_ldd[9] c_ldd[10] c_ldd[11] c_ldd[12] c_ldd[13] c_ldd[14] c_ldd[15] c_ldd[16] c_ldd[17] c_ldd[18] c_ldd[19] c_ldd[20] c_ldd[21] c_ldd[22] c_ldd[23] c_ldd[24] c_ldd[25] c_ldd[26] c_ldd[27] c_ldd[28] c_ldd[29] c_ldd[30] c_ldd[31] c_ldd[32] c_ldd[33] c_ldd[34] c_ldd[35] c_ldd[36] c_ldd[37] c_ldd[38] c_ldd[39] c_ldd[40] c_ldd[41] c_ldd[42] c_ldd[43] c_ldd[44] c_ldd[45] c_ldd[46] c_ldd[47] c_ldd[48] c_ldd[49] c_ldd[50] c_ldd[51] c_ldd[52] c_ldd[53] c_ldd[54] c_ldd[55] c_ldd[56] c_ldd[57] c_ldd[58] c_ldd[59] c_ldd[60] c_ldd[61] c_ldd[62] c_ldd[63] c_ldd[64] c_ldd[65] c_ldd[66] c_ldd[67] c_ldd[68] c_ldd[69] c_ldd[70] c_ldd[71] c_ldd[72] c_ldd[73] c_ldd[74] c_ldd[75] c_ldd[76] c_ldd[77] c_ldd[78] c_ldd[79] c_ldd[80] c_ldd[81] c_ldd[82] c_ldd[83] c_ldd[84] c_ldd[85] c_ldd[86] c_ldd[87] c_ldd[88] c_ldd[89] c_ldd[90] c_ldd[91] c_ldd[92] c_ldd[93] c_ldd[94] c_ldd[95] c_ldd[96] c_ldd[97] c_ldd[98] c_ldd[99] c_ldd[100] c_ldd[101] c_ldd[102] c_ldd[103] c_ldd[104] c_ldd[105] c_ldd[106] c_ldd[107] c_ldd[108] c_ldd[109] c_ldd[110] c_ldd[111] c_ldd[112] c_ldd[113] c_ldd[114] c_ldd[115] c_ldd[116] c_ldd[117] c_ldd[118] c_ldd[119] c_ldd[120] c_ldd[121] c_ldd[122] c_ldd[123] c_ldd[124] c_ldd[125] c_ldd[126] c_ldd[127] c_ldd[128] c_ldd[129] c_ldd[130] c_ldd[131] c_ldd[132] c_ldd[133] c_ldd[134] c_ldd[135] c_ldd[136] c_ldd[137] c_ldd[138] c_ldd[139] c_ldd[140] c_ldd[141] c_ldd[142] c_ldd[143] c_ldd[144] c_ldd[145] c_ldd[146] c_ldd[147] c_ldd[148] c_ldd[149] c_ldd[150] c_ldd[151] c_ldd[152] c_ldd[153] c_ldd[154] c_ldd[155] c_ldd[156] c_ldd[157] c_ldd[158] c_ldd[159] c_ldd[160] c_ldd[161] c_ldd[162] c_ldd[163] c_ldd[164] c_ldd[165] c_ldd[166] c_ldd[167] c_ldd[168] c_ldd[169] c_ldd[170] c_ldd[171] c_ldd[172] c_ldd[173] c_ldd[174] c_ldd[175] c_ldd[176] c_ldd[177] c_ldd[178] c_ldd[179] c_ldd[180] c_ldd[181] c_ldd[182] c_ldd[183] c_ldd[184] c_ldd[185] c_ldd[186] c_ldd[187] c_ldd[188] c_ldd[189] c_ldd[190] c_ldd[191] c_ldd[192] c_ldd[193] c_ldd[194] c_ldd[195] c_ldd[196] c_ldd[197] c_ldd[198] c_ldd[199] c_ldd[200] c_ldd[201] c_ldd[202] c_ldd[203] c_ldd[204] c_ldd[205] c_ldd[206] c_ldd[207] c_ldd[208] c_ldd[209] c_ldd[210] c_ldd[211] c_ldd[212] c_ldd[213] c_ldd[214] c_ldd[215] c_ldd[216] c_ldd[217] c_ldd[218] c_ldd[219] c_ldd[220] c_ldd[221] c_ldd[222] c_ldd[223] c_ldd[224] c_ldd[225] c_ldd[226] c_ldd[227] c_ldd[228] c_ldd[229] c_ldd[230] c_ldd[231] c_ldd[232] c_ldd[233] c_ldd[234] c_ldd[235] c_ldd[236] c_ldd[237] c_ldd[238] c_ldd[239] c_ldd[240] c_ldd[241] c_ldd[242] c_ldd[243] c_ldd[244]
|
||||
@ -1,183 +0,0 @@
|
||||
POD_coefficients: 182
|
||||
-4.35182
|
||||
3.57837
|
||||
2.25497
|
||||
4.84612
|
||||
-2.06319
|
||||
-1.17070
|
||||
-0.23842
|
||||
9.17160
|
||||
36.02366
|
||||
16.65304
|
||||
-141.18403
|
||||
37.17722
|
||||
0.46028
|
||||
-9.76148
|
||||
-0.03681
|
||||
15.64520
|
||||
2.29791
|
||||
0.02143
|
||||
2.69735
|
||||
-0.35336
|
||||
0.51108
|
||||
-2.36290
|
||||
0.18617
|
||||
-0.13079
|
||||
1.02666
|
||||
0.21514
|
||||
0.08075
|
||||
-0.28347
|
||||
-0.45059
|
||||
-0.24762
|
||||
-1.13671
|
||||
-0.30577
|
||||
0.60504
|
||||
0.31285
|
||||
-0.10639
|
||||
-0.06957
|
||||
0.21961
|
||||
-0.10426
|
||||
0.80318
|
||||
-11.41460
|
||||
-10.26102
|
||||
-0.03887
|
||||
-18.86071
|
||||
-4.47372
|
||||
-1.76858
|
||||
-0.92503
|
||||
0.42654
|
||||
0.35849
|
||||
0.56611
|
||||
-0.79354
|
||||
5.65136
|
||||
8.75283
|
||||
-6.22283
|
||||
-4.34623
|
||||
10.20031
|
||||
6.53360
|
||||
7.16688
|
||||
2.19236
|
||||
5.90789
|
||||
3.52173
|
||||
7.97264
|
||||
0.21104
|
||||
-0.01015
|
||||
0.01023
|
||||
0.03088
|
||||
0.10222
|
||||
0.05366
|
||||
-0.08037
|
||||
-3.17612
|
||||
-3.45669
|
||||
-0.79282
|
||||
-2.38323
|
||||
-0.69797
|
||||
-1.44780
|
||||
-0.03351
|
||||
-0.05645
|
||||
0.01901
|
||||
-0.01923
|
||||
0.05401
|
||||
-0.02095
|
||||
1.45651
|
||||
1.58812
|
||||
1.41188
|
||||
2.18122
|
||||
3.04893
|
||||
1.09294
|
||||
3.03781
|
||||
1.07249
|
||||
0.50262
|
||||
0.81150
|
||||
0.35997
|
||||
0.64602
|
||||
-0.04245
|
||||
0.00113
|
||||
-0.02894
|
||||
0.04382
|
||||
-0.06556
|
||||
0.00052
|
||||
4.67541
|
||||
0.11812
|
||||
1.52428
|
||||
-0.17075
|
||||
0.20231
|
||||
0.36857
|
||||
0.61744
|
||||
0.20190
|
||||
-0.00816
|
||||
0.16194
|
||||
-0.12948
|
||||
-0.02136
|
||||
-2.19271
|
||||
0.62510
|
||||
0.20030
|
||||
-0.27621
|
||||
-0.58116
|
||||
-0.21792
|
||||
-1.82295
|
||||
-0.32166
|
||||
-0.64550
|
||||
-0.11580
|
||||
-0.02438
|
||||
-0.08057
|
||||
0.19538
|
||||
0.04119
|
||||
0.00323
|
||||
0.06530
|
||||
-0.02547
|
||||
-0.01404
|
||||
0.22336
|
||||
-0.48191
|
||||
-0.10715
|
||||
-0.25685
|
||||
-0.65069
|
||||
-0.31428
|
||||
-0.06947
|
||||
0.11924
|
||||
0.05467
|
||||
0.12105
|
||||
-0.03980
|
||||
-0.00295
|
||||
-2.14413
|
||||
0.82345
|
||||
0.23083
|
||||
-0.24925
|
||||
-0.36678
|
||||
-0.16709
|
||||
1.20410
|
||||
-0.47756
|
||||
-0.11104
|
||||
0.09587
|
||||
0.03722
|
||||
0.00309
|
||||
-0.29879
|
||||
-0.06463
|
||||
-0.10236
|
||||
-0.02276
|
||||
-0.06012
|
||||
-0.02985
|
||||
12.06876
|
||||
-3.39995
|
||||
0.85590
|
||||
-0.77481
|
||||
-1.13392
|
||||
-0.40511
|
||||
-0.08005
|
||||
-0.07162
|
||||
-0.05978
|
||||
-0.02407
|
||||
-0.06031
|
||||
-0.02307
|
||||
-10.24105
|
||||
2.49356
|
||||
-1.14052
|
||||
0.70453
|
||||
0.99988
|
||||
0.33862
|
||||
2.43469
|
||||
-1.16557
|
||||
-0.23708
|
||||
0.03482
|
||||
-0.05280
|
||||
-0.02735
|
||||
@ -1,33 +0,0 @@
|
||||
# DATE: 2022-11-30 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362
|
||||
# chemical element symbols
|
||||
species Ta
|
||||
|
||||
# periodic boundary conditions
|
||||
pbc 1 1 1
|
||||
|
||||
# inner cut-off radius
|
||||
rin 1.0
|
||||
|
||||
# outer cut-off radius
|
||||
rcut 5.0
|
||||
|
||||
# polynomial degrees for radial basis functions
|
||||
bessel_polynomial_degree 3
|
||||
inverse_polynomial_degree 6
|
||||
|
||||
# one-body potential
|
||||
onebody 1
|
||||
|
||||
# two-body linear POD potential
|
||||
twobody_number_radial_basis_functions 6
|
||||
|
||||
# three-body linear POD potential
|
||||
threebody_number_radial_basis_functions 5
|
||||
threebody_number_angular_basis_functions 5
|
||||
|
||||
# four-body linear SNAP potential
|
||||
fourbody_snap_twojmax 0
|
||||
|
||||
# quadratic POD potential
|
||||
quadratic_pod_potential 1
|
||||
|
||||
@ -1,387 +0,0 @@
|
||||
# Displaced_A15.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
1 64 -754.2481469 -754.220443 0.0004328739544 8.011514562 8.398670477 0.06376624845
|
||||
2 64 -753.8045629 -753.865255 0.0009483144042 9.036674821 9.134430545 0.07283326238
|
||||
3 64 -754.1013214 -754.0221 0.001237834258 8.637024088 9.017261102 0.06364800593
|
||||
4 64 -754.2847414 -754.279613 8.013173542e-05 8.107730622 8.381725092 0.06510174353
|
||||
5 64 -753.8382044 -753.777209 0.0009530527364 9.104258904 9.478314477 0.07200164536
|
||||
6 64 -754.0793448 -754.048643 0.0004797149286 8.152198894 8.465317938 0.06707941365
|
||||
7 64 -754.3310528 -754.317603 0.0002101531052 7.9440922 8.127690491 0.05987172107
|
||||
8 64 -754.0070856 -753.969161 0.0005925720361 9.179443805 9.425464952 0.06695320222
|
||||
9 64 -754.1450602 -754.141988 4.800358611e-05 8.574170786 8.821346913 0.06628506232
|
||||
# Displaced_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
10 54 -630.8081935 -631.019667 0.003916175555 15.97497534 16.625876 0.1021118679
|
||||
11 54 -631.4580134 -631.719595 0.004844103559 15.24068949 15.58666626 0.1043856792
|
||||
12 54 -631.1667566 -631.386255 0.004064785931 15.46091788 15.92378883 0.1062824093
|
||||
13 54 -632.3004944 -632.575826 0.005098733346 14.4261974 14.55977162 0.0983914465
|
||||
14 54 -630.089475 -630.450212 0.006680315456 16.78432947 16.96340726 0.1085102316
|
||||
15 54 -631.3402507 -631.669379 0.006094968558 15.8289421 16.05757315 0.1000888617
|
||||
16 54 -632.0447348 -632.431277 0.007158189539 14.73098416 14.69810718 0.09621569386
|
||||
17 54 -630.7186536 -630.960068 0.004470636457 15.62236511 15.99073148 0.1063789621
|
||||
18 54 -623.3884977 -623.378198 0.0001907343232 23.9739298 24.67640432 0.1519105596
|
||||
# Displaced_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
19 48 -556.0112403 -555.899463 0.002328692864 5.300795546 6.084617063 0.07215982294
|
||||
20 48 -555.9884377 -555.922478 0.001374159425 5.509767245 6.297071211 0.08438730171
|
||||
21 48 -555.8765558 -555.800269 0.001589309295 5.420812146 6.021098636 0.07404418561
|
||||
22 48 -556.2511475 -556.196151 0.001145760427 4.541854917 5.127955094 0.06609455537
|
||||
23 48 -555.6590668 -555.488929 0.003544536845 6.087063152 7.050223459 0.09107542897
|
||||
24 48 -556.1020655 -556.027926 0.001544573067 5.048523277 5.611881174 0.06751584111
|
||||
25 48 -556.0607474 -555.968399 0.001923924855 5.209756732 5.979217189 0.08024047849
|
||||
26 48 -556.0598015 -556.047132 0.0002639485133 4.995519804 5.544452585 0.07745361595
|
||||
27 48 -555.8256424 -555.747848 0.00162071731 5.762702675 6.47892568 0.08480576837
|
||||
# Elastic_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
28 2 -23.69025375 -23.689367 0.0004433751768 0.0006229111456 0.0006222748589 9.850534294e-07
|
||||
29 2 -23.690768 -23.689888 0.0004399996606 0.0006181832344 0.0006166052222 1.005063831e-06
|
||||
30 2 -23.69082186 -23.689996 0.0004129292199 0.0008798076914 0.0008810425642 1.748431771e-06
|
||||
31 2 -23.69166748 -23.690957 0.0003552395228 1.000599546e-06 0 4.011214433e-07
|
||||
32 2 -23.69137648 -23.690521 0.0004277406839 0.0005992884516 0.0005982273815 7.219402767e-07
|
||||
33 2 -23.69120607 -23.69038 0.000413036746 0.000594795449 0.0005925723585 9.949794864e-07
|
||||
34 2 -23.6900782 -23.689202 0.000438099978 0.0006263336007 0.0006279363025 1.111474332e-06
|
||||
35 2 -23.69121642 -23.690482 0.0003672088475 0.00086350893 0.0008640138888 1.400551425e-06
|
||||
36 2 -23.69074792 -23.689902 0.0004229601404 0.0006176589245 0.0006152154094 9.894995842e-07
|
||||
37 2 -23.6914111 -23.690563 0.0004240514006 0.0006052368582 0.0006038725031 4.148713688e-07
|
||||
38 2 -23.69095105 -23.690207 0.0003720253444 0.001071999394 0.00107369735 7.195087511e-07
|
||||
39 2 -23.69007856 -23.689285 0.0003967806815 0.0008875291033 0.000890013483 1.187797446e-06
|
||||
40 2 -23.69061639 -23.689768 0.0004241940528 0.00107874486 0.001080249045 1.09850755e-06
|
||||
41 2 -23.69064479 -23.68968 0.0004823957182 0.0008702114429 0.0008680034562 8.482668094e-07
|
||||
42 2 -23.6910243 -23.690074 0.0004751495365 0.001368926593 0.001373818765 2.351835771e-06
|
||||
43 2 -23.68910107 -23.688108 0.0004965341502 0.0006334704764 0.0006336134468 5.990110163e-07
|
||||
44 2 -23.69003986 -23.689241 0.0003994287496 0.0008886654529 0.0008880101351 1.319380731e-06
|
||||
45 2 -23.69042994 -23.68952 0.0004549677771 0.0008868888968 0.0008860011287 4.688590432e-07
|
||||
46 2 -23.68738487 -23.686278 0.0005534329248 0.0006426681164 0.0006406777661 9.718938063e-07
|
||||
47 2 -23.69095089 -23.690097 0.0004269463837 0.0008409065407 0.0008410160522 1.331153983e-06
|
||||
48 2 -23.69158161 -23.690811 0.0003853032969 0.0008464480591 0.0008500070588 1.611890257e-06
|
||||
49 2 -23.69114597 -23.690266 0.0004399838162 0.001039354626 0.001044322747 3.354760892e-06
|
||||
50 2 -23.6914223 -23.690597 0.0004126524984 0.001045529019 0.001050833003 2.164890519e-06
|
||||
51 2 -23.69157045 -23.690673 0.000448723371 0.0006045419676 0.0006038907186 7.138092253e-07
|
||||
52 2 -23.69135377 -23.690551 0.0004013838132 0.0008554941993 0.0008590064028 1.199818147e-06
|
||||
53 2 -23.6914855 -23.690693 0.0003962481391 0.0008561040807 0.0008590110593 1.062310127e-06
|
||||
54 2 -23.69110782 -23.69021 0.0004489100066 0.0008699576152 0.0008730051546 1.100920756e-06
|
||||
55 2 -23.68987142 -23.688943 0.0004642105928 0.0008789741194 0.0008800306813 8.92018913e-07
|
||||
56 2 -23.69108099 -23.690136 0.0004724937378 0.0005971006713 0.000593996633 9.809423198e-07
|
||||
57 2 -23.6884849 -23.687444 0.0005204491042 0.000904649919 0.000903059245 1.159812589e-06
|
||||
58 2 -23.69061659 -23.689801 0.0004077963743 0.0008734822906 0.0008740011442 2.825876968e-07
|
||||
59 2 -23.69129673 -23.690408 0.0004443659273 8.294238722e-07 0 3.094976672e-07
|
||||
60 2 -23.69128183 -23.690362 0.0004599146039 0.0006083806397 0.0006067503605 7.610598464e-07
|
||||
61 2 -23.68992958 -23.688881 0.0005242884644 0.000821029922 0.0008250054545 1.71686782e-06
|
||||
62 2 -23.6913441 -23.690515 0.0004145518648 0.001475621399 0.001475779794 2.84677577e-06
|
||||
63 2 -23.69141171 -23.690551 0.0004303564504 0.0005957866015 0.0005996599036 1.20514709e-06
|
||||
64 2 -23.69029628 -23.689487 0.0004046403158 0.0006212225944 0.0006194384554 9.873937532e-07
|
||||
65 2 -23.69072139 -23.68986 0.0004306945962 0.0008858828979 0.0008860124153 5.860284088e-07
|
||||
66 2 -23.69018379 -23.689288 0.0004478949008 0.001400963016 0.001396479144 1.244329984e-06
|
||||
67 2 -23.69129611 -23.690457 0.0004195546182 0.0005914019669 0.0005939831647 1.147186262e-06
|
||||
68 2 -23.69084551 -23.689792 0.0005267528672 0.0008274902414 0.0008340587509 2.923475453e-06
|
||||
69 2 -23.69101454 -23.690006 0.0005042723904 0.0005874526839 0.0005897694465 1.183912924e-06
|
||||
70 2 -23.69137638 -23.690571 0.000402691994 0.0005935054979 0.0005939781141 8.884918862e-07
|
||||
71 2 -23.69114123 -23.690213 0.0004641143201 0.001085937193 0.001084315452 6.623820068e-07
|
||||
72 2 -23.69146017 -23.690617 0.0004215869658 0.0005980165481 0.0006024682564 1.268404944e-06
|
||||
73 2 -23.69063494 -23.689761 0.0004369696294 0.0008787872001 0.0008790688255 2.274049375e-06
|
||||
74 2 -23.69116059 -23.69027 0.0004452958397 6.913233052e-07 0 2.060281613e-07
|
||||
75 2 -23.69134793 -23.690599 0.0003744660576 0.0006108390866 0.0006137752031 6.96527736e-07
|
||||
76 2 -23.69149586 -23.69061 0.0004429283645 9.198413091e-07 0 3.754401369e-07
|
||||
77 2 -23.69139951 -23.690603 0.0003982565418 0.0008543320292 0.0008590331775 1.578633627e-06
|
||||
78 2 -23.68884519 -23.687908 0.0004685934904 0.0009053957054 0.0009010105438 1.657834627e-06
|
||||
79 2 -23.69142551 -23.690688 0.0003687527847 0.0008461959647 0.0008470064935 1.246502358e-06
|
||||
80 2 -23.69088798 -23.689988 0.0004499883039 0.0006191457459 0.0006194465272 7.974697206e-07
|
||||
81 2 -23.69054504 -23.689613 0.0004660181693 0.0008740608763 0.0008740732235 7.595219281e-07
|
||||
82 2 -23.69150291 -23.690678 0.0004124547512 0.000610815565 0.0006123757017 8.071847352e-07
|
||||
83 2 -23.69107508 -23.69017 0.0004525405781 0.0008712164372 0.0008750051428 1.391960695e-06
|
||||
84 2 -23.68888774 -23.687892 0.0004978720826 0.001115255323 0.001112070142 1.300271383e-06
|
||||
85 2 -23.69100617 -23.690132 0.0004370853773 0.0008623539978 0.000868018433 1.989797184e-06
|
||||
86 2 -23.69156961 -23.690843 0.0003633026522 0.0006034844173 0.0006081134763 1.367563513e-06
|
||||
87 2 -23.6914135 -23.690598 0.0004077495027 0.001205622469 0.001217674833 4.139579599e-06
|
||||
88 2 -23.69152569 -23.690656 0.0004348453461 0.0005982210923 0.0006024765556 1.339909066e-06
|
||||
89 2 -23.69122964 -23.690254 0.00048782182 0.001039614512 0.001043496047 2.818899799e-06
|
||||
90 2 -23.69160573 -23.690694 0.0004558641588 0.0006005238032 0.0006010740387 4.468144277e-07
|
||||
91 2 -23.69097667 -23.690097 0.0004398327929 0.0008742196236 0.0008730234819 9.401054078e-07
|
||||
92 2 -23.68931978 -23.688402 0.000458891277 0.0006323492378 0.000632180354 2.788895255e-07
|
||||
93 2 -23.68957636 -23.688669 0.0004536814608 0.001093068336 0.001092474256 1.597403354e-06
|
||||
94 2 -23.69136079 -23.690538 0.0004113951269 0.0008559692215 0.0008610145179 1.717480332e-06
|
||||
95 2 -23.69064046 -23.689722 0.0004592296819 0.0006203235661 0.0006251287867 1.466428815e-06
|
||||
96 2 -23.69148677 -23.690581 0.0004528827615 7.127210559e-07 0 2.255863159e-07
|
||||
97 2 -23.68967251 -23.688755 0.0004587561741 0.0006269092047 0.0006251143895 8.456044924e-07
|
||||
98 2 -23.69038245 -23.689312 0.0005352258985 0.0008260738577 0.0008290597083 1.434578094e-06
|
||||
99 2 -23.6885155 -23.687388 0.000563750435 0.001127068066 0.001120237475 2.790106364e-06
|
||||
100 2 -23.69147138 -23.690664 0.0004036883861 0.0006101343713 0.0006109402589 2.333308226e-07
|
||||
101 2 -23.69059185 -23.68941 0.0005909264985 0.0005851627979 0.0005883553348 1.578359791e-06
|
||||
102 2 -23.69082355 -23.690035 0.0003942730081 0.0008795919888 0.0008810062429 8.322915827e-07
|
||||
103 2 -23.69101815 -23.690015 0.0005015766298 0.0008420116739 0.0008450195264 1.339928081e-06
|
||||
104 2 -23.6915919 -23.690752 0.0004199497676 0.0005974770628 0.0005996415596 9.70808844e-07
|
||||
105 2 -23.69060481 -23.689825 0.0003899065755 0.0008774617579 0.0008800215906 1.681761199e-06
|
||||
106 2 -23.69149834 -23.690562 0.0004681676 0.0008527074936 0.0008560011682 1.11226924e-06
|
||||
107 2 -23.69145561 -23.690622 0.0004168050595 0.0008363624298 0.0008390017878 8.930611273e-07
|
||||
108 2 -23.68965306 -23.688764 0.0004445297309 0.0008936263738 0.0008910185183 1.309339573e-06
|
||||
109 2 -23.69077552 -23.690011 0.0003822592712 0.0006203793746 0.0006194287691 3.133550229e-07
|
||||
110 2 -23.68867102 -23.687696 0.0004875100015 0.001086068328 0.001087589996 1.327020171e-06
|
||||
111 2 -23.69172933 -23.691019 0.0003551646935 0.000852013148 0.0008540035129 9.847230007e-07
|
||||
112 2 -23.68991099 -23.689025 0.000442996005 6.46227386e-07 0 2.557212911e-07
|
||||
113 2 -23.69080506 -23.689952 0.0004265318142 7.012777671e-07 0 2.758977769e-07
|
||||
114 2 -23.69152793 -23.69061 0.0004589654148 0.0008542966264 0.0008580011655 1.338482046e-06
|
||||
115 2 -23.69153556 -23.690595 0.0004702783823 0.000867974804 0.0008680069124 6.687384672e-07
|
||||
116 2 -23.69117399 -23.690231 0.000471493636 0.0005924023762 0.0005925892338 1.259776007e-07
|
||||
117 2 -23.69139497 -23.690469 0.0004629856458 0.0008486906688 0.0008500294113 6.344879116e-07
|
||||
118 2 -23.69122801 -23.690482 0.0003730070077 0.0008734801582 0.0008740102974 2.172190141e-07
|
||||
119 2 -23.69055118 -23.689613 0.0004690919274 0.0008237358825 0.0008320192305 2.927942421e-06
|
||||
120 2 -23.68847553 -23.687426 0.0005247657372 0.001093739709 0.00109577735 8.307823424e-07
|
||||
121 2 -23.69041353 -23.689562 0.000425762889 0.0006210724415 0.0006265237426 1.574752432e-06
|
||||
122 2 -23.69137916 -23.6904 0.0004895814578 3.712921801e-07 0 1.509058252e-07
|
||||
123 2 -23.69152029 -23.690561 0.0004796427403 0.0005964911748 0.0005982273815 1.201511775e-06
|
||||
124 2 -23.69012377 -23.689107 0.0005083837539 0.0008124995989 0.0008180073349 1.97846325e-06
|
||||
125 2 -23.69112303 -23.690145 0.000489014125 0.0008742245309 0.0008740766557 1.981010569e-06
|
||||
126 2 -23.6913827 -23.690482 0.00045035056 0.0005944563316 0.0005939983165 2.227151791e-07
|
||||
127 2 -23.69071568 -23.689864 0.0004258388591 0.0008855411376 0.0008860124153 7.974985004e-07
|
||||
# Elastic_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
128 4 -46.43709855 -46.437936 0.0002093617328 0.0008950059332 0.001265949446 0.0001464529791
|
||||
129 4 -46.4407039 -46.438504 0.0005499744469 0.0009975948265 0.001492549497 0.0001384062515
|
||||
130 4 -46.43497365 -46.436378 0.0003510867184 0.0005521282525 0.000810592376 9.989141969e-05
|
||||
131 4 -46.44077415 -46.441551 0.0001942123898 0.001132197907 0.001283675193 6.296966657e-05
|
||||
132 4 -46.41517164 -46.416957 0.0004463408133 0.000917990147 0.001186145859 8.226324971e-05
|
||||
133 4 -46.43849879 -46.440495 0.0004990529713 0.001000780113 0.001212440514 6.935590465e-05
|
||||
134 4 -46.43777706 -46.437972 4.873595839e-05 0.001389269665 0.002358226452 0.0002414827518
|
||||
135 4 -46.44772061 -46.44586 0.0004651524929 0.00136379307 0.002033949852 0.0001874009366
|
||||
136 4 -46.43566097 -46.435744 2.075858871e-05 0.0009531675039 0.001690849491 0.0002499304712
|
||||
137 4 -46.4397151 -46.438209 0.0003765248409 0.0008871611703 0.001160049999 6.827992039e-05
|
||||
138 4 -46.42609455 -46.42629 4.886349894e-05 0.0005556350766 0.0005297018029 1.21651498e-05
|
||||
139 4 -46.44149051 -46.443301 0.0004526223375 0.001132510738 0.001818421568 0.0001734412988
|
||||
140 4 -46.43896893 -46.439002 8.267473937e-06 0.001179879164 0.001416973535 6.937478941e-05
|
||||
141 4 -46.43123555 -46.432438 0.0003006112875 0.001147766739 0.001010469198 6.008540236e-05
|
||||
142 4 -46.41017485 -46.412654 0.0006197883649 0.001371501311 0.001801959766 0.0001610014112
|
||||
143 4 -46.44246774 -46.443231 0.0001908144167 0.0008879088126 0.001691590967 0.0001867981938
|
||||
144 4 -46.43057135 -46.431513 0.0002354128564 0.001455115574 0.001680544852 7.970584502e-05
|
||||
145 4 -46.43314849 -46.435608 0.0006148766383 0.000895665005 0.0009593039143 1.661569891e-05
|
||||
146 4 -46.43895751 -46.437689 0.0003171270659 0.001001644887 0.001217708504 8.864745791e-05
|
||||
147 4 -46.4271122 -46.428447 0.0003336990143 0.001053852574 0.002060081552 0.0002791878204
|
||||
148 4 -46.43182739 -46.432255 0.000106902789 0.0007125255966 0.0006274201144 7.371627608e-05
|
||||
149 4 -46.44177161 -46.442315 0.0001358463057 0.001140463867 0.002424436842 0.0003371037421
|
||||
150 4 -46.43717254 -46.436613 0.000139884251 0.0005515470124 0.0005321240457 4.25980675e-05
|
||||
151 4 -46.43004027 -46.430825 0.0001961823592 0.001008902912 0.001399987143 0.0001075255834
|
||||
152 4 -46.43208405 -46.43312 0.0002589881882 0.0005518528033 0.0007272771136 5.274203147e-05
|
||||
153 4 -46.43371444 -46.434347 0.000158140244 0.0008969169177 0.001284451634 0.000116451331
|
||||
154 4 -46.42879982 -46.430573 0.0004432948912 0.0009069765322 0.001315746176 0.0001014266222
|
||||
155 4 -46.44729799 -46.445665 0.0004082485341 0.001210137892 0.00180789159 0.0001638465464
|
||||
156 4 -46.43544342 -46.435898 0.0001136447769 0.0008978231434 0.001869300939 0.0002335504461
|
||||
157 4 -46.44021163 -46.442107 0.0004738424917 0.0007064270827 0.0006020930161 3.471655618e-05
|
||||
158 4 -46.43498956 -46.434432 0.0001393896227 0.0009533481605 0.001092982159 7.242855265e-05
|
||||
159 4 -46.43803608 -46.436308 0.0004320210529 0.001263659168 0.001839150891 0.0001727461868
|
||||
160 4 -46.42268734 -46.423938 0.0003126642441 0.001014412719 0.001463463016 0.0001717552709
|
||||
161 4 -46.42662921 -46.428115 0.0003714482928 0.0007136207063 0.0008584497656 6.405723837e-05
|
||||
162 4 -46.42531434 -46.4269 0.0003964160099 0.001206355349 0.001845719914 0.0002046485876
|
||||
163 4 -46.42224822 -46.421142 0.00027655517 0.001156356408 0.001309150106 4.994079618e-05
|
||||
164 4 -46.4302643 -46.432233 0.0004921743842 0.0007882966199 0.0007253109678 2.466489974e-05
|
||||
165 4 -46.43017473 -46.429408 0.0001916835518 0.000899021915 0.001068327665 6.208651635e-05
|
||||
166 4 -46.44541887 -46.445145 6.846642975e-05 0.001028604344 0.001776038288 0.0001975509563
|
||||
167 4 -46.43410132 -46.435868 0.0004416698523 0.00126629641 0.002376074704 0.0003279007933
|
||||
168 4 -46.43919494 -46.439663 0.0001170158831 0.0005441672792 0.001119403413 0.0001039537827
|
||||
169 4 -46.42584101 -46.428287 0.0006114968909 0.001286554794 0.001277000392 3.606396056e-05
|
||||
170 4 -46.42254993 -46.424584 0.000508517271 0.0007166928246 0.0008032957114 3.058246984e-05
|
||||
171 4 -46.41053526 -46.413045 0.0006274344802 0.001077488731 0.001248322074 4.395073797e-05
|
||||
172 4 -46.43440112 -46.436994 0.0006482191497 0.0009567631962 0.001331939188 0.0001491134491
|
||||
173 4 -46.44377744 -46.443604 4.335911262e-05 0.0009956173287 0.001177046303 8.761456142e-05
|
||||
174 4 -46.44028269 -46.439718 0.0001411716593 9.067044161e-07 0 2.475504855e-07
|
||||
175 4 -46.43723548 -46.435527 0.0004271206705 0.001133620344 0.0009338393866 8.014312499e-05
|
||||
176 4 -46.43396161 -46.434787 0.0002063465503 0.001150111339 0.00117329195 4.934565354e-05
|
||||
177 4 -46.43612253 -46.434929 0.0002983823621 0.001267526966 0.001349491756 5.093502218e-05
|
||||
178 4 -46.42638491 -46.426499 2.852244117e-05 0.001164859691 0.001248937949 4.347949244e-05
|
||||
179 4 -46.43717201 -46.437025 3.675245971e-05 0.0007725496777 0.000938418883 6.831038049e-05
|
||||
180 4 -46.4281895 -46.428937 0.0001868757356 0.001151243959 0.001286352984 4.994282406e-05
|
||||
181 4 -46.44116364 -46.442516 0.0003380892793 0.0007032387465 0.00094855469 0.0001088604201
|
||||
182 4 -46.42978258 -46.428736 0.0002616440103 0.001009629916 0.001424321593 0.0001089615662
|
||||
183 4 -46.43305551 -46.433359 7.587361447e-05 0.001156682853 0.001276381604 4.128766832e-05
|
||||
184 4 -46.44006475 -46.438799 0.0003164382753 0.0007752996065 0.0008186940821 3.548756745e-05
|
||||
185 4 -46.44169053 -46.441993 7.561864672e-05 0.0008970969052 0.001887735151 0.0002223397932
|
||||
186 4 -46.43727222 -46.439033 0.0004401954936 0.0007708721088 0.000821568013 4.107007018e-05
|
||||
187 4 -46.43632517 -46.436967 0.0001604574289 0.001052390296 0.001482323514 0.0001388091482
|
||||
188 4 -46.42718259 -46.427245 1.560352526e-05 0.001072419721 0.001293885621 7.709435507e-05
|
||||
189 4 -46.43874841 -46.438046 0.0001756024201 0.001260671216 0.001627288542 0.0001002074435
|
||||
190 4 -46.41877429 -46.420083 0.0003271768634 0.00142160315 0.002395244873 0.0003233098312
|
||||
191 4 -46.44621445 -46.445247 0.0002418615665 0.0009904374428 0.001219330964 5.687306262e-05
|
||||
192 4 -46.44511464 -46.446044 0.0002323410927 0.0008790838348 0.001305329077 0.0001107509197
|
||||
193 4 -46.43564394 -46.434472 0.0002929851777 0.000890378693 0.0008323340675 4.743679034e-05
|
||||
194 4 -46.44317175 -46.44458 0.0003520619573 0.0007034014662 0.0009744208536 5.172015881e-05
|
||||
195 4 -46.44087095 -46.441776 0.0002262624122 0.00113922313 0.001339231869 8.765052415e-05
|
||||
196 4 -46.43719326 -46.436389 0.0002010659177 0.001277508928 0.001786741168 0.0001303767454
|
||||
197 4 -46.44563996 -46.446416 0.0001940097871 0.0007007387602 0.0006588778339 5.645487424e-05
|
||||
198 4 -46.44980864 -46.449806 6.606823266e-07 0.001232826529 0.002135055034 0.0002384857832
|
||||
199 4 -46.42466674 -46.427189 0.0006305654832 0.001011828255 0.001050788276 2.797047454e-05
|
||||
200 4 -46.42588993 -46.427857 0.000491766418 0.001010915484 0.001487666629 0.0001398462887
|
||||
201 4 -46.44273693 -46.44004 0.0006742317456 0.0007050795233 0.000757202747 2.506458135e-05
|
||||
202 4 -46.43659247 -46.437214 0.0001553829854 0.0008924045914 0.001505586265 0.0001475571029
|
||||
203 4 -46.42189527 -46.422628 0.0001831835233 0.0009120248848 0.001601713458 0.0002207350143
|
||||
204 4 -46.44387014 -46.443535 8.378431277e-05 0.001253187495 0.001590304373 0.0001006147174
|
||||
205 4 -46.4386991 -46.439922 0.0003057254875 0.001138308324 0.001530493385 0.0001018467819
|
||||
206 4 -46.43732669 -46.437675 8.707637653e-05 0.00144833639 0.002440246094 0.0003149341193
|
||||
207 4 -46.44459348 -46.445558 0.0002411303465 0.0008716893522 0.00113392416 7.56134454e-05
|
||||
208 4 -46.43888136 -46.439106 5.615896373e-05 0.001259801268 0.001830731002 0.0001709222499
|
||||
209 4 -46.44452218 -46.443073 0.000362294488 0.0005355233492 0.0005766870902 1.79131844e-05
|
||||
210 4 -46.44072829 -46.4397 0.0002570727366 0.0008912594074 0.001204174406 7.190949652e-05
|
||||
211 4 -46.43632905 -46.436374 1.123701302e-05 0.00100454144 0.001461656594 0.0001640759619
|
||||
212 4 -46.42622449 -46.426557 8.312836801e-05 0.0009090508417 0.001359624213 9.618645017e-05
|
||||
213 4 -46.43334095 -46.434009 0.0001670117853 0.001064727099 0.001391131194 0.0001118380718
|
||||
214 4 -46.43528491 -46.436262 0.0002442735765 0.001381671175 0.002503347159 0.0002862586192
|
||||
215 4 -46.43302209 -46.434505 0.0003707286996 0.001050895795 0.001041637173 1.894959196e-05
|
||||
216 4 -46.43866543 -46.438768 2.564354619e-05 0.001038218613 0.001098285027 4.514351427e-05
|
||||
217 4 -46.43867092 -46.440254 0.000395771139 0.0005510961745 0.0006069892915 4.783705107e-05
|
||||
218 4 -46.42481603 -46.42286 0.0004890086715 0.0005673661918 0.0007365242698 6.506184883e-05
|
||||
219 4 -46.41707211 -46.418078 0.0002514715464 0.001292943265 0.002028412187 0.0002017017408
|
||||
220 4 -46.44058128 -46.440513 1.706961588e-05 0.0008917162415 0.001158189967 9.459271337e-05
|
||||
221 4 -46.40786735 -46.409824 0.000489161666 0.000915995593 0.001759573812 0.0002027400318
|
||||
222 4 -46.44176165 -46.440329 0.0003581615225 0.0007050784001 0.0009534044263 7.330945846e-05
|
||||
223 4 -46.43764613 -46.43773 2.096761683e-05 0.000774718051 0.000926180328 6.358620287e-05
|
||||
224 4 -46.41646676 -46.416525 1.456068592e-05 0.0007183862165 0.0007573664899 3.367541267e-05
|
||||
225 4 -46.44086814 -46.440293 0.0001437843048 0.0008909024924 0.0007725386722 2.803785114e-05
|
||||
226 4 -46.44027213 -46.43839 0.0004705337314 0.000707862011 0.0005612022808 3.305821092e-05
|
||||
227 4 -46.44117428 -46.438916 0.0005645706045 0.0008843758872 0.001650878554 0.0001728226219
|
||||
# GSF_110.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
228 24 -278.9717069 -279.068761 0.004043919984 1.716820818 1.756353161 0.02195804808
|
||||
229 24 -279.8354387 -279.784296 0.002130947227 0.8360148085 0.9057668891 0.02306494198
|
||||
230 24 -279.920921 -279.901657 0.0008026661363 0.2958425997 0.001565946359 0.01411644584
|
||||
231 24 -279.6113309 -279.584238 0.001128870276 1.136927478 1.035572248 0.0268109436
|
||||
232 24 -279.8354404 -279.784283 0.002131557004 0.8360112083 0.9056396189 0.02305363685
|
||||
233 24 -279.302435 -279.302158 1.154096848e-05 1.736732738 1.771965137 0.03376130194
|
||||
234 24 -279.5958843 -279.55564 0.001676844981 1.457718936 1.405626506 0.02601748107
|
||||
235 24 -279.1575825 -279.246939 0.003723187357 0.7701803397 0.4813964151 0.04047323625
|
||||
236 24 -279.3024375 -279.302157 1.168852836e-05 1.736736025 1.771953347 0.03376039536
|
||||
237 24 -279.1575946 -279.246935 0.003722518226 0.7692677843 0.4809484798 0.04044520421
|
||||
238 24 -279.9208868 -279.896025 0.001035907873 0.2963184571 0.01060549839 0.01410249844
|
||||
239 24 -279.6115695 -279.584237 0.001138852664 1.13770573 1.035836121 0.02686761528
|
||||
240 24 -279.064529 -279.124427 0.002495750967 1.76375665 1.809545887 0.03536482035
|
||||
241 24 -279.3562359 -279.379366 0.000963755899 1.070359933 0.8982692706 0.03586365384
|
||||
242 24 -279.3561337 -279.37937 0.0009681791432 1.070187041 0.898081355 0.03582334182
|
||||
243 24 -279.0645273 -279.124427 0.002495818902 1.763753116 1.809523374 0.03536507377
|
||||
244 24 -279.920921 -279.901657 0.0008026661364 0.295842601 0.001570374478 0.01411415473
|
||||
245 24 -279.835369 -279.79264 0.001780376182 0.7694168746 0.8392614852 0.02365583077
|
||||
246 24 -279.9208868 -279.896025 0.001035907873 0.2963184557 0.01060243293 0.01410273421
|
||||
247 24 -279.0819585 -279.206496 0.005189061107 0.548788431 0.005326518563 0.03225764062
|
||||
248 24 -279.5958869 -279.55564 0.001676956181 1.457719116 1.4056319 0.02601845486
|
||||
249 24 -279.8353874 -279.79264 0.001781141415 0.7694021079 0.8392625708 0.0236575616
|
||||
# GSF_112.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
250 30 -345.1958147 -345.175835 0.0006659888828 1.417827685 1.057395322 0.04924259711
|
||||
251 30 -346.4091654 -346.361714 0.001581712645 1.014644886 1.220284939 0.04659093523
|
||||
252 30 -345.9623042 -345.795524 0.005559340233 1.678459906 2.112860875 0.06265040874
|
||||
253 30 -345.1047773 -345.164602 0.001994157897 1.817583015 1.765832199 0.05258058387
|
||||
254 30 -346.5687925 -346.593523 0.0008243492414 0.5266160053 0.01148867129 0.03755504848
|
||||
255 30 -346.4165137 -346.396186 0.0006775885975 1.101956458 0.9954683928 0.04399110332
|
||||
256 30 -345.2521553 -345.319406 0.00224168982 2.024011434 1.772040852 0.05936118376
|
||||
257 30 -345.5898528 -345.594794 0.0001647082757 2.048144835 1.516014157 0.06040121307
|
||||
258 30 -346.0297765 -345.98566 0.001470549283 1.767327791 1.406252265 0.05243702855
|
||||
259 30 -345.5053828 -345.383994 0.004046292585 1.336428571 0.963574308 0.05104895348
|
||||
260 30 -346.5686342 -346.582564 0.0004643258311 0.5264214865 0.0126740587 0.03760971825
|
||||
261 30 -345.4208872 -345.452139 0.001041727499 3.011665478 2.787719406 0.06345649484
|
||||
262 30 -346.5687922 -346.593523 0.000824358736 0.5266293188 0.01148834 0.03755660424
|
||||
263 30 -345.4303122 -345.281949 0.004945440141 1.947208063 1.873142686 0.05337069289
|
||||
264 30 -345.95932 -345.928661 0.001021967701 2.362723976 2.100874472 0.05002108374
|
||||
265 30 -345.0137677 -345.111657 0.003262976998 3.19378163 3.358068319 0.06536423133
|
||||
266 30 -346.4078756 -346.367123 0.001358420679 1.085591236 1.335797131 0.04639235845
|
||||
267 30 -346.5685864 -346.582565 0.0004659529893 0.5264879505 0.01254743735 0.03760890253
|
||||
268 30 -344.8663405 -344.91356 0.001573984549 2.930408919 3.441834403 0.06926998065
|
||||
269 30 -345.9709087 -345.836703 0.004473521714 1.391835251 1.608769148 0.0557054003
|
||||
270 30 -345.0229891 -344.984307 0.001289401895 2.372016819 2.542628782 0.05571749983
|
||||
271 30 -346.4089445 -346.393931 0.0005004501598 1.297845976 1.211680725 0.04319349672
|
||||
# Liquid.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
272 100 -1105.559726 -1105.601723 0.0004199683753 30.70196346 31.39853886 0.2273901869
|
||||
273 100 -1099.629534 -1099.673012 0.0004347802829 31.98646736 32.03167218 0.2226202775
|
||||
274 100 -1121.43168 -1121.31506 0.001166195007 21.23863202 20.81076453 0.2037539309
|
||||
# Surface.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
275 24 -279.9208871 -279.911828 0.0003774634676 0.2963192975 0.002753093533 0.01433131958
|
||||
276 48 -554.241479 -555.359452 0.02329110353 1.363109446 0.003020630398 0.0573825018
|
||||
277 40 -459.5808398 -459.216162 0.009116945293 3.33149843 5.0461364 0.07877996461
|
||||
278 40 -460.5932467 -461.144076 0.01377073163 0.8854479197 0.005582740008 0.03813349763
|
||||
279 24 -279.8214986 -279.635146 0.007764693427 0.982012045 1.288799837 0.01857540863
|
||||
280 30 -346.5687933 -346.592525 0.000791056775 0.5266154723 0.008446203407 0.03726637101
|
||||
281 30 -346.0051971 -345.744506 0.008689702509 2.266739618 3.124961367 0.06591070739
|
||||
# Volume_A15.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
282 8 -67.00264003 -66.990732 0.001488503243 8.978495355e-15 0 1.554167674e-15
|
||||
283 8 -72.95775645 -72.957807 6.318335608e-06 6.173563626e-14 0 9.086337007e-15
|
||||
284 8 -94.15079079 -94.145745 0.0006307242955 1.257001279e-14 0 1.651353601e-15
|
||||
285 8 -94.55576971 -94.554682 0.0001359640227 7.864226848e-15 0 1.351609702e-15
|
||||
286 8 -79.41650989 -79.438363 0.002731638712 2.922311383e-14 0 4.6112564e-15
|
||||
287 8 -69.6319055 -69.627817 0.0005110626381 3.131450246e-15 0 5.512083845e-16
|
||||
288 8 -82.6140242 -82.604907 0.001139650038 1.015341342e-14 0 1.573105072e-15
|
||||
289 8 14.8871533 14.89048 0.0004158371788 2.179622647e-13 0 3.718594804e-14
|
||||
290 8 -94.35602701 -94.367599 0.001446498413 1.681327296e-14 0 2.430951383e-15
|
||||
291 8 -89.2494361 -89.248227 0.0001511372198 1.602695388e-14 0 2.27566808e-15
|
||||
292 8 -87.22359357 -87.211997 0.001449571359 5.891018761e-15 0 1.023486851e-15
|
||||
293 8 -93.64917633 -93.66897 0.002474209194 1.737070481e-15 0 2.726891929e-16
|
||||
294 8 -7.974970896 -7.989166 0.001774387948 5.346466786e-13 0 7.317740119e-14
|
||||
295 8 -84.99735697 -84.982834 0.001815371577 1.628985705e-15 0 2.68014777e-16
|
||||
296 8 -92.51696442 -92.536373 0.002426072159 3.702813287e-14 0 5.965135793e-15
|
||||
297 8 -26.79883523 -26.77612 0.002839403163 2.314654929e-13 0 3.768467838e-14
|
||||
298 8 -77.53738473 -77.544107 0.0008402842141 2.975839122e-15 0 5.1405639e-16
|
||||
299 8 -80.11476757 -80.114217 6.882064461e-05 9.414427891e-15 0 1.325473296e-15
|
||||
300 8 -42.12903262 -42.143041 0.001751047533 2.610061598e-13 0 3.565304919e-14
|
||||
301 8 -91.02990946 -91.040671 0.001345192241 8.368513177e-15 0 1.310872707e-15
|
||||
302 8 -84.50933121 -84.499231 0.001262526145 5.714110441e-14 0 1.066782658e-14
|
||||
303 8 -61.79844789 -61.825173 0.003340638518 6.62953849e-15 0 1.015391475e-15
|
||||
304 8 -91.13057644 -91.156873 0.003287069749 4.719369293e-15 0 6.76336609e-16
|
||||
305 8 -54.64916677 -54.658744 0.001197153514 1.464956394e-13 0 2.113576767e-14
|
||||
306 8 -72.27319255 -72.277255 0.0005078062019 8.658199332e-16 0 1.410908427e-16
|
||||
307 8 -74.9147183 -74.923334 0.001076962465 4.434219242e-15 0 6.615078855e-16
|
||||
308 8 -64.81833247 -64.798066 0.002533308735 3.748412002e-14 0 5.576268614e-15
|
||||
309 8 -93.03489726 -93.048342 0.001680592822 1.857310674e-14 0 2.604235054e-15
|
||||
310 8 -64.39098013 -64.38702 0.0004950167019 5.001001166e-15 0 5.722057666e-16
|
||||
311 8 -88.36401125 -88.352871 0.001392531574 1.47982807e-14 0 2.645507511e-15
|
||||
# Volume_BCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
312 2 -16.76594323 -16.763625 0.0011591154 3.058627912e-16 0 7.979727989e-17
|
||||
313 2 16.31372699 16.314145 0.0002090027274 8.186542193e-13 0 2.624717573e-13
|
||||
314 2 -21.21034402 -21.209071 0.000636508568 6.029606478e-15 0 1.688464572e-15
|
||||
315 2 -15.7845968 -15.780524 0.002036397536 5.051396178e-14 0 1.863971217e-14
|
||||
316 2 -18.99841038 -19.002205 0.001897311189 3.70201696e-14 0 1.247006253e-14
|
||||
317 2 -22.6245193 -22.620568 0.001975650815 3.866866338e-15 0 1.424786215e-15
|
||||
318 2 4.098164527 4.096885 0.0006397634862 6.334293648e-14 0 2.151519703e-14
|
||||
319 2 56.26275599 56.26276 2.005221472e-06 2.247995559e-12 0 7.580021273e-13
|
||||
320 2 -22.58944012 -22.585113 0.002163562406 1.113168148e-15 0 3.747002708e-16
|
||||
321 2 -21.79724015 -21.795501 0.0008695760695 1.09344287e-15 0 3.700743415e-16
|
||||
322 2 33.11015633 33.110078 3.916354612e-05 4.904232742e-13 0 1.492139745e-13
|
||||
323 2 -20.88315873 -20.885998 0.001419634185 1.859416424e-15 0 7.401486831e-16
|
||||
324 2 -23.59568898 -23.601336 0.002823509954 1.486164289e-15 0 4.916167932e-16
|
||||
325 2 -23.20858071 -23.207313 0.0006338528204 8.900302643e-16 0 3.147520853e-16
|
||||
326 2 -19.89310507 -19.898089 0.002491965758 8.784897284e-16 0 3.064678141e-16
|
||||
327 2 -23.40543384 -23.405474 2.007854096e-05 9.04864091e-16 0 2.55004351e-16
|
||||
328 2 -4.783890314 -4.781324 0.00128315718 1.026901322e-13 0 2.670433319e-14
|
||||
329 2 -18.86311291 -18.864936 0.0009115426716 2.305551267e-16 0 7.864079758e-17
|
||||
330 2 -17.81642588 -17.813086 0.001669937839 1.716587549e-16 0 6.245004514e-17
|
||||
331 2 -11.19369732 -11.197201 0.001751842379 6.247077482e-14 0 2.245483891e-14
|
||||
332 2 -23.6830862 -23.696705 0.006809399945 1.843658888e-15 0 7.087971703e-16
|
||||
# Volume_FCC.xyz
|
||||
config # atoms energy DFT energy energy error force DFT force force error
|
||||
333 4 -19.07363592 -19.075994 0.0005895202867 4.838977351e-14 0 1.162785146e-14
|
||||
334 4 -34.87911157 -34.873619 0.001373142448 2.834773835e-16 0 5.955883934e-17
|
||||
335 4 -43.95312208 -43.950003 0.0007797711561 2.246784353e-15 0 4.928060275e-16
|
||||
336 4 -40.99484531 -40.991909 0.0007340763059 8.408019466e-15 0 2.017013582e-15
|
||||
337 4 -43.44688587 -43.453929 0.001760782795 1.105978561e-14 0 2.960654589e-15
|
||||
338 4 -42.69057259 -42.686077 0.001123896575 2.15077979e-15 0 5.053466326e-16
|
||||
339 4 -33.22567657 -33.224653 0.0002558935333 6.71927174e-16 0 1.601728009e-16
|
||||
340 4 -26.86518979 -26.862709 0.0006201969912 3.31529179e-14 0 7.652202346e-15
|
||||
341 4 -25.52095377 -25.519883 0.0002676922193 3.655453829e-16 0 7.199102425e-17
|
||||
342 4 3.462101367 3.463071 0.0002424081278 1.816025861e-13 0 4.023864575e-14
|
||||
343 4 -31.5932268 -31.59595 0.0006807997919 3.628185658e-16 0 8.557969148e-17
|
||||
344 4 -45.10086835 -45.100466 0.0001005873411 2.465692424e-15 0 5.323999453e-16
|
||||
345 4 -46.05341345 -46.052258 0.0002888629271 8.511696107e-16 0 1.9963776e-16
|
||||
346 4 -29.99832749 -30.001189 0.0007153784531 3.847020655e-16 0 1.014813233e-16
|
||||
347 4 -22.85257327 -22.8504 0.0005433170403 7.603433695e-16 0 2.026735261e-16
|
||||
348 4 -9.165925377 -9.164691 0.0003085942037 6.355991568e-14 0 1.496321874e-14
|
||||
349 4 -24.14844545 -24.150343 0.0004743875843 4.762376771e-16 0 9.887923813e-17
|
||||
350 4 -46.43546878 -46.426795 0.002168445654 2.389854689e-15 0 6.508104241e-16
|
||||
351 4 -28.45126723 -28.451145 3.055783253e-05 7.811231556e-15 0 2.246466901e-15
|
||||
352 4 40.34134283 40.341566 5.579164045e-05 4.392900751e-13 0 1.047052708e-13
|
||||
353 4 19.618876 19.617912 0.0002409995917 2.653013854e-13 0 4.82657932e-14
|
||||
354 4 -26.95747287 -26.954384 0.0007722170381 5.063966549e-16 0 1.225871256e-16
|
||||
355 4 -46.33491981 -46.323696 0.002805953551 3.211950954e-15 0 8.731441496e-16
|
||||
356 4 -45.83316791 -45.828947 0.001055227438 1.228572267e-14 0 3.512236798e-15
|
||||
357 4 -38.16058675 -38.16029 7.418651586e-05 1.457184241e-15 0 3.625572065e-16
|
||||
358 4 -32.91257363 -32.919741 0.001791843199 5.73065335e-14 0 1.529158744e-14
|
||||
359 4 -41.2675262 -41.272675 0.001287199354 7.138843467e-15 0 2.027950471e-15
|
||||
360 4 -39.74460494 -39.753322 0.002179265661 7.861049173e-16 0 1.651275908e-16
|
||||
361 4 -37.55548161 -37.547435 0.002011652753 1.155947671e-14 0 2.497062164e-15
|
||||
362 4 -36.53186908 -36.52595 0.001479769423 3.660718685e-16 0 9.51206706e-17
|
||||
363 4 -45.01550153 -45.016087 0.0001463673621 1.766214736e-15 0 4.760370339e-16
|
||||
@ -1,20 +0,0 @@
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014
|
||||
Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461
|
||||
Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471
|
||||
Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002
|
||||
Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163
|
||||
GSF_110.xyz 22 528 0.001852 0.002260 0.027303 0.044765
|
||||
GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350
|
||||
Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109
|
||||
Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123
|
||||
Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.001053 0.002171 0.059051 0.106960
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
@ -1,5 +0,0 @@
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
|
||||
@ -1,114 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 1
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 150
|
||||
total number of descriptors for all potentials: 182
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
**************** Begin of Data File ****************
|
||||
file format: extxyz
|
||||
file extension: xyz
|
||||
path to training data set: ../Ta/XYZ
|
||||
path to test data set: ../Ta/XYZ
|
||||
training fraction: 1
|
||||
test fraction: 1
|
||||
randomize training data set: 1
|
||||
randomize test data set: 1
|
||||
error analysis for training data set: 1
|
||||
error analysis for test data set: 0
|
||||
energy/force calculation for training data set: 0
|
||||
energy/force calculation for test data set: 0
|
||||
fitting weight for energy: 100
|
||||
fitting weight for force: 1
|
||||
fitting weight for stress: 0
|
||||
fitting regularization parameter: 1e-10
|
||||
**************** End of Data File ****************
|
||||
**************** Begin of Training Data Set ****************
|
||||
---------------------------------------------------------------
|
||||
data file | number of configurations | number of atoms
|
||||
---------------------------------------------------------------
|
||||
Displaced_A15.xyz | 9 | 576
|
||||
Displaced_BCC.xyz | 9 | 486
|
||||
Displaced_FCC.xyz | 9 | 432
|
||||
Elastic_BCC.xyz | 100 | 200
|
||||
Elastic_FCC.xyz | 100 | 400
|
||||
GSF_110.xyz | 22 | 528
|
||||
GSF_112.xyz | 22 | 660
|
||||
Liquid.xyz | 3 | 300
|
||||
Surface.xyz | 7 | 236
|
||||
Volume_A15.xyz | 30 | 240
|
||||
Volume_BCC.xyz | 21 | 42
|
||||
Volume_FCC.xyz | 31 | 124
|
||||
---------------------------------------------------------------
|
||||
number of files: 12
|
||||
number of configurations in all files: 363
|
||||
number of atoms in all files: 4224
|
||||
minimum number of atoms: 2
|
||||
maximum number of atoms: 100
|
||||
**************** End of Training Data Set ****************
|
||||
**************** Begin of Memory Allocation ****************
|
||||
maximum number of atoms in periodic domain: 100
|
||||
maximum number of atoms in extended domain: 2700
|
||||
maximum number of neighbors in extended domain: 270000
|
||||
size of double memory: 223201
|
||||
size of int memory: 14709
|
||||
size of descriptor matrix: 182 x 182
|
||||
**************** End of Memory Allocation ****************
|
||||
**************** Begin of Least-Squares Fitting ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Least-Squares Fitting ****************
|
||||
**************** Begin of Error Calculation ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Error Calculation ****************
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014
|
||||
Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461
|
||||
Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471
|
||||
Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002
|
||||
Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163
|
||||
GSF_110.xyz 22 528 0.001852 0.002260 0.027303 0.044765
|
||||
GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350
|
||||
Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109
|
||||
Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123
|
||||
Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.001053 0.002171 0.059051 0.106960
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,114 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate fitpod for POD potential
|
||||
|
||||
units metal
|
||||
fitpod Ta_param.pod Ta_data.pod
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 1
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 150
|
||||
total number of descriptors for all potentials: 182
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
**************** Begin of Data File ****************
|
||||
file format: extxyz
|
||||
file extension: xyz
|
||||
path to training data set: ../Ta/XYZ
|
||||
path to test data set: ../Ta/XYZ
|
||||
training fraction: 1
|
||||
test fraction: 1
|
||||
randomize training data set: 1
|
||||
randomize test data set: 1
|
||||
error analysis for training data set: 1
|
||||
error analysis for test data set: 0
|
||||
energy/force calculation for training data set: 0
|
||||
energy/force calculation for test data set: 0
|
||||
fitting weight for energy: 100
|
||||
fitting weight for force: 1
|
||||
fitting weight for stress: 0
|
||||
fitting regularization parameter: 1e-10
|
||||
**************** End of Data File ****************
|
||||
**************** Begin of Training Data Set ****************
|
||||
---------------------------------------------------------------
|
||||
data file | number of configurations | number of atoms
|
||||
---------------------------------------------------------------
|
||||
Displaced_A15.xyz | 9 | 576
|
||||
Displaced_BCC.xyz | 9 | 486
|
||||
Displaced_FCC.xyz | 9 | 432
|
||||
Elastic_BCC.xyz | 100 | 200
|
||||
Elastic_FCC.xyz | 100 | 400
|
||||
GSF_110.xyz | 22 | 528
|
||||
GSF_112.xyz | 22 | 660
|
||||
Liquid.xyz | 3 | 300
|
||||
Surface.xyz | 7 | 236
|
||||
Volume_A15.xyz | 30 | 240
|
||||
Volume_BCC.xyz | 21 | 42
|
||||
Volume_FCC.xyz | 31 | 124
|
||||
---------------------------------------------------------------
|
||||
number of files: 12
|
||||
number of configurations in all files: 363
|
||||
number of atoms in all files: 4224
|
||||
minimum number of atoms: 2
|
||||
maximum number of atoms: 100
|
||||
**************** End of Training Data Set ****************
|
||||
**************** Begin of Memory Allocation ****************
|
||||
maximum number of atoms in periodic domain: 100
|
||||
maximum number of atoms in extended domain: 2700
|
||||
maximum number of neighbors in extended domain: 270000
|
||||
size of double memory: 223201
|
||||
size of int memory: 14709
|
||||
size of descriptor matrix: 182 x 182
|
||||
**************** End of Memory Allocation ****************
|
||||
**************** Begin of Least-Squares Fitting ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Least-Squares Fitting ****************
|
||||
**************** Begin of Error Calculation ****************
|
||||
Configuration: # 1
|
||||
Configuration: # 101
|
||||
Configuration: # 201
|
||||
Configuration: # 301
|
||||
**************** End of Error Calculation ****************
|
||||
**************** Begin of Error Analysis for the Training Data Set ****************
|
||||
---------------------------------------------------------------------------------------------------
|
||||
File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force
|
||||
---------------------------------------------------------------------------------------------------
|
||||
Displaced_A15.xyz 9 576 0.000554 0.000680 0.066393 0.083014
|
||||
Displaced_BCC.xyz 9 486 0.004724 0.005103 0.108253 0.139461
|
||||
Displaced_FCC.xyz 9 432 0.001704 0.001900 0.077531 0.097471
|
||||
Elastic_BCC.xyz 100 200 0.000444 0.000446 0.000001 0.000002
|
||||
Elastic_FCC.xyz 100 400 0.000273 0.000327 0.000110 0.000163
|
||||
GSF_110.xyz 22 528 0.001852 0.002260 0.027302 0.044765
|
||||
GSF_112.xyz 22 660 0.001839 0.002404 0.051415 0.080350
|
||||
Liquid.xyz 3 300 0.000674 0.000758 0.217921 0.276109
|
||||
Surface.xyz 7 236 0.009115 0.011661 0.047949 0.105123
|
||||
Volume_A15.xyz 30 240 0.001407 0.001693 0.000000 0.000000
|
||||
Volume_BCC.xyz 21 42 0.001497 0.002077 0.000000 0.000000
|
||||
Volume_FCC.xyz 31 124 0.000870 0.001139 0.000000 0.000000
|
||||
---------------------------------------------------------------------------------------------------
|
||||
All files 363 4224 0.001053 0.002171 0.059051 0.106960
|
||||
---------------------------------------------------------------------------------------------------
|
||||
**************** End of Error Analysis for the Training Data Set ****************
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate POD Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 1
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 150
|
||||
total number of descriptors for all potentials: 182
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
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 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
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 = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.847697 0 -11.809222 13502.169
|
||||
10 296.47494 -11.847245 0 -11.809222 13529.584
|
||||
20 286.0918 -11.845913 0 -11.809222 13613.884
|
||||
30 269.42275 -11.843776 0 -11.809222 13759.746
|
||||
40 247.39423 -11.84095 0 -11.809222 13972.073
|
||||
50 221.23976 -11.837596 0 -11.809222 14253.202
|
||||
60 192.43252 -11.833901 0 -11.809222 14600.367
|
||||
70 162.59874 -11.830075 0 -11.809221 15004.156
|
||||
80 133.41531 -11.826332 0 -11.809221 15448.418
|
||||
90 106.49785 -11.82288 0 -11.809221 15911.638
|
||||
100 83.288219 -11.819903 0 -11.809221 16369.373
|
||||
Loop time of 1.51781 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 2.846 ns/day, 8.432 hours/ns, 65.884 timesteps/s, 8.433 katom-step/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5172 | 1.5172 | 1.5172 | 0.0 | 99.96
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0002542 | 0.0002542 | 0.0002542 | 0.0 | 0.02
|
||||
Output | 0.00013308 | 0.00013308 | 0.00013308 | 0.0 | 0.01
|
||||
Modify | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.01
|
||||
Other | | 0.0001446 | | | 0.01
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 727 ave 727 max 727 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 7424 ave 7424 max 7424 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,142 +0,0 @@
|
||||
LAMMPS (22 Dec 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Demonstrate POD Ta potential
|
||||
|
||||
# Initialize simulation
|
||||
|
||||
variable nsteps index 100
|
||||
variable nrep equal 4
|
||||
variable a equal 3.316
|
||||
units metal
|
||||
|
||||
# generate the box and atom positions using a BCC lattice
|
||||
|
||||
variable nx equal ${nrep}
|
||||
variable nx equal 4
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 4
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 4
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice bcc $a
|
||||
lattice bcc 3.316
|
||||
Lattice spacing in x,y,z = 3.316 3.316 3.316
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 ${ny} 0 ${nz}
|
||||
region box block 0 4 0 4 0 ${nz}
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 128 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass 1 180.88
|
||||
|
||||
|
||||
# POD potential
|
||||
pair_style pod
|
||||
pair_coeff * * Ta_param.pod Ta_coefficients.pod Ta
|
||||
Reading potential file Ta_param.pod with DATE: 2022-11-30
|
||||
**************** Begin of POD Potentials ****************
|
||||
species: Ta
|
||||
periodic boundary conditions: 1 1 1
|
||||
inner cut-off radius: 1
|
||||
outer cut-off radius: 5
|
||||
bessel polynomial degree: 3
|
||||
inverse polynomial degree: 6
|
||||
one-body potential: 1
|
||||
two-body potential: 3 6 6
|
||||
three-body potential: 3 6 5 5
|
||||
four-body SNAP potential: 0 0
|
||||
quadratic POD potential: 1
|
||||
number of basis functions for one-body potential: 1
|
||||
number of basis functions for two-body potential: 6
|
||||
number of basis functions for three-body potential: 25
|
||||
number of basis functions for four-body potential: 0
|
||||
number of descriptors for one-body potential: 1
|
||||
number of descriptors for two-body potential: 6
|
||||
number of descriptors for three-body potential: 25
|
||||
number of descriptors for four-body potential: 0
|
||||
number of descriptors for quadratic POD potential: 150
|
||||
total number of descriptors for all potentials: 182
|
||||
**************** End of POD Potentials ****************
|
||||
|
||||
|
||||
# Setup output
|
||||
|
||||
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 300.0 4928459 loop geom
|
||||
fix 1 all nve
|
||||
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 = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair pod, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -11.847697 0 -11.809222 13502.169
|
||||
10 296.47494 -11.847245 0 -11.809222 13529.584
|
||||
20 286.0918 -11.845913 0 -11.809222 13613.884
|
||||
30 269.42275 -11.843776 0 -11.809222 13759.746
|
||||
40 247.39423 -11.84095 0 -11.809222 13972.073
|
||||
50 221.23976 -11.837596 0 -11.809222 14253.202
|
||||
60 192.43252 -11.833901 0 -11.809222 14600.367
|
||||
70 162.59874 -11.830075 0 -11.809221 15004.156
|
||||
80 133.41531 -11.826332 0 -11.809221 15448.418
|
||||
90 106.49785 -11.82288 0 -11.809221 15911.638
|
||||
100 83.288219 -11.819903 0 -11.809221 16369.373
|
||||
Loop time of 0.427448 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 10.106 ns/day, 2.375 hours/ns, 233.947 timesteps/s, 29.945 katom-step/s
|
||||
97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40622 | 0.40946 | 0.419 | 0.9 | 95.79
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0071192 | 0.016995 | 0.020439 | 4.4 | 3.98
|
||||
Output | 0.00012904 | 0.0002071 | 0.00043132 | 0.0 | 0.05
|
||||
Modify | 3.905e-05 | 4.8089e-05 | 5.5714e-05 | 0.0 | 0.01
|
||||
Other | | 0.0007341 | | | 0.17
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 431 ave 431 max 431 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1856 ave 1856 max 1856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7424
|
||||
Ave neighs/atom = 58
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -62,11 +62,11 @@ EAPOD::EAPOD(LAMMPS *_lmp, const std::string &pod_file, const std::string &coeff
|
||||
true4BodyDesc = 1;
|
||||
ns = nbesselpars*besseldegree + inversedegree;
|
||||
Njmax = 100;
|
||||
nrbf2 = 6;
|
||||
nrbf3 = 5;
|
||||
nrbf2 = 8;
|
||||
nrbf3 = 6;
|
||||
nrbf4 = 4;
|
||||
nabf3 = 5;
|
||||
nabf4 = 4;
|
||||
nabf4 = 3;
|
||||
nrbf23 = 0;
|
||||
nabf23 = 0;
|
||||
nrbf33 = 0;
|
||||
|
||||
@ -242,7 +242,7 @@ int FitPOD::read_data_file(double *fitting_weights, std::string &file_format,
|
||||
auto keywd = words[0];
|
||||
|
||||
if (words.size() != 2)
|
||||
error->one(FLERR,"Improper POD file.", utils::getsyserror());
|
||||
error->one(FLERR,"Improper POD data file.", utils::getsyserror());
|
||||
|
||||
// settings for fitting weights
|
||||
|
||||
@ -622,7 +622,8 @@ void FitPOD::get_data(datastruct &data, const std::vector<std::string> &species)
|
||||
utils::logmesg(lmp, "number of atoms in all files: {}\n", data.num_atom_sum);
|
||||
}
|
||||
|
||||
if (data.data_files.size() < 1) error->all(FLERR, "Cannot fit potential without data files");
|
||||
if (data.data_files.size() < 1)
|
||||
error->all(FLERR, "Cannot fit potential without data files. The data paths may not be valid. Please check the data paths in the POD data file.");
|
||||
|
||||
int n = data.num_config_sum;
|
||||
memory->create(data.lattice, 9*n, "fitpod:lattice");
|
||||
|
||||
Reference in New Issue
Block a user