Move A.Thomson's modifications on doc and examples in:
- doc/src/.rst - examples/USER/pace - potentials
This commit is contained in:
Yury Lysogorskiy
@ -215,6 +215,7 @@ OPT.
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* :doc:`oxrna2/stk <pair_oxrna2>`
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* :doc:`oxrna2/stk <pair_oxrna2>`
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* :doc:`oxrna2/xstk <pair_oxrna2>`
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* :doc:`oxrna2/xstk <pair_oxrna2>`
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* :doc:`oxrna2/coaxstk <pair_oxrna2>`
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* :doc:`oxrna2/coaxstk <pair_oxrna2>`
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* :doc:`pace <pair_pace>`
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* :doc:`peri/eps <pair_peri>`
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* :doc:`peri/eps <pair_peri>`
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* :doc:`peri/lps (o) <pair_peri>`
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* :doc:`peri/lps (o) <pair_peri>`
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* :doc:`peri/pmb (o) <pair_peri>`
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* :doc:`peri/pmb (o) <pair_peri>`
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@ -90,6 +90,7 @@ page gives those details.
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* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
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* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
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* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
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* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
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* :ref:`USER-OMP <PKG-USER-OMP>`
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* :ref:`USER-OMP <PKG-USER-OMP>`
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* :ref:`USER-PACE <PKG-USER-PACE>`
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* :ref:`USER-PHONON <PKG-USER-PHONON>`
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* :ref:`USER-PHONON <PKG-USER-PHONON>`
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* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
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* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
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* :ref:`USER-PTM <PKG-USER-PTM>`
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* :ref:`USER-PTM <PKG-USER-PTM>`
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@ -1349,6 +1350,42 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
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----------
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----------
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.. _PKG-USER-PACE:
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USER-PACE package
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-------------------
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**Contents:**
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A pair style for the Atomic Cluster Expansion potential (ACE).
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ACE is a methodology for deriving a highly accurate classical potential
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fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
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package provides an efficient implementation for running simulations
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with ACE potentials.
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**Authors:**
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This package was written by Yury Lysogorskiy^1,
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Cas van der Oord^2, Anton Bochkarev^1,
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Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
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Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
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^1: Ruhr-University Bochum, Bochum, Germany
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^2: University of Cambridge, Cambridge, United Kingdom
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^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
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^4: University of British Columbia, Vancouver, BC, Canada
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**Supporting info:**
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* src/USER-PACE: filenames -> commands
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* :doc:`pair_style pace <pair_pace>`
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* examples/USER/pace
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----------
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.. _PKG-USER-PLUMED:
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.. _PKG-USER-PLUMED:
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USER-PLUMED package
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USER-PLUMED package
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114
doc/src/pair_pace.rst
Normal file
114
doc/src/pair_pace.rst
Normal file
@ -0,0 +1,114 @@
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.. index:: pair_style pace
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pair_style pace 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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pair_style pace ... keyword values ...
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* an optional keyword may be appended
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* keyword = *product* or *recursive*
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.. parsed-literal::
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*product* = use product algorithm for basis functions
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*recursive* = use recursive algorithm for basis functions
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style pace
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pair_style pace product
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pair_coeff * * Cu-PBE-core-rep.ace Cu
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Description
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"""""""""""
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Pair style *pace* computes interactions using the Atomic Cluster
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Expansion (ACE), which is a general expansion of the atomic energy in
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multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.
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The *pace* pair style
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provides an efficient implementation that
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is described in this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
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In ACE, the total energy is decomposed into a sum over
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atomic energies. The energy of atom *i* is expressed as a
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linear or non-linear function of one or more density functions.
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By projecting the
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density onto a local atomic base, the lowest order contributions
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to the energy can be expressed as a set of scalar polynomials in
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basis function contributions summed over neighbor atoms.
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Only a single pair_coeff command is used with the *pace* style which
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specifies an ACE coefficient file followed by N additional arguments
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specifying the mapping of ACE elements to LAMMPS atom types,
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where N is the number of LAMMPS atom types:
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* ACE coefficient file
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* N element names = mapping of ACE elements to atom types
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Only a single pair_coeff command is used with the *pace* style which
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specifies an ACE file that fully defines the potential.
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Note that unlike for other potentials, cutoffs are
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not set in the pair_style or pair_coeff command; they are specified in
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the ACE file.
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The pair_style *mliap* may be followed by an optional keyword
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*product* or *recursive*, which determines which of two algorithms
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is used for the calculation of basis functions and derivatives.
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The default is *recursive*.
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See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
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to specify the path for the ACE coefficient file.
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, where types I and J correspond to
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two different element types, mixing is performed by LAMMPS with
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user-specifiable parameters as described above. You never need to
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specify a pair_coeff command with I != J arguments for this style.
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This pair style does not support the :doc:`pair_modify <pair_modify>`
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shift, table, and tail options.
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This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
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need to re-specify the pair_style and pair_coeff commands in an input
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script that reads a restart file.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. It does not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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This pair style is part of the USER-PACE package. It is only enabled if LAMMPS
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was built with that package.
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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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Default
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"""""""
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recursive
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.. _Drautz20191:
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**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
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.. _Lysogorskiy20211:
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**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021).
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1
examples/USER/pace/Cu-PBE-core-rep.ace
Symbolic link
1
examples/USER/pace/Cu-PBE-core-rep.ace
Symbolic link
@ -0,0 +1 @@
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../../../potentials/Cu-PBE-core-rep.ace
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38
examples/USER/pace/in.pace.product
Normal file
38
examples/USER/pace/in.pace.product
Normal file
@ -0,0 +1,38 @@
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# simple test of fcc Cu with ACE product
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units metal
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify every 2 delay 10 check yes
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variable a equal 3.597
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lattice fcc $a
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 26.98
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group Al type 1
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pair_style pace product
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pair_coeff * * Cu-PBE-core-rep.ace Cu
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velocity all create 300 8728 loop geom
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timestep 0.0005
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fix 1 all nve
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compute eatom all pe/atom
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compute energy all reduce sum c_eatom
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variable delenergy equal c_energy-pe
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
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variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
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thermo 10
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thermo_style custom step temp epair etotal press v_delenergy v_delpress
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run 100
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38
examples/USER/pace/in.pace.recursive
Normal file
38
examples/USER/pace/in.pace.recursive
Normal file
@ -0,0 +1,38 @@
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# simple test of fcc Cu with ACE recursive
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units metal
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify every 2 delay 10 check yes
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variable a equal 3.597
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lattice fcc $a
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region box block 0 4 0 4 0 4
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create_box 1 box
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create_atoms 1 box
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mass 1 26.98
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group Al type 1
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pair_style pace recursive
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pair_coeff * * Cu-PBE-core-rep.ace Cu
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velocity all create 300 8728 loop geom
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timestep 0.0005
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fix 1 all nve
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compute eatom all pe/atom
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|
compute energy all reduce sum c_eatom
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variable delenergy equal c_energy-pe
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compute satom all stress/atom NULL
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compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
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|
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
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|
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thermo 10
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thermo_style custom step temp epair etotal press v_delenergy v_delpress
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run 100
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108
examples/USER/pace/log.03Feb2021.pace.product.g++.1
Normal file
108
examples/USER/pace/log.03Feb2021.pace.product.g++.1
Normal file
@ -0,0 +1,108 @@
|
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|
LAMMPS (24 Dec 2020)
|
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|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
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|
using 1 OpenMP thread(s) per MPI task
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|
# simple test of fcc Cu with ACE product
|
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|
|
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|
units metal
|
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|
atom_style atomic
|
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|
|
||||||
|
neighbor 0.3 bin
|
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|
neigh_modify every 2 delay 10 check yes
|
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|
|
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|
variable a equal 3.597
|
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|
lattice fcc $a
|
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|
lattice fcc 3.597
|
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|
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
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|
region box block 0 4 0 4 0 4
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|
create_box 1 box
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|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
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|
1 by 1 by 1 MPI processor grid
|
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|
create_atoms 1 box
|
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|
Created 256 atoms
|
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|
create_atoms CPU = 0.000 seconds
|
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|
|
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|
mass 1 26.98
|
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|
|
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|
group Al type 1
|
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|
256 atoms in group Al
|
||||||
|
|
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|
pair_style pace product
|
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|
ACE version: 2021.2.3
|
||||||
|
Product evaluator is used
|
||||||
|
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||||
|
Loading Cu-PBE-core-rep.ace
|
||||||
|
Total number of basis functions
|
||||||
|
Cu: 16 (r=1) 726 (r>1)
|
||||||
|
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||||
|
|
||||||
|
velocity all create 300 8728 loop geom
|
||||||
|
timestep 0.0005
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute eatom all pe/atom
|
||||||
|
compute energy all reduce sum c_eatom
|
||||||
|
variable delenergy equal c_energy-pe
|
||||||
|
|
||||||
|
compute satom all stress/atom NULL
|
||||||
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||||
|
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7.7
|
||||||
|
ghost atom cutoff = 7.7
|
||||||
|
binsize = 3.85, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair pace, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||||
|
0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11
|
||||||
|
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
|
||||||
|
20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11
|
||||||
|
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||||
|
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
|
||||||
|
50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11
|
||||||
|
60 53.124678 -937.84857 -936.09751 56878.948 0 0
|
||||||
|
70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11
|
||||||
|
80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11
|
||||||
|
90 142.02657 -940.77975 -936.09837 52001.1 0 0
|
||||||
|
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
|
||||||
|
Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms
|
||||||
|
|
||||||
|
Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s
|
||||||
|
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96
|
||||||
|
Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01
|
||||||
|
Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01
|
||||||
|
Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01
|
||||||
|
Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00
|
||||||
|
Other | | 0.000397 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 256 max 256 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2201.00 ave 2201 max 2201 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 43118.0 ave 43118 max 43118 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 43118
|
||||||
|
Ave neighs/atom = 168.42969
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:11
|
||||||
108
examples/USER/pace/log.03Feb2021.pace.product.g++.4
Normal file
108
examples/USER/pace/log.03Feb2021.pace.product.g++.4
Normal file
@ -0,0 +1,108 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple test of fcc Cu with ACE product
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify every 2 delay 10 check yes
|
||||||
|
|
||||||
|
variable a equal 3.597
|
||||||
|
lattice fcc $a
|
||||||
|
lattice fcc 3.597
|
||||||
|
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||||
|
region box block 0 4 0 4 0 4
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 256 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 26.98
|
||||||
|
|
||||||
|
group Al type 1
|
||||||
|
256 atoms in group Al
|
||||||
|
|
||||||
|
pair_style pace product
|
||||||
|
ACE version: 2021.2.3
|
||||||
|
Product evaluator is used
|
||||||
|
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||||
|
Loading Cu-PBE-core-rep.ace
|
||||||
|
Total number of basis functions
|
||||||
|
Cu: 16 (r=1) 726 (r>1)
|
||||||
|
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||||
|
|
||||||
|
velocity all create 300 8728 loop geom
|
||||||
|
timestep 0.0005
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute eatom all pe/atom
|
||||||
|
compute energy all reduce sum c_eatom
|
||||||
|
variable delenergy equal c_energy-pe
|
||||||
|
|
||||||
|
compute satom all stress/atom NULL
|
||||||
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||||
|
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7.7
|
||||||
|
ghost atom cutoff = 7.7
|
||||||
|
binsize = 3.85, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair pace, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||||
|
0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11
|
||||||
|
10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11
|
||||||
|
20 228.73618 -943.63789 -936.09844 48903.598 0 0
|
||||||
|
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||||
|
40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11
|
||||||
|
50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11
|
||||||
|
60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12
|
||||||
|
70 74.623347 -938.5575 -936.09782 55565.237 0 0
|
||||||
|
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
|
||||||
|
90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11
|
||||||
|
100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11
|
||||||
|
Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms
|
||||||
|
|
||||||
|
Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s
|
||||||
|
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30
|
||||||
|
Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01
|
||||||
|
Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63
|
||||||
|
Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03
|
||||||
|
Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01
|
||||||
|
Other | | 0.0005298 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 64.0000 ave 71 max 57 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Nghost: 1373.00 ave 1380 max 1366 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 10779.5 ave 11978 max 9604 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 43118
|
||||||
|
Ave neighs/atom = 168.42969
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:03
|
||||||
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.1
Normal file
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.1
Normal file
@ -0,0 +1,108 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple test of fcc Cu with ACE recursive
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify every 2 delay 10 check yes
|
||||||
|
|
||||||
|
variable a equal 3.597
|
||||||
|
lattice fcc $a
|
||||||
|
lattice fcc 3.597
|
||||||
|
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||||
|
region box block 0 4 0 4 0 4
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 256 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 26.98
|
||||||
|
|
||||||
|
group Al type 1
|
||||||
|
256 atoms in group Al
|
||||||
|
|
||||||
|
pair_style pace recursive
|
||||||
|
ACE version: 2021.2.3
|
||||||
|
Recursive evaluator is used
|
||||||
|
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||||
|
Loading Cu-PBE-core-rep.ace
|
||||||
|
Total number of basis functions
|
||||||
|
Cu: 16 (r=1) 726 (r>1)
|
||||||
|
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||||
|
|
||||||
|
velocity all create 300 8728 loop geom
|
||||||
|
timestep 0.0005
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute eatom all pe/atom
|
||||||
|
compute energy all reduce sum c_eatom
|
||||||
|
variable delenergy equal c_energy-pe
|
||||||
|
|
||||||
|
compute satom all stress/atom NULL
|
||||||
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||||
|
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7.7
|
||||||
|
ghost atom cutoff = 7.7
|
||||||
|
binsize = 3.85, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair pace, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||||
|
0 300 -945.9873 -936.0989 45359.818 0 0
|
||||||
|
10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11
|
||||||
|
20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11
|
||||||
|
30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11
|
||||||
|
40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11
|
||||||
|
50 59.165961 -938.04759 -936.0974 56850.103 0 0
|
||||||
|
60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11
|
||||||
|
70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11
|
||||||
|
80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11
|
||||||
|
90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11
|
||||||
|
100 161.73598 -941.42945 -936.09842 51114.997 0 0
|
||||||
|
Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms
|
||||||
|
|
||||||
|
Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s
|
||||||
|
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96
|
||||||
|
Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01
|
||||||
|
Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01
|
||||||
|
Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01
|
||||||
|
Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01
|
||||||
|
Other | | 0.000363 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 256 max 256 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2201.00 ave 2201 max 2201 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 43118.0 ave 43118 max 43118 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 43118
|
||||||
|
Ave neighs/atom = 168.42969
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:09
|
||||||
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.4
Normal file
108
examples/USER/pace/log.03Feb2021.pace.recursive.g++.4
Normal file
@ -0,0 +1,108 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple test of fcc Cu with ACE recursive
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style atomic
|
||||||
|
|
||||||
|
neighbor 0.3 bin
|
||||||
|
neigh_modify every 2 delay 10 check yes
|
||||||
|
|
||||||
|
variable a equal 3.597
|
||||||
|
lattice fcc $a
|
||||||
|
lattice fcc 3.597
|
||||||
|
Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
|
||||||
|
region box block 0 4 0 4 0 4
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 256 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
mass 1 26.98
|
||||||
|
|
||||||
|
group Al type 1
|
||||||
|
256 atoms in group Al
|
||||||
|
|
||||||
|
pair_style pace recursive
|
||||||
|
ACE version: 2021.2.3
|
||||||
|
Recursive evaluator is used
|
||||||
|
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||||
|
Loading Cu-PBE-core-rep.ace
|
||||||
|
Total number of basis functions
|
||||||
|
Cu: 16 (r=1) 726 (r>1)
|
||||||
|
Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
|
||||||
|
|
||||||
|
velocity all create 300 8728 loop geom
|
||||||
|
timestep 0.0005
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
compute eatom all pe/atom
|
||||||
|
compute energy all reduce sum c_eatom
|
||||||
|
variable delenergy equal c_energy-pe
|
||||||
|
|
||||||
|
compute satom all stress/atom NULL
|
||||||
|
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||||
|
variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
thermo_style custom step temp epair etotal press v_delenergy v_delpress
|
||||||
|
|
||||||
|
run 100
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 2 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 7.7
|
||||||
|
ghost atom cutoff = 7.7
|
||||||
|
binsize = 3.85, bins = 4 4 4
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair pace, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin/atomonly
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press v_delenergy v_delpress
|
||||||
|
0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11
|
||||||
|
10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11
|
||||||
|
20 228.73618 -943.63789 -936.09844 48903.598 0 0
|
||||||
|
30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11
|
||||||
|
40 97.732944 -939.31899 -936.09758 55176.875 0 0
|
||||||
|
50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11
|
||||||
|
60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11
|
||||||
|
70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11
|
||||||
|
80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12
|
||||||
|
90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11
|
||||||
|
100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12
|
||||||
|
Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms
|
||||||
|
|
||||||
|
Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s
|
||||||
|
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46
|
||||||
|
Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01
|
||||||
|
Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45
|
||||||
|
Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04
|
||||||
|
Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01
|
||||||
|
Other | | 0.0005595 | | | 0.02
|
||||||
|
|
||||||
|
Nlocal: 64.0000 ave 71 max 57 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Nghost: 1373.00 ave 1380 max 1366 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 10779.5 ave 11978 max 9604 min
|
||||||
|
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 43118
|
||||||
|
Ave neighs/atom = 168.42969
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:03
|
||||||
8980
potentials/Cu-PBE-core-rep.ace
Normal file
8980
potentials/Cu-PBE-core-rep.ace
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user