forked from lijiext/lammps
Merge branch 'remove-reax-meam' into collected-post-stable-patches
This commit is contained in:
Axel Kohlmeyer
commit
02bdda0d05
|
|
@ -171,7 +171,7 @@ set(LAMMPS_DEPS)
|
|||
set(LAMMPS_API_DEFINES)
|
||||
|
||||
set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
|
||||
KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
|
||||
KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
|
||||
SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
|
||||
USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
|
||||
USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
|
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|
|
@ -191,11 +191,11 @@ endforeach()
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######################################################
|
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# packages with special compiler needs or external libs
|
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######################################################
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if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
|
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if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
|
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enable_language(Fortran)
|
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endif()
|
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|
||||
if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
|
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if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
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enable_language(C)
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endif()
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@ -826,7 +826,7 @@ endforeach()
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##############################################
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# add lib sources of (simple) enabled packages
|
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############################################
|
||||
foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
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foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
|
||||
USER-QMMM)
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if(PKG_${SIMPLE_LIB})
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string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
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|
|
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|
|
@ -36,7 +36,6 @@ This is the list of packages that may require additional steps.
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"OPT"_#opt,
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"POEMS"_#poems,
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||||
"PYTHON"_#python,
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"REAX"_#reax,
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"VORONOI"_#voronoi,
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"USER-ATC"_#user-atc,
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||||
"USER-AWPMD"_#user-awpmd,
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@ -536,45 +535,6 @@ build fails.
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|
||||
:line
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|
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REAX package :h4,link(reax)
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|
||||
NOTE: the use of the REAX package and its "pair_style
|
||||
reax"_pair_reax.html command is discouraged, as it is no longer
|
||||
maintained. Please use the USER-REAXC package and its "pair_style
|
||||
reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
|
||||
enabled variant (pair_style reax/c/kk), which has a more robust memory
|
||||
management. See the "pair_style reax/c"_pair_reaxc.html doc page for
|
||||
details.
|
||||
|
||||
[CMake build]:
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|
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No additional settings are needed besides "-D PKG_REAX=yes".
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|
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[Traditional make]:
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|
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Before building LAMMPS, you must build the REAX library in lib/reax.
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You can do this manually if you prefer; follow the instructions in
|
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lib/reax/README. You can also do it in one step from the lammps/src
|
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dir, using a command like these, which simply invoke the
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lib/reax/Install.py script with the specified args:
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|
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make lib-reax # print help message
|
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make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial")
|
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make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi")
|
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make lib-reax args="-m ifort" # build with Intel ifort compiler :pre
|
||||
|
||||
The build should produce two files: lib/reax/libreax.a and
|
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lib/reax/Makefile.lammps. The latter is copied from an existing
|
||||
Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
|
||||
Fortran (REAX library). Typically the two compilers used for LAMMPS
|
||||
and the REAX library need to be consistent (e.g. both Intel or both
|
||||
GNU compilers). If necessary, you can edit/create a new
|
||||
lib/reax/Makefile.machine file for your system, which should define an
|
||||
EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
|
||||
file.
|
||||
|
||||
:line
|
||||
|
||||
VORONOI package :h4,link(voronoi)
|
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|
||||
To build with this package, you must download and build the "Voro++
|
||||
|
|
|
|||
|
|
@ -47,7 +47,6 @@ packages:
|
|||
"OPT"_Build_extras.html#opt,
|
||||
"POEMS"_Build_extras.html#poems,
|
||||
"PYTHON"_Build_extras.html#python,
|
||||
"REAX"_Build_extras.html#reax,
|
||||
"VORONOI"_Build_extras.html#voronoi,
|
||||
"USER-ATC"_Build_extras.html#user-atc,
|
||||
"USER-AWPMD"_Build_extras.html#user-awpmd,
|
||||
|
|
|
|||
|
|
@ -169,8 +169,7 @@ OPT.
|
|||
"qmmm"_fix_qmmm.html,
|
||||
"qtb"_fix_qtb.html,
|
||||
"rattle"_fix_shake.html,
|
||||
"reax/bonds"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reax_bonds.html,
|
||||
"reax/c/bonds (k)"_fix_reaxc_bonds.html,
|
||||
"reax/c/species (k)"_fix_reaxc_species.html,
|
||||
"recenter"_fix_recenter.html,
|
||||
"restrain"_fix_restrain.html,
|
||||
|
|
|
|||
|
|
@ -160,8 +160,7 @@ OPT.
|
|||
"lubricateU/poly"_pair_lubricateU.html,
|
||||
"mdpd"_pair_meso.html,
|
||||
"mdpd/rhosum"_pair_meso.html,
|
||||
"meam"_pair_meam.html,
|
||||
"meam/c"_pair_meam.html,
|
||||
"meam/c"_pair_meamc.html,
|
||||
"meam/spline (o)"_pair_meam_spline.html,
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html,
|
||||
"mgpt"_pair_mgpt.html,
|
||||
|
|
@ -194,7 +193,6 @@ OPT.
|
|||
"polymorphic"_pair_polymorphic.html,
|
||||
"python"_pair_python.html,
|
||||
"quip"_pair_quip.html,
|
||||
"reax"_pair_reax.html,
|
||||
"reax/c (ko)"_pair_reaxc.html,
|
||||
"rebo (io)"_pair_airebo.html,
|
||||
"resquared (go)"_pair_resquared.html,
|
||||
|
|
|
|||
|
|
@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
|
|||
needed to run in parallel.
|
||||
|
||||
The LAMMPS binaries contain all optional packages included in the
|
||||
source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
|
||||
and USER-QMMM. The serial version also does not include the MPIIO and
|
||||
source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
|
||||
The serial version also does not include the MPIIO and
|
||||
USER-LB packages. GPU support is provided for OpenCL.
|
||||
|
||||
The installer site also has instructions on how to run LAMMPS under
|
||||
|
|
|
|||
|
|
@ -45,7 +45,6 @@ as contained in the file name.
|
|||
"LATTE"_#PKG-LATTE,
|
||||
"MANYBODY"_#PKG-MANYBODY,
|
||||
"MC"_#PKG-MC,
|
||||
"MEAM"_#PKG-MEAM,
|
||||
"MESSAGE"_#PKG-MESSAGE,
|
||||
"MISC"_#PKG-MISC,
|
||||
"MOLECULE"_#PKG-MOLECULE,
|
||||
|
|
@ -56,7 +55,6 @@ as contained in the file name.
|
|||
"POEMS"_#PKG-POEMS,
|
||||
"PYTHON"_#PKG-PYTHON,
|
||||
"QEQ"_#PKG-QEQ,
|
||||
"REAX"_#PKG-REAX,
|
||||
"REPLICA"_#PKG-REPLICA2,
|
||||
"RIGID"_#PKG-RIGID,
|
||||
"SHOCK"_#PKG-SHOCK,
|
||||
|
|
@ -533,37 +531,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
|
|||
|
||||
:line
|
||||
|
||||
MEAM package :link(PKG-MEAM),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential.
|
||||
|
||||
Please note that the use of the MEAM package is discouraged as
|
||||
it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
|
||||
which is a direct translation of the MEAM package to C++.
|
||||
USER-MEAMC contains additional optimizations making it run faster
|
||||
than MEAM on most machines, while providing the identical features
|
||||
and user interface.
|
||||
|
||||
[Author:] Greg Wagner (Northwestern U) while at Sandia.
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/MEAM: filenames -> commands
|
||||
src/meam/README
|
||||
lib/meam/README
|
||||
"pair_style meam"_pair_meam.html
|
||||
examples/meam :ul
|
||||
|
||||
:line
|
||||
|
||||
MESSAGE package :link(PKG-MESSAGE),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
@ -834,38 +801,6 @@ examples/streitz :ul
|
|||
|
||||
:line
|
||||
|
||||
REAX package :link(PKG-REAX),h4
|
||||
|
||||
[Contents:]
|
||||
|
||||
NOTE: the use of the REAX package is discouraged, as it is no longer
|
||||
maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
|
||||
and possibly the KOKKOS enabled variant of that, which has a more robust
|
||||
memory management.
|
||||
|
||||
A pair style which wraps a Fortran library which implements the ReaxFF
|
||||
potential, which is a universal reactive force field. Also included is
|
||||
a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
|
||||
as bonds are created and destroyed.
|
||||
|
||||
[Author:] Aidan Thompson (Sandia).
|
||||
|
||||
[Install:]
|
||||
|
||||
This package has "specific installation
|
||||
instructions"_Build_extras.html#gpu on the "Build
|
||||
extras"_Build_extras.html doc page.
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/REAX: filenames -> commands
|
||||
lib/reax/README
|
||||
"pair_style reax"_pair_reax.html
|
||||
"fix reax/bonds"_fix_reax_bonds.html
|
||||
examples/reax :ul
|
||||
|
||||
:line
|
||||
|
||||
REPLICA package :link(PKG-REPLICA2),h4
|
||||
|
||||
[Contents:]
|
||||
|
|
@ -1552,10 +1487,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
|
|||
[Contents:]
|
||||
|
||||
A pair style for the modified embedded atom (MEAM) potential
|
||||
translated from the Fortran version in the "MEAM"_#PKG-MEAM package
|
||||
to plain C++. In contrast to the MEAM package, no library
|
||||
needs to be compiled and the pair style can be instantiated
|
||||
multiple times.
|
||||
translated from the Fortran version in the (obsolete) "MEAM" package
|
||||
to plain C++. The USER-MEAMC fully replaces the MEAM package, which
|
||||
has been removed from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
|
||||
based on the Fortran version of Greg Wagner (Northwestern U) while at
|
||||
|
|
@ -1565,8 +1499,8 @@ Sandia.
|
|||
|
||||
src/USER-MEAMC: filenames -> commands
|
||||
src/USER-MEAMC/README
|
||||
"pair_style meam/c"_pair_meam.html
|
||||
examples/meam :ul
|
||||
"pair_style meam/c"_pair_meamc.html
|
||||
examples/meamc :ul
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -1894,9 +1828,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
|
|||
|
||||
[Contents:]
|
||||
|
||||
A pair style which implements the ReaxFF potential in C/C++ (in
|
||||
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
|
||||
is universal reactive force field. See the src/USER-REAXC/README file
|
||||
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
|
||||
is a universal reactive force field. See the src/USER-REAXC/README file
|
||||
for more info on differences between the two packages. Also two fixes
|
||||
for monitoring molecules as bonds are created and destroyed.
|
||||
|
||||
|
|
@ -1907,7 +1840,7 @@ for monitoring molecules as bonds are created and destroyed.
|
|||
src/USER-REAXC: filenames -> commands
|
||||
src/USER-REAXC/README
|
||||
"pair_style reax/c"_pair_reaxc.html
|
||||
"fix reax/c/bonds"_fix_reax_bonds.html
|
||||
"fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
"fix reax/c/species"_fix_reaxc_species.html
|
||||
examples/reax :ul
|
||||
|
||||
|
|
|
|||
|
|
@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
|
|||
"LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
|
||||
"MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
|
||||
"MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
|
||||
"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
|
||||
"MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
|
||||
"MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
|
||||
"MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
|
||||
|
|
@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
|
|||
"POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
|
||||
"PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
|
||||
"QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
|
||||
"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
|
||||
"REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
|
||||
"RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
|
||||
"SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ Package, Description, Doc page, Example, Library
|
|||
"USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
|
||||
"USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
|
||||
"USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
|
||||
"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
|
||||
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
|
||||
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
|
||||
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
|
||||
|
|
|
|||
|
|
@ -486,8 +486,8 @@ README for more info on Pizza.py and how to use these scripts.
|
|||
reax tool :h4,link(reax_tool)
|
||||
|
||||
The reax sub-directory contains stand-alone codes that can
|
||||
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
|
||||
post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See
|
||||
the README.txt file for more info.
|
||||
|
||||
These tools were written by Aidan Thompson at Sandia.
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
|
|||
compute 1 all pair gauss
|
||||
compute 1 all pair lj/cut/coul/cut ecoul
|
||||
compute 1 all pair tersoff 2 epair
|
||||
compute 1 all pair reax :pre
|
||||
compute 1 all pair reax/c :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
|
|
@ -60,8 +60,8 @@ corrections, even if they are enabled via the
|
|||
"pair_modify"_pair_modify.html command.
|
||||
|
||||
Some pair styles tally additional quantities, e.g. a breakdown of
|
||||
potential energy into a dozen or so components is tallied by the
|
||||
"pair_style reax"_pair_reax.html command. These values (1 or more)
|
||||
potential energy into 14 components is tallied by the "pair_style
|
||||
reax/c"_pair_reaxc.html command. These values (1 or more)
|
||||
are stored as a global vector by this compute. See the doc page for
|
||||
"individual pair styles"_pair_style.html for info on these values.
|
||||
|
||||
|
|
|
|||
|
|
@ -312,9 +312,8 @@ accelerated styles exist.
|
|||
"qmmm"_fix_qmmm.html -
|
||||
"qtb"_fix_qtb.html -
|
||||
"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
|
||||
"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/bonds"_fix_reax_bonds.html -
|
||||
"reax/c/species"_fix_reaxc_species.html -
|
||||
"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
|
||||
"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
|
||||
"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
|
||||
"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
|
||||
"rhok"_fix_rhok.html -
|
||||
|
|
|
|||
|
|
@ -6,13 +6,12 @@
|
|||
|
||||
:line
|
||||
|
||||
fix reax/bonds command :h3
|
||||
fix reax/c/bonds command :h3
|
||||
fix reax/c/bonds/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID reax/bonds Nevery filename :pre
|
||||
fix ID group-ID reaxc/bonds Nevery filename :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command
|
||||
reax/bonds = style name of this fix command
|
||||
|
|
@ -21,16 +20,14 @@ filename = name of output file :ul
|
|||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all reax/bonds 100 bonds.tatb
|
||||
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Write out the bond information computed by the ReaxFF potential
|
||||
specified by "pair_style reax"_pair_reax.html or "pair_style
|
||||
reax/c"_pair_reaxc.html in the exact same format as the original
|
||||
stand-alone ReaxFF code of Adri van Duin. The bond information is
|
||||
written to {filename} on timesteps that are multiples of {Nevery},
|
||||
Write out the bond information computed by the ReaxFF potential specified
|
||||
by "pair_style reax/c"_pair_reaxc.html in the exact same format as the
|
||||
original stand-alone ReaxFF code of Adri van Duin. The bond information
|
||||
is written to {filename} on timesteps that are multiples of {Nevery},
|
||||
including timestep 0. For time-averaged chemical species analysis,
|
||||
please see the "fix reaxc/c/species"_fix_reaxc_species.html command.
|
||||
|
||||
|
|
@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The fix reax/bonds command requires that the "pair_style
|
||||
reax"_pair_reax.html be invoked. This fix is part of the REAX
|
||||
package. It is only enabled if LAMMPS was built with that package,
|
||||
which also requires the REAX library be built and linked with LAMMPS.
|
||||
The fix reax/c/bonds command requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
reax/c"_pair_reaxc.html is invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
|
@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax"_pair_reax.html, "pair_style
|
||||
reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The fix species currently only works with "pair_style
|
||||
The "fix reax/c/species" currently only works with "pair_style
|
||||
reax/c"_pair_reaxc.html and it requires that the "pair_style
|
||||
reax/c"_pair_reaxc.html be invoked. This fix is part of the
|
||||
USER-REAXC package. It is only enabled if LAMMPS was built with that
|
||||
|
|
@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix
|
||||
reax/bonds"_fix_reax_bonds.html
|
||||
"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -135,7 +135,7 @@ Fixes :h1
|
|||
fix_qeq_reax
|
||||
fix_qmmm
|
||||
fix_qtb
|
||||
fix_reax_bonds
|
||||
fix_reaxc_bonds
|
||||
fix_reaxc_species
|
||||
fix_recenter
|
||||
fix_restrain
|
||||
|
|
|
|||
|
|
@ -356,7 +356,7 @@ fix_qeq_comb.html
|
|||
fix_qeq_reax.html
|
||||
fix_qmmm.html
|
||||
fix_qtb.html
|
||||
fix_reax_bonds.html
|
||||
fix_reaxc_bonds.html
|
||||
fix_reaxc_species.html
|
||||
fix_recenter.html
|
||||
fix_restrain.html
|
||||
|
|
@ -598,7 +598,7 @@ pair_lj_soft.html
|
|||
pair_lubricate.html
|
||||
pair_lubricateU.html
|
||||
pair_mdf.html
|
||||
pair_meam.html
|
||||
pair_meamc.html
|
||||
pair_meam_spline.html
|
||||
pair_meam_sw_spline.html
|
||||
pair_meso.html
|
||||
|
|
@ -617,7 +617,6 @@ pair_peri.html
|
|||
pair_polymorphic.html
|
||||
pair_python.html
|
||||
pair_quip.html
|
||||
pair_reax.html
|
||||
pair_reaxc.html
|
||||
pair_resquared.html
|
||||
pair_sdk.html
|
||||
|
|
|
|||
|
|
@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your
|
|||
model, then you should just list the sub-style once and use the
|
||||
pair_coeff command to assign parameters for the different type pairs.
|
||||
|
||||
NOTE: There are two exceptions to this option to list an individual
|
||||
pair style multiple times. The first is for pair styles implemented
|
||||
as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
|
||||
reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
|
||||
This is because unlike a C++ class, they can not be instantiated
|
||||
multiple times, due to the manner in which they were coded in Fortran.
|
||||
The second is for GPU-enabled pair styles in the GPU package. This is
|
||||
b/c the GPU package also currently assumes that only one instance of a
|
||||
pair style is being used.
|
||||
NOTE: There is one exception to this option to list an individual
|
||||
pair style multiple times: GPU-enabled pair styles in the GPU package.
|
||||
This is because the GPU package currently assumes that only one
|
||||
instance of a pair style is being used.
|
||||
|
||||
In the pair_coeff commands, the name of a pair style must be added
|
||||
after the I,J type specification, with the remaining coefficients
|
||||
|
|
|
|||
|
|
@ -152,7 +152,7 @@ info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -116,7 +116,7 @@ info.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html,
|
||||
"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html,
|
||||
"pair_style meam/spline"_pair_meam_spline.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -6,18 +6,17 @@
|
|||
|
||||
:line
|
||||
|
||||
pair_style meam command :h3
|
||||
pair_style meam/c command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style :pre
|
||||
|
||||
style = {meam} or {meam/c}
|
||||
style = {meam/c}
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style meam
|
||||
pair_style meam/c
|
||||
pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
|
||||
pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
|
||||
|
||||
|
|
@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed
|
|||
as of November 2010; see description below of the mixture_ref_t
|
||||
parameter
|
||||
|
||||
Style {meam} computes pairwise interactions for a variety of materials
|
||||
Style {meam/c} computes pairwise interactions for a variety of materials
|
||||
using modified embedded-atom method (MEAM) potentials
|
||||
"(Baskes)"_#Baskes. Conceptually, it is an extension to the original
|
||||
"EAM potentials"_pair_eam.html which adds angular forces. It is
|
||||
thus suitable for modeling metals and alloys with fcc, bcc, hcp and
|
||||
diamond cubic structures, as well as covalently bonded materials like
|
||||
silicon and carbon. Style {meam/c} is a translation of the {meam} code
|
||||
from (mostly) Fortran to C++. It is functionally equivalent to {meam}.
|
||||
silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
|
||||
{meam} code from Fortran to C++. It is functionally equivalent to {meam}
|
||||
but more efficient, and thus {meam} has been removed from LAMMPS after
|
||||
the 12 December 2018 release.
|
||||
|
||||
In the MEAM formulation, the total energy E of a system of atoms is
|
||||
given by:
|
||||
|
|
@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {meam} style is part of the MEAM package. It is only enabled if
|
||||
LAMMPS was built with that package, which also requires the MEAM
|
||||
library be built and linked with LAMMPS. The {meam/c} style is
|
||||
provided in the USER-MEAMC package. It is only enabled if LAMMPS was
|
||||
built with that package. In contrast to the {meam} style, {meam/c}
|
||||
does not require a separate library to be compiled and it can be
|
||||
instantiated multiple times in a "hybrid"_pair_hybrid.html pair style.
|
||||
The {meam/c} style is provided in the USER-MEAMC package. It is
|
||||
only enabled if LAMMPS was built with that package.
|
||||
See the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
|
@ -1,216 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style reax command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style reax hbcut hbnewflag tripflag precision :pre
|
||||
|
||||
hbcut = hydrogen-bond cutoff (optional) (distance units)
|
||||
hbnewflag = use old or new hbond function style (0 or 1) (optional)
|
||||
tripflag = apply stabilization to all triple bonds (0 or 1) (optional)
|
||||
precision = precision for charge equilibration (optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style reax
|
||||
pair_style reax 10.0 0 1 1.0e-5
|
||||
pair_coeff * * ffield.reax 3 1 2 2
|
||||
pair_coeff * * ffield.reax 3 NULL NULL 3 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {reax} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper:
|
||||
"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches
|
||||
the most up-to-date version of ReaxFF as of summer 2010.
|
||||
|
||||
WARNING: pair style reax is now deprecated and will soon be retired. Users
|
||||
should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
|
||||
differs from the {reax/c} style in the lo-level implementation details.
|
||||
The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
|
||||
LAMMPS requires that a file called ffield.reax be provided, containing
|
||||
the ReaxFF parameters for each atom type, bond type, etc. The format
|
||||
is identical to the ffield file used by van Duin and co-workers. The
|
||||
filename is required as an argument in the pair_coeff command. Any
|
||||
value other than "ffield.reax" will be rejected (see below).
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
documented in potentials/README.reax. The default ffield.reax
|
||||
contains parameterizations for the following elements: C, H, O, N.
|
||||
|
||||
NOTE: We do not distribute a wide variety of ReaxFF force field files
|
||||
with LAMMPS. Adri van Duin's group at PSU is the central repository
|
||||
for this kind of data as they are continuously deriving and updating
|
||||
parameterizations for different classes of materials. You can submit
|
||||
a contact request at the Materials Computation Center (MCC) website
|
||||
"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
|
||||
describing the material(s) you are interested in modeling with ReaxFF.
|
||||
They can tell
|
||||
you what is currently available or what it would take to create a
|
||||
suitable ReaxFF parameterization.
|
||||
|
||||
The format of these files is identical to that used originally by van
|
||||
Duin. We have tested the accuracy of {pair_style reax} potential
|
||||
against the original ReaxFF code for the systems mentioned above. You
|
||||
can use other ffield files for specific chemical systems that may be
|
||||
available elsewhere (but note that their accuracy may not have been
|
||||
tested).
|
||||
|
||||
The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are
|
||||
optional arguments. If none are provided, default settings are used:
|
||||
{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use
|
||||
new hbond function style), {tripflag} = 1 (apply stabilization to all
|
||||
triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you
|
||||
wish to override any of these defaults, then all of the settings must
|
||||
be specified.
|
||||
|
||||
Two examples using {pair_style reax} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
|
||||
calculated by both of these pair styles match very closely, the
|
||||
contributions due to the valence angles differ slightly due to
|
||||
the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
|
||||
is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom since the {reax} pair style performs a charge equilibration (QEq)
|
||||
calculation. See the "atom_style"_atom_style.html and
|
||||
"read_data"_read_data.html commands for details on how to specify
|
||||
charges.
|
||||
|
||||
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
|
||||
energy contributions, with the exception of the Coulombic and charge
|
||||
equilibration contributions which are stored in the thermo variable
|
||||
{ecoul}. The output of these quantities is controlled by the
|
||||
"thermo"_thermo.html command.
|
||||
|
||||
This pair style tallies a breakdown of the total ReaxFF potential
|
||||
energy into sub-categories, which can be accessed via the "compute
|
||||
pair"_compute_pair.html command as a vector of values of length 14.
|
||||
The 14 values correspond to the following sub-categories (the variable
|
||||
names in italics match those used in the ReaxFF FORTRAN library):
|
||||
|
||||
{eb} = bond energy
|
||||
{ea} = atom energy
|
||||
{elp} = lone-pair energy
|
||||
{emol} = molecule energy (always 0.0)
|
||||
{ev} = valence angle energy
|
||||
{epen} = double-bond valence angle penalty
|
||||
{ecoa} = valence angle conjugation energy
|
||||
{ehb} = hydrogen bond energy
|
||||
{et} = torsion energy
|
||||
{eco} = conjugation energy
|
||||
{ew} = van der Waals energy
|
||||
{ep} = Coulomb energy
|
||||
{efi} = electric field energy (always 0.0)
|
||||
{eqeq} = charge equilibration energy :ol
|
||||
|
||||
To print these quantities to the log file (with descriptive column
|
||||
headings) the following commands could be included in an input script:
|
||||
|
||||
compute reax all pair reax
|
||||
variable eb equal c_reax\[1\]
|
||||
variable ea equal c_reax\[2\]
|
||||
...
|
||||
variable eqeq equal c_reax\[14\]
|
||||
thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre
|
||||
|
||||
Only a single pair_coeff command is used with the {reax} style which
|
||||
specifies a ReaxFF potential file with parameters for all needed
|
||||
elements. These are mapped to LAMMPS atom types by specifying N
|
||||
additional arguments after the filename in the pair_coeff command,
|
||||
where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
N indices = mapping of ReaxFF elements to atom types :ul
|
||||
|
||||
The specification of the filename and the mapping of LAMMPS atom types
|
||||
recognized by the ReaxFF is done differently than for other LAMMPS
|
||||
potentials, due to the non-portable difficulty of passing character
|
||||
strings (e.g. filename, element names) between C++ and Fortran.
|
||||
|
||||
The filename has to be "ffield.reax" and it has to exist in the
|
||||
directory you are running LAMMPS in. This means you cannot prepend a
|
||||
path to the file in the potentials dir. Rather, you should copy that
|
||||
file into the directory you are running from. If you wish to use
|
||||
another ReaxFF potential file, then name it "ffield.reax" and put it
|
||||
in the directory you run from.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
names, each with a couple dozen numeric parameters. If there are M
|
||||
elements specified in the {ffield} file, think of these as numbered 1
|
||||
to M. Each of the N indices you specify for the N atom types of LAMMPS
|
||||
atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will
|
||||
be mapped to whatever element you specify as the first index value,
|
||||
etc. If a mapping value is specified as NULL, the mapping is not
|
||||
performed. This can be used when a ReaxFF potential is used as part
|
||||
of the {hybrid} pair style. The NULL values are placeholders for atom
|
||||
types that will be used with other potentials.
|
||||
|
||||
NOTE: Currently the reax pair style cannot be used as part of the
|
||||
{hybrid} pair style. Some additional changes still need to be made to
|
||||
enable this.
|
||||
|
||||
As an example, say your LAMMPS simulation has 4 atom types and the
|
||||
elements are ordered as C, H, O, N in the {ffield} file. If you want
|
||||
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
|
||||
H, you would use the following pair_coeff command:
|
||||
|
||||
pair_coeff * * ffield.reax 1 1 4 2 :pre
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, since it is stored in potential files. Thus, you
|
||||
need to re-specify the pair_style and pair_coeff commands in an input
|
||||
script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The ReaxFF potential files provided with LAMMPS in the potentials
|
||||
directory are parameterized for real "units"_units.html. You can use
|
||||
the ReaxFF potential with any LAMMPS units, but you would need to
|
||||
create your own potential file with coefficients listed in the
|
||||
appropriate units if your simulation doesn't use "real" units.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
|
||||
"fix_reax_bonds"_fix_reax_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1,
|
||||
{precision} = 1.0e-6.
|
||||
|
||||
:line
|
||||
|
||||
:link(Chenoweth_20081)
|
||||
[(Chenoweth_2008)] Chenoweth, van Duin and Goddard,
|
||||
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
|
||||
|
|
@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre
|
|||
Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and
|
||||
co-workers. ReaxFF uses distance-dependent bond-order functions to
|
||||
represent the contributions of chemical bonding to the potential
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
energy. There is more than one version of ReaxFF. The version
|
||||
implemented in LAMMPS uses the functional forms documented in the
|
||||
supplemental information of the following paper: "(Chenoweth et al.,
|
||||
2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches
|
||||
|
|
@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either
|
|||
half or full neighbor lists. This setting can be changed using the
|
||||
Kokkos "package"_package.html command.
|
||||
|
||||
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
|
||||
command in the lo-level implementation details. The {reax} style is a
|
||||
Fortran library, linked to LAMMPS. The {reax/c} style was initially
|
||||
implemented as stand-alone C code and is now integrated into LAMMPS as
|
||||
a package.
|
||||
The {reax/c} style differs from the (obsolete) "pair_style reax"
|
||||
command in the implementation details. The {reax} style was a
|
||||
Fortran library, linked to LAMMPS. The {reax} style has been removed
|
||||
from LAMMPS after the 12 December 2018 version.
|
||||
|
||||
LAMMPS provides several different versions of ffield.reax in its
|
||||
potentials dir, each called potentials/ffield.reax.label. These are
|
||||
|
|
@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial
|
|||
code. If these are changed by setting control variables in the control
|
||||
file, the results from LAMMPS and the serial code will not agree.
|
||||
|
||||
Two examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory, along with corresponding examples for
|
||||
"pair_style reax"_pair_reax.html.
|
||||
Examples using {pair_style reax/c} are provided in the examples/reax
|
||||
sub-directory.
|
||||
|
||||
Use of this pair style requires that a charge be defined for every
|
||||
atom. See the "atom_style"_atom_style.html and
|
||||
|
|
@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types:
|
|||
filename
|
||||
N indices = ReaxFF elements :ul
|
||||
|
||||
The filename is the ReaxFF potential file. Unlike for the {reax}
|
||||
pair style, any filename can be used.
|
||||
The filename is the ReaxFF potential file.
|
||||
|
||||
In the ReaxFF potential file, near the top, after the general
|
||||
parameters, is the atomic parameters section that contains element
|
||||
|
|
@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units.
|
|||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
|
||||
reax/c/bonds"_fix_reax_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html, "pair_style
|
||||
reax"_pair_reax.html
|
||||
reax/c/bonds"_fix_reaxc_bonds.html, "fix
|
||||
reax/c/species"_fix_reaxc_species.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -226,8 +226,7 @@ accelerated styles exist.
|
|||
"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
|
||||
"mdpd"_pair_meso.html - mDPD particle interactions
|
||||
"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
|
||||
"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
|
||||
"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
|
||||
"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C
|
||||
"meam/spline"_pair_meam_spline.html - splined version of MEAM
|
||||
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
|
||||
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
|
||||
|
|
@ -260,7 +259,6 @@ accelerated styles exist.
|
|||
"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
|
||||
"python"_pair_python.html -
|
||||
"quip"_pair_quip.html -
|
||||
"reax"_pair_reax.html - ReaxFF potential in Fortran
|
||||
"reax/c"_pair_reaxc.html - ReaxFF potential in C
|
||||
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
|
||||
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
|
|
|
|||
|
|
@ -63,7 +63,7 @@ Pair Styles :h1
|
|||
pair_lubricate
|
||||
pair_lubricateU
|
||||
pair_mdf
|
||||
pair_meam
|
||||
pair_meamc
|
||||
pair_meam_spline
|
||||
pair_meam_sw_spline
|
||||
pair_meso
|
||||
|
|
@ -82,7 +82,6 @@ Pair Styles :h1
|
|||
pair_polymorphic
|
||||
pair_python
|
||||
pair_quip
|
||||
pair_reax
|
||||
pair_reaxc
|
||||
pair_resquared
|
||||
pair_sdk
|
||||
|
|
|
|||
|
|
@ -1526,6 +1526,7 @@ mdf
|
|||
mdpd
|
||||
mDPD
|
||||
meam
|
||||
meamc
|
||||
MEAMC
|
||||
meamf
|
||||
meanDist
|
||||
|
|
|
|||
|
|
@ -1,30 +0,0 @@
|
|||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
|
|
@ -1,96 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file SiC.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
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 = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.0545483 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 158.392 ns/day, 0.152 hours/ns, 1833.239 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.050821 | 0.050821 | 0.050821 | 0.0 | 93.17
|
||||
Neigh | 0.0026484 | 0.0026484 | 0.0026484 | 0.0 | 4.86
|
||||
Comm | 0.0006423 | 0.0006423 | 0.0006423 | 0.0 | 1.18
|
||||
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.21
|
||||
Modify | 0.00021195 | 0.00021195 | 0.00021195 | 0.0 | 0.39
|
||||
Other | | 0.0001101 | | | 0.20
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 543 ave 543 max 543 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1526 ave 1526 max 1526 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3052 ave 3052 max 3052 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,96 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file SiC.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
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 = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 6 6 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.023721 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Performance: 364.234 ns/day, 0.066 hours/ns, 4215.667 timesteps/s
|
||||
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.019888 | 0.020242 | 0.020626 | 0.2 | 85.33
|
||||
Neigh | 0.00071859 | 0.00076133 | 0.00082922 | 0.0 | 3.21
|
||||
Comm | 0.0019681 | 0.0022618 | 0.002651 | 0.5 | 9.53
|
||||
Output | 0.00018048 | 0.0002225 | 0.00034213 | 0.0 | 0.94
|
||||
Modify | 8.2016e-05 | 8.6308e-05 | 9.203e-05 | 0.0 | 0.36
|
||||
Other | | 0.000147 | | | 0.62
|
||||
|
||||
Nlocal: 32 ave 36 max 30 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 293.75 ave 305 max 285 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 381.5 ave 413 max 334 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
FullNghs: 763 ave 866 max 678 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
Time spent = 0.0007267 secs
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 27 17 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
|
||||
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
|
||||
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
|
||||
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
|
||||
Loop time of 0.894544 on 1 procs for 100 steps with 1912 atoms
|
||||
|
||||
Performance: 9.659 ns/day, 2.485 hours/ns, 111.789 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.87012 | 0.87012 | 0.87012 | 0.0 | 97.27
|
||||
Neigh | 0.01798 | 0.01798 | 0.01798 | 0.0 | 2.01
|
||||
Comm | 0.0016143 | 0.0016143 | 0.0016143 | 0.0 | 0.18
|
||||
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.01
|
||||
Modify | 0.0035381 | 0.0035381 | 0.0035381 | 0.0 | 0.40
|
||||
Other | | 0.001176 | | | 0.13
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1672 ave 1672 max 1672 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23806 ave 23806 max 23806 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 47612 ave 47612 max 47612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 47612
|
||||
Ave neighs/atom = 24.9017
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297
|
||||
100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53
|
||||
200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24
|
||||
300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759
|
||||
400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698
|
||||
500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813
|
||||
600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887
|
||||
700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302
|
||||
800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519
|
||||
900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992
|
||||
1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243
|
||||
1100 304.14041 -8096.5041 0 -8060.2573 9646.6972 20888.167
|
||||
1200 302.78454 -8080.5931 0 -8044.5079 11516.208 20995.917
|
||||
1300 308.67064 -8061.6724 0 -8024.8857 11496.471 21130.013
|
||||
1400 309.82994 -8046.27 0 -8009.3451 12926.819 21247.271
|
||||
1500 300 -8035.0317 0 -7999.2784 15346.797 21370.637
|
||||
1600 300 -8030.6636 0 -7994.9102 14803.43 21496.446
|
||||
1700 300 -8024.4819 0 -7988.7286 13175.257 21611.262
|
||||
1800 300 -8022.8531 0 -7987.0998 10315.63 21743.178
|
||||
1900 300 -8028.4095 0 -7992.6561 6882.0635 21855.551
|
||||
2000 300 -8036.9005 0 -8001.1472 3508.9237 21983.802
|
||||
2100 300 -8037.8224 0 -8002.0691 2724.0594 22112.054
|
||||
2200 306.93248 -8035.3297 0 -7998.7501 4400.6008 22228.091
|
||||
2300 306.24125 -8036.748 0 -8000.2508 6075.0546 22352.678
|
||||
2400 300 -8038.8534 0 -8003.1 8701.8498 22465.051
|
||||
2500 308.34129 -8034.0796 0 -7997.3322 10977.68 22600.632
|
||||
2600 299.70072 -8028.8815 0 -7993.1638 15468.97 22715.447
|
||||
2700 298.78276 -8019.1655 0 -7983.5572 18076.132 22844.921
|
||||
2800 305.57845 -8014.3542 0 -7977.936 17573.035 22962.179
|
||||
2900 300 -8015.7677 0 -7980.0144 13461.463 23087.988
|
||||
3000 300 -8010.5908 0 -7974.8375 9333.4855 23199.139
|
||||
Loop time of 29.4592 on 1 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Performance: 8.799 ns/day, 2.728 hours/ns, 101.836 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 | 28.489 | 28.489 | 28.489 | 0.0 | 96.71
|
||||
Neigh | 0.77356 | 0.77356 | 0.77356 | 0.0 | 2.63
|
||||
Comm | 0.052517 | 0.052517 | 0.052517 | 0.0 | 0.18
|
||||
Output | 0.00095224 | 0.00095224 | 0.00095224 | 0.0 | 0.00
|
||||
Modify | 0.10813 | 0.10813 | 0.10813 | 0.0 | 0.37
|
||||
Other | | 0.03525 | | | 0.12
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1668 ave 1668 max 1668 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23391 ave 23391 max 23391 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 46782 ave 46782 max 46782 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46782
|
||||
Ave neighs/atom = 24.4676
|
||||
Neighbor list builds = 219
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:30
|
||||
|
|
@ -1,209 +0,0 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
Time spent = 0.000408649 secs
|
||||
|
||||
pair_style meam
|
||||
WARNING: THE pair_style meam COMMAND IS OBSOLETE AND WILL BE REMOVED VERY SOON. PLEASE USE meam/c (src/MEAM/pair_meam.cpp:51)
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
Reading potential file library.meam with DATE: 2012-06-29
|
||||
Reading potential file Ni.meam with DATE: 2007-06-11
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.3
|
||||
ghost atom cutoff = 4.3
|
||||
binsize = 2.15, bins = 27 17 5
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair meam, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair meam, perpetual, half/full from (1)
|
||||
attributes: half, newton on
|
||||
pair build: halffull/newton
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
|
||||
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
|
||||
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
|
||||
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
|
||||
Loop time of 0.263516 on 4 procs for 100 steps with 1912 atoms
|
||||
|
||||
Performance: 32.787 ns/day, 0.732 hours/ns, 379.483 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.24401 | 0.2486 | 0.25128 | 0.6 | 94.34
|
||||
Neigh | 0.0046518 | 0.0047416 | 0.0048261 | 0.1 | 1.80
|
||||
Comm | 0.0054512 | 0.0082117 | 0.012793 | 3.1 | 3.12
|
||||
Output | 0.00010562 | 0.00013095 | 0.00019932 | 0.0 | 0.05
|
||||
Modify | 0.0010016 | 0.0010275 | 0.0010595 | 0.1 | 0.39
|
||||
Other | | 0.0008045 | | | 0.31
|
||||
|
||||
Nlocal: 478 ave 492 max 465 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 809 ave 822 max 795 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 5916 ave 6133 max 5658 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
FullNghs: 11832 ave 12277 max 11299 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 47328
|
||||
Ave neighs/atom = 24.7531
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93
|
||||
100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765
|
||||
200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877
|
||||
300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714
|
||||
400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012
|
||||
500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256
|
||||
600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848
|
||||
700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046
|
||||
800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183
|
||||
900 304.61422 -8126.9246 0 -8090.6214 6654.0962 20640.213
|
||||
1000 300 -8113.8464 0 -8078.0931 7760.1237 20768.465
|
||||
1100 300.17873 -8097.7469 0 -8061.9722 8438.1259 20874.731
|
||||
1200 306.01441 -8083.3367 0 -8046.8665 10835.588 20994.432
|
||||
1300 300 -8067.022 0 -8031.2687 11216.061 21126.348
|
||||
1400 300 -8053.223 0 -8017.4696 10570.211 21253.378
|
||||
1500 300 -8043.4848 0 -8007.7314 11360.762 21375.523
|
||||
1600 300 -8034.6201 0 -7998.8667 11371.282 21498.889
|
||||
1700 300 -8028.6797 0 -7992.9263 9596.8454 21613.705
|
||||
1800 300 -8033.0802 0 -7997.3268 8767.8176 21743.178
|
||||
1900 303.23288 -8035.1821 0 -7999.0434 8065.2879 21859.215
|
||||
2000 300 -8025.0795 0 -7989.3262 9321.8098 21980.138
|
||||
2100 300 -8041.3621 0 -8005.6088 6674.2623 22108.39
|
||||
2200 300 -8039.7261 0 -8003.9727 7548.8847 22225.648
|
||||
2300 300 -8052.3497 0 -8016.5964 8936.4935 22352.678
|
||||
2400 300 -8049.395 0 -8013.6416 12633.909 22476.044
|
||||
2500 308.48099 -8039.9448 0 -8003.1807 16242.081 22593.303
|
||||
2600 300 -8032.1953 0 -7996.442 18386.669 22722.776
|
||||
2700 303.49413 -8027.6563 0 -7991.4865 14415.581 22829.042
|
||||
2800 304.13476 -8017.3394 0 -7981.0933 7457.1076 22953.629
|
||||
2900 300 -8010.3658 0 -7974.6124 2815.5155 23074.552
|
||||
3000 309.49253 -7999.74 0 -7962.8553 756.7511 23210.132
|
||||
Loop time of 8.57528 on 4 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Performance: 30.226 ns/day, 0.794 hours/ns, 349.843 timesteps/s
|
||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.0046 | 8.0451 | 8.1075 | 1.5 | 93.82
|
||||
Neigh | 0.20142 | 0.20699 | 0.21469 | 1.2 | 2.41
|
||||
Comm | 0.1972 | 0.2657 | 0.312 | 9.3 | 3.10
|
||||
Output | 0.00087762 | 0.0015897 | 0.0037148 | 3.1 | 0.02
|
||||
Modify | 0.030267 | 0.031624 | 0.032929 | 0.7 | 0.37
|
||||
Other | | 0.02427 | | | 0.28
|
||||
|
||||
Nlocal: 478 ave 507 max 447 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Nghost: 799.75 ave 842 max 763 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 5806.5 ave 6097 max 5507 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
FullNghs: 11613 ave 12159 max 11039 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 46452
|
||||
Ave neighs/atom = 24.295
|
||||
Neighbor list builds = 224
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -1,12 +1,8 @@
|
|||
This directory contains input files for two short ReaxFF simulations
|
||||
(RDX and TATB crystals) using the ReaxFF parameterization developed
|
||||
for nitramines. The parameter file ffield.reax is the same as that in
|
||||
subdirectory RDX (see below). Input files for both pair_style reax and
|
||||
pair_style reax/c are provided.
|
||||
|
||||
In addition, each subdirectory contains validated parameter files for
|
||||
a particular published version of ReaxFF. In all cases, the examples
|
||||
use pair_style reax/c.
|
||||
subdirectory RDX (see below). In addition, each subdirectory contains
|
||||
validated parameter files for a particular published version of ReaxFF.
|
||||
|
||||
Disclaimer: Using these force fields for systems they have not been
|
||||
explicitly trained against may produce unrealistic results. Please
|
||||
|
|
|
|||
|
|
@ -1,52 +0,0 @@
|
|||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press &
|
||||
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb &
|
||||
v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
|
|
@ -1,53 +0,0 @@
|
|||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press &
|
||||
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
|
||||
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type &
|
||||
# axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842
|
||||
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115
|
||||
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159
|
||||
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177
|
||||
40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424
|
||||
50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068
|
||||
60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841
|
||||
70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047
|
||||
80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961
|
||||
90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827
|
||||
100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946
|
||||
Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60
|
||||
Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19
|
||||
Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09
|
||||
Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07
|
||||
Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02
|
||||
Other | | 0.000124 | | | 0.03
|
||||
|
||||
Nlocal: 21 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 546 ave 546 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1106 ave 1106 max 1106 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1106
|
||||
Ave neighs/atom = 52.6667
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,107 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for RDX system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.rdx
|
||||
orthogonal box = (35 35 35) to (48 48 48)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
21 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 1.0
|
||||
|
||||
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 10 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 3 3 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428
|
||||
10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152
|
||||
20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168
|
||||
30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765
|
||||
40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473
|
||||
50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791
|
||||
60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383
|
||||
70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091
|
||||
80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512
|
||||
90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716
|
||||
100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043
|
||||
Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms
|
||||
|
||||
Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s
|
||||
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31
|
||||
Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06
|
||||
Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42
|
||||
Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16
|
||||
Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02
|
||||
Other | | 0.0001363 | | | 0.03
|
||||
|
||||
Nlocal: 5.25 ave 15 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 355.5 ave 432 max 282 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 301.25 ave 827 max 0 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1205
|
||||
Ave neighs/atom = 57.381
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
|
||||
5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127
|
||||
10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942
|
||||
15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551
|
||||
20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614
|
||||
25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409
|
||||
Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19
|
||||
Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75
|
||||
Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03
|
||||
Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00
|
||||
Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02
|
||||
Other | | 0.0003309 | | | 0.00
|
||||
|
||||
Nlocal: 384 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7559 ave 7559 max 7559 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 286828 ave 286828 max 286828 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 286828
|
||||
Ave neighs/atom = 746.948
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:08
|
||||
|
|
@ -1,103 +0,0 @@
|
|||
LAMMPS (8 Mar 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# ReaxFF potential for TATB system
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.tatb
|
||||
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
|
||||
# reax args: hbcut hbnewflag tripflag precision
|
||||
pair_style reax 6.0 1 1 1.0e-6
|
||||
WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49)
|
||||
pair_coeff * * ffield.reax 1 2 3 4
|
||||
|
||||
compute reax all pair reax
|
||||
|
||||
variable eb equal c_reax[1]
|
||||
variable ea equal c_reax[2]
|
||||
variable elp equal c_reax[3]
|
||||
variable emol equal c_reax[4]
|
||||
variable ev equal c_reax[5]
|
||||
variable epen equal c_reax[6]
|
||||
variable ecoa equal c_reax[7]
|
||||
variable ehb equal c_reax[8]
|
||||
variable et equal c_reax[9]
|
||||
variable eco equal c_reax[10]
|
||||
variable ew equal c_reax[11]
|
||||
variable ep equal c_reax[12]
|
||||
variable efi equal c_reax[13]
|
||||
variable eqeq equal c_reax[14]
|
||||
|
||||
neighbor 2.5 bin
|
||||
neigh_modify delay 0 every 5 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 5
|
||||
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
|
||||
timestep 0.0625
|
||||
|
||||
#dump 1 all custom 100 dump.reax.tatb id type q x y z
|
||||
|
||||
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
fix 2 all reax/bonds 25 bonds.reax.tatb
|
||||
|
||||
run 25
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.5
|
||||
ghost atom cutoff = 12.5
|
||||
binsize = 6.25, bins = 5 4 3
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair reax, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: half/bin/3d/newtoff
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
|
||||
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
|
||||
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
|
||||
5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581
|
||||
10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083
|
||||
15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505
|
||||
20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629
|
||||
25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682
|
||||
Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms
|
||||
|
||||
Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22
|
||||
Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35
|
||||
Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38
|
||||
Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02
|
||||
Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02
|
||||
Other | | 0.0002663 | | | 0.01
|
||||
|
||||
Nlocal: 96 ave 96 max 96 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5118 ave 5118 max 5118 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 79754 ave 79754 max 79754 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 319016
|
||||
Ave neighs/atom = 830.771
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -33,8 +33,6 @@ kokkos Kokkos package for GPU and many-core acceleration
|
|||
from Kokkos development team (Sandia)
|
||||
linalg set of BLAS and LAPACK routines needed by USER-ATC package
|
||||
from Axel Kohlmeyer (Temple U)
|
||||
meam modified embedded atom method (MEAM) potential, MEAM package
|
||||
from Greg Wagner (Sandia)
|
||||
message client/server communication library via MPI, sockets, files
|
||||
from Steve Plimpton (Sandia)
|
||||
molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package
|
||||
|
|
@ -51,8 +49,6 @@ qmmm quantum mechanics/molecular mechanics coupling interface
|
|||
from Axel Kohlmeyer (Temple U)
|
||||
quip interface to QUIP/libAtoms framework, USER-QUIP package
|
||||
from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
|
||||
reax ReaxFF potential, REAX package
|
||||
from Adri van Duin (Penn State) and Aidan Thompson (Sandia)
|
||||
smd hooks to Eigen library, used by USER-SMD package
|
||||
from Georg Ganzenmueller (Ernst Mach Institute, Germany)
|
||||
voronoi hooks to the Voro++ library, used by compute voronoi/atom command
|
||||
|
|
|
|||
|
|
@ -1,9 +0,0 @@
|
|||
# dependencies. needed for parallel make
|
||||
$(DIR)meam_data.o: meam_data.F
|
||||
$(DIR)meam_cleanup.o: meam_cleanup.F $(DIR)meam_data.o
|
||||
$(DIR)meam_dens_final.o: meam_dens_final.F $(DIR)meam_data.o
|
||||
$(DIR)meam_dens_init.o: meam_dens_init.F $(DIR)meam_data.o
|
||||
$(DIR)meam_force.o: meam_force.F $(DIR)meam_data.o
|
||||
$(DIR)meam_setup_done.o: meam_setup_done.F $(DIR)meam_data.o
|
||||
$(DIR)meam_setup_global.o: meam_setup_global.F $(DIR)meam_data.o
|
||||
$(DIR)meam_setup_param.o: meam_setup_param.F $(DIR)meam_data.o
|
||||
|
|
@ -1 +0,0 @@
|
|||
*.mod
|
||||
|
|
@ -1 +0,0 @@
|
|||
../Install.py
|
||||
|
|
@ -1,57 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.gfortran
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = g95
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1,61 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.gfortran
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = gfortran
|
||||
CC = gcc
|
||||
F90FLAGS = -O3 -fPIC -ffast-math -ftree-vectorize -fexpensive-optimizations -fno-second-underscore -g
|
||||
#F90FLAGS = -O
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
LINK = g++
|
||||
LINKFLAGS = -O
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1,57 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.ifort
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = ifort
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
meam_SYSINC =
|
||||
meam_SYSLIB =
|
||||
meam_SYSPATH =
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
meam_SYSINC =
|
||||
meam_SYSLIB = -lgfortran
|
||||
meam_SYSPATH =
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
meam_SYSINC =
|
||||
meam_SYSLIB = -lifcore -lsvml -lompstub -limf
|
||||
meam_SYSPATH = -L/opt/intel-11.1.046/lib/intel64
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
meam_SYSINC =
|
||||
meam_SYSLIB = -lifcore -lsvml -lompstub -limf
|
||||
meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib
|
||||
|
|
@ -1,61 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = mpifort
|
||||
CC = mpicc
|
||||
F90FLAGS = -O3 -fPIC
|
||||
#F90FLAGS = -O
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
LINK = mpicxx
|
||||
LINKFLAGS = -O
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1,57 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.pgf90
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = pgf90
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1 +0,0 @@
|
|||
Makefile.gfortran
|
||||
|
|
@ -1,59 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * MEAM: MODEFIED EMBEDDED ATOM METHOD *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * AUTHORS: Greg Wagner, Sandia National Laboratories *
|
||||
# * CONTACT: gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.glory
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
|
||||
|
||||
FILES = $(SRC) Makefile
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libmeam.a
|
||||
OBJ = $(SRC:.F=.o) fm_exp.o
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = mpif90
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
LINK = g++
|
||||
LINKFLAGS = -O
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
%.o:%.c
|
||||
$(CC) $(F90FLAGS) -c $<
|
||||
|
||||
include .depend
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o *.mod *~ $(LIB)
|
||||
|
||||
tar:
|
||||
-tar -cvf ../MEAM.tar $(FILES)
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
MEAM (modified embedded atom method) library
|
||||
|
||||
Greg Wagner, Sandia National Labs
|
||||
gjwagne at sandia.gov
|
||||
Jan 2007
|
||||
|
||||
This library is in implementation of the MEAM potential, specifically
|
||||
designed to work with LAMMPS.
|
||||
|
||||
-------------------------------------------------
|
||||
|
||||
This directory has source files to build a library that LAMMPS
|
||||
links against when using the MEAM package.
|
||||
|
||||
This library must be built with a F90 compiler, before LAMMPS is
|
||||
built, so LAMMPS can link against it.
|
||||
|
||||
You can type "make lib-meam" from the src directory to see help on how
|
||||
to build this library via make commands, or you can do the same thing
|
||||
by typing "python Install.py" from within this directory, or you can
|
||||
do it manually by following the instructions below.
|
||||
|
||||
Build the library using one of the provided Makefile.* files or create
|
||||
your own, specific to your compiler and system. For example:
|
||||
|
||||
make -f Makefile.gfortran
|
||||
|
||||
When you are done building this library, two files should
|
||||
exist in this directory:
|
||||
|
||||
libmeam.a the library LAMMPS will link against
|
||||
Makefile.lammps settings the LAMMPS Makefile will import
|
||||
|
||||
Makefile.lammps is created by the make command, by copying one of the
|
||||
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
|
||||
Makefile.* files.
|
||||
|
||||
IMPORTANT: You must examine the final Makefile.lammps to insure it is
|
||||
correct for your system, else the LAMMPS build will likely fail.
|
||||
|
||||
Makefile.lammps has settings for 3 variables:
|
||||
|
||||
user-meam_SYSINC = leave blank for this package
|
||||
user-meam_SYSLIB = auxiliary F90 libs needed to link a F90 lib with
|
||||
a C++ program (LAMMPS) via a C++ compiler
|
||||
user-meam_SYSPATH = path(s) to where those libraries are
|
||||
|
||||
Because you have a F90 compiler on your system, you should have these
|
||||
libraries. But you will have to figure out which ones are needed and
|
||||
where they are. Examples of common configurations are in the
|
||||
Makefile.lammps.* files.
|
||||
|
|
@ -1,133 +0,0 @@
|
|||
/*
|
||||
Copyright (c) 2012,2013 Axel Kohlmeyer <akohlmey@gmail.com>
|
||||
All rights reserved.
|
||||
|
||||
Redistribution and use in source and binary forms, with or without
|
||||
modification, are permitted provided that the following conditions
|
||||
are met:
|
||||
|
||||
* Redistributions of source code must retain the above copyright
|
||||
notice, this list of conditions and the following disclaimer.
|
||||
* Redistributions in binary form must reproduce the above copyright
|
||||
notice, this list of conditions and the following disclaimer in the
|
||||
documentation and/or other materials provided with the distribution.
|
||||
* Neither the name of the <organization> nor the
|
||||
names of its contributors may be used to endorse or promote products
|
||||
derived from this software without specific prior written permission.
|
||||
|
||||
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
||||
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
||||
ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
|
||||
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
|
||||
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
|
||||
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
|
||||
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
|
||||
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
|
||||
THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
||||
*/
|
||||
|
||||
/* faster versions of 2**x, e**x, and 10**x in single and double precision.
|
||||
*
|
||||
* Based on the Cephes math library 2.8
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
#include <stdint.h>
|
||||
|
||||
/* internal definitions for the fastermath library */
|
||||
|
||||
/* IEEE 754 double precision floating point data manipulation */
|
||||
typedef union
|
||||
{
|
||||
double f;
|
||||
uint64_t u;
|
||||
struct {int32_t i0,i1;};
|
||||
} udi_t;
|
||||
#define FM_DOUBLE_BIAS 1023
|
||||
#define FM_DOUBLE_EMASK 2146435072
|
||||
#define FM_DOUBLE_MBITS 20
|
||||
#define FM_DOUBLE_MMASK 1048575
|
||||
#define FM_DOUBLE_EZERO 1072693248
|
||||
|
||||
/* generate 2**num in floating point by bitshifting */
|
||||
#define FM_DOUBLE_INIT_EXP(var,num) \
|
||||
var.i0 = 0; \
|
||||
var.i1 = (((int) num) + FM_DOUBLE_BIAS) << 20
|
||||
|
||||
/* double precision constants */
|
||||
#define FM_DOUBLE_LOG2OFE 1.4426950408889634074
|
||||
#define FM_DOUBLE_LOGEOF2 6.9314718055994530942e-1
|
||||
#define FM_DOUBLE_LOG2OF10 3.32192809488736234789
|
||||
#define FM_DOUBLE_LOG10OF2 3.0102999566398119521e-1
|
||||
#define FM_DOUBLE_LOG10OFE 4.3429448190325182765e-1
|
||||
#define FM_DOUBLE_SQRT2 1.41421356237309504880
|
||||
#define FM_DOUBLE_SQRTH 0.70710678118654752440
|
||||
|
||||
/* optimizer friendly implementation of exp2(x).
|
||||
*
|
||||
* strategy:
|
||||
*
|
||||
* split argument into an integer part and a fraction:
|
||||
* ipart = floor(x+0.5);
|
||||
* fpart = x - ipart;
|
||||
*
|
||||
* compute exp2(ipart) from setting the ieee754 exponent
|
||||
* compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[
|
||||
*
|
||||
* the result becomes: exp2(x) = exp2(ipart) * exp2(fpart)
|
||||
*/
|
||||
|
||||
static const double fm_exp2_q[] = {
|
||||
/* 1.00000000000000000000e0, */
|
||||
2.33184211722314911771e2,
|
||||
4.36821166879210612817e3
|
||||
};
|
||||
static const double fm_exp2_p[] = {
|
||||
2.30933477057345225087e-2,
|
||||
2.02020656693165307700e1,
|
||||
1.51390680115615096133e3
|
||||
};
|
||||
|
||||
static double fm_exp2(double x)
|
||||
{
|
||||
double ipart, fpart, px, qx;
|
||||
udi_t epart;
|
||||
|
||||
ipart = floor(x+0.5);
|
||||
fpart = x - ipart;
|
||||
FM_DOUBLE_INIT_EXP(epart,ipart);
|
||||
|
||||
x = fpart*fpart;
|
||||
|
||||
px = fm_exp2_p[0];
|
||||
px = px*x + fm_exp2_p[1];
|
||||
qx = x + fm_exp2_q[0];
|
||||
px = px*x + fm_exp2_p[2];
|
||||
qx = qx*x + fm_exp2_q[1];
|
||||
|
||||
px = px * fpart;
|
||||
|
||||
x = 1.0 + 2.0*(px/(qx-px));
|
||||
return epart.f*x;
|
||||
}
|
||||
|
||||
double fm_exp_(double *x)
|
||||
{
|
||||
#if defined(__BYTE_ORDER__)
|
||||
#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
|
||||
return fm_exp2(FM_DOUBLE_LOG2OFE * (*x));
|
||||
#endif
|
||||
#endif
|
||||
return exp(*x);
|
||||
}
|
||||
|
||||
/*
|
||||
* Local Variables:
|
||||
* mode: c
|
||||
* compile-command: "make -C .."
|
||||
* c-basic-offset: 4
|
||||
* fill-column: 76
|
||||
* indent-tabs-mode: nil
|
||||
* End:
|
||||
*/
|
||||
|
|
@ -1,26 +0,0 @@
|
|||
c Declaration in pair_meam.h:
|
||||
c
|
||||
c void meam_cleanup()
|
||||
c
|
||||
c Call from PairMEAM destructor
|
||||
c
|
||||
c meam_cleanup()
|
||||
c
|
||||
|
||||
subroutine meam_cleanup
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer dealloc_error
|
||||
|
||||
deallocate(phir,STAT=dealloc_error)
|
||||
deallocate(phirar,STAT=dealloc_error)
|
||||
deallocate(phirar1,STAT=dealloc_error)
|
||||
deallocate(phirar2,STAT=dealloc_error)
|
||||
deallocate(phirar3,STAT=dealloc_error)
|
||||
deallocate(phirar4,STAT=dealloc_error)
|
||||
deallocate(phirar5,STAT=dealloc_error)
|
||||
deallocate(phirar6,STAT=dealloc_error)
|
||||
|
||||
return
|
||||
end
|
||||
|
|
@ -1,87 +0,0 @@
|
|||
|
||||
module meam_data
|
||||
|
||||
integer, parameter :: maxelt = 5
|
||||
real*8 , external :: fm_exp
|
||||
|
||||
c cutforce = force cutoff
|
||||
c cutforcesq = force cutoff squared
|
||||
|
||||
real*8 cutforce,cutforcesq
|
||||
|
||||
c Ec_meam = cohesive energy
|
||||
c re_meam = nearest-neighbor distance
|
||||
c Omega_meam = atomic volume
|
||||
c B_meam = bulk modulus
|
||||
c Z_meam = number of first neighbors for reference structure
|
||||
c ielt_meam = atomic number of element
|
||||
c A_meam = adjustable parameter
|
||||
c alpha_meam = sqrt(9*Omega*B/Ec)
|
||||
c rho0_meam = density scaling parameter
|
||||
c delta_meam = heat of formation for alloys
|
||||
c beta[0-3]_meam = electron density constants
|
||||
c t[0-3]_meam = coefficients on densities in Gamma computation
|
||||
c rho_ref_meam = background density for reference structure
|
||||
c ibar_meam(i) = selection parameter for Gamma function for elt i,
|
||||
c lattce_meam(i,j) = lattce configuration for elt i or alloy (i,j)
|
||||
c neltypes = maximum number of element type defined
|
||||
c eltind = index number of pair (similar to Voigt notation; ij = ji)
|
||||
c phir = pair potential function array
|
||||
c phirar[1-6] = spline coeffs
|
||||
c attrac_meam = attraction parameter in Rose energy
|
||||
c repuls_meam = repulsion parameter in Rose energy
|
||||
c nn2_meam = 1 if second nearest neighbors are to be computed, else 0
|
||||
c zbl_meam = 1 if zbl potential for small r to be use, else 0
|
||||
c emb_lin_neg = 1 if linear embedding function for rhob to be used, else 0
|
||||
c bkgd_dyn = 1 if reference densities follows Dynamo, else 0
|
||||
c Cmin_meam, Cmax_meam = min and max values in screening cutoff
|
||||
c rc_meam = cutoff distance for meam
|
||||
c delr_meam = cutoff region for meam
|
||||
c ebound_meam = factor giving maximum boundary of sceen fcn ellipse
|
||||
c augt1 = flag for whether t1 coefficient should be augmented
|
||||
c ialloy = flag for newer alloy formulation (as in dynamo code)
|
||||
c mix_ref_t = flag to recover "old" way of computing t in reference config
|
||||
c erose_form = selection parameter for form of E_rose function
|
||||
c gsmooth_factor = factor determining length of G smoothing region
|
||||
c vind[23]D = Voight notation index maps for 2 and 3D
|
||||
c v2D,v3D = array of factors to apply for Voight notation
|
||||
|
||||
c nr,dr = pair function discretization parameters
|
||||
c nrar,rdrar = spline coeff array parameters
|
||||
|
||||
real*8 Ec_meam(maxelt,maxelt),re_meam(maxelt,maxelt)
|
||||
real*8 Omega_meam(maxelt),Z_meam(maxelt)
|
||||
real*8 A_meam(maxelt),alpha_meam(maxelt,maxelt),rho0_meam(maxelt)
|
||||
real*8 delta_meam(maxelt,maxelt)
|
||||
real*8 beta0_meam(maxelt),beta1_meam(maxelt)
|
||||
real*8 beta2_meam(maxelt),beta3_meam(maxelt)
|
||||
real*8 t0_meam(maxelt),t1_meam(maxelt)
|
||||
real*8 t2_meam(maxelt),t3_meam(maxelt)
|
||||
real*8 rho_ref_meam(maxelt)
|
||||
integer ibar_meam(maxelt),ielt_meam(maxelt)
|
||||
character*3 lattce_meam(maxelt,maxelt)
|
||||
integer nn2_meam(maxelt,maxelt)
|
||||
integer zbl_meam(maxelt,maxelt)
|
||||
integer eltind(maxelt,maxelt)
|
||||
integer neltypes
|
||||
|
||||
real*8, allocatable :: phir(:,:)
|
||||
|
||||
real*8, allocatable :: phirar(:,:),phirar1(:,:),phirar2(:,:),
|
||||
$ phirar3(:,:),phirar4(:,:),phirar5(:,:),phirar6(:,:)
|
||||
|
||||
real*8 attrac_meam(maxelt,maxelt),repuls_meam(maxelt,maxelt)
|
||||
|
||||
real*8 Cmin_meam(maxelt,maxelt,maxelt)
|
||||
real*8 Cmax_meam(maxelt,maxelt,maxelt)
|
||||
real*8 rc_meam,delr_meam,ebound_meam(maxelt,maxelt)
|
||||
integer augt1, ialloy, mix_ref_t, erose_form
|
||||
integer emb_lin_neg, bkgd_dyn
|
||||
real*8 gsmooth_factor
|
||||
integer vind2D(3,3),vind3D(3,3,3)
|
||||
integer v2D(6),v3D(10)
|
||||
|
||||
integer nr,nrar
|
||||
real*8 dr,rdrar
|
||||
|
||||
end module
|
||||
|
|
@ -1,296 +0,0 @@
|
|||
c Extern "C" declaration has the form:
|
||||
c
|
||||
c void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *,
|
||||
c int *, int *, int *,
|
||||
c double *, double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, int *);
|
||||
c
|
||||
c Call from pair_meam.cpp has the form:
|
||||
c
|
||||
c meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom,
|
||||
c &eng_vdwl,eatom,ntype,type,fmap,
|
||||
c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],
|
||||
c &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1,
|
||||
c dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag);
|
||||
c
|
||||
|
||||
subroutine meam_dens_final(nlocal, nmax,
|
||||
$ eflag_either, eflag_global, eflag_atom, eng_vdwl, eatom,
|
||||
$ ntype, type, fmap,
|
||||
$ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave,
|
||||
$ Gamma, dGamma1, dGamma2, dGamma3,
|
||||
$ rho, rho0, rho1, rho2, rho3, fp, errorflag)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer nlocal, nmax, eflag_either, eflag_global, eflag_atom
|
||||
integer ntype, type, fmap
|
||||
real*8 eng_vdwl, eatom, Arho1, Arho2
|
||||
real*8 Arho2b, Arho3, Arho3b
|
||||
real*8 t_ave, tsq_ave
|
||||
real*8 Gamma, dGamma1, dGamma2, dGamma3
|
||||
real*8 rho, rho0, rho1, rho2, rho3
|
||||
real*8 fp
|
||||
integer errorflag
|
||||
|
||||
dimension eatom(nmax)
|
||||
dimension type(nmax), fmap(ntype)
|
||||
dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax)
|
||||
dimension Arho3(10,nmax), Arho3b(3,nmax), t_ave(3,nmax)
|
||||
dimension tsq_ave(3,nmax)
|
||||
dimension Gamma(nmax), dGamma1(nmax), dGamma2(nmax)
|
||||
dimension dGamma3(nmax), rho(nmax), rho0(nmax)
|
||||
dimension rho1(nmax), rho2(nmax), rho3(nmax)
|
||||
dimension fp(nmax)
|
||||
|
||||
integer i, elti
|
||||
integer m
|
||||
real*8 rhob, G, dG, Gbar, dGbar, gam, shp(3), shpi(3), Z
|
||||
real*8 B, denom, rho_bkgd
|
||||
|
||||
c Complete the calculation of density
|
||||
|
||||
do i = 1,nlocal
|
||||
|
||||
elti = fmap(type(i))
|
||||
if (elti.gt.0) then
|
||||
rho1(i) = 0.d0
|
||||
rho2(i) = -1.d0/3.d0*Arho2b(i)*Arho2b(i)
|
||||
rho3(i) = 0.d0
|
||||
do m = 1,3
|
||||
rho1(i) = rho1(i) + Arho1(m,i)*Arho1(m,i)
|
||||
rho3(i) = rho3(i) - 3.d0/5.d0*Arho3b(m,i)*Arho3b(m,i)
|
||||
enddo
|
||||
do m = 1,6
|
||||
rho2(i) = rho2(i) + v2D(m)*Arho2(m,i)*Arho2(m,i)
|
||||
enddo
|
||||
do m = 1,10
|
||||
rho3(i) = rho3(i) + v3D(m)*Arho3(m,i)*Arho3(m,i)
|
||||
enddo
|
||||
|
||||
if( rho0(i) .gt. 0.0 ) then
|
||||
if (ialloy.eq.1) then
|
||||
if (tsq_ave(1,i) .ne. 0.0d0) then
|
||||
t_ave(1,i) = t_ave(1,i)/tsq_ave(1,i)
|
||||
else
|
||||
t_ave(1,i) = 0.0d0
|
||||
endif
|
||||
if (tsq_ave(2,i) .ne. 0.0d0) then
|
||||
t_ave(2,i) = t_ave(2,i)/tsq_ave(2,i)
|
||||
else
|
||||
t_ave(2,i) = 0.0d0
|
||||
endif
|
||||
if (tsq_ave(3,i) .ne. 0.0d0) then
|
||||
t_ave(3,i) = t_ave(3,i)/tsq_ave(3,i)
|
||||
else
|
||||
t_ave(3,i) = 0.0d0
|
||||
endif
|
||||
else if (ialloy.eq.2) then
|
||||
t_ave(1,i) = t1_meam(elti)
|
||||
t_ave(2,i) = t2_meam(elti)
|
||||
t_ave(3,i) = t3_meam(elti)
|
||||
else
|
||||
t_ave(1,i) = t_ave(1,i)/rho0(i)
|
||||
t_ave(2,i) = t_ave(2,i)/rho0(i)
|
||||
t_ave(3,i) = t_ave(3,i)/rho0(i)
|
||||
endif
|
||||
endif
|
||||
|
||||
Gamma(i) = t_ave(1,i)*rho1(i)
|
||||
$ + t_ave(2,i)*rho2(i) + t_ave(3,i)*rho3(i)
|
||||
|
||||
if( rho0(i) .gt. 0.0 ) then
|
||||
Gamma(i) = Gamma(i)/(rho0(i)*rho0(i))
|
||||
end if
|
||||
|
||||
Z = Z_meam(elti)
|
||||
|
||||
call G_gam(Gamma(i),ibar_meam(elti),
|
||||
$ gsmooth_factor,G,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
call get_shpfcn(shp,lattce_meam(elti,elti))
|
||||
if (ibar_meam(elti).le.0) then
|
||||
Gbar = 1.d0
|
||||
dGbar = 0.d0
|
||||
else
|
||||
if (mix_ref_t.eq.1) then
|
||||
gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
|
||||
$ +t_ave(3,i)*shp(3))/(Z*Z)
|
||||
else
|
||||
gam = (t1_meam(elti)*shp(1)+t2_meam(elti)*shp(2)
|
||||
$ +t3_meam(elti)*shp(3))/(Z*Z)
|
||||
endif
|
||||
call G_gam(gam,ibar_meam(elti),gsmooth_factor,
|
||||
$ Gbar,errorflag)
|
||||
endif
|
||||
rho(i) = rho0(i) * G
|
||||
|
||||
if (mix_ref_t.eq.1) then
|
||||
if (ibar_meam(elti).le.0) then
|
||||
Gbar = 1.d0
|
||||
dGbar = 0.d0
|
||||
else
|
||||
gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2)
|
||||
$ +t_ave(3,i)*shp(3))/(Z*Z)
|
||||
call dG_gam(gam,ibar_meam(elti),gsmooth_factor,
|
||||
$ Gbar,dGbar)
|
||||
endif
|
||||
rho_bkgd = rho0_meam(elti)*Z*Gbar
|
||||
else
|
||||
if (bkgd_dyn.eq.1) then
|
||||
rho_bkgd = rho0_meam(elti)*Z
|
||||
else
|
||||
rho_bkgd = rho_ref_meam(elti)
|
||||
endif
|
||||
endif
|
||||
rhob = rho(i)/rho_bkgd
|
||||
denom = 1.d0/rho_bkgd
|
||||
|
||||
call dG_gam(Gamma(i),ibar_meam(elti),gsmooth_factor,G,dG)
|
||||
|
||||
dGamma1(i) = (G - 2*dG*Gamma(i))*denom
|
||||
|
||||
if( rho0(i) .ne. 0.d0 ) then
|
||||
dGamma2(i) = (dG/rho0(i))*denom
|
||||
else
|
||||
dGamma2(i) = 0.d0
|
||||
end if
|
||||
|
||||
c dGamma3 is nonzero only if we are using the "mixed" rule for
|
||||
c computing t in the reference system (which is not correct, but
|
||||
c included for backward compatibility
|
||||
if (mix_ref_t.eq.1) then
|
||||
dGamma3(i) = rho0(i)*G*dGbar/(Gbar*Z*Z)*denom
|
||||
else
|
||||
dGamma3(i) = 0.0
|
||||
endif
|
||||
|
||||
B = A_meam(elti)*Ec_meam(elti,elti)
|
||||
|
||||
if( rhob .ne. 0.d0 ) then
|
||||
if (emb_lin_neg.eq.1 .and. rhob.le.0) then
|
||||
fp(i) = -B
|
||||
else
|
||||
fp(i) = B*(log(rhob)+1.d0)
|
||||
endif
|
||||
if (eflag_either.ne.0) then
|
||||
if (eflag_global.ne.0) then
|
||||
if (emb_lin_neg.eq.1 .and. rhob.le.0) then
|
||||
eng_vdwl = eng_vdwl - B*rhob
|
||||
else
|
||||
eng_vdwl = eng_vdwl + B*rhob*log(rhob)
|
||||
endif
|
||||
endif
|
||||
if (eflag_atom.ne.0) then
|
||||
if (emb_lin_neg.eq.1 .and. rhob.le.0) then
|
||||
eatom(i) = eatom(i) - B*rhob
|
||||
else
|
||||
eatom(i) = eatom(i) + B*rhob*log(rhob)
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
else
|
||||
if (emb_lin_neg.eq.1) then
|
||||
fp(i) = -B
|
||||
else
|
||||
fp(i) = B
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
enddo
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine G_gam(Gamma,ibar,gsmooth_factor,G,errorflag)
|
||||
c Compute G(Gamma) based on selection flag ibar:
|
||||
c 0 => G = sqrt(1+Gamma)
|
||||
c 1 => G = exp(Gamma/2)
|
||||
c 2 => not implemented
|
||||
c 3 => G = 2/(1+exp(-Gamma))
|
||||
c 4 => G = sqrt(1+Gamma)
|
||||
c -5 => G = +-sqrt(abs(1+Gamma))
|
||||
use meam_data , only: fm_exp
|
||||
implicit none
|
||||
real*8 Gamma,G
|
||||
real*8 gsmooth_factor, gsmooth_switchpoint
|
||||
integer ibar, errorflag
|
||||
if (ibar.eq.0.or.ibar.eq.4) then
|
||||
gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1)
|
||||
if (Gamma.lt.gsmooth_switchpoint) then
|
||||
c e.g. gsmooth_factor is 99, then:
|
||||
c gsmooth_switchpoint = -0.99
|
||||
c G = 0.01*(-0.99/Gamma)**99
|
||||
G = 1/(gsmooth_factor+1)
|
||||
$ *(gsmooth_switchpoint/Gamma)**gsmooth_factor
|
||||
G = sqrt(G)
|
||||
else
|
||||
G = sqrt(1.d0+Gamma)
|
||||
endif
|
||||
else if (ibar.eq.1) then
|
||||
G = fm_exp(Gamma/2.d0)
|
||||
else if (ibar.eq.3) then
|
||||
G = 2.d0/(1.d0+exp(-Gamma))
|
||||
else if (ibar.eq.-5) then
|
||||
if ((1.d0+Gamma).ge.0) then
|
||||
G = sqrt(1.d0+Gamma)
|
||||
else
|
||||
G = -sqrt(-1.d0-Gamma)
|
||||
endif
|
||||
else
|
||||
errorflag = 1
|
||||
endif
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine dG_gam(Gamma,ibar,gsmooth_factor,G,dG)
|
||||
c Compute G(Gamma) and dG(gamma) based on selection flag ibar:
|
||||
c 0 => G = sqrt(1+Gamma)
|
||||
c 1 => G = fm_exp(Gamma/2)
|
||||
c 2 => not implemented
|
||||
c 3 => G = 2/(1+fm_exp(-Gamma))
|
||||
c 4 => G = sqrt(1+Gamma)
|
||||
c -5 => G = +-sqrt(abs(1+Gamma))
|
||||
use meam_data , only: fm_exp
|
||||
real*8 Gamma,G,dG
|
||||
real*8 gsmooth_factor, gsmooth_switchpoint
|
||||
integer ibar
|
||||
if (ibar.eq.0.or.ibar.eq.4) then
|
||||
gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1)
|
||||
if (Gamma.lt.gsmooth_switchpoint) then
|
||||
c e.g. gsmooth_factor is 99, then:
|
||||
c gsmooth_switchpoint = -0.99
|
||||
c G = 0.01*(-0.99/Gamma)**99
|
||||
G = 1/(gsmooth_factor+1)
|
||||
$ *(gsmooth_switchpoint/Gamma)**gsmooth_factor
|
||||
G = sqrt(G)
|
||||
dG = -gsmooth_factor*G/(2.0*Gamma)
|
||||
else
|
||||
G = sqrt(1.d0+Gamma)
|
||||
dG = 1.d0/(2.d0*G)
|
||||
endif
|
||||
else if (ibar.eq.1) then
|
||||
G = fm_exp(Gamma/2.d0)
|
||||
dG = G/2.d0
|
||||
else if (ibar.eq.3) then
|
||||
G = 2.d0/(1.d0+fm_exp(-Gamma))
|
||||
dG = G*(2.d0-G)/2
|
||||
else if (ibar.eq.-5) then
|
||||
if ((1.d0+Gamma).ge.0) then
|
||||
G = sqrt(1.d0+Gamma)
|
||||
dG = 1.d0/(2.d0*G)
|
||||
else
|
||||
G = -sqrt(-1.d0-Gamma)
|
||||
dG = -1.d0/(2.d0*G)
|
||||
endif
|
||||
endif
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
|
@ -1,564 +0,0 @@
|
|||
c Extern "C" declaration has the form:
|
||||
c
|
||||
c void meam_dens_init_(int *, int *, int *, double *, int *, int *, int *, double *,
|
||||
c int *, int *, int *, int *,
|
||||
c double *, double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, int *);
|
||||
c
|
||||
c
|
||||
c Call from pair_meam.cpp has the form:
|
||||
c
|
||||
c meam_dens_init_(&i,&nmax,ntype,type,fmap,&x[0][0],
|
||||
c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i],
|
||||
c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
|
||||
c rho0,&arho1[0][0],&arho2[0][0],arho2b,
|
||||
c &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],&errorflag);
|
||||
c
|
||||
|
||||
subroutine meam_dens_init(i, nmax,
|
||||
$ ntype, type, fmap, x,
|
||||
$ numneigh, firstneigh,
|
||||
$ numneigh_full, firstneigh_full,
|
||||
$ scrfcn, dscrfcn, fcpair, rho0, arho1, arho2, arho2b,
|
||||
$ arho3, arho3b, t_ave, tsq_ave, errorflag)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer i, nmax, ntype, type, fmap
|
||||
real*8 x
|
||||
integer numneigh, firstneigh, numneigh_full, firstneigh_full
|
||||
real*8 scrfcn, dscrfcn, fcpair
|
||||
real*8 rho0, arho1, arho2
|
||||
real*8 arho2b, arho3, arho3b, t_ave, tsq_ave
|
||||
integer errorflag
|
||||
integer j,jn
|
||||
|
||||
dimension x(3,nmax)
|
||||
dimension type(nmax), fmap(ntype)
|
||||
dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
|
||||
dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh)
|
||||
dimension rho0(nmax), arho1(3,nmax), arho2(6,nmax)
|
||||
dimension arho2b(nmax), arho3(10,nmax), arho3b(3,nmax)
|
||||
dimension t_ave(3,nmax), tsq_ave(3,nmax)
|
||||
|
||||
errorflag = 0
|
||||
|
||||
c Compute screening function and derivatives
|
||||
call getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x,
|
||||
$ numneigh, firstneigh,
|
||||
$ numneigh_full, firstneigh_full,
|
||||
$ ntype, type, fmap)
|
||||
|
||||
c Calculate intermediate density terms to be communicated
|
||||
call calc_rho1(i, nmax, ntype, type, fmap, x,
|
||||
$ numneigh, firstneigh,
|
||||
$ scrfcn, fcpair, rho0, arho1, arho2, arho2b,
|
||||
$ arho3, arho3b, t_ave, tsq_ave)
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x,
|
||||
$ numneigh, firstneigh,
|
||||
$ numneigh_full, firstneigh_full,
|
||||
$ ntype, type, fmap)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer i, nmax
|
||||
real*8 scrfcn, dscrfcn, fcpair, x
|
||||
integer numneigh, firstneigh, numneigh_full, firstneigh_full
|
||||
integer ntype, type, fmap
|
||||
|
||||
dimension scrfcn(numneigh), dscrfcn(numneigh)
|
||||
dimension fcpair(numneigh), x(3,nmax)
|
||||
dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
|
||||
dimension type(nmax), fmap(ntype)
|
||||
|
||||
integer jn,j,kn,k
|
||||
integer elti,eltj,eltk
|
||||
real*8 xitmp,yitmp,zitmp,delxij,delyij,delzij,rij2,rij
|
||||
real*8 xjtmp,yjtmp,zjtmp,delxik,delyik,delzik,rik2,rik
|
||||
real*8 xktmp,yktmp,zktmp,delxjk,delyjk,delzjk,rjk2,rjk
|
||||
real*8 xik,xjk,sij,fcij,sfcij,dfcij,sikj,dfikj,cikj
|
||||
real*8 Cmin,Cmax,delc,ebound,rbound,a,coef1,coef2
|
||||
real*8 coef1a,coef1b,coef2a,coef2b
|
||||
real*8 dcikj
|
||||
real*8 dC1a,dC1b,dC2a,dC2b
|
||||
real*8 rnorm,fc,dfc,drinv
|
||||
|
||||
drinv = 1.d0/delr_meam
|
||||
elti = fmap(type(i))
|
||||
|
||||
if (elti.gt.0) then
|
||||
|
||||
xitmp = x(1,i)
|
||||
yitmp = x(2,i)
|
||||
zitmp = x(3,i)
|
||||
|
||||
do jn = 1,numneigh
|
||||
j = firstneigh(jn)
|
||||
|
||||
eltj = fmap(type(j))
|
||||
if (eltj.gt.0) then
|
||||
|
||||
c First compute screening function itself, sij
|
||||
xjtmp = x(1,j)
|
||||
yjtmp = x(2,j)
|
||||
zjtmp = x(3,j)
|
||||
delxij = xjtmp - xitmp
|
||||
delyij = yjtmp - yitmp
|
||||
delzij = zjtmp - zitmp
|
||||
rij2 = delxij*delxij + delyij*delyij + delzij*delzij
|
||||
rij = sqrt(rij2)
|
||||
if (rij.gt.rc_meam) then
|
||||
fcij = 0.0
|
||||
dfcij = 0.d0
|
||||
sij = 0.d0
|
||||
else
|
||||
rnorm = (rc_meam-rij)*drinv
|
||||
call screen(i, j, nmax, x, rij2, sij,
|
||||
$ numneigh_full, firstneigh_full, ntype, type, fmap)
|
||||
call dfcut(rnorm,fc,dfc)
|
||||
fcij = fc
|
||||
dfcij = dfc*drinv
|
||||
endif
|
||||
|
||||
c Now compute derivatives
|
||||
dscrfcn(jn) = 0.d0
|
||||
sfcij = sij*fcij
|
||||
if (sfcij.eq.0.d0.or.sfcij.eq.1.d0) goto 100
|
||||
rbound = ebound_meam(elti,eltj) * rij2
|
||||
do kn = 1,numneigh_full
|
||||
k = firstneigh_full(kn)
|
||||
if (k.eq.j) goto 10
|
||||
eltk = fmap(type(k))
|
||||
if (eltk.eq.0) goto 10
|
||||
xktmp = x(1,k)
|
||||
yktmp = x(2,k)
|
||||
zktmp = x(3,k)
|
||||
delxjk = xktmp - xjtmp
|
||||
delyjk = yktmp - yjtmp
|
||||
delzjk = zktmp - zjtmp
|
||||
rjk2 = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk
|
||||
if (rjk2.gt.rbound) goto 10
|
||||
delxik = xktmp - xitmp
|
||||
delyik = yktmp - yitmp
|
||||
delzik = zktmp - zitmp
|
||||
rik2 = delxik*delxik + delyik*delyik + delzik*delzik
|
||||
if (rik2.gt.rbound) goto 10
|
||||
xik = rik2/rij2
|
||||
xjk = rjk2/rij2
|
||||
a = 1 - (xik-xjk)*(xik-xjk)
|
||||
c if a < 0, then ellipse equation doesn't describe this case and
|
||||
c atom k can't possibly screen i-j
|
||||
if (a.le.0.d0) goto 10
|
||||
cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
|
||||
Cmax = Cmax_meam(elti,eltj,eltk)
|
||||
Cmin = Cmin_meam(elti,eltj,eltk)
|
||||
if (cikj.ge.Cmax) then
|
||||
goto 10
|
||||
c Note that cikj may be slightly negative (within numerical
|
||||
c tolerance) if atoms are colinear, so don't reject that case here
|
||||
c (other negative cikj cases were handled by the test on "a" above)
|
||||
c Note that we never have 0<cikj<Cmin here, else sij=0 (rejected above)
|
||||
else
|
||||
delc = Cmax - Cmin
|
||||
cikj = (cikj-Cmin)/delc
|
||||
call dfcut(cikj,sikj,dfikj)
|
||||
coef1 = dfikj/(delc*sikj)
|
||||
call dCfunc(rij2,rik2,rjk2,dCikj)
|
||||
dscrfcn(jn) = dscrfcn(jn) + coef1*dCikj
|
||||
endif
|
||||
10 continue
|
||||
enddo
|
||||
coef1 = sfcij
|
||||
coef2 = sij*dfcij/rij
|
||||
dscrfcn(jn) = dscrfcn(jn)*coef1 - coef2
|
||||
100 continue
|
||||
|
||||
scrfcn(jn) = sij
|
||||
fcpair(jn) = fcij
|
||||
|
||||
endif
|
||||
|
||||
enddo
|
||||
|
||||
endif
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine calc_rho1(i, nmax, ntype, type, fmap, x,
|
||||
$ numneigh, firstneigh,
|
||||
$ scrfcn, fcpair, rho0, arho1, arho2, arho2b,
|
||||
$ arho3, arho3b, t_ave, tsq_ave)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer i, nmax, ntype, type, fmap
|
||||
real*8 x
|
||||
integer numneigh, firstneigh
|
||||
real*8 scrfcn, fcpair, rho0, arho1, arho2
|
||||
real*8 arho2b, arho3, arho3b, t_ave, tsq_ave
|
||||
|
||||
dimension type(nmax), fmap(ntype), x(3,nmax)
|
||||
dimension firstneigh(numneigh)
|
||||
dimension scrfcn(numneigh), fcpair(numneigh)
|
||||
dimension rho0(nmax), arho1(3,nmax), arho2(6,nmax)
|
||||
dimension arho2b(nmax), arho3(10,nmax), arho3b(3,nmax)
|
||||
dimension t_ave(3,nmax), tsq_ave(3,nmax)
|
||||
|
||||
integer jn,j,m,n,p,elti,eltj
|
||||
integer nv2,nv3
|
||||
real*8 xtmp,ytmp,ztmp,delij(3),rij2,rij,sij
|
||||
real*8 ai,aj,rhoa0j,rhoa1j,rhoa2j,rhoa3j,A1j,A2j,A3j
|
||||
real*8 G,Gbar,gam,shp(3)
|
||||
real*8 ro0i,ro0j
|
||||
real*8 rhoa0i,rhoa1i,rhoa2i,rhoa3i,A1i,A2i,A3i
|
||||
|
||||
elti = fmap(type(i))
|
||||
xtmp = x(1,i)
|
||||
ytmp = x(2,i)
|
||||
ztmp = x(3,i)
|
||||
do jn = 1,numneigh
|
||||
if (scrfcn(jn).ne.0.d0) then
|
||||
j = firstneigh(jn)
|
||||
sij = scrfcn(jn)*fcpair(jn)
|
||||
delij(1) = x(1,j) - xtmp
|
||||
delij(2) = x(2,j) - ytmp
|
||||
delij(3) = x(3,j) - ztmp
|
||||
rij2 = delij(1)*delij(1) + delij(2)*delij(2)
|
||||
$ + delij(3)*delij(3)
|
||||
if (rij2.lt.cutforcesq) then
|
||||
eltj = fmap(type(j))
|
||||
rij = sqrt(rij2)
|
||||
ai = rij/re_meam(elti,elti) - 1.d0
|
||||
aj = rij/re_meam(eltj,eltj) - 1.d0
|
||||
ro0i = rho0_meam(elti)
|
||||
ro0j = rho0_meam(eltj)
|
||||
rhoa0j = ro0j*fm_exp(-beta0_meam(eltj)*aj)*sij
|
||||
rhoa1j = ro0j*fm_exp(-beta1_meam(eltj)*aj)*sij
|
||||
rhoa2j = ro0j*fm_exp(-beta2_meam(eltj)*aj)*sij
|
||||
rhoa3j = ro0j*fm_exp(-beta3_meam(eltj)*aj)*sij
|
||||
rhoa0i = ro0i*fm_exp(-beta0_meam(elti)*ai)*sij
|
||||
rhoa1i = ro0i*fm_exp(-beta1_meam(elti)*ai)*sij
|
||||
rhoa2i = ro0i*fm_exp(-beta2_meam(elti)*ai)*sij
|
||||
rhoa3i = ro0i*fm_exp(-beta3_meam(elti)*ai)*sij
|
||||
if (ialloy.eq.1) then
|
||||
rhoa1j = rhoa1j * t1_meam(eltj)
|
||||
rhoa2j = rhoa2j * t2_meam(eltj)
|
||||
rhoa3j = rhoa3j * t3_meam(eltj)
|
||||
rhoa1i = rhoa1i * t1_meam(elti)
|
||||
rhoa2i = rhoa2i * t2_meam(elti)
|
||||
rhoa3i = rhoa3i * t3_meam(elti)
|
||||
endif
|
||||
rho0(i) = rho0(i) + rhoa0j
|
||||
rho0(j) = rho0(j) + rhoa0i
|
||||
c For ialloy = 2, use single-element value (not average)
|
||||
if (ialloy.ne.2) then
|
||||
t_ave(1,i) = t_ave(1,i) + t1_meam(eltj)*rhoa0j
|
||||
t_ave(2,i) = t_ave(2,i) + t2_meam(eltj)*rhoa0j
|
||||
t_ave(3,i) = t_ave(3,i) + t3_meam(eltj)*rhoa0j
|
||||
t_ave(1,j) = t_ave(1,j) + t1_meam(elti)*rhoa0i
|
||||
t_ave(2,j) = t_ave(2,j) + t2_meam(elti)*rhoa0i
|
||||
t_ave(3,j) = t_ave(3,j) + t3_meam(elti)*rhoa0i
|
||||
endif
|
||||
if (ialloy.eq.1) then
|
||||
tsq_ave(1,i) = tsq_ave(1,i) +
|
||||
$ t1_meam(eltj)*t1_meam(eltj)*rhoa0j
|
||||
tsq_ave(2,i) = tsq_ave(2,i) +
|
||||
$ t2_meam(eltj)*t2_meam(eltj)*rhoa0j
|
||||
tsq_ave(3,i) = tsq_ave(3,i) +
|
||||
$ t3_meam(eltj)*t3_meam(eltj)*rhoa0j
|
||||
tsq_ave(1,j) = tsq_ave(1,j) +
|
||||
$ t1_meam(elti)*t1_meam(elti)*rhoa0i
|
||||
tsq_ave(2,j) = tsq_ave(2,j) +
|
||||
$ t2_meam(elti)*t2_meam(elti)*rhoa0i
|
||||
tsq_ave(3,j) = tsq_ave(3,j) +
|
||||
$ t3_meam(elti)*t3_meam(elti)*rhoa0i
|
||||
endif
|
||||
Arho2b(i) = Arho2b(i) + rhoa2j
|
||||
Arho2b(j) = Arho2b(j) + rhoa2i
|
||||
|
||||
A1j = rhoa1j/rij
|
||||
A2j = rhoa2j/rij2
|
||||
A3j = rhoa3j/(rij2*rij)
|
||||
A1i = rhoa1i/rij
|
||||
A2i = rhoa2i/rij2
|
||||
A3i = rhoa3i/(rij2*rij)
|
||||
nv2 = 1
|
||||
nv3 = 1
|
||||
do m = 1,3
|
||||
Arho1(m,i) = Arho1(m,i) + A1j*delij(m)
|
||||
Arho1(m,j) = Arho1(m,j) - A1i*delij(m)
|
||||
Arho3b(m,i) = Arho3b(m,i) + rhoa3j*delij(m)/rij
|
||||
Arho3b(m,j) = Arho3b(m,j) - rhoa3i*delij(m)/rij
|
||||
do n = m,3
|
||||
Arho2(nv2,i) = Arho2(nv2,i) + A2j*delij(m)*delij(n)
|
||||
Arho2(nv2,j) = Arho2(nv2,j) + A2i*delij(m)*delij(n)
|
||||
nv2 = nv2+1
|
||||
do p = n,3
|
||||
Arho3(nv3,i) = Arho3(nv3,i)
|
||||
$ + A3j*delij(m)*delij(n)*delij(p)
|
||||
Arho3(nv3,j) = Arho3(nv3,j)
|
||||
$ - A3i*delij(m)*delij(n)*delij(p)
|
||||
nv3 = nv3+1
|
||||
enddo
|
||||
enddo
|
||||
enddo
|
||||
endif
|
||||
endif
|
||||
enddo
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine screen(i, j, nmax, x, rijsq, sij,
|
||||
$ numneigh_full, firstneigh_full, ntype, type, fmap)
|
||||
c Screening function
|
||||
c Inputs: i = atom 1 id (integer)
|
||||
c j = atom 2 id (integer)
|
||||
c rijsq = squared distance between i and j
|
||||
c Outputs: sij = screening function
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer i,j,nmax,k,nk,m
|
||||
real*8 x,rijsq,sij
|
||||
integer numneigh_full, firstneigh_full
|
||||
integer ntype, type, fmap
|
||||
|
||||
dimension x(3,nmax), firstneigh_full(numneigh_full)
|
||||
dimension type(nmax), fmap(ntype)
|
||||
|
||||
integer elti,eltj,eltk
|
||||
real*8 delxik,delyik,delzik
|
||||
real*8 delxjk,delyjk,delzjk
|
||||
real*8 riksq,rjksq,xik,xjk,cikj,a,delc,sikj,fcij,rij
|
||||
real*8 Cmax,Cmin,rbound
|
||||
|
||||
sij = 1.d0
|
||||
elti = fmap(type(i))
|
||||
eltj = fmap(type(j))
|
||||
|
||||
c if rjksq > ebound*rijsq, atom k is definitely outside the ellipse
|
||||
rbound = ebound_meam(elti,eltj)*rijsq
|
||||
|
||||
do nk = 1,numneigh_full
|
||||
k = firstneigh_full(nk)
|
||||
eltk = fmap(type(k))
|
||||
if (k.eq.j) goto 10
|
||||
delxjk = x(1,k) - x(1,j)
|
||||
delyjk = x(2,k) - x(2,j)
|
||||
delzjk = x(3,k) - x(3,j)
|
||||
rjksq = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk
|
||||
if (rjksq.gt.rbound) goto 10
|
||||
delxik = x(1,k) - x(1,i)
|
||||
delyik = x(2,k) - x(2,i)
|
||||
delzik = x(3,k) - x(3,i)
|
||||
riksq = delxik*delxik + delyik*delyik + delzik*delzik
|
||||
if (riksq.gt.rbound) goto 10
|
||||
xik = riksq/rijsq
|
||||
xjk = rjksq/rijsq
|
||||
a = 1 - (xik-xjk)*(xik-xjk)
|
||||
c if a < 0, then ellipse equation doesn't describe this case and
|
||||
c atom k can't possibly screen i-j
|
||||
if (a.le.0.d0) goto 10
|
||||
cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
|
||||
Cmax = Cmax_meam(elti,eltj,eltk)
|
||||
Cmin = Cmin_meam(elti,eltj,eltk)
|
||||
if (cikj.ge.Cmax) then
|
||||
goto 10
|
||||
c note that cikj may be slightly negative (within numerical
|
||||
c tolerance) if atoms are colinear, so don't reject that case here
|
||||
c (other negative cikj cases were handled by the test on "a" above)
|
||||
else if (cikj.le.Cmin) then
|
||||
sij = 0.d0
|
||||
goto 20
|
||||
else
|
||||
delc = Cmax - Cmin
|
||||
cikj = (cikj-Cmin)/delc
|
||||
call fcut(cikj,sikj)
|
||||
endif
|
||||
sij = sij * sikj
|
||||
10 continue
|
||||
enddo
|
||||
|
||||
20 continue
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2,
|
||||
$ ntype,type,fmap,x,scrfcn,fcpair)
|
||||
c Inputs: i,j,k = id's of 3 atom triplet
|
||||
c jn = id of i-j pair
|
||||
c rij2 = squared distance between i and j
|
||||
c Outputs: dsij1 = deriv. of sij w.r.t. rik
|
||||
c dsij2 = deriv. of sij w.r.t. rjk
|
||||
use meam_data
|
||||
implicit none
|
||||
integer i,j,k,jn,nmax,numneigh
|
||||
integer elti,eltj,eltk
|
||||
real*8 rij2,rik2,rjk2,dsij1,dsij2
|
||||
integer ntype, type, fmap
|
||||
real*8 x, scrfcn, fcpair
|
||||
|
||||
dimension type(nmax), fmap(ntype)
|
||||
dimension x(3,nmax), scrfcn(numneigh), fcpair(numneigh)
|
||||
|
||||
real*8 dxik,dyik,dzik
|
||||
real*8 dxjk,dyjk,dzjk
|
||||
real*8 rbound,delc,sij,xik,xjk,cikj,sikj,dfc,a
|
||||
real*8 Cmax,Cmin,dCikj1,dCikj2
|
||||
|
||||
sij = scrfcn(jn)*fcpair(jn)
|
||||
elti = fmap(type(i))
|
||||
eltj = fmap(type(j))
|
||||
eltk = fmap(type(k))
|
||||
Cmax = Cmax_meam(elti,eltj,eltk)
|
||||
Cmin = Cmin_meam(elti,eltj,eltk)
|
||||
|
||||
dsij1 = 0.d0
|
||||
dsij2 = 0.d0
|
||||
if ((sij.ne.0.d0).and.(sij.ne.1.d0)) then
|
||||
rbound = rij2*ebound_meam(elti,eltj)
|
||||
delc = Cmax-Cmin
|
||||
dxjk = x(1,k) - x(1,j)
|
||||
dyjk = x(2,k) - x(2,j)
|
||||
dzjk = x(3,k) - x(3,j)
|
||||
rjk2 = dxjk*dxjk + dyjk*dyjk + dzjk*dzjk
|
||||
if (rjk2.le.rbound) then
|
||||
dxik = x(1,k) - x(1,i)
|
||||
dyik = x(2,k) - x(2,i)
|
||||
dzik = x(3,k) - x(3,i)
|
||||
rik2 = dxik*dxik + dyik*dyik + dzik*dzik
|
||||
if (rik2.le.rbound) then
|
||||
xik = rik2/rij2
|
||||
xjk = rjk2/rij2
|
||||
a = 1 - (xik-xjk)*(xik-xjk)
|
||||
if (a.ne.0.d0) then
|
||||
cikj = (2.d0*(xik+xjk) + a - 2.d0)/a
|
||||
if (cikj.ge.Cmin.and.cikj.le.Cmax) then
|
||||
cikj = (cikj-Cmin)/delc
|
||||
call dfcut(cikj,sikj,dfc)
|
||||
call dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2)
|
||||
a = sij/delc*dfc/sikj
|
||||
dsij1 = a*dCikj1
|
||||
dsij2 = a*dCikj2
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
endif
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine fcut(xi,fc)
|
||||
c cutoff function
|
||||
implicit none
|
||||
real*8 xi,fc
|
||||
real*8 a
|
||||
if (xi.ge.1.d0) then
|
||||
fc = 1.d0
|
||||
else if (xi.le.0.d0) then
|
||||
fc = 0.d0
|
||||
else
|
||||
a = 1.d0-xi
|
||||
a = a*a
|
||||
a = a*a
|
||||
a = 1.d0-a
|
||||
fc = a*a
|
||||
c fc = xi
|
||||
endif
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine dfcut(xi,fc,dfc)
|
||||
c cutoff function and its derivative
|
||||
implicit none
|
||||
real*8 xi,fc,dfc,a,a3,a4
|
||||
if (xi.ge.1.d0) then
|
||||
fc = 1.d0
|
||||
dfc = 0.d0
|
||||
else if (xi.le.0.d0) then
|
||||
fc = 0.d0
|
||||
dfc = 0.d0
|
||||
else
|
||||
a = 1.d0-xi
|
||||
a3 = a*a*a
|
||||
a4 = a*a3
|
||||
fc = (1.d0-a4)**2
|
||||
dfc = 8*(1.d0-a4)*a3
|
||||
c fc = xi
|
||||
c dfc = 1.d0
|
||||
endif
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine dCfunc(rij2,rik2,rjk2,dCikj)
|
||||
c Inputs: rij,rij2,rik2,rjk2
|
||||
c Outputs: dCikj = derivative of Cikj w.r.t. rij
|
||||
implicit none
|
||||
real*8 rij2,rik2,rjk2,dCikj
|
||||
real*8 rij4,a,b,denom
|
||||
|
||||
rij4 = rij2*rij2
|
||||
a = rik2-rjk2
|
||||
b = rik2+rjk2
|
||||
denom = rij4 - a*a
|
||||
denom = denom*denom
|
||||
dCikj = -4*(-2*rij2*a*a + rij4*b + a*a*b)/denom
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
subroutine dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2)
|
||||
c Inputs: rij,rij2,rik2,rjk2
|
||||
c Outputs: dCikj1 = derivative of Cikj w.r.t. rik
|
||||
c dCikj2 = derivative of Cikj w.r.t. rjk
|
||||
implicit none
|
||||
real*8 rij2,rik2,rjk2,dCikj1,dCikj2
|
||||
real*8 rij4,rik4,rjk4,a,b,denom
|
||||
|
||||
rij4 = rij2*rij2
|
||||
rik4 = rik2*rik2
|
||||
rjk4 = rjk2*rjk2
|
||||
a = rik2-rjk2
|
||||
b = rik2+rjk2
|
||||
denom = rij4 - a*a
|
||||
denom = denom*denom
|
||||
dCikj1 = 4*rij2*(rij4 + rik4 + 2*rik2*rjk2 - 3*rjk4 - 2*rij2*a)/
|
||||
$ denom
|
||||
dCikj2 = 4*rij2*(rij4 - 3*rik4 + 2*rik2*rjk2 + rjk4 + 2*rij2*a)/
|
||||
$ denom
|
||||
return
|
||||
end
|
||||
|
||||
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -1,608 +0,0 @@
|
|||
c Extern "C" declaration has the form:
|
||||
c
|
||||
c void meam_force_(int *, int *, int *, double *, int *, int *, int *, double *,
|
||||
c int *, int *, int *, int *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *, double *, int *);
|
||||
c
|
||||
c Call from pair_meam.cpp has the form:
|
||||
c
|
||||
c meam_force_(&i,&nmax,&eflag_either,&eflag_global,&eflag_atom,&vflag_atom,
|
||||
c &eng_vdwl,eatom,&ntype,type,fmap,&x[0][0],
|
||||
c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i],
|
||||
c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset],
|
||||
c dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop,
|
||||
c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0],
|
||||
c &t_ave[0][0],&tsq_ave[0][0],&f[0][0],&vatom[0][0],&errorflag);
|
||||
c
|
||||
|
||||
subroutine meam_force(i, nmax,
|
||||
$ eflag_either, eflag_global, eflag_atom, vflag_atom,
|
||||
$ eng_vdwl, eatom, ntype, type, fmap, x,
|
||||
$ numneigh, firstneigh, numneigh_full, firstneigh_full,
|
||||
$ scrfcn, dscrfcn, fcpair,
|
||||
$ dGamma1, dGamma2, dGamma3, rho0, rho1, rho2, rho3, fp,
|
||||
$ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave, f,
|
||||
$ vatom, errorflag)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer eflag_either, eflag_global, eflag_atom, vflag_atom
|
||||
integer nmax, ntype, type, fmap
|
||||
real*8 eng_vdwl, eatom, x
|
||||
integer numneigh, firstneigh, numneigh_full, firstneigh_full
|
||||
real*8 scrfcn, dscrfcn, fcpair
|
||||
real*8 dGamma1, dGamma2, dGamma3
|
||||
real*8 rho0, rho1, rho2, rho3, fp
|
||||
real*8 Arho1, Arho2, Arho2b
|
||||
real*8 Arho3, Arho3b
|
||||
real*8 t_ave, tsq_ave, f, vatom
|
||||
integer errorflag
|
||||
|
||||
dimension eatom(nmax)
|
||||
dimension type(nmax), fmap(ntype)
|
||||
dimension x(3,nmax)
|
||||
dimension firstneigh(numneigh), firstneigh_full(numneigh_full)
|
||||
dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh)
|
||||
dimension dGamma1(nmax), dGamma2(nmax), dGamma3(nmax)
|
||||
dimension rho0(nmax), rho1(nmax), rho2(nmax), rho3(nmax), fp(nmax)
|
||||
dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax)
|
||||
dimension Arho3(10,nmax), Arho3b(3,nmax)
|
||||
dimension t_ave(3,nmax), tsq_ave(3,nmax), f(3,nmax), vatom(6,nmax)
|
||||
|
||||
integer i,j,jn,k,kn,kk,m,n,p,q
|
||||
integer nv2,nv3,elti,eltj,eltk,ind
|
||||
real*8 xitmp,yitmp,zitmp,delij(3),delref(3),rij2,rij,rij3
|
||||
real*8 delik(3),deljk(3),v(6),fi(3),fj(3)
|
||||
real*8 Eu,astar,astarp,third,sixth
|
||||
real*8 pp,phiforce,dUdrij,dUdsij,dUdrijm(3),force,forcem
|
||||
real*8 B,r,recip,phi,phip,rhop,a
|
||||
real*8 sij,fcij,dfcij,ds(3)
|
||||
real*8 a0,a1,a1i,a1j,a2,a2i,a2j
|
||||
real*8 a3i,a3j,a3i1,a3i2,a3j1,a3j2
|
||||
real*8 G,dG,Gbar,dGbar,gam,shpi(3),shpj(3),Z,denom
|
||||
real*8 ai,aj,ro0i,ro0j,invrei,invrej
|
||||
real*8 b0,rhoa0j,drhoa0j,rhoa0i,drhoa0i
|
||||
real*8 b1,rhoa1j,drhoa1j,rhoa1i,drhoa1i
|
||||
real*8 b2,rhoa2j,drhoa2j,rhoa2i,drhoa2i
|
||||
real*8 a3,a3a,b3,rhoa3j,drhoa3j,rhoa3i,drhoa3i
|
||||
real*8 drho0dr1,drho0dr2,drho0ds1,drho0ds2
|
||||
real*8 drho1dr1,drho1dr2,drho1ds1,drho1ds2
|
||||
real*8 drho1drm1(3),drho1drm2(3)
|
||||
real*8 drho2dr1,drho2dr2,drho2ds1,drho2ds2
|
||||
real*8 drho2drm1(3),drho2drm2(3)
|
||||
real*8 drho3dr1,drho3dr2,drho3ds1,drho3ds2
|
||||
real*8 drho3drm1(3),drho3drm2(3)
|
||||
real*8 dt1dr1,dt1dr2,dt1ds1,dt1ds2
|
||||
real*8 dt2dr1,dt2dr2,dt2ds1,dt2ds2
|
||||
real*8 dt3dr1,dt3dr2,dt3ds1,dt3ds2
|
||||
real*8 drhodr1,drhodr2,drhods1,drhods2,drhodrm1(3),drhodrm2(3)
|
||||
real*8 arg,arg1,arg2
|
||||
real*8 arg1i1,arg1j1,arg1i2,arg1j2,arg2i2,arg2j2
|
||||
real*8 arg1i3,arg1j3,arg2i3,arg2j3,arg3i3,arg3j3
|
||||
real*8 dsij1,dsij2,force1,force2
|
||||
real*8 t1i,t2i,t3i,t1j,t2j,t3j
|
||||
|
||||
errorflag = 0
|
||||
third = 1.0/3.0
|
||||
sixth = 1.0/6.0
|
||||
|
||||
c Compute forces atom i
|
||||
|
||||
elti = fmap(type(i))
|
||||
|
||||
if (elti.gt.0) then
|
||||
xitmp = x(1,i)
|
||||
yitmp = x(2,i)
|
||||
zitmp = x(3,i)
|
||||
|
||||
c Treat each pair
|
||||
do jn = 1,numneigh
|
||||
|
||||
j = firstneigh(jn)
|
||||
eltj = fmap(type(j))
|
||||
|
||||
if (scrfcn(jn).ne.0.d0.and.eltj.gt.0) then
|
||||
|
||||
sij = scrfcn(jn)*fcpair(jn)
|
||||
delij(1) = x(1,j) - xitmp
|
||||
delij(2) = x(2,j) - yitmp
|
||||
delij(3) = x(3,j) - zitmp
|
||||
rij2 = delij(1)*delij(1) + delij(2)*delij(2)
|
||||
$ + delij(3)*delij(3)
|
||||
if (rij2.lt.cutforcesq) then
|
||||
rij = sqrt(rij2)
|
||||
r = rij
|
||||
|
||||
c Compute phi and phip
|
||||
ind = eltind(elti,eltj)
|
||||
pp = rij*rdrar + 1.0D0
|
||||
kk = pp
|
||||
kk = min(kk,nrar-1)
|
||||
pp = pp - kk
|
||||
pp = min(pp,1.0D0)
|
||||
phi = ((phirar3(kk,ind)*pp + phirar2(kk,ind))*pp
|
||||
$ + phirar1(kk,ind))*pp + phirar(kk,ind)
|
||||
phip = (phirar6(kk,ind)*pp + phirar5(kk,ind))*pp
|
||||
$ + phirar4(kk,ind)
|
||||
recip = 1.0d0/r
|
||||
|
||||
if (eflag_either.ne.0) then
|
||||
if (eflag_global.ne.0) eng_vdwl = eng_vdwl + phi*sij
|
||||
if (eflag_atom.ne.0) then
|
||||
eatom(i) = eatom(i) + 0.5*phi*sij
|
||||
eatom(j) = eatom(j) + 0.5*phi*sij
|
||||
endif
|
||||
endif
|
||||
|
||||
c write(1,*) "force_meamf: phi: ",phi
|
||||
c write(1,*) "force_meamf: phip: ",phip
|
||||
|
||||
c Compute pair densities and derivatives
|
||||
invrei = 1.d0/re_meam(elti,elti)
|
||||
ai = rij*invrei - 1.d0
|
||||
ro0i = rho0_meam(elti)
|
||||
rhoa0i = ro0i*fm_exp(-beta0_meam(elti)*ai)
|
||||
drhoa0i = -beta0_meam(elti)*invrei*rhoa0i
|
||||
rhoa1i = ro0i*fm_exp(-beta1_meam(elti)*ai)
|
||||
drhoa1i = -beta1_meam(elti)*invrei*rhoa1i
|
||||
rhoa2i = ro0i*fm_exp(-beta2_meam(elti)*ai)
|
||||
drhoa2i = -beta2_meam(elti)*invrei*rhoa2i
|
||||
rhoa3i = ro0i*fm_exp(-beta3_meam(elti)*ai)
|
||||
drhoa3i = -beta3_meam(elti)*invrei*rhoa3i
|
||||
|
||||
if (elti.ne.eltj) then
|
||||
invrej = 1.d0/re_meam(eltj,eltj)
|
||||
aj = rij*invrej - 1.d0
|
||||
ro0j = rho0_meam(eltj)
|
||||
rhoa0j = ro0j*fm_exp(-beta0_meam(eltj)*aj)
|
||||
drhoa0j = -beta0_meam(eltj)*invrej*rhoa0j
|
||||
rhoa1j = ro0j*fm_exp(-beta1_meam(eltj)*aj)
|
||||
drhoa1j = -beta1_meam(eltj)*invrej*rhoa1j
|
||||
rhoa2j = ro0j*fm_exp(-beta2_meam(eltj)*aj)
|
||||
drhoa2j = -beta2_meam(eltj)*invrej*rhoa2j
|
||||
rhoa3j = ro0j*fm_exp(-beta3_meam(eltj)*aj)
|
||||
drhoa3j = -beta3_meam(eltj)*invrej*rhoa3j
|
||||
else
|
||||
rhoa0j = rhoa0i
|
||||
drhoa0j = drhoa0i
|
||||
rhoa1j = rhoa1i
|
||||
drhoa1j = drhoa1i
|
||||
rhoa2j = rhoa2i
|
||||
drhoa2j = drhoa2i
|
||||
rhoa3j = rhoa3i
|
||||
drhoa3j = drhoa3i
|
||||
endif
|
||||
|
||||
if (ialloy.eq.1) then
|
||||
rhoa1j = rhoa1j * t1_meam(eltj)
|
||||
rhoa2j = rhoa2j * t2_meam(eltj)
|
||||
rhoa3j = rhoa3j * t3_meam(eltj)
|
||||
rhoa1i = rhoa1i * t1_meam(elti)
|
||||
rhoa2i = rhoa2i * t2_meam(elti)
|
||||
rhoa3i = rhoa3i * t3_meam(elti)
|
||||
drhoa1j = drhoa1j * t1_meam(eltj)
|
||||
drhoa2j = drhoa2j * t2_meam(eltj)
|
||||
drhoa3j = drhoa3j * t3_meam(eltj)
|
||||
drhoa1i = drhoa1i * t1_meam(elti)
|
||||
drhoa2i = drhoa2i * t2_meam(elti)
|
||||
drhoa3i = drhoa3i * t3_meam(elti)
|
||||
endif
|
||||
|
||||
nv2 = 1
|
||||
nv3 = 1
|
||||
arg1i1 = 0.d0
|
||||
arg1j1 = 0.d0
|
||||
arg1i2 = 0.d0
|
||||
arg1j2 = 0.d0
|
||||
arg1i3 = 0.d0
|
||||
arg1j3 = 0.d0
|
||||
arg3i3 = 0.d0
|
||||
arg3j3 = 0.d0
|
||||
do n = 1,3
|
||||
do p = n,3
|
||||
do q = p,3
|
||||
arg = delij(n)*delij(p)*delij(q)*v3D(nv3)
|
||||
arg1i3 = arg1i3 + Arho3(nv3,i)*arg
|
||||
arg1j3 = arg1j3 - Arho3(nv3,j)*arg
|
||||
nv3 = nv3+1
|
||||
enddo
|
||||
arg = delij(n)*delij(p)*v2D(nv2)
|
||||
arg1i2 = arg1i2 + Arho2(nv2,i)*arg
|
||||
arg1j2 = arg1j2 + Arho2(nv2,j)*arg
|
||||
nv2 = nv2+1
|
||||
enddo
|
||||
arg1i1 = arg1i1 + Arho1(n,i)*delij(n)
|
||||
arg1j1 = arg1j1 - Arho1(n,j)*delij(n)
|
||||
arg3i3 = arg3i3 + Arho3b(n,i)*delij(n)
|
||||
arg3j3 = arg3j3 - Arho3b(n,j)*delij(n)
|
||||
enddo
|
||||
|
||||
c rho0 terms
|
||||
drho0dr1 = drhoa0j * sij
|
||||
drho0dr2 = drhoa0i * sij
|
||||
|
||||
c rho1 terms
|
||||
a1 = 2*sij/rij
|
||||
drho1dr1 = a1*(drhoa1j-rhoa1j/rij)*arg1i1
|
||||
drho1dr2 = a1*(drhoa1i-rhoa1i/rij)*arg1j1
|
||||
a1 = 2.d0*sij/rij
|
||||
do m = 1,3
|
||||
drho1drm1(m) = a1*rhoa1j*Arho1(m,i)
|
||||
drho1drm2(m) = -a1*rhoa1i*Arho1(m,j)
|
||||
enddo
|
||||
|
||||
c rho2 terms
|
||||
a2 = 2*sij/rij2
|
||||
drho2dr1 = a2*(drhoa2j - 2*rhoa2j/rij)*arg1i2
|
||||
$ - 2.d0/3.d0*Arho2b(i)*drhoa2j*sij
|
||||
drho2dr2 = a2*(drhoa2i - 2*rhoa2i/rij)*arg1j2
|
||||
$ - 2.d0/3.d0*Arho2b(j)*drhoa2i*sij
|
||||
a2 = 4*sij/rij2
|
||||
do m = 1,3
|
||||
drho2drm1(m) = 0.d0
|
||||
drho2drm2(m) = 0.d0
|
||||
do n = 1,3
|
||||
drho2drm1(m) = drho2drm1(m)
|
||||
$ + Arho2(vind2D(m,n),i)*delij(n)
|
||||
drho2drm2(m) = drho2drm2(m)
|
||||
$ - Arho2(vind2D(m,n),j)*delij(n)
|
||||
enddo
|
||||
drho2drm1(m) = a2*rhoa2j*drho2drm1(m)
|
||||
drho2drm2(m) = -a2*rhoa2i*drho2drm2(m)
|
||||
enddo
|
||||
|
||||
c rho3 terms
|
||||
rij3 = rij*rij2
|
||||
a3 = 2*sij/rij3
|
||||
a3a = 6.d0/5.d0*sij/rij
|
||||
drho3dr1 = a3*(drhoa3j - 3*rhoa3j/rij)*arg1i3
|
||||
$ - a3a*(drhoa3j - rhoa3j/rij)*arg3i3
|
||||
drho3dr2 = a3*(drhoa3i - 3*rhoa3i/rij)*arg1j3
|
||||
$ - a3a*(drhoa3i - rhoa3i/rij)*arg3j3
|
||||
a3 = 6*sij/rij3
|
||||
a3a = 6*sij/(5*rij)
|
||||
do m = 1,3
|
||||
drho3drm1(m) = 0.d0
|
||||
drho3drm2(m) = 0.d0
|
||||
nv2 = 1
|
||||
do n = 1,3
|
||||
do p = n,3
|
||||
arg = delij(n)*delij(p)*v2D(nv2)
|
||||
drho3drm1(m) = drho3drm1(m)
|
||||
$ + Arho3(vind3D(m,n,p),i)*arg
|
||||
drho3drm2(m) = drho3drm2(m)
|
||||
$ + Arho3(vind3D(m,n,p),j)*arg
|
||||
nv2 = nv2 + 1
|
||||
enddo
|
||||
enddo
|
||||
drho3drm1(m) = (a3*drho3drm1(m) - a3a*Arho3b(m,i))
|
||||
$ *rhoa3j
|
||||
drho3drm2(m) = (-a3*drho3drm2(m) + a3a*Arho3b(m,j))
|
||||
$ *rhoa3i
|
||||
enddo
|
||||
|
||||
c Compute derivatives of weighting functions t wrt rij
|
||||
t1i = t_ave(1,i)
|
||||
t2i = t_ave(2,i)
|
||||
t3i = t_ave(3,i)
|
||||
t1j = t_ave(1,j)
|
||||
t2j = t_ave(2,j)
|
||||
t3j = t_ave(3,j)
|
||||
|
||||
if (ialloy.eq.1) then
|
||||
|
||||
a1i = 0.d0
|
||||
a1j = 0.d0
|
||||
a2i = 0.d0
|
||||
a2j = 0.d0
|
||||
a3i = 0.d0
|
||||
a3j = 0.d0
|
||||
if ( tsq_ave(1,i) .ne. 0.d0 ) then
|
||||
a1i = drhoa0j*sij/tsq_ave(1,i)
|
||||
endif
|
||||
if ( tsq_ave(1,j) .ne. 0.d0 ) then
|
||||
a1j = drhoa0i*sij/tsq_ave(1,j)
|
||||
endif
|
||||
if ( tsq_ave(2,i) .ne. 0.d0 ) then
|
||||
a2i = drhoa0j*sij/tsq_ave(2,i)
|
||||
endif
|
||||
if ( tsq_ave(2,j) .ne. 0.d0 ) then
|
||||
a2j = drhoa0i*sij/tsq_ave(2,j)
|
||||
endif
|
||||
if ( tsq_ave(3,i) .ne. 0.d0 ) then
|
||||
a3i = drhoa0j*sij/tsq_ave(3,i)
|
||||
endif
|
||||
if ( tsq_ave(3,j) .ne. 0.d0 ) then
|
||||
a3j = drhoa0i*sij/tsq_ave(3,j)
|
||||
endif
|
||||
|
||||
dt1dr1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2)
|
||||
dt1dr2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2)
|
||||
dt2dr1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2)
|
||||
dt2dr2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2)
|
||||
dt3dr1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2)
|
||||
dt3dr2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2)
|
||||
|
||||
else if (ialloy.eq.2) then
|
||||
|
||||
dt1dr1 = 0.d0
|
||||
dt1dr2 = 0.d0
|
||||
dt2dr1 = 0.d0
|
||||
dt2dr2 = 0.d0
|
||||
dt3dr1 = 0.d0
|
||||
dt3dr2 = 0.d0
|
||||
|
||||
else
|
||||
|
||||
ai = 0.d0
|
||||
if( rho0(i) .ne. 0.d0 ) then
|
||||
ai = drhoa0j*sij/rho0(i)
|
||||
end if
|
||||
aj = 0.d0
|
||||
if( rho0(j) .ne. 0.d0 ) then
|
||||
aj = drhoa0i*sij/rho0(j)
|
||||
end if
|
||||
|
||||
dt1dr1 = ai*(t1_meam(eltj)-t1i)
|
||||
dt1dr2 = aj*(t1_meam(elti)-t1j)
|
||||
dt2dr1 = ai*(t2_meam(eltj)-t2i)
|
||||
dt2dr2 = aj*(t2_meam(elti)-t2j)
|
||||
dt3dr1 = ai*(t3_meam(eltj)-t3i)
|
||||
dt3dr2 = aj*(t3_meam(elti)-t3j)
|
||||
|
||||
endif
|
||||
|
||||
c Compute derivatives of total density wrt rij, sij and rij(3)
|
||||
call get_shpfcn(shpi,lattce_meam(elti,elti))
|
||||
call get_shpfcn(shpj,lattce_meam(eltj,eltj))
|
||||
drhodr1 = dGamma1(i)*drho0dr1
|
||||
$ + dGamma2(i)*
|
||||
$ (dt1dr1*rho1(i)+t1i*drho1dr1
|
||||
$ + dt2dr1*rho2(i)+t2i*drho2dr1
|
||||
$ + dt3dr1*rho3(i)+t3i*drho3dr1)
|
||||
$ - dGamma3(i)*
|
||||
$ (shpi(1)*dt1dr1+shpi(2)*dt2dr1+shpi(3)*dt3dr1)
|
||||
drhodr2 = dGamma1(j)*drho0dr2
|
||||
$ + dGamma2(j)*
|
||||
$ (dt1dr2*rho1(j)+t1j*drho1dr2
|
||||
$ + dt2dr2*rho2(j)+t2j*drho2dr2
|
||||
$ + dt3dr2*rho3(j)+t3j*drho3dr2)
|
||||
$ - dGamma3(j)*
|
||||
$ (shpj(1)*dt1dr2+shpj(2)*dt2dr2+shpj(3)*dt3dr2)
|
||||
do m = 1,3
|
||||
drhodrm1(m) = 0.d0
|
||||
drhodrm2(m) = 0.d0
|
||||
drhodrm1(m) = dGamma2(i)*
|
||||
$ (t1i*drho1drm1(m)
|
||||
$ + t2i*drho2drm1(m)
|
||||
$ + t3i*drho3drm1(m))
|
||||
drhodrm2(m) = dGamma2(j)*
|
||||
$ (t1j*drho1drm2(m)
|
||||
$ + t2j*drho2drm2(m)
|
||||
$ + t3j*drho3drm2(m))
|
||||
enddo
|
||||
|
||||
c Compute derivatives wrt sij, but only if necessary
|
||||
if (dscrfcn(jn).ne.0.d0) then
|
||||
drho0ds1 = rhoa0j
|
||||
drho0ds2 = rhoa0i
|
||||
a1 = 2.d0/rij
|
||||
drho1ds1 = a1*rhoa1j*arg1i1
|
||||
drho1ds2 = a1*rhoa1i*arg1j1
|
||||
a2 = 2.d0/rij2
|
||||
drho2ds1 = a2*rhoa2j*arg1i2
|
||||
$ - 2.d0/3.d0*Arho2b(i)*rhoa2j
|
||||
drho2ds2 = a2*rhoa2i*arg1j2
|
||||
$ - 2.d0/3.d0*Arho2b(j)*rhoa2i
|
||||
a3 = 2.d0/rij3
|
||||
a3a = 6.d0/(5.d0*rij)
|
||||
drho3ds1 = a3*rhoa3j*arg1i3 - a3a*rhoa3j*arg3i3
|
||||
drho3ds2 = a3*rhoa3i*arg1j3 - a3a*rhoa3i*arg3j3
|
||||
|
||||
if (ialloy.eq.1) then
|
||||
|
||||
a1i = 0.d0
|
||||
a1j = 0.d0
|
||||
a2i = 0.d0
|
||||
a2j = 0.d0
|
||||
a3i = 0.d0
|
||||
a3j = 0.d0
|
||||
if ( tsq_ave(1,i) .ne. 0.d0 ) then
|
||||
a1i = rhoa0j/tsq_ave(1,i)
|
||||
endif
|
||||
if ( tsq_ave(1,j) .ne. 0.d0 ) then
|
||||
a1j = rhoa0i/tsq_ave(1,j)
|
||||
endif
|
||||
if ( tsq_ave(2,i) .ne. 0.d0 ) then
|
||||
a2i = rhoa0j/tsq_ave(2,i)
|
||||
endif
|
||||
if ( tsq_ave(2,j) .ne. 0.d0 ) then
|
||||
a2j = rhoa0i/tsq_ave(2,j)
|
||||
endif
|
||||
if ( tsq_ave(3,i) .ne. 0.d0 ) then
|
||||
a3i = rhoa0j/tsq_ave(3,i)
|
||||
endif
|
||||
if ( tsq_ave(3,j) .ne. 0.d0 ) then
|
||||
a3j = rhoa0i/tsq_ave(3,j)
|
||||
endif
|
||||
|
||||
dt1ds1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2)
|
||||
dt1ds2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2)
|
||||
dt2ds1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2)
|
||||
dt2ds2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2)
|
||||
dt3ds1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2)
|
||||
dt3ds2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2)
|
||||
|
||||
else if (ialloy.eq.2) then
|
||||
|
||||
dt1ds1 = 0.d0
|
||||
dt1ds2 = 0.d0
|
||||
dt2ds1 = 0.d0
|
||||
dt2ds2 = 0.d0
|
||||
dt3ds1 = 0.d0
|
||||
dt3ds2 = 0.d0
|
||||
|
||||
else
|
||||
|
||||
ai = 0.d0
|
||||
if( rho0(i) .ne. 0.d0 ) then
|
||||
ai = rhoa0j/rho0(i)
|
||||
end if
|
||||
aj = 0.d0
|
||||
if( rho0(j) .ne. 0.d0 ) then
|
||||
aj = rhoa0i/rho0(j)
|
||||
end if
|
||||
|
||||
dt1ds1 = ai*(t1_meam(eltj)-t1i)
|
||||
dt1ds2 = aj*(t1_meam(elti)-t1j)
|
||||
dt2ds1 = ai*(t2_meam(eltj)-t2i)
|
||||
dt2ds2 = aj*(t2_meam(elti)-t2j)
|
||||
dt3ds1 = ai*(t3_meam(eltj)-t3i)
|
||||
dt3ds2 = aj*(t3_meam(elti)-t3j)
|
||||
|
||||
endif
|
||||
|
||||
drhods1 = dGamma1(i)*drho0ds1
|
||||
$ + dGamma2(i)*
|
||||
$ (dt1ds1*rho1(i)+t1i*drho1ds1
|
||||
$ + dt2ds1*rho2(i)+t2i*drho2ds1
|
||||
$ + dt3ds1*rho3(i)+t3i*drho3ds1)
|
||||
$ - dGamma3(i)*
|
||||
$ (shpi(1)*dt1ds1+shpi(2)*dt2ds1+shpi(3)*dt3ds1)
|
||||
drhods2 = dGamma1(j)*drho0ds2
|
||||
$ + dGamma2(j)*
|
||||
$ (dt1ds2*rho1(j)+t1j*drho1ds2
|
||||
$ + dt2ds2*rho2(j)+t2j*drho2ds2
|
||||
$ + dt3ds2*rho3(j)+t3j*drho3ds2)
|
||||
$ - dGamma3(j)*
|
||||
$ (shpj(1)*dt1ds2+shpj(2)*dt2ds2+shpj(3)*dt3ds2)
|
||||
endif
|
||||
|
||||
c Compute derivatives of energy wrt rij, sij and rij(3)
|
||||
dUdrij = phip*sij
|
||||
$ + fp(i)*drhodr1 + fp(j)*drhodr2
|
||||
dUdsij = 0.d0
|
||||
if (dscrfcn(jn).ne.0.d0) then
|
||||
dUdsij = phi
|
||||
$ + fp(i)*drhods1 + fp(j)*drhods2
|
||||
endif
|
||||
do m = 1,3
|
||||
dUdrijm(m) = fp(i)*drhodrm1(m) + fp(j)*drhodrm2(m)
|
||||
enddo
|
||||
|
||||
c Add the part of the force due to dUdrij and dUdsij
|
||||
|
||||
force = dUdrij*recip + dUdsij*dscrfcn(jn)
|
||||
do m = 1,3
|
||||
forcem = delij(m)*force + dUdrijm(m)
|
||||
f(m,i) = f(m,i) + forcem
|
||||
f(m,j) = f(m,j) - forcem
|
||||
enddo
|
||||
|
||||
c Tabulate per-atom virial as symmetrized stress tensor
|
||||
|
||||
if (vflag_atom.ne.0) then
|
||||
fi(1) = delij(1)*force + dUdrijm(1)
|
||||
fi(2) = delij(2)*force + dUdrijm(2)
|
||||
fi(3) = delij(3)*force + dUdrijm(3)
|
||||
v(1) = -0.5 * (delij(1) * fi(1))
|
||||
v(2) = -0.5 * (delij(2) * fi(2))
|
||||
v(3) = -0.5 * (delij(3) * fi(3))
|
||||
v(4) = -0.25 * (delij(1)*fi(2) + delij(2)*fi(1))
|
||||
v(5) = -0.25 * (delij(1)*fi(3) + delij(3)*fi(1))
|
||||
v(6) = -0.25 * (delij(2)*fi(3) + delij(3)*fi(2))
|
||||
|
||||
vatom(1,i) = vatom(1,i) + v(1)
|
||||
vatom(2,i) = vatom(2,i) + v(2)
|
||||
vatom(3,i) = vatom(3,i) + v(3)
|
||||
vatom(4,i) = vatom(4,i) + v(4)
|
||||
vatom(5,i) = vatom(5,i) + v(5)
|
||||
vatom(6,i) = vatom(6,i) + v(6)
|
||||
vatom(1,j) = vatom(1,j) + v(1)
|
||||
vatom(2,j) = vatom(2,j) + v(2)
|
||||
vatom(3,j) = vatom(3,j) + v(3)
|
||||
vatom(4,j) = vatom(4,j) + v(4)
|
||||
vatom(5,j) = vatom(5,j) + v(5)
|
||||
vatom(6,j) = vatom(6,j) + v(6)
|
||||
endif
|
||||
|
||||
c Now compute forces on other atoms k due to change in sij
|
||||
|
||||
if (sij.eq.0.d0.or.sij.eq.1.d0) goto 100
|
||||
do kn = 1,numneigh_full
|
||||
k = firstneigh_full(kn)
|
||||
eltk = fmap(type(k))
|
||||
if (k.ne.j.and.eltk.gt.0) then
|
||||
call dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2,
|
||||
$ ntype,type,fmap,x,scrfcn,fcpair)
|
||||
if (dsij1.ne.0.d0.or.dsij2.ne.0.d0) then
|
||||
force1 = dUdsij*dsij1
|
||||
force2 = dUdsij*dsij2
|
||||
do m = 1,3
|
||||
delik(m) = x(m,k) - x(m,i)
|
||||
deljk(m) = x(m,k) - x(m,j)
|
||||
enddo
|
||||
do m = 1,3
|
||||
f(m,i) = f(m,i) + force1*delik(m)
|
||||
f(m,j) = f(m,j) + force2*deljk(m)
|
||||
f(m,k) = f(m,k) - force1*delik(m)
|
||||
$ - force2*deljk(m)
|
||||
enddo
|
||||
|
||||
c Tabulate per-atom virial as symmetrized stress tensor
|
||||
|
||||
if (vflag_atom.ne.0) then
|
||||
fi(1) = force1*delik(1)
|
||||
fi(2) = force1*delik(2)
|
||||
fi(3) = force1*delik(3)
|
||||
fj(1) = force2*deljk(1)
|
||||
fj(2) = force2*deljk(2)
|
||||
fj(3) = force2*deljk(3)
|
||||
v(1) = -third * (delik(1)*fi(1) + deljk(1)*fj(1))
|
||||
v(2) = -third * (delik(2)*fi(2) + deljk(2)*fj(2))
|
||||
v(3) = -third * (delik(3)*fi(3) + deljk(3)*fj(3))
|
||||
v(4) = -sixth * (delik(1)*fi(2) + deljk(1)*fj(2) +
|
||||
$ delik(2)*fi(1) + deljk(2)*fj(1))
|
||||
v(5) = -sixth * (delik(1)*fi(3) + deljk(1)*fj(3) +
|
||||
$ delik(3)*fi(1) + deljk(3)*fj(1))
|
||||
v(6) = -sixth * (delik(2)*fi(3) + deljk(2)*fj(3) +
|
||||
$ delik(3)*fi(2) + deljk(3)*fj(2))
|
||||
|
||||
vatom(1,i) = vatom(1,i) + v(1)
|
||||
vatom(2,i) = vatom(2,i) + v(2)
|
||||
vatom(3,i) = vatom(3,i) + v(3)
|
||||
vatom(4,i) = vatom(4,i) + v(4)
|
||||
vatom(5,i) = vatom(5,i) + v(5)
|
||||
vatom(6,i) = vatom(6,i) + v(6)
|
||||
vatom(1,j) = vatom(1,j) + v(1)
|
||||
vatom(2,j) = vatom(2,j) + v(2)
|
||||
vatom(3,j) = vatom(3,j) + v(3)
|
||||
vatom(4,j) = vatom(4,j) + v(4)
|
||||
vatom(5,j) = vatom(5,j) + v(5)
|
||||
vatom(6,j) = vatom(6,j) + v(6)
|
||||
vatom(1,k) = vatom(1,k) + v(1)
|
||||
vatom(2,k) = vatom(2,k) + v(2)
|
||||
vatom(3,k) = vatom(3,k) + v(3)
|
||||
vatom(4,k) = vatom(4,k) + v(4)
|
||||
vatom(5,k) = vatom(5,k) + v(5)
|
||||
vatom(6,k) = vatom(6,k) + v(6)
|
||||
endif
|
||||
|
||||
endif
|
||||
endif
|
||||
c end of k loop
|
||||
enddo
|
||||
endif
|
||||
100 continue
|
||||
endif
|
||||
c end of j loop
|
||||
enddo
|
||||
|
||||
c else if elti=0, this is not a meam atom
|
||||
endif
|
||||
|
||||
return
|
||||
end
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,111 +0,0 @@
|
|||
c
|
||||
c declaration in pair_meam.h:
|
||||
c
|
||||
c void meam_setup_global(int *, int *, double *, int *, double *, double *,
|
||||
c double *, double *, double *, double *, double *,
|
||||
c double *, double *, double *, double *, double *,
|
||||
c double *, double *, int *);
|
||||
c
|
||||
c call in pair_meam.cpp:
|
||||
c
|
||||
c meam_setup_global(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3,
|
||||
c alat,esub,asub,t0,t1,t2,t3,rozero,ibar);
|
||||
c
|
||||
c
|
||||
|
||||
subroutine meam_setup_global(nelt, lat, z, ielement, atwt, alpha,
|
||||
$ b0, b1, b2, b3, alat, esub, asub,
|
||||
$ t0, t1, t2, t3, rozero, ibar)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer nelt, lat, ielement, ibar
|
||||
real*8 z, atwt, alpha, b0, b1, b2, b3
|
||||
real*8 alat, esub, asub, t0, t1, t2, t3
|
||||
real*8 rozero
|
||||
|
||||
dimension lat(nelt), ielement(nelt), ibar(nelt)
|
||||
dimension z(nelt), atwt(nelt), alpha(nelt)
|
||||
dimension b0(nelt), b1(nelt), b2(nelt), b3(nelt)
|
||||
dimension alat(nelt), esub(nelt), asub(nelt)
|
||||
dimension t0(nelt), t1(nelt), t2(nelt), t3(nelt), rozero(nelt)
|
||||
|
||||
integer i
|
||||
real*8 tmplat(maxelt)
|
||||
|
||||
neltypes = nelt
|
||||
|
||||
do i = 1,nelt
|
||||
|
||||
if (lat(i).eq.0) then
|
||||
lattce_meam(i,i) = 'fcc'
|
||||
else if (lat(i).eq.1) then
|
||||
lattce_meam(i,i) = 'bcc'
|
||||
else if (lat(i).eq.2) then
|
||||
lattce_meam(i,i) = 'hcp'
|
||||
else if (lat(i).eq.3) then
|
||||
lattce_meam(i,i) = 'dim'
|
||||
else if (lat(i).eq.4) then
|
||||
lattce_meam(i,i) = 'dia'
|
||||
else
|
||||
c unknown
|
||||
endif
|
||||
|
||||
Z_meam(i) = z(i)
|
||||
ielt_meam(i) = ielement(i)
|
||||
alpha_meam(i,i) = alpha(i)
|
||||
beta0_meam(i) = b0(i)
|
||||
beta1_meam(i) = b1(i)
|
||||
beta2_meam(i) = b2(i)
|
||||
beta3_meam(i) = b3(i)
|
||||
tmplat(i) = alat(i)
|
||||
Ec_meam(i,i) = esub(i)
|
||||
A_meam(i) = asub(i)
|
||||
t0_meam(i) = t0(i)
|
||||
t1_meam(i) = t1(i)
|
||||
t2_meam(i) = t2(i)
|
||||
t3_meam(i) = t3(i)
|
||||
rho0_meam(i) = rozero(i)
|
||||
ibar_meam(i) = ibar(i)
|
||||
|
||||
if (lattce_meam(i,i).eq.'fcc') then
|
||||
re_meam(i,i) = tmplat(i)/sqrt(2.d0)
|
||||
elseif (lattce_meam(i,i).eq.'bcc') then
|
||||
re_meam(i,i) = tmplat(i)*sqrt(3.d0)/2.d0
|
||||
elseif (lattce_meam(i,i).eq.'hcp') then
|
||||
re_meam(i,i) = tmplat(i)
|
||||
elseif (lattce_meam(i,i).eq.'dim') then
|
||||
re_meam(i,i) = tmplat(i)
|
||||
elseif (lattce_meam(i,i).eq.'dia') then
|
||||
re_meam(i,i) = tmplat(i)*sqrt(3.d0)/4.d0
|
||||
else
|
||||
c error
|
||||
endif
|
||||
|
||||
enddo
|
||||
|
||||
|
||||
c Set some defaults
|
||||
rc_meam = 4.0
|
||||
delr_meam = 0.1
|
||||
attrac_meam(:,:) = 0.0
|
||||
repuls_meam(:,:) = 0.0
|
||||
Cmax_meam(:,:,:) = 2.8
|
||||
Cmin_meam(:,:,:) = 2.0
|
||||
ebound_meam(:,:) = (2.8d0**2)/(4.d0*(2.8d0-1.d0))
|
||||
delta_meam(:,:) = 0.0
|
||||
nn2_meam(:,:) = 0
|
||||
zbl_meam(:,:) = 1
|
||||
gsmooth_factor = 99.0
|
||||
augt1 = 1
|
||||
ialloy = 0
|
||||
mix_ref_t = 0
|
||||
emb_lin_neg = 0
|
||||
bkgd_dyn = 0
|
||||
erose_form = 0
|
||||
|
||||
return
|
||||
end
|
||||
|
||||
|
||||
|
|
@ -1,204 +0,0 @@
|
|||
c
|
||||
c do a sanity check on index parameters
|
||||
subroutine meam_checkindex(num,lim,nidx,idx,ierr)
|
||||
implicit none
|
||||
integer i,num,lim,nidx,idx(3),ierr
|
||||
|
||||
ierr = 0
|
||||
if (nidx.lt.num) then
|
||||
ierr = 2
|
||||
return
|
||||
endif
|
||||
|
||||
do i=1,num
|
||||
if ((idx(i).lt.1).or.(idx(i).gt.lim)) then
|
||||
ierr = 3
|
||||
return
|
||||
endif
|
||||
enddo
|
||||
end
|
||||
|
||||
c
|
||||
c Declaration in pair_meam.h:
|
||||
c
|
||||
c void meam_setup_param(int *, double *, int *, int *, int *);
|
||||
c
|
||||
c Call in pair_meam.cpp
|
||||
c
|
||||
c meam_setup_param(&which,&value,&nindex,index,&errorflag);
|
||||
c
|
||||
c
|
||||
c
|
||||
c The "which" argument corresponds to the index of the "keyword" array
|
||||
c in pair_meam.cpp:
|
||||
c
|
||||
c 0 = Ec_meam
|
||||
c 1 = alpha_meam
|
||||
c 2 = rho0_meam
|
||||
c 3 = delta_meam
|
||||
c 4 = lattce_meam
|
||||
c 5 = attrac_meam
|
||||
c 6 = repuls_meam
|
||||
c 7 = nn2_meam
|
||||
c 8 = Cmin_meam
|
||||
c 9 = Cmax_meam
|
||||
c 10 = rc_meam
|
||||
c 11 = delr_meam
|
||||
c 12 = augt1
|
||||
c 13 = gsmooth_factor
|
||||
c 14 = re_meam
|
||||
c 15 = ialloy
|
||||
c 16 = mixture_ref_t
|
||||
c 17 = erose_form
|
||||
c 18 = zbl_meam
|
||||
c 19 = emb_lin_neg
|
||||
c 20 = bkgd_dyn
|
||||
|
||||
subroutine meam_setup_param(which, value, nindex,
|
||||
$ index, errorflag)
|
||||
|
||||
use meam_data
|
||||
implicit none
|
||||
|
||||
integer which, nindex, index(3), errorflag
|
||||
real*8 value
|
||||
integer i1, i2
|
||||
|
||||
errorflag = 0
|
||||
|
||||
c 0 = Ec_meam
|
||||
if (which.eq.0) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
Ec_meam(index(1),index(2)) = value
|
||||
|
||||
c 1 = alpha_meam
|
||||
else if (which.eq.1) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
alpha_meam(index(1),index(2)) = value
|
||||
|
||||
c 2 = rho0_meam
|
||||
else if (which.eq.2) then
|
||||
call meam_checkindex(1,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
rho0_meam(index(1)) = value
|
||||
|
||||
c 3 = delta_meam
|
||||
else if (which.eq.3) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
delta_meam(index(1),index(2)) = value
|
||||
|
||||
c 4 = lattce_meam
|
||||
else if (which.eq.4) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
if (value.eq.0) then
|
||||
lattce_meam(index(1),index(2)) = "fcc"
|
||||
else if (value.eq.1) then
|
||||
lattce_meam(index(1),index(2)) = "bcc"
|
||||
else if (value.eq.2) then
|
||||
lattce_meam(index(1),index(2)) = "hcp"
|
||||
else if (value.eq.3) then
|
||||
lattce_meam(index(1),index(2)) = "dim"
|
||||
else if (value.eq.4) then
|
||||
lattce_meam(index(1),index(2)) = "dia"
|
||||
else if (value.eq.5) then
|
||||
lattce_meam(index(1),index(2)) = 'b1'
|
||||
else if (value.eq.6) then
|
||||
lattce_meam(index(1),index(2)) = 'c11'
|
||||
else if (value.eq.7) then
|
||||
lattce_meam(index(1),index(2)) = 'l12'
|
||||
else if (value.eq.8) then
|
||||
lattce_meam(index(1),index(2)) = 'b2'
|
||||
endif
|
||||
|
||||
c 5 = attrac_meam
|
||||
else if (which.eq.5) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
attrac_meam(index(1),index(2)) = value
|
||||
|
||||
c 6 = repuls_meam
|
||||
else if (which.eq.6) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
repuls_meam(index(1),index(2)) = value
|
||||
|
||||
c 7 = nn2_meam
|
||||
else if (which.eq.7) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
i1 = min(index(1),index(2))
|
||||
i2 = max(index(1),index(2))
|
||||
nn2_meam(i1,i2) = value
|
||||
|
||||
c 8 = Cmin_meam
|
||||
else if (which.eq.8) then
|
||||
call meam_checkindex(3,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
Cmin_meam(index(1),index(2),index(3)) = value
|
||||
|
||||
c 9 = Cmax_meam
|
||||
else if (which.eq.9) then
|
||||
call meam_checkindex(3,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
Cmax_meam(index(1),index(2),index(3)) = value
|
||||
|
||||
c 10 = rc_meam
|
||||
else if (which.eq.10) then
|
||||
rc_meam = value
|
||||
|
||||
c 11 = delr_meam
|
||||
else if (which.eq.11) then
|
||||
delr_meam = value
|
||||
|
||||
c 12 = augt1
|
||||
else if (which.eq.12) then
|
||||
augt1 = value
|
||||
|
||||
c 13 = gsmooth
|
||||
else if (which.eq.13) then
|
||||
gsmooth_factor = value
|
||||
|
||||
c 14 = re_meam
|
||||
else if (which.eq.14) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
re_meam(index(1),index(2)) = value
|
||||
|
||||
c 15 = ialloy
|
||||
else if (which.eq.15) then
|
||||
ialloy = value
|
||||
|
||||
c 16 = mixture_ref_t
|
||||
else if (which.eq.16) then
|
||||
mix_ref_t = value
|
||||
|
||||
c 17 = erose_form
|
||||
else if (which.eq.17) then
|
||||
erose_form = value
|
||||
|
||||
c 18 = zbl_meam
|
||||
else if (which.eq.18) then
|
||||
call meam_checkindex(2,maxelt,nindex,index,errorflag)
|
||||
if (errorflag.ne.0) return
|
||||
i1 = min(index(1),index(2))
|
||||
i2 = max(index(1),index(2))
|
||||
zbl_meam(i1,i2) = value
|
||||
|
||||
c 19 = emb_lin_neg
|
||||
else if (which.eq.19) then
|
||||
emb_lin_neg = value
|
||||
|
||||
c 20 = bkgd_dyn
|
||||
else if (which.eq.20) then
|
||||
bkgd_dyn = value
|
||||
|
||||
else
|
||||
errorflag = 1
|
||||
endif
|
||||
|
||||
return
|
||||
end
|
||||
|
|
@ -1 +0,0 @@
|
|||
../Install.py
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.gfortran
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = g95
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.gfortran
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = gfortran
|
||||
F90FLAGS = -O3 -fPIC -fno-second-underscore
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.ifort
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = ifort
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
reax_SYSINC =
|
||||
reax_SYSLIB =
|
||||
reax_SYSPATH =
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
reax_SYSINC =
|
||||
reax_SYSLIB = -lgfortran
|
||||
reax_SYSPATH =
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
# Settings that the LAMMPS build will import when this package library is used
|
||||
|
||||
reax_SYSINC =
|
||||
reax_SYSLIB = -lifcore
|
||||
reax_SYSPATH =
|
||||
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.empty
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = mpifort
|
||||
F90FLAGS = -O3 -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.pgf90
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = pgf90
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.ifort
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = mpif90
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1 +0,0 @@
|
|||
Makefile.gfortran
|
||||
|
|
@ -1,51 +0,0 @@
|
|||
# *
|
||||
# *_________________________________________________________________________*
|
||||
# * Fortran Library for Reactive Force Field *
|
||||
# * DESCRIPTION: SEE READ-ME *
|
||||
# * FILE NAME: Makefile *
|
||||
# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) *
|
||||
# * and Greg Wagner(SNL) *
|
||||
# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov *
|
||||
# *_________________________________________________________________________*/
|
||||
|
||||
SHELL = /bin/sh
|
||||
|
||||
# which file will be copied to Makefile.lammps
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.ifort
|
||||
|
||||
# ------ FILES ------
|
||||
|
||||
SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F
|
||||
|
||||
HEADERFILES = reax_defs.h *.blk
|
||||
|
||||
# ------ DEFINITIONS ------
|
||||
|
||||
LIB = libreax.a
|
||||
OBJ = $(SRC:.F=.o)
|
||||
|
||||
# ------ SETTINGS ------
|
||||
|
||||
F90 = mpif90
|
||||
F90FLAGS = -O -fPIC
|
||||
ARCHIVE = ar
|
||||
ARCHFLAG = -rc
|
||||
USRLIB =
|
||||
SYSLIB =
|
||||
|
||||
# ------ MAKE PROCEDURE ------
|
||||
|
||||
lib: $(OBJ)
|
||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
||||
@cp $(EXTRAMAKE) Makefile.lammps
|
||||
|
||||
# ------ COMPILE RULES ------
|
||||
|
||||
%.o:%.F $(HEADERFILES)
|
||||
$(F90) $(F90FLAGS) -c $<
|
||||
|
||||
# ------ CLEAN ------
|
||||
|
||||
clean:
|
||||
-rm *.o $(LIB)
|
||||
|
|
@ -1,78 +0,0 @@
|
|||
ReaxFF library
|
||||
|
||||
Aidan Thompson, Sandia National Labs
|
||||
athomps at sandia.gov
|
||||
Jan 2008
|
||||
|
||||
This library is an implementation of the ReaxFF potential,
|
||||
specifically designed to work with LAMMPS. It is derived from Adri van
|
||||
Duin's original serial code, with intervening incarnations in CMDF and
|
||||
GRASP.
|
||||
|
||||
-------------------------------------------------
|
||||
|
||||
This directory has source files to build a library that LAMMPS
|
||||
links against when using the REAX package.
|
||||
|
||||
This library must be built with a F90 compiler, before LAMMPS is
|
||||
built, so LAMMPS can link against it.
|
||||
|
||||
You can type "make lib-reax" from the src directory to see help on how
|
||||
to build this library via make commands, or you can do the same thing
|
||||
by typing "python Install.py" from within this directory, or you can
|
||||
do it manually by following the instructions below.
|
||||
|
||||
Build the library using one of the provided Makefile.* files or create
|
||||
your own, specific to your compiler and system. For example:
|
||||
|
||||
make -f Makefile.gfortran
|
||||
|
||||
When you are done building this library, two files should
|
||||
exist in this directory:
|
||||
|
||||
libreax.a the library LAMMPS will link against
|
||||
Makefile.lammps settings the LAMMPS Makefile will import
|
||||
|
||||
Makefile.lammps is created by the make command, by copying one of the
|
||||
Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the
|
||||
Makefile.* files.
|
||||
|
||||
IMPORTANT: You must examine the final Makefile.lammps to insure it is
|
||||
correct for your system, else the LAMMPS build will likely fail.
|
||||
|
||||
Makefile.lammps has settings for 3 variables:
|
||||
|
||||
user-reax_SYSINC = leave blank for this package
|
||||
user-reax_SYSLIB = auxiliary F90 libs needed to link a F90 lib with
|
||||
a C++ program (LAMMPS) via a C++ compiler
|
||||
user-reax_SYSPATH = path(s) to where those libraries are
|
||||
|
||||
Because you have a F90 compiler on your system, you should have these
|
||||
libraries. But you will have to figure out which ones are needed and
|
||||
where they are. Examples of common configurations are in the
|
||||
Makefile.lammps.* files.
|
||||
|
||||
-------------------------------------------------
|
||||
|
||||
Additional build notes:
|
||||
|
||||
The include file reax_defs.h is used by both the ReaxFF library source
|
||||
files and the LAMMPS pair_reax.cpp source file (in package src/REAX).
|
||||
It contains dimensions of statically-allocated arrays created by the
|
||||
ReaxFF library. The size of these arrays must be set small enough to
|
||||
avoid exceeding the available machine memory, and large enough to fit
|
||||
the actual data generated by ReaxFF. If you change the values in
|
||||
reax_defs.h, you must first rebuild the library and then rebuild
|
||||
LAMMPS.
|
||||
|
||||
This library is called by functions in pair_reax.cpp. The C++ to
|
||||
FORTRAN function calls in pair_reax.cpp assume that FORTRAN object
|
||||
names are converted to C object names by appending an underscore
|
||||
character. This is generally the case, but on machines that do not
|
||||
conform to this convention, you will need to modify either the C++
|
||||
code or your compiler settings. The name conversion is handled by the
|
||||
preprocessor macro called FORTRAN in the file pair_reax_fortran.h,
|
||||
which is included by pair_reax.cpp. Different definitions of this
|
||||
macro can be obtained by adding a machine-specific macro definition to
|
||||
the CCFLAGS variable in your your LAMMPS Makefile e.g. -D_IBM. See
|
||||
pair_reax_fortran.h for more info.
|
||||
|
|
@ -1,116 +0,0 @@
|
|||
#include "reax_defs.h"
|
||||
implicit real*8 (a-h,o-z),integer(i-n)
|
||||
parameter (nneighmax=NNEIGHMAXDEF)
|
||||
parameter (nat=NATDEF) !Max number of atoms
|
||||
parameter (nattot=NATTOTDEF) !Max number of global atoms
|
||||
parameter (nsort=NSORTDEF) !Max number of atom types
|
||||
parameter (mbond=MBONDDEF) !Max number of bonds connected to one atom
|
||||
parameter (na1mx3=3*nat) !3*max number of atoms
|
||||
parameter (navib=NAVIBDEF) !for 2nd derivatives
|
||||
parameter (nbotym=NBOTYMDEF) !Max number of bond types
|
||||
parameter (nvatym=NVATYMDEF) !Max number of valency angle types
|
||||
parameter (ntotym=NTOTYMDEF) !Max number of torsion angle types
|
||||
parameter (nhbtym=NHBTYMDEF) !Max number of hydrogen bond types
|
||||
parameter (nodmtym=NODMTYMDEF) !Max number of off-diagonal Morse types
|
||||
parameter (nboallmax=NBOALLMAXDEF) !Max number of all bonds
|
||||
parameter (nbomax=NBOMAXDEF) !Max number of bonds
|
||||
parameter (nhbmax=NHBMAXDEF) !Max number of hydrogen bonds
|
||||
parameter (nvamax=NVAMAXDEF) !Max number of valency angles
|
||||
parameter (nopmax=NOPMAXDEF) !Max number of out of plane angles
|
||||
parameter (ntomax=NTOMAXDEF) !Max number of torsion angles
|
||||
parameter (npamax=NPAMAXDEF) !Max number of general parameters in force field
|
||||
parameter (nmolmax=NMOLMAXDEF) !Max number of molecules in system
|
||||
parameter (nmolset=NMOLSETDEF) !Max number of molecules in training set
|
||||
parameter (mrestra=MRESTRADEF) !Max number of restraints
|
||||
parameter (mtreg=MTREGDEF) !Max number of temperature regimes
|
||||
parameter (mtzone=MTZONEDEF) !Max number of temperature zones
|
||||
parameter (mvreg=MVREGDEF) !Max number of volume regimes
|
||||
parameter (mvzone=MVZONEDEF) !Max number of volume zones
|
||||
parameter (mereg=MEREGDEF) !Max number of electric field regimes
|
||||
parameter (mezone=MEZONEDEF) !Max number of electric field zones
|
||||
character*1 qr,qrset,qresi2
|
||||
character*2 qaset,qadd
|
||||
character*3 qresi1
|
||||
character*5 qlabel,qffty,qbgfaxes,qbgfsgn,qresi3
|
||||
character*20 qkeyw
|
||||
character*25 qfile
|
||||
character*40 qffield,qformat,qstrana2
|
||||
character*60 qremark,qremset,qmolset
|
||||
character*200 qstrana1
|
||||
common
|
||||
$/cbka/ dhbdc(nhbmax,3,3),cp(nat,3),
|
||||
$ cadd(nat,3),d2(3*navib,3*navib),
|
||||
$ veladd(3,nat),
|
||||
$ aold(3,nat),dic(3,nat),pvdw1(nsort,nsort),
|
||||
$ pvdw2(nsort,nsort),angimp(nat,6),
|
||||
$ yt(na1mx3),pt(na1mx3),gi(na1mx3),enmolset(nmolset),
|
||||
$ ai(na1mx3),bi(na1mx3),yi(na1mx3),pn(na1mx3),tbo(nat),
|
||||
$ chgbgf(nattot),
|
||||
$ abo2(nat),bor4(nat),bos(nbomax),
|
||||
$ eldef(nat),vradic(nat),
|
||||
$ vmo2(nat),
|
||||
$ ro(nbomax),dbondr(nbomax),
|
||||
$ dbosidr(nbomax),thgo(nopmax),
|
||||
$ elmol(nmolmax),
|
||||
$ elaf(nsort),vpq(nsort),
|
||||
$ rvdw(nsort),alf(nsort),eps(nsort),chat(nsort),
|
||||
$ rcore(nsort,nsort),ecore(nsort,nsort),acore(nsort,nsort),
|
||||
$ vlp2(nsort),
|
||||
$ valp2(nsort),vincr(nsort),
|
||||
$ vval3(nsort),
|
||||
$ vuncor(nbotym),
|
||||
$ vop(nsort),
|
||||
$ sigqeq(nsort),
|
||||
$ rrcha(mrestra),
|
||||
$ rmstra3(mrestra),
|
||||
$ rmcha(mrestra),
|
||||
$ rtcha(mrestra),rvcha(mrestra),
|
||||
$ v2bo(ntotym),v3bo(ntotym),
|
||||
$ eel,fctor,elr,
|
||||
$ presx2,presy2,presz2,
|
||||
$ tset2,
|
||||
$ enmol,formol,vvol,tpnrad,
|
||||
$ delvib,
|
||||
$ taut2,tincr,xmasmd,
|
||||
$ gdicmax,parc1,parc2,sumelec,
|
||||
$ xinh,fsnh,vqnh,snh,ham,errnh,sumhe,
|
||||
$ swa,swb2,swc0,swc1,swc2,swc3,swc4,swc5,swc6,
|
||||
$ swc7,plr,endpo2,ccpar,
|
||||
$ c4,estrmin,endpo,accincr,
|
||||
$ endpoold,xadd,yadd,zadd,addist,taddmol,
|
||||
$ Hug_E0, Hug_P0, Hug_V0, xImpVcm, shock_vel,
|
||||
$ shock_z_sep
|
||||
common
|
||||
$/cbka/
|
||||
$ ioop(nopmax,9),ifreqset(nmolset),
|
||||
$ ijk(nat,4),icgeopt(nmolset),
|
||||
$ irap(50),irdo(50,2),
|
||||
$ ityadd(nat),
|
||||
$ nmoloo(nat),iradic(nat),idef(nsort),nasort(nsort),
|
||||
$ ibgr1(nattot),ibgr2(nattot),idupc(6),
|
||||
$ imolsta(nat),
|
||||
$ ncent2(nbomax),irads,nrdd,nrddf,nbiolab,nuge,
|
||||
$ nbon2,npar,nodmty,ngnh,irac,nincrop,
|
||||
$ nboty,mdstep,
|
||||
$ nreac,
|
||||
$ nbonop,icelo2,
|
||||
$ iaddfreq,iveladd,invt,
|
||||
$ noop,ndtau,
|
||||
$ nelc3,nfc,nsav2,nmmax,ibh2,
|
||||
$ nmmaxold,nfcold,icellold,imodfile,
|
||||
$ icelo2old,inmov1,inmov2,nchaold,naa,nadattempt,
|
||||
$ nequi,iadj,
|
||||
$ ntest,nmm,
|
||||
$ nmolo5o,nradcount,nmollset,iflga,
|
||||
$ iperiod,ibgfversion,iremark,iconne,
|
||||
$ kx,ky,kz,iexco,iruid,ibity,nvlist,
|
||||
$ ityrad,iredo,iexx,iexy,iexz,ncellopt,
|
||||
$ ndata2,nprob,nit,i5758,ingeo,nmoloold,itemp,
|
||||
$ icgeo,ishock_type,isymm,
|
||||
$ qadd(nat),qlabel(nattot),qffty(nattot),qresi1(nattot),
|
||||
$ qresi2(nattot),qresi3(nattot),
|
||||
$ qremark(20),qformat(20),qr,qffield,
|
||||
$ qstrana1,qstrana2,qmolset(nmolset)
|
||||
***********************************************************************
|
||||
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
common
|
||||
$/cbkabo/ abo(nat)
|
||||
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkatomcoord/ id(nat,3),xmasat(nat),vel(3,nat),accel(3,nat)
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkbo/ bo(nbomax)
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
common
|
||||
$/cbkboncor/ dbosindc(nbomax,3,2*mbond+2),dbosidc(nbomax,3,2),
|
||||
$ bo131(nsort),bo132(nsort),bo133(nsort),
|
||||
$ ovc(nbotym),v13cor(nbotym)
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkbopi/ bopi(nbomax)
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkbopi2/ bopi2(nbomax)
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
common
|
||||
$/cbkbosi/ bosi(nbomax)
|
||||
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
common
|
||||
$/cbkc/ c(nat,3),cglobal(nattot,3),itag(nat),
|
||||
$chgglobal(nattot)
|
||||
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
common
|
||||
$/cbkch/ ch(nat)
|
||||
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
common
|
||||
$/cbkcha/ ech,syscha,chisys
|
||||
$ vfieldx,vfieldy,vfieldz,nmcharge,ioldchg
|
||||
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
common
|
||||
$/cbkcharmol/ vmcha(nmolmax),
|
||||
$ iat1mc(nmolmax),iat2mc(nmolmax)
|
||||
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkchb/ chi(nsort),eta(nsort),gam(nsort)
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
|
||||
common
|
||||
$/cbkconst/ dgrrdn,one,half,three,zero,caljou,rgasc,xjouca
|
||||
$ convmd
|
||||
|
||||
|
|
@ -1,7 +0,0 @@
|
|||
|
||||
|
||||
common
|
||||
$/cbkcovbon/ de2(nbotym),de3(nbotym),psi(nbotym),
|
||||
$ psp(nbotym),
|
||||
$ ltripstaball
|
||||
|
||||
|
|
@ -1,7 +0,0 @@
|
|||
integer Lvirial,Latomvirial
|
||||
|
||||
common
|
||||
$/cbkd/ d(3,nat),estrain(nat)
|
||||
|
||||
common
|
||||
$/cbkvirial/ atomvirial(6,nat),virial(6),Lvirial,Latomvirial
|
||||
|
|
@ -1,3 +0,0 @@
|
|||
common
|
||||
$/cbkdbodc/ dbodc(nbomax,3,2)
|
||||
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
|
||||
|
||||
|
||||
common
|
||||
$/cbkdbopi2ndc/ dbopi2ndc(nbomax,3,2*mbond+2)
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
|
||||
|
||||
common
|
||||
$/dbopidc/ dbopi2dc(nbomax,3,2),dbopidc(nbomax,3,2)
|
||||
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
|
||||
|
||||
|
||||
common
|
||||
$/dbopindc/ dbopindc(nbomax,3,2*mbond+2)
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
|
||||
|
||||
common
|
||||
$/cbkdcell/ dcell(3,nat,27)
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
|
||||
|
||||
common
|
||||
$/cbkdhdc/ dhdc(nvamax,3,3)
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
common
|
||||
$/cbkdistan/ axis(3),aaxh,baxh,caxh,iortho
|
||||
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
|
||||
|
||||
common
|
||||
$/cbkdrdc/ drdc(nbomax,3,2)
|
||||
|
||||
|
|
@ -1,4 +0,0 @@
|
|||
|
||||
common
|
||||
$/cbkefield/ efix,efiy,efiz,c1
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue