Merge branch 'lammps:develop' into fortran-tinkering
This commit is contained in:
hammondkd
@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
|
|||||||
pkg_depends(CG-DNA MOLECULE)
|
pkg_depends(CG-DNA MOLECULE)
|
||||||
pkg_depends(CG-DNA ASPHERE)
|
pkg_depends(CG-DNA ASPHERE)
|
||||||
pkg_depends(ELECTRODE KSPACE)
|
pkg_depends(ELECTRODE KSPACE)
|
||||||
|
pkg_depends(EXTRA-MOLECULE MOLECULE)
|
||||||
|
|
||||||
# detect if we may enable OpenMP support by default
|
# detect if we may enable OpenMP support by default
|
||||||
set(BUILD_OMP_DEFAULT OFF)
|
set(BUILD_OMP_DEFAULT OFF)
|
||||||
|
|||||||
@ -6,13 +6,10 @@ else()
|
|||||||
endif()
|
endif()
|
||||||
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
|
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
if(DOWNLOAD_MDI)
|
if(DOWNLOAD_MDI)
|
||||||
message(STATUS "MDI download requested - we will build our own")
|
message(STATUS "MDI download requested - we will build our own")
|
||||||
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.10.tar.gz" CACHE STRING "URL for MDI tarball")
|
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
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||||||
set(MDI_MD5 "1c203b7fd462d9934834f643f09f3c06" CACHE STRING "MD5 checksum for MDI tarball")
|
set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
|
||||||
mark_as_advanced(MDI_URL)
|
mark_as_advanced(MDI_URL)
|
||||||
mark_as_advanced(MDI_MD5)
|
mark_as_advanced(MDI_MD5)
|
||||||
enable_language(C)
|
enable_language(C)
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||||||
|
|||||||
@ -3,6 +3,13 @@
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|||||||
# prefer flang over gfortran, if available
|
# prefer flang over gfortran, if available
|
||||||
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
|
find_program(CLANG_FORTRAN NAMES flang gfortran f95)
|
||||||
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
|
set(ENV{OMPI_FC} ${CLANG_FORTRAN})
|
||||||
|
get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
|
||||||
|
if (_tmp_fc STREQUAL "flang")
|
||||||
|
set(FC_STD_VERSION "-std=f2018")
|
||||||
|
set(BUILD_MPI OFF)
|
||||||
|
else()
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||||||
|
set(FC_STD_VERSION "-std=f2003")
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||||||
|
endif()
|
||||||
|
|
||||||
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
|
set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
|
set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
|
||||||
@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
|
|||||||
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
|
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
|
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
|
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
|
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
|
||||||
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
|
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
|
||||||
|
|||||||
@ -932,6 +932,10 @@ EXTRA-MOLECULE package
|
|||||||
|
|
||||||
Additional bond, angle, dihedral, and improper styles that are less commonly used.
|
Additional bond, angle, dihedral, and improper styles that are less commonly used.
|
||||||
|
|
||||||
|
**Install:**
|
||||||
|
|
||||||
|
To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
|
||||||
|
|
||||||
**Supporting info:**
|
**Supporting info:**
|
||||||
|
|
||||||
* src/EXTRA-MOLECULE: filenames -> commands
|
* src/EXTRA-MOLECULE: filenames -> commands
|
||||||
|
|||||||
@ -176,6 +176,31 @@ extra buffering.
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
.. versionadded:: 4May2022
|
||||||
|
|
||||||
|
The *colname* keyword can be used to change the default header keyword
|
||||||
|
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
|
||||||
|
and MPIIO variants. The setting for *ID string* replaces the default
|
||||||
|
text with the provided string. *ID* can be a positive integer when it
|
||||||
|
represents the column number counting from the left, a negative integer
|
||||||
|
when it represents the column number from the right (i.e. -1 is the last
|
||||||
|
column/keyword), or a custom dump keyword (or compute, fix, property, or
|
||||||
|
variable reference) and then it replaces the string for that specific
|
||||||
|
keyword. For *atom* dump styles only the keywords "id", "type", "x",
|
||||||
|
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
|
||||||
|
whether scaled or unwrapped coordinates were enabled or disabled, and
|
||||||
|
it always assumes 8 columns for indexing regardless of whether image
|
||||||
|
flags are enabled or not. For dump style *cfg* only changes to the
|
||||||
|
"auxiliary" keywords (6th or later keyword) will become visible.
|
||||||
|
|
||||||
|
The *colname* keyword can be used multiple times. If multiple *colname*
|
||||||
|
settings refer to the same keyword, the last setting has precedence. A
|
||||||
|
setting of *default* clears all previous settings, reverting all values
|
||||||
|
to their default names. Using the *scale* or *image* keyword will also
|
||||||
|
reset all header keywords to their default values.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
The *delay* keyword applies to all dump styles. No snapshots will be
|
The *delay* keyword applies to all dump styles. No snapshots will be
|
||||||
output until the specified *Dstep* timestep or later. Specifying
|
output until the specified *Dstep* timestep or later. Specifying
|
||||||
*Dstep* < 0 is the same as turning off the delay setting. This is a
|
*Dstep* < 0 is the same as turning off the delay setting. This is a
|
||||||
@ -365,7 +390,7 @@ always occur if the current timestep is a multiple of $N$, the
|
|||||||
frequency specified in the :doc:`dump <dump>` command or
|
frequency specified in the :doc:`dump <dump>` command or
|
||||||
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
|
:doc:`dump_modify every <dump_modify>` command, including timestep 0.
|
||||||
It will also always occur if the current simulation time is a multiple
|
It will also always occur if the current simulation time is a multiple
|
||||||
of *Delta*, the time interval specified in the doc:`dump_modify
|
of *Delta*, the time interval specified in the :doc:`dump_modify
|
||||||
every/time <dump_modify>` command.
|
every/time <dump_modify>` command.
|
||||||
|
|
||||||
But if this is not the case, a dump snapshot will only be written if
|
But if this is not the case, a dump snapshot will only be written if
|
||||||
@ -373,7 +398,7 @@ the setting of this keyword is *yes*\ . If it is *no*, which is the
|
|||||||
default, then it will not be written.
|
default, then it will not be written.
|
||||||
|
|
||||||
Note that if the argument to the :doc:`dump_modify every
|
Note that if the argument to the :doc:`dump_modify every
|
||||||
<dump_modify>` doc:`dump_modify every/time <dump_modify>` commands is
|
<dump_modify>` :doc:`dump_modify every/time <dump_modify>` commands is
|
||||||
a variable and not a numeric value, then specifying *first yes* is the
|
a variable and not a numeric value, then specifying *first yes* is the
|
||||||
only way to write a dump snapshot on the first timestep after the dump
|
only way to write a dump snapshot on the first timestep after the dump
|
||||||
command is invoked.
|
command is invoked.
|
||||||
@ -388,30 +413,6 @@ performed with dump style *xtc*\ .
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. versionadded:: 4May2022
|
|
||||||
|
|
||||||
The *colname* keyword can be used to change the default header keyword
|
|
||||||
for dump styles: *atom*, *custom*, and *cfg* and their compressed, ADIOS,
|
|
||||||
and MPIIO variants. The setting for *ID string* replaces the default
|
|
||||||
text with the provided string. *ID* can be a positive integer when it
|
|
||||||
represents the column number counting from the left, a negative integer
|
|
||||||
when it represents the column number from the right (i.e. -1 is the last
|
|
||||||
column/keyword), or a custom dump keyword (or compute, fix, property, or
|
|
||||||
variable reference) and then it replaces the string for that specific
|
|
||||||
keyword. For *atom* dump styles only the keywords "id", "type", "x",
|
|
||||||
"y", "z", "ix", "iy", "iz" can be accessed via string regardless of
|
|
||||||
whether scaled or unwrapped coordinates were enabled or disabled, and
|
|
||||||
it always assumes 8 columns for indexing regardless of whether image
|
|
||||||
flags are enabled or not. For dump style *cfg* only changes to the
|
|
||||||
"auxiliary" keywords (6th or later keyword) will become visible.
|
|
||||||
|
|
||||||
The *colname* keyword can be used multiple times. If multiple *colname*
|
|
||||||
settings refer to the same keyword, the last setting has precedence. A
|
|
||||||
setting of *default* clears all previous settings, reverting all values
|
|
||||||
to their default names.
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
The *format* keyword can be used to change the default numeric format output
|
The *format* keyword can be used to change the default numeric format output
|
||||||
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
|
by the text-based dump styles: *atom*, *local*, *custom*, *cfg*, and
|
||||||
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
|
*xyz* styles, and their MPIIO variants. Only the *line* or *none*
|
||||||
@ -498,6 +499,8 @@ boundary twice and is really two box lengths to the left of its
|
|||||||
current coordinate. Note that for dump style *custom* these various
|
current coordinate. Note that for dump style *custom* these various
|
||||||
values can be printed in the dump file by using the appropriate atom
|
values can be printed in the dump file by using the appropriate atom
|
||||||
attributes in the dump command itself.
|
attributes in the dump command itself.
|
||||||
|
Using this keyword will reset all custom header names set with
|
||||||
|
*dump_modify colname* to their respective default values.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -671,6 +674,8 @@ value of *yes* means atom coords are written in normalized units from
|
|||||||
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
(tilted), then all atom coords will still be between 0.0 and 1.0. A
|
||||||
value of *no* means they are written in absolute distance units
|
value of *no* means they are written in absolute distance units
|
||||||
(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
|
(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`).
|
||||||
|
Using this keyword will reset all custom header names set with
|
||||||
|
*dump_modify colname* to their respective default values.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -8,18 +8,27 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
fix ID group-ID latte peID
|
fix ID group-ID latte keyword value ...
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* latte = style name of this fix command
|
* latte = style name of this fix command
|
||||||
* peID = NULL or ID of compute used to calculate per-atom energy
|
* zero or more keyword/value pairs may be appended
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
keyword = *coulomb* or *exclude*
|
||||||
|
*coulomb* value = peID
|
||||||
|
peID = ID of compute used to calculate per-atom energy
|
||||||
|
*exclude* value = fixID
|
||||||
|
fixID = ID of fix which potentially excludes atoms before calling LATTE
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix dftb all latte NULL
|
fix dftb all latte
|
||||||
|
fix dftb all exclude GCMC
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
@ -48,10 +57,41 @@ found in examples/latte.
|
|||||||
|
|
||||||
A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
|
A step-by-step tutorial can be followed at: `LAMMPS-LATTE tutorial <https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS>`_
|
||||||
|
|
||||||
The *peID* argument is not yet supported by fix latte, so it must be
|
Currently, LAMMPS must be run in serial or as a single MPI task, to
|
||||||
specified as NULL. Eventually it will be used to enable LAMMPS to
|
use this fix. This is because the version of the LATTE library LAMMPS
|
||||||
calculate a Coulomb potential as an alternative to LATTE performing
|
uses does not support MPI. On the LAMMPS size, this is typically not
|
||||||
the calculation.
|
a bottleneck, since LATTE will be doing 99% or more of the work to
|
||||||
|
compute quantum-accurate forces. On the LATTE side, the LATTE library
|
||||||
|
does support threaded parallelism via OpenMP. You must build the
|
||||||
|
LATTE library with OpenMP support, then set the OMP_NUM_THREADS
|
||||||
|
environment variable before performing a LAMMPS + LATTE simulation to
|
||||||
|
tell LATTE how many threads to invoke.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
NEB calculations can be done using this fix using multiple
|
||||||
|
replicas and running LAMMPS in parallel. However, each replica must
|
||||||
|
be run on a single MPI task. For details, see the :doc:`neb <neb>`
|
||||||
|
command page and the :doc:`-partition command-line switch <Run_options>`
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
The *coulomb* argument is not yet supported by fix latte (as of Sept
|
||||||
|
2022). Eventually it will be used to enable LAMMPS to calculate a
|
||||||
|
Coulomb potential as an alternative to LATTE performing the
|
||||||
|
calculation.
|
||||||
|
|
||||||
|
The *exclude* argument allows this fix to work in tandem with another
|
||||||
|
fix which may decide to delete one or more atoms of molecules. The
|
||||||
|
specified fixID is the ID of the other fix.
|
||||||
|
|
||||||
|
The one current example of such a fix is the :doc:`fix gcmc
|
||||||
|
<fix_gcmc>` command which performs Monte Carlo insertions and
|
||||||
|
deletions. If a trial deletion is performed, then LAMMPS needs to
|
||||||
|
only pass LATTE the atoms which remain. Fix gcmc does not actually
|
||||||
|
remove any atoms until after the new energy is computed (in this case
|
||||||
|
by LATTE), and a Monte Carlo accept/reject decision is made for the
|
||||||
|
trial deletion.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -153,18 +193,8 @@ use this fix.
|
|||||||
|
|
||||||
LATTE does not currently compute per-atom energy or per-atom virial
|
LATTE does not currently compute per-atom energy or per-atom virial
|
||||||
contributions. So they will not show up as part of the calculations
|
contributions. So they will not show up as part of the calculations
|
||||||
performed by the :doc:`compute pe/atom <compute_pe_atom>` or :doc:`compute stress/atom <compute_stress_atom>` commands.
|
performed by the :doc:`compute pe/atom <compute_pe_atom>` or
|
||||||
|
:doc:`compute stress/atom <compute_stress_atom>` commands.
|
||||||
Currently, LAMMPS must be run in serial or as a single MPI task, to
|
|
||||||
use this fix. This is typically not a bottleneck, since LATTE will be
|
|
||||||
doing 99% or more of the work to compute quantum-accurate forces.
|
|
||||||
|
|
||||||
.. note::
|
|
||||||
|
|
||||||
NEB calculations can be done using this fix using multiple
|
|
||||||
replicas and running LAMMPS in parallel. However, each replica must
|
|
||||||
be run on a single MPI task. For details, see the :doc:`neb <neb>`
|
|
||||||
command page and the :doc:`-partition command-line switch <Run_options>`
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|||||||
@ -86,6 +86,8 @@ This command must come after the simulation box is defined by a
|
|||||||
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
|
||||||
:doc:`create_box <create_box>` command.
|
:doc:`create_box <create_box>` command.
|
||||||
|
|
||||||
|
Label maps are currently not supported when using the KOKKOS package.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
|
|||||||
@ -249,7 +249,7 @@ Style *lj/long/dipole/long* has the same functionality as style
|
|||||||
*lj/cut/dipole/long*, except it also has an option to compute 12/6
|
*lj/cut/dipole/long*, except it also has an option to compute 12/6
|
||||||
Lennard-Jones interactions for use with a long-range dispersion kspace
|
Lennard-Jones interactions for use with a long-range dispersion kspace
|
||||||
style. This is done by setting its *flag_lj* argument to *long*. For
|
style. This is done by setting its *flag_lj* argument to *long*. For
|
||||||
long-range LJ interactions, the doc:`kspace_style ewald/disp
|
long-range LJ interactions, the :doc:`kspace_style ewald/disp
|
||||||
<kspace_style>` command must be used.
|
<kspace_style>` command must be used.
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|||||||
@ -81,12 +81,12 @@ only the global settings in that command are reset. Any previous
|
|||||||
doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify <pair_modify>`
|
doc:`pair_coeff <pair_coeff>` and :doc:`pair_modify <pair_modify>`
|
||||||
command settings are preserved. The only exception is that if the
|
command settings are preserved. The only exception is that if the
|
||||||
global cutoff in the pair_style command is changed, it will override
|
global cutoff in the pair_style command is changed, it will override
|
||||||
the corresponding cutoff in any of the previous doc:`pair_modify
|
the corresponding cutoff in any of the previous :doc:`pair_modify
|
||||||
<pair_coeff>` commands.
|
<pair_coeff>` commands.
|
||||||
|
|
||||||
Two pair styles which do not follow this rule are the pair_style
|
Two pair styles which do not follow this rule are the pair_style
|
||||||
*table* and *hybrid* commands. A new pair_style command for these
|
*table* and *hybrid* commands. A new pair_style command for these
|
||||||
styles will wipe out all previously specified doc:`pair_coeff
|
styles will wipe out all previously specified :doc:`pair_coeff
|
||||||
<pair_coeff>` and :doc:`pair_modify <pair_modify>` settings, including
|
<pair_coeff>` and :doc:`pair_modify <pair_modify>` settings, including
|
||||||
for the sub-styles of the *hybrid* command.
|
for the sub-styles of the *hybrid* command.
|
||||||
|
|
||||||
|
|||||||
@ -1519,11 +1519,14 @@ To read gzipped data files, you must compile LAMMPS with the
|
|||||||
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
|
-DLAMMPS_GZIP option. See the :doc:`Build settings <Build_settings>`
|
||||||
doc page for details.
|
doc page for details.
|
||||||
|
|
||||||
|
Label maps are currently not supported when using the KOKKOS package.
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`read_dump <read_dump>`, :doc:`read_restart <read_restart>`,
|
:doc:`read_dump <read_dump>`, :doc:`read_restart <read_restart>`,
|
||||||
:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`
|
:doc:`create_atoms <create_atoms>`, :doc:`write_data <write_data>`,
|
||||||
|
:doc:`labelmap <labelmap>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -12,7 +12,7 @@ Syntax
|
|||||||
restart N root keyword value ...
|
restart N root keyword value ...
|
||||||
restart N file1 file2 keyword value ...
|
restart N file1 file2 keyword value ...
|
||||||
|
|
||||||
* N = write a restart file on timesteps which are multipls of N
|
* N = write a restart file on timesteps which are multiples of N
|
||||||
* N can be a variable (see below)
|
* N can be a variable (see below)
|
||||||
* root = filename to which timestep # is appended
|
* root = filename to which timestep # is appended
|
||||||
* file1,file2 = two full filenames, toggle between them when writing file
|
* file1,file2 = two full filenames, toggle between them when writing file
|
||||||
|
|||||||
@ -54,7 +54,19 @@ Building 3 codes needed to run these examples
|
|||||||
(3) Build LAMMPS with its MDI package
|
(3) Build LAMMPS with its MDI package
|
||||||
also with the MOLECULE package for these example scripts
|
also with the MOLECULE package for these example scripts
|
||||||
|
|
||||||
Build with CMake (NOTE: do not use traditional make for this use case)
|
Build with traditional make
|
||||||
|
|
||||||
|
% cd lammps/lib/mdi
|
||||||
|
% python Install.py -m mpi # downloads and builds MDI
|
||||||
|
% cd ../../src
|
||||||
|
% make yes-mdi yes-molecule
|
||||||
|
$ make mpi # creates lmp_mpi
|
||||||
|
|
||||||
|
% mkdir build; cd build
|
||||||
|
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
|
||||||
|
% make # creates lmp
|
||||||
|
|
||||||
|
Build with CMake
|
||||||
|
|
||||||
% cd lammps
|
% cd lammps
|
||||||
% mkdir build; cd build
|
% mkdir build; cd build
|
||||||
@ -63,7 +75,7 @@ Build with CMake (NOTE: do not use traditional make for this use case)
|
|||||||
|
|
||||||
(4) Copy LAMMPS and LATTE executables into this dir
|
(4) Copy LAMMPS and LATTE executables into this dir
|
||||||
|
|
||||||
Copy the LAMMPS executable into this dir as lmp_mpi.
|
Copy the LAMMPS executable (lmp_mpi or lmp) into this dir as lmp_mpi.
|
||||||
Copy the LATTE executable LATTE_DOUBLE into this dir.
|
Copy the LATTE executable LATTE_DOUBLE into this dir.
|
||||||
The run commands below assume you have done this.
|
The run commands below assume you have done this.
|
||||||
|
|
||||||
|
|||||||
@ -1,35 +1,35 @@
|
|||||||
# Simple water model with LATTE
|
# Simple water model with LATTE
|
||||||
|
|
||||||
units metal
|
units metal
|
||||||
atom_style full
|
atom_style full
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
read_data data.graphene
|
read_data data.graphene
|
||||||
|
|
||||||
# replicate system if requested
|
# replicate system if requested
|
||||||
|
|
||||||
variable x index 1
|
variable x index 1
|
||||||
variable y index 1
|
variable y index 1
|
||||||
variable z index 1
|
variable z index 1
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
variable nrep equal v_x*v_y*v_z
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
# initialize system
|
# initialize system
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
timestep 0.00025
|
timestep 0.00025
|
||||||
|
|
||||||
fix 1 all box/relax iso 0.0 vmax 0.001
|
fix 1 all box/relax iso 0.0 vmax 0.001
|
||||||
|
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom etotal
|
thermo_style custom etotal
|
||||||
@ -9,7 +9,7 @@ read_data data.water
|
|||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
@ -17,7 +17,7 @@ neigh_modify every 1 delay 0 check yes
|
|||||||
timestep 0.00025
|
timestep 0.00025
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
thermo_style custom step temp pe etotal press
|
||||||
@ -44,7 +44,7 @@ read_data data.ch4
|
|||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
@ -53,7 +53,7 @@ timestep 0.00025
|
|||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
thermo_style custom step temp pe etotal press
|
||||||
|
|||||||
@ -1,40 +0,0 @@
|
|||||||
# simple sucrose model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.sucrose
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
@ -1,35 +1,35 @@
|
|||||||
# simple sucrose model with LATTE
|
# simple sucrose model with LATTE
|
||||||
|
|
||||||
units metal
|
units metal
|
||||||
atom_style full
|
atom_style full
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
read_data data.sucrose
|
read_data data.sucrose
|
||||||
|
|
||||||
# replicate system if requested
|
# replicate system if requested
|
||||||
|
|
||||||
variable x index 1
|
variable x index 1
|
||||||
variable y index 1
|
variable y index 1
|
||||||
variable z index 1
|
variable z index 1
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
variable nrep equal v_x*v_y*v_z
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
# initialize system
|
# initialize system
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
timestep 0.00025
|
timestep 0.00025
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
thermo_style custom step temp pe etotal press
|
||||||
@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press
|
|||||||
# dynamics
|
# dynamics
|
||||||
|
|
||||||
thermo 10
|
thermo 10
|
||||||
run 100
|
run 100
|
||||||
|
|||||||
@ -1,40 +0,0 @@
|
|||||||
# simple water model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.water
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
@ -1,35 +1,35 @@
|
|||||||
# simple water model with LATTE
|
# simple water model with LATTE
|
||||||
|
|
||||||
units metal
|
units metal
|
||||||
atom_style full
|
atom_style full
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
read_data data.water
|
read_data data.water
|
||||||
|
|
||||||
# replicate system if requested
|
# replicate system if requested
|
||||||
|
|
||||||
variable x index 1
|
variable x index 1
|
||||||
variable y index 1
|
variable y index 1
|
||||||
variable z index 1
|
variable z index 1
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
variable nrep equal v_x*v_y*v_z
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
# initialize system
|
# initialize system
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
timestep 0.00025
|
timestep 0.00025
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
thermo_style custom step temp pe etotal press
|
||||||
@ -37,4 +37,4 @@ thermo_style custom step temp pe etotal press
|
|||||||
# dynamics
|
# dynamics
|
||||||
|
|
||||||
thermo 10
|
thermo 10
|
||||||
run 100
|
run 100
|
||||||
|
|||||||
@ -1,35 +1,35 @@
|
|||||||
# simple water model with LATTE
|
# simple water model with LATTE
|
||||||
|
|
||||||
units metal
|
units metal
|
||||||
atom_style full
|
atom_style full
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
read_data data.water
|
read_data data.water
|
||||||
|
|
||||||
# replicate system if requested
|
# replicate system if requested
|
||||||
|
|
||||||
variable x index 1
|
variable x index 1
|
||||||
variable y index 1
|
variable y index 1
|
||||||
variable z index 1
|
variable z index 1
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
variable nrep equal v_x*v_y*v_z
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
# initialize system
|
# initialize system
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
pair_style zero 1.0
|
pair_style zero 1.0
|
||||||
pair_coeff * *
|
pair_coeff * *
|
||||||
|
|
||||||
neighbor 1.0 bin
|
neighbor 1.0 bin
|
||||||
neigh_modify every 1 delay 0 check yes
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
timestep 0.00025
|
timestep 0.00025
|
||||||
|
|
||||||
fix 1 all nve
|
fix 1 all nve
|
||||||
|
|
||||||
fix 2 all latte NULL
|
fix 2 all latte
|
||||||
fix_modify 2 energy yes
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
thermo_style custom step temp pe etotal press
|
||||||
|
|||||||
179
examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1
Normal file
179
examples/latte/log.13Sep22.latte.graphene.boxrelax.g++.1
Normal file
@ -0,0 +1,179 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Simple water model with LATTE
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.graphene
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (10 8 20) with tilt (4.8985872e-16 1.2246468e-15 1.2246468e-15)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
32 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# replicate system if requested
|
||||||
|
|
||||||
|
variable x index 1
|
||||||
|
variable y index 1
|
||||||
|
variable z index 1
|
||||||
|
|
||||||
|
variable nrep equal v_x*v_y*v_z
|
||||||
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all box/relax iso 0.0 vmax 0.001
|
||||||
|
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom etotal
|
||||||
|
|
||||||
|
# minimization
|
||||||
|
|
||||||
|
thermo 1
|
||||||
|
fix 3 all print 1 "Total Energy ="
|
||||||
|
min_style cg
|
||||||
|
min_modify dmax 0.1
|
||||||
|
min_modify line quadratic
|
||||||
|
minimize 1.0e-4 1.0e-4 10000 10000
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 11 9 20
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.03 | 7.03 | 7.03 Mbytes
|
||||||
|
TotEng
|
||||||
|
-247.46002
|
||||||
|
-247.67224
|
||||||
|
-247.87937
|
||||||
|
-248.08148
|
||||||
|
-248.27865
|
||||||
|
-248.47096
|
||||||
|
-248.65851
|
||||||
|
-248.84137
|
||||||
|
-249.01964
|
||||||
|
-249.19342
|
||||||
|
-249.36281
|
||||||
|
-249.52791
|
||||||
|
-249.68883
|
||||||
|
-249.8457
|
||||||
|
-249.99865
|
||||||
|
-250.1478
|
||||||
|
-250.29332
|
||||||
|
-250.43535
|
||||||
|
-250.57409
|
||||||
|
-250.70972
|
||||||
|
-250.84247
|
||||||
|
-250.97258
|
||||||
|
-251.10035
|
||||||
|
-251.2261
|
||||||
|
-251.35021
|
||||||
|
-251.47314
|
||||||
|
-251.59543
|
||||||
|
-251.71776
|
||||||
|
-251.84096
|
||||||
|
-251.9661
|
||||||
|
-252.09459
|
||||||
|
-252.22833
|
||||||
|
-252.37003
|
||||||
|
-252.52371
|
||||||
|
-252.69578
|
||||||
|
-252.89752
|
||||||
|
-253.15197
|
||||||
|
-253.52044
|
||||||
|
-254.31418
|
||||||
|
-255.6175
|
||||||
|
-256.8162
|
||||||
|
-258.1227
|
||||||
|
-259.38401
|
||||||
|
-260.74831
|
||||||
|
-262.03991
|
||||||
|
-263.5463
|
||||||
|
-264.70486
|
||||||
|
-267.69143
|
||||||
|
-267.88682
|
||||||
|
-269.0352
|
||||||
|
-270.602
|
||||||
|
-270.65395
|
||||||
|
-270.7429
|
||||||
|
-271.55831
|
||||||
|
-271.81159
|
||||||
|
-271.87447
|
||||||
|
-273.03096
|
||||||
|
-273.23109
|
||||||
|
-273.27869
|
||||||
|
-273.34621
|
||||||
|
-273.4082
|
||||||
|
-273.45599
|
||||||
|
-273.53849
|
||||||
|
-273.57478
|
||||||
|
-273.71381
|
||||||
|
-273.74092
|
||||||
|
Loop time of 20.5496 on 1 procs for 65 steps with 32 atoms
|
||||||
|
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-247.460020562055 -273.713813242259 -273.740918498854
|
||||||
|
Force two-norm initial, final = 201.60784 9.4927634
|
||||||
|
Force max component initial, final = 188.92406 2.4327308
|
||||||
|
Final line search alpha, max atom move = 0.00022885545 0.0005567437
|
||||||
|
Iterations, force evaluations = 65 65
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 7.7869e-05 | 7.7869e-05 | 7.7869e-05 | 0.0 | 0.00
|
||||||
|
Bond | 3.531e-06 | 3.531e-06 | 3.531e-06 | 0.0 | 0.00
|
||||||
|
Neigh | 1.3988e-05 | 1.3988e-05 | 1.3988e-05 | 0.0 | 0.00
|
||||||
|
Comm | 0.00014355 | 0.00014355 | 0.00014355 | 0.0 | 0.00
|
||||||
|
Output | 0.00071475 | 0.00071475 | 0.00071475 | 0.0 | 0.00
|
||||||
|
Modify | 20.547 | 20.547 | 20.547 | 0.0 | 99.99
|
||||||
|
Other | | 0.001683 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 32 ave 32 max 32 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 100 ave 100 max 100 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 48 ave 48 max 48 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 48
|
||||||
|
Ave neighs/atom = 1.5
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:20
|
||||||
189
examples/latte/log.13Sep22.latte.multiple.g++.1
Normal file
189
examples/latte/log.13Sep22.latte.multiple.g++.1
Normal file
@ -0,0 +1,189 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.water
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
24 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press
|
||||||
|
|
||||||
|
# dynamics
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 10
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press
|
||||||
|
0 0 -104.95596 -104.95596 48235.442
|
||||||
|
10 336.53107 -105.96027 -104.95977 97996.851
|
||||||
|
Loop time of 0.334108 on 1 procs for 10 steps with 24 atoms
|
||||||
|
|
||||||
|
Performance: 0.646 ns/day, 37.123 hours/ns, 29.930 timesteps/s
|
||||||
|
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 3.714e-06 | 3.714e-06 | 3.714e-06 | 0.0 | 0.00
|
||||||
|
Bond | 5.02e-07 | 5.02e-07 | 5.02e-07 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 1.1209e-05 | 1.1209e-05 | 1.1209e-05 | 0.0 | 0.00
|
||||||
|
Output | 2.3638e-05 | 2.3638e-05 | 2.3638e-05 | 0.0 | 0.01
|
||||||
|
Modify | 0.33404 | 0.33404 | 0.33404 | 0.0 | 99.98
|
||||||
|
Other | | 2.795e-05 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 24 ave 24 max 24 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 71 ave 71 max 71 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 37 ave 37 max 37 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 37
|
||||||
|
Ave neighs/atom = 1.5416667
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# Clear up previus calculation
|
||||||
|
|
||||||
|
clear
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
|
||||||
|
# simple CH4 molecule with LATTE
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.ch4
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (0 0 0) to (19.523 12.758 11.692) with tilt (0 0 0)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
5 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.007 seconds
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press
|
||||||
|
|
||||||
|
# dynamics
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 10
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 20 13 12
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton/tri
|
||||||
|
stencil: half/bin/3d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.902 | 5.902 | 5.902 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press
|
||||||
|
0 0 -23.980353 -23.980353 348.02716
|
||||||
|
10 19.123149 -23.990297 -23.98041 18.774332
|
||||||
|
Loop time of 0.0121573 on 1 procs for 10 steps with 5 atoms
|
||||||
|
|
||||||
|
Performance: 17.767 ns/day, 1.351 hours/ns, 822.549 timesteps/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.224e-06 | 1.224e-06 | 1.224e-06 | 0.0 | 0.01
|
||||||
|
Bond | 2.93e-07 | 2.93e-07 | 2.93e-07 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 3.845e-06 | 3.845e-06 | 3.845e-06 | 0.0 | 0.03
|
||||||
|
Output | 8.633e-06 | 8.633e-06 | 8.633e-06 | 0.0 | 0.07
|
||||||
|
Modify | 0.012132 | 0.012132 | 0.012132 | 0.0 | 99.80
|
||||||
|
Other | | 1.089e-05 | | | 0.09
|
||||||
|
|
||||||
|
Nlocal: 5 ave 5 max 5 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 7 ave 7 max 7 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 10 ave 10 max 10 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 10
|
||||||
|
Ave neighs/atom = 2
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
112
examples/latte/log.13Sep22.latte.sucrose.md.g++.1
Normal file
112
examples/latte/log.13Sep22.latte.sucrose.md.g++.1
Normal file
@ -0,0 +1,112 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple sucrose model with LATTE
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.sucrose
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
45 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# replicate system if requested
|
||||||
|
|
||||||
|
variable x index 1
|
||||||
|
variable y index 1
|
||||||
|
variable z index 1
|
||||||
|
|
||||||
|
variable nrep equal v_x*v_y*v_z
|
||||||
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press
|
||||||
|
|
||||||
|
# dynamics
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 100
|
||||||
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 18 19 22
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.93 | 5.93 | 5.93 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press
|
||||||
|
0 0 -251.26617 -251.26617 16.617233
|
||||||
|
10 0.025263738 -251.26631 -251.26617 8.0576369
|
||||||
|
20 0.034232485 -251.26636 -251.26617 1.6672772
|
||||||
|
30 0.059079585 -251.2665 -251.26617 11.058355
|
||||||
|
40 0.055499785 -251.26648 -251.26617 14.837599
|
||||||
|
50 0.058499496 -251.2665 -251.26617 6.7180488
|
||||||
|
60 0.071094531 -251.26657 -251.26617 6.6131215
|
||||||
|
70 0.084309398 -251.26665 -251.26617 12.372502
|
||||||
|
80 0.1089929 -251.26679 -251.26617 8.8352747
|
||||||
|
90 0.11378255 -251.26681 -251.26617 5.1175071
|
||||||
|
100 0.13003967 -251.26691 -251.26617 8.2429118
|
||||||
|
Loop time of 14.4456 on 1 procs for 100 steps with 45 atoms
|
||||||
|
|
||||||
|
Performance: 0.150 ns/day, 160.507 hours/ns, 6.923 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 | 7.5758e-05 | 7.5758e-05 | 7.5758e-05 | 0.0 | 0.00
|
||||||
|
Bond | 6.748e-06 | 6.748e-06 | 6.748e-06 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 9.0137e-05 | 9.0137e-05 | 9.0137e-05 | 0.0 | 0.00
|
||||||
|
Output | 0.00025976 | 0.00025976 | 0.00025976 | 0.0 | 0.00
|
||||||
|
Modify | 14.445 | 14.445 | 14.445 | 0.0 | 99.99
|
||||||
|
Other | | 0.0005283 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 45 ave 45 max 45 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 59 ave 59 max 59 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 59
|
||||||
|
Ave neighs/atom = 1.3111111
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:14
|
||||||
112
examples/latte/log.13Sep22.latte.water.md.g++.1
Normal file
112
examples/latte/log.13Sep22.latte.water.md.g++.1
Normal file
@ -0,0 +1,112 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple water model with LATTE
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.water
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
24 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# replicate system if requested
|
||||||
|
|
||||||
|
variable x index 1
|
||||||
|
variable y index 1
|
||||||
|
variable z index 1
|
||||||
|
|
||||||
|
variable nrep equal v_x*v_y*v_z
|
||||||
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press
|
||||||
|
|
||||||
|
# dynamics
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
run 100
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press
|
||||||
|
0 0 -104.95596 -104.95596 48235.442
|
||||||
|
10 336.53107 -105.96027 -104.95977 97996.851
|
||||||
|
20 529.06408 -106.53023 -104.95733 131519.85
|
||||||
|
30 753.62603 -107.19952 -104.959 49296.66
|
||||||
|
40 716.65648 -107.08803 -104.95742 28307.121
|
||||||
|
50 824.04392 -107.40823 -104.95836 102167.59
|
||||||
|
60 933.56146 -107.73479 -104.95933 92508.517
|
||||||
|
70 851.18489 -107.48767 -104.95711 13993.262
|
||||||
|
80 999.8028 -107.93147 -104.95907 36700.736
|
||||||
|
90 998.77488 -107.9257 -104.95636 107233.54
|
||||||
|
100 1281.4438 -108.76963 -104.95992 49702.386
|
||||||
|
Loop time of 3.14578 on 1 procs for 100 steps with 24 atoms
|
||||||
|
|
||||||
|
Performance: 0.687 ns/day, 34.953 hours/ns, 31.789 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 | 3.0818e-05 | 3.0818e-05 | 3.0818e-05 | 0.0 | 0.00
|
||||||
|
Bond | 4.704e-06 | 4.704e-06 | 4.704e-06 | 0.0 | 0.00
|
||||||
|
Neigh | 1.8668e-05 | 1.8668e-05 | 1.8668e-05 | 0.0 | 0.00
|
||||||
|
Comm | 0.00010831 | 0.00010831 | 0.00010831 | 0.0 | 0.00
|
||||||
|
Output | 0.00021087 | 0.00021087 | 0.00021087 | 0.0 | 0.01
|
||||||
|
Modify | 3.1452 | 3.1452 | 3.1452 | 0.0 | 99.98
|
||||||
|
Other | | 0.0002339 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 24 ave 24 max 24 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 77 ave 77 max 77 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 31 ave 31 max 31 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 31
|
||||||
|
Ave neighs/atom = 1.2916667
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 2
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
122
examples/latte/log.13Sep22.latte.water.min.g++.1
Normal file
122
examples/latte/log.13Sep22.latte.water.min.g++.1
Normal file
@ -0,0 +1,122 @@
|
|||||||
|
LAMMPS (3 Aug 2022)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# simple water model with LATTE
|
||||||
|
|
||||||
|
units metal
|
||||||
|
atom_style full
|
||||||
|
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
||||||
|
|
||||||
|
read_data data.water
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
24 atoms
|
||||||
|
Finding 1-2 1-3 1-4 neighbors ...
|
||||||
|
special bond factors lj: 0 0 0
|
||||||
|
special bond factors coul: 0 0 0
|
||||||
|
0 = max # of 1-2 neighbors
|
||||||
|
0 = max # of 1-3 neighbors
|
||||||
|
0 = max # of 1-4 neighbors
|
||||||
|
1 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000 seconds
|
||||||
|
read_data CPU = 0.001 seconds
|
||||||
|
|
||||||
|
# replicate system if requested
|
||||||
|
|
||||||
|
variable x index 1
|
||||||
|
variable y index 1
|
||||||
|
variable z index 1
|
||||||
|
|
||||||
|
variable nrep equal v_x*v_y*v_z
|
||||||
|
if "${nrep} > 1" then "replicate $x $y $z"
|
||||||
|
|
||||||
|
# initialize system
|
||||||
|
|
||||||
|
velocity all create 0.0 87287 loop geom
|
||||||
|
|
||||||
|
pair_style zero 1.0
|
||||||
|
pair_coeff * *
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 0 check yes
|
||||||
|
|
||||||
|
timestep 0.00025
|
||||||
|
|
||||||
|
fix 1 all nve
|
||||||
|
|
||||||
|
fix 2 all latte
|
||||||
|
fix_modify 2 energy yes
|
||||||
|
|
||||||
|
thermo_style custom step temp pe etotal press
|
||||||
|
|
||||||
|
# minimization
|
||||||
|
|
||||||
|
thermo 10
|
||||||
|
|
||||||
|
min_style fire
|
||||||
|
minimize 1.0e-4 1.0e-4 500 500
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
Neighbor list info ...
|
||||||
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2
|
||||||
|
ghost atom cutoff = 2
|
||||||
|
binsize = 1, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair zero, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Parameters for fire:
|
||||||
|
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
|
||||||
|
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.88 | 5.88 | 5.88 Mbytes
|
||||||
|
Step Temp PotEng TotEng Press
|
||||||
|
0 0 -104.95596 -104.95596 48235.442
|
||||||
|
10 853.69689 -106.31143 -103.7734 79191.444
|
||||||
|
20 1112.0893 -107.2723 -103.96607 82675.468
|
||||||
|
30 1897.6249 -108.36769 -102.72608 71447.508
|
||||||
|
40 3068.3491 -110.06452 -100.94237 47627.967
|
||||||
|
50 3.730935 -110.16042 -110.14932 5913.0643
|
||||||
|
60 28.603141 -110.18885 -110.10381 5778.8586
|
||||||
|
66 54.717686 -110.21503 -110.05236 5739.5831
|
||||||
|
Loop time of 2.48723 on 1 procs for 66 steps with 24 atoms
|
||||||
|
|
||||||
|
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
Minimization stats:
|
||||||
|
Stopping criterion = energy tolerance
|
||||||
|
Energy initial, next-to-last, final =
|
||||||
|
-104.955957263186 -110.209885831179 -110.215033825672
|
||||||
|
Force two-norm initial, final = 19.119006 0.51695213
|
||||||
|
Force max component initial, final = 11.775801 0.1663917
|
||||||
|
Final line search alpha, max atom move = 0 0
|
||||||
|
Iterations, force evaluations = 66 69
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.7159e-05 | 2.7159e-05 | 2.7159e-05 | 0.0 | 0.00
|
||||||
|
Bond | 3.124e-06 | 3.124e-06 | 3.124e-06 | 0.0 | 0.00
|
||||||
|
Neigh | 1.0201e-05 | 1.0201e-05 | 1.0201e-05 | 0.0 | 0.00
|
||||||
|
Comm | 0.000109 | 0.000109 | 0.000109 | 0.0 | 0.00
|
||||||
|
Output | 0.00010568 | 0.00010568 | 0.00010568 | 0.0 | 0.00
|
||||||
|
Modify | 2.4866 | 2.4866 | 2.4866 | 0.0 | 99.98
|
||||||
|
Other | | 0.0003552 | | | 0.01
|
||||||
|
|
||||||
|
Nlocal: 24 ave 24 max 24 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 75 ave 75 max 75 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 33 ave 33 max 33 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 33
|
||||||
|
Ave neighs/atom = 1.375
|
||||||
|
Ave special neighs/atom = 0
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -1,406 +0,0 @@
|
|||||||
The log file for latte_lib
|
|
||||||
|
|
||||||
CONTROL{ }
|
|
||||||
|
|
||||||
WARNING: variable JobName= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DEBUGON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable FERMIM= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CGORLIB= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NORECS= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable VDWON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable LCNON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable LCNITER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MDON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PBCON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RESTART= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NGPU= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DOSFIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable QFIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPFITON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ALLFITON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPSTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BISTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PP2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPNMOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PARREP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable VERBOSE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MIXER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CGTOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULACC= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULCUT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULR1= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CHTOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BETA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPBETA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
|
|
||||||
|
|
||||||
|
|
||||||
############### Parameters used for this run ################
|
|
||||||
CONTROL{
|
|
||||||
xControl= 1
|
|
||||||
DEBUGON= 0
|
|
||||||
FERMIM= 6
|
|
||||||
CGORLIB= 1
|
|
||||||
NORECS= 1
|
|
||||||
ENTROPYKIND= 1
|
|
||||||
PPOTON= 1
|
|
||||||
VDWON= 0
|
|
||||||
SPINON= 0
|
|
||||||
ELECTRO= 1
|
|
||||||
ELECMETH= 0
|
|
||||||
MAXSCF= 450
|
|
||||||
MINSP2ITER= 22
|
|
||||||
FULLQCONV= 1
|
|
||||||
QITER= 3
|
|
||||||
ORDERNMOL= 0
|
|
||||||
SPARSEON= 1
|
|
||||||
THRESHOLDON= 1
|
|
||||||
FILLINSTOP= 100
|
|
||||||
BLKSZ= 4
|
|
||||||
MSPARSE= 1500
|
|
||||||
LCNON= 0
|
|
||||||
LCNITER= 4
|
|
||||||
RELAX= 0
|
|
||||||
MAXITER= 100000
|
|
||||||
MDON= 1
|
|
||||||
PBCON= 1
|
|
||||||
RESTART= 0
|
|
||||||
CHARGE= 0
|
|
||||||
XBO= 1
|
|
||||||
XBODISON= 1
|
|
||||||
XBODISORDER= 5
|
|
||||||
NGPU= 2
|
|
||||||
KON= 0
|
|
||||||
COMPFORCE= 1
|
|
||||||
DOSFIT= 0
|
|
||||||
INTS2FIT= 1
|
|
||||||
NFITSTEP= 5000
|
|
||||||
QFIT= 0
|
|
||||||
PPFITON= 0
|
|
||||||
ALLFITON= 0
|
|
||||||
PPSTEP= 500
|
|
||||||
BISTEP= 500
|
|
||||||
PP2FIT= 2
|
|
||||||
BINT2FIT= 6
|
|
||||||
PPNMOL= 10
|
|
||||||
PPNGEOM= 200
|
|
||||||
PARREP= 0
|
|
||||||
VERBOSE= 0
|
|
||||||
MIXER= 0
|
|
||||||
RESTARTLIB= 0
|
|
||||||
CGTOL= 9.9999999747524271E-007
|
|
||||||
KBT= 0.0000000000000000
|
|
||||||
SPINTOL= 1.0000000000000000E-004
|
|
||||||
ELEC_ETOL= 1.0000000474974513E-003
|
|
||||||
ELEC_QTOL= 1.0000000000000000E-008
|
|
||||||
COULACC= 9.9999999747524271E-007
|
|
||||||
COULCUT= -500.00000000000000
|
|
||||||
COULR1= 500.00000000000000
|
|
||||||
BREAKTOL= 9.9999999999999995E-007
|
|
||||||
QMIX= 0.25000000000000000
|
|
||||||
SPINMIX= 0.25000000000000000
|
|
||||||
MDMIX= 0.25000000000000000
|
|
||||||
NUMTHRESH= 9.9999999999999995E-007
|
|
||||||
CHTOL= 9.9999997764825821E-003
|
|
||||||
SKIN= 1.0000000000000000
|
|
||||||
RLXFTOL= 9.9999999999999995E-008
|
|
||||||
BETA= 1000.0000000000000
|
|
||||||
MCSIGMA= 0.20000000298023224
|
|
||||||
PPBETA= 1000.0000000000000
|
|
||||||
PPSIGMA= 9.9999997764825821E-003
|
|
||||||
ER= 1.0000000000000000
|
|
||||||
JobName=MyJob
|
|
||||||
BASISTYPE=NONORTHO
|
|
||||||
SP2CONV=REL
|
|
||||||
RELAXTYPE=SD
|
|
||||||
PARAMPATH=./TBparam
|
|
||||||
COORDSFILE=./coords.dat
|
|
||||||
INITIALIZED= F
|
|
||||||
}
|
|
||||||
|
|
||||||
./TBparam/electrons.dat
|
|
||||||
MDCONTROL{ }
|
|
||||||
|
|
||||||
WARNING: variable RNDIST= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RSFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable THERMPER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable THERMRUN= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NVTON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NPTON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable AVEPER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SEED= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MDADAPT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable GETHUG= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable FRICTION= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PTARGET= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable USHOCK= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable C0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable E0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable V0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable P0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DUMMY= is missing. I will use a default value instead ...
|
|
||||||
|
|
||||||
|
|
||||||
############### Parameters used for this run ################
|
|
||||||
MDCONTROL{
|
|
||||||
MAXITER= -1
|
|
||||||
UDNEIGH= 1
|
|
||||||
DUMPFREQ= 250
|
|
||||||
RSFREQ= 500
|
|
||||||
WRTFREQ= 25
|
|
||||||
TOINITTEMP5= 1
|
|
||||||
THERMPER= 500
|
|
||||||
THERMRUN= 50000
|
|
||||||
NVTON= 0
|
|
||||||
NPTON= 0
|
|
||||||
AVEPER= 1000
|
|
||||||
SEED= 54
|
|
||||||
SHOCKON= 0
|
|
||||||
SHOCKSTART= 100000
|
|
||||||
SHOCKDIR= 1
|
|
||||||
MDADAPT= 0
|
|
||||||
GETHUG= 0
|
|
||||||
RSLEVEL= 0
|
|
||||||
DT= 0.25000000000000000
|
|
||||||
TEMPERATURE= 300.00000000000000
|
|
||||||
FRICTION= 1000.0000000000000
|
|
||||||
PTARGET= 0.0000000000000000
|
|
||||||
UPARTICLE= 500.00000000000000
|
|
||||||
USHOCK= -4590.0000000000000
|
|
||||||
C0= 1300.0000000000000
|
|
||||||
E0= -795.72497558593750
|
|
||||||
V0= 896.98486328125000
|
|
||||||
P0= 8.3149001002311707E-002
|
|
||||||
RNDIST=GAUSSIAN
|
|
||||||
SEEDINIT=UNIFORM
|
|
||||||
NPTTYPE=ISO
|
|
||||||
DUMMY= F
|
|
||||||
}
|
|
||||||
|
|
||||||
LIBCALLS 0
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15165627147849 13.850829743067372 0.0000000000000000 3.9653384620309846
|
|
||||||
LIBCALLS 1
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15142147081917 13.850596160685321 0.0000000000000000 3.9653428217526296
|
|
||||||
LIBCALLS 2
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15072431717670 13.849902902335046 0.0000000000000000 3.9653556077235628
|
|
||||||
LIBCALLS 3
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14958682134301 13.848772166382796 0.0000000000000000 3.9653762812719782
|
|
||||||
LIBCALLS 4
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14804481054080 13.847240065975685 0.0000000000000000 3.9654039257311324
|
|
||||||
LIBCALLS 5
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14614669298459 13.845355347298943 0.0000000000000000 3.9654372593625880
|
|
||||||
LIBCALLS 6
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14395200541782 13.843177681164811 0.0000000000000000 3.9654747563744728
|
|
||||||
LIBCALLS 7
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14152950027858 13.840775605612510 0.0000000000000000 3.9655146828204026
|
|
||||||
LIBCALLS 8
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13895477239572 13.838224210058369 0.0000000000000000 3.9655551214573213
|
|
||||||
LIBCALLS 9
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13630808318862 13.835602658269416 0.0000000000000000 3.9655940696401335
|
|
||||||
LIBCALLS 10
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13367156672246 13.832991646694552 0.0000000000000000 3.9656294961085377
|
|
||||||
LIBCALLS 11
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13112695791978 13.830470890853416 0.0000000000000000 3.9656594331001127
|
|
||||||
LIBCALLS 12
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12875304084571 13.828116721514562 0.0000000000000000 3.9656820468287637
|
|
||||||
LIBCALLS 13
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12662314462005 13.825999860613845 0.0000000000000000 3.9656956633599689
|
|
||||||
LIBCALLS 14
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12480303363179 13.824183432931337 0.0000000000000000 3.9656988576578489
|
|
||||||
LIBCALLS 15
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12334906554690 13.822721254684298 0.0000000000000000 3.9656905013961525
|
|
||||||
LIBCALLS 16
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12230649281338 13.821656427050725 0.0000000000000000 3.9656697961568699
|
|
||||||
LIBCALLS 17
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12170820445976 13.821020251989051 0.0000000000000000 3.9656362957330207
|
|
||||||
LIBCALLS 18
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12157378544725 13.820831478957400 0.0000000000000000 3.9655899465557289
|
|
||||||
LIBCALLS 19
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12190902409918 13.821095885466233 0.0000000000000000 3.9655310732858191
|
|
||||||
LIBCALLS 20
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12270578464654 13.821806190548854 0.0000000000000000 3.9654603894825375
|
|
||||||
LIBCALLS 21
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12394226924755 13.822942298269552 0.0000000000000000 3.9653789701528157
|
|
||||||
LIBCALLS 22
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12558369933174 13.824471866833779 0.0000000000000000 3.9652882392864672
|
|
||||||
LIBCALLS 23
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12758334335854 13.826351196916939 0.0000000000000000 3.9651899208403507
|
|
||||||
LIBCALLS 24
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12988392857540 13.828526429544008 0.0000000000000000 3.9650859962581815
|
|
||||||
LIBCALLS 25
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13241933900565 13.830935038404082 0.0000000000000000 3.9649786471076300
|
|
||||||
LIBCALLS 26
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13511663668885 13.833507593821677 0.0000000000000000 3.9648702062183578
|
|
||||||
LIBCALLS 27
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13789821166085 13.836169765592846 0.0000000000000000 3.9647630647732250
|
|
||||||
LIBCALLS 28
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14068416314257 13.838844520440762 0.0000000000000000 3.9646596094056243
|
|
||||||
LIBCALLS 29
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14339478125902 13.841454456993119 0.0000000000000000 3.9645621614306648
|
|
||||||
LIBCALLS 30
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14595299166797 13.843924209084781 0.0000000000000000 3.9644728862209537
|
|
||||||
LIBCALLS 31
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14828672908391 13.846182838096166 0.0000000000000000 3.9643937231592781
|
|
||||||
LIBCALLS 32
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15033121417270 13.848166127650318 0.0000000000000000 3.9643263326484774
|
|
||||||
LIBCALLS 33
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15203097820654 13.849818691045462 0.0000000000000000 3.9642720350529470
|
|
||||||
LIBCALLS 34
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15334158494318 13.851095804201121 0.0000000000000000 3.9642317563508436
|
|
||||||
LIBCALLS 35
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15423101277941 13.851964884709183 0.0000000000000000 3.9642060118064197
|
|
||||||
LIBCALLS 36
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468060067406 13.852406550643760 0.0000000000000000 3.9641948735126151
|
|
||||||
LIBCALLS 37
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15468556770435 13.852415210893483 0.0000000000000000 3.9641979705462513
|
|
||||||
LIBCALLS 38
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15425506702360 13.851999160128511 0.0000000000000000 3.9642145018322728
|
|
||||||
LIBCALLS 39
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15341177086162 13.851180175004831 0.0000000000000000 3.9642432622019754
|
|
||||||
LIBCALLS 40
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219100341108 13.849992631968849 0.0000000000000000 3.9642826797086155
|
|
||||||
LIBCALLS 41
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15063948253476 13.848482189284203 0.0000000000000000 3.9643308764467280
|
|
||||||
LIBCALLS 42
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14881366363778 13.846704095034502 0.0000000000000000 3.9643857194231229
|
|
||||||
LIBCALLS 43
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14677783841711 13.844721197666447 0.0000000000000000 3.9644449063996254
|
|
||||||
LIBCALLS 44
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14460195130079 13.842601745208173 0.0000000000000000 3.9645060327113080
|
|
||||||
LIBCALLS 45
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14235930197236 13.840417063344470 0.0000000000000000 3.9645666751650537
|
|
||||||
LIBCALLS 46
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14012416839108 13.838239201362184 0.0000000000000000 3.9646244709241216
|
|
||||||
LIBCALLS 47
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13796944534135 13.836138629087953 0.0000000000000000 3.9646771958199687
|
|
||||||
LIBCALLS 48
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13596436459642 13.834182058508610 0.0000000000000000 3.9647228360374207
|
|
||||||
LIBCALLS 49
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13417236277201 13.832430452024822 0.0000000000000000 3.9647596471475066
|
|
||||||
LIBCALLS 50
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13264918465853 13.830937266579358 0.0000000000000000 3.9647862263274365
|
|
||||||
LIBCALLS 51
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13144121811348 13.829746970164395 0.0000000000000000 3.9648015300858930
|
|
||||||
LIBCALLS 52
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13058418584075 13.828893856279002 0.0000000000000000 3.9648049379175174
|
|
||||||
LIBCALLS 53
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13010212355317 13.828401171909800 0.0000000000000000 3.9647962482159476
|
|
||||||
LIBCALLS 54
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000675986638 13.828280567696357 0.0000000000000000 3.9647757005033171
|
|
||||||
LIBCALLS 55
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13029725443062 13.828531873218640 0.0000000000000000 3.9647439679967813
|
|
||||||
LIBCALLS 56
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13096031859556 13.829143196581525 0.0000000000000000 3.9647021412055241
|
|
||||||
LIBCALLS 57
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13197071275096 13.830091344339912 0.0000000000000000 3.9646517009757813
|
|
||||||
LIBCALLS 58
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13329208290526 13.831342554670950 0.0000000000000000 3.9645944691057076
|
|
||||||
LIBCALLS 59
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13487817952188 13.832853532802908 0.0000000000000000 3.9645325717081379
|
|
||||||
LIBCALLS 60
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13667431785007 13.834572772174083 0.0000000000000000 3.9644683636269380
|
|
||||||
LIBCALLS 61
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13861917436014 13.836442137716100 0.0000000000000000 3.9644043716683206
|
|
||||||
LIBCALLS 62
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14064674344610 13.838398678492441 0.0000000000000000 3.9643432117931376
|
|
||||||
LIBCALLS 63
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14268847880851 13.840376626541268 0.0000000000000000 3.9642875107994442
|
|
||||||
LIBCALLS 64
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14467552446979 13.842309527587247 0.0000000000000000 3.9642398279114381
|
|
||||||
LIBCALLS 65
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14654097615647 13.844132438475109 0.0000000000000000 3.9642025589783412
|
|
||||||
LIBCALLS 66
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14822207995957 13.845784117078871 0.0000000000000000 3.9641778771678413
|
|
||||||
LIBCALLS 67
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14966231911774 13.847209123749478 0.0000000000000000 3.9641676470155103
|
|
||||||
LIBCALLS 68
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15081329445576 13.848359751049152 0.0000000000000000 3.9641733618391299
|
|
||||||
LIBCALLS 69
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15163634076458 13.849197700537186 0.0000000000000000 3.9641960937768981
|
|
||||||
LIBCALLS 70
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15210380659516 13.849695432596437 0.0000000000000000 3.9642364336978391
|
|
||||||
LIBCALLS 71
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15219997215792 13.849837127658775 0.0000000000000000 3.9642944914660605
|
|
||||||
LIBCALLS 72
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15192153900722 13.849619213627008 0.0000000000000000 3.9643698667021590
|
|
||||||
LIBCALLS 73
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15127769530471 13.849050434626310 0.0000000000000000 3.9644616585289247
|
|
||||||
LIBCALLS 74
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.15028974592457 13.848151458176057 0.0000000000000000 3.9645684873567908
|
|
||||||
LIBCALLS 75
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14899032381624 13.846954040343237 0.0000000000000000 3.9646885325372980
|
|
||||||
LIBCALLS 76
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14742221364327 13.845499789571511 0.0000000000000000 3.9648195821504211
|
|
||||||
LIBCALLS 77
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14563684020112 13.843838588134755 0.0000000000000000 3.9649591055666282
|
|
||||||
LIBCALLS 78
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14369246883172 13.842026744273829 0.0000000000000000 3.9651043223068876
|
|
||||||
LIBCALLS 79
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14165219754119 13.840124957235691 0.0000000000000000 3.9652522794782556
|
|
||||||
LIBCALLS 80
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13958181195608 13.838196181062383 0.0000000000000000 3.9653999492835532
|
|
||||||
LIBCALLS 81
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13754757713065 13.836303471774007 0.0000000000000000 3.9655443071963385
|
|
||||||
LIBCALLS 82
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13561405478509 13.834507896249461 0.0000000000000000 3.9656824354232736
|
|
||||||
LIBCALLS 83
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13384198639028 13.832866571528193 0.0000000000000000 3.9658115908515681
|
|
||||||
LIBCALLS 84
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13228634940748 13.831430891696755 0.0000000000000000 3.9659292903699495
|
|
||||||
LIBCALLS 85
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13099461122306 13.830244986101496 0.0000000000000000 3.9660333724384569
|
|
||||||
LIBCALLS 86
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13000526350720 13.829344440260281 0.0000000000000000 3.9661220782532145
|
|
||||||
LIBCALLS 87
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12934661713206 13.828755299191645 0.0000000000000000 3.9661940662588862
|
|
||||||
LIBCALLS 88
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12903595764971 13.828493364127572 0.0000000000000000 3.9662484623936765
|
|
||||||
LIBCALLS 89
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12907904533250 13.828563786156602 0.0000000000000000 3.9662848954537067
|
|
||||||
LIBCALLS 90
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.12946994320248 13.828960955791626 0.0000000000000000 3.9663034756730777
|
|
||||||
LIBCALLS 91
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13019123489619 13.829668684955367 0.0000000000000000 3.9663048073711558
|
|
||||||
LIBCALLS 92
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13121457766835 13.830660675785223 0.0000000000000000 3.9662899643566578
|
|
||||||
LIBCALLS 93
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13250159637499 13.831901269302985 0.0000000000000000 3.9662604605307470
|
|
||||||
LIBCALLS 94
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13400508153813 13.833346464674193 0.0000000000000000 3.9662181906403653
|
|
||||||
LIBCALLS 95
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13567049003717 13.834945196074795 0.0000000000000000 3.9661653991148187
|
|
||||||
LIBCALLS 96
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13743766487022 13.836640848231452 0.0000000000000000 3.9661045863001441
|
|
||||||
LIBCALLS 97
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.13924277096038 13.838372983906890 0.0000000000000000 3.9660384593805307
|
|
||||||
LIBCALLS 98
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14102036682124 13.840079246589914 0.0000000000000000 3.9659698320311318
|
|
||||||
LIBCALLS 99
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14270555407057 13.841697390518378 0.0000000000000000 3.9659015537535014
|
|
||||||
LIBCALLS 100
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -261.14423615166146 13.843167378892108 0.0000000000000000 3.9658364191978137
|
|
||||||
@ -1,406 +0,0 @@
|
|||||||
The log file for latte_lib
|
|
||||||
|
|
||||||
CONTROL{ }
|
|
||||||
|
|
||||||
WARNING: variable JobName= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PARAMPATH= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DEBUGON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable FERMIM= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CGORLIB= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NORECS= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable VDWON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ORDERNMOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable LCNON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable LCNITER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MDON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PBCON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RESTART= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NGPU= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COMPFORCE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DOSFIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable INTS2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NFITSTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable QFIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPFITON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ALLFITON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPSTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BISTEP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PP2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BINT2FIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPNMOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPNGEOM= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PARREP= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable VERBOSE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MIXER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RESTARTLIB= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CGTOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULACC= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULCUT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable COULR1= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable CHTOL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable BETA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MCSIGMA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPBETA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PPSIGMA= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable ER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable INITIALIZED= is missing. I will use a default value instead ...
|
|
||||||
|
|
||||||
|
|
||||||
############### Parameters used for this run ################
|
|
||||||
CONTROL{
|
|
||||||
xControl= 1
|
|
||||||
DEBUGON= 0
|
|
||||||
FERMIM= 6
|
|
||||||
CGORLIB= 1
|
|
||||||
NORECS= 1
|
|
||||||
ENTROPYKIND= 1
|
|
||||||
PPOTON= 1
|
|
||||||
VDWON= 0
|
|
||||||
SPINON= 0
|
|
||||||
ELECTRO= 1
|
|
||||||
ELECMETH= 0
|
|
||||||
MAXSCF= 450
|
|
||||||
MINSP2ITER= 22
|
|
||||||
FULLQCONV= 1
|
|
||||||
QITER= 3
|
|
||||||
ORDERNMOL= 0
|
|
||||||
SPARSEON= 1
|
|
||||||
THRESHOLDON= 1
|
|
||||||
FILLINSTOP= 100
|
|
||||||
BLKSZ= 4
|
|
||||||
MSPARSE= 1500
|
|
||||||
LCNON= 0
|
|
||||||
LCNITER= 4
|
|
||||||
RELAX= 0
|
|
||||||
MAXITER= 100000
|
|
||||||
MDON= 1
|
|
||||||
PBCON= 1
|
|
||||||
RESTART= 0
|
|
||||||
CHARGE= 0
|
|
||||||
XBO= 1
|
|
||||||
XBODISON= 1
|
|
||||||
XBODISORDER= 5
|
|
||||||
NGPU= 2
|
|
||||||
KON= 0
|
|
||||||
COMPFORCE= 1
|
|
||||||
DOSFIT= 0
|
|
||||||
INTS2FIT= 1
|
|
||||||
NFITSTEP= 5000
|
|
||||||
QFIT= 0
|
|
||||||
PPFITON= 0
|
|
||||||
ALLFITON= 0
|
|
||||||
PPSTEP= 500
|
|
||||||
BISTEP= 500
|
|
||||||
PP2FIT= 2
|
|
||||||
BINT2FIT= 6
|
|
||||||
PPNMOL= 10
|
|
||||||
PPNGEOM= 200
|
|
||||||
PARREP= 0
|
|
||||||
VERBOSE= 0
|
|
||||||
MIXER= 0
|
|
||||||
RESTARTLIB= 0
|
|
||||||
CGTOL= 9.9999999747524271E-007
|
|
||||||
KBT= 0.0000000000000000
|
|
||||||
SPINTOL= 1.0000000000000000E-004
|
|
||||||
ELEC_ETOL= 1.0000000474974513E-003
|
|
||||||
ELEC_QTOL= 1.0000000000000000E-008
|
|
||||||
COULACC= 9.9999999747524271E-007
|
|
||||||
COULCUT= -500.00000000000000
|
|
||||||
COULR1= 500.00000000000000
|
|
||||||
BREAKTOL= 9.9999999999999995E-007
|
|
||||||
QMIX= 0.25000000000000000
|
|
||||||
SPINMIX= 0.25000000000000000
|
|
||||||
MDMIX= 0.25000000000000000
|
|
||||||
NUMTHRESH= 9.9999999999999995E-007
|
|
||||||
CHTOL= 9.9999997764825821E-003
|
|
||||||
SKIN= 1.0000000000000000
|
|
||||||
RLXFTOL= 9.9999999999999995E-008
|
|
||||||
BETA= 1000.0000000000000
|
|
||||||
MCSIGMA= 0.20000000298023224
|
|
||||||
PPBETA= 1000.0000000000000
|
|
||||||
PPSIGMA= 9.9999997764825821E-003
|
|
||||||
ER= 1.0000000000000000
|
|
||||||
JobName=MyJob
|
|
||||||
BASISTYPE=NONORTHO
|
|
||||||
SP2CONV=REL
|
|
||||||
RELAXTYPE=SD
|
|
||||||
PARAMPATH=./TBparam
|
|
||||||
COORDSFILE=./coords.dat
|
|
||||||
INITIALIZED= F
|
|
||||||
}
|
|
||||||
|
|
||||||
./TBparam/electrons.dat
|
|
||||||
MDCONTROL{ }
|
|
||||||
|
|
||||||
WARNING: variable RNDIST= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SEEDINIT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NPTTYPE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable UDNEIGH= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DUMPFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RSFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable WRTFREQ= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable THERMPER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable THERMRUN= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NVTON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable NPTON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable AVEPER= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SEED= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKON= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKSTART= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable SHOCKDIR= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable MDADAPT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable GETHUG= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable RSLEVEL= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DT= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable TEMPERATURE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable FRICTION= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable PTARGET= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable UPARTICLE= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable USHOCK= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable C0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable E0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable V0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable P0= is missing. I will use a default value instead ...
|
|
||||||
WARNING: variable DUMMY= is missing. I will use a default value instead ...
|
|
||||||
|
|
||||||
|
|
||||||
############### Parameters used for this run ################
|
|
||||||
MDCONTROL{
|
|
||||||
MAXITER= -1
|
|
||||||
UDNEIGH= 1
|
|
||||||
DUMPFREQ= 250
|
|
||||||
RSFREQ= 500
|
|
||||||
WRTFREQ= 25
|
|
||||||
TOINITTEMP5= 1
|
|
||||||
THERMPER= 500
|
|
||||||
THERMRUN= 50000
|
|
||||||
NVTON= 0
|
|
||||||
NPTON= 0
|
|
||||||
AVEPER= 1000
|
|
||||||
SEED= 54
|
|
||||||
SHOCKON= 0
|
|
||||||
SHOCKSTART= 100000
|
|
||||||
SHOCKDIR= 1
|
|
||||||
MDADAPT= 0
|
|
||||||
GETHUG= 0
|
|
||||||
RSLEVEL= 0
|
|
||||||
DT= 0.25000000000000000
|
|
||||||
TEMPERATURE= 300.00000000000000
|
|
||||||
FRICTION= 1000.0000000000000
|
|
||||||
PTARGET= 0.0000000000000000
|
|
||||||
UPARTICLE= 500.00000000000000
|
|
||||||
USHOCK= -4590.0000000000000
|
|
||||||
C0= 1300.0000000000000
|
|
||||||
E0= -795.72497558593750
|
|
||||||
V0= 896.98486328125000
|
|
||||||
P0= 8.3149001002311707E-002
|
|
||||||
RNDIST=GAUSSIAN
|
|
||||||
SEEDINIT=UNIFORM
|
|
||||||
NPTTYPE=ISO
|
|
||||||
DUMMY= F
|
|
||||||
}
|
|
||||||
|
|
||||||
LIBCALLS 0
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -110.94281402417451 9.3197859655447317 0.0000000000000000 3.3331152608769714
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|
||||||
LIBCALLS 1
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.00875524736128 9.3653691493930946 0.0000000000000000 3.3307590218500454
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|
||||||
LIBCALLS 2
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.20542679804305 9.5022104076319209 0.0000000000000000 3.3237269236958826
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|
||||||
LIBCALLS 3
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.52938059528239 9.7304811436977623 0.0000000000000000 3.3121168872278743
|
|
||||||
LIBCALLS 4
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.97463249071366 10.050121693432235 0.0000000000000000 3.2961492065207088
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|
||||||
LIBCALLS 5
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.53270518796754 10.460328095449432 0.0000000000000000 3.2761112890303719
|
|
||||||
LIBCALLS 6
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.19233973551384 10.958848347453728 0.0000000000000000 3.2524094948032394
|
|
||||||
LIBCALLS 7
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.93936061504219 11.541120618354967 0.0000000000000000 3.2255715906285793
|
|
||||||
LIBCALLS 8
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.75657630591589 12.199315594286325 0.0000000000000000 3.1962412869596100
|
|
||||||
LIBCALLS 9
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.62363727592754 12.921383532128770 0.0000000000000000 3.1652236023838971
|
|
||||||
LIBCALLS 10
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.51738028417616 13.690253224922545 0.0000000000000000 3.1333864449223818
|
|
||||||
LIBCALLS 11
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.41167836078414 14.483370804317431 0.0000000000000000 3.1018474945925432
|
|
||||||
LIBCALLS 12
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.27888830961329 15.272791625586624 0.0000000000000000 3.0716022180609772
|
|
||||||
LIBCALLS 13
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.09006809777934 16.026020995592610 0.0000000000000000 3.0437832241644842
|
|
||||||
LIBCALLS 14
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.81665859965702 16.707725410478066 0.0000000000000000 3.0194382402972129
|
|
||||||
LIBCALLS 15
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.43171665196000 17.282293509806884 0.0000000000000000 2.9995944159949395
|
|
||||||
LIBCALLS 16
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.91202932933264 17.717025741135480 0.0000000000000000 2.9850159611897484
|
|
||||||
LIBCALLS 17
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.23935305628714 17.985521384886379 0.0000000000000000 2.9763132734231292
|
|
||||||
LIBCALLS 18
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.40195013006486 18.070687763205626 0.0000000000000000 2.9738279411203812
|
|
||||||
LIBCALLS 19
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.39540873020161 17.966785565900089 0.0000000000000000 2.9776410698341418
|
|
||||||
LIBCALLS 20
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.22299732491055 17.680085363043698 0.0000000000000000 2.9875419962840417
|
|
||||||
LIBCALLS 21
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.89520311723561 17.228004261852682 0.0000000000000000 3.0030824758482719
|
|
||||||
LIBCALLS 22
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.42892991839108 16.636927104987372 0.0000000000000000 3.0235548851138652
|
|
||||||
LIBCALLS 23
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.84603562384113 15.939176953031323 0.0000000000000000 3.0480682132279808
|
|
||||||
LIBCALLS 24
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.17151378155378 15.169713318754383 0.0000000000000000 3.0757033760823562
|
|
||||||
LIBCALLS 25
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.43237009319661 14.363090728730079 0.0000000000000000 3.1053593079625457
|
|
||||||
LIBCALLS 26
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.65587959220025 13.551051330611342 0.0000000000000000 3.1359367589132958
|
|
||||||
LIBCALLS 27
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.86794783202731 12.760928656005802 0.0000000000000000 3.1665525874091585
|
|
||||||
LIBCALLS 28
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.09314111752745 12.014864684105008 0.0000000000000000 3.1962157162544820
|
|
||||||
LIBCALLS 29
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.35329645548983 11.329720850249741 0.0000000000000000 3.2241713466126849
|
|
||||||
LIBCALLS 30
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.66766945168203 10.717501941208962 0.0000000000000000 3.2497326120829619
|
|
||||||
LIBCALLS 31
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.05267853351812 10.186102377105355 0.0000000000000000 3.2723439005172468
|
|
||||||
LIBCALLS 32
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.52195471723405 9.7402032028335377 0.0000000000000000 3.2915777178346559
|
|
||||||
LIBCALLS 33
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.08654808143162 9.3821857555240076 0.0000000000000000 3.3070881064986164
|
|
||||||
LIBCALLS 34
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.75494140290169 9.1129669843369658 0.0000000000000000 3.3186769594405297
|
|
||||||
LIBCALLS 35
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.53346080566452 8.9326971516334606 0.0000000000000000 3.3261797960311763
|
|
||||||
LIBCALLS 36
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.42631053676025 8.8412887543407273 0.0000000000000000 3.3295101207595583
|
|
||||||
LIBCALLS 37
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.43567911088179 8.8387604511711384 0.0000000000000000 3.3286360397306387
|
|
||||||
LIBCALLS 38
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.56180874683180 8.9253908783870841 0.0000000000000000 3.3235794828927934
|
|
||||||
LIBCALLS 39
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.80290981416660 9.1016780459478674 0.0000000000000000 3.3144303393175201
|
|
||||||
LIBCALLS 40
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.15529209572232 9.3681021116147463 0.0000000000000000 3.3012719922659173
|
|
||||||
LIBCALLS 41
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.61284717182851 9.7246892073080176 0.0000000000000000 3.2843276907821406
|
|
||||||
LIBCALLS 42
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.16711238367500 10.170382433756300 0.0000000000000000 3.2638758866524444
|
|
||||||
LIBCALLS 43
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.80697882175535 10.702240750749448 0.0000000000000000 3.2402928278295451
|
|
||||||
LIBCALLS 44
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.51862249254057 11.314512276989859 0.0000000000000000 3.2140189987358694
|
|
||||||
LIBCALLS 45
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.28534475502829 11.997664972113199 0.0000000000000000 3.1855791836729437
|
|
||||||
LIBCALLS 46
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.08723294353808 12.737504349188432 0.0000000000000000 3.1557205936583181
|
|
||||||
LIBCALLS 47
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.90172272355942 13.514542609912253 0.0000000000000000 3.1252466759266087
|
|
||||||
LIBCALLS 48
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.70392627447073 14.303827027310493 0.0000000000000000 3.0950533786893732
|
|
||||||
LIBCALLS 49
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.46728361372288 15.075425279261220 0.0000000000000000 3.0661202668284480
|
|
||||||
LIBCALLS 50
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.16480071670361 15.795723720235596 0.0000000000000000 3.0394030522382605
|
|
||||||
LIBCALLS 51
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.77012122199473 16.429579578207949 0.0000000000000000 3.0158910566711334
|
|
||||||
LIBCALLS 52
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.25943485841766 16.943195338409559 0.0000000000000000 2.9964108616830281
|
|
||||||
LIBCALLS 53
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.61275582007269 17.307379355481601 0.0000000000000000 2.9817016064731785
|
|
||||||
LIBCALLS 54
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.81557415209883 17.500688554193868 0.0000000000000000 2.9722905637821611
|
|
||||||
LIBCALLS 55
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.85979389563140 17.511877645177901 0.0000000000000000 2.9685356305551474
|
|
||||||
LIBCALLS 56
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.74454585055143 17.341170281709367 0.0000000000000000 2.9705149057151141
|
|
||||||
LIBCALLS 57
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.47625724150488 17.000096879575938 0.0000000000000000 2.9780008785307088
|
|
||||||
LIBCALLS 58
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.06771474420596 16.509959464438374 0.0000000000000000 2.9906138266349656
|
|
||||||
LIBCALLS 59
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.53702830874704 15.899266098308772 0.0000000000000000 3.0078351734174715
|
|
||||||
LIBCALLS 60
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.90667912574422 15.200652842845301 0.0000000000000000 3.0288733658622142
|
|
||||||
LIBCALLS 61
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.20142467775943 14.447825469624703 0.0000000000000000 3.0529481020908245
|
|
||||||
LIBCALLS 62
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.44747494197328 13.672949108115853 0.0000000000000000 3.0790791220573088
|
|
||||||
LIBCALLS 63
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.67063237406208 12.904741667499017 0.0000000000000000 3.1063745183559131
|
|
||||||
LIBCALLS 64
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.89550228683500 12.167344616151606 0.0000000000000000 3.1339818740985033
|
|
||||||
LIBCALLS 65
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.14487351718614 11.479908971904207 0.0000000000000000 3.1610748652786995
|
|
||||||
LIBCALLS 66
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.43917601644073 10.856755674815151 0.0000000000000000 3.1869042214936911
|
|
||||||
LIBCALLS 67
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.79630542914917 10.307930318909381 0.0000000000000000 3.2107896540741994
|
|
||||||
LIBCALLS 68
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.23118520942130 9.8399835349372715 0.0000000000000000 3.2322754400486997
|
|
||||||
LIBCALLS 69
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.75645667348935 9.4568320682906393 0.0000000000000000 3.2508686207040949
|
|
||||||
LIBCALLS 70
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.38220191758144 9.1605931457952803 0.0000000000000000 3.2662052636761625
|
|
||||||
LIBCALLS 71
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.11651461323785 8.9523172650382463 0.0000000000000000 3.2778578161416640
|
|
||||||
LIBCALLS 72
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.96490300473705 8.8325758589074610 0.0000000000000000 3.2856373346184280
|
|
||||||
LIBCALLS 73
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -112.93101384064629 8.8018792766284140 0.0000000000000000 3.2893376450243901
|
|
||||||
LIBCALLS 74
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.01657988020818 8.8609123616606951 0.0000000000000000 3.2887786713823335
|
|
||||||
LIBCALLS 75
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.22122702505257 9.0105808374276855 0.0000000000000000 3.2838806809960044
|
|
||||||
LIBCALLS 76
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.54255812607462 9.2518619694254909 0.0000000000000000 3.2746170980725564
|
|
||||||
LIBCALLS 77
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -113.97595003796289 9.5854566564348804 0.0000000000000000 3.2610495238703536
|
|
||||||
LIBCALLS 78
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -114.51445216471619 10.011242264155852 0.0000000000000000 3.2433103887056101
|
|
||||||
LIBCALLS 79
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.14835871057100 10.527538366743359 0.0000000000000000 3.2217018278255036
|
|
||||||
LIBCALLS 80
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -115.86512618816471 11.130220642932718 0.0000000000000000 3.1966546818138903
|
|
||||||
LIBCALLS 81
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -116.64916580084807 11.811746817430592 0.0000000000000000 3.1687509169099037
|
|
||||||
LIBCALLS 82
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -117.48162972769103 12.560201275368994 0.0000000000000000 3.1387793445426220
|
|
||||||
LIBCALLS 83
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.34080112521505 13.358507776606700 0.0000000000000000 3.1076005013428842
|
|
||||||
LIBCALLS 84
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.20206255799097 14.183999576696523 0.0000000000000000 3.0762625451098367
|
|
||||||
LIBCALLS 85
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.03875955947012 15.008549885925623 0.0000000000000000 3.0458557745855401
|
|
||||||
LIBCALLS 86
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.82281065648482 15.799445052997022 0.0000000000000000 3.0175902569508040
|
|
||||||
LIBCALLS 87
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.52638053902615 16.521105731022047 0.0000000000000000 2.9925661691795984
|
|
||||||
LIBCALLS 88
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.12297505178334 17.137613862262167 0.0000000000000000 2.9718740800190462
|
|
||||||
LIBCALLS 89
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.58954501498538 17.615819283155187 0.0000000000000000 2.9563457612376758
|
|
||||||
LIBCALLS 90
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.90768650775293 17.928615619513138 0.0000000000000000 2.9466637669908935
|
|
||||||
LIBCALLS 91
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -123.06510359278838 18.057846294334183 0.0000000000000000 2.9432773288779130
|
|
||||||
LIBCALLS 92
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -123.05653995529889 17.996310208253615 0.0000000000000000 2.9463730237128352
|
|
||||||
LIBCALLS 93
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.88443709725219 17.748486968230267 0.0000000000000000 2.9557418006906766
|
|
||||||
LIBCALLS 94
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.55804625906457 17.329857520510558 0.0000000000000000 2.9710497340098647
|
|
||||||
LIBCALLS 95
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -122.09316916859144 16.764989519228550 0.0000000000000000 2.9916333369114647
|
|
||||||
LIBCALLS 96
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -121.51050736457847 16.084787212290774 0.0000000000000000 3.0167038701280053
|
|
||||||
LIBCALLS 97
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.83475656442954 15.323405512114466 0.0000000000000000 3.0451593241515909
|
|
||||||
LIBCALLS 98
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -120.09218577985371 14.515310319889227 0.0000000000000000 3.0759929793994090
|
|
||||||
LIBCALLS 99
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -119.30969482099719 13.692843612811791 0.0000000000000000 3.1081426979179545
|
|
||||||
LIBCALLS 100
|
|
||||||
Energy Components (TRRHOH, EREP, ENTE, ECOUL) -118.51358261827596 12.884492109393644 0.0000000000000000 3.1405428597121636
|
|
||||||
@ -1,170 +0,0 @@
|
|||||||
LAMMPS (11 May 2018)
|
|
||||||
# Simple water model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.graphene.boxrel
|
|
||||||
triclinic box = (0 0 0) to (10 8 20) with tilt (4.89859e-16 1.22465e-15 1.22465e-15)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
32 atoms
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all box/relax iso 0.0 vmax 0.001
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom etotal
|
|
||||||
|
|
||||||
# minimization
|
|
||||||
|
|
||||||
thermo 1
|
|
||||||
fix 3 all print 1 "Total Energy ="
|
|
||||||
min_style cg
|
|
||||||
min_modify dmax 0.1
|
|
||||||
min_modify line quadratic
|
|
||||||
minimize 1.0e-4 1.0e-4 10000 10000
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 11 9 20
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton/tri
|
|
||||||
stencil: half/bin/3d/newton/tri
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 6.779 | 6.779 | 6.779 Mbytes
|
|
||||||
TotEng
|
|
||||||
-247.46002
|
|
||||||
-247.67224
|
|
||||||
-247.87937
|
|
||||||
-248.08148
|
|
||||||
-248.27865
|
|
||||||
-248.47096
|
|
||||||
-248.65851
|
|
||||||
-248.84137
|
|
||||||
-249.01964
|
|
||||||
-249.19342
|
|
||||||
-249.36281
|
|
||||||
-249.52791
|
|
||||||
-249.68883
|
|
||||||
-249.8457
|
|
||||||
-249.99865
|
|
||||||
-250.1478
|
|
||||||
-250.29332
|
|
||||||
-250.43535
|
|
||||||
-250.57409
|
|
||||||
-250.70972
|
|
||||||
-250.84247
|
|
||||||
-250.97258
|
|
||||||
-251.10035
|
|
||||||
-251.2261
|
|
||||||
-251.35021
|
|
||||||
-251.47314
|
|
||||||
-251.59543
|
|
||||||
-251.71776
|
|
||||||
-251.84096
|
|
||||||
-251.9661
|
|
||||||
-252.09459
|
|
||||||
-252.22833
|
|
||||||
-252.37003
|
|
||||||
-252.52371
|
|
||||||
-252.69578
|
|
||||||
-252.89752
|
|
||||||
-253.15197
|
|
||||||
-253.52044
|
|
||||||
-254.31418
|
|
||||||
-255.6175
|
|
||||||
-256.8162
|
|
||||||
-258.1227
|
|
||||||
-259.38401
|
|
||||||
-260.74831
|
|
||||||
-262.03991
|
|
||||||
-263.5463
|
|
||||||
-264.70486
|
|
||||||
-267.69144
|
|
||||||
-267.88682
|
|
||||||
-269.03519
|
|
||||||
-270.60187
|
|
||||||
-270.65382
|
|
||||||
-270.74279
|
|
||||||
-271.55883
|
|
||||||
-271.81248
|
|
||||||
-271.87529
|
|
||||||
-273.01494
|
|
||||||
-273.23948
|
|
||||||
-273.28719
|
|
||||||
-273.35272
|
|
||||||
-273.41591
|
|
||||||
-273.46274
|
|
||||||
-273.54755
|
|
||||||
-273.58318
|
|
||||||
-273.73111
|
|
||||||
-273.75754
|
|
||||||
Loop time of 39.4155 on 1 procs for 65 steps with 32 atoms
|
|
||||||
|
|
||||||
1582.4% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
Minimization stats:
|
|
||||||
Stopping criterion = energy tolerance
|
|
||||||
Energy initial, next-to-last, final =
|
|
||||||
-247.460020579 -273.731112592 -273.757543461
|
|
||||||
Force two-norm initial, final = 201.608 9.43485
|
|
||||||
Force max component initial, final = 188.924 2.41297
|
|
||||||
Final line search alpha, max atom move = 0.000223273 0.00053875
|
|
||||||
Iterations, force evaluations = 65 65
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.00012159 | 0.00012159 | 0.00012159 | 0.0 | 0.00
|
|
||||||
Bond | 5.1975e-05 | 5.1975e-05 | 5.1975e-05 | 0.0 | 0.00
|
|
||||||
Neigh | 4.1962e-05 | 4.1962e-05 | 4.1962e-05 | 0.0 | 0.00
|
|
||||||
Comm | 0.00026107 | 0.00026107 | 0.00026107 | 0.0 | 0.00
|
|
||||||
Output | 0.0013342 | 0.0013342 | 0.0013342 | 0.0 | 0.00
|
|
||||||
Modify | 39.412 | 39.412 | 39.412 | 0.0 | 99.99
|
|
||||||
Other | | 0.00127 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 32 ave 32 max 32 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 100 ave 100 max 100 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 48 ave 48 max 48 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 48
|
|
||||||
Ave neighs/atom = 1.5
|
|
||||||
Ave special neighs/atom = 0
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:40
|
|
||||||
@ -1,103 +0,0 @@
|
|||||||
LAMMPS (11 May 2018)
|
|
||||||
# simple sucrose model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.sucrose
|
|
||||||
orthogonal box = (0 0 0) to (17.203 18.009 21.643)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
45 atoms
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 18 19 22
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 0.5064 | 0.5064 | 0.5064 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press
|
|
||||||
0 0 -251.26617 -251.26617 16.617234
|
|
||||||
10 0.025263709 -251.26631 -251.26617 8.0576708
|
|
||||||
20 0.034232467 -251.26636 -251.26617 1.6673442
|
|
||||||
30 0.059079556 -251.2665 -251.26617 11.058458
|
|
||||||
40 0.055499766 -251.26648 -251.26617 14.837775
|
|
||||||
50 0.058499509 -251.2665 -251.26617 6.7183113
|
|
||||||
60 0.071094535 -251.26657 -251.26617 6.6133687
|
|
||||||
70 0.084309439 -251.26665 -251.26617 12.372721
|
|
||||||
80 0.1089929 -251.26679 -251.26617 8.8355516
|
|
||||||
90 0.11378257 -251.26681 -251.26617 5.1177922
|
|
||||||
100 0.13003966 -251.26691 -251.26617 8.2431185
|
|
||||||
Loop time of 27.8386 on 1 procs for 100 steps with 45 atoms
|
|
||||||
|
|
||||||
Performance: 0.078 ns/day, 309.318 hours/ns, 3.592 timesteps/s
|
|
||||||
1799.6% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 8.3685e-05 | 8.3685e-05 | 8.3685e-05 | 0.0 | 0.00
|
|
||||||
Bond | 7.4148e-05 | 7.4148e-05 | 7.4148e-05 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00016689 | 0.00016689 | 0.00016689 | 0.0 | 0.00
|
|
||||||
Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00
|
|
||||||
Modify | 27.837 | 27.837 | 27.837 | 0.0 |100.00
|
|
||||||
Other | | 0.0005403 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 45 ave 45 max 45 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 59 ave 59 max 59 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 59
|
|
||||||
Ave neighs/atom = 1.31111
|
|
||||||
Ave special neighs/atom = 0
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:28
|
|
||||||
@ -1,103 +0,0 @@
|
|||||||
LAMMPS (11 May 2018)
|
|
||||||
# simple water model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.water
|
|
||||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
24 atoms
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press
|
|
||||||
0 0 -104.95594 -104.95594 48236.006
|
|
||||||
10 336.5303 -105.96026 -104.95976 97997.303
|
|
||||||
20 529.06385 -106.53021 -104.95731 131520.49
|
|
||||||
30 753.62616 -107.1995 -104.95898 49297.371
|
|
||||||
40 716.6565 -107.08802 -104.95741 28307.272
|
|
||||||
50 824.04417 -107.40822 -104.95835 102167.48
|
|
||||||
60 933.56056 -107.73478 -104.95932 92508.792
|
|
||||||
70 851.18518 -107.48766 -104.95711 13993.28
|
|
||||||
80 999.80265 -107.93146 -104.95906 36700.417
|
|
||||||
90 998.77707 -107.92569 -104.95634 107233.7
|
|
||||||
100 1281.4446 -108.76961 -104.95989 49703.193
|
|
||||||
Loop time of 10.6388 on 1 procs for 100 steps with 24 atoms
|
|
||||||
|
|
||||||
Performance: 0.203 ns/day, 118.209 hours/ns, 9.400 timesteps/s
|
|
||||||
6459.7% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.6771e-05 | 7.6771e-05 | 7.6771e-05 | 0.0 | 0.00
|
|
||||||
Bond | 7.5817e-05 | 7.5817e-05 | 7.5817e-05 | 0.0 | 0.00
|
|
||||||
Neigh | 4.6015e-05 | 4.6015e-05 | 4.6015e-05 | 0.0 | 0.00
|
|
||||||
Comm | 0.00031829 | 0.00031829 | 0.00031829 | 0.0 | 0.00
|
|
||||||
Output | 0.00032401 | 0.00032401 | 0.00032401 | 0.0 | 0.00
|
|
||||||
Modify | 10.637 | 10.637 | 10.637 | 0.0 | 99.99
|
|
||||||
Other | | 0.00052 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 24 ave 24 max 24 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 77 ave 77 max 77 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 31 ave 31 max 31 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 31
|
|
||||||
Ave neighs/atom = 1.29167
|
|
||||||
Ave special neighs/atom = 0
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:10
|
|
||||||
@ -1,108 +0,0 @@
|
|||||||
LAMMPS (11 May 2018)
|
|
||||||
# simple water model with LATTE
|
|
||||||
|
|
||||||
units metal
|
|
||||||
atom_style full
|
|
||||||
atom_modify sort 0 0.0 # turn off sorting of the coordinates
|
|
||||||
|
|
||||||
read_data data.water
|
|
||||||
orthogonal box = (0 0 0) to (6.267 6.267 6.267)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
24 atoms
|
|
||||||
0 = max # of 1-2 neighbors
|
|
||||||
0 = max # of 1-3 neighbors
|
|
||||||
0 = max # of 1-4 neighbors
|
|
||||||
1 = max # of special neighbors
|
|
||||||
|
|
||||||
# replicate system if requested
|
|
||||||
|
|
||||||
variable x index 1
|
|
||||||
variable y index 1
|
|
||||||
variable z index 1
|
|
||||||
|
|
||||||
variable nrep equal v_x*v_y*v_z
|
|
||||||
if "${nrep} > 1" then "replicate $x $y $z"
|
|
||||||
|
|
||||||
# initialize system
|
|
||||||
|
|
||||||
velocity all create 0.0 87287 loop geom
|
|
||||||
|
|
||||||
pair_style zero 1.0
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 1 delay 0 check yes
|
|
||||||
|
|
||||||
timestep 0.00025
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
fix 2 all latte NULL
|
|
||||||
fix_modify 2 energy yes
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press
|
|
||||||
|
|
||||||
# minimization
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
min_style fire
|
|
||||||
minimize 1.0e-4 1.0e-4 500 500
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2
|
|
||||||
ghost atom cutoff = 2
|
|
||||||
binsize = 1, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair zero, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press
|
|
||||||
0 0 -104.95594 -104.95594 48236.006
|
|
||||||
10 349.4534 -105.50948 -104.47056 62157.729
|
|
||||||
20 1253.6636 -107.00863 -103.28151 116456.71
|
|
||||||
30 134.64051 -107.56155 -107.16127 59864.196
|
|
||||||
40 2.4044989 -108.1527 -108.14556 32695.648
|
|
||||||
47 137.26885 -108.30413 -107.89603 60177.442
|
|
||||||
Loop time of 6.42677 on 1 procs for 47 steps with 24 atoms
|
|
||||||
|
|
||||||
6481.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
Minimization stats:
|
|
||||||
Stopping criterion = energy tolerance
|
|
||||||
Energy initial, next-to-last, final =
|
|
||||||
-104.955944301 -108.302982895 -108.304126127
|
|
||||||
Force two-norm initial, final = 19.119 3.44609
|
|
||||||
Force max component initial, final = 11.7758 1.3408
|
|
||||||
Final line search alpha, max atom move = 0 0
|
|
||||||
Iterations, force evaluations = 47 47
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 4.6253e-05 | 4.6253e-05 | 4.6253e-05 | 0.0 | 0.00
|
|
||||||
Bond | 3.1948e-05 | 3.1948e-05 | 3.1948e-05 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 0.00
|
|
||||||
Output | 0.00012302 | 0.00012302 | 0.00012302 | 0.0 | 0.00
|
|
||||||
Modify | 6.426 | 6.426 | 6.426 | 0.0 | 99.99
|
|
||||||
Other | | 0.0004699 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 24 ave 24 max 24 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 71 ave 71 max 71 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 37 ave 37 max 37 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 37
|
|
||||||
Ave neighs/atom = 1.54167
|
|
||||||
Ave special neighs/atom = 0
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:06
|
|
||||||
@ -32,12 +32,12 @@ make lib-mdi args="-m mpi" # build MDI lib with same settings as in the mpi Make
|
|||||||
|
|
||||||
# settings
|
# settings
|
||||||
|
|
||||||
version = "1.4.10"
|
version = "1.4.11"
|
||||||
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
|
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
|
||||||
|
|
||||||
# known checksums for different MDI versions. used to validate the download.
|
# known checksums for different MDI versions. used to validate the download.
|
||||||
checksums = { \
|
checksums = { \
|
||||||
'1.4.10' : '1c203b7fd462d9934834f643f09f3c06', \
|
'1.4.11' : '3791fe5081405c14aac07d4687f1cc58', \
|
||||||
}
|
}
|
||||||
|
|
||||||
# print error message or help
|
# print error message or help
|
||||||
|
|||||||
@ -416,7 +416,7 @@ void PairAmoeba::read_keyfile(char *filename)
|
|||||||
|
|
||||||
const auto words = Tokenizer(trimmed).as_vector();
|
const auto words = Tokenizer(trimmed).as_vector();
|
||||||
const int nwords = words.size();
|
const int nwords = words.size();
|
||||||
const auto keyword = words[0];
|
const auto &keyword = words[0];
|
||||||
|
|
||||||
if (utils::strmatch(keyword, "^[^a-z]+")) {
|
if (utils::strmatch(keyword, "^[^a-z]+")) {
|
||||||
; // ignore keywords that do not start with text
|
; // ignore keywords that do not start with text
|
||||||
|
|||||||
@ -43,9 +43,9 @@ void ComputeERotateAsphere::init()
|
|||||||
{
|
{
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec_ellipsoid = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
avec_line = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
avec_line = dynamic_cast<AtomVecLine *>(atom->style_match("line"));
|
||||||
avec_tri = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
avec_tri = dynamic_cast<AtomVecTri *>(atom->style_match("tri"));
|
||||||
if (!avec_ellipsoid && !avec_line && !avec_tri)
|
if (!avec_ellipsoid && !avec_line && !avec_tri)
|
||||||
error->all(FLERR,"Compute erotate/asphere requires "
|
error->all(FLERR,"Compute erotate/asphere requires "
|
||||||
"atom style ellipsoid or line or tri");
|
"atom style ellipsoid or line or tri");
|
||||||
|
|||||||
@ -94,7 +94,7 @@ void ComputeTempAsphere::init()
|
|||||||
{
|
{
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
|
error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
|
||||||
|
|
||||||
|
|||||||
@ -36,7 +36,7 @@ FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixNHAsphere::init()
|
void FixNHAsphere::init()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,
|
error->all(FLERR,
|
||||||
"Compute nvt/nph/npt asphere requires atom style ellipsoid");
|
"Compute nvt/nph/npt asphere requires atom style ellipsoid");
|
||||||
|
|||||||
@ -37,7 +37,7 @@ FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixNVEAsphere::init()
|
void FixNVEAsphere::init()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
|
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
|
||||||
|
|
||||||
|
|||||||
@ -37,7 +37,7 @@ void FixNVEAsphereNoforce::init()
|
|||||||
{
|
{
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!atom->ellipsoid_flag)
|
if (!atom->ellipsoid_flag)
|
||||||
error->all(FLERR,"Fix nve/asphere/noforce requires atom style ellipsoid");
|
error->all(FLERR,"Fix nve/asphere/noforce requires atom style ellipsoid");
|
||||||
|
|
||||||
|
|||||||
@ -56,7 +56,7 @@ void FixNVELine::init()
|
|||||||
{
|
{
|
||||||
// error checks
|
// error checks
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
avec = dynamic_cast<AtomVecLine *>(atom->style_match("line"));
|
||||||
if (!avec) error->all(FLERR,"Fix nve/line requires atom style line");
|
if (!avec) error->all(FLERR,"Fix nve/line requires atom style line");
|
||||||
|
|
||||||
if (domain->dimension != 2)
|
if (domain->dimension != 2)
|
||||||
|
|||||||
@ -50,7 +50,7 @@ void FixNVETri::init()
|
|||||||
{
|
{
|
||||||
// error checks
|
// error checks
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
avec = dynamic_cast<AtomVecTri *>(atom->style_match("tri"));
|
||||||
if (!avec) error->all(FLERR,"Fix nve/tri requires atom style tri");
|
if (!avec) error->all(FLERR,"Fix nve/tri requires atom style tri");
|
||||||
|
|
||||||
if (domain->dimension != 3)
|
if (domain->dimension != 3)
|
||||||
|
|||||||
@ -346,7 +346,7 @@ void PairGayBerne::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairGayBerne::init_style()
|
void PairGayBerne::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!avec) error->all(FLERR,"Pair gayberne requires atom style ellipsoid");
|
if (!avec) error->all(FLERR,"Pair gayberne requires atom style ellipsoid");
|
||||||
|
|
||||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||||
|
|||||||
@ -402,7 +402,7 @@ void PairLineLJ::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairLineLJ::init_style()
|
void PairLineLJ::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecLine *>( atom->style_match("line"));
|
avec = dynamic_cast<AtomVecLine *>(atom->style_match("line"));
|
||||||
if (!avec) error->all(FLERR,"Pair line/lj requires atom style line");
|
if (!avec) error->all(FLERR,"Pair line/lj requires atom style line");
|
||||||
|
|
||||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||||
|
|||||||
@ -467,7 +467,7 @@ void PairTriLJ::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairTriLJ::init_style()
|
void PairTriLJ::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecTri *>( atom->style_match("tri"));
|
avec = dynamic_cast<AtomVecTri *>(atom->style_match("tri"));
|
||||||
if (!avec) error->all(FLERR,"Pair tri/lj requires atom style tri");
|
if (!avec) error->all(FLERR,"Pair tri/lj requires atom style tri");
|
||||||
|
|
||||||
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
neighbor->add_request(this,NeighConst::REQ_DEFAULT);
|
||||||
|
|||||||
@ -39,7 +39,7 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
|
|||||||
// order of fields in a string does not matter
|
// order of fields in a string does not matter
|
||||||
// except: fields_data_atom & fields_data_vel must match data file
|
// except: fields_data_atom & fields_data_vel must match data file
|
||||||
|
|
||||||
fields_grow = {"q", "espin", "eradius", "ervel", "erforce",
|
fields_grow = {"q", "espin", "eradius", "ervel", "erforce",
|
||||||
"cs", "csforce", "vforce", "ervelforce", "etag"};
|
"cs", "csforce", "vforce", "ervelforce", "etag"};
|
||||||
fields_copy = {"q", "espin", "eradius", "ervel", "cs", "etag"};
|
fields_copy = {"q", "espin", "eradius", "ervel", "cs", "etag"};
|
||||||
fields_comm = {"eradius"};
|
fields_comm = {"eradius"};
|
||||||
@ -108,7 +108,7 @@ void AtomVecWavepacket::data_atom_post(int ilocal)
|
|||||||
int AtomVecWavepacket::property_atom(const std::string &name)
|
int AtomVecWavepacket::property_atom(const std::string &name)
|
||||||
{
|
{
|
||||||
if (name == "espin") return 0;
|
if (name == "espin") return 0;
|
||||||
if (name == "spin") return 0; // backward compatibility
|
if (name == "spin") return 0; // backward compatibility
|
||||||
if (name == "eradius") return 1;
|
if (name == "eradius") return 1;
|
||||||
if (name == "ervel") return 2;
|
if (name == "ervel") return 2;
|
||||||
if (name == "erforce") return 3;
|
if (name == "erforce") return 3;
|
||||||
|
|||||||
@ -61,7 +61,7 @@ void FixNVEAwpmd::init()
|
|||||||
dtf = 0.5 * update->dt * force->ftm2v;
|
dtf = 0.5 * update->dt * force->ftm2v;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
|
|
||||||
awpmd_pair=dynamic_cast<PairAWPMDCut *>(force->pair);
|
awpmd_pair=dynamic_cast<PairAWPMDCut *>(force->pair);
|
||||||
awpmd_pair->wpmd->norm_needed=1;
|
awpmd_pair->wpmd->norm_needed=1;
|
||||||
|
|||||||
@ -491,7 +491,7 @@ void FixBocs::init()
|
|||||||
{
|
{
|
||||||
for (int i = 0; i < modify->nfix; i++)
|
for (int i = 0; i < modify->nfix; i++)
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
int *dimflag = (dynamic_cast<FixDeform *>( modify->fix[i]))->dimflag;
|
int *dimflag = (dynamic_cast<FixDeform *>(modify->fix[i]))->dimflag;
|
||||||
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
|
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
|
||||||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
|
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
|
||||||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
|
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
|
||||||
@ -591,8 +591,8 @@ void FixBocs::init()
|
|||||||
else kspace_flag = 0;
|
else kspace_flag = 0;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
|
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
dto = 0.5*step_respa[0];
|
dto = 0.5*step_respa[0];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -53,7 +53,7 @@ ComputeBodyLocal::ComputeBodyLocal(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec) error->all(FLERR,"Compute body/local requires atom style body");
|
if (!avec) error->all(FLERR,"Compute body/local requires atom style body");
|
||||||
bptr = avec->bptr;
|
bptr = avec->bptr;
|
||||||
|
|
||||||
|
|||||||
@ -87,7 +87,7 @@ void ComputeTempBody::init()
|
|||||||
{
|
{
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Compute temp/body requires atom style body");
|
error->all(FLERR,"Compute temp/body requires atom style body");
|
||||||
|
|
||||||
|
|||||||
@ -37,7 +37,7 @@ FixNHBody::FixNHBody(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixNHBody::init()
|
void FixNHBody::init()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,
|
error->all(FLERR,
|
||||||
"Compute nvt/nph/npt body requires atom style body");
|
"Compute nvt/nph/npt body requires atom style body");
|
||||||
|
|||||||
@ -30,7 +30,7 @@ FixNVEBody::FixNVEBody(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixNVEBody::init()
|
void FixNVEBody::init()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec) error->all(FLERR,"Fix nve/body requires atom style body");
|
if (!avec) error->all(FLERR,"Fix nve/body requires atom style body");
|
||||||
|
|
||||||
// check that all particles are bodies
|
// check that all particles are bodies
|
||||||
|
|||||||
@ -179,13 +179,13 @@ void FixWallBodyPolygon::init()
|
|||||||
{
|
{
|
||||||
dt = update->dt;
|
dt = update->dt;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
||||||
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
||||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||||
"body style rounded/polygon");
|
"body style rounded/polygon");
|
||||||
bptr = dynamic_cast<BodyRoundedPolygon *>( avec->bptr);
|
bptr = dynamic_cast<BodyRoundedPolygon *>(avec->bptr);
|
||||||
|
|
||||||
// set pairstyle from body/polygonular pair style
|
// set pairstyle from body/polygonular pair style
|
||||||
|
|
||||||
|
|||||||
@ -184,13 +184,13 @@ void FixWallBodyPolyhedron::init()
|
|||||||
{
|
{
|
||||||
dt = update->dt;
|
dt = update->dt;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body");
|
error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body");
|
||||||
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
||||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||||
"body style rounded/polyhedron");
|
"body style rounded/polyhedron");
|
||||||
bptr = dynamic_cast<BodyRoundedPolyhedron *>( avec->bptr);
|
bptr = dynamic_cast<BodyRoundedPolyhedron *>(avec->bptr);
|
||||||
|
|
||||||
// set pairstyle from body/polyhedronular pair style
|
// set pairstyle from body/polyhedronular pair style
|
||||||
|
|
||||||
|
|||||||
@ -416,11 +416,11 @@ void PairBodyNparticle::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairBodyNparticle::init_style()
|
void PairBodyNparticle::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body");
|
if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body");
|
||||||
if (strcmp(avec->bptr->style,"nparticle") != 0)
|
if (strcmp(avec->bptr->style,"nparticle") != 0)
|
||||||
error->all(FLERR,"Pair body/nparticle requires body style nparticle");
|
error->all(FLERR,"Pair body/nparticle requires body style nparticle");
|
||||||
bptr = dynamic_cast<BodyNparticle *>( avec->bptr);
|
bptr = dynamic_cast<BodyNparticle *>(avec->bptr);
|
||||||
|
|
||||||
neighbor->add_request(this);
|
neighbor->add_request(this);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -411,13 +411,13 @@ void PairBodyRoundedPolygon::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairBodyRoundedPolygon::init_style()
|
void PairBodyRoundedPolygon::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
||||||
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
||||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||||
"body style rounded/polygon");
|
"body style rounded/polygon");
|
||||||
bptr = dynamic_cast<BodyRoundedPolygon *>( avec->bptr);
|
bptr = dynamic_cast<BodyRoundedPolygon *>(avec->bptr);
|
||||||
|
|
||||||
if (force->newton_pair == 0)
|
if (force->newton_pair == 0)
|
||||||
error->all(FLERR,"Pair style body/rounded/polygon requires "
|
error->all(FLERR,"Pair style body/rounded/polygon requires "
|
||||||
|
|||||||
@ -390,13 +390,13 @@ void PairBodyRoundedPolyhedron::coeff(int narg, char **arg)
|
|||||||
|
|
||||||
void PairBodyRoundedPolyhedron::init_style()
|
void PairBodyRoundedPolyhedron::init_style()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecBody *>( atom->style_match("body"));
|
avec = dynamic_cast<AtomVecBody *>(atom->style_match("body"));
|
||||||
if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
if (!avec) error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||||
"atom style body");
|
"atom style body");
|
||||||
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
||||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||||
"body style rounded/polyhedron");
|
"body style rounded/polyhedron");
|
||||||
bptr = dynamic_cast<BodyRoundedPolyhedron *>( avec->bptr);
|
bptr = dynamic_cast<BodyRoundedPolyhedron *>(avec->bptr);
|
||||||
|
|
||||||
if (force->newton_pair == 0)
|
if (force->newton_pair == 0)
|
||||||
error->all(FLERR,"Pair style body/rounded/polyhedron requires "
|
error->all(FLERR,"Pair style body/rounded/polyhedron requires "
|
||||||
|
|||||||
@ -84,9 +84,9 @@ void BondBPM::init_style()
|
|||||||
{
|
{
|
||||||
if (id_fix_store_local) {
|
if (id_fix_store_local) {
|
||||||
auto ifix = modify->get_fix_by_id(id_fix_store_local);
|
auto ifix = modify->get_fix_by_id(id_fix_store_local);
|
||||||
if (!ifix) error->all(FLERR, "Cannot find fix STORE/LOCAL id {}",id_fix_store_local);
|
if (!ifix) error->all(FLERR, "Cannot find fix STORE/LOCAL id {}", id_fix_store_local);
|
||||||
if (strcmp(ifix->style, "STORE/LOCAL") != 0)
|
if (strcmp(ifix->style, "STORE/LOCAL") != 0)
|
||||||
error->all(FLERR, "Incorrect fix style matched, not STORE/LOCAL: {}",ifix->style);
|
error->all(FLERR, "Incorrect fix style matched, not STORE/LOCAL: {}", ifix->style);
|
||||||
fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
|
fix_store_local = dynamic_cast<FixStoreLocal *>(ifix);
|
||||||
fix_store_local->nvalues = nvalues;
|
fix_store_local->nvalues = nvalues;
|
||||||
}
|
}
|
||||||
|
|||||||
@ -70,7 +70,7 @@ void FixBrownian::initial_integrate(int /*vflag */)
|
|||||||
initial_integrate_templated<1, 0, 0>();
|
initial_integrate_templated<1, 0, 0>();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -126,4 +126,4 @@ template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void FixBrownian::initial_int
|
|||||||
v[i][2] = dz / dt;
|
v[i][2] = dz / dt;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -157,7 +157,7 @@ void FixBrownianAsphere::initial_integrate(int /*vflag */)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -296,5 +296,4 @@ void FixBrownianAsphere::initial_integrate_templated()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
}
|
|
||||||
|
|||||||
@ -85,7 +85,7 @@ void FixBrownianSphere::initial_integrate(int /*vflag */)
|
|||||||
initial_integrate_templated<1, 0, 0, 0>();
|
initial_integrate_templated<1, 0, 0, 0>();
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
|||||||
@ -37,7 +37,7 @@ FixNVEDot::FixNVEDot(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
void FixNVEDot::init()
|
void FixNVEDot::init()
|
||||||
{
|
{
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Compute nve/dot requires atom style ellipsoid");
|
error->all(FLERR,"Compute nve/dot requires atom style ellipsoid");
|
||||||
|
|
||||||
|
|||||||
@ -89,7 +89,7 @@ void FixNVEDotcLangevin::init()
|
|||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
|
|
||||||
if (!avec)
|
if (!avec)
|
||||||
error->all(FLERR,"Fix nve/dotc/langevin requires atom style ellipsoid");
|
error->all(FLERR,"Fix nve/dotc/langevin requires atom style ellipsoid");
|
||||||
|
|||||||
@ -139,7 +139,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag)
|
|||||||
int newton_pair = force->newton_pair;
|
int newton_pair = force->newton_pair;
|
||||||
int *alist,*blist,*numneigh,**firstneigh;
|
int *alist,*blist,*numneigh,**firstneigh;
|
||||||
|
|
||||||
auto avec = dynamic_cast<AtomVecEllipsoid *>( atom->style_match("ellipsoid"));
|
auto avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
|
||||||
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||||
int *ellipsoid = atom->ellipsoid;
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
|
||||||
|
|||||||
@ -362,7 +362,7 @@ void PairBrownianPoly::init_style()
|
|||||||
error->all(FLERR,
|
error->all(FLERR,
|
||||||
"Cannot use multiple fix wall commands with pair brownian");
|
"Cannot use multiple fix wall commands with pair brownian");
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -563,7 +563,7 @@ void PairLubricate::init_style()
|
|||||||
for (int i = 0; i < modify->nfix; i++) {
|
for (int i = 0; i < modify->nfix; i++) {
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
shearing = flagdeform = 1;
|
shearing = flagdeform = 1;
|
||||||
if ((dynamic_cast<FixDeform *>( modify->fix[i]))->remapflag != Domain::V_REMAP)
|
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
|
||||||
error->all(FLERR,"Using pair lubricate with inconsistent "
|
error->all(FLERR,"Using pair lubricate with inconsistent "
|
||||||
"fix deform remap option");
|
"fix deform remap option");
|
||||||
}
|
}
|
||||||
@ -572,7 +572,7 @@ void PairLubricate::init_style()
|
|||||||
error->all(FLERR,
|
error->all(FLERR,
|
||||||
"Cannot use multiple fix wall commands with pair lubricate");
|
"Cannot use multiple fix wall commands with pair lubricate");
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1801,7 +1801,7 @@ void PairLubricateU::init_style()
|
|||||||
"Cannot use multiple fix wall commands with "
|
"Cannot use multiple fix wall commands with "
|
||||||
"pair lubricateU");
|
"pair lubricateU");
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -1165,7 +1165,7 @@ void PairLubricateUPoly::init_style()
|
|||||||
"Cannot use multiple fix wall commands with "
|
"Cannot use multiple fix wall commands with "
|
||||||
"pair lubricateU");
|
"pair lubricateU");
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -463,7 +463,7 @@ void PairLubricatePoly::init_style()
|
|||||||
for (int i = 0; i < modify->nfix; i++) {
|
for (int i = 0; i < modify->nfix; i++) {
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
shearing = flagdeform = 1;
|
shearing = flagdeform = 1;
|
||||||
if ((dynamic_cast<FixDeform *>( modify->fix[i]))->remapflag != Domain::V_REMAP)
|
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
|
||||||
error->all(FLERR,"Using pair lubricate with inconsistent "
|
error->all(FLERR,"Using pair lubricate with inconsistent "
|
||||||
"fix deform remap option");
|
"fix deform remap option");
|
||||||
}
|
}
|
||||||
@ -473,15 +473,15 @@ void PairLubricatePoly::init_style()
|
|||||||
"Cannot use multiple fix wall commands with "
|
"Cannot use multiple fix wall commands with "
|
||||||
"pair lubricate/poly");
|
"pair lubricate/poly");
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
if (wallfix->xflag) flagwall = 2; // Moving walls exist
|
||||||
}
|
}
|
||||||
|
|
||||||
if (strstr(modify->fix[i]->style,"wall") != nullptr) {
|
if (strstr(modify->fix[i]->style,"wall") != nullptr) {
|
||||||
flagwall = 1; // Walls exist
|
flagwall = 1; // Walls exist
|
||||||
if ((dynamic_cast<FixWall *>( modify->fix[i]))->xflag) {
|
if ((dynamic_cast<FixWall *>(modify->fix[i]))->xflag) {
|
||||||
flagwall = 2; // Moving walls exist
|
flagwall = 2; // Moving walls exist
|
||||||
wallfix = dynamic_cast<FixWall *>( modify->fix[i]);
|
wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -539,7 +539,7 @@ void PairLubricatePoly::init_style()
|
|||||||
for (int i = 0; i < modify->nfix; i++)
|
for (int i = 0; i < modify->nfix; i++)
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
shearing = 1;
|
shearing = 1;
|
||||||
if ((dynamic_cast<FixDeform *>( modify->fix[i]))->remapflag != Domain::V_REMAP)
|
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
|
||||||
error->all(FLERR,"Using pair lubricate/poly with inconsistent "
|
error->all(FLERR,"Using pair lubricate/poly with inconsistent "
|
||||||
"fix deform remap option");
|
"fix deform remap option");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -101,7 +101,8 @@ class colvarproxy_lammps : public colvarproxy {
|
|||||||
void log(std::string const &message) override;
|
void log(std::string const &message) override;
|
||||||
void error(std::string const &message) override;
|
void error(std::string const &message) override;
|
||||||
|
|
||||||
cvm::rvector position_distance(cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const override;
|
cvm::rvector position_distance(cvm::atom_pos const &pos1,
|
||||||
|
cvm::atom_pos const &pos2) const override;
|
||||||
|
|
||||||
cvm::real rand_gaussian(void) override { return _random->gaussian(); };
|
cvm::real rand_gaussian(void) override { return _random->gaussian(); };
|
||||||
|
|
||||||
|
|||||||
@ -21,7 +21,7 @@
|
|||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
GzFileWriter::GzFileWriter() : compression_level(Z_BEST_COMPRESSION), gzFp(nullptr) {}
|
GzFileWriter::GzFileWriter() : compression_level(Z_BEST_COMPRESSION), gzFp(nullptr) {}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
|||||||
@ -24,7 +24,7 @@
|
|||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
ZstdFileWriter::ZstdFileWriter() :
|
ZstdFileWriter::ZstdFileWriter() :
|
||||||
compression_level(0), checksum_flag(1), cctx(nullptr), fp(nullptr)
|
compression_level(0), checksum_flag(1), cctx(nullptr), fp(nullptr)
|
||||||
{
|
{
|
||||||
out_buffer_size = ZSTD_CStreamOutSize();
|
out_buffer_size = ZSTD_CStreamOutSize();
|
||||||
out_buffer = new char[out_buffer_size];
|
out_buffer = new char[out_buffer_size];
|
||||||
|
|||||||
@ -101,29 +101,30 @@ void AtomVecDielectric::init()
|
|||||||
// with pair styles using coulomb without dielectric support.
|
// with pair styles using coulomb without dielectric support.
|
||||||
|
|
||||||
std::string pair_style(force->pair_style);
|
std::string pair_style(force->pair_style);
|
||||||
if ((pair_style != "none") && (pair_style != "zero") && !utils::strmatch(force->pair_style,"/dielectric")) {
|
if ((pair_style != "none") && (pair_style != "zero") &&
|
||||||
|
!utils::strmatch(force->pair_style, "/dielectric")) {
|
||||||
bool mismatch = false;
|
bool mismatch = false;
|
||||||
if (utils::strmatch(force->pair_style,"^reaxff")) mismatch = true;
|
if (utils::strmatch(force->pair_style, "^reaxff")) mismatch = true;
|
||||||
if (utils::strmatch(force->pair_style,"^comb")) mismatch = true;
|
if (utils::strmatch(force->pair_style, "^comb")) mismatch = true;
|
||||||
if (utils::strmatch(force->pair_style,"coul")) mismatch = true;
|
if (utils::strmatch(force->pair_style, "coul")) mismatch = true;
|
||||||
if (utils::strmatch(force->pair_style,"tip4p")) mismatch = true;
|
if (utils::strmatch(force->pair_style, "tip4p")) mismatch = true;
|
||||||
if (utils::strmatch(force->pair_style,"dipole")) mismatch = true;
|
if (utils::strmatch(force->pair_style, "dipole")) mismatch = true;
|
||||||
|
|
||||||
if (utils::strmatch(force->pair_style,"^hybrid")) {
|
if (utils::strmatch(force->pair_style, "^hybrid")) {
|
||||||
auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
|
auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
|
||||||
if (hybrid) {
|
if (hybrid) {
|
||||||
for (int i = 0; i < hybrid->nstyles; i++) {
|
for (int i = 0; i < hybrid->nstyles; i++) {
|
||||||
if (utils::strmatch(hybrid->keywords[i],"^reaxff")) mismatch = true;
|
if (utils::strmatch(hybrid->keywords[i], "^reaxff")) mismatch = true;
|
||||||
if (utils::strmatch(hybrid->keywords[i],"^comb")) mismatch = true;
|
if (utils::strmatch(hybrid->keywords[i], "^comb")) mismatch = true;
|
||||||
if (utils::strmatch(hybrid->keywords[i],"coul")) mismatch = true;
|
if (utils::strmatch(hybrid->keywords[i], "coul")) mismatch = true;
|
||||||
if (utils::strmatch(hybrid->keywords[i],"tip4p")) mismatch = true;
|
if (utils::strmatch(hybrid->keywords[i], "tip4p")) mismatch = true;
|
||||||
if (utils::strmatch(hybrid->keywords[i],"dipole")) mismatch = true;
|
if (utils::strmatch(hybrid->keywords[i], "dipole")) mismatch = true;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
if (mismatch)
|
if (mismatch)
|
||||||
error->all(FLERR, "Pair style {} is not compatible with atom style {}",
|
error->all(FLERR, "Pair style {} is not compatible with atom style {}", pair_style,
|
||||||
pair_style, atom->get_style());
|
atom->get_style());
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -58,7 +58,7 @@ void MSMDielectric::init()
|
|||||||
{
|
{
|
||||||
MSM::init();
|
MSM::init();
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
|
avec = dynamic_cast<AtomVecDielectric *>(atom->style_match("dielectric"));
|
||||||
if (!avec) error->all(FLERR,"msm/dielectric requires atom style dielectric");
|
if (!avec) error->all(FLERR,"msm/dielectric requires atom style dielectric");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -36,8 +36,7 @@ using MathConst::MY_PIS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
PairCoulLongDielectric::PairCoulLongDielectric(LAMMPS *_lmp) :
|
PairCoulLongDielectric::PairCoulLongDielectric(LAMMPS *_lmp) : PairCoulLong(_lmp), efield(nullptr)
|
||||||
PairCoulLong(_lmp), efield(nullptr)
|
|
||||||
{
|
{
|
||||||
nmax = 0;
|
nmax = 0;
|
||||||
single_enable = 0;
|
single_enable = 0;
|
||||||
@ -177,7 +176,8 @@ void PairCoulLongDielectric::compute(int eflag, int vflag)
|
|||||||
ecoul = scale[itype][jtype] * qtmp * q[j] * 0.5 * (etmp + eps[j]) * table;
|
ecoul = scale[itype][jtype] * qtmp * q[j] * 0.5 * (etmp + eps[j]) * table;
|
||||||
}
|
}
|
||||||
if (factor_coul < 1.0) ecoul -= (1.0 - factor_coul) * prefactor;
|
if (factor_coul < 1.0) ecoul -= (1.0 - factor_coul) * prefactor;
|
||||||
} else ecoul = 0.0;
|
} else
|
||||||
|
ecoul = 0.0;
|
||||||
|
|
||||||
if (evflag) ev_tally_full(i, 0.0, ecoul, fpair_i, delx, dely, delz);
|
if (evflag) ev_tally_full(i, 0.0, ecoul, fpair_i, delx, dely, delz);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -159,7 +159,7 @@ void PairLJCutCoulCutDielectric::compute(int eflag, int vflag)
|
|||||||
|
|
||||||
if (eflag) {
|
if (eflag) {
|
||||||
if (rsq < cut_coulsq[itype][jtype]) {
|
if (rsq < cut_coulsq[itype][jtype]) {
|
||||||
ecoul = factor_coul * qqrd2e * qtmp * q[j] * 0.5 * (etmp + eps[j]) *rinv;
|
ecoul = factor_coul * qqrd2e * qtmp * q[j] * 0.5 * (etmp + eps[j]) * rinv;
|
||||||
} else
|
} else
|
||||||
ecoul = 0.0;
|
ecoul = 0.0;
|
||||||
if (rsq < cut_ljsq[itype][jtype]) {
|
if (rsq < cut_ljsq[itype][jtype]) {
|
||||||
|
|||||||
@ -61,7 +61,7 @@ PPPMDielectric::PPPMDielectric(LAMMPS *_lmp) : PPPM(_lmp)
|
|||||||
// no warnings about non-neutral systems from qsum_qsq()
|
// no warnings about non-neutral systems from qsum_qsq()
|
||||||
warn_nonneutral = 2;
|
warn_nonneutral = 2;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
|
avec = dynamic_cast<AtomVecDielectric *>(atom->style_match("dielectric"));
|
||||||
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -72,7 +72,7 @@ PPPMDispDielectric::PPPMDispDielectric(LAMMPS *_lmp) : PPPMDisp(_lmp)
|
|||||||
phi = nullptr;
|
phi = nullptr;
|
||||||
potflag = 0;
|
potflag = 0;
|
||||||
|
|
||||||
avec = dynamic_cast<AtomVecDielectric *>( atom->style_match("dielectric"));
|
avec = dynamic_cast<AtomVecDielectric *>(atom->style_match("dielectric"));
|
||||||
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
if (!avec) error->all(FLERR,"pppm/dielectric requires atom style dielectric");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -67,7 +67,7 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
|
error->all(FLERR,"Compute ID for fix saed/vtk does not exist");
|
||||||
|
|
||||||
// Check that specified compute is for SAED
|
// Check that specified compute is for SAED
|
||||||
compute_saed = dynamic_cast<ComputeSAED *>( modify->compute[icompute]);
|
compute_saed = dynamic_cast<ComputeSAED *>(modify->compute[icompute]);
|
||||||
if (strcmp(compute_saed->style,"saed") != 0)
|
if (strcmp(compute_saed->style,"saed") != 0)
|
||||||
error->all(FLERR,"Fix saed/vtk has invalid compute assigned");
|
error->all(FLERR,"Fix saed/vtk has invalid compute assigned");
|
||||||
|
|
||||||
|
|||||||
@ -30,9 +30,9 @@ FixDPDenergy::FixDPDenergy(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
if (narg != 3 ) error->all(FLERR,"Illegal fix dpd/energy command");
|
if (narg != 3 ) error->all(FLERR,"Illegal fix dpd/energy command");
|
||||||
|
|
||||||
pairDPDE = nullptr;
|
pairDPDE = nullptr;
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy",1));
|
||||||
if (pairDPDE == nullptr)
|
if (pairDPDE == nullptr)
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy/kk",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy/kk",1));
|
||||||
|
|
||||||
if (pairDPDE == nullptr)
|
if (pairDPDE == nullptr)
|
||||||
error->all(FLERR,"Must use pair_style dpd/fdt/energy with fix dpd/energy");
|
error->all(FLERR,"Must use pair_style dpd/fdt/energy with fix dpd/energy");
|
||||||
|
|||||||
@ -319,9 +319,9 @@ void FixRX::post_constructor()
|
|||||||
newcmd1 += " ghost yes";
|
newcmd1 += " ghost yes";
|
||||||
newcmd2 += " ghost yes";
|
newcmd2 += " ghost yes";
|
||||||
|
|
||||||
fix_species = dynamic_cast<FixPropertyAtom *>( modify->add_fix(newcmd1));
|
fix_species = dynamic_cast<FixPropertyAtom *>(modify->add_fix(newcmd1));
|
||||||
restartFlag = fix_species->restart_reset;
|
restartFlag = fix_species->restart_reset;
|
||||||
fix_species_old = dynamic_cast<FixPropertyAtom *>( modify->add_fix(newcmd2));
|
fix_species_old = dynamic_cast<FixPropertyAtom *>(modify->add_fix(newcmd2));
|
||||||
|
|
||||||
if (nspecies==0) error->all(FLERR,"There are no rx species specified.");
|
if (nspecies==0) error->all(FLERR,"There are no rx species specified.");
|
||||||
|
|
||||||
@ -579,9 +579,9 @@ int FixRX::setmask()
|
|||||||
|
|
||||||
void FixRX::init()
|
void FixRX::init()
|
||||||
{
|
{
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy",1));
|
||||||
if (pairDPDE == nullptr)
|
if (pairDPDE == nullptr)
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy/kk",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy/kk",1));
|
||||||
|
|
||||||
if (pairDPDE == nullptr)
|
if (pairDPDE == nullptr)
|
||||||
error->all(FLERR,"Must use pair_style dpd/fdt/energy with fix rx");
|
error->all(FLERR,"Must use pair_style dpd/fdt/energy with fix rx");
|
||||||
|
|||||||
@ -94,10 +94,10 @@ FixShardlow::FixShardlow(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
pairDPD = nullptr;
|
pairDPD = nullptr;
|
||||||
pairDPDE = nullptr;
|
pairDPDE = nullptr;
|
||||||
pairDPD = dynamic_cast<PairDPDfdt *>( force->pair_match("dpd/fdt",1));
|
pairDPD = dynamic_cast<PairDPDfdt *>(force->pair_match("dpd/fdt",1));
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy",1));
|
||||||
if (pairDPDE == nullptr)
|
if (pairDPDE == nullptr)
|
||||||
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>( force->pair_match("dpd/fdt/energy/kk",1));
|
pairDPDE = dynamic_cast<PairDPDfdtEnergy *>(force->pair_match("dpd/fdt/energy/kk",1));
|
||||||
|
|
||||||
maxRNG = 0;
|
maxRNG = 0;
|
||||||
if (pairDPDE) {
|
if (pairDPDE) {
|
||||||
|
|||||||
@ -67,7 +67,7 @@ void ComputeTempDrude::init()
|
|||||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||||
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
||||||
if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
|
if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
|
|
||||||
if (!comm->ghost_velocity)
|
if (!comm->ghost_velocity)
|
||||||
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
|
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
|
||||||
|
|||||||
@ -148,7 +148,7 @@ void FixLangevinDrude::init()
|
|||||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||||
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
||||||
if (ifix == modify->nfix) error->all(FLERR, "fix langevin/drude requires fix drude");
|
if (ifix == modify->nfix) error->all(FLERR, "fix langevin/drude requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -523,7 +523,7 @@ FixTGNHDrude::FixTGNHDrude(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||||
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
||||||
if (ifix == modify->nfix) error->all(FLERR, "fix tgnh/drude requires fix drude");
|
if (ifix == modify->nfix) error->all(FLERR, "fix tgnh/drude requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
|
|
||||||
// make sure ghost atoms have velocity
|
// make sure ghost atoms have velocity
|
||||||
if (!comm->ghost_velocity)
|
if (!comm->ghost_velocity)
|
||||||
@ -595,7 +595,7 @@ void FixTGNHDrude::init()
|
|||||||
if (pstat_flag)
|
if (pstat_flag)
|
||||||
for (int i = 0; i < modify->nfix; i++)
|
for (int i = 0; i < modify->nfix; i++)
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
int *dimflag = (dynamic_cast<FixDeform *>( modify->fix[i]))->dimflag;
|
int *dimflag = (dynamic_cast<FixDeform *>(modify->fix[i]))->dimflag;
|
||||||
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
|
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
|
||||||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
|
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
|
||||||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
|
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
|
||||||
@ -664,8 +664,8 @@ void FixTGNHDrude::init()
|
|||||||
else kspace_flag = 0;
|
else kspace_flag = 0;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
|
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
dto = 0.5*step_respa[0];
|
dto = 0.5*step_respa[0];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -289,7 +289,7 @@ void PairCoulTT::init_style()
|
|||||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||||
if (utils::strmatch(modify->fix[ifix]->style,"^drude")) break;
|
if (utils::strmatch(modify->fix[ifix]->style,"^drude")) break;
|
||||||
if (ifix == modify->nfix) error->all(FLERR, "Pair coul/tt requires fix drude");
|
if (ifix == modify->nfix) error->all(FLERR, "Pair coul/tt requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
|
|
||||||
neighbor->add_request(this);
|
neighbor->add_request(this);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -364,7 +364,7 @@ void PairLJCutTholeLong::init_style()
|
|||||||
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
||||||
if (ifix == modify->nfix)
|
if (ifix == modify->nfix)
|
||||||
error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude");
|
error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
|
|
||||||
neighbor->add_request(this);
|
neighbor->add_request(this);
|
||||||
|
|
||||||
|
|||||||
@ -258,7 +258,7 @@ void PairThole::init_style()
|
|||||||
for (ifix = 0; ifix < modify->nfix; ifix++)
|
for (ifix = 0; ifix < modify->nfix; ifix++)
|
||||||
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
|
||||||
if (ifix == modify->nfix) error->all(FLERR, "Pair thole requires fix drude");
|
if (ifix == modify->nfix) error->all(FLERR, "Pair thole requires fix drude");
|
||||||
fix_drude = dynamic_cast<FixDrude *>( modify->fix[ifix]);
|
fix_drude = dynamic_cast<FixDrude *>(modify->fix[ifix]);
|
||||||
|
|
||||||
neighbor->add_request(this);
|
neighbor->add_request(this);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -120,7 +120,7 @@ void AtomVecElectron::data_atom_post(int ilocal)
|
|||||||
int AtomVecElectron::property_atom(const std::string &name)
|
int AtomVecElectron::property_atom(const std::string &name)
|
||||||
{
|
{
|
||||||
if (name == "espin") return 0;
|
if (name == "espin") return 0;
|
||||||
if (name == "spin") return 0; // backward compatibility
|
if (name == "spin") return 0; // backward compatibility
|
||||||
if (name == "eradius") return 1;
|
if (name == "eradius") return 1;
|
||||||
if (name == "ervel") return 2;
|
if (name == "ervel") return 2;
|
||||||
if (name == "erforce") return 3;
|
if (name == "erforce") return 3;
|
||||||
|
|||||||
@ -74,7 +74,7 @@ void ComputeTempDeformEff::init()
|
|||||||
int i;
|
int i;
|
||||||
for (i = 0; i < modify->nfix; i++)
|
for (i = 0; i < modify->nfix; i++)
|
||||||
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
if (strcmp(modify->fix[i]->style,"deform") == 0) {
|
||||||
if ((dynamic_cast<FixDeform *>( modify->fix[i]))->remapflag == Domain::X_REMAP &&
|
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag == Domain::X_REMAP &&
|
||||||
comm->me == 0)
|
comm->me == 0)
|
||||||
error->warning(FLERR,"Using compute temp/deform/eff with inconsistent "
|
error->warning(FLERR,"Using compute temp/deform/eff with inconsistent "
|
||||||
"fix deform remap option");
|
"fix deform remap option");
|
||||||
|
|||||||
@ -59,7 +59,7 @@ void FixNVEEff::init()
|
|||||||
dtf = 0.5 * update->dt * force->ftm2v;
|
dtf = 0.5 * update->dt * force->ftm2v;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
@ -70,7 +70,7 @@ void FixNVTSllodEff::init()
|
|||||||
int i;
|
int i;
|
||||||
for (i = 0; i < modify->nfix; i++)
|
for (i = 0; i < modify->nfix; i++)
|
||||||
if (strncmp(modify->fix[i]->style,"deform",6) == 0) {
|
if (strncmp(modify->fix[i]->style,"deform",6) == 0) {
|
||||||
if ((dynamic_cast<FixDeform *>( modify->fix[i]))->remapflag != Domain::V_REMAP)
|
if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
|
||||||
error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform "
|
error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform "
|
||||||
"remap option");
|
"remap option");
|
||||||
break;
|
break;
|
||||||
|
|||||||
@ -57,8 +57,9 @@ ElectrodeVector::~ElectrodeVector()
|
|||||||
utils::logmesg(lmp, fmt::format("B time: {:.4g} s\n", b_time_total));
|
utils::logmesg(lmp, fmt::format("B time: {:.4g} s\n", b_time_total));
|
||||||
utils::logmesg(lmp, fmt::format("B kspace time: {:.4g} s\n", kspace_time_total));
|
utils::logmesg(lmp, fmt::format("B kspace time: {:.4g} s\n", kspace_time_total));
|
||||||
utils::logmesg(lmp, fmt::format("B pair time: {:.4g} s\n", pair_time_total));
|
utils::logmesg(lmp, fmt::format("B pair time: {:.4g} s\n", pair_time_total));
|
||||||
utils::logmesg(lmp, fmt::format("B boundary time: {:.4g} s\n", boundary_time_total));
|
utils::logmesg(lmp, fmt::format("B boundary time: {:.4g} s\n", boundary_time_total));
|
||||||
} catch (std::exception &) {}
|
} catch (std::exception &) {
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -1058,7 +1058,8 @@ FixElectrodeConp::~FixElectrodeConp()
|
|||||||
try {
|
try {
|
||||||
utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time));
|
utils::logmesg(lmp, fmt::format("Multiplication time: {:.4g} s\n", mult_time));
|
||||||
utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time));
|
utils::logmesg(lmp, fmt::format("Update time: {:.4g} s\n", update_time));
|
||||||
} catch (std::exception &) {}
|
} catch (std::exception &) {
|
||||||
|
}
|
||||||
}
|
}
|
||||||
if (!modify->get_fix_by_id(id)) // avoid segfault if derived fixes' ctor throws err
|
if (!modify->get_fix_by_id(id)) // avoid segfault if derived fixes' ctor throws err
|
||||||
atom->delete_callback(id, Atom::GROW); // atomvec track local electrode atoms
|
atom->delete_callback(id, Atom::GROW); // atomvec track local electrode atoms
|
||||||
@ -1107,7 +1108,7 @@ void FixElectrodeConp::write_to_file(FILE *file, const std::vector<tagint> &tags
|
|||||||
|
|
||||||
/*----------------------------------------------------------------------- */
|
/*----------------------------------------------------------------------- */
|
||||||
|
|
||||||
void FixElectrodeConp::read_from_file(const std::string& input_file, double **array,
|
void FixElectrodeConp::read_from_file(const std::string &input_file, double **array,
|
||||||
const std::string &filetype)
|
const std::string &filetype)
|
||||||
{
|
{
|
||||||
if (comm->me == 0) {
|
if (comm->me == 0) {
|
||||||
|
|||||||
@ -101,7 +101,7 @@ class FixElectrodeConp : public Fix {
|
|||||||
double potential_energy(int);
|
double potential_energy(int);
|
||||||
double self_energy(int);
|
double self_energy(int);
|
||||||
void write_to_file(FILE *, const std::vector<tagint> &, const std::vector<std::vector<double>> &);
|
void write_to_file(FILE *, const std::vector<tagint> &, const std::vector<std::vector<double>> &);
|
||||||
void read_from_file(const std::string& input_file, double **, const std::string &);
|
void read_from_file(const std::string &input_file, double **, const std::string &);
|
||||||
void compute_sd_vectors();
|
void compute_sd_vectors();
|
||||||
void compute_sd_vectors_ffield();
|
void compute_sd_vectors_ffield();
|
||||||
std::vector<int> setvars_types, setvars_groups, setvars_vars;
|
std::vector<int> setvars_types, setvars_groups, setvars_vars;
|
||||||
|
|||||||
@ -55,7 +55,7 @@ FixElectrodeThermo::FixElectrodeThermo(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
FixElectrodeThermo::~FixElectrodeThermo()
|
FixElectrodeThermo::~FixElectrodeThermo()
|
||||||
{
|
{
|
||||||
delete thermo_random;
|
delete thermo_random;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------- */
|
/* ----------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -130,7 +130,7 @@ void FixAddTorque::init()
|
|||||||
else varflag = CONSTANT;
|
else varflag = CONSTANT;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
ilevel_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels-1;
|
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels-1;
|
||||||
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
|
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -142,9 +142,9 @@ void FixAddTorque::setup(int vflag)
|
|||||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
else {
|
else {
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(ilevel_respa);
|
||||||
post_force_respa(vflag,ilevel_respa,0);
|
post_force_respa(vflag,ilevel_respa,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(ilevel_respa);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -71,7 +71,7 @@ int FixDrag::setmask()
|
|||||||
void FixDrag::init()
|
void FixDrag::init()
|
||||||
{
|
{
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
ilevel_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels-1;
|
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels-1;
|
||||||
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
|
if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -83,9 +83,9 @@ void FixDrag::setup(int vflag)
|
|||||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
else {
|
else {
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(ilevel_respa);
|
||||||
post_force_respa(vflag,ilevel_respa,0);
|
post_force_respa(vflag,ilevel_respa,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(ilevel_respa);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -139,9 +139,9 @@ void FixElectronStoppingFit::setup(int vflag)
|
|||||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
else {
|
else {
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(nlevels_respa-1);
|
||||||
post_force_respa(vflag,nlevels_respa-1,0);
|
post_force_respa(vflag,nlevels_respa-1,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(nlevels_respa-1);
|
||||||
};
|
};
|
||||||
};
|
};
|
||||||
|
|
||||||
|
|||||||
@ -158,8 +158,8 @@ void FixFFL::init() {
|
|||||||
}
|
}
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
|
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
}
|
}
|
||||||
|
|
||||||
init_ffl();
|
init_ffl();
|
||||||
@ -182,9 +182,9 @@ void FixFFL::setup(int vflag) {
|
|||||||
if (utils::strmatch(update->integrate_style,"^verlet"))
|
if (utils::strmatch(update->integrate_style,"^verlet"))
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
else {
|
else {
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(nlevels_respa-1);
|
||||||
post_force_respa(vflag,nlevels_respa-1,0);
|
post_force_respa(vflag,nlevels_respa-1,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(nlevels_respa-1);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -279,7 +279,7 @@ void FixFilterCorotate::init()
|
|||||||
// set ptrs to rRESPA variables
|
// set ptrs to rRESPA variables
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
nlevels_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels;
|
nlevels_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels;
|
||||||
}
|
}
|
||||||
else error->all(FLERR,"Fix filter/corotate requires rRESPA!");
|
else error->all(FLERR,"Fix filter/corotate requires rRESPA!");
|
||||||
|
|
||||||
@ -656,9 +656,9 @@ void FixFilterCorotate::pre_neighbor()
|
|||||||
|
|
||||||
void FixFilterCorotate::setup(int vflag)
|
void FixFilterCorotate::setup(int vflag)
|
||||||
{
|
{
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(nlevels_respa-1);
|
||||||
post_force_respa(vflag,nlevels_respa-1,0);
|
post_force_respa(vflag,nlevels_respa-1,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(nlevels_respa-1);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(nlevels_respa-1);
|
||||||
}
|
}
|
||||||
|
|
||||||
void FixFilterCorotate::setup_pre_force_respa(int vflag,int ilevel) {
|
void FixFilterCorotate::setup_pre_force_respa(int vflag,int ilevel) {
|
||||||
|
|||||||
@ -123,7 +123,7 @@ void FixFlowGauss::init()
|
|||||||
//if respa level specified by fix_modify, then override default (outermost)
|
//if respa level specified by fix_modify, then override default (outermost)
|
||||||
//if specified level too high, set to max level
|
//if specified level too high, set to max level
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
ilevel_respa = (dynamic_cast<Respa *>( update->integrate))->nlevels-1;
|
ilevel_respa = (dynamic_cast<Respa *>(update->integrate))->nlevels-1;
|
||||||
if (respa_level >= 0)
|
if (respa_level >= 0)
|
||||||
ilevel_respa = MIN(respa_level,ilevel_respa);
|
ilevel_respa = MIN(respa_level,ilevel_respa);
|
||||||
}
|
}
|
||||||
@ -146,9 +146,9 @@ void FixFlowGauss::setup(int vflag)
|
|||||||
error->all(FLERR,"Invalid group mass in fix flow/gauss");
|
error->all(FLERR,"Invalid group mass in fix flow/gauss");
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa")) {
|
if (utils::strmatch(update->integrate_style,"^respa")) {
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_flevel_f(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_flevel_f(ilevel_respa);
|
||||||
post_force_respa(vflag,ilevel_respa,0);
|
post_force_respa(vflag,ilevel_respa,0);
|
||||||
(dynamic_cast<Respa *>( update->integrate))->copy_f_flevel(ilevel_respa);
|
(dynamic_cast<Respa *>(update->integrate))->copy_f_flevel(ilevel_respa);
|
||||||
}
|
}
|
||||||
else
|
else
|
||||||
post_force(vflag);
|
post_force(vflag);
|
||||||
|
|||||||
@ -197,7 +197,7 @@ void FixGLD::init()
|
|||||||
dtf = 0.5 * update->dt * force->ftm2v;
|
dtf = 0.5 * update->dt * force->ftm2v;
|
||||||
|
|
||||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||||
step_respa = (dynamic_cast<Respa *>( update->integrate))->step;
|
step_respa = (dynamic_cast<Respa *>(update->integrate))->step;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user