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Merge branch 'master' into collected-small-changes

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This commit is contained in:
Richard Berger
2020-11-29 12:26:30 -05:00
parent 62f5f3a3b8 a5858e350c
commit bddbc516b5
38 changed files with 2528 additions and 443 deletions
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31
cmake/Modules/Packages/KIM.cmake
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@ -34,8 +34,8 @@ if(DOWNLOAD_KIM)
enable_language(C) enable_language(C)
enable_language(Fortran) enable_language(Fortran)
ExternalProject_Add(kim_build ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz URL https://s3.openkim.org/kim-api/kim-api-2.2.0.txz
URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8 URL_MD5 e7f944e1593cffd7444679a660607f6c
BINARY_DIR build BINARY_DIR build
CMAKE_ARGS ${CMAKE_REQUEST_PIC} CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@ -53,11 +53,28 @@ if(DOWNLOAD_KIM)
add_library(LAMMPS::KIM UNKNOWN IMPORTED) add_library(LAMMPS::KIM UNKNOWN IMPORTED)
set_target_properties(LAMMPS::KIM PROPERTIES set_target_properties(LAMMPS::KIM PROPERTIES
IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}" IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}"
INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api") INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api"
target_link_libraries(lammps PRIVATE LAMMPS::KIM) )
add_dependencies(LAMMPS::KIM kim_build) add_dependencies(LAMMPS::KIM kim_build)
target_link_libraries(lammps PRIVATE LAMMPS::KIM)
# Set rpath so lammps build directory is relocatable
if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
set(_rpath_prefix "@loader_path")
else()
set(_rpath_prefix "$ORIGIN")
endif()
set_target_properties(lmp PROPERTIES
BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
)
else() else()
find_package(PkgConfig REQUIRED) if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION}) # For kim-api >= 2.2.0
target_link_libraries(lammps PRIVATE PkgConfig::KIM-API) find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
target_link_libraries(lammps PRIVATE KIM-API::kim-api)
else()
# For kim-api 2.1.3 (consistent with previous version of this file)
find_package(PkgConfig REQUIRED)
pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
endif()
endif() endif()

2
doc/src/Commands_bond.rst
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@ -35,6 +35,7 @@ OPT.
* :doc:`class2 (ko) <bond_class2>` * :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>` * :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>` * :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>` * :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>` * :doc:`harmonic (iko) <bond_harmonic>`
* :doc:`harmonic/shift (o) <bond_harmonic_shift>` * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
@ -84,6 +85,7 @@ OPT.
* :doc:`dipole (o) <angle_dipole>` * :doc:`dipole (o) <angle_dipole>`
* :doc:`fourier (o) <angle_fourier>` * :doc:`fourier (o) <angle_fourier>`
* :doc:`fourier/simple (o) <angle_fourier_simple>` * :doc:`fourier/simple (o) <angle_fourier_simple>`
* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
* :doc:`harmonic (iko) <angle_harmonic>` * :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>` * :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>` * :doc:`quartic (o) <angle_quartic>`

1
doc/src/Commands_fix.rst
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@ -62,6 +62,7 @@ OPT.
* :doc:`efield <fix_efield>` * :doc:`efield <fix_efield>`
* :doc:`ehex <fix_ehex>` * :doc:`ehex <fix_ehex>`
* :doc:`electron/stopping <fix_electron_stopping>` * :doc:`electron/stopping <fix_electron_stopping>`
* :doc:`electron/stopping/fit <fix_electron_stopping>`
* :doc:`enforce2d (k) <fix_enforce2d>` * :doc:`enforce2d (k) <fix_enforce2d>`
* :doc:`eos/cv <fix_eos_cv>` * :doc:`eos/cv <fix_eos_cv>`
* :doc:`eos/table <fix_eos_table>` * :doc:`eos/table <fix_eos_table>`

69
doc/src/angle_gaussian.rst Normal file
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@ -0,0 +1,69 @@
.. index:: angle_style gaussian
angle_style gaussian command
================================
Syntax
""""""
.. code-block:: LAMMPS
angle_style gaussian
Examples
""""""""
.. code-block:: LAMMPS
angle_style gaussian
angle_coeff 1 300.0 2 0.0128 0.375 80.0 0.0730 0.148 123.0
Description
"""""""""""
The *gaussian* angle style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`\theta_1` (degrees)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`\theta_n` (degrees)
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none
----------
.. _Milano1:
**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

1
doc/src/angle_style.rst
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@ -87,6 +87,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
* :doc:`fourier <angle_fourier>` - angle with multiple cosine terms * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
* :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
* :doc:`harmonic <angle_harmonic>` - harmonic angle * :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle * :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms

70
doc/src/bond_gaussian.rst Normal file
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@ -0,0 +1,70 @@
.. index:: bond_style gaussian
bond_style gaussian command
================================
Syntax
""""""
.. code-block:: LAMMPS
bond_style gaussian
Examples
""""""""
.. code-block:: LAMMPS
bond_style gaussian
bond_coeff 1 300.0 2 0.0128 0.375 3.37 0.0730 0.148 3.63
Description
"""""""""""
The *gaussian* bond style uses the potential:
.. math::
E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
This analytical form is a suitable potential for obtaining
mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
* T temperature at which the potential was derived
* :math:`n` (integer >=1)
* :math:`A_1` (-)
* :math:`w_1` (-)
* :math:`r_1` (length)
* ...
* :math:`A_n` (-)
* :math:`w_n` (-)
* :math:`r_n` (length)
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`
Default
"""""""
none
----------
.. _Milano0:
**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

1
doc/src/bond_style.rst
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@ -87,6 +87,7 @@ accelerated styles exist.
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond * :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond * :doc:`harmonic <bond_harmonic>` - harmonic bond
* :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond

1
doc/src/fix.rst
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@ -205,6 +205,7 @@ accelerated styles exist.
* :doc:`efield <fix_efield>` - impose electric field on system * :doc:`efield <fix_efield>` - impose electric field on system
* :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm * :doc:`ehex <fix_ehex>` - enhanced heat exchange algorithm
* :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force * :doc:`electron/stopping <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`electron/stopping/fit <fix_electron_stopping>` - electronic stopping power as a friction force
* :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force * :doc:`enforce2d <fix_enforce2d>` - zero out z-dimension velocity and force
* :doc:`eos/cv <fix_eos_cv>` - * :doc:`eos/cv <fix_eos_cv>` -
* :doc:`eos/table <fix_eos_table>` - * :doc:`eos/table <fix_eos_table>` -

52
doc/src/fix_electron_stopping.rst
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@ -1,28 +1,41 @@
.. index:: fix electron/stopping .. index:: fix electron/stopping
.. index:: fix electron/stopping/fit
fix electron/stopping command fix electron/stopping command
============================= =============================
fix electron/stopping/fit command
=================================
Syntax Syntax
"""""" """"""
.. parsed-literal:: .. parsed-literal::
fix ID group-ID electron/stopping Ecut file keyword value ... fix ID group-ID style args
* ID, group-ID are documented in :doc:`fix <fix>` command * ID, group-ID are documented in :doc:`fix <fix>` command
* electron/stopping = style name of this fix command * style = *electron/stopping* or *electron/stopping/fit*
* Ecut = minimum kinetic energy for electronic stopping (energy units)
* file = name of the file containing the electronic stopping power table
* zero or more keyword/value pairs may be appended to args
* keyword = *region* or *minneigh*
.. parsed-literal:: .. parsed-literal::
*electron/stopping* args = Ecut file keyword value ...
Ecut = minimum kinetic energy for electronic stopping (energy units)
file = name of the file containing the electronic stopping power table
*electron/stopping/fit* args = Ecut c1 c2 ...
Ecut = minimum kinetic energy for electronic stopping (energy units)
c1 c2 = linear and quadratic coefficients for the fitted quadratic polynomial
* zero or more keyword/value pairs may be appended to args for style = *electron/stopping*
.. parsed-literal::
keyword = *region* or *minneigh*
*region* value = region-ID *region* value = region-ID
region-ID = region, whose atoms will be affected by this fix region-ID = region whose atoms will be affected by this fix
*minneigh* value = minneigh *minneigh* value = minneigh
minneigh = minimum number of neighbors an atom to have stopping applied minneigh = minimum number of neighbors an atom to have stopping applied
Examples Examples
"""""""" """"""""
@ -32,6 +45,8 @@ Examples
fix el all electron/stopping 10.0 elstop-table.txt fix el all electron/stopping 10.0 elstop-table.txt
fix el all electron/stopping 10.0 elstop-table.txt minneigh 3 fix el all electron/stopping 10.0 elstop-table.txt minneigh 3
fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk fix el mygroup electron/stopping 1.0 elstop-table.txt region bulk
fix 1 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
fix 1 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
Description Description
""""""""""" """""""""""
@ -129,6 +144,19 @@ scientific publications, experimental databases or by using
of the impact parameter of the ion; these results can be used of the impact parameter of the ion; these results can be used
to derive the stopping power. to derive the stopping power.
----------
Style *electron/stopping/fit* calculates the electronic stopping power
and cumulative energy lost to the electron gas via a quadratic functional
and applies a drag force to the classical equations-of-motion for all
atoms moving above some minimum cutoff velocity (i.e., kinetic energy).
These coefficients can be determined by fitting a quadratic polynomial to
electronic stopping data predicted by, for example, SRIM or TD-DFT. Multiple
'Ecut c1 c2' values can be provided for multi-species simulations in the order
of the atom types. There is an examples/USER/misc/electron_stopping/ directory,
which illustrates uses of this command. Details of this implementation are
further described in :ref:`Stewart2018 <Stewart2018>` and :ref:`Lee2020 <Lee2020>`.
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@ -181,3 +209,11 @@ The default is no limitation by region, and minneigh = 1.
.. _PASS: .. _PASS:
**(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS **(PASS)** PASS webpage: https://www.sdu.dk/en/DPASS
.. _Stewart2018:
**(Stewart2018)** J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
.. _Lee2020:
**(Lee2020)** C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.

3
doc/src/package.rst
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@ -448,8 +448,7 @@ does not require atomic operations in the calculation of pair forces. For
that reason, *full* is the default setting for GPUs. However, when that reason, *full* is the default setting for GPUs. However, when
running on CPUs, a *half* neighbor list is the default because it are running on CPUs, a *half* neighbor list is the default because it are
often faster, just as it is for non-accelerated pair styles. Similarly, often faster, just as it is for non-accelerated pair styles. Similarly,
the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`. If not explicitly set, the value of the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
*neigh/qeq* will match *neigh*\ .
If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
threads only over atoms. However, for small systems, this may not expose threads only over atoms. However, for small systems, this may not expose

6
doc/utils/sphinx-config/false_positives.txt
View File

@ -1128,6 +1128,7 @@ Gonzalez-Melchor
googlemail googlemail
googletest googletest
Gordan Gordan
Goudeau
GPa GPa
gpu gpu
gpuID gpuID
@ -1887,6 +1888,7 @@ mie
Mie Mie
Mij Mij
Mikami Mikami
Milano
Militzer Militzer
Minary Minary
mincap mincap
@ -1990,6 +1992,7 @@ multi
multibody multibody
Multibody Multibody
multicenter multicenter
multicentered
multicmd multicmd
multicomponent multicomponent
multicore multicore
@ -2010,6 +2013,7 @@ muVT
mux mux
muy muy
muz muz
Müller
mv mv
mV mV
Mvapich Mvapich
@ -2457,6 +2461,7 @@ polydispersity
polyelectrolyte polyelectrolyte
polyhedra polyhedra
polymorphism polymorphism
Polym
popen popen
Popov Popov
popstore popstore
@ -2788,6 +2793,7 @@ Schulten
Schunk Schunk
Schuring Schuring
Schwen Schwen
Sci
screenshot screenshot
screenshots screenshots
Scripps Scripps

38
examples/USER/misc/electron_stopping/in.cascade_AlCu Normal file
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@ -0,0 +1,38 @@
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
region box block -10 10 -10 10 -10 10
create_box 2 box
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100

36
examples/USER/misc/electron_stopping/in.cascade_SiSi Normal file
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@ -0,0 +1,36 @@
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
region box block -10 10 -10 10 -10 10
create_box 1 box
create_atoms 1 box
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100

115
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.1 Normal file
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@ -0,0 +1,115 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
Lattice spacing in x,y,z = 4.0495000 4.0495000 4.0495000
region box block -10 10 -10 10 -10 10
create_box 2 box
Created orthogonal box = (-40.495000 -40.495000 -40.495000) to (40.495000 40.495000 40.495000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.004 seconds
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
Reading eam/alloy potential file ../../../../potentials/AlCu.eam.alloy with DATE: 2008-10-01
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
Setting atom values ...
1 settings made for type
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.27 | 23.27 | 23.27 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 53029.167 -106186.96 219339 0
5 2.4881895e-05 0.00012440247 53019.542 -106184.2 219299.18 36.968257
10 1.0341799e-05 0.00021830163 53006.803 -106159.67 219246.49 64.866504
15 5.6753071e-06 0.0002583636 52996.09 -106127.26 219202.18 76.766363
20 4.0862476e-06 0.0002830119 52987.566 -106099.31 219166.93 84.086344
25 3.3677164e-06 0.00030179992 52980.99 -106077.67 219139.73 89.665096
30 3.0218093e-06 0.00031784053 52976.302 -106063.03 219120.34 94.427505
35 2.8935922e-06 0.00033262008 52973.489 -106055.77 219108.7 98.815168
40 2.9394209e-06 0.00034711037 52972.541 -106056.15 219104.78 103.11678
45 3.1822694e-06 0.00036220043 52973.425 -106064.3 219108.44 107.59642
50 3.743784e-06 0.00037905999 52976.072 -106080.26 219119.38 112.60152
55 5.0685177e-06 0.0003999287 52980.344 -106104.15 219137.05 118.79722
60 1.0189784e-05 0.00043198334 52985.861 -106136.52 219159.88 128.31484
65 1.8636384e-05 0.00052946777 52985.275 -106162.53 219157.45 157.2625
70 1.844772e-05 0.00061001061 52977.927 -106155.89 219127.06 181.17691
75 2.4893022e-05 0.00072690857 52972.391 -106168.08 219104.16 215.88136
80 7.390618e-06 0.00081149431 52959.379 -106139.89 219050.34 240.98969
85 4.1547853e-06 0.00084037647 52948.078 -106101.74 219003.59 249.56079
90 2.9763749e-06 0.00085843347 52938.03 -106065.54 218962.03 254.91825
95 2.3727508e-06 0.00087197081 52929.043 -106032.37 218924.86 258.93397
100 2.0138478e-06 0.00088304936 52921.103 -106002.81 218892.02 262.21977
Loop time of 9.53154 on 1 procs for 100 steps with 32000 atoms
Performance: 0.002 ns/day, 13147.213 hours/ns, 10.491 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.815 | 8.815 | 8.815 | 0.0 | 92.48
Neigh | 0.38408 | 0.38408 | 0.38408 | 0.0 | 4.03
Comm | 0.029049 | 0.029049 | 0.029049 | 0.0 | 0.30
Output | 0.0025912 | 0.0025912 | 0.0025912 | 0.0 | 0.03
Modify | 0.28624 | 0.28624 | 0.28624 | 0.0 | 3.00
Other | | 0.01456 | | | 0.15
Nlocal: 32000.0 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 26825.0 ave 26825 max 26825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.81599e+06 ave 2.81599e+06 max 2.81599e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2815993
Ave neighs/atom = 87.999781
Neighbor list builds = 5
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

115
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_AlCu.intel.4 Normal file
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@ -0,0 +1,115 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Al lattice with a single incident Cu atom - multiple species simulation
# ***
units metal
boundary p p p
lattice fcc 4.0495
Lattice spacing in x,y,z = 4.0495000 4.0495000 4.0495000
region box block -10 10 -10 10 -10 10
create_box 2 box
Created orthogonal box = (-40.495000 -40.495000 -40.495000) to (40.495000 40.495000 40.495000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 32000 atoms
create_atoms CPU = 0.001 seconds
pair_style eam/alloy
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
Reading eam/alloy potential file ../../../../potentials/AlCu.eam.alloy with DATE: 2008-10-01
mass 1 26.982
mass 2 63.546
velocity all create 300 42534 mom yes rot yes
set atom 1 type 2
Setting atom values ...
1 settings made for type
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 3.49 1.8e-3 9.0e-8 7.57 4.2e-3 5.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.6825
ghost atom cutoff = 8.6825
binsize = 4.34125, bins = 19 19 19
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/alloy, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.014 | 9.014 | 9.014 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 53029.167 -106186.96 219339 0
5 2.4881895e-05 0.00012440247 53019.542 -106184.2 219299.18 36.968257
10 1.0341742e-05 0.00021830123 53006.803 -106159.67 219246.49 64.866388
15 5.6752732e-06 0.00025836298 52996.09 -106127.26 219202.18 76.76618
20 4.0862174e-06 0.00028301112 52987.566 -106099.31 219166.93 84.086114
25 3.3676848e-06 0.00030179899 52980.99 -106077.67 219139.73 89.664821
30 3.021773e-06 0.00031783944 52976.302 -106063.02 219120.33 94.427181
35 2.8935472e-06 0.00033261879 52973.489 -106055.77 219108.7 98.814784
40 2.9393606e-06 0.00034710883 52972.541 -106056.15 219104.78 103.11632
45 3.1821803e-06 0.00036219854 52973.425 -106064.29 219108.43 107.59586
50 3.7436309e-06 0.00037905755 52976.071 -106080.26 219119.38 112.60079
55 5.0681667e-06 0.0003999252 52980.343 -106104.15 219137.05 118.79618
60 1.0187808e-05 0.00043197649 52985.861 -106136.51 219159.87 128.3128
65 1.8643099e-05 0.00052944037 52985.278 -106162.53 219157.46 157.25436
70 1.8445045e-05 0.00060999223 52977.928 -106155.89 219127.06 181.17146
75 2.4893021e-05 0.00072688076 52972.393 -106168.08 219104.17 215.8731
80 7.3916674e-06 0.0008114874 52959.382 -106139.9 219050.35 240.98764
85 4.1550998e-06 0.00084037284 52948.08 -106101.75 219003.6 249.55971
90 2.976545e-06 0.00085843108 52938.032 -106065.55 218962.04 254.91754
95 2.3728646e-06 0.00087196913 52929.045 -106032.38 218924.87 258.93348
100 2.0139362e-06 0.00088304819 52921.106 -106002.82 218892.03 262.21943
Loop time of 2.45676 on 4 procs for 100 steps with 32000 atoms
Performance: 0.007 ns/day, 3388.559 hours/ns, 40.704 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2127 | 2.2257 | 2.2399 | 0.8 | 90.59
Neigh | 0.095856 | 0.097842 | 0.10197 | 0.8 | 3.98
Comm | 0.03626 | 0.054908 | 0.069787 | 6.3 | 2.23
Output | 0.00088538 | 0.0011005 | 0.0017236 | 1.1 | 0.04
Modify | 0.072449 | 0.072553 | 0.072611 | 0.0 | 2.95
Other | | 0.004684 | | | 0.19
Nlocal: 8000.00 ave 8033 max 7977 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 12605.0 ave 12628 max 12572 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 703998.0 ave 706570 max 702282 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 2815992
Ave neighs/atom = 87.999750
Neighbor list builds = 5
Dangerous builds = 3
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

113
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.1 Normal file
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@ -0,0 +1,113 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block -10 10 -10 10 -10 10
create_box 1 box
Created orthogonal box = (-54.310000 -54.310000 -54.310000) to (54.310000 54.310000 54.310000)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 64000 atoms
create_atoms CPU = 0.008 seconds
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
Reading tersoff/zbl potential file ../../../../potentials/SiC.tersoff.zbl with DATE: 2009-04-15
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.91 | 23.91 | 23.91 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 21258.724 -296293.96 175863.22 0
5 9.2462185e-06 9.0354398e-05 21252.059 -296277.65 175808.08 38.834393
10 6.1558479e-06 0.00013003059 21246.736 -296250.63 175764.05 55.881868
15 4.9002335e-06 0.00015681379 21242.649 -296228.27 175730.24 67.386915
20 5.853687e-06 0.00018286317 21239.571 -296213.99 175704.78 78.574676
25 7.0182823e-06 0.00021483214 21237.286 -296208.81 175685.87 92.303028
30 8.2570048e-06 0.00025083646 21236.034 -296213.99 175675.52 107.76296
35 6.4734302e-06 0.00029194185 21233.473 -296210.33 175654.33 125.41212
40 7.3445302e-06 0.00032561085 21231.196 -296205.94 175635.5 139.86641
45 6.9480705e-06 0.00036268325 21230.21 -296213.68 175627.33 155.78046
50 7.2224188e-06 0.00039655436 21230.512 -296230.74 175629.84 170.32001
55 1.0773409e-05 0.00044221823 21230.023 -296246.37 175625.79 189.92217
60 5.7527075e-06 0.00048339879 21226.064 -296231.33 175593.04 207.5982
65 5.8568503e-06 0.0005110075 21222.544 -296213.97 175563.92 219.44643
70 6.7430644e-06 0.00054252027 21220.179 -296207.92 175544.35 232.96808
75 7.0523029e-06 0.00057648256 21219.781 -296219.19 175541.06 247.53974
80 1.784394e-05 0.00062210154 21221.276 -296251.35 175553.43 267.11364
85 2.1885193e-05 0.0007395532 21218.037 -296274.94 175526.64 317.50995
90 8.233509e-06 0.00081518257 21211.247 -296251.53 175470.47 349.95382
95 5.1490725e-06 0.00084789415 21205.33 -296216.55 175421.52 363.982
100 5.7628664e-06 0.0008764946 21200.168 -296186.27 175378.81 376.24357
Loop time of 20.4868 on 1 procs for 100 steps with 64000 atoms
Performance: 0.002 ns/day, 9874.909 hours/ns, 4.881 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.397 | 19.397 | 19.397 | 0.0 | 94.68
Neigh | 0.45332 | 0.45332 | 0.45332 | 0.0 | 2.21
Comm | 0.035144 | 0.035144 | 0.035144 | 0.0 | 0.17
Output | 0.0040397 | 0.0040397 | 0.0040397 | 0.0 | 0.02
Modify | 0.5739 | 0.5739 | 0.5739 | 0.0 | 2.80
Other | | 0.0229 | | | 0.11
Nlocal: 64000.0 ave 64000 max 64000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 18341.0 ave 18341 max 18341 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: 1.79199e+06 ave 1.79199e+06 max 1.79199e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1791990
Ave neighs/atom = 27.999844
Neighbor list builds = 7
Dangerous builds = 2
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:20

113
examples/USER/misc/electron_stopping/log.18Sep2020.cascade_SiSi.intel.4 Normal file
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@ -0,0 +1,113 @@
LAMMPS (18 Sep 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# ***
# Example input for including electronic stopping effects using fix electron/stopping/fit
# Si lattice with one primary knock-on atom (PKA) - single species simulation
# ***
units metal
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.4310000 5.4310000 5.4310000
region box block -10 10 -10 10 -10 10
create_box 1 box
Created orthogonal box = (-54.310000 -54.310000 -54.310000) to (54.310000 54.310000 54.310000)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 64000 atoms
create_atoms CPU = 0.003 seconds
pair_style tersoff/zbl
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
Reading tersoff/zbl potential file ../../../../potentials/SiC.tersoff.zbl with DATE: 2009-04-15
mass 1 28.0855
velocity all create 300 42534 mom yes rot yes
group pka id 1
1 atoms in group pka
velocity pka set 1120 1620 400
fix 1 all nve
fix 2 all dt/reset 1 NULL 0.001 0.05 emax 10.0
fix 3 all electron/stopping/fit 4.63 3.3e-3 4.0e-8
thermo 5
thermo_style custom step dt time temp pe ke f_3
thermo_modify lost warn flush yes
#dump 0 all custom 10 dump.pka_* id type x y z vx vy vz fx fy fz
#dump_modify 0 first yes
run 100
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5
ghost atom cutoff = 5
binsize = 2.5, bins = 44 44 44
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair tersoff/zbl, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.777 | 7.777 Mbytes
Step Dt Time Temp PotEng KinEng f_3
0 2.4879625e-05 0 21258.724 -296293.96 175863.22 0
5 9.2462211e-06 9.0354422e-05 21252.059 -296277.66 175808.08 38.834403
10 6.1568847e-06 0.00013003069 21246.736 -296250.63 175764.05 55.881913
15 4.8997821e-06 0.00015681555 21242.649 -296228.27 175730.24 67.387669
20 5.8536714e-06 0.00018286203 21239.571 -296213.99 175704.78 78.574187
25 7.0160073e-06 0.00021483347 21237.285 -296208.8 175685.86 92.303599
30 8.2556386e-06 0.00025082046 21236.035 -296213.99 175675.53 107.75609
35 6.4735852e-06 0.00029193023 21233.474 -296210.34 175654.34 125.40713
40 7.3441556e-06 0.00032559783 21231.197 -296205.94 175635.5 139.86082
45 6.9483099e-06 0.00036267022 21230.21 -296213.68 175627.34 155.77487
50 7.2213562e-06 0.0003965413 21230.513 -296230.74 175629.84 170.31441
55 1.0776037e-05 0.00044219672 21230.024 -296246.38 175625.8 189.91293
60 5.7538246e-06 0.0004833796 21226.067 -296231.34 175593.06 207.58996
65 5.856213e-06 0.00051099409 21222.546 -296213.98 175563.94 219.44067
70 6.7431217e-06 0.00054250526 21220.18 -296207.92 175544.37 232.96164
75 7.0518411e-06 0.00057646788 21219.781 -296219.18 175541.07 247.53344
80 1.7829072e-05 0.00062207162 21221.276 -296251.34 175553.43 267.1008
85 2.1894958e-05 0.0007395084 21218.04 -296274.95 175526.66 317.49073
90 8.2365472e-06 0.00081516502 21211.25 -296251.55 175470.49 349.94629
95 5.1493496e-06 0.00084788428 21205.333 -296216.57 175421.54 363.97777
100 5.7652664e-06 0.00087648406 21200.171 -296186.3 175378.84 376.23905
Loop time of 5.23182 on 4 procs for 100 steps with 64000 atoms
Performance: 0.010 ns/day, 2520.759 hours/ns, 19.114 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8069 | 4.8618 | 4.9229 | 2.0 | 92.93
Neigh | 0.11442 | 0.11856 | 0.12948 | 1.8 | 2.27
Comm | 0.040943 | 0.098988 | 0.15807 | 14.7 | 1.89
Output | 0.0013075 | 0.0014801 | 0.0019936 | 0.8 | 0.03
Modify | 0.14496 | 0.14502 | 0.1451 | 0.0 | 2.77
Other | | 0.005981 | | | 0.11
Nlocal: 16000.0 ave 16017 max 15987 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 8044.00 ave 8058 max 8026 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 447998.0 ave 448471 max 447634 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 1791990
Ave neighs/atom = 27.999844
Neighbor list builds = 7
Dangerous builds = 2
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

3
lib/kim/Install.py
View File

@ -18,12 +18,13 @@ parser = ArgumentParser(prog='Install.py',
# settings # settings
thisdir = fullpath('.') thisdir = fullpath('.')
version = "2.1.3" version = "2.2.0"
# known checksums for different KIM-API versions. used to validate the download. # known checksums for different KIM-API versions. used to validate the download.
checksums = { \ checksums = { \
'2.1.2' : '6ac52e14ef52967fc7858220b208cba5', \ '2.1.2' : '6ac52e14ef52967fc7858220b208cba5', \
'2.1.3' : '6ee829a1bbba5f8b9874c88c4c4ebff8', \ '2.1.3' : '6ee829a1bbba5f8b9874c88c4c4ebff8', \
'2.2.0' : 'e7f944e1593cffd7444679a660607f6c', \
} }

117
src/KIM/kim_init.cpp
View File

@ -92,7 +92,12 @@ void KimInit::command(int narg, char **arg)
strcpy(user_units,arg[1]); strcpy(user_units,arg[1]);
if (narg == 3) { if (narg == 3) {
if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true; if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true;
else { error->all(FLERR,"Illegal kim_init command"); } else {
error->all(FLERR,fmt::format("Illegal kim_init command.\nThe argument "
"followed by unit_style {} is an optional "
"argument and when is used must "
"be unit_conversion_mode", user_units));
}
} else unit_conversion_mode = false; } else unit_conversion_mode = false;
char *model_units; char *model_units;
@ -122,38 +127,41 @@ void get_kim_unit_names(
KIM_TimeUnit & timeUnit, KIM_TimeUnit & timeUnit,
Error * error) Error * error)
{ {
if ((strcmp(system,"real")==0)) { if (strcmp(system,"real") == 0) {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol; energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system,"metal")==0)) { } else if (strcmp(system,"metal") == 0) {
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV; energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps; timeUnit = KIM_TIME_UNIT_ps;
} else if ((strcmp(system,"si")==0)) { } else if (strcmp(system,"si") == 0) {
lengthUnit = KIM_LENGTH_UNIT_m; lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J; energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C; chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system,"cgs")==0)) { } else if (strcmp(system,"cgs") == 0) {
lengthUnit = KIM_LENGTH_UNIT_cm; lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg; energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC; chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system,"electron")==0)) { } else if (strcmp(system,"electron") == 0) {
lengthUnit = KIM_LENGTH_UNIT_Bohr; lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree; energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system,"lj")==0)) { } else if (strcmp(system,"lj") == 0 ||
error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); strcmp(system,"micro") ==0 ||
strcmp(system,"nano")==0) {
error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system));
} else { } else {
error->all(FLERR,"Unknown unit_style"); error->all(FLERR,"Unknown unit_style");
} }
@ -171,19 +179,19 @@ void KimInit::determine_model_type_and_units(char * model_name,
KIM_TemperatureUnit temperatureUnit; KIM_TemperatureUnit temperatureUnit;
KIM_TimeUnit timeUnit; KIM_TimeUnit timeUnit;
int units_accepted; int units_accepted;
KIM_Collections * kim_Coll; KIM_Collections * collections;
KIM_CollectionItemType itemType; KIM_CollectionItemType itemType;
int kim_error = KIM_Collections_Create(&kim_Coll); int kim_error = KIM_Collections_Create(&collections);
if (kim_error) { if (kim_error)
error->all(FLERR,"Unable to access KIM Collections to find Model."); error->all(FLERR,"Unable to access KIM Collections to find Model");
}
kim_error = KIM_Collections_GetItemType(kim_Coll, model_name, &itemType); auto logID = fmt::format("{}_Collections", comm->me);
if (kim_error) { KIM_Collections_SetLogID(collections, logID.c_str());
error->all(FLERR,"KIM Model name not found.");
} kim_error = KIM_Collections_GetItemType(collections, model_name, &itemType);
KIM_Collections_Destroy(&kim_Coll); if (kim_error) error->all(FLERR,"KIM Model name not found");
KIM_Collections_Destroy(&collections);
if (KIM_CollectionItemType_Equal(itemType, if (KIM_CollectionItemType_Equal(itemType,
KIM_COLLECTION_ITEM_TYPE_portableModel)) { KIM_COLLECTION_ITEM_TYPE_portableModel)) {
@ -199,12 +207,13 @@ void KimInit::determine_model_type_and_units(char * model_name,
&units_accepted, &units_accepted,
&pkim); &pkim);
if (kim_error) if (kim_error) error->all(FLERR,"Unable to load KIM Simulator Model");
error->all(FLERR,"Unable to load KIM Simulator Model.");
model_type = MO; model_type = MO;
if (units_accepted) { if (units_accepted) {
logID = fmt::format("{}_Model", comm->me);
KIM_Model_SetLogID(pkim, logID.c_str());
*model_units = new char[strlen(user_units)+1]; *model_units = new char[strlen(user_units)+1];
strcpy(*model_units,user_units); strcpy(*model_units,user_units);
return; return;
@ -226,6 +235,8 @@ void KimInit::determine_model_type_and_units(char * model_name,
&units_accepted, &units_accepted,
&pkim); &pkim);
if (units_accepted) { if (units_accepted) {
logID = fmt::format("{}_Model", comm->me);
KIM_Model_SetLogID(pkim, logID.c_str());
*model_units = new char[strlen(systems[i])+1]; *model_units = new char[strlen(systems[i])+1];
strcpy(*model_units,systems[i]); strcpy(*model_units,systems[i]);
return; return;
@ -238,37 +249,40 @@ void KimInit::determine_model_type_and_units(char * model_name,
error->all(FLERR,"KIM Model does not support the requested unit system"); error->all(FLERR,"KIM Model does not support the requested unit system");
} }
} else if (KIM_CollectionItemType_Equal( } else if (KIM_CollectionItemType_Equal(
itemType, KIM_COLLECTION_ITEM_TYPE_simulatorModel)) { itemType, KIM_COLLECTION_ITEM_TYPE_simulatorModel)) {
KIM_SimulatorModel * kim_SM; KIM_SimulatorModel * simulatorModel;
kim_error = KIM_SimulatorModel_Create(model_name, &kim_SM); kim_error = KIM_SimulatorModel_Create(model_name, &simulatorModel);
if (kim_error) if (kim_error)
error->all(FLERR,"Unable to load KIM Simulator Model."); error->all(FLERR,"Unable to load KIM Simulator Model");
model_type = SM; model_type = SM;
logID = fmt::format("{}_SimulatorModel", comm->me);
KIM_SimulatorModel_SetLogID(simulatorModel, logID.c_str());
int sim_fields; int sim_fields;
int sim_lines; int sim_lines;
char const * sim_field; char const * sim_field;
char const * sim_value; char const * sim_value;
KIM_SimulatorModel_GetNumberOfSimulatorFields(kim_SM, &sim_fields); KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
KIM_SimulatorModel_CloseTemplateMap(kim_SM); KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
for (int i=0; i < sim_fields; ++i) { for (int i=0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
kim_SM,i,&sim_lines,&sim_field); simulatorModel, i, &sim_lines, &sim_field);
if (0 == strcmp(sim_field,"units")) { if (0 == strcmp(sim_field,"units")) {
KIM_SimulatorModel_GetSimulatorFieldLine(kim_SM,i,0,&sim_value); KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel, i, 0, &sim_value);
int len=strlen(sim_value)+1; int len=strlen(sim_value)+1;
*model_units = new char[len]; strcpy(*model_units,sim_value); *model_units = new char[len];
strcpy(*model_units,sim_value);
break; break;
} }
} }
KIM_SimulatorModel_Destroy(&kim_SM); KIM_SimulatorModel_Destroy(&simulatorModel);
if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) { if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0)) {
std::string mesg("Incompatible units for KIM Simulator Model, " error->all(FLERR,fmt::format("Incompatible units for KIM Simulator Model"
"required units = "); ", required units = {}", *model_units));
mesg += *model_units;
error->all(FLERR,mesg);
} }
} }
} }
@ -295,13 +309,16 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
KIM_SimulatorModel * simulatorModel; KIM_SimulatorModel * simulatorModel;
if (model_type == SM) { if (model_type == SM) {
int kim_error = int kim_error =
KIM_SimulatorModel_Create(model_name,&simulatorModel); KIM_SimulatorModel_Create(model_name, &simulatorModel);
if (kim_error) if (kim_error)
error->all(FLERR,"Unable to load KIM Simulator Model."); error->all(FLERR,"Unable to load KIM Simulator Model");
auto logID = fmt::format("{}_SimulatorModel", comm->me);
KIM_SimulatorModel_SetLogID(simulatorModel, logID.c_str());
char const *sim_name, *sim_version; char const *sim_name, *sim_version;
KIM_SimulatorModel_GetSimulatorNameAndVersion( KIM_SimulatorModel_GetSimulatorNameAndVersion(
simulatorModel,&sim_name, &sim_version); simulatorModel, &sim_name, &sim_version);
if (0 != strcmp(sim_name,"LAMMPS")) if (0 != strcmp(sim_name,"LAMMPS"))
error->all(FLERR,"Incompatible KIM Simulator Model"); error->all(FLERR,"Incompatible KIM Simulator Model");
@ -389,7 +406,7 @@ void KimInit::do_init(char *model_name, char *user_units, char *model_units, KIM
mesg += fmt::format(" {:<8} | {:<{}} | {:<10} | {}\n",i+1,str_name, mesg += fmt::format(" {:<8} | {:<{}} | {:<10} | {}\n",i+1,str_name,
max_len,data_type,extent); max_len,data_type,extent);
} }
} else mesg += "No mutable parameters. \n"; } else mesg += "No mutable parameters.\n";
KIM_Model_Destroy(&pkim); KIM_Model_Destroy(&pkim);
input->write_echo(mesg); input->write_echo(mesg);
@ -447,7 +464,7 @@ void KimInit::do_variables(const std::string &from, const std::string &to)
conversion_factor); conversion_factor);
if (ier != 0) if (ier != 0)
error->all(FLERR,fmt::format("Unable to obtain conversion factor: " error->all(FLERR,fmt::format("Unable to obtain conversion factor: "
"unit = {}; from = {}; to = {}.", "unit = {}; from = {}; to = {}",
units[i], from, to)); units[i], from, to));
variable->internal_set(v_unit,conversion_factor); variable->internal_set(v_unit,conversion_factor);
@ -461,23 +478,28 @@ void KimInit::do_variables(const std::string &from, const std::string &to)
void KimInit::write_log_cite(char *model_name) void KimInit::write_log_cite(char *model_name)
{ {
KIM_Collections * coll; KIM_Collections * collections;
int err = KIM_Collections_Create(&coll); int err = KIM_Collections_Create(&collections);
if (err) return; if (err) return;
auto logID = fmt::format("{}_Collections", comm->me);
KIM_Collections_SetLogID(collections, logID.c_str());
int extent; int extent;
if (model_type == MO) { if (model_type == MO) {
err = KIM_Collections_CacheListOfItemMetadataFiles( err = KIM_Collections_CacheListOfItemMetadataFiles(
coll,KIM_COLLECTION_ITEM_TYPE_portableModel,model_name,&extent); collections, KIM_COLLECTION_ITEM_TYPE_portableModel,
model_name,&extent);
} else if (model_type == SM) { } else if (model_type == SM) {
err = KIM_Collections_CacheListOfItemMetadataFiles( err = KIM_Collections_CacheListOfItemMetadataFiles(
coll,KIM_COLLECTION_ITEM_TYPE_simulatorModel,model_name,&extent); collections, KIM_COLLECTION_ITEM_TYPE_simulatorModel,
model_name, &extent);
} else { } else {
error->all(FLERR,"Unknown model type."); error->all(FLERR,"Unknown model type");
} }
if (err) { if (err) {
KIM_Collections_Destroy(&coll); KIM_Collections_Destroy(&collections);
return; return;
} }
@ -486,7 +508,8 @@ void KimInit::write_log_cite(char *model_name)
int availableAsString; int availableAsString;
char const * fileString; char const * fileString;
err = KIM_Collections_GetItemMetadataFile( err = KIM_Collections_GetItemMetadataFile(
coll,i,&fileName,nullptr,nullptr,&availableAsString,&fileString); collections, i, &fileName, nullptr, nullptr,
&availableAsString, &fileString);
if (err) continue; if (err) continue;
if (0 == strncmp("kimcite",fileName,7)) { if (0 == strncmp("kimcite",fileName,7)) {
@ -494,5 +517,5 @@ void KimInit::write_log_cite(char *model_name)
} }
} }
KIM_Collections_Destroy(&coll); KIM_Collections_Destroy(&collections);
} }

137
src/KIM/kim_interactions.cpp
View File

@ -16,6 +16,7 @@
Ryan S. Elliott (UMN) Ryan S. Elliott (UMN)
Ellad B. Tadmor (UMN) Ellad B. Tadmor (UMN)
Ronald Miller (Carleton U) Ronald Miller (Carleton U)
Yaser Afshar (UMN)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -87,6 +88,7 @@ void KimInteractions::command(int narg, char **arg)
if (!domain->box_exist) if (!domain->box_exist)
error->all(FLERR,"Must use 'kim_interactions' command after " error->all(FLERR,"Must use 'kim_interactions' command after "
"simulation box is defined"); "simulation box is defined");
do_setup(narg,arg); do_setup(narg,arg);
} }
@ -98,7 +100,11 @@ void KimInteractions::do_setup(int narg, char **arg)
if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) { if ((narg == 1) && (0 == strcmp("fixed_types",arg[0]))) {
fixed_types = true; fixed_types = true;
} else if (narg != atom->ntypes) { } else if (narg != atom->ntypes) {
error->all(FLERR,"Illegal kim_interactions command"); error->all(FLERR,fmt::format("Illegal kim_interactions command.\nThe "
"LAMMPS simulation has {} atom type(s), but "
"{} chemical species passed to the "
"kim_interactions command",
atom->ntypes, narg));
} else { } else {
fixed_types = false; fixed_types = false;
} }
@ -121,22 +127,20 @@ void KimInteractions::do_setup(int narg, char **arg)
input->write_echo("#=== BEGIN kim_interactions ==================================\n"); input->write_echo("#=== BEGIN kim_interactions ==================================\n");
if (simulatorModel) { if (simulatorModel) {
if (!fixed_types) { if (!fixed_types) {
std::string delimiter(""); std::string atom_type_sym_list =
std::string atom_type_sym_list; fmt::format("{}", fmt::join(arg, arg + narg, " "));
std::string atom_type_num_list;
std::string atom_type_num_list =
fmt::format("{}", species_to_atomic_no(arg[0]));
for (int i = 0; i < narg; i++) { for (int i = 1; i < narg; ++i)
atom_type_sym_list += delimiter + arg[i]; atom_type_num_list += fmt::format(" {}", species_to_atomic_no(arg[i]));
atom_type_num_list += delimiter + std::to_string(species_to_atomic_no(arg[i]));
delimiter = " ";
}
KIM_SimulatorModel_AddTemplateMap( KIM_SimulatorModel_AddTemplateMap(
simulatorModel,"atom-type-sym-list",atom_type_sym_list.c_str()); simulatorModel, "atom-type-sym-list", atom_type_sym_list.c_str());
KIM_SimulatorModel_AddTemplateMap( KIM_SimulatorModel_AddTemplateMap(
simulatorModel,"atom-type-num-list",atom_type_num_list.c_str()); simulatorModel, "atom-type-num-list", atom_type_num_list.c_str());
KIM_SimulatorModel_CloseTemplateMap(simulatorModel); KIM_SimulatorModel_CloseTemplateMap(simulatorModel);
// validate species selection // validate species selection
@ -150,14 +154,14 @@ void KimInteractions::do_setup(int narg, char **arg)
for (auto atom_type_sym : utils::split_words(atom_type_sym_list)) { for (auto atom_type_sym : utils::split_words(atom_type_sym_list)) {
species_is_supported = false; species_is_supported = false;
if (atom_type_sym == "NULL") continue; if (atom_type_sym == "NULL") continue;
for (int i=0; i < sim_num_species; ++i) { for (int i = 0; i < sim_num_species; ++i) {
KIM_SimulatorModel_GetSupportedSpecies(simulatorModel,i,&sim_species); KIM_SimulatorModel_GetSupportedSpecies(
simulatorModel, i, &sim_species);
if (atom_type_sym == sim_species) species_is_supported = true; if (atom_type_sym == sim_species) species_is_supported = true;
} }
if (!species_is_supported) { if (!species_is_supported) {
std::string msg = "Species '"; error->all(FLERR,fmt::format("Species '{}' is not supported by this "
msg += atom_type_sym + "' is not supported by this KIM Simulator Model"; "KIM Simulator Model", atom_type_sym));
error->all(FLERR,msg);
} }
} }
} else { } else {
@ -169,29 +173,39 @@ void KimInteractions::do_setup(int narg, char **arg)
int sim_fields, sim_lines; int sim_fields, sim_lines;
const char *sim_field, *sim_value; const char *sim_field, *sim_value;
KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields); KIM_SimulatorModel_GetNumberOfSimulatorFields(simulatorModel, &sim_fields);
for (int i=0; i < sim_fields; ++i) { for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel,i,&sim_lines,&sim_field); simulatorModel, i, &sim_lines, &sim_field);
if (0 == strcmp(sim_field,"units")) { if (strcmp(sim_field,"units") == 0) {
KIM_SimulatorModel_GetSimulatorFieldLine(simulatorModel,i,0,&sim_value); KIM_SimulatorModel_GetSimulatorFieldLine(
if (0 != strcmp(sim_value,update->unit_style)) simulatorModel, i, 0, &sim_value);
if (strcmp(sim_value,update->unit_style) != 0)
error->all(FLERR,"Incompatible units for KIM Simulator Model"); error->all(FLERR,"Incompatible units for KIM Simulator Model");
} }
} }
int sim_model_idx=-1; bool no_model_definition = true;
for (int i=0; i < sim_fields; ++i) { for (int i = 0; i < sim_fields; ++i) {
KIM_SimulatorModel_GetSimulatorFieldMetadata( KIM_SimulatorModel_GetSimulatorFieldMetadata(
simulatorModel,i,&sim_lines,&sim_field); simulatorModel, i, &sim_lines, &sim_field);
if (0 == strcmp(sim_field,"model-defn")) { if (strcmp(sim_field,"model-defn") == 0) {
if (domain->periodicity[0]&&domain->periodicity[1]&&domain->periodicity[2]) input->one("variable kim_periodic equal 1"); if (domain->periodicity[0]&&
else if (domain->periodicity[0]&&domain->periodicity[1]&&!domain->periodicity[2]) input->one("variable kim_periodic equal 2"); domain->periodicity[1]&&
domain->periodicity[2])
input->one("variable kim_periodic equal 1");
else if (domain->periodicity[0]&&
domain->periodicity[1]&&
!domain->periodicity[2])
input->one("variable kim_periodic equal 2");
else input->one("variable kim_periodic equal 0"); else input->one("variable kim_periodic equal 0");
sim_model_idx = i;
for (int j=0; j < sim_lines; ++j) { // KIM Simulator Model has a Model definition
no_model_definition = false;
for (int j = 0; j < sim_lines; ++j) {
KIM_SimulatorModel_GetSimulatorFieldLine( KIM_SimulatorModel_GetSimulatorFieldLine(
simulatorModel,sim_model_idx,j,&sim_value); simulatorModel, i, j, &sim_value);
if (utils::strmatch(sim_value,"^KIM_SET_TYPE_PARAMETERS")) { if (utils::strmatch(sim_value,"^KIM_SET_TYPE_PARAMETERS")) {
// Notes regarding the KIM_SET_TYPE_PARAMETERS command // Notes regarding the KIM_SET_TYPE_PARAMETERS command
// * This is an INTERNAL command. // * This is an INTERNAL command.
@ -212,7 +226,7 @@ void KimInteractions::do_setup(int narg, char **arg)
} }
} }
if (sim_model_idx < 0) if (no_model_definition)
error->all(FLERR,"KIM Simulator Model has no Model definition"); error->all(FLERR,"KIM Simulator Model has no Model definition");
KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel); KIM_SimulatorModel_OpenAndInitializeTemplateMap(simulatorModel);
@ -227,14 +241,9 @@ void KimInteractions::do_setup(int narg, char **arg)
// NOTE: all references to arg must appear before calls to input->one() // NOTE: all references to arg must appear before calls to input->one()
// as that will reset the argument vector. // as that will reset the argument vector.
std::string cmd1("pair_style kim "); auto cmd1 = fmt::format("pair_style kim {}", model_name);
cmd1 += model_name; auto cmd2 =
fmt::format("pair_coeff * * {}", fmt::join(arg, arg + narg, " "));
std::string cmd2("pair_coeff * * ");
for (int i=0; i < narg; ++i) {
cmd2 += arg[i];
cmd2 += " ";
}
input->one(cmd1); input->one(cmd1);
input->one(cmd2); input->one(cmd2);
@ -248,22 +257,25 @@ void KimInteractions::do_setup(int narg, char **arg)
void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) const void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) const
{ {
int nocomment;
auto words = utils::split_words(input_line); auto words = utils::split_words(input_line);
std::string key = words[1]; const std::string key = words[1];
if (key != "pair" && key != "charge")
error->one(FLERR,fmt::format("Unrecognized KEY {} for "
"KIM_SET_TYPE_PARAMETERS command", key));
std::string filename = words[2]; std::string filename = words[2];
std::vector<std::string> species(words.begin()+3,words.end()); std::vector<std::string> species(words.begin()+3,words.end());
if ((int)species.size() != atom->ntypes) if ((int)species.size() != atom->ntypes)
error->one(FLERR,"Incorrect args for KIM_SET_TYPE_PARAMETERS command"); error->one(FLERR,"Incorrect args for KIM_SET_TYPE_PARAMETERS command");
FILE *fp; FILE *fp = nullptr;
fp = fopen(filename.c_str(),"r"); if (comm->me == 0) {
if (fp == nullptr) { fp = fopen(filename.c_str(),"r");
error->one(FLERR,"Parameter file not found"); if (fp == nullptr) error->one(FLERR,"Parameter file not found");
} }
char line[MAXLINE],*ptr; char line[MAXLINE], *ptr;
int n, eof = 0; int n, eof = 0;
while (1) { while (1) {
@ -279,27 +291,24 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(const std::string &input_line) con
MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world);
nocomment = line[0] != '#'; if (ptr = strchr(line,'#')) *ptr = '\0';
if (strspn(line," \t\n\r") == strlen(line)) continue;
if(nocomment) { words = utils::split_words(line);
words = utils::split_words(line); if (key == "pair") {
if (key == "pair") { for (int ia = 0; ia < atom->ntypes; ++ia) {
for (int ia = 0; ia < atom->ntypes; ++ia) { for (int ib = ia; ib < atom->ntypes; ++ib)
for (int ib = ia; ib < atom->ntypes; ++ib) if (((species[ia] == words[0]) && (species[ib] == words[1]))
if (((species[ia] == words[0]) && (species[ib] == words[1])) || ((species[ib] == words[0]) && (species[ia] == words[1])))
|| ((species[ib] == words[0]) && (species[ia] == words[1]))) input->one(fmt::format("pair_coeff {} {} {}",ia+1,ib+1,
input->one(fmt::format("pair_coeff {} {} {}",ia+1,ib+1,fmt::join(words.begin()+2,words.end()," "))); fmt::join(words.begin()+2,words.end()," ")));
}
} else if (key == "charge") {
for (int ia = 0; ia < atom->ntypes; ++ia)
if (species[ia] == words[0])
input->one(fmt::format("set type {} charge {}",ia+1,words[1]));
} else {
error->one(FLERR,"Unrecognized KEY for KIM_SET_TYPE_PARAMETERS command");
} }
} else {
for (int ia = 0; ia < atom->ntypes; ++ia)
if (species[ia] == words[0])
input->one(fmt::format("set type {} charge {}",ia+1,words[1]));
} }
} }
fclose(fp);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

203
src/KIM/kim_param.cpp
View File

@ -57,6 +57,7 @@
#include "kim_param.h" #include "kim_param.h"
#include "comm.h"
#include "error.h" #include "error.h"
#include "fix_store_kim.h" #include "fix_store_kim.h"
#include "force.h" #include "force.h"
@ -65,8 +66,9 @@
#include "pair_kim.h" #include "pair_kim.h"
#include "variable.h" #include "variable.h"
#include <cstdlib>
#include <cstring> #include <cstring>
#include <sstream> #include <vector>
extern "C" extern "C"
{ {
@ -118,8 +120,11 @@ void get_kim_unit_names(
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system, "lj") == 0)) { } else if (strcmp(system,"lj") == 0 ||
error->all(FLERR, "LAMMPS unit_style lj not supported by KIM models"); strcmp(system,"micro") ==0 ||
strcmp(system,"nano")==0) {
error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", system));
} else } else
error->all(FLERR, "Unknown unit_style"); error->all(FLERR, "Unknown unit_style");
} }
@ -240,6 +245,9 @@ void KimParam::command(int narg, char **arg)
&pkim); &pkim);
if (kim_error) if (kim_error)
error->all(FLERR, "Unable to create KIM Portable Model"); error->all(FLERR, "Unable to create KIM Portable Model");
auto logID = fmt::format("{}_Model", comm->me);
KIM_Model_SetLogID(pkim, logID.c_str());
} }
} }
@ -253,7 +261,7 @@ void KimParam::command(int narg, char **arg)
// Parameter name // Parameter name
char *paramname = nullptr; char *paramname = nullptr;
// Variable name // Variable name
char *varname = nullptr; std::string varname;
// Loop over all the arguments // Loop over all the arguments
for (int i = 1; i < narg;) { for (int i = 1; i < narg;) {
@ -277,15 +285,13 @@ void KimParam::command(int narg, char **arg)
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterMetadata returned error"); error->all(FLERR, "KIM GetParameterMetadata returned error");
if (strcmp(paramname, str_name) == 0) if (strcmp(paramname, str_name) == 0) break;
break;
} }
if (param_index >= numberOfParameters) { if (param_index >= numberOfParameters) {
std::string msg("Wrong argument in kim_param get command.\n"); auto msg = fmt::format("Wrong argument in kim_param get command.\n"
msg += "This Model does not have the requested '"; "This Model does not have the requested '{}' "
msg += paramname; "parameter", paramname);
msg += "' parameter";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
@ -299,60 +305,53 @@ void KimParam::command(int narg, char **arg)
// Check to see if the indices range contains // Check to see if the indices range contains
// only integer numbers and/or range : // only integer numbers and/or range :
if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { if (argtostr.find_first_not_of("0123456789:") != std::string::npos) {
std::string msg("Illegal index_range.\n"); auto msg = fmt::format("Illegal index_range.\nExpected integer "
msg += "Expected integer parameter(s) instead of '"; "parameter(s) instead of '{}' in "
msg += argtostr; "index_range", argtostr);
msg += "' in index_range";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
std::string::size_type npos = argtostr.find(':'); std::string::size_type npos = argtostr.find(':');
if (npos != std::string::npos) { if (npos != std::string::npos) {
argtostr[npos] = ' '; argtostr[npos] = ' ';
std::stringstream str(argtostr); auto words = utils::split_words(argtostr);
str >> nlbound >> nubound; nlbound = atoi(words[0].c_str());
nubound = atoi(words[1].c_str());
if (nubound < 1 || nubound > extent || if (nubound < 1 || nubound > extent ||
nlbound < 1 || nlbound > nubound) { nlbound < 1 || nlbound > nubound) {
std::string msg("Illegal index_range '"); auto msg = fmt::format("Illegal index_range '{}-{}' for '{}' "
msg += std::to_string(nlbound) + "-"; "parameter with the extent of '{}'",
msg += std::to_string(nubound) + "' for '"; nlbound, nubound, paramname, extent);
msg += paramname;
msg += "' parameter with the extent of '";
msg += std::to_string(extent);
msg += "'";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
} else { } else {
std::stringstream str(argtostr); nlbound = atoi(argtostr.c_str());
str >> nlbound;
if (nlbound < 1 || nlbound > extent) { if (nlbound < 1 || nlbound > extent) {
std::string msg("Illegal index '"); auto msg = fmt::format("Illegal index '{}' for '{}' parameter "
msg += std::to_string(nlbound) + "' for '"; "with the extent of '{}'", nlbound,
msg += paramname; paramname, extent);
msg += "' parameter with the extent of '";
msg += std::to_string(extent);
msg += "'";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
nubound = nlbound; nubound = nlbound;
} }
} else { } else {
std::string msg("Wrong number of arguments in "); std::string msg("Wrong number of arguments in 'kim_param get' ");
msg += "'kim_param get' command.\n"; msg += "command.\nIndex range after parameter name is mandatory";
msg += "Index range after parameter name is mandatory";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
int const nvars = nubound - nlbound + 1; int const nvars = nubound - nlbound + 1;
char **varsname = nullptr; std::vector<std::string> varsname;
if (i < narg) { if (i < narg) {
// Get the variable/variable_base name // Get the variable/variable_base name
varname = arg[i++]; varname = arg[i++];
} else { } else {
std::string msg("Wrong number of arguments in "); std::string msg("Wrong number of arguments in 'kim_param get' ");
msg += "'kim_param get' command.\n"; msg += "command.\nThe LAMMPS variable name is mandatory";
msg += "The LAMMPS variable name is mandatory";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
@ -362,56 +361,47 @@ void KimParam::command(int narg, char **arg)
if (nvars > 1) { if (nvars > 1) {
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "split") == 0) { if (strcmp(arg[i], "split") == 0) {
varsname = new char *[nvars]; varsname.resize(nvars);
for (int j = 0, k = nlbound; j < nvars; ++j, ++k) { for (int j = 0, k = nlbound; j < nvars; ++j, ++k) {
std::stringstream str; varsname[j] = fmt::format("{}_{}", varname, k);
str << varname << "_" << k;
varsname[j] = const_cast<char *>(str.str().c_str());
} }
} else if (strcmp(arg[i], "list") == 0) { } else if (strcmp(arg[i], "list") == 0) {
list_requested = true; list_requested = true;
varsname = new char *[1]; varsname.resize(1);
varsname[0] = varname; varsname[0] = varname;
// Default explicit (optional) formatarg // Default explicit (optional) formatarg
} else if (i - 1 + nvars < narg) { } else if (i - 1 + nvars < narg) {
varsname = new char *[nvars]; varsname.resize(nvars);
--i; --i;
for (int j = 0; j < nvars; ++j, ++i) for (int j = 0; j < nvars; ++j, ++i) varsname[j] = arg[i];
varsname[j] = arg[i];
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "explicit") == 0) if (strcmp(arg[i], "explicit") == 0) ++i;
++i;
} }
} else { } else {
std::string msg("Wrong number of arguments in "); auto msg =
msg += "'kim_param get' command.\nThe LAMMPS '"; fmt::format("Wrong number of arguments in 'kim_param get' "
msg += std::to_string(nvars); "command.\nThe LAMMPS '{}' variable names or "
msg += "' variable names or '"; "'{} split' is mandatory", nvars, varname);
msg += varname;
msg += " split' is mandatory";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
} else { } else {
std::string msg("Wrong number of arguments in "); auto msg =
msg += "'kim_param get' command.\nThe LAMMPS '"; fmt::format("Wrong number of arguments in 'kim_param get' "
msg += std::to_string(nvars); "command.\nThe LAMMPS '{}' variable names or "
msg += "' variable names or '"; "'{} split/list' is mandatory", nvars, varname);
msg += varname;
msg += " split/list' is mandatory";
error->all(FLERR, msg); error->all(FLERR, msg);
} }
} else { } else {
varsname = new char *[1]; varsname.resize(1);
if (i < narg) { if (i < narg) {
if (strcmp(arg[i], "split") == 0) { if (strcmp(arg[i], "split") == 0) {
std::stringstream str; varsname[0] = fmt::format("{}_{}", varname, nlbound);
str << varname << "_" << nlbound;
varsname[0] = const_cast<char *>(str.str().c_str());
++i; ++i;
} else { } else {
if ((strcmp(arg[i], "list") == 0) || if ((strcmp(arg[i], "list") == 0) ||
(strcmp(arg[i], "explicit") == 0)) (strcmp(arg[i], "explicit") == 0))
++i; ++i;
varsname[0] = varname; varsname[0] = varname;
} }
} else { } else {
@ -419,98 +409,90 @@ void KimParam::command(int narg, char **arg)
} }
} }
char **varcmd = new char *[3];
varcmd[1] = const_cast<char *>("string");
if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) { if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Double)) {
if (list_requested) { if (list_requested) {
std::stringstream str; std::string str;
double V; double V;
{ {
kim_error = KIM_Model_GetParameterDouble(pkim, param_index, kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
nlbound - 1, &V); nlbound - 1, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterDouble returned error"); error->all(FLERR, "KIM GetParameterDouble returned error");
str << V;
str = fmt::format("{}", V);
} }
for (int j = 1; j < nvars; ++j) { for (int j = 1; j < nvars; ++j) {
kim_error = KIM_Model_GetParameterDouble(pkim, param_index, kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
nlbound - 1 + j, &V); nlbound - 1 + j, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterDouble returned error"); error->all(FLERR, "KIM GetParameterDouble returned error");
str << " " << V;
str += fmt::format(" {}", V);
} }
varcmd[0] = varsname[0];
varcmd[2] = const_cast<char *>(str.str().c_str()); auto setcmd = fmt::format("{} string {}", varsname[0], str);
input->variable->set(3, varcmd); input->variable->set(setcmd);
echo_var_assign(varcmd[0], varcmd[2]); input->write_echo(fmt::format("variable {}\n", setcmd));
} else { } else {
double V;
for (int j = 0; j < nvars; ++j) { for (int j = 0; j < nvars; ++j) {
varcmd[0] = varsname[j];
double V;
kim_error = KIM_Model_GetParameterDouble(pkim, param_index, kim_error = KIM_Model_GetParameterDouble(pkim, param_index,
nlbound - 1 + j, &V); nlbound - 1 + j, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterDouble returned error"); error->all(FLERR, "KIM GetParameterDouble returned error");
std::stringstream str;
str << V; auto setcmd = fmt::format("{} string {}", varsname[j], V);
varcmd[2] = const_cast<char *>(str.str().c_str()); input->variable->set(setcmd);
input->variable->set(3, varcmd); input->write_echo(fmt::format("variable {}\n", setcmd));
echo_var_assign(varcmd[0], varcmd[2]);
} }
} }
} else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) { } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) {
if (list_requested) { if (list_requested) {
std::stringstream str; std::string str;
int V; int V;
{ {
kim_error = KIM_Model_GetParameterInteger(pkim, param_index, kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
nlbound - 1, &V); nlbound - 1, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterInteger returned error"); error->all(FLERR, "KIM GetParameterInteger returned error");
str << V;
str = fmt::format("{}", V);
} }
for (int j = 1; j < nvars; ++j) { for (int j = 1; j < nvars; ++j) {
kim_error = KIM_Model_GetParameterInteger(pkim, param_index, kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
nlbound - 1 + j, &V); nlbound - 1 + j, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterInteger returned error"); error->all(FLERR, "KIM GetParameterInteger returned error");
str << " " << V;
str += fmt::format(" {}", V);
} }
varcmd[0] = varsname[0];
varcmd[2] = const_cast<char *>(str.str().c_str()); auto setcmd = fmt::format("{} string {}", varsname[0], str);
input->variable->set(3, varcmd); input->variable->set(setcmd);
echo_var_assign(varcmd[0], varcmd[2]); input->write_echo(fmt::format("variable {}\n", setcmd));
} else { } else {
int V;
for (int j = 0; j < nvars; ++j) { for (int j = 0; j < nvars; ++j) {
varcmd[0] = varsname[j];
int V;
kim_error = KIM_Model_GetParameterInteger(pkim, param_index, kim_error = KIM_Model_GetParameterInteger(pkim, param_index,
nlbound - 1 + j, &V); nlbound - 1 + j, &V);
if (kim_error) if (kim_error)
error->all(FLERR, "KIM GetParameterInteger returned error"); error->all(FLERR, "KIM GetParameterInteger returned error");
std::stringstream str;
str << V; auto setcmd = fmt::format("{} string {}", varsname[j], V);
varcmd[2] = const_cast<char *>(str.str().c_str()); input->variable->set(setcmd);
input->variable->set(3, varcmd); input->write_echo(fmt::format("variable {}\n", setcmd));
echo_var_assign(varcmd[0], varcmd[2]);
} }
} }
} else } else
error->all(FLERR, "Wrong parameter type"); error->all(FLERR, "Wrong parameter type");
delete[] varcmd;
delete[] varsname;
} // End of loop over all the arguments } // End of loop over all the arguments
// Set the parameters // Set the parameters
} else { } else {
std::string set_cmd("pair_coeff * * "); auto setcmd = fmt::format("pair_coeff * * {} {}", atom_type_list,
set_cmd += atom_type_list; fmt::join(arg + 1, arg + narg, " "));
for (int i = 1; i < narg; ++i) { input->one(setcmd);
set_cmd += " ";
set_cmd += arg[i];
}
input->one(set_cmd);
} }
} else } else
error->all(FLERR, "This model has No mutable parameters"); error->all(FLERR, "This model has No mutable parameters");
@ -521,12 +503,3 @@ void KimParam::command(int narg, char **arg)
input->write_echo(fmt::format("#=== END kim-param {} =====================" input->write_echo(fmt::format("#=== END kim-param {} ====================="
"==================\n",kim_param_get_set)); "==================\n",kim_param_get_set));
} }
/* ---------------------------------------------------------------------- */
void KimParam::echo_var_assign(const std::string &name,
const std::string &value) const
{
input->write_echo(fmt::format("variable {} string {}\n",
name, value));
}

3
src/KIM/kim_param.h
View File

@ -77,9 +77,6 @@ public:
~KimParam(); ~KimParam();
void command(int, char **); void command(int, char **);
private:
void echo_var_assign(const std::string &name, const std::string &value) const;
}; };
} // namespace LAMMPS_NS } // namespace LAMMPS_NS

6
src/KIM/kim_property.cpp
View File

@ -100,11 +100,7 @@ void kimProperty::command(int narg, char **arg)
error->all(FLERR, msg); error->all(FLERR, msg);
} }
if (comm->me == 0) { input->write_echo("#=== kim-property ===========================================\n");
std::string msg;
msg = "#=== kim-property ===========================================\n";
input->write_echo(msg);
}
// Get the kim_str ptr to the data associated with a kim_property_str // Get the kim_str ptr to the data associated with a kim_property_str
// variable // variable

207
src/KIM/kim_query.cpp
View File

@ -63,11 +63,15 @@
#include "info.h" #include "info.h"
#include "input.h" #include "input.h"
#include "modify.h" #include "modify.h"
#include "utils.h"
#include "variable.h" #include "variable.h"
#include "version.h" #include "version.h"
#include "tokenizer.h"
#include "fmt/format.h"
#include <cstdlib>
#include <cstring> #include <cstring>
#include <sstream> #include <string>
#if defined(LMP_KIM_CURL) #if defined(LMP_KIM_CURL)
#include <sys/types.h> #include <sys/types.h>
@ -92,26 +96,28 @@ static size_t write_callback(void *, size_t, size_t, void *);
void KimQuery::command(int narg, char **arg) void KimQuery::command(int narg, char **arg)
{ {
char *varname, *function, *value;
if (narg < 2) error->all(FLERR,"Illegal kim_query command"); if (narg < 2) error->all(FLERR,"Illegal kim_query command");
// check if we had a kim_init command by finding fix STORE/KIM // check if we had a kim_init command by finding fix STORE/KIM
// retrieve model name. // retrieve model name.
char * model_name; char *model_name;
int ifix = modify->find_fix("KIM_MODEL_STORE"); const int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) { if (ifix >= 0) {
FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix]; FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
model_name = (char *)fix_store->getptr("model_name"); model_name = (char *)fix_store->getptr("model_name");
} else error->all(FLERR,"Must use 'kim_init' before 'kim_query'"); } else error->all(FLERR,"Must use 'kim_init' before 'kim_query'");
varname = arg[0]; char *varname = arg[0];
bool split = false; bool split = false;
if (0 == strcmp("split",arg[1])) { if (strcmp("split",arg[1]) == 0) {
if (narg == 2) error->all(FLERR,"Illegal kim_query command"); if (narg == 2) error->all(FLERR,"Illegal kim_query command.\nThe keyword "
if (0 == strcmp("list",arg[2])) "'split' must be followed by the name of "
error->all(FLERR,"Illegal kim_query command"); "the query function");
if (strcmp("list",arg[2]) == 0)
error->all(FLERR,"Illegal kim_query command.\nThe 'list' keyword "
"can not be used after 'split'");
split = true; split = true;
arg++; arg++;
narg--; narg--;
@ -119,78 +125,69 @@ void KimQuery::command(int narg, char **arg)
// The “list” is the default setting // The “list” is the default setting
// the result is returned as a space-separated list of values in variable // the result is returned as a space-separated list of values in variable
if (0 == strcmp("list",arg[1])) { if (strcmp("list",arg[1]) == 0) {
if (narg == 2) error->all(FLERR,"Illegal kim_query command"); if (narg == 2) error->all(FLERR,"Illegal kim_query command.\nThe 'list' "
if (split) error->all(FLERR,"Illegal kim_query command"); "keyword must be followed by ('split' "
"and) the name of the query function");
arg++; arg++;
narg--; narg--;
} }
function = arg[1];
for (int i = 2; i < narg; ++i) {
if (0 == strncmp("model=",arg[i], 6)) {
error->all(FLERR,"Illegal 'model' key in kim_query command");
}
}
char *function = arg[1];
for (int i = 2; i < narg; ++i) {
if (strncmp("model=",arg[i],6) == 0)
error->all(FLERR,"Illegal 'model' key in kim_query command");
if (!strchr(arg[i], '=') || !strchr(arg[i], '[') || !strchr(arg[i], ']'))
error->all(FLERR,fmt::format("Illegal query format.\nInput argument of "
"`{}` to kim_query is wrong. The query "
"format is the keyword=[value], where value "
"is always an array of one or more "
"comma-separated items", arg[i]));
}
#if defined(LMP_KIM_CURL) #if defined(LMP_KIM_CURL)
value = do_query(function, model_name, narg-2, arg+2, comm->me, world); char *value = do_query(function, model_name, narg-2, arg+2, comm->me, world);
// check for valid result // check for valid result
// on error the content of "value" is a '\0' byte // on error the content of "value" is a '\0' byte
// as the first element, and then the error message // as the first element, and then the error message
// that was returned by the web server // that was returned by the web server
char errmsg[1024]; if (strlen(value) == 0) {
if (0 == strlen(value)) { error->all(FLERR,fmt::format("OpenKIM query failed: {}", value+1));
sprintf(errmsg,"OpenKIM query failed: %s",value+1); } else if (strcmp(value,"EMPTY") == 0) {
error->all(FLERR,errmsg); error->all(FLERR,fmt::format("OpenKIM query returned no results"));
} else if (0 == strcmp(value,"EMPTY")) {
sprintf(errmsg,"OpenKIM query returned no results");
error->all(FLERR,errmsg);
} }
input->write_echo("#=== BEGIN kim-query =========================================\n"); input->write_echo("#=== BEGIN kim-query =========================================\n");
char **varcmd = new char*[3]; ValueTokenizer values(value, ",");
varcmd[1] = (char *) "string";
std::stringstream ss(value);
std::string token;
if (split) { if (split) {
int counter = 1; int counter = 1;
while(std::getline(ss, token, ',')) { while (values.has_next()) {
token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim auto svalue = values.next_string();
token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim auto setcmd = fmt::format("{}_{} string {}", varname, counter++, svalue);
std::stringstream splitname; input->variable->set(setcmd);
splitname << varname << "_" << counter++; input->write_echo(fmt::format("variable {}\n", setcmd));
varcmd[0] = const_cast<char *>(splitname.str().c_str());
varcmd[2] = const_cast<char *>(token.c_str());
input->variable->set(3,varcmd);
echo_var_assign(splitname.str(), varcmd[2]);
} }
} else { } else {
varcmd[0] = varname; auto svalue = values.next_string();
std::string value_string; std::string setcmd = fmt::format("{} string \"{}", varname, svalue);
while(std::getline(ss, token, ',')) { while (values.has_next()) {
token.erase(0,token.find_first_not_of(" \n\r\t")); // ltrim svalue = values.next_string();
token.erase(token.find_last_not_of(" \n\r\t") + 1); // rtrim setcmd += fmt::format(" {}", svalue);
if (value_string.size() && token.size())
value_string += " ";
value_string += token;
} }
varcmd[2] = const_cast<char *>(value_string.c_str());; setcmd += "\"";
input->variable->set(3,varcmd); input->variable->set(setcmd);
echo_var_assign(varname, value_string); input->write_echo(fmt::format("variable {}\n", setcmd));
} }
input->write_echo("#=== END kim-query ===========================================\n\n"); input->write_echo("#=== END kim-query ===========================================\n\n");
delete[] varcmd;
delete[] value; delete[] value;
#else #else
error->all(FLERR,"Cannot use 'kim_query' command when KIM package " error->all(FLERR,"Cannot use 'kim_query' command when KIM package "
"is compiled without support for libcurl"); "is compiled without support for libcurl");
#endif #endif
} }
@ -201,17 +198,18 @@ void KimQuery::command(int narg, char **arg)
size_t write_callback(void *data, size_t size, size_t nmemb, void *userp) size_t write_callback(void *data, size_t size, size_t nmemb, void *userp)
{ {
struct WriteBuf *buf = (struct WriteBuf *)userp; struct WriteBuf *buf = (struct WriteBuf *)userp;
size_t buffer_size = size*nmemb;
// copy chunks into the buffer for as long as there is space left // copy chunks into the buffer for as long as there is space left
if (buf->sizeleft) { if (buf->sizeleft) {
size_t copy_this_much = buf->sizeleft; const size_t buffer_size = size * nmemb;
if (copy_this_much > buffer_size) const size_t copy_this_much =
copy_this_much = buffer_size; buf->sizeleft > buffer_size ? buffer_size : buf->sizeleft;
memcpy(buf->dataptr, data, copy_this_much); memcpy(buf->dataptr, data, copy_this_much);
buf->dataptr += copy_this_much; buf->dataptr += copy_this_much;
buf->sizeleft -= copy_this_much; buf->sizeleft -= copy_this_much;
return copy_this_much; return copy_this_much;
} }
return 0; // done return 0; // done
@ -220,16 +218,12 @@ size_t write_callback(void *data, size_t size, size_t nmemb, void *userp)
char *do_query(char *qfunction, char * model_name, int narg, char **arg, char *do_query(char *qfunction, char * model_name, int narg, char **arg,
int rank, MPI_Comm comm) int rank, MPI_Comm comm)
{ {
char value[512], *retval; char value[512];
// run the web query from rank 0 only // run the web query from rank 0 only
if (rank == 0) { if (rank == 0) {
CURL *handle;
CURLcode res;
// set up and clear receive buffer // set up and clear receive buffer
struct WriteBuf buf; struct WriteBuf buf;
buf.dataptr = value; buf.dataptr = value;
buf.sizeleft = 511; buf.sizeleft = 511;
@ -237,19 +231,43 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
// create curl web query instance // create curl web query instance
curl_global_init(CURL_GLOBAL_DEFAULT); curl_global_init(CURL_GLOBAL_DEFAULT);
handle = curl_easy_init(); CURL *handle = curl_easy_init();
if (handle) { if (handle) {
std::string url("https://query.openkim.org/api/"); auto url = fmt::format("https://query.openkim.org/api/{}", qfunction);
url += qfunction; auto query = fmt::format("model=[\"{}\"]", model_name);
for (int i = 0; i < narg; ++i) {
std::string query(arg[0]); ValueTokenizer values(arg[i], "=[]");
query += "&model=[\""; std::string key = values.next_string();
query += model_name; std::string val = values.next_string();
query += "\"]"; std::string::size_type n = val.find(",");
for (int i=1; i < narg; ++i) { if (n == std::string::npos) {
query += '&'; if (utils::is_integer(val) ||
query += arg[i]; utils::is_double(val) ||
(val.front() == '"' &&
val.back() == '"')) {
query += fmt::format("&{}", arg[i]);
} else {
query += fmt::format("&{}=[\"{}\"]", key, val);
}
} else {
query += fmt::format("&{}=[", key);
while (n != std::string::npos){
std::string sval = val.substr(0, n);
if (utils::is_integer(sval) ||
utils::is_double(sval) ||
(val.front() == '"' &&
val.back() == '"')) {
query += fmt::format("{},", sval);
} else {
query += fmt::format("\"{}\",", sval);
}
val = val.substr(n + 1);
n = val.find(",");
}
if (val.size()) query += fmt::format("\"{}\"]", val);
else query[query.size() - 1]=']';
}
} }
#if LMP_DEBUG_CURL #if LMP_DEBUG_CURL
@ -274,23 +292,21 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
} }
} }
std::string user_agent = std::string("kim_query--LAMMPS/") std::string user_agent = fmt::format("kim_query--LAMMPS/{} ({})",
+ LAMMPS_VERSION LAMMPS_VERSION, Info::get_os_info());
+ " (" + Info::get_os_info() + ")";
curl_easy_setopt(handle, CURLOPT_USERAGENT, user_agent.c_str()); curl_easy_setopt(handle, CURLOPT_USERAGENT, user_agent.c_str());
curl_easy_setopt(handle, CURLOPT_URL, url.c_str()); curl_easy_setopt(handle, CURLOPT_URL, url.c_str());
curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L); curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L);
curl_easy_setopt(handle, CURLOPT_POSTFIELDS, query.c_str()); curl_easy_setopt(handle, CURLOPT_POSTFIELDS, query.c_str());
curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION, write_callback);
curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION,write_callback);
curl_easy_setopt(handle, CURLOPT_WRITEDATA,&buf); curl_easy_setopt(handle, CURLOPT_WRITEDATA,&buf);
// perform OpenKIM query and check for errors // perform OpenKIM query and check for errors
res = curl_easy_perform(handle); CURLcode res = curl_easy_perform(handle);
if (res != CURLE_OK) { if (res != CURLE_OK) {
// on error we return an "empty" string but add error message after it // on error we return an "empty" string but add error message after it
value[0]= '\0'; value[0] = '\0';
strcpy(value+1,curl_easy_strerror(res)); strcpy(value+1,curl_easy_strerror(res));
} }
curl_easy_cleanup(handle); curl_easy_cleanup(handle);
@ -302,30 +318,31 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
// we must make a proper copy of the query, as the stack allocation // we must make a proper copy of the query, as the stack allocation
// for "value" will go out of scope. a valid query has a '[' as // for "value" will go out of scope. a valid query has a '[' as
// the first character. skip over it (and the last character ']', too) // the first character. skip over it (and the last character ']', too)
// an error messages starts with a '\0' character. copy that and // an error message starts with a '\0' character. copy that and
// the remaining string, as that is the error message. // the remaining string, as that is the error message.
char *retval;
// a valid query has a '[' as the first character
if (value[0] == '[') { if (value[0] == '[') {
int len = strlen(value)-1; int len = strlen(value) - 1;
if (value[len] == ']') { if (value[len] == ']') {
retval = new char[len];
value[len] = '\0'; value[len] = '\0';
if (0 == strcmp(value+1, "")) { retval = new char[len];
strcpy(retval,"EMPTY"); if (strcmp(value+1, "") == 0) strcpy(retval,"EMPTY");
} else else strcpy(retval,value+1);
strcpy(retval,value+1);
} else { } else {
retval = new char[len+2]; retval = new char[len+2];
retval[0] = '\0'; retval[0] = '\0';
strcpy(retval+1,value); strcpy(retval+1,value);
} }
// an error message starts with a '\0' character
} else if (value[0] == '\0') { } else if (value[0] == '\0') {
int len = strlen(value+1)+2; int len = strlen(value+1)+2;
retval = new char[len]; retval = new char[len];
retval[0] = '\0'; retval[0] = '\0';
strcpy(retval+1,value+1); strcpy(retval+1,value+1);
// unknown response type. we should not get here.
} else { } else {
// unknown response type. we should not get here.
// we return an "empty" string but add error message after it // we return an "empty" string but add error message after it
int len = strlen(value)+2; int len = strlen(value)+2;
retval = new char[len]; retval = new char[len];
@ -335,11 +352,3 @@ char *do_query(char *qfunction, char * model_name, int narg, char **arg,
return retval; return retval;
} }
#endif #endif
/* ---------------------------------------------------------------------- */
void KimQuery::echo_var_assign(const std::string &name,
const std::string &value) const
{
input->write_echo(fmt::format("variable {} string {}\n",name,value));
}

6
src/KIM/kim_query.h
View File

@ -13,7 +13,8 @@
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U), Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN) Ryan S. Elliott (UMN),
Yaser Afshar (UMN)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -71,9 +72,6 @@ class KimQuery : protected Pointers {
public: public:
KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; KimQuery(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **); void command(int, char **);
private:
void echo_var_assign(const std::string &name, const std::string &value)
const;
}; };
} }

167
src/KIM/pair_kim.cpp
View File

@ -67,8 +67,9 @@
#include "neighbor.h" #include "neighbor.h"
#include "update.h" #include "update.h"
#include <cstdlib>
#include <cstring> #include <cstring>
#include <sstream> #include <vector>
using namespace LAMMPS_NS; using namespace LAMMPS_NS;
@ -204,8 +205,8 @@ void PairKIM::compute(int eflag, int vflag)
KIM_COMPUTE_ARGUMENT_NAME_particleContributing, KIM_COMPUTE_ARGUMENT_NAME_particleContributing,
kim_particleContributing); kim_particleContributing);
if (kimerror) if (kimerror)
error->all(FLERR, error->all(FLERR,"Unable to set KIM particle species "
"Unable to set KIM particle species codes and/or contributing"); "codes and/or contributing");
} }
// kim_particleSpecies = KIM atom species for each LAMMPS atom // kim_particleSpecies = KIM atom species for each LAMMPS atom
@ -339,7 +340,9 @@ void PairKIM::coeff(int narg, char **arg)
// insure I,J args are * * // insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients"); error->all(FLERR,"Incorrect args for pair coefficients.\nThe first two "
"arguments of pair_coeff command must be * * to span "
"all LAMMPS atom types");
int ilo,ihi,jlo,jhi; int ilo,ihi,jlo,jhi;
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error); utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
@ -410,9 +413,8 @@ void PairKIM::coeff(int narg, char **arg)
if (supported) { if (supported) {
kim_particle_codes[i] = code; kim_particle_codes[i] = code;
} else { } else {
std::string msg("create_kim_particle_codes: symbol not found: "); error->all(FLERR,fmt::format("GetSpeciesSupportAndCode: symbol not "
msg += lmps_unique_elements[i]; "found: {}",lmps_unique_elements[i]));
error->all(FLERR, msg);
} }
} }
// Set the new values for PM parameters // Set the new values for PM parameters
@ -421,11 +423,9 @@ void PairKIM::coeff(int narg, char **arg)
int numberOfParameters(0); int numberOfParameters(0);
KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters); KIM_Model_GetNumberOfParameters(pkim, &numberOfParameters);
if (!numberOfParameters) { if (!numberOfParameters)
std::string msg("Incorrect args for pair coefficients \n"); error->all(FLERR,"Incorrect args for pair coefficients\n"
msg += "This model has No mutable parameters"; "This model has No mutable parameters");
error->all(FLERR, msg);
}
int kimerror; int kimerror;
@ -456,11 +456,10 @@ void PairKIM::coeff(int narg, char **arg)
} }
if (param_index >= numberOfParameters) { if (param_index >= numberOfParameters) {
std::string msg("Wrong argument for pair coefficients.\n"); auto msg = fmt::format("Wrong argument for pair coefficients.\n"
msg += "This Model does not have the requested '"; "This Model does not have the requested "
msg += paramname; "'{}' parameter", paramname);
msg += "' parameter"; error->all(FLERR,msg);
error->all(FLERR, msg);
} }
// Get the index_range for the requested parameter // Get the index_range for the requested parameter
@ -472,48 +471,41 @@ void PairKIM::coeff(int narg, char **arg)
// Check to see if the indices range contains only integer numbers & : // Check to see if the indices range contains only integer numbers & :
if (argtostr.find_first_not_of("0123456789:") != std::string::npos) { if (argtostr.find_first_not_of("0123456789:") != std::string::npos) {
std::string msg("Illegal index_range.\n"); auto msg = fmt::format("Illegal index_range.\nExpected integer "
msg += "Expected integer parameter(s) instead of '"; "parameter(s) instead of '{}' in "
msg += argtostr; "index_range", argtostr);
msg += "' in index_range"; error->all(FLERR,msg);
error->all(FLERR, msg);
} }
std::string::size_type npos = argtostr.find(':'); std::string::size_type npos = argtostr.find(':');
if (npos != std::string::npos) { if (npos != std::string::npos) {
argtostr[npos] = ' '; argtostr[npos] = ' ';
std::stringstream str(argtostr); auto words = utils::split_words(argtostr);
str >> nlbound >> nubound; nlbound = atoi(words[0].c_str());
nubound = atoi(words[1].c_str());
if (nubound < 1 || nubound > extent || if (nubound < 1 || nubound > extent ||
nlbound < 1 || nlbound > nubound) { nlbound < 1 || nlbound > nubound) {
std::string msg("Illegal index_range '"); auto msg = fmt::format("Illegal index_range '{}-{}' for '{}' "
msg += std::to_string(nlbound) + "-" ; "parameter with the extent of '{}'",
msg += std::to_string(nubound) + "' for '"; nlbound, nubound, paramname, extent);
msg += paramname; error->all(FLERR,msg);
msg += "' parameter with the extent of '";
msg += std::to_string(extent);
msg += "'";
error->all(FLERR, msg);
} }
} else { } else {
std::stringstream str(argtostr); nlbound = atoi(argtostr.c_str());
str >> nlbound;
if (nlbound < 1 || nlbound > extent) { if (nlbound < 1 || nlbound > extent) {
std::string msg("Illegal index '"); auto msg = fmt::format("Illegal index '{}' for '{}' parameter "
msg += std::to_string(nlbound) + "' for '"; "with the extent of '{}'", nlbound,
msg += paramname; paramname, extent);
msg += "' parameter with the extent of '"; error->all(FLERR,msg);
msg += std::to_string(extent);
msg += "'";
error->all(FLERR, msg);
} }
nubound = nlbound; nubound = nlbound;
} }
} else { } else {
std::string msg = error->all(FLERR,"Wrong number of arguments for pair coefficients.\n"
"Wrong number of arguments for pair coefficients.\n"; "Index range after parameter name is mandatory");
msg += "Index range after parameter name is mandatory";
error->all(FLERR, msg);
} }
// Parameter values // Parameter values
@ -524,7 +516,7 @@ void PairKIM::coeff(int narg, char **arg)
kimerror = KIM_Model_SetParameterDouble(pkim, param_index, kimerror = KIM_Model_SetParameterDouble(pkim, param_index,
nlbound - 1 + j, V); nlbound - 1 + j, V);
if (kimerror) if (kimerror)
error->all(FLERR, "KIM SetParameterDouble returned error"); error->all(FLERR,"KIM SetParameterDouble returned error");
} }
} else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) { } else if (KIM_DataType_Equal(kim_DataType, KIM_DATA_TYPE_Integer)) {
for (int j = 0; j < nubound - nlbound + 1; ++j) { for (int j = 0; j < nubound - nlbound + 1; ++j) {
@ -532,25 +524,22 @@ void PairKIM::coeff(int narg, char **arg)
kimerror = KIM_Model_SetParameterInteger(pkim, param_index, kimerror = KIM_Model_SetParameterInteger(pkim, param_index,
nlbound - 1 + j, V); nlbound - 1 + j, V);
if (kimerror) if (kimerror)
error->all(FLERR, "KIM SetParameterInteger returned error"); error->all(FLERR,"KIM SetParameterInteger returned error");
} }
} else } else
error->all(FLERR, "Wrong parameter type to update"); error->all(FLERR,"Wrong parameter type to update");
} else { } else {
std::string msg = auto msg = fmt::format("Wrong number of variable values for pair "
"Wrong number of variable values for pair coefficients.\n"; "coefficients.\n'{}' values are requested "
msg += "'"; "for '{}' parameter", nubound - nlbound + 1,
msg += std::to_string(nubound - nlbound + 1); paramname);
msg += "' values are requested for '"; error->all(FLERR,msg);
msg += paramname;
msg += "' parameter.";
error->all(FLERR, msg);
} }
} }
kimerror = KIM_Model_ClearThenRefresh(pkim); kimerror = KIM_Model_ClearThenRefresh(pkim);
if (kimerror) if (kimerror)
error->all(FLERR, "KIM KIM_Model_ClearThenRefresh returned error"); error->all(FLERR,"KIM KIM_Model_ClearThenRefresh returned error");
} }
} }
@ -842,11 +831,13 @@ void PairKIM::kim_init()
else if (!requestedUnitsAccepted) else if (!requestedUnitsAccepted)
error->all(FLERR,"KIM Model did not accept the requested unit system"); error->all(FLERR,"KIM Model did not accept the requested unit system");
auto logID = fmt::format("{}_Model", comm->me);
KIM_Model_SetLogID(pkim, logID.c_str());
// check that the model does not require unknown capabilities // check that the model does not require unknown capabilities
kimerror = check_for_routine_compatibility(); kimerror = check_for_routine_compatibility();
if (kimerror) if (kimerror)
error->all(FLERR, error->all(FLERR,"KIM Model requires unknown Routines. Unable to proceed");
"KIM Model requires unknown Routines. Unable to proceed");
kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs);
if (kimerror) { if (kimerror) {
@ -854,6 +845,9 @@ void PairKIM::kim_init()
error->all(FLERR,"KIM ComputeArgumentsCreate failed"); error->all(FLERR,"KIM ComputeArgumentsCreate failed");
} else kim_init_ok = true; } else kim_init_ok = true;
logID = fmt::format("{}_ComputeArguments", comm->me);
KIM_ComputeArguments_SetLogID(pargs, logID.c_str());
// determine KIM Model capabilities (used in this function below) // determine KIM Model capabilities (used in this function below)
set_kim_model_has_flags(); set_kim_model_has_flags();
@ -985,43 +979,46 @@ void PairKIM::set_lmps_flags()
error->all(FLERR,"pair_kim does not support hybrid"); error->all(FLERR,"pair_kim does not support hybrid");
// determine unit system and set lmps_units flag // determine unit system and set lmps_units flag
if ((strcmp(update->unit_style,"real")==0)) { if (strcmp(update->unit_style,"real") == 0) {
lmps_units = REAL; lmps_units = REAL;
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol; energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(update->unit_style,"metal")==0)) { } else if (strcmp(update->unit_style,"metal") == 0) {
lmps_units = METAL; lmps_units = METAL;
lengthUnit = KIM_LENGTH_UNIT_A; lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV; energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps; timeUnit = KIM_TIME_UNIT_ps;
} else if ((strcmp(update->unit_style,"si")==0)) { } else if (strcmp(update->unit_style,"si") == 0) {
lmps_units = SI; lmps_units = SI;
lengthUnit = KIM_LENGTH_UNIT_m; lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J; energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C; chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(update->unit_style,"cgs")==0)) { } else if (strcmp(update->unit_style,"cgs") == 0) {
lmps_units = CGS; lmps_units = CGS;
lengthUnit = KIM_LENGTH_UNIT_cm; lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg; energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC; chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s; timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(update->unit_style,"electron")==0)) { } else if (strcmp(update->unit_style,"electron") == 0) {
lmps_units = ELECTRON; lmps_units = ELECTRON;
lengthUnit = KIM_LENGTH_UNIT_Bohr; lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree; energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e; chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K; temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs; timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(update->unit_style,"lj")==0)) { } else if (strcmp(update->unit_style,"lj") == 0 ||
error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); strcmp(update->unit_style,"micro") == 0 ||
strcmp(update->unit_style,"nano") == 0) {
error->all(FLERR,fmt::format("LAMMPS unit_style {} not supported "
"by KIM models", update->unit_style));
} else { } else {
error->all(FLERR,"Unknown unit_style"); error->all(FLERR,"Unknown unit_style");
} }
@ -1102,29 +1099,33 @@ void PairKIM::set_kim_model_has_flags()
KIM_SUPPORT_STATUS_required)) { KIM_SUPPORT_STATUS_required)) {
std::string msg("KIM Model requires unsupported compute argument: "); std::string msg("KIM Model requires unsupported compute argument: ");
msg += KIM_ComputeArgumentName_ToString(computeArgumentName); msg += KIM_ComputeArgumentName_ToString(computeArgumentName);
error->all(FLERR, msg); error->all(FLERR,msg);
} }
} }
if (KIM_SupportStatus_Equal(kim_model_support_for_energy, if (comm->me == 0) {
KIM_SUPPORT_STATUS_notSupported)) if (KIM_SupportStatus_Equal(kim_model_support_for_energy,
error->warning(FLERR,"KIM Model does not provide `partialEnergy'; " KIM_SUPPORT_STATUS_notSupported))
"Potential energy will be zero"); error->warning(FLERR,"KIM Model does not provide 'partialEnergy'; "
"Potential energy will be zero");
if (KIM_SupportStatus_Equal(kim_model_support_for_forces, if (KIM_SupportStatus_Equal(kim_model_support_for_forces,
KIM_SUPPORT_STATUS_notSupported)) KIM_SUPPORT_STATUS_notSupported))
error->warning(FLERR,"KIM Model does not provide `partialForce'; " error->warning(FLERR,"KIM Model does not provide 'partialForce'; "
"Forces will be zero"); "Forces will be zero");
if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy,
KIM_SUPPORT_STATUS_notSupported)) KIM_SUPPORT_STATUS_notSupported))
error->warning(FLERR,"KIM Model does not provide `partialParticleEnergy'; " error->warning(FLERR,"KIM Model does not provide "
"energy per atom will be zero"); "'partialParticleEnergy'; "
"energy per atom will be zero");
if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial,
KIM_SUPPORT_STATUS_notSupported)) KIM_SUPPORT_STATUS_notSupported))
error->warning(FLERR,"KIM Model does not provide `partialParticleVirial'; " error->warning(FLERR,"KIM Model does not provide "
"virial per atom will be zero"); "'partialParticleVirial'; "
"virial per atom will be zero");
}
int numberOfComputeCallbackNames; int numberOfComputeCallbackNames;
KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames( KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames(

3
src/KOKKOS/kokkos.cpp
View File

@ -199,7 +199,6 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
#endif #endif
neigh_thread = 0; neigh_thread = 0;
neigh_thread_set = 0; neigh_thread_set = 0;
neighflag_qeq_set = 0;
if (ngpus > 0) { if (ngpus > 0) {
neighflag = FULL; neighflag = FULL;
neighflag_qeq = FULL; neighflag_qeq = FULL;
@ -314,7 +313,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
neighflag = HALF; neighflag = HALF;
} }
else error->all(FLERR,"Illegal package kokkos command"); else error->all(FLERR,"Illegal package kokkos command");
if (!neighflag_qeq_set) neighflag_qeq = neighflag;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"neigh/qeq") == 0) { } else if (strcmp(arg[iarg],"neigh/qeq") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command");
@ -326,7 +324,6 @@ void KokkosLMP::accelerator(int narg, char **arg)
neighflag_qeq = HALF; neighflag_qeq = HALF;
} }
else error->all(FLERR,"Illegal package kokkos command"); else error->all(FLERR,"Illegal package kokkos command");
neighflag_qeq_set = 1;
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"binsize") == 0) { } else if (strcmp(arg[iarg],"binsize") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command"); if (iarg+2 > narg) error->all(FLERR,"Illegal package kokkos command");

2
src/KOKKOS/kokkos_type.h
View File

@ -405,7 +405,7 @@ struct s_EV_FLOAT_REAX {
E_FLOAT evdwl; E_FLOAT evdwl;
E_FLOAT ecoul; E_FLOAT ecoul;
E_FLOAT v[6]; E_FLOAT v[6];
E_FLOAT ereax[10]; E_FLOAT ereax[9];
KOKKOS_INLINE_FUNCTION KOKKOS_INLINE_FUNCTION
s_EV_FLOAT_REAX() { s_EV_FLOAT_REAX() {
evdwl = 0; evdwl = 0;

3
src/USER-MISC/README
View File

@ -22,10 +22,12 @@ angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
angle_style gaussian, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 Nov 2020
angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12 angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12
angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12
bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11
bond_style gaussian, Evangelos Voyiatzis, evoyiatzis at gmail.com, 25 Nov 2020
bond_style special, David Nicholson, davidanich at gmail.com, 31 Jan 2020 bond_style special, David Nicholson, davidanich at gmail.com, 31 Jan 2020
compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007
compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013
@ -51,6 +53,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18
fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20
fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11
fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015
fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020
fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019
fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018
fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "angle_gaussian.h"
#include <cmath>
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMAL 0.001
#define SMALL 1.0e-8
/* ---------------------------------------------------------------------- */
AngleGaussian::AngleGaussian(LAMMPS *lmp) : Angle(lmp)
{
}
/* ---------------------------------------------------------------------- */
AngleGaussian::~AngleGaussian()
{
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(nterms);
memory->destroy(angle_temperature);
for (int i = 1; i <= atom->nangletypes; i++) {
if (alpha[i]) delete [] alpha[i];
if (width[i]) delete [] width[i];
if (theta0[i]) delete [] theta0[i];
}
delete [] alpha;
delete [] width;
delete [] theta0;
}
}
/* ---------------------------------------------------------------------- */
void AngleGaussian::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type;
double delx1,dely1,delz1,delx2,dely2,delz2;
double eangle,f1[3],f3[3];
double dtheta,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
double prefactor, exponent, g_i, sum_g_i, sum_numerator;
eangle = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMAL) s = SMAL;
s = 1.0/s;
// force & energy
double theta = acos(c);
sum_g_i = 0.0;
sum_numerator = 0.0;
for (int i = 0; i < nterms[type]; i++) {
dtheta = theta - theta0[type][i];
prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
exponent = -2*dtheta*dtheta/(width[type][i]*width[type][i]);
g_i = prefactor*exp(exponent);
sum_g_i += g_i;
sum_numerator += g_i*dtheta/(width[type][i]*width[type][i]);
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (eflag) eangle = -(force->boltz*angle_temperature[type])*log(sum_g_i);
// I should check about the sign of this expression
a = -4.0*(force->boltz*angle_temperature[type])*(sum_numerator/sum_g_i)*s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
f3[0] = a22*delx2 + a12*delx1;
f3[1] = a22*dely2 + a12*dely1;
f3[2] = a22*delz2 + a12*delz1;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += f1[0];
f[i1][1] += f1[1];
f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= f1[0] + f3[0];
f[i2][1] -= f1[1] + f3[1];
f[i2][2] -= f1[2] + f3[2];
}
if (newton_bond || i3 < nlocal) {
f[i3][0] += f3[0];
f[i3][1] += f3[1];
f[i3][2] += f3[2];
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
/* ---------------------------------------------------------------------- */
void AngleGaussian::allocate()
{
allocated = 1;
int n = atom->nangletypes;
memory->create(nterms,n+1,"angle:nterms");
memory->create(angle_temperature,n+1,"angle:angle_temperature");
alpha = new double *[n+1];
width = new double *[n+1];
theta0 = new double *[n+1];
for (int i = 1; i <= n; i++) {
alpha[i] = 0;
width[i] = 0;
theta0[i] = 0;
}
memory->create(setflag,n+1,"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleGaussian::coeff(int narg, char **arg)
{
if (narg < 6) error->all(FLERR,"Incorrect args for angle coefficients");
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nangletypes,ilo,ihi,error);
double angle_temperature_one = utils::numeric(FLERR,arg[1],false,lmp);
int n = utils::inumeric(FLERR,arg[2],false,lmp);
if (narg != 3*n + 3)
error->all(FLERR,"Incorrect args for angle coefficients");
if (!allocated) allocate();
// convert theta0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
angle_temperature[i] = angle_temperature_one;
nterms[i] = n;
alpha[i] = new double [n];
width[i] = new double [n];
theta0[i] = new double [n];
for (int j = 0; j < n; j++ ) {
alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
theta0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp)* MY_PI / 180.0;
setflag[i] = 1;
}
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleGaussian::equilibrium_angle(int i)
{
return theta0[i][0];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleGaussian::write_restart(FILE *fp)
{
fwrite(&angle_temperature[1],sizeof(double),atom->nangletypes,fp);
fwrite(&nterms[1],sizeof(int),atom->nangletypes,fp);
for(int i = 1; i <= atom->nangletypes; i++) {
fwrite(alpha[i],sizeof(double),nterms[i],fp);
fwrite(width[i],sizeof(double),nterms[i],fp);
fwrite(theta0[i],sizeof(double),nterms[i],fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleGaussian::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&angle_temperature[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nangletypes,fp,nullptr,error);
}
MPI_Bcast(&angle_temperature[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&nterms[1],atom->nangletypes,MPI_INT,0,world);
// allocate
for(int i = 1; i <= atom->nangletypes; i++) {
alpha[i] = new double [nterms[i]];
width[i] = new double [nterms[i]];
theta0[i] = new double [nterms[i]];
}
if (comm->me == 0) {
for(int i = 1; i <= atom->nangletypes; i++) {
utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,theta0[i],sizeof(double),nterms[i],fp,nullptr,error);
}
}
for(int i = 1; i <= atom->nangletypes; i++) {
MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(theta0[i],nterms[i],MPI_DOUBLE,0,world);
}
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void AngleGaussian::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nangletypes; i++) {
fprintf(fp,"%d %g %d",i,angle_temperature[i],nterms[i]);
for (int j = 0; j < nterms[i]; j++) {
fprintf(fp," %g %g %g",alpha[i][j],width[i][j],(theta0[i][j]/MY_PI)*180.0);
}
fprintf(fp, "\n");
}
}
/* ---------------------------------------------------------------------- */
double AngleGaussian::single(int type, int i1, int i2, int i3)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(delx1,dely1,delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(delx2,dely2,delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double theta = acos(c) ;
double sum_g_i = 0.0;
double sum_numerator = 0.0;
for (int i = 0; i < nterms[type]; i++) {
double dtheta = theta - theta0[type][i];
double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
double exponent = -2*dtheta*dtheta/(width[type][i]*width[type][i]);
double g_i = prefactor*exp(exponent);
sum_g_i += g_i;
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
return -(force->boltz*angle_temperature[type])*log(sum_g_i);
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef ANGLE_CLASS
AngleStyle(gaussian,AngleGaussian)
#else
#ifndef LMP_ANGLE_GAUSSIAN_H
#define LMP_ANGLE_GAUSSIAN_H
#include "angle.h"
namespace LAMMPS_NS {
class AngleGaussian : public Angle {
public:
AngleGaussian(class LAMMPS *);
virtual ~AngleGaussian();
virtual void compute(int, int);
virtual void coeff(int, char **);
double equilibrium_angle(int);
void write_restart(FILE *);
virtual void read_restart(FILE *);
void write_data(FILE *);
double single(int, int, int, int);
protected:
int *nterms;
double *angle_temperature;
double **alpha,**width,**theta0;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Incorrect args for angle coefficients
Self-explanatory. Check the input script or data file.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "bond_gaussian.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "neighbor.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 1.0e-10
/* ---------------------------------------------------------------------- */
BondGaussian::BondGaussian(LAMMPS *lmp) : Bond(lmp)
{
reinitflag = 1;
}
/* ---------------------------------------------------------------------- */
BondGaussian::~BondGaussian()
{
if (allocated && !copymode) {
memory->destroy(setflag);
memory->destroy(nterms);
memory->destroy(bond_temperature);
for (int i = 1; i <= atom->nbondtypes; i++) {
if (alpha[i]) delete [] alpha[i];
if (width[i]) delete [] width[i];
if (r0[i]) delete [] r0[i];
}
delete [] alpha;
delete [] width;
delete [] r0;
}
}
/* ---------------------------------------------------------------------- */
void BondGaussian::compute(int eflag, int vflag)
{
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r,dr;
double prefactor, exponent, g_i, sum_g_i, sum_numerator;
ebond = 0.0;
ev_init(eflag,vflag);
double **x = atom->x;
double **f = atom->f;
int **bondlist = neighbor->bondlist;
int nbondlist = neighbor->nbondlist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nbondlist; n++) {
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
delz = x[i1][2] - x[i2][2];
rsq = delx*delx + dely*dely + delz*delz;
r = sqrt(rsq);
sum_g_i = 0.0;
sum_numerator = 0.0;
for (int i = 0; i < nterms[type]; i++) {
dr = r - r0[type][i];
prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
exponent = -2*dr*dr/(width[type][i]*width[type][i]);
g_i = prefactor*exp(exponent);
sum_g_i += g_i;
sum_numerator += g_i*dr/(width[type][i]*width[type][i]);
}
// force & energy
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (r > 0.0) fbond = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
else fbond = 0.0;
if (eflag) ebond = -(force->boltz*bond_temperature[type])*log(sum_g_i);
// apply force to each of 2 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] += delx*fbond;
f[i1][1] += dely*fbond;
f[i1][2] += delz*fbond;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] -= delx*fbond;
f[i2][1] -= dely*fbond;
f[i2][2] -= delz*fbond;
}
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
}
}
/* ---------------------------------------------------------------------- */
void BondGaussian::allocate()
{
allocated = 1;
int n = atom->nbondtypes;
memory->create(nterms,n+1,"bond:nterms");
memory->create(bond_temperature,n+1,"bond:bond_temperature");
alpha = new double *[n+1];
width = new double *[n+1];
r0 = new double *[n+1];
for (int i = 1; i <= n; i++) {
alpha[i] = 0;
width[i] = 0;
r0[i] = 0;
}
memory->create(setflag,n+1,"bond:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void BondGaussian::coeff(int narg, char **arg)
{
if (narg < 6) error->all(FLERR,"Incorrect args for bond coefficients");
int ilo,ihi;
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
double bond_temp_one = utils::numeric(FLERR,arg[1],false,lmp);
int n = utils::inumeric(FLERR,arg[2],false,lmp);
if (narg != 3*n + 3)
error->all(FLERR,"Incorrect args for bond coefficients");
if (!allocated) allocate();
int count = 0;
for (int i = ilo; i <= ihi; i++) {
bond_temperature[i] = bond_temp_one;
nterms[i] = n;
alpha[i] = new double [n];
width[i] = new double [n];
r0[i] = new double [n];
for (int j = 0; j < n; j++ ) {
alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
r0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp);
setflag[i] = 1;
}
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondGaussian::equilibrium_distance(int i)
{
return r0[i][0];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondGaussian::write_restart(FILE *fp)
{
fwrite(&bond_temperature[1],sizeof(double),atom->nbondtypes,fp);
fwrite(&nterms[1],sizeof(int),atom->nbondtypes,fp);
for(int i = 1; i <= atom->nbondtypes; i++) {
fwrite(alpha[i],sizeof(double),nterms[i],fp);
fwrite(width[i],sizeof(double),nterms[i],fp);
fwrite(r0[i],sizeof(double),nterms[i],fp);
}
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondGaussian::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
utils::sfread(FLERR,&bond_temperature[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nbondtypes,fp,nullptr,error);
}
MPI_Bcast(&bond_temperature[1],atom->nbondtypes,MPI_DOUBLE,0,world);
MPI_Bcast(&nterms[1],atom->nbondtypes,MPI_INT,0,world);
// allocate
for(int i = 1; i <= atom->nbondtypes; i++) {
alpha[i] = new double [nterms[i]];
width[i] = new double [nterms[i]];
r0[i] = new double [nterms[i]];
}
if (comm->me == 0) {
for(int i = 1; i <= atom->nbondtypes; i++) {
utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
utils::sfread(FLERR,r0[i],sizeof(double),nterms[i],fp,nullptr,error);
}
}
for(int i = 1; i <= atom->nbondtypes; i++) {
MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
MPI_Bcast(r0[i],nterms[i],MPI_DOUBLE,0,world);
}
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void BondGaussian::write_data(FILE *fp)
{
for (int i = 1; i <= atom->nbondtypes; i++) {
fprintf(fp,"%d %g %d",i,bond_temperature[i],nterms[i]);
for (int j = 0; j < nterms[i]; j++) {
fprintf(fp," %g %g %g",alpha[i][j],width[i][j],r0[i][j]);
}
fprintf(fp, "\n");
}
}
/* ---------------------------------------------------------------------- */
double BondGaussian::single(int type, double rsq, int /*i*/, int /*j*/,
double &fforce)
{
double r = sqrt(rsq);
fforce = 0;
double sum_g_i = 0.0;
double sum_numerator = 0.0;
for (int i = 0; i < nterms[type]; i++) {
double dr = r - r0[type][i];
double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
double exponent = -2*dr*dr/(width[type][i]*width[type][i]);
double g_i = prefactor*exp(exponent);
sum_g_i += g_i;
sum_numerator += g_i*dr/(width[type][i]*width[type][i]);
}
if (sum_g_i < SMALL) sum_g_i = SMALL;
if (r > 0.0) fforce = -4.0*(force->boltz*bond_temperature[type])*(sum_numerator/sum_g_i)/r;
return -(force->boltz*bond_temperature[type])*log(sum_g_i);
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef BOND_CLASS
BondStyle(gaussian,BondGaussian)
#else
#ifndef LMP_BOND_GAUSSIAN_H
#define LMP_BOND_GAUSSIAN_H
#include "bond.h"
namespace LAMMPS_NS {
class BondGaussian : public Bond {
public:
BondGaussian(class LAMMPS *);
virtual ~BondGaussian();
virtual void compute(int, int);
virtual void coeff(int, char **);
double equilibrium_distance(int);
void write_restart(FILE *);
virtual void read_restart(FILE *);
void write_data(FILE *);
double single(int, double, int, int, double &);
protected:
int *nterms;
double *bond_temperature;
double **alpha,**width,**r0;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Incorrect args for bond coefficients
Self-explanatory. Check the input script or data file.
*/

208
src/USER-MISC/fix_electron_stopping_fit.cpp Normal file
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@ -0,0 +1,208 @@
/* ---------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------ */
/* ---------------------------------------------------------------------
Contributing authors: Stephen M. Foiles (SNL)
James A. Stewart (SNL)
------------------------------------------------------------------ */
#include "fix_electron_stopping_fit.h"
#include "atom.h"
#include "citeme.h"
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_special.h"
#include "modify.h"
#include "region.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;
// ---------------------------------------------------------------------
static const char cite_fix_electron_stopping_fit_c[] =
"fix electron/stopping/fit command:\n\n"
"@Article{Stewart2018,\n"
" author = { J.A. Stewart and G. Brookman and P. Price and M. Franco and W. Ji and K. Hattar and R. Dingreville },\n"
" title = { Characterizing single isolated radiation-damage events from molecular dynamics via virtual diffraction methods },\n"
" journal = { Journal of Applied Physics },\n"
" year = { 2018 },\n"
" volume = { 123 },\n"
" number = { 16 },\n"
" pages = { 165902 }\n"
"}\n\n"
"@Article{Lee2020,\n"
" author = { C.W. Lee and J.A. Stewart and S.M. Foiles and R. Dingreville and A. Schleife },\n"
" title = { Multiscale simulations of electron and ion dynamics in self-irradiated silicon },\n"
" journal = { Physical Review B },\n"
" year = { 2020 },\n"
" volume = { 102 },\n"
" number = { 2 },\n"
" pages = { 024107 }\n"
"}\n\n";
// ---------------------------------------------------------------------
FixElectronStoppingFit::FixElectronStoppingFit(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp,narg,arg), energy_coh_in(nullptr), drag_fac_in_1(nullptr),
drag_fac_in_2(nullptr), drag_fac_1(nullptr), drag_fac_2(nullptr),
v_min_sq(nullptr), v_max_sq(nullptr)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_electron_stopping_fit_c);
if (narg < 3 + 3*atom->ntypes) {
error->all(FLERR,"Incorrect number of fix electron/stopping/fit arguments");
}
scalar_flag = 1;
global_freq = 1;
energy_coh_in = new double[atom->ntypes+1];
drag_fac_in_1 = new double[atom->ntypes+1];
drag_fac_in_2 = new double[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) {
energy_coh_in[i] = utils::numeric(FLERR,arg[3*i],false,lmp);
drag_fac_in_1[i] = utils::numeric(FLERR,arg[3*i+1],false,lmp);
drag_fac_in_2[i] = utils::numeric(FLERR,arg[3*i+2],false,lmp);
};
v_min_sq = new double[atom->ntypes+1];
v_max_sq = new double[atom->ntypes+1];
drag_fac_1 = new double[atom->ntypes+1];
drag_fac_2 = new double[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) {
double mvv;
mvv = 2.0*energy_coh_in[i]/force->mvv2e;
v_min_sq[i] = 1.0*mvv/atom->mass[i];
v_max_sq[i] = 2.0*mvv/atom->mass[i];
drag_fac_1[i] = drag_fac_in_1[i];
drag_fac_2[i] = drag_fac_in_2[i];
};
};
// ---------------------------------------------------------------------
FixElectronStoppingFit::~FixElectronStoppingFit()
{
delete [] energy_coh_in;
delete [] drag_fac_in_1;
delete [] drag_fac_in_2;
delete [] drag_fac_1;
delete [] drag_fac_2;
delete [] v_min_sq;
delete [] v_max_sq;
};
// ---------------------------------------------------------------------
int FixElectronStoppingFit::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::init()
{
electronic_loss_this_node = 0.;
electronic_loss = 0.;
f_dot_v_prior = 0.;
f_dot_v_current = 0.;
last_step = update->ntimestep;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::setup(int vflag)
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
};
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::post_force(int vflag)
{
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
f_dot_v_current = 0.0;
for (int i = 0; i < nlocal; i++) {
double vv = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (vv > v_min_sq[type[i]]) {
double gamma_x;
double gamma_y;
double gamma_z;
double v_mag = sqrt(vv);
if (vv < v_max_sq[type[i]]) {
double frac = (vv - v_min_sq[type[i]])/(v_max_sq[type[i]] - v_min_sq[type[i]]);
gamma_x = frac*(drag_fac_2[type[i]]*v[i][0] + drag_fac_1[type[i]]);
gamma_y = frac*(drag_fac_2[type[i]]*v[i][1] + drag_fac_1[type[i]]);
gamma_z = frac*(drag_fac_2[type[i]]*v[i][2] + drag_fac_1[type[i]]);
} else {
gamma_x = drag_fac_2[type[i]]*v[i][0] + drag_fac_1[type[i]];
gamma_y = drag_fac_2[type[i]]*v[i][1] + drag_fac_1[type[i]];
gamma_z = drag_fac_2[type[i]]*v[i][2] + drag_fac_1[type[i]];
};
f[i][0] -= gamma_x*v[i][0];
f[i][1] -= gamma_y*v[i][1];
f[i][2] -= gamma_z*v[i][2];
f_dot_v_current += v_mag*sqrt( MathSpecial::square(gamma_x*v[i][0])
+ MathSpecial::square(gamma_y*v[i][1])
+ MathSpecial::square(gamma_z*v[i][2]) );
};
};
this_step = update->ntimestep;
electronic_loss_this_node += (this_step - last_step)*update->dt*0.5*(f_dot_v_prior + f_dot_v_current);
last_step = this_step;
f_dot_v_prior = f_dot_v_current;
};
// ---------------------------------------------------------------------
void FixElectronStoppingFit::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
};
// ---------------------------------------------------------------------
double FixElectronStoppingFit::compute_scalar()
{
MPI_Allreduce(&electronic_loss_this_node,&electronic_loss,1,MPI_DOUBLE,MPI_SUM,world);
return electronic_loss;
};
// ---------------------------------------------------------------------

54
src/USER-MISC/fix_electron_stopping_fit.h Normal file
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@ -0,0 +1,54 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Stephen M. Foiles (SNL)
James A. Stewart (SNL)
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(electron/stopping/fit,FixElectronStoppingFit)
#else
#ifndef LMP_FIX_ELECTRON_STOPPING_FIT_H
#define LMP_FIX_ELECTRON_STOPPING_FIT_H
#include "fix.h"
namespace LAMMPS_NS {
class FixElectronStoppingFit : public Fix {
public:
FixElectronStoppingFit(class LAMMPS *, int, char **);
~FixElectronStoppingFit();
int setmask();
void init();
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
double compute_scalar();
private:
double *energy_coh_in,*v_min_sq,*v_max_sq,*drag_fac_in_1,*drag_fac_in_2,*drag_fac_1,*drag_fac_2;
double electronic_loss,electronic_loss_this_node;
double f_dot_v_prior,f_dot_v_current;
int last_step,this_step;
int nlevels_respa;
};
}
#endif
#endif

163
unittest/commands/test_kim_commands.cpp
View File

@ -17,6 +17,7 @@
#include "lammps.h" #include "lammps.h"
#include "lmppython.h" #include "lmppython.h"
#include "modify.h" #include "modify.h"
#include "output.h"
#include "utils.h" #include "utils.h"
#include "variable.h" #include "variable.h"
#include "gmock/gmock.h" #include "gmock/gmock.h"
@ -82,17 +83,24 @@ TEST_F(KimCommandsTest, kim_init)
{ {
if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP(); if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP();
TEST_FAILURE(".*ERROR: Illegal kim_init command.*", lmp->input->one("kim_init");); TEST_FAILURE(".*ERROR: Illegal kim_init command.*",
lmp->input->one("kim_init"););
TEST_FAILURE(".*ERROR: Illegal kim_init command.*", TEST_FAILURE(".*ERROR: Illegal kim_init command.*",
lmp->input->one("kim_init LennardJones_Ar real si");); lmp->input->one("kim_init LennardJones_Ar real si"););
TEST_FAILURE(".*ERROR: LAMMPS unit_style lj not supported by KIM models.*", TEST_FAILURE(".*ERROR: LAMMPS unit_style lj not supported by KIM models.*",
lmp->input->one("kim_init LennardJones_Ar lj");); lmp->input->one("kim_init LennardJones_Ar lj"););
TEST_FAILURE(".*ERROR: LAMMPS unit_style micro not supported by KIM models.*",
lmp->input->one("kim_init LennardJones_Ar micro"););
TEST_FAILURE(".*ERROR: LAMMPS unit_style nano not supported by KIM models.*",
lmp->input->one("kim_init LennardJones_Ar nano"););
TEST_FAILURE(".*ERROR: Unknown unit_style.*", TEST_FAILURE(".*ERROR: Unknown unit_style.*",
lmp->input->one("kim_init LennardJones_Ar new_style");); lmp->input->one("kim_init LennardJones_Ar new_style"););
TEST_FAILURE(".*ERROR: KIM Model name not found.*", TEST_FAILURE(".*ERROR: KIM Model name not found.*",
lmp->input->one("kim_init Unknown_Model real");); lmp->input->one("kim_init Unknown_Model real"););
TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model, required units = metal.*", TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model, required units = metal.*",
lmp->input->one("kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real");); lmp->input->one("kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real"););
// TEST_FAILURE(".*ERROR: KIM Model does not support the requested unit system.*",
// lmp->input->one("kim_init ex_model_Ar_P_Morse real"););
if (!verbose) ::testing::internal::CaptureStdout(); if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("kim_init LennardJones_Ar real"); lmp->input->one("kim_init LennardJones_Ar real");
@ -125,6 +133,17 @@ TEST_F(KimCommandsTest, kim_interactions)
lmp->input->one("create_atoms 1 box"); lmp->input->one("create_atoms 1 box");
if (!verbose) ::testing::internal::GetCapturedStdout(); if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Illegal kim_interactions command.*",
lmp->input->one("kim_interactions Ar Ar"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("lattice fcc 4.4300");
lmp->input->one("region box block 0 20 0 20 0 20");
lmp->input->one("create_box 4 box");
lmp->input->one("create_atoms 4 box");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Illegal kim_interactions command.*", TEST_FAILURE(".*ERROR: Illegal kim_interactions command.*",
lmp->input->one("kim_interactions Ar Ar");); lmp->input->one("kim_interactions Ar Ar"););
@ -172,6 +191,21 @@ TEST_F(KimCommandsTest, kim_interactions)
TEST_FAILURE(".*ERROR: Species 'Ar' is not supported by this KIM Simulator Model.*", TEST_FAILURE(".*ERROR: Species 'Ar' is not supported by this KIM Simulator Model.*",
lmp->input->one("kim_interactions Ar");); lmp->input->one("kim_interactions Ar"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("kim_init Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu metal");
lmp->input->one("lattice fcc 4.08");
lmp->input->one("region box block 0 10 0 10 0 10");
lmp->input->one("create_box 1 box");
lmp->input->one("create_atoms 1 box");
lmp->input->one("kim_interactions Au");
if (!verbose) ::testing::internal::GetCapturedStdout();
// ASSERT_EQ(lmp->output->var_kim_periodic, 1);
// TEST_FAILURE(".*ERROR: Incompatible units for KIM Simulator Model.*",
// lmp->input->one("kim_interactions Au"););
if (!verbose) ::testing::internal::CaptureStdout(); if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear"); lmp->input->one("clear");
lmp->input->one("kim_init LennardJones_Ar real"); lmp->input->one("kim_init LennardJones_Ar real");
@ -302,6 +336,133 @@ TEST_F(KimCommandsTest, kim_property)
} }
} }
TEST_F(KimCommandsTest, kim_query)
{
if (!LAMMPS::is_installed_pkg("KIM")) GTEST_SKIP();
TEST_FAILURE(".*ERROR: Illegal kim_query command.*",
lmp->input->one("kim_query"););
TEST_FAILURE(".*ERROR: Must use 'kim_init' before 'kim_query'.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic"););
if (!verbose) ::testing::internal::CaptureStdout();
lmp->input->one("clear");
lmp->input->one("kim_init LennardJones612_UniversalShifted__MO_959249795837_003 real");
if (!verbose) ::testing::internal::GetCapturedStdout();
TEST_FAILURE(".*ERROR: Illegal kim_query command.\nThe keyword 'split' "
"must be followed by the name of the query function.*",
lmp->input->one("kim_query a0 split"););
TEST_FAILURE(".*ERROR: Illegal kim_query command.\nThe 'list' keyword "
"can not be used after 'split'.*",
lmp->input->one("kim_query a0 split list"););
TEST_FAILURE(".*ERROR: Illegal kim_query command.\nThe 'list' keyword "
"must be followed by \\('split' and\\) the name of the query "
"function.*", lmp->input->one("kim_query a0 list"););
TEST_FAILURE(".*ERROR: Illegal 'model' key in kim_query command.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic "
"model=[MO_959249795837_003]"););
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `crystal` "
"to kim_query is wrong. The query format is the "
"keyword=\\[value\\], where value is always an array of one "
"or more comma-separated items.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic "
"crystal"););
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `"
"crystal=fcc` to kim_query is wrong. The query format is the "
"keyword=\\[value\\], where value is always an array of one "
"or more comma-separated items.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic "
"crystal=fcc"););
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `"
"crystal=\\[fcc` to kim_query is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic "
"crystal=[fcc"););
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `"
"crystal=fcc\\]` to kim_query is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one("kim_query a0 get_lattice_constant_cubic "
"crystal=fcc]"););
std::string squery("kim_query a0 get_lattice_constant_cubic ");
squery += "crystal=[\"fcc\"] species=\"Al\",\"Ni\" units=[\"angstrom\"]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"\"Al\",\"Ni\"` to kim_query is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim_query a0 get_lattice_constant_cubic ";
squery += "crystal=[\"fcc\"] species=\"Al\",\"Ni\", units=[\"angstrom\"]";
TEST_FAILURE(".*ERROR: Illegal query format.\nInput argument of `species="
"\"Al\",\"Ni\",` to kim_query is wrong. The query format is "
"the keyword=\\[value\\], where value is always an array of "
"one or more comma-separated items.*",
lmp->input->one(squery););
squery = "kim_query a0 get_lattice_constant_cubic crystal=[fcc] "
"species=[Al]";
TEST_FAILURE(".*ERROR: OpenKIM query failed:.*", lmp->input->one(squery););
squery = "kim_query a0 get_lattice_constant_cubic crystal=[fcc] "
"units=[\"angstrom\"]";
TEST_FAILURE(".*ERROR: OpenKIM query failed:.*", lmp->input->one(squery););
// if (!verbose) ::testing::internal::CaptureStdout();
// lmp->input->one("clear");
// lmp->input->one("kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal");
// squery = "kim_query latconst split get_lattice_constant_hexagonal ";
// squery += "crystal=[\"hcp\"] species=[\"Zr\"] units=[\"angstrom\"]";
// lmp->input->one(squery);
// if (!verbose) ::testing::internal::GetCapturedStdout();
// ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_1")) ==
// std::string("3.234055244384789")));
// ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst_2")) ==
// std::string("5.167650199630013")));
// if (!verbose) ::testing::internal::CaptureStdout();
// lmp->input->one("clear");
// lmp->input->one("kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal");
// squery = "kim_query latconst list get_lattice_constant_hexagonal ";
// squery += "crystal=[hcp] species=[Zr] units=[angstrom]";
// lmp->input->one(squery);
// if (!verbose) ::testing::internal::GetCapturedStdout();
// ASSERT_TRUE((std::string(lmp->input->variable->retrieve("latconst")) ==
// std::string("3.234055244384789 5.167650199630013")));
// squery = "kim_query latconst list get_lattice_constant_hexagonal ";
// squery += "crystal=[bcc] species=[Zr] units=[angstrom]";
// TEST_FAILURE(".*ERROR: OpenKIM query failed:.*", lmp->input->one(squery););
// if (!verbose) ::testing::internal::CaptureStdout();
// lmp->input->one("clear");
// lmp->input->one("kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal");
// squery = "kim_query alpha get_linear_thermal_expansion_coefficient_cubic ";
// squery += "crystal=[fcc] species=[Al] units=[1/K] temperature=[293.15] ";
// squery += "temperature_units=[K]";
// lmp->input->one(squery);
// if (!verbose) ::testing::internal::GetCapturedStdout();
// ASSERT_TRUE((std::string(lmp->input->variable->retrieve("alpha")) ==
// std::string("1.654960564704273e-05")));
}
} // namespace LAMMPS_NS } // namespace LAMMPS_NS
int main(int argc, char **argv) int main(int argc, char **argv)

86
unittest/force-styles/tests/angle-gaussian.yaml Normal file
View File

@ -0,0 +1,86 @@
---
lammps_version: 29 Oct 2020
date_generated: Sat Nov 14 17:18:12 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
angle gaussian
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
angle_style: gaussian
angle_coeff: ! |
1 300.0 3 0.2189 8.66 88.1 0.5439 9.94 142.7 0.2307 17.14 167.0
2 300.0 3 0.0214 14.29 85.3 0.3934 18.22 118.1 0.9411 31.21 136.2
3 300.0 2 0.2189 8.66 88.1 0.5439 9.94 142.7
4 300.0 2 0.0214 14.29 85.3 0.3934 18.22 118.1
equilibrium: 4 1.5376350710070041 1.4887658519511628 1.5376350710070041 1.4887658519511628
extract: ! ""
natoms: 29
init_energy: 57.7940091589437
init_stress: ! |2-
1.8540667929702014e-02 -2.1128225814185397e-02 2.5875578844833853e-03 1.9120388327532396e-02 4.4564216146325795e-03 9.8400107526492309e-03
init_forces: ! |2
1 2.0043481356521267e-03 -2.0981767618283602e-04 -2.3209495543181176e-03
2 3.5529860865363239e-05 2.8767662992335252e-04 2.3132719898919820e-04
3 -3.8667546050125514e-04 2.0816982895064929e-03 3.3491343253347289e-03
4 -4.7471002298472755e-04 -1.0657600563862162e-03 2.4796171798629677e-04
5 -1.6406411064805123e-03 -1.9359456692002001e-03 -9.0394626833801086e-04
6 7.6979393607576755e-03 -8.1291748957998018e-03 -9.9817242122740776e-03
7 -4.2572919294439045e-03 3.8055081960951839e-03 -9.2914562787063215e-04
8 -5.6354813852788994e-03 -2.4077018853792594e-03 2.2075705642764603e-02
9 -8.5366182106296319e-04 7.7489027943554716e-04 4.3064306944232773e-06
10 5.1692145475614156e-03 1.1913856117509856e-02 -1.2167886610859078e-02
11 -1.1932769900266460e-03 -5.6695560883419894e-04 6.3912856495926295e-04
12 1.5380901789534356e-03 -4.4133578770737883e-03 -3.1448353955117270e-03
13 1.0633492902104076e-04 2.6203621306745674e-04 1.4238358783950607e-04
14 7.0133753297702093e-04 -2.4463789752656221e-04 -2.8963548243354467e-04
15 4.8989433563144716e-04 -2.8356800785119403e-04 8.3150095382329269e-04
16 -3.7177027531705075e-03 6.9883235686930205e-04 1.9103996085473906e-03
17 4.1675258752988943e-04 -5.6757850817313379e-04 3.0627512066648804e-04
18 2.4034769486436930e-04 2.5116260424105398e-03 -1.0192991295370015e-02
19 -2.9428816898762833e-03 -3.6662332265825250e-03 4.3652227193094872e-03
20 2.7025339950119140e-03 1.1546071841719852e-03 5.8277685760605271e-03
21 2.8475989038751108e-03 3.5647233204607149e-03 -1.0653298109293498e-02
22 -5.0707463777986093e-03 -3.4572321794689781e-03 3.7660889578173145e-03
23 2.2231474739234985e-03 -1.0749114099173709e-04 6.8872091514761841e-03
24 -2.2557311483102044e-03 8.7681606485922377e-03 -5.2202265270714686e-03
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...

87
unittest/force-styles/tests/bond-gaussian.yaml Normal file
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@ -0,0 +1,87 @@
---
lammps_version: 29 Oct 2020
date_generated: Sat Nov 14 16:49:01 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
bond gaussian
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
bond_style: gaussian
bond_coeff: ! |
1 300.0 1 0.0100 0.098 1.45
2 300.0 2 0.0128 0.375 1.37 0.0730 0.148 2.63
3 300.0 3 0.0003 0.657 1.61 0.0050 0.360 1.07 0.0048 0.157 1.31
4 300.0 1 0.0100 0.098 2.45
5 300.0 1 0.0100 0.098 2.85
equilibrium: 5 1.45 1.37 1.61 2.45 2.85
extract: ! ""
natoms: 29
init_energy: 194.978038221632
init_stress: ! |-
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init_forces: ! |2
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run_energy: 194.96889016686
run_stress: ! |-
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...