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.
|
||||
* :doc:`oxrna2/stk <pair_oxrna2>`
|
||||
* :doc:`oxrna2/xstk <pair_oxrna2>`
|
||||
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
|
||||
* :doc:`pace <pair_pace>`
|
||||
* :doc:`peri/eps <pair_peri>`
|
||||
* :doc:`peri/lps (o) <pair_peri>`
|
||||
* :doc:`peri/pmb (o) <pair_peri>`
|
||||
|
||||
@ -90,6 +90,7 @@ page gives those details.
|
||||
* :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
|
||||
* :ref:`USER-NETCDF <PKG-USER-NETCDF>`
|
||||
* :ref:`USER-OMP <PKG-USER-OMP>`
|
||||
* :ref:`USER-PACE <PKG-USER-PACE>`
|
||||
* :ref:`USER-PHONON <PKG-USER-PHONON>`
|
||||
* :ref:`USER-PLUMED <PKG-USER-PLUMED>`
|
||||
* :ref:`USER-PTM <PKG-USER-PTM>`
|
||||
@ -1349,6 +1350,42 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-USER-PACE:
|
||||
|
||||
USER-PACE package
|
||||
-------------------
|
||||
|
||||
**Contents:**
|
||||
|
||||
A pair style for the Atomic Cluster Expansion potential (ACE).
|
||||
ACE is a methodology for deriving a highly accurate classical potential
|
||||
fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
|
||||
package provides an efficient implementation for running simulations
|
||||
with ACE potentials.
|
||||
|
||||
**Authors:**
|
||||
|
||||
This package was written by Yury Lysogorskiy^1,
|
||||
Cas van der Oord^2, Anton Bochkarev^1,
|
||||
Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
|
||||
Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
|
||||
|
||||
^1: Ruhr-University Bochum, Bochum, Germany
|
||||
|
||||
^2: University of Cambridge, Cambridge, United Kingdom
|
||||
|
||||
^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
|
||||
|
||||
^4: University of British Columbia, Vancouver, BC, Canada
|
||||
|
||||
**Supporting info:**
|
||||
|
||||
* src/USER-PACE: filenames -> commands
|
||||
* :doc:`pair_style pace <pair_pace>`
|
||||
* examples/USER/pace
|
||||
|
||||
----------
|
||||
|
||||
.. _PKG-USER-PLUMED:
|
||||
|
||||
USER-PLUMED package
|
||||
|
||||
114
doc/src/pair_pace.rst
Normal file
114
doc/src/pair_pace.rst
Normal file
@ -0,0 +1,114 @@
|
||||
.. index:: pair_style pace
|
||||
|
||||
pair_style pace command
|
||||
========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style pace ... keyword values ...
|
||||
|
||||
* an optional keyword may be appended
|
||||
* keyword = *product* or *recursive*
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*product* = use product algorithm for basis functions
|
||||
*recursive* = use recursive algorithm for basis functions
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style pace
|
||||
pair_style pace product
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
Pair style *pace* computes interactions using the Atomic Cluster
|
||||
Expansion (ACE), which is a general expansion of the atomic energy in
|
||||
multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.
|
||||
The *pace* pair style
|
||||
provides an efficient implementation that
|
||||
is described in this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
|
||||
|
||||
In ACE, the total energy is decomposed into a sum over
|
||||
atomic energies. The energy of atom *i* is expressed as a
|
||||
linear or non-linear function of one or more density functions.
|
||||
By projecting the
|
||||
density onto a local atomic base, the lowest order contributions
|
||||
to the energy can be expressed as a set of scalar polynomials in
|
||||
basis function contributions summed over neighbor atoms.
|
||||
|
||||
Only a single pair_coeff command is used with the *pace* style which
|
||||
specifies an ACE coefficient file followed by N additional arguments
|
||||
specifying the mapping of ACE elements to LAMMPS atom types,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
* ACE coefficient file
|
||||
* N element names = mapping of ACE elements to atom types
|
||||
|
||||
Only a single pair_coeff command is used with the *pace* style which
|
||||
specifies an ACE file that fully defines the potential.
|
||||
Note that unlike for other potentials, cutoffs are
|
||||
not set in the pair_style or pair_coeff command; they are specified in
|
||||
the ACE file.
|
||||
|
||||
The pair_style *mliap* may be followed by an optional keyword
|
||||
*product* or *recursive*, which determines which of two algorithms
|
||||
is used for the calculation of basis functions and derivatives.
|
||||
The default is *recursive*.
|
||||
|
||||
See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
|
||||
to specify the path for the ACE coefficient file.
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
For atom type pairs I,J and I != J, where types I and J correspond to
|
||||
two different element types, mixing is performed by LAMMPS with
|
||||
user-specifiable parameters as described above. You never need to
|
||||
specify a pair_coeff command with I != J arguments for this style.
|
||||
|
||||
This pair style does not support the :doc:`pair_modify <pair_modify>`
|
||||
shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the *pair* keyword of the
|
||||
:doc:`run_style respa <run_style>` command. It does not support the
|
||||
*inner*\ , *middle*\ , *outer* keywords.
|
||||
|
||||
----------
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
This pair style is part of the USER-PACE package. It is only enabled if LAMMPS
|
||||
was built with that package.
|
||||
See the :doc:`Build package <Build_package>` doc page for more info.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`pair_style snap <pair_snap>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
recursive
|
||||
|
||||
.. _Drautz20191:
|
||||
|
||||
**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
|
||||
|
||||
.. _Lysogorskiy20211:
|
||||
|
||||
**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021).
|
||||
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 @@
|
||||
../../../potentials/Cu-PBE-core-rep.ace
|
||||
38
examples/USER/pace/in.pace.product
Normal file
38
examples/USER/pace/in.pace.product
Normal file
@ -0,0 +1,38 @@
|
||||
# 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
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
|
||||
pair_style pace product
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
|
||||
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
|
||||
|
||||
38
examples/USER/pace/in.pace.recursive
Normal file
38
examples/USER/pace/in.pace.recursive
Normal file
@ -0,0 +1,38 @@
|
||||
# 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
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
group Al type 1
|
||||
|
||||
pair_style pace recursive
|
||||
pair_coeff * * Cu-PBE-core-rep.ace Cu
|
||||
|
||||
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
|
||||
|
||||
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 @@
|
||||
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 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 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) = 4.036 | 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