Merge branch 'master' into progguide-axel
This commit is contained in:
Axel Kohlmeyer
@ -81,6 +81,7 @@ OPT.
|
||||
* :doc:`coul/slater/long <pair_coul_slater>`
|
||||
* :doc:`coul/shield <pair_coul_shield>`
|
||||
* :doc:`coul/streitz <pair_coul>`
|
||||
* :doc:`coul/tt <pair_coul_tt>`
|
||||
* :doc:`coul/wolf (ko) <pair_coul>`
|
||||
* :doc:`coul/wolf/cs <pair_cs>`
|
||||
* :doc:`dpd (gio) <pair_dpd>`
|
||||
|
||||
@ -24,7 +24,7 @@ of the source files: the lammps.f90 file needs to be compiled first,
|
||||
since it provides the ``LIBLAMMPS`` module that is imported by the
|
||||
Fortran code using the interface.
|
||||
|
||||
.. versionadded:: 30Sep2020
|
||||
.. versionadded:: 6Oct2020
|
||||
|
||||
.. admonition:: Work in Progress
|
||||
:class: note
|
||||
|
||||
131
doc/src/pair_coul_tt.rst
Normal file
131
doc/src/pair_coul_tt.rst
Normal file
@ -0,0 +1,131 @@
|
||||
.. index:: pair_style coul/tt
|
||||
|
||||
pair_style coul/tt command
|
||||
==========================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style style args
|
||||
|
||||
* style = *coul/tt*
|
||||
* args = list of arguments for a particular style
|
||||
|
||||
.. parsed-literal::
|
||||
|
||||
*coul/tt* args = n cutoff
|
||||
n = degree of polynomial
|
||||
cutoff = global cutoff (distance units)
|
||||
|
||||
Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
||||
pair_style hybrid/overlay ... coul/tt 4 12.0
|
||||
pair_coeff 1 2 coul/tt 4.5 1.0
|
||||
pair_coeff 1 2 coul/tt 4.0 1.0 4 12.0
|
||||
pair_coeff 1 3* coul/tt 4.5 1.0 4
|
||||
|
||||
|
||||
Description
|
||||
"""""""""""
|
||||
|
||||
The *coul/tt* pair style is meant to be used with force fields that
|
||||
include explicit polarization through Drude dipoles.
|
||||
|
||||
The *coul/tt* pair style should be used as a sub-style within in the
|
||||
:doc:`pair_style hybrid/overlay <pair_hybrid>` command, in conjunction with a
|
||||
main pair style including Coulomb interactions and *thole* pair style,
|
||||
or with *lj/cut/thole/long* pair style that is equivalent to the combination
|
||||
of preceding two.
|
||||
|
||||
The *coul/tt* pair styles compute the charge-dipole Coulomb interaction damped
|
||||
at short distances by a function
|
||||
|
||||
.. math::
|
||||
|
||||
f_{n,ij}(r) = 1 - c_{ij} \cdot e^{-b_{ij} r} \sum_{k=0}^n \frac{(b_{ij} r)^k}{k!}
|
||||
|
||||
This function results from an adaptation to the Coulomb interaction :ref:`(Salanne)
|
||||
<Salanne1>` of the damping function originally proposed
|
||||
by :ref:`Tang Toennies <TangToennies1>` for van der Waals interactions.
|
||||
|
||||
The polynomial takes the degree 4 for damping the Coulomb interaction.
|
||||
The parameters :math:`b_{ij}` and :math:`c_{ij}` could be determined from
|
||||
first-principle calculations for small, mainly mono-atomic, ions :ref:`(Salanne)
|
||||
<Salanne1>`, or else treated as empirical for large molecules.
|
||||
|
||||
In pair styles with Drude induced dipoles, this damping function is typically
|
||||
applied to the interactions between a Drude charge (either :math:`q_{D,i}` on
|
||||
a Drude particle or :math:`-q_{D,i}` on the respective
|
||||
Drude core)) and a charge on a non-polarizable atom, :math:`q_{j}`.
|
||||
|
||||
The Tang-Toennies function could also be used to damp electrostatic
|
||||
interactions between the (non-polarizable part of the) charge of a core,
|
||||
:math:`q_{i}-q_{D,i}`, and the Drude charge of another, :math:`-q_{D,j}`.
|
||||
The :math:`b_{ij}` and :math:`c_{ij}` are equal to :math:`b_{ji}` and
|
||||
:math:`c_{ji}` in the case of core-core interactions.
|
||||
|
||||
For pair_style *coul/tt*\ , the following coefficients must be defined for
|
||||
each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command
|
||||
as in the example above.
|
||||
|
||||
* :math:`b_{ij}`
|
||||
* :math:`c_{ij}`
|
||||
* degree of polynomial (positive integer)
|
||||
* cutoff (distance units)
|
||||
|
||||
The last two coefficients are optional. If not specified the global
|
||||
degree of the polynomial or the global cutoff specified in the pair_style
|
||||
command are used. In order to specify a cutoff (forth argument), the degree of
|
||||
the polynomial (third argument) must also be specified.
|
||||
|
||||
----------
|
||||
|
||||
Mixing, shift, table, tail correction, restart, rRESPA info
|
||||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
The *coul/tt* pair style does not support mixing. Thus, coefficients
|
||||
for all I,J pairs must be specified explicitly.
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
These pair styles are part of the USER-DRUDE package. They are only
|
||||
enabled if LAMMPS was built with that package. See the :doc:`Build package
|
||||
<Build_package>` doc page for more info.
|
||||
|
||||
This pair_style should currently not be used with the :doc:`charmm dihedral
|
||||
style <dihedral_charmm>` if the latter has non-zero 1-4 weighting
|
||||
factors. This is because the *coul/tt* pair style does not know which
|
||||
pairs are 1-4 partners of which dihedrals.
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`fix drude <fix_drude>`, :doc:`fix langevin/drude <fix_langevin_drude>`,
|
||||
:doc:`fix drude/transform <fix_drude_transform>`,
|
||||
:doc:`compute temp/drude <compute_temp_drude>`,
|
||||
:doc:`pair_style thole <pair_thole>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _Thole1:
|
||||
|
||||
**(Thole)** Chem Phys, 59, 341 (1981).
|
||||
|
||||
.. _Salanne1:
|
||||
|
||||
**(Salanne)** Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
|
||||
|
||||
.. _TangToennies1:
|
||||
|
||||
**(Tang and Toennies)** J Chem Phys, 80, 3726 (1984).
|
||||
@ -144,6 +144,7 @@ accelerated styles exist.
|
||||
* :doc:`coul/slater/long <pair_coul>` - long-range smeared out Coulomb
|
||||
* :doc:`coul/shield <pair_coul_shield>` - Coulomb for boron nitride for use with :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` potential
|
||||
* :doc:`coul/streitz <pair_coul>` - Coulomb via Streitz/Mintmire Slater orbitals
|
||||
* :doc:`coul/tt <pair_coul_tt>` - damped charge-dipole Coulomb for Drude dipoles
|
||||
* :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
|
||||
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
|
||||
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
|
||||
|
||||
@ -1410,6 +1410,7 @@ Izz
|
||||
Jacobsen
|
||||
Jadhav
|
||||
jagreat
|
||||
Jahn
|
||||
Jalalvand
|
||||
james
|
||||
Janssen
|
||||
@ -2715,6 +2716,7 @@ Rosenberger
|
||||
Rossky
|
||||
rosybrown
|
||||
rotationally
|
||||
Rotenberg
|
||||
Rovigatti
|
||||
royalblue
|
||||
rozero
|
||||
@ -2749,6 +2751,7 @@ safezone
|
||||
Safran
|
||||
Sagui
|
||||
Saidi
|
||||
Salanne
|
||||
Salles
|
||||
sandia
|
||||
Sandia
|
||||
@ -3112,6 +3115,7 @@ Tohoku
|
||||
tokenizer
|
||||
tokyo
|
||||
tol
|
||||
Toennies
|
||||
tomic
|
||||
toolchain
|
||||
topologies
|
||||
@ -3340,6 +3344,7 @@ vtp
|
||||
vtr
|
||||
vtu
|
||||
Vu
|
||||
Vuilleumier
|
||||
vv
|
||||
vx
|
||||
Vx
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -7,8 +7,9 @@ LAMMPS_SRC = $(LAMMPS_ROOT)/src
|
||||
# Uncomment the line below if using the MPI stubs library
|
||||
MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS
|
||||
|
||||
FC = mpif90 # replace with your Fortran compiler
|
||||
CXX = mpicxx # replace with your C++ compiler
|
||||
FC = mpifort # replace with your Fortran compiler
|
||||
CXX = mpicxx # replace with your C++ compiler
|
||||
CXXLIB = -lstdc++ # replace with your C++ runtime libs
|
||||
|
||||
# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively
|
||||
FFLAGS = -O2 -fPIC
|
||||
@ -18,7 +19,7 @@ CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX
|
||||
all : liblammps_fortran.a liblammps_fortran.so
|
||||
|
||||
liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o
|
||||
$(FC) $(FFLAGS) -shared -o $@ $^
|
||||
$(FC) $(FFLAGS) -shared -o $@ $^ $(CXXLIB)
|
||||
|
||||
liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o
|
||||
$(AR) rs $@ $^
|
||||
@ -1,265 +1,265 @@
|
||||
LAMMPS.F90 defines a Fortran 2003 module, LAMMPS, which wraps all functions in
|
||||
src/library.h so they can be used directly from Fortran-encoded programs.
|
||||
|
||||
All functions in src/library.h that use and/or return C-style pointers have
|
||||
Fortran wrapper functions that use Fortran-style arrays, pointers, and
|
||||
strings; all C-style memory management is handled internally with no user
|
||||
intervention. See --USE-- for notes on how this interface differs from the
|
||||
C interface (and the Python interface).
|
||||
|
||||
This interface was created by Karl Hammond who you can contact with
|
||||
questions:
|
||||
|
||||
Karl D. Hammond
|
||||
University of Tennessee, Knoxville
|
||||
karlh at ugcs.caltech.edu
|
||||
karlh at utk.edu
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--COMPILATION--
|
||||
|
||||
First, be advised that mixed-language programming is not trivial. It requires
|
||||
you to link in the required libraries of all languages you use (in this case,
|
||||
those for Fortran, C, and C++), as well as any other libraries required.
|
||||
You are also advised to read the --USE-- section below before trying to
|
||||
compile.
|
||||
|
||||
The following steps will work to compile this module (replace ${LAMMPS_SRC}
|
||||
with the path to your LAMMPS source directory).
|
||||
|
||||
Steps 3-5 are accomplished, possibly after some modifications to
|
||||
the makefile, by make using the attached makefile. Said makefile also builds
|
||||
the dynamically-linkable library (liblammps_fortran.so).
|
||||
|
||||
** STATIC LIBRARY INSTRUCTIONS **
|
||||
(1) Compile LAMMPS as a static library.
|
||||
Call the resulting file ${LAMMPS_LIB}, which will have an actual name
|
||||
like liblmp_openmpi.a. If compiling using the MPI stubs in
|
||||
${LAMMPS_SRC}/STUBS, you will need to know where libmpi_stubs.a
|
||||
is as well (I'll call it ${MPI_STUBS} hereafter)
|
||||
(2) Copy said library to your Fortran program's source directory or replace
|
||||
${LAMMPS_LIB} with its full path in the instructions below.
|
||||
(3) Compile (but don't link!) LAMMPS.F90. Example:
|
||||
mpif90 -c LAMMPS.f90
|
||||
OR
|
||||
gfortran -c LAMMPS.F90
|
||||
NOTE: you may get a warning such as,
|
||||
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
|
||||
Variable 'communicator' at (1) is a parameter to the BIND(C)
|
||||
procedure 'lammps_open_wrapper' but may not be C interoperable
|
||||
This is normal (see --IMPLEMENTATION NOTES--).
|
||||
|
||||
(4) Compile (but don't link) LAMMPS-wrapper.cpp. You will need its header
|
||||
file as well. You will have to provide the locations of LAMMPS's
|
||||
header files. For example,
|
||||
mpicxx -c -I${LAMMPS_SRC} LAMMPS-wrapper.cpp
|
||||
OR
|
||||
g++ -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
|
||||
OR
|
||||
icpc -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
|
||||
(5) OPTIONAL: Make a library from the object files so you can carry around
|
||||
two files instead of three. Example:
|
||||
ar rs liblammps_fortran.a LAMMPS.o LAMMPS-wrapper.o
|
||||
This will create the file liblammps_fortran.a that you can use in place
|
||||
of "LAMMPS.o LAMMPS-wrapper.o" later. Note that you will still
|
||||
need to have the .mod file from part (3).
|
||||
|
||||
It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
|
||||
LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
|
||||
library, like so:
|
||||
ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
|
||||
In this case, you can now use the Fortran wrapper functions as if they
|
||||
were part of the usual LAMMPS library interface (if you have the module
|
||||
file visible to the compiler, that is).
|
||||
(6) Compile (but don't link) your Fortran program. Example:
|
||||
mpif90 -c myfreeformatfile.f90
|
||||
mpif90 -c myfixedformatfile.f
|
||||
OR
|
||||
gfortran -c myfreeformatfile.f90
|
||||
gfortran -c myfixedformatfile.f
|
||||
The object files generated by these steps are collectively referred to
|
||||
as ${my_object_files} in the next step(s).
|
||||
|
||||
IMPORTANT: If the Fortran module from part (3) is not in the current
|
||||
directory or in one searched by the compiler for module files, you will
|
||||
need to include that location via the -I flag to the compiler, like so:
|
||||
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
|
||||
|
||||
(7) Link everything together, including any libraries needed by LAMMPS (such
|
||||
as the C++ standard library, the C math library, the JPEG library, fftw,
|
||||
etc.) For example,
|
||||
mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
|
||||
OR
|
||||
gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} ${MPI_STUBS} -lstdc++ -lm
|
||||
OR
|
||||
ifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} ${MPI_STUBS} -cxxlib -lm
|
||||
Any other required libraries (e.g. -ljpeg, -lfftw) should be added to
|
||||
the end of this line.
|
||||
|
||||
You should now have a working executable.
|
||||
|
||||
** DYNAMIC LIBRARY INSTRUCTIONS **
|
||||
(1) Compile LAMMPS as a dynamic library
|
||||
(make makeshlib && make -f Makefile.shlib [targetname]).
|
||||
(2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
|
||||
mpif90 -fPIC -c LAMMPS.f90
|
||||
(3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
|
||||
mpicxx -fPIC -c LAMMPS-wrapper.cpp
|
||||
(4) Make the dynamic library, like so:
|
||||
mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
|
||||
(5) Compile your program, such as,
|
||||
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
|
||||
where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
|
||||
step (3)
|
||||
(6) Link everything together, such as
|
||||
mpif90 ${my_object_files} -L${LAMMPS_SRC} \
|
||||
-L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
|
||||
-llammps_openmpi -lmpi_cxx -lstdc++ -lm
|
||||
|
||||
If you wish to avoid the -L flags, add the directories containing your
|
||||
shared libraries to the LIBRARY_PATH environment variable. At run time, you
|
||||
will have to add these directories to LD_LIBRARY_PATH as well; otherwise,
|
||||
your executable will not find the libraries it needs.
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--USAGE--
|
||||
|
||||
To use this API, your program unit (PROGRAM/SUBROUTINE/FUNCTION/MODULE/etc.)
|
||||
should look something like this:
|
||||
program call_lammps
|
||||
use LAMMPS
|
||||
! Other modules, etc.
|
||||
implicit none
|
||||
type (lammps_instance) :: lmp ! This is a pointer to your LAMMPS instance
|
||||
real (C_double) :: fix
|
||||
real (C_double), dimension(:), pointer :: fix2
|
||||
! Rest of declarations
|
||||
call lammps_open_no_mpi ('lmp -in /dev/null -screen out.lammps',lmp)
|
||||
! Set up rest of program here
|
||||
call lammps_file (lmp, 'in.example')
|
||||
call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
|
||||
call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
|
||||
call lammps_close (lmp)
|
||||
end program call_lammps
|
||||
|
||||
Important notes:
|
||||
* Though I dislike the use of pointers, they are necessary when communicating
|
||||
with C and C++, which do not support Fortran's ALLOCATABLE attribute.
|
||||
* There is no need to deallocate C-allocated memory; this is done for you in
|
||||
the cases when it is done (which are all cases when pointers are not
|
||||
accepted, such as global fix data)
|
||||
* All arguments which are char* variables in library.cpp are character (len=*)
|
||||
variables here. For example,
|
||||
call lammps_command (lmp, 'units metal')
|
||||
will work as expected.
|
||||
* The public functions (the only ones you can use) have interfaces as
|
||||
described in the comments at the top of LAMMPS.F90. They are not always
|
||||
the same as those in library.h, since C strings are replaced by Fortran
|
||||
strings and the like.
|
||||
* The module attempts to check whether you have done something stupid (such
|
||||
as assign a 2D array to a scalar), but it's not perfect. For example, the
|
||||
command
|
||||
call lammps_extract_global (nlocal, ptr, 'nlocal')
|
||||
will give nlocal correctly if nlocal is a pointer to type INTEGER, but it
|
||||
will give the wrong answer if nlocal is a pointer to type REAL. This is a
|
||||
feature of the (void*) type cast in library.cpp. There is no way I can
|
||||
check this for you! It WILL catch you if you pass it an allocatable or
|
||||
fixed-size array when it expects a pointer.
|
||||
* Arrays constructed from temporary data from LAMMPS are ALLOCATABLE, and
|
||||
represent COPIES of data, not the originals. Functions like
|
||||
lammps_extract_atom, which return actual LAMMPS data, are pointers.
|
||||
* IMPORTANT: Due to the differences between C and Fortran arrays (C uses
|
||||
row-major vectors, Fortran uses column-major vectors), all arrays returned
|
||||
from LAMMPS have their indices swapped.
|
||||
* An example of a complete program, simple.f90, is included with this
|
||||
package.
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--TROUBLESHOOTING--
|
||||
|
||||
Compile-time errors (when compiling LAMMPS.F90, that is) probably indicate
|
||||
that your compiler is not new enough to support Fortran 2003 features. For
|
||||
example, GCC 4.1.2 will not compile this module, but GCC 4.4.0 will.
|
||||
|
||||
If your compiler balks at 'use, intrinsic :: ISO_C_binding,' try removing the
|
||||
intrinsic part so it looks like an ordinary module. However, it is likely
|
||||
that such a compiler will also have problems with everything else in the
|
||||
file as well.
|
||||
|
||||
If you get a segfault as soon as the lammps_open call is made, check that you
|
||||
compiled your program AND LAMMPS-wrapper.cpp using the same MPI headers. Using
|
||||
the stubs for one and the actual MPI library for the other will cause Bad
|
||||
Things to happen.
|
||||
|
||||
If you find run-time errors, please pass them along via the LAMMPS Users
|
||||
mailing list (please CC me as well; address above). Please provide a minimal
|
||||
working example along with the names and versions of the compilers you are
|
||||
using. Please make sure the error is repeatable and is in MY code, not yours
|
||||
(generating a minimal working example will usually ensure this anyway).
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--IMPLEMENTATION NOTES--
|
||||
|
||||
The Fortran procedures have the same names as the C procedures, and
|
||||
their purpose is the same, but they may take different arguments. Here are
|
||||
some of the important differences:
|
||||
* lammps_open and lammps_open_no_mpi take a string instead of argc and
|
||||
argv. This is necessary because C and C++ have a very different way
|
||||
of treating strings than Fortran. If you want the command line to be
|
||||
passed to lammps_open (as it often would be from C/C++), use the
|
||||
GET_COMMAND intrinsic to obtain it.
|
||||
* All C++ functions that accept char* pointers now accept Fortran-style
|
||||
strings within this interface instead.
|
||||
* All of the lammps_extract_[something] functions, which return void*
|
||||
C-style pointers, have been replaced by generic subroutines that return
|
||||
Fortran variables (which may be arrays). The first argument houses the
|
||||
variable/pointer to be returned (pretend it's on the left-hand side); all
|
||||
other arguments are identical except as stipulated above.
|
||||
Note that it is not possible to declare generic functions that are selected
|
||||
based solely on the type/kind/rank (TKR) signature of the return value,
|
||||
only based on the TKR of the arguments.
|
||||
* The SHAPE of the first argument to lammps_extract_[something] is checked
|
||||
against the "shape" of the C array (e.g., double vs. double* vs. double**).
|
||||
Calling a subroutine with arguments of inappropriate rank will result in an
|
||||
error at run time.
|
||||
* The indices i and j in lammps_extract_fix are used the same way they
|
||||
are in f_ID[i][j] references in LAMMPS (i.e., starting from 1). This is
|
||||
different than the way library.cpp uses these numbers, but is more
|
||||
consistent with the way arrays are accessed in LAMMPS and in Fortran.
|
||||
* The char* pointer normally returned by lammps_command is thrown away
|
||||
in this version; note also that lammps_command is now a subroutine
|
||||
instead of a function.
|
||||
* The pointer to LAMMPS itself is of type(lammps_instance), which is itself
|
||||
a synonym for type(C_ptr), part of ISO_C_BINDING. Type (C_ptr) is
|
||||
C's void* data type.
|
||||
* This module will almost certainly generate a compile-time warning,
|
||||
such as,
|
||||
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
|
||||
Variable 'communicator' at (1) is a parameter to the BIND(C)
|
||||
procedure 'lammps_open_wrapper' but may not be C interoperable
|
||||
This happens because lammps_open_wrapper actually takes a Fortran
|
||||
INTEGER argument, whose type is defined by the MPI library itself. The
|
||||
Fortran integer is converted to a C integer by the MPI library (if such
|
||||
conversion is actually necessary).
|
||||
* lammps_extract_global returns COPIES of the (scalar) data, as does the
|
||||
C version.
|
||||
* lammps_extract_atom, lammps_extract_compute, and lammps_extract_fix
|
||||
have a first argument that will be associated with ACTUAL LAMMPS DATA.
|
||||
This means the first argument must be:
|
||||
* The right rank (via the DIMENSION modifier)
|
||||
* A C-interoperable POINTER type (i.e., INTEGER (C_int) or
|
||||
REAL (C_double)).
|
||||
* lammps_extract_variable returns COPIES of the data, as the C library
|
||||
interface does. There is no need to deallocate using lammps_free.
|
||||
* The 'data' argument to lammps_gather_atoms and lammps_scatter atoms must
|
||||
be ALLOCATABLE. It should be of type INTEGER or DOUBLE PRECISION. It
|
||||
does NOT need to be C inter-operable (and indeed should not be).
|
||||
* The 'count' argument of lammps_scatter_atoms is unnecessary; the shape of
|
||||
the array determines the number of elements LAMMPS will read.
|
||||
LAMMPS.F90 defines a Fortran 2003 module, LAMMPS, which wraps all functions in
|
||||
src/library.h so they can be used directly from Fortran-encoded programs.
|
||||
|
||||
All functions in src/library.h that use and/or return C-style pointers have
|
||||
Fortran wrapper functions that use Fortran-style arrays, pointers, and
|
||||
strings; all C-style memory management is handled internally with no user
|
||||
intervention. See --USE-- for notes on how this interface differs from the
|
||||
C interface (and the Python interface).
|
||||
|
||||
This interface was created by Karl Hammond who you can contact with
|
||||
questions:
|
||||
|
||||
Karl D. Hammond
|
||||
University of Tennessee, Knoxville
|
||||
karlh at ugcs.caltech.edu
|
||||
karlh at utk.edu
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--COMPILATION--
|
||||
|
||||
First, be advised that mixed-language programming is not trivial. It requires
|
||||
you to link in the required libraries of all languages you use (in this case,
|
||||
those for Fortran, C, and C++), as well as any other libraries required.
|
||||
You are also advised to read the --USE-- section below before trying to
|
||||
compile.
|
||||
|
||||
The following steps will work to compile this module (replace ${LAMMPS_SRC}
|
||||
with the path to your LAMMPS source directory).
|
||||
|
||||
Steps 3-5 are accomplished, possibly after some modifications to
|
||||
the makefile, by make using the attached makefile. Said makefile also builds
|
||||
the dynamically-linkable library (liblammps_fortran.so).
|
||||
|
||||
** STATIC LIBRARY INSTRUCTIONS **
|
||||
(1) Compile LAMMPS as a static library.
|
||||
Call the resulting file ${LAMMPS_LIB}, which will have an actual name
|
||||
like liblmp_openmpi.a. If compiling using the MPI stubs in
|
||||
${LAMMPS_SRC}/STUBS, you will need to know where libmpi_stubs.a
|
||||
is as well (I'll call it ${MPI_STUBS} hereafter)
|
||||
(2) Copy said library to your Fortran program's source directory or replace
|
||||
${LAMMPS_LIB} with its full path in the instructions below.
|
||||
(3) Compile (but don't link!) LAMMPS.F90. Example:
|
||||
mpif90 -c LAMMPS.f90
|
||||
OR
|
||||
gfortran -c LAMMPS.F90
|
||||
NOTE: you may get a warning such as,
|
||||
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
|
||||
Variable 'communicator' at (1) is a parameter to the BIND(C)
|
||||
procedure 'lammps_open_wrapper' but may not be C interoperable
|
||||
This is normal (see --IMPLEMENTATION NOTES--).
|
||||
|
||||
(4) Compile (but don't link) LAMMPS-wrapper.cpp. You will need its header
|
||||
file as well. You will have to provide the locations of LAMMPS's
|
||||
header files. For example,
|
||||
mpicxx -c -I${LAMMPS_SRC} LAMMPS-wrapper.cpp
|
||||
OR
|
||||
g++ -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
|
||||
OR
|
||||
icpc -c -I${LAMMPS_SRC} -I${LAMMPS_SRC}/STUBS LAMMPS-wrapper.cpp
|
||||
(5) OPTIONAL: Make a library from the object files so you can carry around
|
||||
two files instead of three. Example:
|
||||
ar rs liblammps_fortran.a LAMMPS.o LAMMPS-wrapper.o
|
||||
This will create the file liblammps_fortran.a that you can use in place
|
||||
of "LAMMPS.o LAMMPS-wrapper.o" later. Note that you will still
|
||||
need to have the .mod file from part (3).
|
||||
|
||||
It is also possible to add LAMMPS.o and LAMMPS-wrapper.o into the
|
||||
LAMMPS library (e.g., liblmp_openmpi.a) instead of creating a separate
|
||||
library, like so:
|
||||
ar rs ${LAMMPS_LIB} LAMMPS.o LAMMPS-wrapper.o
|
||||
In this case, you can now use the Fortran wrapper functions as if they
|
||||
were part of the usual LAMMPS library interface (if you have the module
|
||||
file visible to the compiler, that is).
|
||||
(6) Compile (but don't link) your Fortran program. Example:
|
||||
mpif90 -c myfreeformatfile.f90
|
||||
mpif90 -c myfixedformatfile.f
|
||||
OR
|
||||
gfortran -c myfreeformatfile.f90
|
||||
gfortran -c myfixedformatfile.f
|
||||
The object files generated by these steps are collectively referred to
|
||||
as ${my_object_files} in the next step(s).
|
||||
|
||||
IMPORTANT: If the Fortran module from part (3) is not in the current
|
||||
directory or in one searched by the compiler for module files, you will
|
||||
need to include that location via the -I flag to the compiler, like so:
|
||||
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
|
||||
|
||||
(7) Link everything together, including any libraries needed by LAMMPS (such
|
||||
as the C++ standard library, the C math library, the JPEG library, fftw,
|
||||
etc.) For example,
|
||||
mpif90 LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} -lmpi_cxx -lstdc++ -lm
|
||||
OR
|
||||
gfortran LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} ${MPI_STUBS} -lstdc++ -lm
|
||||
OR
|
||||
ifort LAMMPS.o LAMMPS-wrapper.o ${my_object_files} \
|
||||
${LAMMPS_LIB} ${MPI_STUBS} -cxxlib -lm
|
||||
Any other required libraries (e.g. -ljpeg, -lfftw) should be added to
|
||||
the end of this line.
|
||||
|
||||
You should now have a working executable.
|
||||
|
||||
** DYNAMIC LIBRARY INSTRUCTIONS **
|
||||
(1) Compile LAMMPS as a dynamic library
|
||||
(make makeshlib && make -f Makefile.shlib [targetname]).
|
||||
(2) Compile, but don't link, LAMMPS.F90 using the -fPIC flag, such as
|
||||
mpif90 -fPIC -c LAMMPS.f90
|
||||
(3) Compile, but don't link, LAMMPS-wrapper.cpp in the same manner, e.g.
|
||||
mpicxx -fPIC -c LAMMPS-wrapper.cpp
|
||||
(4) Make the dynamic library, like so:
|
||||
mpif90 -fPIC -shared -o liblammps_fortran.so LAMMPS.o LAMMPS-wrapper.o
|
||||
(5) Compile your program, such as,
|
||||
mpif90 -I${LAMMPS_SRC}/examples/COUPLE/fortran2 -c myfreeformatfile.f90
|
||||
where ${LAMMPS_SRC}/examples/COUPLE/fortran2 contains the .mod file from
|
||||
step (3)
|
||||
(6) Link everything together, such as
|
||||
mpif90 ${my_object_files} -L${LAMMPS_SRC} \
|
||||
-L${LAMMPS_SRC}/examples/COUPLE/fortran2 -llammps_fortran \
|
||||
-llammps_openmpi -lmpi_cxx -lstdc++ -lm
|
||||
|
||||
If you wish to avoid the -L flags, add the directories containing your
|
||||
shared libraries to the LIBRARY_PATH environment variable. At run time, you
|
||||
will have to add these directories to LD_LIBRARY_PATH as well; otherwise,
|
||||
your executable will not find the libraries it needs.
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--USAGE--
|
||||
|
||||
To use this API, your program unit (PROGRAM/SUBROUTINE/FUNCTION/MODULE/etc.)
|
||||
should look something like this:
|
||||
program call_lammps
|
||||
use LAMMPS
|
||||
! Other modules, etc.
|
||||
implicit none
|
||||
type (lammps_instance) :: lmp ! This is a pointer to your LAMMPS instance
|
||||
real (C_double) :: fix
|
||||
real (C_double), dimension(:), pointer :: fix2
|
||||
! Rest of declarations
|
||||
call lammps_open_no_mpi ('lmp -in /dev/null -screen out.lammps',lmp)
|
||||
! Set up rest of program here
|
||||
call lammps_file (lmp, 'in.example')
|
||||
call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
|
||||
call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
|
||||
call lammps_close (lmp)
|
||||
end program call_lammps
|
||||
|
||||
Important notes:
|
||||
* Though I dislike the use of pointers, they are necessary when communicating
|
||||
with C and C++, which do not support Fortran's ALLOCATABLE attribute.
|
||||
* There is no need to deallocate C-allocated memory; this is done for you in
|
||||
the cases when it is done (which are all cases when pointers are not
|
||||
accepted, such as global fix data)
|
||||
* All arguments which are char* variables in library.cpp are character (len=*)
|
||||
variables here. For example,
|
||||
call lammps_command (lmp, 'units metal')
|
||||
will work as expected.
|
||||
* The public functions (the only ones you can use) have interfaces as
|
||||
described in the comments at the top of LAMMPS.F90. They are not always
|
||||
the same as those in library.h, since C strings are replaced by Fortran
|
||||
strings and the like.
|
||||
* The module attempts to check whether you have done something stupid (such
|
||||
as assign a 2D array to a scalar), but it's not perfect. For example, the
|
||||
command
|
||||
call lammps_extract_global (nlocal, ptr, 'nlocal')
|
||||
will give nlocal correctly if nlocal is a pointer to type INTEGER, but it
|
||||
will give the wrong answer if nlocal is a pointer to type REAL. This is a
|
||||
feature of the (void*) type cast in library.cpp. There is no way I can
|
||||
check this for you! It WILL catch you if you pass it an allocatable or
|
||||
fixed-size array when it expects a pointer.
|
||||
* Arrays constructed from temporary data from LAMMPS are ALLOCATABLE, and
|
||||
represent COPIES of data, not the originals. Functions like
|
||||
lammps_extract_atom, which return actual LAMMPS data, are pointers.
|
||||
* IMPORTANT: Due to the differences between C and Fortran arrays (C uses
|
||||
row-major vectors, Fortran uses column-major vectors), all arrays returned
|
||||
from LAMMPS have their indices swapped.
|
||||
* An example of a complete program, simple.f90, is included with this
|
||||
package.
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--TROUBLESHOOTING--
|
||||
|
||||
Compile-time errors (when compiling LAMMPS.F90, that is) probably indicate
|
||||
that your compiler is not new enough to support Fortran 2003 features. For
|
||||
example, GCC 4.1.2 will not compile this module, but GCC 4.4.0 will.
|
||||
|
||||
If your compiler balks at 'use, intrinsic :: ISO_C_binding,' try removing the
|
||||
intrinsic part so it looks like an ordinary module. However, it is likely
|
||||
that such a compiler will also have problems with everything else in the
|
||||
file as well.
|
||||
|
||||
If you get a segfault as soon as the lammps_open call is made, check that you
|
||||
compiled your program AND LAMMPS-wrapper.cpp using the same MPI headers. Using
|
||||
the stubs for one and the actual MPI library for the other will cause Bad
|
||||
Things to happen.
|
||||
|
||||
If you find run-time errors, please pass them along via the LAMMPS Users
|
||||
mailing list (please CC me as well; address above). Please provide a minimal
|
||||
working example along with the names and versions of the compilers you are
|
||||
using. Please make sure the error is repeatable and is in MY code, not yours
|
||||
(generating a minimal working example will usually ensure this anyway).
|
||||
|
||||
-------------------------------------
|
||||
|
||||
--IMPLEMENTATION NOTES--
|
||||
|
||||
The Fortran procedures have the same names as the C procedures, and
|
||||
their purpose is the same, but they may take different arguments. Here are
|
||||
some of the important differences:
|
||||
* lammps_open and lammps_open_no_mpi take a string instead of argc and
|
||||
argv. This is necessary because C and C++ have a very different way
|
||||
of treating strings than Fortran. If you want the command line to be
|
||||
passed to lammps_open (as it often would be from C/C++), use the
|
||||
GET_COMMAND intrinsic to obtain it.
|
||||
* All C++ functions that accept char* pointers now accept Fortran-style
|
||||
strings within this interface instead.
|
||||
* All of the lammps_extract_[something] functions, which return void*
|
||||
C-style pointers, have been replaced by generic subroutines that return
|
||||
Fortran variables (which may be arrays). The first argument houses the
|
||||
variable/pointer to be returned (pretend it's on the left-hand side); all
|
||||
other arguments are identical except as stipulated above.
|
||||
Note that it is not possible to declare generic functions that are selected
|
||||
based solely on the type/kind/rank (TKR) signature of the return value,
|
||||
only based on the TKR of the arguments.
|
||||
* The SHAPE of the first argument to lammps_extract_[something] is checked
|
||||
against the "shape" of the C array (e.g., double vs. double* vs. double**).
|
||||
Calling a subroutine with arguments of inappropriate rank will result in an
|
||||
error at run time.
|
||||
* The indices i and j in lammps_extract_fix are used the same way they
|
||||
are in f_ID[i][j] references in LAMMPS (i.e., starting from 1). This is
|
||||
different than the way library.cpp uses these numbers, but is more
|
||||
consistent with the way arrays are accessed in LAMMPS and in Fortran.
|
||||
* The char* pointer normally returned by lammps_command is thrown away
|
||||
in this version; note also that lammps_command is now a subroutine
|
||||
instead of a function.
|
||||
* The pointer to LAMMPS itself is of type(lammps_instance), which is itself
|
||||
a synonym for type(C_ptr), part of ISO_C_BINDING. Type (C_ptr) is
|
||||
C's void* data type.
|
||||
* This module will almost certainly generate a compile-time warning,
|
||||
such as,
|
||||
subroutine lammps_open_wrapper (argc, argv, communicator, ptr) &
|
||||
Variable 'communicator' at (1) is a parameter to the BIND(C)
|
||||
procedure 'lammps_open_wrapper' but may not be C interoperable
|
||||
This happens because lammps_open_wrapper actually takes a Fortran
|
||||
INTEGER argument, whose type is defined by the MPI library itself. The
|
||||
Fortran integer is converted to a C integer by the MPI library (if such
|
||||
conversion is actually necessary).
|
||||
* lammps_extract_global returns COPIES of the (scalar) data, as does the
|
||||
C version.
|
||||
* lammps_extract_atom, lammps_extract_compute, and lammps_extract_fix
|
||||
have a first argument that will be associated with ACTUAL LAMMPS DATA.
|
||||
This means the first argument must be:
|
||||
* The right rank (via the DIMENSION modifier)
|
||||
* A C-interoperable POINTER type (i.e., INTEGER (C_int) or
|
||||
REAL (C_double)).
|
||||
* lammps_extract_variable returns COPIES of the data, as the C library
|
||||
interface does. There is no need to deallocate using lammps_free.
|
||||
* The 'data' argument to lammps_gather_atoms and lammps_scatter atoms must
|
||||
be ALLOCATABLE. It should be of type INTEGER or DOUBLE PRECISION. It
|
||||
does NOT need to be C inter-operable (and indeed should not be).
|
||||
* The 'count' argument of lammps_scatter_atoms is unnecessary; the shape of
|
||||
the array determines the number of elements LAMMPS will read.
|
||||
|
||||
@ -60,19 +60,19 @@ program simple
|
||||
call lammps_command (lmp, 'run 500')
|
||||
|
||||
! This extracts f_2 as a scalar (the last two arguments can be arbitrary)
|
||||
call lammps_extract_fix (fix, lmp, '2', 0, 1, 1, 1)
|
||||
call lammps_extract_fix (fix, lmp, '2', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR, 1, 1)
|
||||
print *, 'Fix is ', fix
|
||||
|
||||
! This extracts f_4[1][1] as a scalar
|
||||
call lammps_extract_fix (fix2, lmp, '4', 0, 2, 1, 1)
|
||||
call lammps_extract_fix (fix2, lmp, '4', LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY, 1, 1)
|
||||
print *, 'Fix 2 is ', fix2
|
||||
|
||||
! This extracts the scalar compute of compute thermo_temp
|
||||
call lammps_extract_compute (compute, lmp, 'thermo_temp', 0, 0)
|
||||
call lammps_extract_compute (compute, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR)
|
||||
print *, 'Compute is ', compute
|
||||
|
||||
! This extracts the vector compute of compute thermo_temp
|
||||
call lammps_extract_compute (compute_v, lmp, 'thermo_temp', 0, 1)
|
||||
call lammps_extract_compute (compute_v, lmp, 'thermo_temp', LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR)
|
||||
print *, 'Vector is ', compute_v
|
||||
|
||||
! This extracts the masses
|
||||
@ -90,6 +90,7 @@ program simple
|
||||
|
||||
! Allocates an array and assigns all positions to it
|
||||
call lammps_gather_atoms (lmp, 'x', 3, r)
|
||||
print *, 'natoms = ', int(lammps_get_natoms(lmp))
|
||||
print *, 'size(r) = ', size(r)
|
||||
print *, 'r is ', r(1:6)
|
||||
|
||||
|
||||
@ -14,3 +14,6 @@ use of the `extra/special/per/atom` keyword
|
||||
* `swm4-ndp` -- 4-site rigid water model in NpT ensemble (no Thole
|
||||
damping)
|
||||
|
||||
* `ethylene_glycol` -- simulation in NpT ensemble with Thole
|
||||
and Tang-Toennies damping and with Nosé-Hoover thermostat
|
||||
|
||||
|
||||
11259
examples/USER/drude/ethylene_glycol/data.ethylene_glycol
Normal file
11259
examples/USER/drude/ethylene_glycol/data.ethylene_glycol
Normal file
File diff suppressed because it is too large
Load Diff
80
examples/USER/drude/ethylene_glycol/in.ethylene_glycol
Normal file
80
examples/USER/drude/ethylene_glycol/in.ethylene_glycol
Normal file
@ -0,0 +1,80 @@
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
|
||||
pair_coeff 1 5 thole 1.662
|
||||
pair_coeff 1 6 thole 1.561
|
||||
pair_coeff 2 2 thole 1.467
|
||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
|
||||
pair_coeff 5 5 thole 1.662
|
||||
pair_coeff 5 6 thole 1.561
|
||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
|
||||
group CORES type 1 2
|
||||
group DRUDES type 5 6
|
||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong &
|
||||
press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
|
||||
@ -0,0 +1,200 @@
|
||||
LAMMPS (24 Aug 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (35.000000 35.000000 35.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2800 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2600 bonds
|
||||
reading angles ...
|
||||
2800 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
13 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.023 seconds
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
|
||||
pair_coeff 1 5 thole 1.662
|
||||
pair_coeff 1 6 thole 1.561
|
||||
pair_coeff 2 2 thole 1.467
|
||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
|
||||
pair_coeff 5 5 thole 1.662
|
||||
pair_coeff 5 6 thole 1.561
|
||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1 2
|
||||
800 atoms in group CORES
|
||||
group DRUDES type 5 6
|
||||
800 atoms in group DRUDES
|
||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
400 = # of size 2 clusters
|
||||
400 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 298 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1428)
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 1 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.41206781
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0040479865
|
||||
estimated relative force accuracy = 1.2190391e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 250047 157464
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 13
|
||||
New max number of 1-2 to 1-4 neighbors: 13 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 7 7 7
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair coul/tt, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 39.43 | 39.43 | 39.43 Mbytes
|
||||
Step TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
0 2707.9246 1420.362 1287.5627 1474.8647 30.734202 -461.31379 540022.21 -539778.93 -9408.4231 42875 0.48077588 298 294.34401 6.9394757
|
||||
50 1418.4664 1249.502 168.96443 309.99547 480.01554 -495.04808 539716.53 -540017.02 3344.2851 42776.949 0.48187789 252.07241 255.56807 12.841403
|
||||
100 1391.631 1287.2692 104.36186 333.86636 427.43215 -456.38003 539638.17 -540023.61 -3962.1786 42668.283 0.48310512 265.74273 268.23371 3.3477444
|
||||
150 1404.7861 1334.1949 70.591169 285.69315 480.49154 -340.69071 539518.01 -540045.75 -2082.9182 42395.713 0.48621109 274.19438 278.9463 1.6008228
|
||||
200 1425.8199 1378.4982 47.321668 460.35813 459.3409 -415.44782 539411.67 -540044.6 6205.8012 42117.045 0.48942811 284.32248 288.46225 1.1474711
|
||||
250 1451.5312 1408.0791 43.452124 376.36315 598.2256 -302.5574 539235.03 -540053.8 -3523.5224 41843.302 0.49263001 290.29735 294.90585 0.66499891
|
||||
300 1460.3317 1532.45 -72.118296 394.63946 561.19451 -334.56109 539192.83 -540050.12 4984.7253 41569.486 0.49587493 316.03909 320.8862 0.85911251
|
||||
350 1465.3219 1564.1529 -98.830958 418.42916 585.9688 -296.62501 539077.24 -540036.78 740.62275 41386.895 0.49806264 322.55774 327.69261 0.54088355
|
||||
400 1446.0613 1528.77 -82.708678 414.47172 582.41623 -279.89537 539064.81 -540045.35 -1758.0709 41241.935 0.49981326 314.95112 320.11103 0.86624717
|
||||
450 1411.6647 1569.3338 -157.66914 380.54196 668.12309 -290.80881 538968.32 -540032.63 3122.7219 41154.153 0.50087936 323.38401 328.46391 1.1709084
|
||||
500 1366.0173 1653.6398 -287.62246 433.22615 598.36853 -281.95956 538837.44 -540025.77 -2920.9274 41080.823 0.50177344 340.53461 346.03932 1.3737011
|
||||
Loop time of 21.2526 on 1 procs for 500 steps with 2800 atoms
|
||||
|
||||
Performance: 2.033 ns/day, 11.807 hours/ns, 23.526 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 | 5.0143 | 5.0143 | 5.0143 | 0.0 | 23.59
|
||||
Bond | 0.34285 | 0.34285 | 0.34285 | 0.0 | 1.61
|
||||
Kspace | 7.6454 | 7.6454 | 7.6454 | 0.0 | 35.97
|
||||
Neigh | 0.36282 | 0.36282 | 0.36282 | 0.0 | 1.71
|
||||
Comm | 0.035159 | 0.035159 | 0.035159 | 0.0 | 0.17
|
||||
Output | 0.00068069 | 0.00068069 | 0.00068069 | 0.0 | 0.00
|
||||
Modify | 7.8451 | 7.8451 | 7.8451 | 0.0 | 36.91
|
||||
Other | | 0.006337 | | | 0.03
|
||||
|
||||
Nlocal: 2800.00 ave 2800 max 2800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6816.00 ave 6816 max 6816 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 446966.0 ave 446966 max 446966 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 446966
|
||||
Ave neighs/atom = 159.63071
|
||||
Ave special neighs/atom = 11.714286
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:21
|
||||
@ -0,0 +1,200 @@
|
||||
LAMMPS (24 Aug 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# created by fftool
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style opls
|
||||
|
||||
special_bonds lj/coul 0.0 0.0 0.5
|
||||
|
||||
pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 coul/tt 4 8.0
|
||||
pair_modify tail yes
|
||||
kspace_style pppm 1.0e-5
|
||||
|
||||
read_data data.ethylene_glycol
|
||||
Reading data file ...
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (35.000000 35.000000 35.000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2800 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
9 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
2600 bonds
|
||||
reading angles ...
|
||||
2800 angles
|
||||
reading dihedrals ...
|
||||
3000 dihedrals
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0.0 0.0 0.5
|
||||
special bond factors coul: 0.0 0.0 0.5
|
||||
5 = max # of 1-2 neighbors
|
||||
6 = max # of 1-3 neighbors
|
||||
10 = max # of 1-4 neighbors
|
||||
13 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.057289 3.500000 # CTO CTO ~
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.091945 3.304542 # CTO OHG ~
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038625 2.958040 # CTO H1O ~
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.000000 0.000000 # CTO HOG ~
|
||||
pair_coeff 2 2 lj/cut/coul/long 0.147565 3.120000 # OHG OHG ~
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.061990 2.792848 # OHG H1O ~
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.000000 0.000000 # OHG HOG ~
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.026041 2.500000 # H1O H1O ~
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.000000 0.000000 # H1O HOG ~
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.000000 0.000000 # HOG HOG ~
|
||||
pair_coeff * 5* lj/cut/coul/long 0.000000 0.000000
|
||||
pair_coeff 1 1 thole 1.662
|
||||
pair_coeff 1 2 thole 1.561
|
||||
pair_coeff 1 5 thole 1.662
|
||||
pair_coeff 1 6 thole 1.561
|
||||
pair_coeff 2 2 thole 1.467
|
||||
pair_coeff 2 5 thole 1.561
|
||||
pair_coeff 2 6 thole 1.467
|
||||
pair_coeff 5 5 thole 1.662
|
||||
pair_coeff 5 6 thole 1.561
|
||||
pair_coeff 6 6 thole 1.467
|
||||
pair_coeff 2 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 6 coul/tt 4.5 1.0
|
||||
pair_coeff 1 4 coul/tt 4.5 1.0
|
||||
pair_coeff 4 5 coul/tt 4.5 1.0
|
||||
|
||||
group ATOMS type 1 2 3 4
|
||||
2000 atoms in group ATOMS
|
||||
group CORES type 1 2
|
||||
800 atoms in group CORES
|
||||
group DRUDES type 5 6
|
||||
800 atoms in group DRUDES
|
||||
|
||||
fix DRUDE all drude C C N N D D
|
||||
|
||||
fix SHAKE ATOMS shake 0.0001 20 0 b 3 4
|
||||
400 = # of size 2 clusters
|
||||
400 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
0 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
timestep 1.0
|
||||
|
||||
variable TK equal 298.0
|
||||
variable TDK equal 1.0
|
||||
variable PBAR equal 1.0
|
||||
|
||||
comm_modify vel yes
|
||||
velocity ATOMS create ${TK} 12345
|
||||
velocity ATOMS create 298 12345
|
||||
|
||||
compute TATOM ATOMS temp
|
||||
compute TDRUDE all temp/drude
|
||||
|
||||
fix DTDIR all drude/transform/direct
|
||||
fix TSTAT ATOMS npt temp ${TK} ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 ${TK} 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso ${PBAR} ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 ${PBAR} 1000
|
||||
fix TSTAT ATOMS npt temp 298 298 200 iso 1 1 1000
|
||||
fix_modify TSTAT temp TATOM press thermo_press
|
||||
WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1428)
|
||||
fix TSTDR DRUDES nvt temp ${TDK} ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 ${TDK} 50
|
||||
fix TSTDR DRUDES nvt temp 1 1 50
|
||||
fix DTINV all drude/transform/inverse
|
||||
|
||||
fix ICECUBE all momentum 1000 linear 1 1 1
|
||||
|
||||
thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
thermo 50
|
||||
|
||||
run 500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
|
||||
G vector (1/distance) = 0.41206781
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0040479865
|
||||
estimated relative force accuracy = 1.2190391e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 81648 40824
|
||||
Rebuild special list taking Drude particles into account
|
||||
Old max number of 1-2 to 1-4 neighbors: 13
|
||||
New max number of 1-2 to 1-4 neighbors: 13 (+0)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
||||
ghost atom cutoff = 10
|
||||
binsize = 5, bins = 7 7 7
|
||||
3 neighbor lists, perpetual/occasional/extra = 3 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) pair thole, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) pair coul/tt, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.28 | 21.36 | 21.43 Mbytes
|
||||
Step TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Density c_TATOM c_TDRUDE[1] c_TDRUDE[2]
|
||||
0 2707.9246 1420.362 1287.5627 1474.8647 30.734202 -461.31379 540022.21 -539778.93 -9408.4231 42875 0.48077588 298 294.34401 6.9394757
|
||||
50 1418.4665 1249.502 168.96445 309.99547 480.01554 -495.04808 539716.53 -540017.02 3344.2849 42776.949 0.48187789 252.07241 255.56807 12.841403
|
||||
100 1391.631 1287.2692 104.36189 333.86638 427.43215 -456.38003 539638.17 -540023.61 -3962.1786 42668.283 0.48310512 265.74272 268.23371 3.3477454
|
||||
150 1404.786 1334.1949 70.59104 285.69317 480.49154 -340.6907 539518.01 -540045.75 -2082.9181 42395.713 0.48621109 274.19439 278.9463 1.6008224
|
||||
200 1425.8201 1378.4982 47.32185 460.35819 459.34089 -415.44783 539411.67 -540044.6 6205.8014 42117.045 0.48942811 284.32247 288.46225 1.1474763
|
||||
250 1451.5312 1408.0791 43.45212 376.3631 598.22557 -302.55737 539235.03 -540053.8 -3523.5218 41843.302 0.49263001 290.29734 294.90584 0.66500219
|
||||
300 1460.3316 1532.4498 -72.118238 394.63949 561.1946 -334.56112 539192.83 -540050.12 4984.7226 41569.486 0.49587493 316.03906 320.88617 0.85911374
|
||||
350 1465.322 1564.1496 -98.827597 418.43029 585.96947 -296.62447 539077.24 -540036.78 740.63702 41386.895 0.49806264 322.55705 327.69192 0.54088385
|
||||
400 1446.0613 1528.7739 -82.712576 414.46626 582.41806 -279.89551 539064.81 -540045.35 -1758.0964 41241.935 0.49981326 314.95192 320.11185 0.86625313
|
||||
450 1411.6627 1569.3001 -157.63739 380.53709 668.13885 -290.80678 538968.36 -540032.62 3122.8773 41154.153 0.50087936 323.37686 328.45689 1.170821
|
||||
500 1366.0164 1653.6078 -287.59139 433.23854 598.39638 -281.95272 538837.43 -540025.77 -2921.1108 41080.827 0.50177339 340.52802 346.03257 1.3738053
|
||||
Loop time of 8.54338 on 4 procs for 500 steps with 2800 atoms
|
||||
|
||||
Performance: 5.057 ns/day, 4.746 hours/ns, 58.525 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1432 | 1.2405 | 1.3019 | 5.3 | 14.52
|
||||
Bond | 0.085337 | 0.091544 | 0.097553 | 1.4 | 1.07
|
||||
Kspace | 4.3889 | 4.4519 | 4.5415 | 2.6 | 52.11
|
||||
Neigh | 0.098468 | 0.098565 | 0.098639 | 0.0 | 1.15
|
||||
Comm | 0.090891 | 0.096061 | 0.102 | 1.3 | 1.12
|
||||
Output | 0.00051045 | 0.00081128 | 0.0016632 | 0.0 | 0.01
|
||||
Modify | 2.549 | 2.5525 | 2.5554 | 0.1 | 29.88
|
||||
Other | | 0.01154 | | | 0.14
|
||||
|
||||
Nlocal: 700.000 ave 721 max 665 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 4229.75 ave 4342 max 4122 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 111742.0 ave 117831 max 101992 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 446967
|
||||
Ave neighs/atom = 159.63107
|
||||
Ave special neighs/atom = 11.714286
|
||||
Neighbor list builds = 28
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:08
|
||||
@ -16,8 +16,8 @@
|
||||
! and library.h using the ISO_C_BINDING module of the Fortran compiler.
|
||||
!
|
||||
! Based on the LAMMPS Fortran 2003 module contributed by:
|
||||
! Karl D. Hammond <karlh@ugcs.caltech.edu>
|
||||
! University of Tennessee, Knoxville (USA), 2012
|
||||
! Karl D. Hammond <hammondkd@missouri.edu>
|
||||
! University of Missouri, 2012-2020
|
||||
!
|
||||
! The Fortran module tries to follow the API of the C-library interface
|
||||
! closely, but like the Python wrapper it employs an object oriented
|
||||
@ -30,7 +30,7 @@
|
||||
MODULE LIBLAMMPS
|
||||
|
||||
USE, INTRINSIC :: ISO_C_BINDING, ONLY: c_ptr, c_null_ptr, c_loc, &
|
||||
c_int, c_char, c_null_char, c_double
|
||||
c_int, c_char, c_null_char, c_double, c_size_t, c_f_pointer
|
||||
|
||||
IMPLICIT NONE
|
||||
PRIVATE
|
||||
@ -114,6 +114,12 @@ MODULE LIBLAMMPS
|
||||
TYPE(c_ptr), VALUE :: str
|
||||
END SUBROUTINE lammps_commands_string
|
||||
|
||||
FUNCTION lammps_malloc(size) BIND(C, name='malloc')
|
||||
IMPORT :: c_ptr, c_size_t
|
||||
INTEGER(c_size_t), value :: size
|
||||
TYPE(c_ptr) :: lammps_malloc
|
||||
END FUNCTION lammps_malloc
|
||||
|
||||
SUBROUTINE lammps_free(ptr) BIND(C, name='lammps_free')
|
||||
IMPORT :: c_ptr
|
||||
TYPE(c_ptr), VALUE :: ptr
|
||||
@ -267,14 +273,14 @@ CONTAINS
|
||||
CHARACTER (len=*), INTENT(in) :: f_string
|
||||
CHARACTER (len=1, kind=c_char), POINTER :: c_string(:)
|
||||
TYPE(c_ptr) :: ptr
|
||||
INTEGER :: i, n
|
||||
INTEGER(c_size_t) :: i, n
|
||||
|
||||
n = LEN_TRIM(f_string)
|
||||
ALLOCATE(c_string(n+1))
|
||||
ptr = lammps_malloc(n+1)
|
||||
CALL C_F_POINTER(ptr,c_string,[1])
|
||||
DO i=1,n
|
||||
c_string(i) = f_string(i:i)
|
||||
END DO
|
||||
c_string(n+1) = c_null_char
|
||||
ptr = c_loc(c_string(1))
|
||||
END FUNCTION f2c_string
|
||||
END MODULE LIBLAMMPS
|
||||
|
||||
@ -7,6 +7,7 @@ features:
|
||||
using Langevin or Nosé-Hoover thermostats
|
||||
* computation of the atom and dipole temperatures
|
||||
* damping induced dipole interactions using Thole's function
|
||||
* charge-dipole damping using Tang-Toennies function
|
||||
|
||||
See the file doc/drude_tutorial.html for getting started.
|
||||
|
||||
@ -18,4 +19,5 @@ The person who created this package is Alain Dequidt at the
|
||||
Chemistry Institute of Clermont-Ferrand, Clermont University, France
|
||||
(alain.dequidt at uca.fr). Contact him directly if you have questions.
|
||||
Co-authors: Julien Devémy, Agilio Padua.
|
||||
Contributors: Kateryna Goloviznina, Zheng Gong.
|
||||
|
||||
|
||||
446
src/USER-DRUDE/pair_coul_tt.cpp
Normal file
446
src/USER-DRUDE/pair_coul_tt.cpp
Normal file
@ -0,0 +1,446 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_coul_tt.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "fix.h"
|
||||
#include "fix_drude.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "error.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairCoulTT::PairCoulTT(LAMMPS *lmp) : Pair(lmp) {
|
||||
fix_drude = nullptr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairCoulTT::~PairCoulTT()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
memory->destroy(b);
|
||||
memory->destroy(c);
|
||||
memory->destroy(ntt);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(scale);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qi,qj,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
|
||||
double r,rsq,r2inv,rinv,factor_coul;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
double factor_f,factor_e;
|
||||
int di,dj;
|
||||
double dcoul;
|
||||
double beta, gamma, betaprime, gammaprime, gammatmp;
|
||||
|
||||
ecoul = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
int *drudetype = fix_drude->drudetype;
|
||||
tagint *drudeid = fix_drude->drudeid;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
|
||||
qi = q[i];
|
||||
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
if (drudetype[type[i]] == drudetype[type[j]] && drudetype[type[j]] != CORE_TYPE)
|
||||
continue;
|
||||
|
||||
qj = q[j];
|
||||
|
||||
if (drudetype[type[i]] == CORE_TYPE) {
|
||||
di = domain->closest_image(i, atom->map(drudeid[i]));
|
||||
if (di == j)
|
||||
continue;
|
||||
switch (drudetype[type[j]]) {
|
||||
case DRUDE_TYPE:
|
||||
qi = q[i]+q[di];
|
||||
break;
|
||||
case NOPOL_TYPE:
|
||||
qi = -q[di];
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (drudetype[type[j]] == CORE_TYPE) {
|
||||
dj = domain->closest_image(j, atom->map(drudeid[j]));
|
||||
if (dj == i)
|
||||
continue;
|
||||
switch (drudetype[type[i]]) {
|
||||
case DRUDE_TYPE:
|
||||
qj = q[j]+q[dj];
|
||||
break;
|
||||
case NOPOL_TYPE:
|
||||
qj = -q[dj];
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
rinv = sqrt(r2inv);
|
||||
|
||||
r = sqrt(rsq);
|
||||
beta = c[itype][jtype] * exp(-b[itype][jtype] * r);
|
||||
betaprime = -b[itype][jtype] * beta;
|
||||
gamma = 1.0 + b[itype][jtype] * r;
|
||||
gammaprime = b[itype][jtype];
|
||||
gammatmp = 1.0;
|
||||
for (int k = 2; k <= ntt[itype][jtype]; k++) {
|
||||
gammatmp *= b[itype][jtype] * r / k;
|
||||
gamma += gammatmp * b[itype][jtype] * r;
|
||||
gammaprime += gammatmp * b[itype][jtype] * k;
|
||||
}
|
||||
|
||||
if (drudetype[type[i]] == CORE_TYPE && drudetype[type[j]] == CORE_TYPE)
|
||||
dcoul = qqrd2e * ( -(q[i]+q[di])*q[dj] - q[di]*(q[j]+q[dj]) ) * scale[itype][jtype] * rinv;
|
||||
else
|
||||
dcoul = qqrd2e * qi * qj *scale[itype][jtype] * rinv;
|
||||
|
||||
factor_f = (-beta*gamma + r*betaprime*gamma + r*beta*gammaprime)*factor_coul;
|
||||
if(eflag) factor_e = - beta*gamma*factor_coul;
|
||||
fpair = factor_f * dcoul * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag)
|
||||
ecoul = factor_e * dcoul;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
0.0,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(scale,n+1,n+1,"pair:scale");
|
||||
memory->create(b, n + 1, n + 1, "pair:b");
|
||||
memory->create(c, n + 1, n + 1, "pair:c");
|
||||
memory->create(ntt, n + 1, n + 1, "pair:ntt");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 2) error->all(FLERR, "Illegal pair_style command");
|
||||
|
||||
n_global = utils::inumeric(FLERR,arg[0],false,lmp);
|
||||
cut_global = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) {
|
||||
ntt[i][j] = n_global;
|
||||
cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 3 || narg > 6)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
|
||||
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
|
||||
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
|
||||
|
||||
double b_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double c_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
int n_one = n_global;
|
||||
double cut_one = cut_global;
|
||||
if (narg >= 5) n_one = utils::inumeric(FLERR,arg[4],false,lmp);
|
||||
if (narg == 6) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
|
||||
if (n_one > n_global)
|
||||
error->all(FLERR, "Incorrect coefficients for pair style coul/tt: n should not be larger than global setting");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
b[i][j] = b_one;
|
||||
c[i][j] = c_one;
|
||||
ntt[i][j] = n_one;
|
||||
cut[i][j] = cut_one;
|
||||
scale[i][j] = 1.0;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style coul/tt requires atom attribute q");
|
||||
int ifix;
|
||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||
if (utils::strmatch(modify->fix[ifix]->style,"^drude")) break;
|
||||
if (ifix == modify->nfix) error->all(FLERR, "Pair coul/tt requires fix drude");
|
||||
fix_drude = (FixDrude *) modify->fix[ifix];
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairCoulTT::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0)
|
||||
cut[i][j] = mix_distance(cut[i][i], cut[j][j]);
|
||||
|
||||
b[j][i] = b[i][j];
|
||||
c[j][i] = c[i][j];
|
||||
ntt[j][i] = ntt[i][j];
|
||||
scale[j][i] = scale[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&b[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&c[i][j], sizeof(double), 1, fp);
|
||||
fwrite(&ntt[i][j], sizeof(int), 1, fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
utils::sfread(FLERR,&b[i][j],sizeof(double),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&c[i][j],sizeof(double),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&ntt[i][j],sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
|
||||
}
|
||||
MPI_Bcast(&b[i][j], 1, MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&c[i][j], 1, MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&ntt[i][j], 1, MPI_INT,0,world);
|
||||
MPI_Bcast(&cut[i][j],1, MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&n_global, sizeof(int), 1, fp);
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairCoulTT::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&n_global,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
|
||||
}
|
||||
MPI_Bcast(&n_global, 1, MPI_INT, 0, world);
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairCoulTT::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double /*factor_lj*/,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,rinv,r,phicoul;
|
||||
double qi,qj,factor_f,factor_e,dcoul;
|
||||
double beta, betaprime, gamma, gammaprime, gammatmp;
|
||||
|
||||
// single() is used in Pair::write_file where there is no information about topology
|
||||
// it corresponds to pair_write command in input file
|
||||
// charges qi and qj are defined by the user (or 1.0 by defaut)
|
||||
|
||||
qi = atom->q[i];
|
||||
qj = atom->q[j];
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
fforce = phicoul = 0.0;
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
rinv = sqrt(r2inv);
|
||||
r = sqrt(rsq);
|
||||
beta = c[itype][jtype] * exp(-b[itype][jtype] * r);
|
||||
betaprime = -b[itype][jtype] * beta;
|
||||
gamma = 1 + b[itype][jtype] * r;
|
||||
gammaprime = b[itype][jtype];
|
||||
gammatmp = 1;
|
||||
for (int k = 2; k <= ntt[itype][jtype]; k++) {
|
||||
gammatmp *= b[itype][jtype] * r / k;
|
||||
gamma += gammatmp * b[itype][jtype] * r;
|
||||
gammaprime += gammatmp * b[itype][jtype] * k;
|
||||
}
|
||||
dcoul = force->qqrd2e * qi * qj * scale[itype][jtype] * rinv;
|
||||
factor_f = (-beta*gamma+r*betaprime*gamma+r*beta*gammaprime)*factor_coul;
|
||||
fforce = factor_f * dcoul * r2inv;
|
||||
factor_e = - beta*gamma*factor_coul;
|
||||
phicoul = factor_e * dcoul;
|
||||
}
|
||||
|
||||
return phicoul;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairCoulTT::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"scale") == 0) return (void *) scale;
|
||||
if (strcmp(str,"b") == 0) return (void *) b;
|
||||
if (strcmp(str,"c") == 0) return (void *) c;
|
||||
if (strcmp(str,"ntt") == 0) return (void *) ntt;
|
||||
return nullptr;
|
||||
}
|
||||
75
src/USER-DRUDE/pair_coul_tt.h
Normal file
75
src/USER-DRUDE/pair_coul_tt.h
Normal file
@ -0,0 +1,75 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(coul/tt,PairCoulTT)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_COULTT_H
|
||||
#define LMP_PAIR_COULTT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairCoulTT: public Pair {
|
||||
public:
|
||||
PairCoulTT(class LAMMPS *);
|
||||
virtual ~PairCoulTT();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
int n_global;
|
||||
double cut_global;
|
||||
double **cut,**scale;
|
||||
double **b,**c;
|
||||
int **ntt;
|
||||
class FixDrude * fix_drude;
|
||||
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style thole requires atom attribute q
|
||||
|
||||
The atom style defined does not have these attributes.
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user