mirror of https://github.com/lammps/lammps.git
Added doc page for compute mliap and updated examples
This commit is contained in:
Aidan Thompson
parent
28bbb6afbc
commit
9d0aee7426
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@ -1,21 +1,36 @@
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.. index:: compute mliap
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compute mliap command
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====================
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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 mliap
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compute ID group-ID mliap ... keyword values ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* mliap = style name of this compute command
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* two keyword/value pairs must be appended
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* keyword = *model* or *descriptor*
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.. parsed-literal::
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*model* values = style Nelems Nparams
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style = *linear* or *quadratic*
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Nelems = number of elements
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Nparams = number of parameters per element
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*descriptor* values = style filename
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style = *sna*
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filename = name of file containing descriptor definitions
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute mliap model linear nelems nparams descriptor sna InP.mliap.descriptor
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compute mliap model linear 2 31 descriptor sna Ta06A.mliap.descriptor
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Description
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"""""""""""
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@ -24,7 +39,7 @@ Compute style *mliap* provides a general interface to the gradient
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of machine-learning interatomic potentials w.r.t. model parameters.
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It is used primarily for calculating the gradient of energy, force, and
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stress components w.r.t. model parameters, which is useful when training
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:doc:`MLIAP pair_style <pair_mliap>` to match target data.
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:doc:`mliap pair_style <pair_mliap>` models to match target data.
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It provides separate
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definitions of the interatomic potential functional form (*model*)
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and the geometric quantities that characterize the atomic positions
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@ -46,7 +61,7 @@ either *linear* or *quadratic*. In both cases,
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this is followed by two arguments. *nelems* is the number of elements.
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It must be equal to the number of LAMMPS atom types. *nparams*
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is the number of parameters per element for this model i.e.
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the number of paramter gradients for each element. Note these definitions
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the number of parameter gradients for each element. Note these definitions
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are identical to those of *nelems* and *nparams* in the
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:doc:`pair_style mliap <pair_mliap>` model file.
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@ -58,43 +73,44 @@ The \'p\' in SNAP is dropped, because keywords that match pair_styles are silent
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out by the LAMMPS command parser. A single additional argument specifies the descriptor filename
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containing the parameters and setting used by the SNAP descriptor.
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The descriptor filename usually ends in the *.mliap.descriptor* extension.
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The format of this file is identical to descriptor file in the
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The format of this file is identical to the descriptor file in the
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:doc:`pair_style mliap <pair_mliap>`, and is described in detail
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there.
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.. note::
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The number of LAMMPS atom types (and the value of *nelems* in the model)
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must match the value of *nelems* in the descriptor file.
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The number of LAMMPS atom types (and the value of *nelems* in the model)
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must match the value of *nelems* in the descriptor file.
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Compute *mliap* calculates a global array containing gradient information.
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The number of columns in the array is the :math:`nelems \times nparams + 1`.
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The first row of the array contain the derivative of potential energy w.r.t to
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The number of columns in the array is :math:`nelems \times nparams + 1`.
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The first row of the array contain the derivative of potential energy w.r.t. to
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each parameter and each element. The last six rows
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of the array contain the corresponding derivatives of the
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virial stress tensor, listed in Voigt notation: *pxx*, *pyy*, *pzz*,
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*pyz*, *pxz*, *pxy*. In between 3\*\ *N* rows containing the derivatives
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of the force components.
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*pyz*, *pxz*, *pxy*. In between the energy and stress rows are
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the 3\*\ *N* rows containing the derivatives of the force components.
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See section below on output for a detailed description of how
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rows and columns are ordered.
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The element in the last column of each row contains
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the potential energy, force, or stress, according to the row.
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These quantities correspond to the user-specified reference potential
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that must be subtracted from the target data when fitting SNAP.
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that must be subtracted from the target data when training a model.
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The potential energy calculation uses the built in compute *thermo_pe*.
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The stress calculation uses a compute called *snap_press* that is
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The stress calculation uses a compute called *mliap_press* that is
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automatically created behind the scenes, according to the following
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command:
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.. code-block:: LAMMPS
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compute snap_press all pressure NULL virial
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compute mliap_press all pressure NULL virial
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See section below on output for a detailed explanation of the data
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layout in the global array.
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Atoms not in the group do not contribute to this compute.
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Neighbor atoms not in the group do not contribute to this compute.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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@ -102,17 +118,19 @@ too frequently.
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.. note::
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If you have a bonded system, then the settings of
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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If the user-specified reference potentials includes bonded and
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non-bonded pairwise interactions, then the settings of
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the :doc:`special_bonds <special_bonds>`
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the calculation. One way to get
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around this, is to write a dump file, and use the :doc:`rerun <rerun>`
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command to compute the bispectrum components for snapshots in the dump
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file. The rerun script can use a :doc:`special_bonds <special_bonds>`
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command that includes all pairs in the neighbor list.
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those pairs will not be included in the calculation. The :doc:`rerun <rerun>`
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command is not an option here, since the reference potential is required
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for the last column of the global array. A work-around is to prevent
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pairwise interactions from being removed by explicitly adding a
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*tiny* positive value for every pairwise interaction that would otherwise be
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set to zero in the :doc:`special_bonds <special_bonds>` command.
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----------
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@ -127,15 +145,14 @@ on an atom, or virial stress component. The rows of the array appear
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in the following order:
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* 1 row: Derivatives of potential energy w.r.t. each parameter of each element.
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* 3\*\ *N* rows: Derivatives of force components. x, y, and z components of
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force on atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
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* 6 rows: Derivatives of virial stress tensor w.r.t. each parameter of each element.
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The ordering of the rows follows Voigt notation: *pxx*, *pyy*, *pzz*,
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*pyz*, *pxz*, *pxy*.
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* 3\*\ *N* rows: Derivatives of force components. x, y, and z components of force on atom *i* appearing in consecutive rows. The atoms are sorted based on atom ID.
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* 6 rows: Derivatives of virial stress tensor w.r.t. each parameter of each element. The ordering of the rows follows Voigt notation: *pxx*, *pyy*, *pzz*, *pyz*, *pxz*, *pxy*.
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These values can be accessed by any command that uses per-atom values
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These values can be accessed by any command that uses a global array
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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page for an overview of LAMMPS output options. To see how this command
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can be used within a Python workflow to train machine-learning interatomic
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potentials, see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
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Restrictions
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""""""""""""
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@ -144,11 +161,10 @@ This compute is part of the MLIAP package. It is only enabled if
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LAMMPS was built with that package. In addition, building LAMMPS with the MLIAP package
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requires building LAMMPS with the SNAP package.
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See the :doc:`Build package <Build_package>` doc page for more info.
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doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_style snap <pair_mliap>`
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:doc:`pair_style mliap <pair_mliap>`
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**Default:** none
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@ -391,7 +391,9 @@ of :math:`K N_{elem}^3` columns.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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page for an overview of LAMMPS output options. To see how this command
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can be used within a Python workflow to train SNAP potentials,
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see the examples in `FitSNAP <https://github.com/FitSNAP/FitSNAP>`_.
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Restrictions
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""""""""""""
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@ -8,7 +8,19 @@ Syntax
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.. code-block:: LAMMPS
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pair_style mliap
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pair_style mliap ... keyword values ...
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* two keyword/value pairs must be appended
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* keyword = *model* or *descriptor*
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.. parsed-literal::
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*model* values = style filename
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style = *linear* or *quadratic*
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filename = name of file containing model definitions
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*descriptor* values = style filename
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style = *sna*
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filename = name of file containing descriptor definitions
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Examples
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""""""""
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@ -23,7 +35,7 @@ Description
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"""""""""""
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Pair style *mliap* provides a general interface to families of
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machine-learning interatomic potentials. It provides separate
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machine-learning interatomic potentials. It allows separate
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definitions of the interatomic potential functional form (*model*)
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and the geometric quantities that characterize the atomic positions
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(*descriptor*). By defining *model* and *descriptor* separately,
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@ -34,6 +46,9 @@ and one descriptor, *sna*, the SNAP descriptor used by :doc:`pair_style snap <pa
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and chem variants. Work is currently underway to extend
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the interface to handle neural network energy models,
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and it is also straightforward to add new descriptor styles.
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In order to train a model, it is useful to know the gradient or derivative
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of energy, force, and stress w.r.t. model parameters. This information
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can be accessed using the related :doc:`compute mliap <compute_mliap>` command.
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The pair_style *mliap* command must be followed by two keywords
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*model* and *descriptor* in either order. A single
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@ -131,6 +146,6 @@ See the :doc:`Build package <Build_package>` doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`pair_style snap <pair_snap>`,
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:doc:`pair_style snap <pair_snap>`, :doc:`compute mliap <compute_mliap>`
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**Default:** none
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@ -0,0 +1,199 @@
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LAMMPS (15 Jun 2020)
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# Demonstrate MLIAP quadratic compute
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# initialize simulation
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variable nsteps index 0
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variable nrep equal 1
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variable a equal 2.0
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable nx equal 1
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variable ny equal ${nrep}
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variable ny equal 1
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variable nz equal ${nrep}
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variable nz equal 1
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boundary p p p
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atom_modify map hash
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lattice bcc $a
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lattice bcc 2
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Lattice spacing in x,y,z = 2 2 2
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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region box block 0 1 0 ${ny} 0 ${nz}
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region box block 0 1 0 1 0 ${nz}
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region box block 0 1 0 1 0 1
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create_box 2 box
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Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
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1 by 1 by 1 MPI processor grid
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create_atoms 2 box
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Created 2 atoms
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create_atoms CPU = 0.000 seconds
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mass * 180.88
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displace_atoms all random 0.1 0.1 0.1 123456
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# set up reference potential
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variable zblcutinner equal 4
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variable zblcutouter equal 4.8
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variable zblz equal 73
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pair_style zbl ${zblcutinner} ${zblcutouter}
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pair_style zbl 4 ${zblcutouter}
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pair_style zbl 4 4.8
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pair_coeff * * ${zblz} ${zblz}
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pair_coeff * * 73 ${zblz}
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pair_coeff * * 73 73
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# choose SNA parameters
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variable twojmax equal 2
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variable rcutfac equal 1.0
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable radelem1 equal 2.3
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variable radelem2 equal 2.0
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variable wj1 equal 1.0
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variable wj2 equal 0.96
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variable quadratic equal 1
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variable bzero equal 0
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variable switch equal 0
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variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
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1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
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1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# set up per-atom computes
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compute b all sna/atom ${snap_options}
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compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute vb all snav/atom ${snap_options}
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compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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compute db all snad/atom ${snap_options}
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compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
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# perform sums over atoms
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group snapgroup1 type 1
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0 atoms in group snapgroup1
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group snapgroup2 type 2
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2 atoms in group snapgroup2
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compute bsum1 snapgroup1 reduce sum c_b[*]
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compute bsum2 snapgroup2 reduce sum c_b[*]
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# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
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# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
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compute vbsum all reduce sum c_vb[*]
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# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
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variable db_2_100 equal c_db[2][100]
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# set up compute snap generating global array
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compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
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SNAP keyword rcutfac 1.0
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SNAP keyword twojmax 2
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SNAP keyword nelems 2
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SNAP keyword elems A
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SNAP keyword radelems 2.3
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SNAP keyword welems 1.0
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SNAP keyword rfac0 0.99363
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SNAP keyword rmin0 0
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SNAP keyword bzeroflag 0
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SNAP keyword switchflag 0
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fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
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thermo 100
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# test output: 1: total potential energy
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# 2: xy component of stress tensor
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# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
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# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
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# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
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#
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# followed by 5 counterparts from compute snap
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thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
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thermo_modify norm no
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# dump mydump_db all custom 1000 dump_db id c_db[*]
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# dump_modify mydump_db sort id
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# Run MD
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run ${nsteps}
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run 0
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6.8
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ghost atom cutoff = 6.8
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binsize = 3.4, bins = 1 1 1
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5 neighbor lists, perpetual/occasional/extra = 1 4 0
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(1) pair zbl, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) compute sna/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(3) compute snav/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(4) compute snad/atom, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(5) compute mliap, occasional
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.45 | 22.45 | 22.45 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,200 @@
|
|||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate MLIAP quadratic compute
|
||||
|
||||
# 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 nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2 2 2
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 1
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 1 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_100 equal c_db[2][100]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model quadratic 2 21
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.quadratic.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.18 | 22.18 | 22.18 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][43] c_snap[13][43] c_snap[1][42] c_snap[12][42] c_snap[6][42]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 2e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 734.5 ave 735 max 734 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 82.5 ave 177 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
FullNghs: 165 ave 330 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,199 @@
|
|||
LAMMPS (15 Jun 2020)
|
||||
# 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 nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2 2 2
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 0
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.73 | 10.73 | 10.73 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 0 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
0.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0 | | | 0.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 853 ave 853 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 330 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 660 ave 660 max 660 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,200 @@
|
|||
LAMMPS (15 Jun 2020)
|
||||
# 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 nx equal 1
|
||||
variable ny equal ${nrep}
|
||||
variable ny equal 1
|
||||
variable nz equal ${nrep}
|
||||
variable nz equal 1
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_modify map hash
|
||||
lattice bcc $a
|
||||
lattice bcc 2
|
||||
Lattice spacing in x,y,z = 2 2 2
|
||||
region box block 0 ${nx} 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 ${ny} 0 ${nz}
|
||||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 123456
|
||||
|
||||
# set up reference potential
|
||||
|
||||
variable zblcutinner equal 4
|
||||
variable zblcutouter equal 4.8
|
||||
variable zblz equal 73
|
||||
pair_style zbl ${zblcutinner} ${zblcutouter}
|
||||
pair_style zbl 4 ${zblcutouter}
|
||||
pair_style zbl 4 4.8
|
||||
pair_coeff * * ${zblz} ${zblz}
|
||||
pair_coeff * * 73 ${zblz}
|
||||
pair_coeff * * 73 73
|
||||
|
||||
# choose SNA parameters
|
||||
|
||||
variable twojmax equal 2
|
||||
variable rcutfac equal 1.0
|
||||
variable rfac0 equal 0.99363
|
||||
variable rmin0 equal 0
|
||||
variable radelem1 equal 2.3
|
||||
variable radelem2 equal 2.0
|
||||
variable wj1 equal 1.0
|
||||
variable wj2 equal 0.96
|
||||
variable quadratic equal 0
|
||||
variable bzero equal 0
|
||||
variable switch equal 0
|
||||
variable snap_options string "${rcutfac} ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}"
|
||||
1 ${rfac0} ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 ${twojmax} ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 ${radelem1} ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 ${radelem2} ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 ${wj1} ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 ${wj2} rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 ${rmin0} quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag ${quadratic} bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag ${bzero} switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag ${switch}
|
||||
1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# set up per-atom computes
|
||||
|
||||
compute b all sna/atom ${snap_options}
|
||||
compute b all sna/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute vb all snav/atom ${snap_options}
|
||||
compute vb all snav/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
compute db all snad/atom ${snap_options}
|
||||
compute db all snad/atom 1 0.99363 2 2.3 2 1 0.96 rmin0 0 quadraticflag 0 bzeroflag 0 switchflag 0
|
||||
|
||||
# perform sums over atoms
|
||||
|
||||
group snapgroup1 type 1
|
||||
0 atoms in group snapgroup1
|
||||
group snapgroup2 type 2
|
||||
2 atoms in group snapgroup2
|
||||
compute bsum1 snapgroup1 reduce sum c_b[*]
|
||||
compute bsum2 snapgroup2 reduce sum c_b[*]
|
||||
# fix bsum1 all ave/time 1 1 1 c_bsum1 file bsum1.dat mode vector
|
||||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
compute snap all mliap descriptor sna compute.mliap.descriptor model linear 2 6
|
||||
SNAP keyword rcutfac 1.0
|
||||
SNAP keyword twojmax 2
|
||||
SNAP keyword nelems 2
|
||||
SNAP keyword elems A
|
||||
SNAP keyword radelems 2.3
|
||||
SNAP keyword welems 1.0
|
||||
SNAP keyword rfac0 0.99363
|
||||
SNAP keyword rmin0 0
|
||||
SNAP keyword bzeroflag 0
|
||||
SNAP keyword switchflag 0
|
||||
fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
||||
|
||||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
# dump_modify mydump_db sort id
|
||||
|
||||
# Run MD
|
||||
|
||||
run ${nsteps}
|
||||
run 0
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.8
|
||||
ghost atom cutoff = 6.8
|
||||
binsize = 3.4, bins = 1 1 1
|
||||
5 neighbor lists, perpetual/occasional/extra = 1 4 0
|
||||
(1) pair zbl, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute sna/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(3) compute snav/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(4) compute snad/atom, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(5) compute mliap, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.69 | 10.69 | 10.7 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][13] c_snap[13][13] c_snap[1][8] c_snap[12][12] c_snap[6][12]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 3.25e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
115.4% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 3.25e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 734.5 ave 735 max 734 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 82.5 ave 177 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
FullNghs: 165 ave 330 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 660
|
||||
Ave neighs/atom = 330
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -80,9 +80,9 @@ fix snap all ave/time 1 1 1 c_snap[*] file compute.snap.dat mode vector
|
|||
thermo 100
|
||||
|
||||
# test output: 1: total potential energy
|
||||
# 2: xz component of stress tensor
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
|
|
|||
|
|
@ -1,6 +1,4 @@
|
|||
LAMMPS (20 Nov 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
|
@ -30,11 +28,11 @@ region box block 0 1 0 ${ny} 0 ${nz}
|
|||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.000478029 secs
|
||||
create_atoms CPU = 0.000 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
|
|
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
|
|||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_30 equal c_db[2][30]
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
|
|
@ -118,12 +116,12 @@ thermo 100
|
|||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
|
|
@ -166,11 +164,11 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.06 | 10.06 | 10.06 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||
322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
|
||||
Loop time of 9.53674e-07 on 1 procs for 0 steps with 2 atoms
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
104.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
200.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
|
|
@ -180,7 +178,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 9.537e-07 | | |100.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,6 +1,4 @@
|
|||
LAMMPS (20 Nov 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
|
@ -30,11 +28,11 @@ region box block 0 1 0 ${ny} 0 ${nz}
|
|||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.000610113 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
|
|
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
|
|||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_30 equal c_db[2][30]
|
||||
variable db_2_25 equal c_db[2][25]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
|
|
@ -118,12 +116,12 @@ thermo 100
|
|||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(B_{000}^i, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: z component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*dB_{222}^i/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(B_{222}^i)/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||
thermo_style custom pe pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
|
|
@ -165,13 +163,13 @@ Neighbor list info ...
|
|||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.211 | 8.254 | 8.295 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[60] v_db_2_30 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[13][10] c_snap[7][10]
|
||||
322.86952 1505558.1 364182.88 381.32218 -855.04473 322.86952 1505558.1 364182.88 381.32218 -855.04473
|
||||
Loop time of 2.38419e-06 on 4 procs for 0 steps with 2 atoms
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.945 | 9.988 | 10.03 Mbytes
|
||||
PotEng Pxy c_bsum2[1] c_vbsum[55] v_db_2_25 c_snap[1][11] c_snap[13][11] c_snap[1][6] c_snap[12][10] c_snap[6][10]
|
||||
322.86952 1505558.1 364182.88 -240.25066 1381.7961 322.86952 1505558.1 364182.88 -240.25066 1381.7961
|
||||
Loop time of 2.75e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
104.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
90.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
|
|
@ -181,7 +179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.384e-06 | | |100.00
|
||||
Other | | 2.75e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
|
@ -1,6 +1,4 @@
|
|||
LAMMPS (20 Nov 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
|
@ -30,11 +28,11 @@ region box block 0 1 0 ${ny} 0 ${nz}
|
|||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.000473976 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
|
|
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
|
|||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_120 equal c_db[2][120]
|
||||
variable db_2_100 equal c_db[2][100]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
|
|
@ -118,12 +116,12 @@ thermo 100
|
|||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
|
|
@ -166,11 +164,11 @@ Neighbor list info ...
|
|||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.78 | 21.78 | 21.78 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
|
||||
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 2 atoms
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 1e-06 on 1 procs for 0 steps with 2 atoms
|
||||
|
||||
93.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
200.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
|
|
@ -180,7 +178,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.146e-06 | | |100.00
|
||||
Other | | 1e-06 | | |100.00
|
||||
|
||||
Nlocal: 2 ave 2 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
|
@ -1,6 +1,4 @@
|
|||
LAMMPS (20 Nov 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:93)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
LAMMPS (15 Jun 2020)
|
||||
# Demonstrate bispectrum computes
|
||||
|
||||
# initialize simulation
|
||||
|
|
@ -30,11 +28,11 @@ region box block 0 1 0 ${ny} 0 ${nz}
|
|||
region box block 0 1 0 1 0 ${nz}
|
||||
region box block 0 1 0 1 0 1
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 0) to (2 2 2)
|
||||
Created orthogonal box = (0.0 0.0 0.0) to (2.0 2.0 2.0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 2 box
|
||||
Created 2 atoms
|
||||
create_atoms CPU = 0.000118971 secs
|
||||
create_atoms CPU = 0.001 seconds
|
||||
|
||||
mass * 180.88
|
||||
|
||||
|
|
@ -105,7 +103,7 @@ compute bsum2 snapgroup2 reduce sum c_b[*]
|
|||
# fix bsum2 all ave/time 1 1 1 c_bsum2 file bsum2.dat mode vector
|
||||
compute vbsum all reduce sum c_vb[*]
|
||||
# fix vbsum all ave/time 1 1 1 c_vbsum file vbsum.dat mode vector
|
||||
variable db_2_120 equal c_db[2][120]
|
||||
variable db_2_100 equal c_db[2][100]
|
||||
|
||||
# set up compute snap generating global array
|
||||
|
||||
|
|
@ -118,12 +116,12 @@ thermo 100
|
|||
# test output: 1: total potential energy
|
||||
# 2: xy component of stress tensor
|
||||
# 3: Sum(0.5*(B_{222}^i)^2, all i of type 2)
|
||||
# 4: xy component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: z component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
# 4: xz component of Sum(Sum(r_j*(0.5*(dB_{222}^i)^2/dR[j]), all i of type 2), all j)
|
||||
# 5: y component of -Sum(d(0.5*(B_{222}^i)^2/dR[2]), all i of type 2)
|
||||
#
|
||||
# followed by 5 counterparts from compute snap
|
||||
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
|
||||
thermo_style custom pe pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
|
||||
thermo_modify norm no
|
||||
|
||||
# dump mydump_db all custom 1000 dump_db id c_db[*]
|
||||
|
|
@ -165,13 +163,13 @@ Neighbor list info ...
|
|||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:936)
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.7 | 19.74 | 19.78 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[240] v_db_2_120 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[13][40] c_snap[7][40]
|
||||
322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699 322.86952 1505558.1 4.2492771e+08 7860489.6 -17625699
|
||||
Loop time of 2.80142e-06 on 4 procs for 0 steps with 2 atoms
|
||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:964)
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.43 | 21.47 | 21.52 Mbytes
|
||||
PotEng Pxy c_bsum2[20] c_vbsum[220] v_db_2_100 c_snap[1][41] c_snap[13][41] c_snap[1][40] c_snap[12][40] c_snap[6][40]
|
||||
322.86952 1505558.1 4.2492771e+08 -4952473 28484035 322.86952 1505558.1 4.2492771e+08 -4952473 28484035
|
||||
Loop time of 2.25e-06 on 4 procs for 0 steps with 2 atoms
|
||||
|
||||
107.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
111.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
|
|
@ -181,7 +179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 2.801e-06 | | |100.00
|
||||
Other | | 2.25e-06 | | |100.00
|
||||
|
||||
Nlocal: 0.5 ave 1 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Loading…
Reference in New Issue