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Merge branch 'develop' into intel_fixes_2023Jun

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Axel Kohlmeyer
2023-06-12 15:18:08 -04:00
parent 0dab1910db 54286ce4dd
commit 90416faf0a
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2
doc/src/Build_manual.rst
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@ -52,7 +52,7 @@ can be translated to different output format using the `Sphinx
incorporates programmer documentation extracted from the LAMMPS C++
sources through the `Doxygen <https://doxygen.nl/>`_ program. Currently
the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
and MOBI (for Amazon Kindle(tm) readers) are supported. For that to work a
and MOBI (for Amazon Kindle readers) are supported. For that to work a
Python interpreter version 3.8 or later, the ``doxygen`` tools and
internet access to download additional files and tools are required.
This download is usually only required once or after the documentation

1
doc/src/Commands_fix.rst
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@ -171,6 +171,7 @@ OPT.
* :doc:`pafi <fix_pafi>`
* :doc:`pair <fix_pair>`
* :doc:`phonon <fix_phonon>`
* :doc:`pimd/langevin <fix_pimd>`
* :doc:`pimd/nvt <fix_pimd>`
* :doc:`planeforce <fix_planeforce>`
* :doc:`plumed <fix_plumed>`

1
doc/src/Commands_pair.rst
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@ -37,6 +37,7 @@ OPT.
*
* :doc:`adp (ko) <pair_adp>`
* :doc:`agni (o) <pair_agni>`
* :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba (g) <pair_amoeba>`

191
doc/src/Fortran.rst
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@ -203,40 +203,62 @@ Below is an example demonstrating some of the possible uses.
.. code-block:: fortran
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms
REAL(KIND=c_double), POINTER :: dt
INTEGER(KIND=c_int64_t), POINTER :: ntimestep
REAL(KIND=c_double) :: pe, ke
PROGRAM testprop
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
REAL(KIND=c_double), POINTER :: dt, dval
INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
INTEGER(KIND=c_int) :: i
CHARACTER(LEN=11) :: key
REAL(KIND=c_double) :: pe, ke
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
lmp = lammps()
CALL lmp%file('in.sysinit')
natoms = lmp%extract_global('natoms')
WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
lmp%extract_setting('ntypes'), ' atom types'
CALL lmp%command('run 2 post no')
dt = lmp%extract_global('dt')
ntimestep = lmp%extract_global('ntimestep')
WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
' Changing timestep from', dt, ' to 0.5'
dt = 0.5_c_double
CALL lmp%command('run 2 post no')
CALL lmp%command('run 2 post no')
WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
pe = lmp%get_thermo('pe')
ke = lmp%get_thermo('ke')
PRINT*, 'PE = ', pe
PRINT*, 'KE = ', ke
ntimestep = lmp%last_thermo('step', 0)
nfield = lmp%last_thermo('num', 0)
WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') 'Last thermo output on step: ', ntimestep, &
', number of fields: ', nfield
DO i=1, nfield
key = lmp%last_thermo('keyword',i)
typ = lmp%last_thermo('type',i)
IF (typ == lmp%dtype%i32) THEN
ival = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', ival
ELSE IF (typ == lmp%dtype%i64) THEN
bval = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', bval
ELSE IF (typ == lmp%dtype%r64) THEN
dval = lmp%last_thermo('data',i)
WRITE(OUTPUT_UNIT,*) key, ':', dval
END IF
END DO
CALL lmp%close(.TRUE.)
END PROGRAM testprop
dt = lmp%extract_global('dt')
ntimestep = lmp%extract_global('ntimestep')
WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
' Changing timestep from', dt, ' to 0.5'
dt = 0.5_c_double
CALL lmp%command('run 2 post no')
WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
pe = lmp%get_thermo('pe')
ke = lmp%get_thermo('ke')
WRITE(OUTPUT_UNIT,*) 'PE = ', pe
WRITE(OUTPUT_UNIT,*) 'KE = ', ke
CALL lmp%close(.TRUE.)
END PROGRAM testprop
---------------
@ -262,6 +284,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype style: type(lammps_style)
:f type: derived type to access lammps type constants
:ftype type: type(lammps_type)
:f dtype: derived type to access lammps data type constants
:ftype dtype: type(lammps_dtype)
:f close: :f:subr:`close`
:ftype close: subroutine
:f subroutine error: :f:subr:`error`
@ -278,6 +302,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype get_natoms: function
:f get_thermo: :f:func:`get_thermo`
:ftype get_thermo: function
:f last_thermo: :f:func:`last_thermo`
:ftype last_thermo: function
:f extract_box: :f:subr:`extract_box`
:ftype extract_box: subroutine
:f reset_box: :f:subr:`reset_box`
@ -587,6 +613,96 @@ Procedures Bound to the :f:type:`lammps` Derived Type
--------
.. f:function:: last_thermo(what, index)
This function will call :cpp:func:`lammps_last_thermo` and returns
either a string or a pointer to a cached copy of LAMMPS last thermodynamic
output, depending on the data requested through *what*. Note that *index*
uses 1-based indexing to access thermo output columns.
.. versionadded:: TBD
Note that this function actually does not return a value, but rather
associates the pointer on the left side of the assignment to point to
internal LAMMPS data (with the exception of string data, which are
copied and returned as ordinary Fortran strings). Pointers must be
of the correct data type to point to said data (typically
``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``).
The pointer being associated with LAMMPS data is type-checked at
run-time via an overloaded assignment operator. The pointers
returned by this function point to temporary, read-only data that may
be overwritten at any time, so their target values need to be copied
to local storage if they are supposed to persist.
For example,
.. code-block:: fortran
PROGRAM thermo
USE LIBLAMMPS
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
TYPE(lammps) :: lmp
INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval
REAL(KIND=c_double), POINTER :: dval
INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
INTEGER(KIND=c_int) :: i
CHARACTER(LEN=11) :: key
lmp = lammps()
CALL lmp%file('in.sysinit')
ntimestep = lmp%last_thermo('step', 0)
nfield = lmp%last_thermo('num', 0)
PRINT*, 'Last thermo output on step: ', ntimestep, ' Number of fields: ', nfield
DO i=1, nfield
key = lmp%last_thermo('keyword',i)
typ = lmp%last_thermo('type',i)
IF (typ == lmp%dtype%i32) THEN
ival = lmp%last_thermo('data',i)
PRINT*, key, ':', ival
ELSE IF (typ == lmp%dtype%i64) THEN
bval = lmp%last_thermo('data',i)
PRINT*, key, ':', bval
ELSE IF (typ == lmp%dtype%r64) THEN
dval = lmp%last_thermo('data',i)
PRINT*, key, ':', dval
END IF
END DO
CALL lmp%close(.TRUE.)
END PROGRAM thermo
would extract the last timestep where thermo output was done and the number
of columns it printed. Then it loops over the columns to print out column
header keywords and the corresponding data.
.. note::
If :f:func:`last_thermo` returns a string, the string must have a length
greater than or equal to the length of the string (not including the
terminal ``NULL`` character) that LAMMPS returns. If the variable's
length is too short, the string will be truncated. As usual in Fortran,
strings are padded with spaces at the end. If you use an allocatable
string, the string **must be allocated** prior to calling this function.
:p character(len=\*) what: string with the name of the thermo keyword
:p integer(c_int) index: 1-based column index
:to: :cpp:func:`lammps_last_thermo`
:r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the
assignment should be either a string (if expecting string data) or a
C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the
extracted property.
.. warning::
Modifying the data in the location pointed to by the returned pointer
may lead to inconsistent internal data and thus may cause failures,
crashes, or bogus simulations. In general, it is much better
to use a LAMMPS input command that sets or changes these parameters.
Using an input command will take care of all side effects and necessary
updates of settings derived from such settings.
--------
.. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
This subroutine will call :cpp:func:`lammps_extract_box`. All
@ -764,13 +880,14 @@ Procedures Bound to the :f:type:`lammps` Derived Type
.. note::
If :f:func:`extract_global` returns a string, the string must have length
greater than or equal to the length of the string (not including the
terminal ``NULL`` character) that LAMMPS returns. If the variable's
length is too short, the string will be truncated. As usual in Fortran,
strings are padded with spaces at the end. If you use an allocatable
string, the string **must be allocated** prior to calling this function,
but you can automatically reallocate it to the correct length after the
If :f:func:`extract_global` returns a string, the string must have
a length greater than or equal to the length of the string (not
including the terminal ``NULL`` character) that LAMMPS returns. If
the variable's length is too short, the string will be
truncated. As usual in Fortran, strings are padded with spaces at
the end. If you use an allocatable string, the string **must be
allocated** prior to calling this function, but you can
automatically reallocate it to the correct length after the
function returns, viz.,
.. code-block :: fortran

6
doc/src/Howto_spc.rst
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@ -69,15 +69,13 @@ SPC/E with rigid bonds.
timestep 1.0
fix rigid all shake 0.0001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
velocity all create 300.0 5463576
fix integrate all nvt temp 300.0 300.0 1.0
fix integrate all nvt temp 300.0 300.0 100.0
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000 upto
write_data tip4p.data nocoeff
write_data spce.data nocoeff
.. _spce_molecule:
.. code-block::

4
doc/src/Howto_tip3p.rst
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@ -128,11 +128,11 @@ TIP3P with rigid bonds.
fix rigid all shake 0.001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
timestep 1.0
velocity all create 300.0 5463576
fix integrate all nvt temp 300 300 1.0
fix integrate all nvt temp 300 300 100.0
thermo_style custom step temp press etotal pe

13
doc/src/Howto_tip4p.rst
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@ -180,17 +180,17 @@ file changed):
fix rigid all shake 0.001 10 10000 b 1 a 1
minimize 0.0 0.0 1000 10000
run 0 post no
reset_timestep 0
timestep 1.0
velocity all create 300.0 5463576
fix integrate all nvt temp 300 300 1.0
fix integrate all nvt temp 300 300 100.0
thermo_style custom step temp press etotal pe
thermo 1000
run 20000
write_data tip3p.data nocoeff
write_data tip4p-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small
@ -203,6 +203,7 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
units real
atom_style charge
atom_modify map array
region box block -5 5 -5 5 -5 5
create_box 3 box
@ -219,14 +220,14 @@ rigid/nvt/small can identify rigid bodies by their molecule ID:
molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
timestep 0.1
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
velocity all create 300.0 5463576
thermo_style custom step temp press etotal density pe ke
thermo 1000
run 20000
write_data tip4p.data nocoeff
write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule:
.. code-block::

5
doc/src/Howto_tip5p.rst
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@ -91,6 +91,7 @@ ID:
units real
atom_style charge
atom_modify map array
region box block -5 5 -5 5 -5 5
create_box 3 box
@ -107,8 +108,8 @@ ID:
molecule water tip5p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
timestep 0.20
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
timestep 0.5
fix integrate all rigid/nvt/small molecule temp 300.0 300.0 100.0
reset_timestep 0
velocity all create 300.0 5463576

6
doc/src/Library_properties.rst
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@ -5,6 +5,7 @@ This section documents the following functions:
- :cpp:func:`lammps_get_natoms`
- :cpp:func:`lammps_get_thermo`
- :cpp:func:`lammps_last_thermo`
- :cpp:func:`lammps_extract_box`
- :cpp:func:`lammps_reset_box`
- :cpp:func:`lammps_memory_usage`
@ -81,6 +82,11 @@ subdomains and processors.
-----------------------
.. doxygenfunction:: lammps_last_thermo
:project: progguide
-----------------------
.. doxygenfunction:: lammps_extract_box
:project: progguide

18
doc/src/bond_bpm_rotational.rst
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@ -24,14 +24,17 @@ Syntax
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
*overlay/pair* value = none
*overlay/pair* value = *yes* or *no*
bonded particles will still interact with pair forces
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
*normalize* value = *yes* or *no*
normalizes normal and shear forces by the reference length
*break* value = *yes* or *no*
indicates whether bonds break during a run
Examples
""""""""
@ -136,16 +139,19 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\gamma_r` (force*distance/velocity units)
* :math:`\gamma_t` (force*distance/velocity units)
However, the *normalize* option will normalize the radial and shear forces
by :math:`r_0` such that :math:`k_r` and :math:`k_s` are unit less.
By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific
the *overlay/pair* option. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
If the *break* option is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
@ -251,7 +257,7 @@ Related commands
Default
"""""""
The option defaults are *smooth* = *yes*
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
----------

20
doc/src/bond_bpm_spring.rst
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@ -24,14 +24,17 @@ Syntax
*x, y, z* = the center of mass position of the 2 atoms when the bond broke (distance units)
*x/ref, y/ref, z/ref* = the initial center of mass position of the 2 atoms (distance units)
*overlay/pair* value = none
*overlay/pair* value = *yes* or *no*
bonded particles will still interact with pair forces
*smooth* value = *yes* or *no*
smooths bond forces near the breaking point
*break/no*
indicates that bonds should not break during a run
*normalize* value = *yes* or *no*
normalizes bond forces by the reference length
*break* value = *yes* or *no*
indicates whether bonds break during a run
Examples
""""""""
@ -66,7 +69,7 @@ particles based on a model described by Clemmer and Robbins
F = k (r - r_0) w
where :math:`k_r` is a stiffness, :math:`r` is the current distance
where :math:`k` is a stiffness, :math:`r` is the current distance
and :math:`r_0` is the initial distance between the two particles, and
:math:`w` is an optional smoothing factor discussed below. Bonds will
break at a strain of :math:`\epsilon_c`. This is done by setting by
@ -102,16 +105,19 @@ the data file or restart files read by the :doc:`read_data
* :math:`\epsilon_c` (unit less)
* :math:`\gamma` (force/velocity units)
However, the *normalize* option will normalize the elastic bond force by
:math:`r_0` such that :math:`k` is unit less.
By default, pair forces are not calculated between bonded particles.
Pair forces can alternatively be overlaid on top of bond forces using
the *overlay/pair* keyword. These settings require specific
the *overlay/pair* option. These settings require specific
:doc:`special_bonds <special_bonds>` settings described in the
restrictions. Further details can be found in the `:doc: how to
<Howto_BPM>` page on BPMs.
.. versionadded:: 28Mar2023
If the *break/no* keyword is used, then LAMMPS assumes bonds should not break
If the *break* option is used, then LAMMPS assumes bonds should not break
during a simulation run. This will prevent some unnecessary calculation.
However, if a bond does break, it will trigger an error.
@ -206,7 +212,7 @@ Related commands
Default
"""""""
The option defaults are *smooth* = *yes*
The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
----------

5
doc/src/compute_bond_local.rst
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@ -76,7 +76,10 @@ The value *force* is the magnitude of the force acting between the
pair of atoms in the bond.
The values *fx*, *fy*, and *fz* are the xyz components of
*force* between the pair of atoms in the bond.
*force* between the pair of atoms in the bond. For bond styles that apply
non-central forces, such as :doc:`bond_style bpm/rotational
<bond_bpm_rotational>`, these values only include the :math:`(x,y,z)`
components of the normal force component.
The remaining properties are all computed for motion of the two atoms
relative to the center of mass (COM) velocity of the 2 atoms in the

12
doc/src/compute_fabric.rst
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@ -146,13 +146,13 @@ m to :math:`M` (inclusive). A middle asterisk means all types from m to n
Output info
"""""""""""
This compute calculates a local vector of doubles and a scalar. The vector
stores the unique components of the first requested tensor in the order
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`
followed by the same components for all subsequent tensors.
This compute calculates a global vector of doubles and a global scalar. The
vector stores the unique components of the first requested tensor in the
order :math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`,
:math:`yz` followed by the same components for all subsequent tensors.
The length of the vector is therefore six times the number of requested
tensors. The scalar output is the number of pairwise interactions included in
the calculation of the fabric tensor.
tensors. The scalar output is the number of pairwise interactions included
in the calculation of the fabric tensor.
Restrictions
""""""""""""

4
doc/src/compute_pair_local.rst
View File

@ -66,7 +66,9 @@ The value *eng* is the interaction energy for the pair of atoms.
The value *force* is the force acting between the pair of atoms, which
is positive for a repulsive force and negative for an attractive
force. The values *fx*, *fy*, and *fz* are the :math:`(x,y,z)` components of
*force* on atom I.
*force* on atom I. For pair styles that apply non-central forces,
such as :doc:`granular pair styles <pair_gran>`, these values only include
the :math:`(x,y,z)` components of the normal force component.
A pair style may define additional pairwise quantities which can be
accessed as *p1* to *pN*, where :math:`N` is defined by the pair style.

118
doc/src/compute_stress_mop.rst
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@ -18,7 +18,7 @@ Syntax
* style = *stress/mop* or *stress/mop/profile*
* dir = *x* or *y* or *z* is the direction normal to the plane
* args = argument specific to the compute style
* keywords = *kin* or *conf* or *total* (one of more can be specified)
* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
.. parsed-literal::
@ -45,85 +45,107 @@ Examples
Description
"""""""""""
Compute *stress/mop* and compute *stress/mop/profile* define computations that
calculate components of the local stress tensor using the method of
planes :ref:`(Todd) <mop-todd>`. Specifically in compute *stress/mop* calculates 3
components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and
*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while
in compute *stress/mop/profile* the profile of the stress is computed.
Compute *stress/mop* and compute *stress/mop/profile* define
computations that calculate components of the local stress tensor using
the method of planes :ref:`(Todd) <mop-todd>`. Specifically in compute
*stress/mop* calculates 3 components are computed in directions *dir*,\
*x*\ ; *dir*,\ *y*\ ; and *dir*,\ *z*\ ; where *dir* is the direction
normal to the plane, while in compute *stress/mop/profile* the profile
of the stress is computed.
Contrary to methods based on histograms of atomic stress (i.e., using
:doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
compatible with mechanical balance in heterogeneous systems and at
:doc:`compute stress/atom <compute_stress_atom>`), the method of planes
is compatible with mechanical balance in heterogeneous systems and at
interfaces :ref:`(Todd) <mop-todd>`.
The stress tensor is the sum of a kinetic term and a configurational
term, which are given respectively by Eq. (21) and Eq. (16) in
:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
atoms have crossed the plane if their positions at times :math:`t-\Delta t`
and :math:`t` are one on either side of the plane, and uses the velocity at
time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers
that atoms have crossed the plane if their positions at times
:math:`t-\Delta t` and :math:`t` are one on either side of the plane,
and uses the velocity at time :math:`t-\Delta t/2` given by the velocity
Verlet algorithm.
Between one and three keywords can be used to indicate which
contributions to the stress must be computed: kinetic stress (kin),
configurational stress (conf), and/or total stress (total).
.. versionadded:: TBD
NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
contributions from bond and angle potentials
Between one and six keywords can be used to indicate which contributions
to the stress must be computed: total stress (total), kinetic stress
(kin), configurational stress (conf), stress due to bond stretching
(bond), stress due to angle bending (angle) and/or due to pairwise
non-bonded interactions (pair). The angle keyword is currently
available only for the *stress/mop* command and **not** the
*stress/mop/profile* command.
NOTE 1: The configurational stress is computed considering all pairs of
atoms where at least one atom belongs to group group-ID.
NOTE 2: The local stress does not include any Lennard-Jones tail
corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
command, since those are contributions to the global system pressure.
corrections to the stress added by the :doc:`pair_modify tail yes
<pair_modify>` command, since those are contributions to the global
system pressure.
NOTE 3: The local stress profile generated by compute *stress/mop/profile*
is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_profile>`.
A key difference is that compute *stress/mop/profile* considers particles
crossing a set of planes, while compute *stress/cartesian* computes averages
for a set of small volumes. More information
on the similarities and differences can be found in
:ref:`(Ikeshoji)<Ikeshoji2>`.
NOTE 3: The local stress profile generated by compute
*stress/mop/profile* is similar to that obtained by compute
:doc:`stress/cartesian <compute_stress_profile>`. A key difference is
that compute *stress/mop/profile* considers particles crossing a set of
planes, while compute *stress/cartesian* computes averages for a set of
small volumes. More information on the similarities and differences can
be found in :ref:`(Ikeshoji)<Ikeshoji2>`.
Output info
"""""""""""
Compute *stress/mop* calculates a global vector (indices starting at 1), with 3
values for each declared keyword (in the order the keywords have been
declared). For each keyword, the stress tensor components are ordered as
follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute *stress/mop* calculates a global vector (indices starting at 1),
with 3 values for each declared keyword (in the order the keywords have
been declared). For each keyword, the stress tensor components are
ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
Compute *stress/mop/profile* instead calculates a global array, with 1 column
giving the position of the planes where the stress tensor was computed,
and with 3 columns of values for each declared keyword (in the order the
keywords have been declared). For each keyword, the profiles of stress
tensor components are ordered as follows: stress_dir,x; stress_dir,y;
and stress_dir,z.
Compute *stress/mop/profile* instead calculates a global array, with 1
column giving the position of the planes where the stress tensor was
computed, and with 3 columns of values for each declared keyword (in the
order the keywords have been declared). For each keyword, the profiles
of stress tensor components are ordered as follows: stress_dir,x;
stress_dir,y; and stress_dir,z.
The values are in pressure :doc:`units <units>`.
The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
For instance, the results can be written to a file using the
:doc:`fix ave/time <fix_ave_time>` command. Please see the example
in the examples/PACKAGES/mop folder.
The values produced by this compute can be accessed by various
:doc:`output commands <Howto_output>`. For instance, the results can be
written to a file using the :doc:`fix ave/time <fix_ave_time>`
command. Please see the example in the examples/PACKAGES/mop folder.
Restrictions
""""""""""""
These styles are part of the EXTRA-COMPUTE package. They are only enabled if
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
doc page on for more info.
These styles are part of the EXTRA-COMPUTE package. They are only
enabled if LAMMPS is built with that package. See the :doc:`Build
package <Build_package>` doc page on for more info.
The method is only implemented for 3d orthogonal simulation boxes whose
size does not change in time, and axis-aligned planes.
The method only works with two-body pair interactions, because it
requires the class method pair->single() to be implemented. In
particular, it does not work with more than two-body pair interactions,
intra-molecular interactions, and long range (kspace) interactions.
requires the class method ``Pair::single()`` to be implemented, which is
not possible for manybody potentials. In particular, compute
*stress/mop/profile* does not work with more than two-body pair
interactions, long range (kspace) interactions and
angle/dihedral/improper intramolecular interactions. Similarly, compute
*stress/mop* does not work with more than two-body pair interactions,
long range (kspace) interactions and dihedral/improper intramolecular
interactions but works with all bond interactions with the class method
single() implemented and all angle interactions with the class method
born_matrix() implemented.
Related commands
""""""""""""""""
:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
:doc:`compute stress/atom <compute_stress_atom>`,
:doc:`compute pressure <compute_pressure>`,
:doc:`compute stress/cartesian <compute_stress_profile>`,
:doc:`compute stress/cylinder <compute_stress_profile>`,
:doc:`compute stress/spherical <compute_stress_profile>`
Default
"""""""

10
doc/src/dump_modify.rst
View File

@ -753,9 +753,13 @@ run, this option is ignored since the output is already balanced.
----------
The *thermo* keyword only applies the dump styles *netcdf* and *yaml*.
It triggers writing of :doc:`thermo <thermo>` information to the dump file
alongside per-atom data. The values included in the dump file are
identical to the values specified by :doc:`thermo_style <thermo_style>`.
It triggers writing of :doc:`thermo <thermo>` information to the dump
file alongside per-atom data. The values included in the dump file are
cached values from the last thermo output and include the exact same the
values as specified by the :doc:`thermo_style <thermo_style>` command.
Because these are cached values, they are only up-to-date when dump
output is on a timestep that also has thermo output. Dump style *yaml*
will skip thermo output on incompatible steps.
----------

3
doc/src/fix.rst
View File

@ -323,7 +323,8 @@ accelerated styles exist.
* :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
* :doc:`pair <fix_pair>` - access per-atom info from pair styles
* :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
* :doc:`pimd/nvt <fix_pimd>` - Feynman path integral molecular dynamics with Nose-Hoover thermostat
* :doc:`pimd/langevin <fix_pimd>` - Feynman path-integral molecular dynamics with stochastic thermostat
* :doc:`pimd/nvt <fix_pimd>` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
* :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
* :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
* :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies

293
doc/src/fix_pimd.rst
View File

@ -1,5 +1,9 @@
.. index:: fix pimd/langevin
.. index:: fix pimd/nvt
fix pimd/langevin command
=========================
fix pimd/nvt command
====================
@ -8,72 +12,107 @@ Syntax
.. parsed-literal::
fix ID group-ID pimd/nvt keyword value ...
fix ID group-ID style keyword value ...
* ID, group-ID are documented in :doc:`fix <fix>` command
* pimd/nvt = style name of this fix command
* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
* zero or more keyword/value pairs may be appended
* keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
* keywords for style *pimd/nvt*
.. parsed-literal::
*keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
*method* value = *pimd* or *nmpimd* or *cmd*
*fmass* value = scaling factor on mass
*sp* value = scaling factor on Planck constant
*temp* value = temperature (temperarate units)
*temp* value = temperature (temperature units)
*nhc* value = Nc = number of chains in Nose-Hoover thermostat
* keywords for style *pimd/langevin*
.. parsed-literal::
*keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
*method* value = *nmpimd*
*integrator* value = *obabo* or *baoab*
*fmmode* value = *physical* or *normal*
*fmass* value = scaling factor on mass
*temp* value = temperature (temperature unit)
temperature = target temperature of the thermostat
*thermostat* values = style seed
style value = *PILE_L*
seed = random number generator seed
*tau* value = thermostat damping parameter (time unit)
*scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat
*iso* or *aniso* values = pressure (pressure unit)
pressure = scalar external pressure of the barostat
*barostat* value = *BZP* or *MTTK*
*taup* value = barostat damping parameter (time unit)
*fixcom* value = *yes* or *no*
*lj* values = epsilon sigma mass planck mvv2e
epsilon = energy scale for reduced units (energy units)
sigma = length scale for reduced units (length units)
mass = mass scale for reduced units (mass units)
planck = Planck's constant for other unit style
mvv2e = mass * velocity^2 to energy conversion factor for other unit style
Examples
""""""""
.. code-block:: LAMMPS
fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 iso 1.0 barostat BZP taup 1.0
Description
"""""""""""
.. versionchanged:: 28Mar2023
Fix pimd was renamed to fix pimd/nvt.
Fix pimd was renamed to fix *pimd/nvt* and fix *pimd/langevin* was added.
This command performs quantum molecular dynamics simulations based on
the Feynman path integral to include effects of tunneling and
These fix commands perform quantum molecular dynamics simulations based
on the Feynman path-integral to include effects of tunneling and
zero-point motion. In this formalism, the isomorphism of a quantum
partition function for the original system to a classical partition
function for a ring-polymer system is exploited, to efficiently sample
configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
The classical partition function and its components are given
by the following equations:
.. math::
Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff} \\
H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
:math:`M_i` is the fictitious mass of the :math:`i`-th mode, and m is the actual mass of the atoms.
The interested user is referred to any of the numerous references on
this methodology, but briefly, each quantum particle in a path
integral simulation is represented by a ring-polymer of P quasi-beads,
labeled from 1 to P. During the simulation, each quasi-bead interacts
with beads on the other ring-polymers with the same imaginary time
index (the second term in the effective potential above). The
quasi-beads also interact with the two neighboring quasi-beads through
the spring potential in imaginary-time space (first term in effective
potential). To sample the canonical ensemble, a Nose-Hoover massive
chain thermostat is applied :ref:`(Tuckerman) <pimd-Tuckerman>`. With the
massive chain algorithm, a chain of NH thermostats is coupled to each
degree of freedom for each quasi-bead. The keyword *temp* sets the
target temperature for the system and the keyword *nhc* sets the
number *Nc* of thermostats in each chain. For example, for a
simulation of N particles with P beads in each ring-polymer, the total
number of NH thermostats would be 3 x N x P x Nc.
this methodology, but briefly, each quantum particle in a path integral
simulation is represented by a ring-polymer of P quasi-beads, labeled
from 1 to P. During the simulation, each quasi-bead interacts with
beads on the other ring-polymers with the same imaginary time index (the
second term in the effective potential above). The quasi-beads also
interact with the two neighboring quasi-beads through the spring
potential in imaginary-time space (first term in effective potential).
To sample the canonical ensemble, any thermostat can be applied.
Fix *pimd/nvt* applies a Nose-Hoover massive chain thermostat
:ref:`(Tuckerman) <pimd-Tuckerman>`. With the massive chain
algorithm, a chain of NH thermostats is coupled to each degree of
freedom for each quasi-bead. The keyword *temp* sets the target
temperature for the system and the keyword *nhc* sets the number *Nc* of
thermostats in each chain. For example, for a simulation of N particles
with P beads in each ring-polymer, the total number of NH thermostats
would be 3 x N x P x Nc.
Fix *pimd/langevin* implements a Langevin thermostat in the normal mode
representation, and also provides a barostat to sample the NPH/NPT ensembles.
.. note::
Fix pimd/nvt implements a complete velocity-verlet integrator
combined with NH massive chain thermostat, so no other time
integration fix should be used.
Both these *fix* styles implement a complete velocity-verlet integrator
combined with a thermostat, so no other time integration fix should be used.
The *method* keyword determines what style of PIMD is performed. A
value of *pimd* is standard PIMD. A value of *nmpimd* is for
@ -81,7 +120,7 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
(CMD). The difference between the styles is as follows.
In standard PIMD, the value used for a bead's fictitious mass is
arbitrary. A common choice is to use Mi = m/P, which results in the
arbitrary. A common choice is to use :math:`M_i = m/P`, which results in the
mass of the entire ring-polymer being equal to the real quantum
particle. But it can be difficult to efficiently integrate the
equations of motion for the stiff harmonic interactions in the ring
@ -97,6 +136,10 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
overall translation of the ring-polymer and is assigned the mass of
the real particle.
.. note::
Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
for most PIMD applications for quantum thermodynamics purpose.
Motion of the centroid can be effectively uncoupled from the other
normal modes by scaling the fictitious masses to achieve a partial
adiabatic separation. This is called a Centroid Molecular Dynamics
@ -108,17 +151,86 @@ normal-mode PIMD. A value of *cmd* is for centroid molecular dynamics
only the k > 0 modes are thermostatted, not the centroid degrees of
freedom.
The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
either of the two should work fine.
The keyword *fmass* sets a further scaling factor for the fictitious
masses of beads, which can be used for the Partial Adiabatic CMD
:ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
masses to be equal to the real particle masses.
The keyword *fmmode* of *fix pimd/langevin* determines the mode of fictitious
mass preconditioning. There are two options: *physical* and *normal*. If *fmmode* is
*physical*, then the physical mass of the particles are used (and then multiplied by
*fmass*). If *fmmode* is *normal*, then the physical mass is first multiplied by the
eigenvalue of each normal mode, and then multiplied by *fmass*. More precisely, the
fictitious mass of *fix pimd/langevin* is determined by two factors: *fmmode* and *fmass*.
If *fmmode* is *physical*, then the fictitious mass is
.. math::
M_i = \mathrm{fmass} \times m
If *fmmode* is *normal*, then the fictitious mass is
.. math::
M_i = \mathrm{fmass} \times \lambda_i \times m
where :math:`\lambda_i` is the eigenvalue of the :math:`i`-th normal mode.
.. note::
Fictitious mass is only used in the momentum of the equation of motion
(:math:`\mathbf{p}_i=M_i\mathbf{v}_i`), and not used in the spring elastic energy
(:math:`\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2`, :math:`m` is always the
actual mass of the particles).
The keyword *sp* is a scaling factor on Planck's constant, which can
be useful for debugging or other purposes. The default value of 1.0
is appropriate for most situations.
The keyword *ensemble* for fix style *pimd/langevin* determines which ensemble is it
going to sample. The value can be *nve* (microcanonical), *nvt* (canonical), *nph* (isoenthalpic),
and *npt* (isothermal-isobaric).
The keyword *temp* specifies temperature parameter for fix styles *pimd/nvt* and *pimd/langevin*. It should read
a positive floating-point number.
.. note::
For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
.. note::
The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
The keyword *tau* specifies the thermostat damping time parameter for fix style *pimd/langevin*. It is in time unit. It only works on the centroid mode.
The keyword *scale* specifies a scaling parameter for the damping times of the non-centroid modes for fix style *pimd/langevin*. The default
damping time of the non-centroid mode :math:`i` is :math:`\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}` (*fmmode* is *physical*) or :math:`\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}` (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*.
The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso*
keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure.
The keyword *barostat* reads *style* of barostat for fix style *pimd/langevin*. *style* can
be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`Bussi <Bussi>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`Martyna1 <Martyna3>` and :ref:`Martyna2 <Martyna4>`).
The keyword *taup* specifies the barostat damping time parameter for fix style *pimd/langevin*. It is in time unit.
The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation.
Once *fixcom* is set to be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
The keyword *lj* should be used if :doc:`lj units <units>` is used for *fix pimd/langevin*. Typically one may want to use
reduced units to run the simulation, and then convert the results into some physical units (for example, :doc:`metal units <units>`). In this case, the 5 quantities in the physical mass units are needed: epsilon (energy scale), sigma (length scale), mass, Planck's constant, mvv2e (mass * velocity^2 to energy conversion factor). Planck's constant and mvv2e can be found in src/update.cpp. If there is no need to convert reduced units to physical units, set all these five value to 1.
The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
as described in :ref:`(Calhoun) <Calhoun>`. In LAMMPS this is done by using
as described in :ref:`Calhoun <Calhoun>`. In LAMMPS this is done by using
:doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
quasi-particle system is stored and simulated on a separate partition
of processors. The following diagram illustrates this approach. The
@ -152,22 +264,49 @@ related tasks for each of the partitions, e.g.
.. code-block:: LAMMPS
dump dcd all dcd 10 system_${ibead}.dcd
dump 1 all custom 100 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
read_restart system_${ibead}.restart2
.. note::
Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
forces in the normal mode representation. If the Cartesian velocities and forces are
needed, it is easy to perform the transformation when doing post-processing.
It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It
will be useful if you want to calculate some estimators during post-processing.
Major differences of *fix pimd/nvt* and *fix pimd/langevin* are:
#. *Fix pimd/nvt* includes Cartesian pimd, normal mode pimd, and centroid md. *Fix pimd/langevin* only intends to support normal mode pimd, as it is commonly enough for thermodynamic sampling.
#. *Fix pimd/nvt* uses Nose-Hoover chain thermostat. *Fix pimd/langevin* uses Langevin thermostat.
#. *Fix pimd/langevin* provides barostat, so the npt ensemble can be sampled. *Fix pimd/nvt* only support nvt ensemble.
#. *Fix pimd/langevin* provides several quantum estimators in output.
#. *Fix pimd/langevin* allows multiple processes for each bead. For *fix pimd/nvt*, there is a large chance that multi-process tasks for each bead may fail.
#. The dump of *fix pimd/nvt* are all Cartesian. *Fix pimd/langevin* dumps normal-mode velocities and forces, and Cartesian coordinates.
Initially, the inter-replica communication and normal mode transformation parts of *fix pimd/langevin* are written based on
those of *fix pimd/nvt*, but are significantly revised.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Fix pimd/nvt writes the state of the Nose/Hoover thermostat over all
Fix *pimd/nvt* writes the state of the Nose/Hoover thermostat over all
quasi-beads to :doc:`binary restart files <restart>`. See the
:doc:`read_restart <read_restart>` command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
Fix *pimd/langevin* writes the state of the barostat overall beads to
:doc:`binary restart files <restart>`. Since it uses a stochastic thermostat,
the state of the thermostat is not written. However, the state of the system
can be restored by reading the restart file, except that it will re-initialize
the random number generator.
None of the :doc:`fix_modify <fix_modify>` options
are relevant to fix pimd/nvt.
Fix pimd/nvt computes a global 3-vector, which can be accessed by
Fix *pimd/nvt* computes a global 3-vector, which can be accessed by
various :doc:`output commands <Howto_output>`. The three quantities in
the global vector are:
@ -176,21 +315,80 @@ the global vector are:
#. the current value of the scalar virial estimator for the kinetic
energy of the quantum system :ref:`(Herman) <Herman>`.
The vector values calculated by fix pimd/nvt are "extensive", except for the
The vector values calculated by fix *pimd/nvt* are "extensive", except for the
temperature, which is "intensive".
No parameter of fix pimd/nvt can be used with the *start/stop* keywords
of the :doc:`run <run>` command. Fix pimd/nvt is not invoked during
Fix *pimd/langevin* computes a global vector of quantities, which
can be accessed by various :doc:`output commands <Howto_output>`. Note that
it outputs multiple log files, and different log files contain information
about different beads or modes (see detailed explanations below). If *ensemble*
is *nve* or *nvt*, the vector has 10 values:
#. kinetic energy of the normal mode
#. spring elastic energy of the normal mode
#. potential energy of the bead
#. total energy of all beads (conserved if *ensemble* is *nve*)
#. primitive kinetic energy estimator
#. virial energy estimator
#. centroid-virial energy estimator
#. primitive pressure estimator
#. thermodynamic pressure estimator
#. centroid-virial pressure estimator
The first 3 are different for different log files, and the others are the same for different log files.
If *ensemble* is *nph* or *npt*, the vector stores internal variables of the barostat. If *iso* is used,
the vector has 15 values:
#. kinetic energy of the normal mode
#. spring elastic energy of the normal mode
#. potential energy of the bead
#. total energy of all beads (conserved if *ensemble* is *nve*)
#. primitive kinetic energy estimator
#. virial energy estimator
#. centroid-virial energy estimator
#. primitive pressure estimator
#. thermodynamic pressure estimator
#. centroid-virial pressure estimator
#. barostat velocity
#. barostat kinetic energy
#. barostat potential energy
#. barostat cell Jacobian
#. enthalpy of the extended system (sum of 4, 12, 13, and 14; conserved if *ensemble* is *nph*)
If *aniso* or *x* or *y* or *z* is used for the barostat, the vector has 17 values:
#. kinetic energy of the normal mode
#. spring elastic energy of the normal mode
#. potential energy of the bead
#. total energy of all beads (conserved if *ensemble* is *nve*)
#. primitive kinetic energy estimator
#. virial energy estimator
#. centroid-virial energy estimator
#. primitive pressure estimator
#. thermodynamic pressure estimator
#. centroid-virial pressure estimator
#. x component of barostat velocity
#. y component of barostat velocity
#. z component of barostat velocity
#. barostat kinetic energy
#. barostat potential energy
#. barostat cell Jacobian
#. enthalpy of the extended system (sum of 4, 14, 15, and 16; conserved if *ensemble* is *nph*)
No parameter of fix *pimd/nvt* or *pimd/langevin* can be used with the *start/stop* keywords
of the :doc:`run <run>` command. Fix *pimd/nvt* or *pimd/langevin* is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions
""""""""""""
This fix is part of the REPLICA package. It is only enabled if LAMMPS
was built with that package. See the :doc:`Build package
These fixes are part of the REPLICA package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
Fix pimd/nvt cannot be used with :doc:`lj units <units>`.
Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
Fix *pimd/langevin* can be used with :doc:`lj units <units>`. See the above part for how to use it.
A PIMD simulation can be initialized with a single data file read via
the :doc:`read_data <read_data>` command. However, this means all
@ -207,7 +405,7 @@ variable, e.g.
Default
"""""""
The keyword defaults for fix pimd/nvt are method = pimd, fmass = 1.0, sp
The keyword defaults for fix *pimd/nvt* are method = pimd, fmass = 1.0, sp
= 1.0, temp = 300.0, and nhc = 2.
----------
@ -243,3 +441,22 @@ Path Integrals, McGraw-Hill, New York (1965).
**(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
.. _Bussi:
**(Bussi)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
.. _Ceriotti3:
**(Ceriotti)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
.. _Martyna3:
**(Martyna1)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
.. _Martyna4:
**(Martyna2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
.. _Liujian:
**(Liu)** J. Liu, D. Li, X. Liu, J. Chem. Phys. 145, 024103 (2016).

23
doc/src/fix_reaxff_species.rst
View File

@ -25,7 +25,7 @@ Syntax
.. parsed-literal::
*cutoff* value = I J Cutoff
I, J = atom types
I, J = atom types (see asterisk form below)
Cutoff = Bond-order cutoff value for this pair of atom types
*element* value = Element1, Element2, ...
*position* value = posfreq filepos
@ -49,7 +49,7 @@ Examples
.. code-block:: LAMMPS
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
@ -88,13 +88,24 @@ If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text version,
but will also take longer to write.
.. versionadded:: TBD
Support for wildcards added
Optional keyword *cutoff* can be assigned to change the minimum
bond-order values used in identifying chemical bonds between pairs of
atoms. Bond-order cutoffs should be carefully chosen, as bond-order
cutoffs that are too small may include too many bonds (which will
result in an error), while cutoffs that are too large will result in
fragmented molecules. The default cutoff of 0.3 usually gives good
results.
cutoffs that are too small may include too many bonds (which will result
in an error), while cutoffs that are too large will result in fragmented
molecules. The default cutoff of 0.3 usually gives good results. A
wildcard asterisk can be used in place of or in conjunction with the I,J
arguments to set the bond-order cutoff for multiple pairs of atom types.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If :math:`N` is
the number of atom types, then an asterisk with no numeric values means
all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
The optional keyword *element* can be used to specify the chemical
symbol printed for each LAMMPS atom type. The number of symbols must

167
doc/src/pair_aip_water_2dm.rst Normal file
View File

@ -0,0 +1,167 @@
.. index:: pair_style aip/water/2dm
.. index:: pair_style aip/water/2dm/opt
pair_style aip/water/2dm command
===================================
Accelerator Variant: *aip/water/2dm/opt*
Syntax
""""""
.. code-block:: LAMMPS
pair_style [hybrid/overlay ...] aip/water/2dm cutoff tap_flag
* cutoff = global cutoff (distance units)
* tap_flag = 0/1 to turn off/on the taper function
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay aip/water/2dm 16.0 1
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw
Description
"""""""""""
.. versionadded:: TBD
The *aip/water/2dm* style computes the anisotropic interfacial potential
(AIP) potential for interfaces of water with two-dimensional (2D)
materials as described in :ref:`(Feng) <Feng>`.
.. math::
E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\
\rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
\rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
f(\rho) = & C e^{ -( \rho / \delta )^2 } \\
{\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides
a continuous cutoff (up to third derivative) for interatomic separations
larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn
<pair_ilp_graphene_hbn>`.
.. note::
This pair style uses the atomic normal vector definition from
:ref:`(Feng) <Feng>`), where the atomic normal vectors of the
hydrogen atoms are assumed to lie along the corresponding
oxygen-hydrogen bonds and the normal vector of the central oxygen
atom is defined as their average.
The provided parameter file, ``COH.aip.water.2dm``, is intended for use
with *metal* :doc:`units <units>`, with energies in meV. Two additional
parameters, *S*, and *rcut* are included in the parameter file. *S* is
designed to facilitate scaling of energies; *rcut* is the cutoff for an
internal, short distance neighbor list that is generated for speeding up
the calculation of the normals for all atom pairs.
.. note::
The parameters presented in the provided parameter file,
``COH.aip.water.2dm``, are fitted with the taper function enabled by
setting the cutoff equal to 16.0 Angstrom. Using a different cutoff
or taper function setting should be carefully checked as they can
lead to significant errors. These parameters provide a good
description in both short- and long-range interaction regimes. This
is essential for simulations in high pressure regime (i.e., the
interlayer distance is smaller than the equilibrium distance).
This potential must be used in combination with hybrid/overlay. Other
interactions can be set to zero using :doc:`pair_coeff settings
<pair_coeff>` with the pair style set to *none*\ .
This pair style tallies a breakdown of the total interlayer potential
energy into sub-categories, which can be accessed via the :doc:`compute
pair <compute_pair>` command as a vector of values of length 2. The 2
values correspond to the following sub-categories:
1. *E_vdW* = vdW (attractive) energy
2. *E_Rep* = Repulsive energy
To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:
.. code-block:: LAMMPS
compute 0 all pair aip/water/2dm
variable Evdw equal c_0[1]
variable Erep equal c_0[2]
thermo_style custom step temp epair v_Erep v_Evdw
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support the pair_modify mix, shift, table, and
tail options.
This pair style does not write their information to binary restart
files, since it is stored in potential files. Thus, you need to
re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
Restrictions
""""""""""""
This pair style is part of the INTERLAYER package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the newton setting to be *on* for pair
interactions.
The ``COH.aip.water.2dm`` potential file provided with LAMMPS is
parameterized for *metal* units. You can use this pair style with any
LAMMPS units, but you would need to create your own potential file with
parameters in the appropriate units, if your simulation does not use
*metal* units.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_none <pair_none>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style drip <pair_drip>`,
:doc:`pair_style ilp_tmd <pair_ilp_tmd>`,
:doc:`pair_style saip_metal <pair_saip_metal>`,
:doc:`pair_style ilp_graphene_hbn <pair_ilp_graphene_hbn>`,
:doc:`pair_style pair_kolmogorov_crespi_z <pair_kolmogorov_crespi_z>`,
:doc:`pair_style pair_kolmogorov_crespi_full <pair_kolmogorov_crespi_full>`,
:doc:`pair_style pair_lebedeva_z <pair_lebedeva_z>`,
:doc:`pair_style pair_coul_shield <pair_coul_shield>`.
Default
"""""""
tap_flag = 1
----------
.. _Feng:
**(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023).

2
doc/src/pair_granular.rst
View File

@ -736,7 +736,7 @@ or
.. math::
E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij})}
E_{eff,ij} = \frac{E_{ij}}{2(1-\nu_{ij}^2)}
These pair styles write their information to :doc:`binary restart files <restart>`, so a pair_style command does not need to be
specified in an input script that reads a restart file.

20
doc/src/pair_ilp_graphene_hbn.rst
View File

@ -155,8 +155,8 @@ interactions.
The BNCH.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom BNCH.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands
@ -181,6 +181,14 @@ tap_flag = 1
----------
.. _Ouyang1:
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang2:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
.. _Leven1:
**(Leven1)** I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
@ -196,11 +204,3 @@ tap_flag = 1
.. _Kolmogorov2:
**(Kolmogorov)** A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
.. _Ouyang1:
**(Ouyang1)** W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
.. _Ouyang2:
**(Ouyang2)** W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).

4
doc/src/pair_ilp_tmd.rst
View File

@ -135,8 +135,8 @@ interactions.
The TMD.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom TMD.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands

2
doc/src/pair_kolmogorov_crespi_full.rst
View File

@ -129,7 +129,7 @@ interactions.
The CH.KC potential file provided with LAMMPS (see the potentials
folder) is parameterized for metal units. You can use this pair style
with any LAMMPS units, but you would need to create your own custom
CC.KC potential file with all coefficients converted to the appropriate
CH.KC potential file with all coefficients converted to the appropriate
units.
Related commands

4
doc/src/pair_saip_metal.rst
View File

@ -134,8 +134,8 @@ interactions.
The CHAu.ILP potential file provided with LAMMPS (see the potentials
directory) are parameterized for *metal* units. You can use this
potential with any LAMMPS units, but you would need to create your
BNCH.ILP potential file with coefficients listed in the appropriate
potential with any LAMMPS units, but you would need to create your own
custom CHAu.ILP potential file with coefficients listed in the appropriate
units, if your simulation does not use *metal* units.
Related commands

1
doc/src/pair_style.rst
View File

@ -114,6 +114,7 @@ accelerated styles exist.
* :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
* :doc:`agni <pair_agni>` - AGNI machine-learning potential
* :doc:`aip/water/2dm <pair_aip_water_2dm>` - anisotropic interfacial potential for water in 2d geometries
* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`amoeba <pair_amoeba>` -

2
doc/src/variable.rst
View File

@ -1481,7 +1481,7 @@ commands
.. code-block:: LAMMPS
# delete_atoms random fraction 0.5 yes all NULL 49839
# run 0
# run 0 post no
variable t equal temp # this thermo keyword invokes a temperature compute
print "Temperature of system = $t"
run 1000

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -55,6 +55,7 @@ Ai
Aidan
aij
aimd
aip
airebo
Aj
ajaramil
@ -528,6 +529,7 @@ collisional
Columic
colvars
Colvars
COH
COLVARS
comID
Commun
@ -1090,6 +1092,7 @@ Fellinger
femtosecond
femtoseconds
fene
Feng
Fennell
fep
FEP
@ -1621,6 +1624,7 @@ Izumi
Izvekov
izz
Izz
Jacobian
Jacobsen
Jadhao
Jadhav
@ -2027,6 +2031,7 @@ Marchetti
Marchi
Mariella
Marinica
Markland
Marrink
Marroquin
Marsaglia
@ -3595,6 +3600,7 @@ THz
Tigran
Tij
Tildesley
Timan
timeI
timespan
timestamp
@ -3736,6 +3742,7 @@ Umin
un
unary
uncomment
uncommented
uncompress
uncompute
underprediction
@ -4090,4 +4097,5 @@ zu
zx
zy
Zybin
Zykova
zz

1
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -90,6 +90,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(get_natoms);
ADDSYM(get_thermo);
ADDSYM(last_thermo);
ADDSYM(extract_box);
ADDSYM(reset_box);

1
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -133,6 +133,7 @@ struct _liblammpsplugin {
double (*get_natoms)(void *);
double (*get_thermo)(void *, const char *);
void *(*last_thermo)(void *, const char *, int);
void (*extract_box)(void *, double *, double *,
double *, double *, double *, int *, int *);

6
examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/in.lammps
View File

@ -1,6 +1,6 @@
dimension 2
units micro
atom_style meso
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
@ -37,12 +37,12 @@ group upper_wall type 3
group lower_wall type 4
mass * ${mass}
set group all meso/rho ${rho_0}
set group all sph/rho ${rho_0}
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_coeff * * ${rho_0} ${c_0} ${h}
fix 1 fluid meso
fix 1 fluid sph
fix 2 sphere rigid/meso single
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box

247
examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1
View File

@ -1,247 +0,0 @@
LAMMPS (24 Oct 2018)
dimension 2
units micro
atom_style meso
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable Lf equal $R*3
variable Lf equal 0.5*3
variable Lb equal $R*4
variable Lb equal 0.5*4
variable wall_velocity equal 0.01 # micrometers/microsecond
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -2 ${Lb} 0 ${a} units box
region box block -2 2 -2 2 0 ${a} units box
region box block -2 2 -2 2 0 0.1 units box
create_box 4 box
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
1 by 1 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 1600 atoms
Time spent = 0.00169706 secs
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
81 settings made for type
region upper_wall block INF INF +${Lf} INF INF INF units box
region upper_wall block INF INF +1.5 INF INF INF units box
set region upper_wall type 3
200 settings made for type
region lower_wall block INF INF INF -${Lf} INF INF units box
region lower_wall block INF INF INF -1.5 INF INF units box
set region lower_wall type 4
240 settings made for type
group fluid type 1
1079 atoms in group fluid
group sphere type 2
81 atoms in group sphere
group upper_wall type 3
200 atoms in group upper_wall
group lower_wall type 4
240 atoms in group lower_wall
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
1600 settings made for meso/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid meso
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
fix 3 upper_wall meso/move linear +0.01 0 0 units box
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
fix 4 lower_wall meso/move linear -0.01 0 0 units box
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 15 15 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 0 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 5 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 6 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 10 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 11 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 14 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 17 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 19 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 20 0
6100 6.1 20 0
6200 6.2 21 0
6300 6.3 21 0
6400 6.4 21 0
6500 6.5 22 0
6600 6.6 22 0
6700 6.7 22 0
6800 6.8 23 0
6900 6.9 23 0
7000 7 23 0
7100 7.1 24 0
7200 7.2 24 0
7300 7.3 25 0
7400 7.4 25 0
7500 7.5 25 0
7600 7.6 26 0
7700 7.7 26 0
7800 7.8 26 0
7900 7.9 27 0
8000 8 27 0
8100 8.1 27 0
8200 8.2 28 0
8300 8.3 28 0
8400 8.4 28 0
8500 8.5 29 0
8600 8.6 29 0
8700 8.7 30 0
8800 8.8 30 0
8900 8.9 30 0
9000 9 31 0
9100 9.1 31 0
9200 9.2 31 0
9300 9.3 32 0
9400 9.4 32 0
9500 9.5 32 0
9600 9.6 33 0
9700 9.7 33 0
9800 9.8 33 0
9900 9.9 34 0
10000 10 34 0
Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 143.08 | 143.08 | 143.08 | 0.0 | 99.22
Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02
Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17
Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08
Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43
Other | | 0.117 | | | 0.08
Nlocal: 1600 ave 1600 max 1600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 993 ave 993 max 993 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73236 ave 73236 max 73236 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 73236
Ave neighs/atom = 45.7725
Neighbor list builds = 34
Dangerous builds = 0
Total wall time: 0:02:24

247
examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4
View File

@ -1,247 +0,0 @@
LAMMPS (24 Oct 2018)
dimension 2
units micro
atom_style meso
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable Lf equal $R*3
variable Lf equal 0.5*3
variable Lb equal $R*4
variable Lb equal 0.5*4
variable wall_velocity equal 0.01 # micrometers/microsecond
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -2 ${Lb} 0 ${a} units box
region box block -2 2 -2 2 0 ${a} units box
region box block -2 2 -2 2 0 0.1 units box
create_box 4 box
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
2 by 2 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 1600 atoms
Time spent = 0.000589566 secs
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
81 settings made for type
region upper_wall block INF INF +${Lf} INF INF INF units box
region upper_wall block INF INF +1.5 INF INF INF units box
set region upper_wall type 3
200 settings made for type
region lower_wall block INF INF INF -${Lf} INF INF units box
region lower_wall block INF INF INF -1.5 INF INF units box
set region lower_wall type 4
240 settings made for type
group fluid type 1
1079 atoms in group fluid
group sphere type 2
81 atoms in group sphere
group upper_wall type 3
200 atoms in group upper_wall
group lower_wall type 4
240 atoms in group lower_wall
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
1600 settings made for meso/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid meso
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
fix 3 upper_wall meso/move linear +0.01 0 0 units box
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
fix 4 lower_wall meso/move linear -0.01 0 0 units box
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 15 15 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 4 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 5 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 6 0
2200 2.2 6 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 7 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 8 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 9 0
3200 3.2 10 0
3300 3.3 10 0
3400 3.4 10 0
3500 3.5 11 0
3600 3.6 11 0
3700 3.7 11 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 12 0
4100 4.1 13 0
4200 4.2 13 0
4300 4.3 13 0
4400 4.4 14 0
4500 4.5 14 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 15 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 17 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 18 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 20 0
6100 6.1 20 0
6200 6.2 20 0
6300 6.3 21 0
6400 6.4 21 0
6500 6.5 21 0
6600 6.6 22 0
6700 6.7 22 0
6800 6.8 22 0
6900 6.9 23 0
7000 7 23 0
7100 7.1 23 0
7200 7.2 24 0
7300 7.3 24 0
7400 7.4 25 0
7500 7.5 25 0
7600 7.6 25 0
7700 7.7 25 0
7800 7.8 26 0
7900 7.9 26 0
8000 8 26 0
8100 8.1 27 0
8200 8.2 27 0
8300 8.3 27 0
8400 8.4 28 0
8500 8.5 28 0
8600 8.6 28 0
8700 8.7 29 0
8800 8.8 29 0
8900 8.9 29 0
9000 9 30 0
9100 9.1 30 0
9200 9.2 31 0
9300 9.3 31 0
9400 9.4 31 0
9500 9.5 32 0
9600 9.6 32 0
9700 9.7 32 0
9800 9.8 32 0
9900 9.9 33 0
10000 10 33 0
Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms
Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
94.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86
Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02
Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51
Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20
Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09
Other | | 0.2038 | | | 0.32
Nlocal: 400 ave 411 max 388 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 552.25 ave 567 max 539 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 18298.8 ave 18781 max 17829 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 73195
Ave neighs/atom = 45.7469
Neighbor list builds = 33
Dangerous builds = 0
Total wall time: 0:01:03

253
examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.1 Normal file
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@ -0,0 +1,253 @@
LAMMPS (28 Mar 2023 - Development)
dimension 2
units micro
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable Lf equal $R*3
variable Lf equal 0.5*3
variable Lb equal $R*4
variable Lb equal 0.5*4
variable wall_velocity equal 0.01 # micrometers/microsecond
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -2 ${Lb} 0 ${a} units box
region box block -2 2 -2 2 0 ${a} units box
region box block -2 2 -2 2 0 0.1 units box
create_box 4 box
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
1 by 1 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 1600 atoms
using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
create_atoms CPU = 0.001 seconds
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
Setting atom values ...
81 settings made for type
region upper_wall block INF INF +${Lf} INF INF INF units box
region upper_wall block INF INF +1.5 INF INF INF units box
set region upper_wall type 3
Setting atom values ...
200 settings made for type
region lower_wall block INF INF INF -${Lf} INF INF units box
region lower_wall block INF INF INF -1.5 INF INF units box
set region lower_wall type 4
Setting atom values ...
240 settings made for type
group fluid type 1
1079 atoms in group fluid
group sphere type 2
81 atoms in group sphere
group upper_wall type 3
200 atoms in group upper_wall
group lower_wall type 4
240 atoms in group lower_wall
mass * ${mass}
mass * 0.001
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
1600 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid sph
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
fix 3 upper_wall meso/move linear +0.01 0 0 units box
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
fix 4 lower_wall meso/move linear -0.01 0 0 units box
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Generated 0 of 6 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 = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 15 15 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.313 | 7.313 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 0 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 5 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 6 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 10 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 11 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 14 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 17 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 19 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 20 0
6100 6.1 20 0
6200 6.2 21 0
6300 6.3 21 0
6400 6.4 21 0
6500 6.5 22 0
6600 6.6 22 0
6700 6.7 22 0
6800 6.8 23 0
6900 6.9 23 0
7000 7 23 0
7100 7.1 24 0
7200 7.2 24 0
7300 7.3 25 0
7400 7.4 25 0
7500 7.5 25 0
7600 7.6 26 0
7700 7.7 26 0
7800 7.8 26 0
7900 7.9 27 0
8000 8 27 0
8100 8.1 27 0
8200 8.2 28 0
8300 8.3 28 0
8400 8.4 28 0
8500 8.5 29 0
8600 8.6 29 0
8700 8.7 30 0
8800 8.8 30 0
8900 8.9 30 0
9000 9 31 0
9100 9.1 31 0
9200 9.2 31 0
9300 9.3 32 0
9400 9.4 32 0
9500 9.5 32 0
9600 9.6 33 0
9700 9.7 33 0
9800 9.8 33 0
9900 9.9 34 0
10000 10 34 0
Loop time of 131.724 on 1 procs for 10000 steps with 1600 atoms
Performance: 6559168.339 ns/day, 0.000 hours/ns, 75.916 timesteps/s, 121.466 katom-step/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 130.89 | 130.89 | 130.89 | 0.0 | 99.37
Neigh | 0.02884 | 0.02884 | 0.02884 | 0.0 | 0.02
Comm | 0.17863 | 0.17863 | 0.17863 | 0.0 | 0.14
Output | 0.095497 | 0.095497 | 0.095497 | 0.0 | 0.07
Modify | 0.42063 | 0.42063 | 0.42063 | 0.0 | 0.32
Other | | 0.1069 | | | 0.08
Nlocal: 1600 ave 1600 max 1600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 993 ave 993 max 993 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73236 ave 73236 max 73236 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 73236
Ave neighs/atom = 45.7725
Neighbor list builds = 34
Dangerous builds = 0
Total wall time: 0:02:11

253
examples/PACKAGES/dpd-smooth/2d-diffusion-in-shear-flow/log.28Mar23.2d-diffusion-in-shear-flow.g++.4 Normal file
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@ -0,0 +1,253 @@
LAMMPS (28 Mar 2023 - Development)
dimension 2
units micro
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable Lf equal $R*3
variable Lf equal 0.5*3
variable Lb equal $R*4
variable Lb equal 0.5*4
variable wall_velocity equal 0.01 # micrometers/microsecond
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
region box block -2 2 -2 ${Lb} 0 ${a} units box
region box block -2 2 -2 2 0 ${a} units box
region box block -2 2 -2 2 0 0.1 units box
create_box 4 box
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
2 by 2 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 1600 atoms
using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
create_atoms CPU = 0.001 seconds
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
Setting atom values ...
81 settings made for type
region upper_wall block INF INF +${Lf} INF INF INF units box
region upper_wall block INF INF +1.5 INF INF INF units box
set region upper_wall type 3
Setting atom values ...
200 settings made for type
region lower_wall block INF INF INF -${Lf} INF INF units box
region lower_wall block INF INF INF -1.5 INF INF units box
set region lower_wall type 4
Setting atom values ...
240 settings made for type
group fluid type 1
1079 atoms in group fluid
group sphere type 2
81 atoms in group sphere
group upper_wall type 3
200 atoms in group upper_wall
group lower_wall type 4
240 atoms in group lower_wall
mass * ${mass}
mass * 0.001
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
1600 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid sph
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
fix 3 upper_wall meso/move linear +0.01 0 0 units box
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
fix 4 lower_wall meso/move linear -0.01 0 0 units box
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Generated 0 of 6 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 = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 15 15 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.23 | 7.23 | 7.23 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 5 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 6 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 10 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 11 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 13 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 14 0
4600 4.6 14 0
4700 4.7 15 0
4800 4.8 15 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 16 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 17 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 18 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 20 0
6100 6.1 20 0
6200 6.2 20 0
6300 6.3 21 0
6400 6.4 21 0
6500 6.5 21 0
6600 6.6 22 0
6700 6.7 22 0
6800 6.8 22 0
6900 6.9 23 0
7000 7 23 0
7100 7.1 23 0
7200 7.2 24 0
7300 7.3 24 0
7400 7.4 24 0
7500 7.5 25 0
7600 7.6 25 0
7700 7.7 25 0
7800 7.8 25 0
7900 7.9 26 0
8000 8 26 0
8100 8.1 26 0
8200 8.2 27 0
8300 8.3 27 0
8400 8.4 28 0
8500 8.5 28 0
8600 8.6 28 0
8700 8.7 29 0
8800 8.8 29 0
8900 8.9 29 0
9000 9 30 0
9100 9.1 30 0
9200 9.2 30 0
9300 9.3 31 0
9400 9.4 31 0
9500 9.5 31 0
9600 9.6 32 0
9700 9.7 32 0
9800 9.8 32 0
9900 9.9 32 0
10000 10 33 0
Loop time of 24.8261 on 4 procs for 10000 steps with 1600 atoms
Performance: 34802055.618 ns/day, 0.000 hours/ns, 402.802 timesteps/s, 644.483 katom-step/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.84 | 22.879 | 23.944 | 21.4 | 92.16
Neigh | 0.007446 | 0.0079435 | 0.0084435 | 0.6 | 0.03
Comm | 0.5271 | 1.5894 | 2.6259 | 80.9 | 6.40
Output | 0.034799 | 0.035302 | 0.036437 | 0.4 | 0.14
Modify | 0.20079 | 0.21033 | 0.2202 | 1.7 | 0.85
Other | | 0.1041 | | | 0.42
Nlocal: 400 ave 414 max 390 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 555.5 ave 564 max 543 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 18299.2 ave 18820 max 17906 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 73197
Ave neighs/atom = 45.748125
Neighbor list builds = 33
Dangerous builds = 0
Total wall time: 0:00:24

6
examples/PACKAGES/dpd-smooth/2d-diffusion/in.lammps
View File

@ -1,6 +1,6 @@
dimension 2
units micro
atom_style meso
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
@ -27,12 +27,12 @@ group fluid type 1
group sphere type 2
mass * ${mass}
set group all meso/rho ${rho_0}
set group all sph/rho ${rho_0}
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_coeff * * ${rho_0} ${c_0} ${h}
fix 1 fluid meso
fix 1 fluid sph
fix 2 sphere rigid/meso single
fix 2d all enforce2d

226
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LAMMPS (24 Oct 2018)
dimension 2
units micro
atom_style meso
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable L equal $R*3
variable L equal 0.5*3
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -$L $L -$L $L 0 $a units box
region box block -1.5 $L -$L $L 0 $a units box
region box block -1.5 1.5 -$L $L 0 $a units box
region box block -1.5 1.5 -1.5 $L 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
create_box 2 box
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
1 by 1 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 900 atoms
Time spent = 0.0015769 secs
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
81 settings made for type
group fluid type 1
819 atoms in group fluid
group sphere type 2
81 atoms in group sphere
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
900 settings made for meso/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid meso
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 6 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 7 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 10 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 11 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 12 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 13 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 14 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 17 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 18 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 19 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 19 0
6100 6.1 20 0
6200 6.2 20 0
6300 6.3 20 0
6400 6.4 21 0
6500 6.5 21 0
6600 6.6 21 0
6700 6.7 21 0
6800 6.8 22 0
6900 6.9 22 0
7000 7 22 0
7100 7.1 23 0
7200 7.2 23 0
7300 7.3 23 0
7400 7.4 24 0
7500 7.5 24 0
7600 7.6 24 0
7700 7.7 25 0
7800 7.8 25 0
7900 7.9 26 0
8000 8 26 0
8100 8.1 26 0
8200 8.2 26 0
8300 8.3 27 0
8400 8.4 27 0
8500 8.5 27 0
8600 8.6 28 0
8700 8.7 28 0
8800 8.8 28 0
8900 8.9 29 0
9000 9 29 0
9100 9.1 29 0
9200 9.2 30 0
9300 9.3 30 0
9400 9.4 30 0
9500 9.5 30 0
9600 9.6 31 0
9700 9.7 31 0
9800 9.8 32 0
9900 9.9 32 0
10000 10 32 0
Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 80.306 | 80.306 | 80.306 | 0.0 | 99.21
Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02
Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21
Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09
Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39
Other | | 0.067 | | | 0.08
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 762 ave 762 max 762 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40697 ave 40697 max 40697 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40697
Ave neighs/atom = 45.2189
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:01:20

226
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LAMMPS (24 Oct 2018)
dimension 2
units micro
atom_style meso
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable L equal $R*3
variable L equal 0.5*3
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -$L $L -$L $L 0 $a units box
region box block -1.5 $L -$L $L 0 $a units box
region box block -1.5 1.5 -$L $L 0 $a units box
region box block -1.5 1.5 -1.5 $L 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
create_box 2 box
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
2 by 2 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 900 atoms
Time spent = 0.0010246 secs
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
81 settings made for type
group fluid type 1
819 atoms in group fluid
group sphere type 2
81 atoms in group sphere
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
900 settings made for meso/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid meso
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 5 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 6 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 7 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 8 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 9 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 10 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 11 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 13 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 16 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 18 0
5500 5.5 18 0
5600 5.6 19 0
5700 5.7 19 0
5800 5.8 19 0
5900 5.9 20 0
6000 6 20 0
6100 6.1 20 0
6200 6.2 21 0
6300 6.3 21 0
6400 6.4 21 0
6500 6.5 22 0
6600 6.6 22 0
6700 6.7 22 0
6800 6.8 23 0
6900 6.9 23 0
7000 7 23 0
7100 7.1 24 0
7200 7.2 24 0
7300 7.3 24 0
7400 7.4 25 0
7500 7.5 25 0
7600 7.6 25 0
7700 7.7 26 0
7800 7.8 26 0
7900 7.9 26 0
8000 8 27 0
8100 8.1 27 0
8200 8.2 27 0
8300 8.3 28 0
8400 8.4 28 0
8500 8.5 28 0
8600 8.6 28 0
8700 8.7 29 0
8800 8.8 29 0
8900 8.9 29 0
9000 9 30 0
9100 9.1 30 0
9200 9.2 31 0
9300 9.3 31 0
9400 9.4 31 0
9500 9.5 31 0
9600 9.6 32 0
9700 9.7 32 0
9800 9.8 32 0
9900 9.9 33 0
10000 10 33 0
Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms
Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s
48.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 56.528 | 57.936 | 58.729 | 11.0 | 83.95
Neigh | 0.013157 | 0.013382 | 0.013551 | 0.1 | 0.02
Comm | 8.9594 | 9.7555 | 11.113 | 26.7 | 14.14
Output | 0.14644 | 0.15009 | 0.15809 | 1.2 | 0.22
Modify | 0.72913 | 0.91574 | 1.0524 | 12.4 | 1.33
Other | | 0.2389 | | | 0.35
Nlocal: 225 ave 229 max 223 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 442 ave 444 max 439 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 10188.8 ave 10437 max 9932 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 40755
Ave neighs/atom = 45.2833
Neighbor list builds = 33
Dangerous builds = 0
Total wall time: 0:01:09

230
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LAMMPS (28 Mar 2023 - Development)
dimension 2
units micro
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable L equal $R*3
variable L equal 0.5*3
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -$L $L -$L $L 0 $a units box
region box block -1.5 $L -$L $L 0 $a units box
region box block -1.5 1.5 -$L $L 0 $a units box
region box block -1.5 1.5 -1.5 $L 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
create_box 2 box
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
1 by 1 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 900 atoms
using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
create_atoms CPU = 0.001 seconds
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
Setting atom values ...
81 settings made for type
group fluid type 1
819 atoms in group fluid
group sphere type 2
81 atoms in group sphere
mass * ${mass}
mass * 0.001
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
900 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid sph
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
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 = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.512 | 6.512 | 6.512 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 6 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 7 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 10 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 11 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 12 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 13 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 14 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 17 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 18 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 19 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 19 0
6100 6.1 20 0
6200 6.2 20 0
6300 6.3 20 0
6400 6.4 21 0
6500 6.5 21 0
6600 6.6 21 0
6700 6.7 21 0
6800 6.8 22 0
6900 6.9 22 0
7000 7 22 0
7100 7.1 23 0
7200 7.2 23 0
7300 7.3 23 0
7400 7.4 24 0
7500 7.5 24 0
7600 7.6 24 0
7700 7.7 25 0
7800 7.8 25 0
7900 7.9 26 0
8000 8 26 0
8100 8.1 26 0
8200 8.2 26 0
8300 8.3 27 0
8400 8.4 27 0
8500 8.5 27 0
8600 8.6 28 0
8700 8.7 28 0
8800 8.8 28 0
8900 8.9 29 0
9000 9 29 0
9100 9.1 29 0
9200 9.2 30 0
9300 9.3 30 0
9400 9.4 30 0
9500 9.5 30 0
9600 9.6 31 0
9700 9.7 31 0
9800 9.8 32 0
9900 9.9 32 0
10000 10 32 0
Loop time of 78.0094 on 1 procs for 10000 steps with 900 atoms
Performance: 11075589.479 ns/day, 0.000 hours/ns, 128.190 timesteps/s, 115.371 katom-step/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 77.441 | 77.441 | 77.441 | 0.0 | 99.27
Neigh | 0.016471 | 0.016471 | 0.016471 | 0.0 | 0.02
Comm | 0.14821 | 0.14821 | 0.14821 | 0.0 | 0.19
Output | 0.062415 | 0.062415 | 0.062415 | 0.0 | 0.08
Modify | 0.25323 | 0.25323 | 0.25323 | 0.0 | 0.32
Other | | 0.0877 | | | 0.11
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 762 ave 762 max 762 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 40697 ave 40697 max 40697 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 40697
Ave neighs/atom = 45.218889
Neighbor list builds = 32
Dangerous builds = 0
Total wall time: 0:01:18

230
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LAMMPS (28 Mar 2023 - Development)
dimension 2
units micro
atom_style sph
variable R equal 0.5 # radius of sphere micrometers
variable a equal $R/5 # lattice spacing micrometers
variable a equal 0.5/5
variable L equal $R*3
variable L equal 0.5*3
variable T equal 300.
variable rho_0 equal 1. # density picograms/micrometer^3
variable c_0 equal 100. # speed of sound micrometers/microsecond
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
variable h equal $a*4.5 # kernel function cutoff micrometers
variable h equal 0.1*4.5
variable mass equal $a*$a*$a*${rho_0}
variable mass equal 0.1*$a*$a*${rho_0}
variable mass equal 0.1*0.1*$a*${rho_0}
variable mass equal 0.1*0.1*0.1*${rho_0}
variable mass equal 0.1*0.1*0.1*1
variable dt equal 1e-3 # timestep microseconds
variable skin equal 0.2*$h
variable skin equal 0.2*0.45
region box block -$L $L -$L $L 0 $a units box
region box block -1.5 $L -$L $L 0 $a units box
region box block -1.5 1.5 -$L $L 0 $a units box
region box block -1.5 1.5 -1.5 $L 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 $a units box
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
create_box 2 box
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
2 by 2 by 1 MPI processor grid
lattice sq $a
lattice sq 0.1
Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 900 atoms
using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
create_atoms CPU = 0.001 seconds
region sphere sphere 0 0 0 $R units box
region sphere sphere 0 0 0 0.5 units box
set region sphere type 2
Setting atom values ...
81 settings made for type
group fluid type 1
819 atoms in group fluid
group sphere type 2
81 atoms in group sphere
mass * ${mass}
mass * 0.001
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
900 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
pair_style sdpd/taitwater/isothermal 300 1 76787
pair_coeff * * ${rho_0} ${c_0} ${h}
pair_coeff * * 1 ${c_0} ${h}
pair_coeff * * 1 100 ${h}
pair_coeff * * 1 100 0.45
fix 1 fluid sph
fix 2 sphere rigid/meso single
1 rigid bodies with 81 atoms
fix 2d all enforce2d
neighbor ${skin} bin
neighbor 0.09 bin
neigh_modify delay 0 every 1 check yes
timestep ${dt}
timestep 0.001
dump dump_id all atom 100 dump.lammpstrj
thermo 100
thermo_style custom step time nbuild ndanger
run 10000
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 = 0.54
ghost atom cutoff = 0.54
binsize = 0.27, bins = 12 12 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/2d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.463 | 6.463 | 6.463 Mbytes
Step Time Nbuild Ndanger
0 0 0 0
100 0.1 0 0
200 0.2 0 0
300 0.3 0 0
400 0.4 1 0
500 0.5 1 0
600 0.6 1 0
700 0.7 2 0
800 0.8 2 0
900 0.9 2 0
1000 1 3 0
1100 1.1 3 0
1200 1.2 3 0
1300 1.3 4 0
1400 1.4 4 0
1500 1.5 4 0
1600 1.6 5 0
1700 1.7 5 0
1800 1.8 5 0
1900 1.9 6 0
2000 2 6 0
2100 2.1 6 0
2200 2.2 7 0
2300 2.3 7 0
2400 2.4 7 0
2500 2.5 8 0
2600 2.6 8 0
2700 2.7 8 0
2800 2.8 9 0
2900 2.9 9 0
3000 3 9 0
3100 3.1 10 0
3200 3.2 10 0
3300 3.3 11 0
3400 3.4 11 0
3500 3.5 11 0
3600 3.6 12 0
3700 3.7 12 0
3800 3.8 12 0
3900 3.9 12 0
4000 4 13 0
4100 4.1 13 0
4200 4.2 14 0
4300 4.3 14 0
4400 4.4 14 0
4500 4.5 15 0
4600 4.6 15 0
4700 4.7 15 0
4800 4.8 16 0
4900 4.9 16 0
5000 5 16 0
5100 5.1 17 0
5200 5.2 17 0
5300 5.3 17 0
5400 5.4 17 0
5500 5.5 18 0
5600 5.6 18 0
5700 5.7 18 0
5800 5.8 19 0
5900 5.9 19 0
6000 6 19 0
6100 6.1 20 0
6200 6.2 20 0
6300 6.3 20 0
6400 6.4 21 0
6500 6.5 21 0
6600 6.6 21 0
6700 6.7 22 0
6800 6.8 22 0
6900 6.9 22 0
7000 7 23 0
7100 7.1 23 0
7200 7.2 23 0
7300 7.3 24 0
7400 7.4 24 0
7500 7.5 24 0
7600 7.6 25 0
7700 7.7 25 0
7800 7.8 26 0
7900 7.9 26 0
8000 8 26 0
8100 8.1 26 0
8200 8.2 27 0
8300 8.3 27 0
8400 8.4 28 0
8500 8.5 28 0
8600 8.6 28 0
8700 8.7 29 0
8800 8.8 29 0
8900 8.9 29 0
9000 9 30 0
9100 9.1 30 0
9200 9.2 30 0
9300 9.3 30 0
9400 9.4 31 0
9500 9.5 31 0
9600 9.6 31 0
9700 9.7 32 0
9800 9.8 32 0
9900 9.9 32 0
10000 10 33 0
Loop time of 13.5306 on 4 procs for 10000 steps with 900 atoms
Performance: 63855371.888 ns/day, 0.000 hours/ns, 739.067 timesteps/s, 665.160 katom-step/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.327 | 12.56 | 12.738 | 4.3 | 92.83
Neigh | 0.0043391 | 0.0044297 | 0.0045381 | 0.1 | 0.03
Comm | 0.53746 | 0.71463 | 0.94685 | 18.1 | 5.28
Output | 0.021884 | 0.02228 | 0.023428 | 0.4 | 0.16
Modify | 0.14457 | 0.14548 | 0.14643 | 0.2 | 1.08
Other | | 0.08351 | | | 0.62
Nlocal: 225 ave 228 max 222 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 438.25 ave 442 max 434 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 10152.2 ave 10328 max 9853 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 40609
Ave neighs/atom = 45.121111
Neighbor list builds = 33
Dangerous builds = 0
Total wall time: 0:00:13

6
examples/PACKAGES/dpd-smooth/equipartition-verification/in.lammps
View File

@ -1,6 +1,6 @@
dimension 3
units micro
atom_style meso
atom_style sph
variable a equal 0.1 # lattice spacing micrometers
variable L equal $a*10
@ -21,7 +21,7 @@ lattice sc $a
create_atoms 1 box
mass * ${mass}
set group all meso/rho ${rho_0}
set group all sph/rho ${rho_0}
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_coeff * * ${rho_0} ${c_0} ${h}
@ -34,7 +34,7 @@ variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
fix 1 all meso
fix 1 all sph
neighbor ${skin} bin
timestep ${dt}

91
examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.1 → examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.1
View File

@ -1,7 +1,7 @@
LAMMPS (24 Oct 2018)
LAMMPS (28 Mar 2023 - Development)
dimension 3
units micro
atom_style meso
atom_style sph
variable a equal 0.1 # lattice spacing micrometers
variable L equal $a*10
@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 8000 atoms
Time spent = 0.00285411 secs
using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
create_atoms CPU = 0.002 seconds
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
8000 settings made for meso/rho
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
8000 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
fix 1 all meso
fix 1 all sph
neighbor ${skin} bin
neighbor 0.04 bin
@ -82,8 +84,9 @@ thermo 10
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
run 200
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.44
ghost atom cutoff = 0.44
@ -92,55 +95,55 @@ Neighbor list info ...
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
0 0 0 0 0
10 0.005 0.70973271 0.71495693 0.71910087
20 0.01 0.90418096 0.88845437 0.89659567
30 0.015 0.9590736 0.97880338 0.9619016
40 0.02 0.98533774 0.96057682 0.95600448
50 0.025 0.96433662 0.96650071 0.95509683
60 0.03 0.96598029 0.96373656 0.96734888
70 0.035 0.95433045 0.98004764 0.96255924
80 0.04 0.97872906 0.95987289 0.96623598
90 0.045 0.99913888 0.99255731 0.95616142
100 0.05 0.98872675 0.97141018 0.95338841
110 0.055 0.97794592 0.97389258 0.98473719
120 0.06 0.98389266 0.96716284 0.95504862
130 0.065 0.98572886 0.96680923 0.95599065
140 0.07 0.97602684 0.97580081 0.9886878
150 0.075 0.99172003 0.95027467 0.96028033
160 0.08 0.96793247 0.94590928 0.95644301
170 0.085 0.94167619 0.98048861 0.93439426
180 0.09 0.97277934 0.97383622 0.96900866
190 0.095 0.96647288 1.0027643 0.96230782
200 0.1 0.94864291 0.95902585 0.96398175
Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
Per MPI rank memory allocation (min/avg/max) = 14.29 | 14.29 | 14.29 Mbytes
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
0 0 0 0 0
10 0.005 0.70973271 0.71495693 0.71910087
20 0.01 0.90418096 0.88845437 0.89659567
30 0.015 0.9590736 0.97880338 0.9619016
40 0.02 0.98533774 0.96057682 0.95600448
50 0.025 0.96433662 0.96650071 0.95509683
60 0.03 0.96598029 0.96373656 0.96734888
70 0.035 0.95433045 0.98004764 0.96255924
80 0.04 0.97872906 0.95987289 0.96623598
90 0.045 0.99913888 0.99255731 0.95616142
100 0.05 0.98872675 0.97141018 0.95338841
110 0.055 0.97794592 0.97389258 0.98473719
120 0.06 0.98389266 0.96716284 0.95504862
130 0.065 0.98572886 0.96680923 0.95599065
140 0.07 0.97602684 0.97580081 0.9886878
150 0.075 0.99172003 0.95027467 0.96028033
160 0.08 0.96793247 0.94590928 0.95644301
170 0.085 0.94167619 0.98048861 0.93439426
180 0.09 0.97277934 0.97383622 0.96900866
190 0.095 0.96647288 1.0027643 0.96230782
200 0.1 0.94864291 0.95902585 0.96398175
Loop time of 55.7542 on 1 procs for 200 steps with 8000 atoms
Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 154965.922 ns/day, 0.000 hours/ns, 3.587 timesteps/s, 28.697 katom-step/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68
Pair | 55.642 | 55.642 | 55.642 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19
Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01
Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07
Other | | 0.02811 | | | 0.05
Comm | 0.060977 | 0.060977 | 0.060977 | 0.0 | 0.11
Output | 0.0066393 | 0.0066393 | 0.0066393 | 0.0 | 0.01
Modify | 0.028354 | 0.028354 | 0.028354 | 0.0 | 0.05
Other | | 0.01623 | | | 0.03
Nlocal: 8000 ave 8000 max 8000 min
Nlocal: 8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 16389 ave 16389 max 16389 min
Nghost: 16389 ave 16389 max 16389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min
Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1456000
Ave neighs/atom = 182
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:01:00
Total wall time: 0:00:56

91
examples/PACKAGES/dpd-smooth/equipartition-verification/log.24Oct18.equipartition.g++.4 → examples/PACKAGES/dpd-smooth/equipartition-verification/log.28Mar23.equipartition.g++.4
View File

@ -1,7 +1,7 @@
LAMMPS (24 Oct 2018)
LAMMPS (28 Mar 2023 - Development)
dimension 3
units micro
atom_style meso
atom_style sph
variable a equal 0.1 # lattice spacing micrometers
variable L equal $a*10
@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
create_atoms 1 box
Created 8000 atoms
Time spent = 0.00252754 secs
using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
create_atoms CPU = 0.001 seconds
mass * ${mass}
mass * 0.001
set group all meso/rho ${rho_0}
set group all meso/rho 1
8000 settings made for meso/rho
set group all sph/rho ${rho_0}
set group all sph/rho 1
Setting atom values ...
8000 settings made for sph/rho
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
fix 1 all meso
fix 1 all sph
neighbor ${skin} bin
neighbor 0.04 bin
@ -82,8 +84,9 @@ thermo 10
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
run 200
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.44
ghost atom cutoff = 0.44
@ -92,55 +95,55 @@ Neighbor list info ...
(1) pair sdpd/taitwater/isothermal, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
0 0 0 0 0
10 0.005 0.71224819 0.71470372 0.7008956
20 0.01 0.90627589 0.90683966 0.90116506
30 0.015 0.938505 0.95884272 0.93337542
40 0.02 0.94394649 0.93668038 0.96468004
50 0.025 0.97152309 0.97546161 0.95107762
60 0.03 0.94710871 0.95678322 0.97285504
70 0.035 0.96253148 0.95838642 0.95450883
80 0.04 0.97581495 0.95278681 0.95099478
90 0.045 0.96251614 0.9740684 0.96081505
100 0.05 0.94191275 0.97137523 0.94084858
110 0.055 0.953406 0.95739684 0.98574522
120 0.06 0.99001614 0.99608287 0.9839996
130 0.065 0.96575225 0.94309655 0.92847798
140 0.07 0.97642687 0.97458638 0.94696406
150 0.075 0.99316381 0.96876814 0.95440106
160 0.08 0.94589744 0.95264791 0.95495169
170 0.085 0.97599092 0.95336014 0.97687718
180 0.09 0.97214242 0.9726305 0.9726035
190 0.095 0.97577583 0.96523645 0.9756968
200 0.1 0.96386053 0.97268854 0.94582436
Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
Per MPI rank memory allocation (min/avg/max) = 6.172 | 6.172 | 6.172 Mbytes
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
0 0 0 0 0
10 0.005 0.71224819 0.71470372 0.7008956
20 0.01 0.90627589 0.90683966 0.90116506
30 0.015 0.938505 0.95884272 0.93337542
40 0.02 0.94394649 0.93668038 0.96468004
50 0.025 0.97152309 0.97546161 0.95107762
60 0.03 0.94710871 0.95678322 0.97285504
70 0.035 0.96253148 0.95838642 0.95450883
80 0.04 0.97581495 0.95278681 0.95099478
90 0.045 0.96251614 0.9740684 0.96081505
100 0.05 0.94191275 0.97137523 0.94084858
110 0.055 0.953406 0.95739684 0.98574522
120 0.06 0.99001614 0.99608287 0.9839996
130 0.065 0.96575225 0.94309655 0.92847798
140 0.07 0.97642687 0.97458638 0.94696406
150 0.075 0.99316381 0.96876814 0.95440106
160 0.08 0.94589744 0.95264791 0.95495169
170 0.085 0.97599092 0.95336014 0.97687718
180 0.09 0.97214242 0.9726305 0.9726035
190 0.095 0.97577583 0.96523645 0.9756968
200 0.1 0.96386053 0.97268854 0.94582436
Loop time of 9.59181 on 4 procs for 200 steps with 8000 atoms
Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
73.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 900768.333 ns/day, 0.000 hours/ns, 20.851 timesteps/s, 166.809 katom-step/s
98.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34
Pair | 8.9729 | 9.2147 | 9.4383 | 5.5 | 96.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10
Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08
Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10
Other | | 0.1226 | | | 0.38
Comm | 0.13739 | 0.36068 | 0.60216 | 27.6 | 3.76
Output | 0.0022724 | 0.002394 | 0.0026506 | 0.3 | 0.02
Modify | 0.0068559 | 0.0069926 | 0.0070974 | 0.1 | 0.07
Other | | 0.007004 | | | 0.07
Nlocal: 2000 ave 2000 max 2000 min
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 8469 ave 8469 max 8469 min
Nghost: 8469 ave 8469 max 8469 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 364000 ave 376628 max 351184 min
Neighs: 364000 ave 376628 max 351184 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 1456000
Ave neighs/atom = 182
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:32
Total wall time: 0:00:09

1
examples/PACKAGES/interlayer/aip_water_2dm/COH.aip.water.2dm Symbolic link
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@ -0,0 +1 @@
../../../../potentials/COH.aip.water.2dm

2040
examples/PACKAGES/interlayer/aip_water_2dm/gra_water.data Normal file
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File diff suppressed because it is too large Load Diff

51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water Normal file
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@ -0,0 +1,51 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

51
examples/PACKAGES/interlayer/aip_water_2dm/in.gr_water.opt Normal file
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@ -0,0 +1,51 @@
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
group water molecule 2
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000

239
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 Normal file
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@ -0,0 +1,239 @@
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J.~Chem.\ Theory Comput.},
volume = 17,
pages = {7237--7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 84320 48000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair aip/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 32.9 | 32.9 | 32.9 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491435 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24516e-05 48
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50422e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496703 -21.072663 3.5759596 188.2777 -1.9833956 291.20871
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15262e-06 96
Angle: 1 104.52 7.02157e-05 48
800 -17.478623 -20.819504 3.3408809 188.37868 -1.9112996 272.06505
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14138e-07 96
Angle: 1 104.52 6.98742e-05 48
900 -17.48086 -20.728495 3.2476349 188.59022 -1.8922102 264.47155
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00586e-06 96
Angle: 1 104.52 0.000111712 48
1000 -17.498465 -20.331545 2.8330804 188.87473 -1.812177 230.71225
Loop time of 20.3334 on 1 procs for 1000 steps with 936 atoms
Performance: 4.249 ns/day, 5.648 hours/ns, 49.180 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.179 | 16.179 | 16.179 | 0.0 | 79.57
Bond | 0.00021103 | 0.00021103 | 0.00021103 | 0.0 | 0.00
Kspace | 3.3118 | 3.3118 | 3.3118 | 0.0 | 16.29
Neigh | 0.79017 | 0.79017 | 0.79017 | 0.0 | 3.89
Comm | 0.026379 | 0.026379 | 0.026379 | 0.0 | 0.13
Output | 0.00046496 | 0.00046496 | 0.00046496 | 0.0 | 0.00
Modify | 0.017013 | 0.017013 | 0.017013 | 0.0 | 0.08
Other | | 0.008835 | | | 0.04
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5242 ave 5242 max 5242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 431382 ave 431382 max 431382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:20

239
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 Normal file
View File

@ -0,0 +1,239 @@
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.017 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J.~Chem.\ Theory Comput.},
volume = 17,
pages = {7237--7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 30685 12480
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair aip/water/2dm, perpetual
attributes: full, newton on, ghost
pair build: full/bin/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 25.22 | 25.25 | 25.29 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24517e-05 48
600 -17.505683 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50425e-07 96
Angle: 1 104.52 5.62422e-05 48
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15256e-06 96
Angle: 1 104.52 7.02177e-05 48
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.06489
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14163e-07 96
Angle: 1 104.52 6.98849e-05 48
900 -17.480865 -20.728504 3.2476386 188.5902 -1.8922108 264.47185
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00568e-06 96
Angle: 1 104.52 0.000111707 48
1000 -17.498474 -20.331607 2.833133 188.87466 -1.8121689 230.71654
Loop time of 9.05361 on 4 procs for 1000 steps with 936 atoms
Performance: 9.543 ns/day, 2.515 hours/ns, 110.453 timesteps/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.462 | 4.2266 | 7.1075 | 89.3 | 46.68
Bond | 0.00018424 | 0.00019878 | 0.00022125 | 0.0 | 0.00
Kspace | 1.4698 | 4.338 | 6.1001 | 87.8 | 47.91
Neigh | 0.39462 | 0.39489 | 0.39518 | 0.0 | 4.36
Comm | 0.043753 | 0.055826 | 0.062746 | 3.1 | 0.62
Output | 0.00048755 | 0.00053971 | 0.00062785 | 0.0 | 0.01
Modify | 0.027255 | 0.028664 | 0.030278 | 0.7 | 0.32
Other | | 0.008904 | | | 0.10
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2876.5 ave 3122 max 2632 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 107846 ave 150684 max 82181 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:09

256
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 Normal file
View File

@ -0,0 +1,256 @@
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
1 by 1 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J.~Chem.\ Theory Comput.},
volume = 17,
pages = {7237--7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
@inproceedings{gao2021lmff
author = {Gao, Ping and Duan, Xiaohui and Others},
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
year = {2021},
isbn = {9781450384421},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3458817.3476137},
doi = {10.1145/3458817.3476137},
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
articleno = {42},
numpages = {14},
location = {St. Louis, Missouri},
series = {SC'21},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 84320 48000
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair aip/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 25.27 | 25.27 | 25.27 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494868 -20.796993 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.486271 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502844 -20.993704 3.49086 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495287 -20.828353 3.3330658 188.48002 -1.8429075 271.42862
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443044 2.9516084 188.7589 -1.8566335 240.36459
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24516e-05 48
600 -17.505684 -20.608457 3.1027731 188.72078 -1.9560796 252.67471
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50422e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496701 -21.07266 3.5759595 188.2777 -1.9833956 291.20871
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15262e-06 96
Angle: 1 104.52 7.02158e-05 48
800 -17.478623 -20.819504 3.340881 188.37868 -1.9112996 272.06506
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14138e-07 96
Angle: 1 104.52 6.98742e-05 48
900 -17.480864 -20.728498 3.2476343 188.59022 -1.8922102 264.4715
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00586e-06 96
Angle: 1 104.52 0.000111711 48
1000 -17.498466 -20.331547 2.8330808 188.87473 -1.8121768 230.71228
Loop time of 8.11929 on 1 procs for 1000 steps with 936 atoms
Performance: 10.641 ns/day, 2.255 hours/ns, 123.163 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 | 4.6849 | 4.6849 | 4.6849 | 0.0 | 57.70
Bond | 0.00017678 | 0.00017678 | 0.00017678 | 0.0 | 0.00
Kspace | 3.2098 | 3.2098 | 3.2098 | 0.0 | 39.53
Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 2.16
Comm | 0.024693 | 0.024693 | 0.024693 | 0.0 | 0.30
Output | 0.00037798 | 0.00037798 | 0.00037798 | 0.0 | 0.00
Modify | 0.015853 | 0.015853 | 0.015853 | 0.0 | 0.20
Other | | 0.007983 | | | 0.10
Nlocal: 936 ave 936 max 936 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5242 ave 5242 max 5242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 431382 ave 431382 max 431382 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:08

256
examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 Normal file
View File

@ -0,0 +1,256 @@
LAMMPS (23 Jun 2022 - Update 4)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Initialization
units metal
boundary p p p
atom_style full
processors * * 1 # domain decomposition over x and y
read_data ./gra_water.data
Reading data file ...
orthogonal box = (0 0 0) to (46.92336 44.331078 200)
2 by 2 by 1 MPI processor grid
reading atoms ...
936 atoms
reading velocities ...
936 velocities
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
96 bonds
reading angles ...
48 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
mass 1 12.0107 # carbon mass (g/mole)
mass 2 15.9994 # oxygen mass (g/mole)
mass 3 1.008 # hydrogen mass (g/mole)
# Separate atom groups
group gr molecule 1
792 atoms in group gr
group water molecule 2
144 atoms in group water
######################## Potential defition ##############################
# Interlayer potential
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
####################################################################
pair_coeff 1 1 none
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02
# bond and angle
bond_style harmonic
bond_coeff 1 0.0 0.9572
angle_style harmonic
angle_coeff 1 0.0 104.52
# define kspace calculation
kspace_style pppm/tip4p 1E-5
# Neighbor update settings
neighbor 2.0 bin
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
####################################################################
# Calculate pair energy
compute 1 all pair lj/cut/tip4p/long
compute 2 all pair aip/water/2dm/opt
compute wt water temp
variable TIP4P equal c_1
variable EILP equal c_2 # total interlayer energy
variable temp_wt equal c_wt
############# Output ##############
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
thermo 100
thermo_modify lost error
fix subf gr setforce 0.0 0.0 0.0
fix 1 water shake 0.0001 20 100 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
48 = # of frozen angles
find clusters CPU = 0.000 seconds
timestep 1e-3
velocity water create 300.0 12345 dist gaussian mom yes rot yes
fix 2 water nve
run 1000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848
@Article{Ouyang2018
author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod},
title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},
journal = {Nano Letters},
volume = 18,
pages = 6009,
year = 2018,
}
- ilp/tmd potential doi:10.1021/acs.jctc.1c00782
@Article{Ouyang2021
author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and
A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod},
title = {Anisotropic Interlayer Force Field for Transition
Metal Dichalcogenides: The Case of Molybdenum Disulfide},
journal = {J.~Chem.\ Theory Comput.},
volume = 17,
pages = {7237--7245}
year = 2021,
}
- ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464
@Article{Feng2023
author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},
title = {Registry-Dependent Potential for Interfaces of Water with Graphene},
journal = {J. Phys. Chem. C},
volume = 127,
pages = {8704-8713}
year = 2023,
}
- ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137
@inproceedings{gao2021lmff
author = {Gao, Ping and Duan, Xiaohui and Others},
title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors},
year = {2021},
isbn = {9781450384421},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3458817.3476137},
doi = {10.1145/3458817.3476137},
booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
articleno = {42},
numpages = {14},
location = {St. Louis, Missouri},
series = {SC'21},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (../kspace.cpp:342)
G vector (1/distance) = 0.28684806
grid = 25 24 80
stencil order = 5
estimated absolute RMS force accuracy = 0.0001640931
estimated relative force accuracy = 1.1395635e-05
using single precision MKL FFT
3d grid and FFT values/proc = 30685 12480
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727)
WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484)
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 100000, page size: 1000000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 5 23
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair aip/water/2dm/opt, perpetual
attributes: full, newton on
pair build: full/bin
stencil: full/bin/3d
bin: standard
(2) pair lj/cut/tip4p/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual, half/full from (1)
attributes: half, newton on
pair build: halffull/newton
stencil: none
bin: none
WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736)
SHAKE stats (type/ave/delta/count) on step 0
Bond: 1 0.957201 2.19705e-06 96
Angle: 1 104.52 0.000203056 48
Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 Mbytes
Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt
0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300
SHAKE stats (type/ave/delta/count) on step 100
Bond: 1 0.9572 9.54949e-07 96
Angle: 1 104.52 6.01522e-05 48
100 -17.494869 -20.796995 3.3021253 188.4955 -1.8981262 268.90898
SHAKE stats (type/ave/delta/count) on step 200
Bond: 1 0.9572 9.63922e-07 96
Angle: 1 104.52 7.7021e-05 48
200 -17.48627 -21.194892 3.7086213 188.14561 -1.9871708 302.01203
SHAKE stats (type/ave/delta/count) on step 300
Bond: 1 0.9572 1.4264e-06 96
Angle: 1 104.52 6.48393e-05 48
300 -17.502843 -20.993703 3.4908599 188.23268 -1.8457229 284.27861
SHAKE stats (type/ave/delta/count) on step 400
Bond: 1 0.9572 1.33728e-06 96
Angle: 1 104.52 7.6239e-05 48
400 -17.495285 -20.82835 3.333065 188.48003 -1.8429074 271.42856
SHAKE stats (type/ave/delta/count) on step 500
Bond: 1 0.9572 1.14685e-06 96
Angle: 1 104.52 8.58621e-05 48
500 -17.491436 -20.443043 2.9516075 188.7589 -1.8566335 240.36452
SHAKE stats (type/ave/delta/count) on step 600
Bond: 1 0.9572 9.17601e-07 96
Angle: 1 104.52 8.24517e-05 48
600 -17.505682 -20.608456 3.1027734 188.72078 -1.9560795 252.67474
SHAKE stats (type/ave/delta/count) on step 700
Bond: 1 0.9572 9.50425e-07 96
Angle: 1 104.52 5.62423e-05 48
700 -17.496706 -21.072664 3.575958 188.2777 -1.9833951 291.20858
SHAKE stats (type/ave/delta/count) on step 800
Bond: 1 0.9572 1.15256e-06 96
Angle: 1 104.52 7.02177e-05 48
800 -17.478628 -20.819507 3.340879 188.37868 -1.9113009 272.0649
SHAKE stats (type/ave/delta/count) on step 900
Bond: 1 0.9572 9.14163e-07 96
Angle: 1 104.52 6.98849e-05 48
900 -17.480868 -20.728506 3.2476383 188.5902 -1.8922108 264.47182
SHAKE stats (type/ave/delta/count) on step 1000
Bond: 1 0.9572 1.00568e-06 96
Angle: 1 104.52 0.000111707 48
1000 -17.498472 -20.331605 2.8331335 188.87466 -1.8121689 230.71657
Loop time of 4.24862 on 4 procs for 1000 steps with 936 atoms
Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25749 | 1.1806 | 2.6872 | 89.0 | 27.79
Bond | 0.00018656 | 0.00020786 | 0.00025377 | 0.0 | 0.00
Kspace | 1.4259 | 2.9204 | 3.8414 | 56.3 | 68.74
Neigh | 0.057504 | 0.057852 | 0.05818 | 0.1 | 1.36
Comm | 0.041952 | 0.053593 | 0.05876 | 3.0 | 1.26
Output | 0.0004296 | 0.00046809 | 0.00055317 | 0.0 | 0.01
Modify | 0.026204 | 0.027251 | 0.028382 | 0.6 | 0.64
Other | | 0.008209 | | | 0.19
Nlocal: 234 ave 302 max 198 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2876.5 ave 3122 max 2632 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 107846 ave 150684 max 82181 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 431382
Ave neighs/atom = 460.87821
Ave special neighs/atom = 0.30769231
Neighbor list builds = 28
Dangerous builds = 0
Total wall time: 0:00:04

422
examples/PACKAGES/pimd/lj/data.metalnpt01 Normal file
View File

@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
39 1 -10.338208372875723 -8.724519590498623 -8.445612139491281 0 -1 1
82 1 -7.5133824622188925 -6.978636164411631 -10.191775661279799 0 0 0
57 1 -6.093878587859262 -9.276313581141936 -7.744358551066254 1 0 0
8 1 -7.188384493977925 -11.000743174865285 -10.566868392413127 0 1 1
49 1 -0.45896030511450936 -8.721648062141405 -7.76988436909876 0 1 0
54 1 4.36019737005205 -9.840722628422576 -9.652200105153977 0 -1 1
114 1 3.904944042667676 -8.560258519206736 -6.227256449483399 -1 0 1
128 1 1.537670815459421 11.367557646509137 -7.44113189883349 0 0 -2
102 1 2.6467980910798623 -6.300231690446356 -10.839747469959917 1 -1 -1
157 1 6.599214138053117 -6.278630725537236 -7.389049268829837 -1 0 1
20 1 8.160418209241914 -11.236890922228888 -9.90427297873004 0 1 0
147 1 10.464052914243185 -5.834517788008704 -9.403782126876184 -1 2 0
169 1 9.355540563360105 -8.982132042608429 -6.861385656669775 0 1 1
123 1 -6.908328795781873 -3.2942152122483694 -10.871702946953768 -1 0 -1
130 1 -6.59789640513614 -2.559000332768779 -7.109058819418416 -1 1 0
140 1 -9.12121182032633 -1.3228381271313019 -9.248705124201138 -1 1 0
153 1 -4.57209419001429 -5.197951679459013 -8.806559015841044 0 1 0
129 1 -0.17714454435176596 -5.056145756511569 -8.582370909018262 0 1 1
148 1 -3.197585507102101 -2.0540921199407465 -9.77932871778502 0 0 0
119 1 -3.51954842440485 -3.8478081846346726 10.678236929073831 0 -1 -1
174 1 3.1384595215939513 -1.9078182147633918 -10.748237231758047 -1 1 -1
134 1 -0.0032185119392025285 -0.36841629060197645 -8.631895429784365 -1 0 2
189 1 2.892780086534627 -1.3587472579142499 -6.410113256095116 0 0 2
28 1 6.224912481821424 -1.100900418829165 -9.316948573538184 0 0 -1
1 1 7.533342646866252 -2.8858379557892953 -6.5588822497649195 1 -1 0
24 1 10.891564390761006 -2.1693511431878143 -8.14872153065027 0 -1 1
176 1 10.35065200687287 -3.6683271215630047 -4.32699396695263 0 0 0
182 1 -10.764131367809398 0.5730937842904389 -5.180063181396292 0 1 -1
137 1 -8.194528746006949 3.76661130396705 -8.596433076900993 -1 1 0
89 1 -5.793296966734716 0.9591211322466908 -8.532912969707475 0 0 -1
88 1 -3.2415549382910047 2.6063473128515433 -11.019658141847422 0 1 -1
160 1 -0.17978720428819353 5.335367005111222 -5.961111228150678 0 0 1
125 1 -3.2595127311899836 3.541669787125592 -7.094678802230409 0 1 0
167 1 2.6101389699783257 2.7016950511217104 -7.510579719545417 0 1 0
107 1 2.478905108002845 1.3710464608203452 -11.241338409619438 -1 1 1
45 1 -0.2728444271939366 3.4472072045614333 -9.803824961885091 0 1 0
95 1 7.005885045149228 1.8641755193621776 -11.033503201926393 0 2 -1
111 1 11.28085723924775 1.3577973865073396 -8.404143782130012 0 1 1
37 1 7.50412447792306 1.5806311975228182 -7.696866725729485 1 0 2
53 1 9.464056637143884 5.181490576538966 -10.160960273108417 -1 -1 1
122 1 -8.61454149114821 11.46923394337289 -7.097906043887797 2 -1 -1
126 1 -8.658911027419105 9.160142379367757 -10.196432851978876 0 0 -1
72 1 -11.223582472260205 7.275428216701358 10.836645274139237 2 0 0
144 1 -3.0387339366126 -9.918200912273784 -9.896452956043586 0 1 1
135 1 0.03771056281680529 7.830565362407303 -8.390686664231268 1 0 0
183 1 2.8786138768293665 5.221499246050073 -10.100270572243783 0 0 0
155 1 3.821499942128122 9.224610559399695 -9.359914290522674 0 0 0
21 1 6.6299071097705 6.818271712520994 -8.197268594363944 1 0 0
66 1 9.53812274637967 7.559409537149467 -6.194715694404919 -2 -1 0
22 1 11.107750453110658 10.72621054512756 -6.232964722376559 -1 0 0
42 1 9.127119842763733 9.280850325093446 -10.249747757735628 -1 1 0
77 1 -6.840159982144716 -10.92057206639582 -3.876267638432264 1 -1 1
47 1 -8.742923464684916 -8.023408201112765 -5.403173093100989 1 2 1
18 1 -10.63751608820882 -11.30186343558728 -3.9206887105699195 1 0 -1
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422
examples/PACKAGES/pimd/lj/data.metalnpt02 Normal file
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@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
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171 2.1156964930224973 3.568443790163169 -3.4488134770961105
94 2.1701428589622624 4.886850980047828 3.260178593455835
41 6.033712104492915 2.2785562972718627 -1.4849735175385876
141 1.4706522295431979 -1.8195923066965298 0.019053288005804775
159 -4.554564437682667 0.05936456417819991 -1.932073129933284

422
examples/PACKAGES/pimd/lj/data.metalnpt03 Normal file
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LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
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128 1 1.5947628847115236 11.435941489344966 -7.415359628481937 0 0 -2
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Velocities
39 -2.179321628468343 1.1511761233721014 -0.5234785181560597
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68 -0.8806574381084391 3.664356747058979 4.498638804868755
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422
examples/PACKAGES/pimd/lj/data.metalnpt04 Normal file
View File

@ -0,0 +1,422 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
200 atoms
1 atom types
-11.876696863105703 11.876696863105703 xlo xhi
-11.876696863105703 11.876696863105703 ylo yhi
-11.876696863105703 11.876696863105703 zlo zhi
Masses
1 39.948
Pair Coeffs # lj/cut
1 0.00965188 3.4
Atoms # atomic
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175 -4.72131850682648 -1.6008946774115904 -3.6054426092000593
158 -5.274680729271083 -0.4457302148856164 4.174272671309751
85 2.9757034033315444 -0.5103121033627565 1.99919210117291
63 1.600933165736236 1.4604641421860185 5.197681341346513
133 0.3650834395918216 4.123541846312257 2.1615515366543354
67 2.0607792864448453 2.3124375339420076 0.21959246817514527
83 -6.156022387564482 -1.1548915743184078 -0.4948872456362283
162 -2.1450070724040025 3.9286059442169066 2.007885747151935
170 1.8166139807691821 -1.95234066921456 -1.8559861240898843
181 -1.587457433365127 -3.2094890956838205 2.212401241994942
71 1.7829689662908779 -3.6713609566551657 1.3773962271622693
31 3.918178411733008 -0.5772484115851036 0.16726508680219976
139 -4.560722486125075 -0.5471630166750243 5.863010868871481
3 -3.9686726349917825 3.6173076990026054 2.5273959166862507
108 0.3042801304200664 4.847444330423647 -0.35518169829313484
16 -2.4685650045584717 5.98056595230015 0.9384145704518219
110 -0.6129548866614436 1.8199747299312752 -0.6050782543434758
50 -1.8884152067915962 -1.4877561250799833 -3.9811275374353494
191 1.500896458072849 -1.9099553342822155 -5.024921011162899
187 -2.013243274912701 -0.8604266013822317 -1.038480536601888
180 1.4966822969502809 2.2104050426784707 3.732721924128324
30 -2.3551911487538373 -1.0313809690434763 -1.4871503115129143
2 2.4972367326603697 -1.5125466361921762 1.0762650051734106
17 0.43112912988867413 -1.9548201848493156 -0.43017998184207773
7 6.622180146484479 4.7673609572662725 0.19425898871224434
164 2.301415823751322 0.4827221772498991 4.559127095693677
69 -3.4364505629674733 -1.1594038113628669 -1.2078137888752072
61 1.7869953777023173 0.9935547623401149 0.14745693195171444
34 -0.027807484985171937 -3.1354780466577754 -1.036977576868685
43 -1.3037743820903311 -5.61028065095172 -4.306710886889687
177 2.1781720801097206 -1.516912077043328 -2.054689845757315
179 0.4934049365569875 -4.8639422788504625 -6.225153590664796
65 2.6970228261721383 0.19294320506195817 6.683323231860031
27 -1.6731814501881797 0.7519385590564082 3.2183027406212203
58 -0.7774753429967389 -0.6669437971456971 3.5183225900940927
32 -5.389835933890947 -0.4954507654154201 0.4594525916972694
26 0.7382474998065096 -3.102724138188651 -2.185686698723454
142 -1.944479379421283 -1.2761486898263725 0.72348529709274
100 -2.739025692998968 -2.6245009262596986 3.182008026346906
184 1.4210317521782347 3.1395926369797884 5.319543188841913
105 -1.2308708716614136 -1.2494207925918743 -3.3415190888725443
75 -1.8835854547991517 -1.3807763884880995 3.052239941977269
99 2.3501462152911015 -0.09098282020287418 -2.963130739502538
193 3.2483282921859455 -6.045063326765766 -1.2297831607518321
33 -1.5552221515820004 2.623852853566988 -0.3953508079233695
79 2.0518370606822334 1.899510113710928 2.0859744201323727
92 1.5026700715390955 0.9352029472761221 -5.528904283783295
165 -2.240438523644089 -0.6103912799862421 0.40653914875448993
199 -1.2653571662196268 3.710626862073433 1.4730516528440072
70 1.655492430853343 0.17760859693009826 -1.650919734678463
146 -1.4225048482747793 2.74232833480091 -3.413198079564811
106 -1.093901348299414 0.20953760114868714 -0.7298112830112282
52 6.647000075136453 -0.30141024565553315 1.2035752428962934
86 0.6741589587443484 4.365068713763016 3.5677961016049315
197 -0.666824417721529 0.7257967702216201 6.272517109849018
185 -1.1845876194928404 2.1001111189632264 2.457366035714506
190 -1.6517508143986053 2.271851696760304 3.7976228734124575
145 -0.6660913411508007 -2.1887913545610314 1.427073342591097
131 3.4923356345857024 1.8910870819349503 0.22757964871813297
156 1.3901143776938099 -0.5912367128957199 -1.945898273856384
10 -3.3254266550003906 2.363446512042732 -2.8505669909097167
196 1.9772342503358795 2.9791453967072834 5.0702556945320305
143 1.3619198656944898 -4.070780999483669 0.554762511858757
13 -3.6607073229889986 -6.103961980753075 3.3895476442791126
59 1.3424546798513801 -0.012418821554116527 -1.0607350515292961
186 -0.19147109350375446 -0.14042042908600805 -5.06183250631794
136 10.318783006250738 -0.33198398090799297 -3.1695432610471372
62 -0.9320061937291512 -8.919718141167188 -1.0031472261072583
192 -6.036717500669019 -0.4626110813075395 -5.283002697165421
113 -1.9312339562598033 1.2868323831429733 -0.27836767602350954
74 0.289298974376203 4.639184114550362 -1.3074893268836063
118 2.3186362762712704 0.014757210175651903 -1.9096714905556824
117 2.917320124569121 -0.927139463682407 -2.038093079844118
23 3.445296199640721 -2.484450168397722 6.150025302403371
171 -1.3488599922862394 -0.40015537573335275 5.541824987776105
94 2.7016234671889183 -4.500360725821148 -0.3771036206116729
41 0.040051409073174504 1.3144504850460685 -2.628956804481983
141 0.8101589418958534 -0.40901282998394567 2.3777914588666906
159 -2.168905163137191 -3.9077440516609387 3.1238186982134213

28
examples/PACKAGES/pimd/lj/in.lmp Normal file
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@ -0,0 +1,28 @@
variable ibead uloop 99 pad
units metal
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 9.5251
read_data data.metalnpt${ibead}
pair_coeff * * 0.00965188 3.4
pair_modify shift yes
mass 1 39.948
timestep 0.001
velocity all create 0.0 ${ibead}
fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
dump dcd all custom 100 ${ibead}.xyz id type xu yu zu vx vy vz ix iy iz fx fy fz
dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

1
examples/PACKAGES/pimd/lj/run.sh Normal file
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@ -0,0 +1 @@
mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen

219
examples/PACKAGES/pimd/lj_reduced_units/data.lj01 Normal file
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@ -0,0 +1,219 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 2000
200 atoms
1 atom types
-3.4945130603740377 3.4945130603740377 xlo xhi
-3.4945130603740377 3.4945130603740377 ylo yhi
-3.4945130603740377 3.4945130603740377 zlo zhi
Masses
1 1
Pair Coeffs # lj/cut
1 1 1
Atoms # atomic
108 1 -2.7795690566068996 -2.0367677788080942 3.4238258338844894 2 1 -1
102 1 -2.609481280743025 -1.8912619121268304 -2.399753092988466 1 -1 -1
141 1 -3.140749645549514 -2.8903241627869427 -2.7071762462261537 2 0 0
49 1 -2.3658136681990007 -3.088812044820056 3.4760124445890623 0 1 -1
88 1 -1.6158710173914035 -2.3369020600614756 3.233517474511907 0 1 -1
192 1 -1.2960228223928079 -3.237522585981233 -3.1506262911155765 1 1 2
113 1 -0.5058112539671865 -2.175265580488635 -2.895948573481031 -1 0 0
147 1 -0.22721902013037146 -3.2095321965856187 -2.5444416457809185 0 1 0
55 1 0.6250447384071113 -2.6446349401275255 -2.959767417439857 -1 0 -1
63 1 1.6783992808137906 -3.22203513406057 -3.1652676844989256 -1 1 1
95 1 1.3579478870419064 -2.684729254303277 -2.052496056604152 0 2 -1
105 1 1.4496281787006915 -1.9673030959679096 -3.332658945278261 0 0 0
84 1 2.4045875426768606 -1.8297724699275564 -2.7874627893944544 0 0 0
65 1 -2.68682939849047 -0.8114540186440395 -3.126687818057689 0 -1 0
112 1 -1.7203801180145006 -0.8038481618523634 -2.0163240721427838 0 0 0
174 1 -1.4968933339977661 -1.3290620346554367 -3.064010040861048 -1 0 -1
189 1 -0.6249709402997541 -1.252931712435372 -1.9882716349469658 0 0 2
9 1 -0.23886293275872486 -1.0612344376875333 -3.025432389188406 0 0 1
146 1 -0.9802936024515303 -0.3953988402073487 -2.8364522494017708 2 1 2
171 1 0.39730078560778914 -1.7846492070113664 -2.443607407553737 0 2 -1
140 1 0.5573788374911133 -0.5990036144148324 -2.402963062521378 -1 0 0
152 1 3.4379847727225346 -1.3055938268830742 -2.4905074589410936 -2 -1 0
11 1 3.1992117767992068 -1.191883736793153 -3.4723419170834338 -1 2 1
69 1 2.6376153053668867 -0.2845436411244765 -2.788279844473203 0 -2 0
173 1 -1.967038944001471 0.06098718735032446 -2.58940519609616 1 0 1
190 1 -2.8711350478349926 0.9129034739862979 -3.477848194666021 0 0 0
164 1 -2.8409776961511124 1.1599509265598786 -2.2464830240939375 0 0 1
161 1 -1.6469671018177567 0.9360204597700993 -3.3491365145788827 1 0 2
74 1 -0.028453987680887038 0.3739399392930446 -2.9891764409930484 1 -1 1
162 1 -0.9152119867762214 1.8538003710645874 -2.0787458665529313 0 0 1
165 1 0.20472499231506947 0.41157279287578097 -1.7804952487691292 0 0 0
28 1 0.9556568956317052 0.9070586383550882 -3.051580171737043 0 -1 -1
107 1 0.27101548210140264 1.6697625775553313 3.256398876364515 -1 1 0
53 1 -2.2768986954542476 1.9520208666344268 -2.905899876141582 -1 -1 1
60 1 -2.3748565234893153 3.1415519659534046 -2.6903226937570888 1 1 0
172 1 -1.3831407623603917 2.6439383680022495 -2.988114399273657 0 0 2
35 1 -1.9040946957475922 2.4850230251463294 -1.8238074088896814 1 -1 0
90 1 -0.6407155002729499 2.891205873820353 -2.184576201275668 0 -1 1
183 1 -0.7452468270399182 1.6958511415691964 -3.2646018242495516 1 0 0
46 1 -0.22701759376730096 2.672935498985858 -3.2296828094464414 1 -1 -1
26 1 0.3607641531328818 1.9915770180932266 -2.4322620664253045 0 -1 1
41 1 0.6373758855225722 3.1576967379383136 -2.2076729513672273 0 0 1
62 1 1.2599715479139464 2.4637352645229535 -2.996655642771261 0 0 1
114 1 0.7095094175128512 3.3529225376529834 -3.446569928809617 0 -1 1
29 1 -3.4441516076858747 3.186682881361427 -3.164290558791177 1 -1 0
120 1 -2.7699397214807666 -3.0679149510930377 -1.4586405778286127 2 1 1
166 1 -2.9639598123456348 -1.8230569851379879 -1.1336421298957986 0 1 0
19 1 -2.219481001384856 -2.718720936926987 -0.17152653954078959 1 1 -1
143 1 -3.3367462911096637 -2.646710289319255 -0.08639804580378332 1 1 0
14 1 -0.8080539703460301 -3.3138674801902015 -1.5513416052298858 -1 0 1
17 1 -1.2519028473371163 -1.9834151764617522 -0.4751925051419198 -2 0 0
7 1 -0.6422036076119758 -2.1822637849150257 -1.309964136714573 -1 0 1
76 1 0.002896678458885543 -2.2620445897063184 -0.2330303144789453 0 0 0
25 1 0.3195487317939559 -2.5915964162672633 -1.6847661018972104 -1 0 1
122 1 0.9437732996524034 -3.076308154774796 -1.0301951566376644 1 0 -1
188 1 1.3149323047475332 -2.0202232851439175 -0.9332517483120624 -1 0 0
196 1 2.4252816482051065 -2.9991133261256717 -0.2915609413585816 0 2 1
154 1 1.617010887740887 -2.199305270305938 0.15712874770371849 -1 2 0
64 1 2.934967635633404 -1.92620475221537 -0.7077313528493354 0 1 0
79 1 -2.8111804533557017 -0.5176533778232942 -2.0486672107634094 0 1 0
80 1 -2.079807139196039 -1.2506968999173758 -0.6878784167189951 0 0 1
12 1 -2.996784469690298 -1.494057160171672 -0.09378065633433766 0 0 1
87 1 -1.4786937501974577 -0.24572242955022147 -1.0411298155891553 0 -1 1
118 1 -1.5219571471797697 -0.6469152337096267 0.07790607124041445 0 1 0
106 1 1.1039107347748043 -0.9982945968846851 -1.4358613477546331 -1 0 0
6 1 0.2994229743009 -1.5755502164022743 -1.1025451212735877 2 0 0
98 1 0.14422647245316755 -0.4562748967814887 -1.1288823927075846 -1 0 0
36 1 1.117403260546369 -0.6258611972204157 -0.45746732579129296 1 -1 0
133 1 0.859517194013173 -1.4579095853876511 0.2223121798831755 1 1 1
1 1 1.9750704226304612 -1.2226584851722493 -0.5050391499153623 0 -1 0
91 1 2.930212504963826 -0.8900603772487206 0.31326990070574257 0 -1 -1
135 1 -1.8704119131145511 1.4151617424236407 -2.0299493395071555 1 0 0
145 1 -2.5978280185456044 0.23771261564216897 -0.6973478660383656 0 -2 -1
194 1 -0.802106175542123 1.5380363524561962 -1.0014646333327863 0 1 -1
177 1 -0.4209642163497379 1.4081511815239465 0.048786606404428355 0 1 -1
56 1 0.1655081354187105 0.488612868229853 -0.6685586469118172 0 0 1
137 1 1.0403444543974962 0.29392106264506496 -1.157047853549803 -1 1 -1
3 1 1.426791637331859 1.1994824011018168 -0.7391487398561316 0 -1 1
125 1 0.6384933993980926 1.4087406696008793 -0.04513978672724809 0 1 0
85 1 3.492386221258323 -0.022918569575539983 -0.18415289757087 1 0 1
37 1 1.9446560065460998 0.32690249887078415 -1.557848909197346 1 0 1
157 1 2.2693311785439514 1.4234672203444076 -1.3950756204319474 -1 -1 1
81 1 2.2043144165939133 0.7734976358785483 -0.1443989261496442 -1 0 1
193 1 -2.800913203549158 3.3913795040038752 -0.3002902442199323 1 0 0
127 1 -1.832485514575906 -3.475177695698571 -1.0143919033965547 0 0 0
104 1 -0.9864189902172598 -3.128510029811542 -0.3946109581791233 0 0 -1
72 1 -1.091863924309645 2.651695772194485 -1.1525574140711645 1 -1 0
99 1 -1.376188772302252 2.1367308970905112 -0.22414000562735564 0 -1 0
24 1 1.0798151658945965 1.8088284522753606 -1.611839691529319 1 -1 0
42 1 3.3099578488331143 2.7636832208891664 -0.11775790598994411 -1 1 -1
38 1 -2.6469918571054945 -2.446265188540552 0.8006326688775777 1 0 1
86 1 -3.3982593364606077 -1.9911707046121028 1.4129412590921573 -1 0 0
116 1 -3.3782151164102614 3.3939134790192074 0.6418244028431277 1 0 0
144 1 -2.152212571536467 -2.8119708535854224 1.6778364082976118 0 1 0
179 1 -0.8263021362457004 -1.7214596406733806 0.6812305480127513 -1 3 1
151 1 -1.5217298498042864 -2.5933593936403763 0.7963122225368328 0 1 2
130 1 -0.41366866285633624 -2.851509016203123 0.6773665297002652 -1 1 0
149 1 -0.8196954968551895 -2.4620140380344058 1.6681749543249536 1 1 0
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142 1 1.7676090653529768 -2.7694388971884765 1.0411093428968425 1 1 0
43 1 1.2651581412723922 -1.7350310325188918 1.2119129817343088 -1 -1 1
156 1 2.796603060966876 -1.975811297437484 0.5269881248554414 0 -1 0
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75 1 -3.264195451754593 -0.2758623474229462 0.8501703715118789 1 -1 0
199 1 -1.8606891200301348 -0.81109530705794 1.234068196576104 1 -1 1
119 1 -1.8952925629684365 -1.6742391291961565 0.3056526633582653 0 -1 0
153 1 -0.6179778569135823 -0.6812551828045249 0.8822634033092613 1 1 0
31 1 0.1434804396367878 -0.5352374975985325 0.00065681711961239 0 -1 0
8 1 0.9896949675708329 -0.5825805499366115 0.8390036708294969 0 0 0
198 1 0.20957042666083733 -1.2300305579788615 1.1505092305231928 0 0 1
22 1 0.11282413745771128 -0.029722367543426716 1.1299864513218787 -1 0 -1
195 1 2.9662277270739343 -0.9097471611972223 1.378968815531931 1 0 2
32 1 1.9176581701385829 -1.0963885598161285 0.612637989357651 1 0 -1
139 1 2.2034635745403706 -0.09403988556633318 0.8645554281632429 -1 2 0
77 1 1.7035877859699526 -0.8133688575022073 1.6318409740615665 0 -1 1
111 1 -3.223221512681343 0.8515794477136406 0.5304444380887284 1 1 1
138 1 -2.102339643808083 0.3205080511040257 0.6397061187151873 0 1 -1
103 1 -2.8441279458234914 0.5800051690180812 1.512417106043963 -1 1 0
184 1 -2.4512811422970944 1.4407376078485292 1.024840909070544 0 0 1
73 1 -1.2083083753201984 0.16913042396249212 1.31830897028215 0 -2 0
89 1 -0.622943103836138 0.15695545887374523 0.03344907944561345 0 0 -1
93 1 -0.6871612783719626 1.4782545941619265 1.7130745398216136 0 -1 0
94 1 -1.209899480419889 1.1419050120740204 0.768566708093127 0 0 0
181 1 0.8338139283938067 0.2955625473112081 0.1708175991674893 -1 1 -1
129 1 1.1355758059362249 0.3630461551808931 1.290797674214222 -1 0 0
182 1 0.08831527814343061 0.9709201913937692 0.9217855950625892 0 1 -1
158 1 1.4062820374169525 1.1517166598840343 0.6269036353613398 0 0 0
100 1 2.8360458941172935 1.5280995172170748 0.62642849190607 0 1 0
59 1 3.120666407088228 0.49773318717092796 1.2390797462592613 0 -1 1
40 1 2.1784673001300465 0.9493086808156442 1.37690657576216 0 0 0
110 1 3.092811420136352 1.457598231264991 1.8333488137634408 0 0 -2
71 1 -2.704068160468349 3.198799130983575 1.5420861670955985 0 -1 -1
187 1 -3.3809787804159894 2.339193447924602 0.9253127201661663 1 1 0
58 1 -1.8161128905276918 3.295453805825648 0.4419286058239596 0 -1 0
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115 1 -1.3188418056778684 -3.426962627878111 1.3071043811339145 1 1 0
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48 1 1.212990075236676 2.7637861839630933 1.668138216427735 0 0 -1
44 1 1.8875283020177747 2.01954806585405 0.15097670327664356 -1 -1 1
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101 1 -2.7232595674410254 -2.5310321070553594 2.520173028347837 1 3 1
121 1 -0.1371595891679715 -2.734037361783574 3.2547541081110136 -1 1 -1
131 1 -1.616105025949218 -1.97873290984862 2.2250110182725185 1 0 0
50 1 -0.9774458776093428 -3.080336575399165 2.647294574069851 0 1 0
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27 1 0.9216706073777299 -2.620009754961919 2.980059759810019 0 0 1
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92 1 3.2579931163558924 -3.0623298587917547 1.8252693484803535 0 2 -1
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96 1 2.599921016729558 -2.6427367710738228 3.4145177684858803 -2 2 -1
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169 1 2.1185477137097575 2.27540363851787 2.3296903855745934 0 0 0

219
examples/PACKAGES/pimd/lj_reduced_units/data.lj02 Normal file
View File

@ -0,0 +1,219 @@
LAMMPS data file via write_data, version 8 Feb 2023, timestep = 8000
200 atoms
1 atom types
-3.4945130603740377 3.4945130603740377 xlo xhi
-3.4945130603740377 3.4945130603740377 ylo yhi
-3.4945130603740377 3.4945130603740377 zlo zhi
Masses
1 1
Pair Coeffs # lj/cut
1 1 1
Atoms # atomic
141 1 -1.763209980389579 -2.6156484242195064 -2.931843780833984 2 0 0
152 1 -1.5928871542954757 3.3501884422702433 -1.8656866405706811 -1 -2 0
49 1 -2.7539752553137182 -3.2181862303090325 -3.2982185001231508 0 1 0
113 1 -0.7003027892165357 -2.1799819378730754 -2.999588953057854 -1 0 0
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7 1 -1.155032969500839 -2.109409697780318 -2.01960214884411 -1 0 1
122 1 -0.11210230788570166 -2.6275713274626975 -1.900506384406081 1 0 -1
55 1 0.23346664931542635 -2.573966195106371 -3.0437128589517024 -1 0 -1
95 1 0.716981854784511 -1.7560064219465084 -1.6999612600924723 0 2 -1
105 1 1.1248014998718883 -1.7403082354703703 -3.356758018801178 0 0 0
84 1 2.225043764737794 -2.1031554472806464 -3.42558560520243 0 0 0
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174 1 -1.4393153013859372 -1.4595317956467175 -2.895392195630071 -1 0 -1
189 1 -0.9035292808774392 -0.8049470303120404 -2.0013910310988474 0 0 2
171 1 -0.09043747063992294 -1.5712222691835853 -2.3464524824680155 0 2 -1
9 1 -0.38933479997274456 -0.745737254721562 -3.0928316849953847 0 0 1
37 1 0.8181444837942082 -0.7091668788083872 -2.594933610756206 1 0 1
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90 1 -0.9570316941978154 2.7341944347748575 -2.39704430602322 0 -1 1
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14 1 -0.7531800111600084 -3.202737076324235 -1.3992046647831564 -1 0 1
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66 1 -0.23373724912576396 -0.5882558302750734 2.5656269999794135 -1 -1 -1
160 1 -1.1132775718863501 0.16126595419727965 2.3994619853672896 0 0 0
18 1 0.6168554097448792 -0.8675105647197154 3.3233443940314107 0 -1 -2
5 1 0.21124689546372627 -1.527936340282886 2.128421015823146 0 -1 -1
167 1 1.157996163161525 -1.3890474926504965 2.5930120556899743 0 1 -1
176 1 0.7227757787132028 -0.4265054817409199 2.130677354553178 0 0 0
77 1 2.0007502274099562 -0.6930768409753575 2.0562080526704536 0 -1 1
136 1 2.059758900185651 -1.052357318680519 3.1194387358517117 0 -1 -2
163 1 3.3650479388293877 -0.7812523229666395 2.7231341802578797 -1 -1 0
53 1 -2.3141819292399695 1.20855609162257 -3.127003289906138 -1 -1 1
34 1 -2.2520285035649175 0.34377072469492165 3.2433897655354262 1 0 -1
82 1 -3.1361148993392707 0.2917712829104399 2.508598507937298 0 -1 -1
47 1 -2.903472142580087 1.2996380231419302 2.6614912616951822 0 1 0
159 1 -1.8421866316781088 1.3742261871908503 2.7832166426856038 0 0 0
161 1 -1.2319440636738626 0.9387211724622819 -3.4892930122068617 1 0 2
33 1 -0.4449542140900899 0.2769280403688486 3.289217283277774 0 -1 -1
191 1 -0.8687075277531521 1.281273999295463 2.3493691514045447 1 -1 0
20 1 -0.12835229617409075 0.4001437971686418 2.091186274425671 1 0 -1
21 1 1.5590447736292827 0.23116165627532026 2.4331182207698356 1 0 -1
83 1 0.6019872094726322 0.17868421219256525 2.965010196172179 0 -2 0
107 1 -0.09314344901480053 1.8386195873289717 2.9198165047206524 -1 1 0
97 1 0.9500008570521725 1.1147256892756756 2.5445482565685626 0 -1 -1
15 1 2.6866827472081427 0.05611542822496954 2.621280841687164 -1 0 -1
40 1 2.0535009935702107 1.3482348414084473 2.153119101811638 0 0 0
110 1 3.037377950690711 1.1454318013031137 2.4602998295324308 0 0 -2
54 1 2.1368310833242825 0.6989281938007096 3.190545712320829 0 -1 -1
71 1 -2.6906257490825327 2.3188264822083675 1.851572369390678 0 -1 -1
45 1 -1.8822606439217724 2.5464355632785174 2.887157746831732 1 0 -1
2 1 -1.527738763941238 2.1784215473644295 1.8498426738676617 1 -2 -1
67 1 -1.014923597719753 2.0522310481028465 3.091487536680741 1 0 0
192 1 -0.8672155474955553 3.087168735274927 2.6165250257240618 1 0 1
124 1 -0.37769468839105996 2.5506571887551175 1.8053870882842125 1 -1 -1
46 1 -0.2092884053324724 2.562694157698328 -3.2372195292692605 1 -1 -1
114 1 -0.2001222858286487 -3.429888000295159 1.8301280696628333 0 0 0
61 1 0.5140644440329998 2.208326878392573 2.2153556959139413 -1 -2 0
169 1 1.5629071468921552 2.2983930760888316 2.2366483189031316 0 0 0
128 1 -3.438885935852406 3.376929578988928 3.002455750479755 1 0 -2
52 1 -3.4549495641597217 2.178628786705743 2.923210719991474 0 -1 0
48 1 2.502392696348409 2.9340155922847346 2.5991521468190113 0 0 -1

26
examples/PACKAGES/pimd/lj_reduced_units/in.lmp Normal file
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@ -0,0 +1,26 @@
variable ibead uloop 32 pad
units lj
atom_style atomic
atom_modify map yes
boundary p p p
pair_style lj/cut 2.8015
read_data data.lj${ibead}
pair_coeff * * 1.0 1.0
pair_modify shift yes
mass 1 1.0
timestep 0.00044905847
fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
thermo_style custom step temp f_1[*] vol press
thermo 100
thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
dump dcd all custom 1 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
run 1000

1
examples/PACKAGES/pimd/lj_reduced_units/run.sh Normal file
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@ -0,0 +1 @@
mpirun -np 2 $LMP -in in.lmp -p 2x1 -log log -screen screen

80
fortran/lammps.f90
View File

@ -87,10 +87,15 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: scalar, vector, array
END TYPE lammps_type
TYPE lammps_dtype
INTEGER(c_int) :: i32, i64, r64, str
END TYPE lammps_dtype
TYPE lammps
TYPE(c_ptr) :: handle = c_null_ptr
TYPE(lammps_style) :: style
TYPE(lammps_type) :: type
TYPE(lammps_dtype) :: dtype
CONTAINS
PROCEDURE :: close => lmp_close
PROCEDURE :: error => lmp_error
@ -100,6 +105,7 @@ MODULE LIBLAMMPS
PROCEDURE :: commands_string => lmp_commands_string
PROCEDURE :: get_natoms => lmp_get_natoms
PROCEDURE :: get_thermo => lmp_get_thermo
PROCEDURE :: last_thermo => lmp_last_thermo
PROCEDURE :: extract_box => lmp_extract_box
PROCEDURE :: reset_box => lmp_reset_box
PROCEDURE :: memory_usage => lmp_memory_usage
@ -243,7 +249,7 @@ MODULE LIBLAMMPS
END TYPE lammps_data_baseclass
! Derived type for receiving LAMMPS data (in lieu of the ability to type cast
! pointers). Used for extract_compute, extract_atom
! pointers). Used for extract_compute, extract_atom, last_thermo
TYPE, EXTENDS(lammps_data_baseclass) :: lammps_data
INTEGER(c_int), POINTER :: i32 => NULL()
INTEGER(c_int), DIMENSION(:), POINTER :: i32_vec => NULL()
@ -439,6 +445,15 @@ MODULE LIBLAMMPS
TYPE(c_ptr), INTENT(IN), VALUE :: name
END FUNCTION lammps_get_thermo
FUNCTION lammps_last_thermo(handle,what,index) BIND(C)
IMPORT :: c_ptr, c_int
IMPLICIT NONE
TYPE(c_ptr) :: lammps_last_thermo
TYPE(c_ptr), INTENT(IN), VALUE :: handle
TYPE(c_ptr), INTENT(IN), VALUE :: what
INTEGER(c_int), INTENT(IN), VALUE :: index
END FUNCTION lammps_last_thermo
SUBROUTINE lammps_extract_box(handle,boxlo,boxhi,xy,yz,xz,pflags, &
boxflag) BIND(C)
IMPORT :: c_ptr, c_double, c_int
@ -995,6 +1010,10 @@ CONTAINS
lmp_open%type%scalar = LMP_TYPE_SCALAR
lmp_open%type%vector = LMP_TYPE_VECTOR
lmp_open%type%array = LMP_TYPE_ARRAY
lmp_open%dtype%i32 = LAMMPS_INT
lmp_open%dtype%i64 = LAMMPS_INT64
lmp_open%dtype%r64 = LAMMPS_DOUBLE
lmp_open%dtype%str = LAMMPS_STRING
! Assign constants for bigint and tagint for use elsewhere
SIZE_TAGINT = lmp_extract_setting(lmp_open, 'tagint')
@ -1103,6 +1122,65 @@ CONTAINS
CALL lammps_free(Cname)
END FUNCTION lmp_get_thermo
! equivalent function to lammps_last_thermo
FUNCTION lmp_last_thermo(self,what,index) RESULT(thermo_data)
CLASS(lammps), INTENT(IN), TARGET :: self
CHARACTER(LEN=*), INTENT(IN) :: what
INTEGER(c_int) :: index
TYPE(lammps_data) :: thermo_data, type_data
INTEGER(c_int) :: datatype
TYPE(c_ptr) :: Cname, Cptr
! set data type for known cases
SELECT CASE (what)
CASE ('step')
IF (SIZE_BIGINT == 4_c_int) THEN
datatype = LAMMPS_INT
ELSE
datatype = LAMMPS_INT64
END IF
CASE ('num')
datatype = LAMMPS_INT
CASE ('type')
datatype = LAMMPS_INT
CASE ('keyword')
datatype = LAMMPS_STRING
CASE ('data')
Cname = f2c_string('type')
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
type_data%lammps_instance => self
type_data%datatype = DATA_INT
CALL C_F_POINTER(Cptr, type_data%i32)
datatype = type_data%i32
CALL lammps_free(Cname)
CASE DEFAULT
datatype = -1
END SELECT
Cname = f2c_string(what)
Cptr = lammps_last_thermo(self%handle,Cname,index-1)
CALL lammps_free(Cname)
thermo_data%lammps_instance => self
SELECT CASE (datatype)
CASE (LAMMPS_INT)
thermo_data%datatype = DATA_INT
CALL C_F_POINTER(Cptr, thermo_data%i32)
CASE (LAMMPS_INT64)
thermo_data%datatype = DATA_INT64
CALL C_F_POINTER(Cptr, thermo_data%i64)
CASE (LAMMPS_DOUBLE)
thermo_data%datatype = DATA_DOUBLE
CALL C_F_POINTER(Cptr, thermo_data%r64)
CASE (LAMMPS_STRING)
thermo_data%datatype = DATA_STRING
thermo_data%str = c2f_string(Cptr)
CASE DEFAULT
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
'Unknown pointer type in last_thermo')
END SELECT
END FUNCTION lmp_last_thermo
! equivalent subroutine to lammps_extract_box
SUBROUTINE lmp_extract_box(self, boxlo, boxhi, xy, yz, xz, pflags, boxflag)
CLASS(lammps), INTENT(IN) :: self

28
potentials/COH.DMC.aip.water.2dm Normal file
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@ -0,0 +1,28 @@
# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
# The parameters below are fitted against the DMC reference data that rescaled from PBE+MBD-NL.
#
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
# For graphene and hydrocarbons
C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0
H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2
C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
# For water-graphene
C Ow 4.03686677 15.09817069 1.00000323 1.03838111 0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222 1.0 2.0
C Hw 3.08246994 6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099 4652.78021666 1.0 2.0
Ow C 4.03686677 15.09817069 1.00000323 1.03838111 0.16372013 9.00010553 1.12057182 2.96484087 21887.14173222 1.0 1.2
Hw C 3.08246994 6.412090180 1.00000265 2.89390420 -1.85748759 9.00009101 1.04574423 2.21642099 4652.78021666 1.0 1.2
# # The ILPs for other systems are set to zero
H Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
H Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2

28
potentials/COH.aip.water.2dm Normal file
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@ -0,0 +1,28 @@
# DATE: 2022-12-02 UNITS: metal CONTRIBUTOR: Wengen Ouyang w.g.ouyang@gmail.com CITATION: Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C 127, 8704 (2023).
# Anisotropic Interfacial Potential (AIP) parameters for water/graphene heterojunctions
# The parameters below are fitted against the PBE + MBD-NL DFT reference data from 2.5 A to 15 A.
#
# ----------------- Repulsion Potential ------------------++++++++++++++ Vdw Potential ++++++++++++++++************
# beta(A) alpha delta(A) epsilon(meV) C(meV) d sR reff(A) C6(meV*A^6) S rcut
# For graphene and hydrocarbons
C C 3.205843 7.511126 1.235334 1.528338E-5 37.530428 15.499947 0.7954443 3.681440 25.714535E3 1.0 2.0
H H 3.974540 6.53799 1.080633 0.6700556 0.8333833 15.022371 0.7490632 2.767223 1.6159581E3 1.0 1.2
C H 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
H C 2.642950 12.91410 1.020257 0.9750012 25.340996 15.222927 0.8115998 3.887324 5.6874617E3 1.0 1.5
# For water-graphene
C Ow 5.45369612 6.18172364 1.25025450 3.34909245 0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127 1.0 2.0
C Hw 2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571 7409.12856378 1.0 2.0
Ow C 5.45369612 6.18172364 1.25025450 3.34909245 0.68780636 9.05706482 1.23249498 2.77577173 100226.55503127 1.0 1.2
Hw C 2.55380862 9.68664390 1.96489198 41.77617053 -16.30012807 9.01568534 0.74415463 2.41545571 7409.12856378 1.0 1.2
# # The ILPs for other systems are set to zero
H Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
H Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw H 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Ow Hw 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2
Hw Ow 5.45369612 6.18172364 1.25025450 0.00000000 0.00000000 9.05706482 1.23249498 2.77577173 0.00000000 1.0 1.2

124
python/lammps/core.py
View File

@ -272,6 +272,9 @@ class lammps(object):
self.lib.lammps_get_thermo.argtypes = [c_void_p, c_char_p]
self.lib.lammps_get_thermo.restype = c_double
self.lib.lammps_last_thermo.argtypes = [c_void_p, c_char_p, c_int]
self.lib.lammps_last_thermo.restype = c_void_p
self.lib.lammps_encode_image_flags.restype = self.c_imageint
self.lib.lammps_config_has_package.argtypes = [c_char_p]
@ -503,9 +506,9 @@ class lammps(object):
def error(self, error_type, error_text):
"""Forward error to the LAMMPS Error class.
This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
.. versionadded:: 3Nov2022
.. versionadded:: TBD
This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
:param error_type:
:type error_type: int
@ -744,6 +747,56 @@ class lammps(object):
# -------------------------------------------------------------------------
def last_thermo(self):
"""Get a dictionary of the last thermodynamic output
This is a wrapper around the :cpp:func:`lammps_last_thermo`
function of the C-library interface. It collects the cached thermo
data from the last timestep into a dictionary. The return value
is None, if there has not been any thermo output yet.
:return: value of thermo keyword
:rtype: dict or None
"""
rv = dict()
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("step".encode()), 0)
mystep = cast(ptr, POINTER(self.c_bigint)).contents.value
if mystep < 0:
return None
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("num".encode()), 0)
nfield = cast(ptr, POINTER(c_int)).contents.value
for i in range(nfield):
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("keyword".encode()), i)
kw = cast(ptr, c_char_p).value.decode()
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("type".encode()), i)
typ = cast(ptr, POINTER(c_int)).contents.value
with ExceptionCheck(self):
ptr = self.lib.lammps_last_thermo(self.lmp, c_char_p("data".encode()), i)
if typ == LAMMPS_DOUBLE:
val = cast(ptr, POINTER(c_double)).contents.value
elif typ == LAMMPS_INT:
val = cast(ptr, POINTER(c_int)).contents.value
elif typ == LAMMPS_INT64:
val = cast(ptr, POINTER(c_int64)).contents.value
else:
# we should not get here
raise TypeError("Unknown LAMMPS data type " + str(typ))
rv[kw] = val
return rv
# -------------------------------------------------------------------------
def extract_setting(self, name):
"""Query LAMMPS about global settings that can be expressed as an integer.
@ -1289,6 +1342,8 @@ class lammps(object):
def gather_bonds(self):
"""Retrieve global list of bonds
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_gather_bonds`
function of the C-library interface.
@ -1296,8 +1351,6 @@ class lammps(object):
flat list of ctypes integer values with the bond type, bond atom1,
bond atom2 for each bond.
.. versionadded:: 28Jul2021
:return: a tuple with the number of bonds and a list of c_int or c_long
:rtype: (int, 3*nbonds*c_tagint)
"""
@ -1312,6 +1365,8 @@ class lammps(object):
def gather_angles(self):
"""Retrieve global list of angles
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_angles`
function of the C-library interface.
@ -1319,8 +1374,6 @@ class lammps(object):
flat list of ctypes integer values with the angle type, angle atom1,
angle atom2, angle atom3 for each angle.
.. versionadded:: TBD
:return: a tuple with the number of angles and a list of c_int or c_long
:rtype: (int, 4*nangles*c_tagint)
"""
@ -1335,6 +1388,8 @@ class lammps(object):
def gather_dihedrals(self):
"""Retrieve global list of dihedrals
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_dihedrals`
function of the C-library interface.
@ -1342,8 +1397,6 @@ class lammps(object):
flat list of ctypes integer values with the dihedral type, dihedral atom1,
dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.
.. versionadded:: TBD
:return: a tuple with the number of dihedrals and a list of c_int or c_long
:rtype: (int, 5*ndihedrals*c_tagint)
"""
@ -1358,6 +1411,8 @@ class lammps(object):
def gather_impropers(self):
"""Retrieve global list of impropers
.. versionadded:: 8Feb2023
This is a wrapper around the :cpp:func:`lammps_gather_impropers`
function of the C-library interface.
@ -1365,8 +1420,6 @@ class lammps(object):
flat list of ctypes integer values with the improper type, improper atom1,
improper atom2, improper atom3, improper atom4 for each improper.
.. versionadded:: TBD
:return: a tuple with the number of impropers and a list of c_int or c_long
:rtype: (int, 5*nimpropers*c_tagint)
"""
@ -1605,13 +1658,13 @@ class lammps(object):
def is_running(self):
""" Report whether being called from a function during a run or a minimization
.. versionadded:: 9Oct2020
Various LAMMPS commands must not be called during an ongoing
run or minimization. This property allows to check for that.
This is a wrapper around the :cpp:func:`lammps_is_running`
function of the library interface.
.. versionadded:: 9Oct2020
:return: True when called during a run otherwise false
:rtype: bool
"""
@ -1622,12 +1675,13 @@ class lammps(object):
def force_timeout(self):
""" Trigger an immediate timeout, i.e. a "soft stop" of a run.
.. versionadded:: 9Oct2020
This function allows to cleanly stop an ongoing run or minimization
at the next loop iteration.
This is a wrapper around the :cpp:func:`lammps_force_timeout`
function of the library interface.
.. versionadded:: 9Oct2020
"""
self.lib.lammps_force_timeout(self.lmp)
@ -1710,11 +1764,11 @@ class lammps(object):
def has_package(self, name):
""" Report if the named package has been enabled in the LAMMPS shared library.
.. versionadded:: 3Nov2022
This is a wrapper around the :cpp:func:`lammps_config_has_package`
function of the library interface.
.. versionadded:: TBD
:param name: name of the package
:type name: string
@ -1854,11 +1908,11 @@ class lammps(object):
def has_id(self, category, name):
"""Returns whether a given ID name is available in a given category
.. versionadded:: 9Oct2020
This is a wrapper around the function :cpp:func:`lammps_has_id`
of the library interface.
.. versionadded:: 9Oct2020
:param category: name of category
:type category: string
:param name: name of the ID
@ -1874,11 +1928,11 @@ class lammps(object):
def available_ids(self, category):
"""Returns a list of IDs available for a given category
.. versionadded:: 9Oct2020
This is a wrapper around the functions :cpp:func:`lammps_id_count()`
and :cpp:func:`lammps_id_name()` of the library interface.
.. versionadded:: 9Oct2020
:param category: name of category
:type category: string
@ -1901,11 +1955,11 @@ class lammps(object):
def available_plugins(self, category):
"""Returns a list of plugins available for a given category
.. versionadded:: 10Mar2021
This is a wrapper around the functions :cpp:func:`lammps_plugin_count()`
and :cpp:func:`lammps_plugin_name()` of the library interface.
.. versionadded:: 10Mar2021
:return: list of style/name pairs of loaded plugins
:rtype: list
"""
@ -1970,11 +2024,11 @@ class lammps(object):
def fix_external_get_force(self, fix_id):
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -1989,11 +2043,11 @@ class lammps(object):
def fix_external_set_energy_global(self, fix_id, eng):
"""Set the global energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: potential energy value to be added by fix external
@ -2008,11 +2062,11 @@ class lammps(object):
def fix_external_set_virial_global(self, fix_id, virial):
"""Set the global virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eng: list of 6 floating point numbers with the virial to be added by fix external
@ -2028,11 +2082,11 @@ class lammps(object):
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the per-atom energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: list of potential energy values for local atoms to be added by fix external
@ -2051,11 +2105,11 @@ class lammps(object):
def fix_external_set_virial_peratom(self, fix_id, vatom):
"""Set the per-atom virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param vatom: list of natoms lists with 6 floating point numbers to be added by fix external
@ -2083,11 +2137,11 @@ class lammps(object):
def fix_external_set_vector_length(self, fix_id, length):
"""Set the vector length for a global vector stored with fix external for analysis
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param length: length of the global vector
@ -2101,11 +2155,11 @@ class lammps(object):
def fix_external_set_vector(self, fix_id, idx, val):
"""Store a global vector value for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
of the C-library interface.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param idx: 1-based index of the value in the global vector

28
python/lammps/numpy_wrapper.py
View File

@ -262,12 +262,12 @@ class numpy_wrapper:
def gather_bonds(self):
"""Retrieve global list of bonds as NumPy array
.. versionadded:: 28Jul2021
This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: 28Jul2021
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nbonds,3)
"""
@ -280,12 +280,12 @@ class numpy_wrapper:
def gather_angles(self):
""" Retrieve global list of angles as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nangles,4)
"""
@ -298,12 +298,12 @@ class numpy_wrapper:
def gather_dihedrals(self):
""" Retrieve global list of dihedrals as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(ndihedrals,5)
"""
@ -316,12 +316,12 @@ class numpy_wrapper:
def gather_impropers(self):
""" Retrieve global list of impropers as NumPy array
.. versionadded:: 8Feb2023
This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` list.
.. versionadded:: TBD
:return: the requested data as a 2d-integer numpy array
:rtype: numpy.array(nimpropers,5)
"""
@ -334,13 +334,13 @@ class numpy_wrapper:
def fix_external_get_force(self, fix_id):
"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
.. versionchanged:: 28Jul2021
This function is a wrapper around the
:py:meth:`lammps.fix_external_get_force() <lammps.lammps.fix_external_get_force()>`
method. It behaves the same as the original method, but returns a NumPy array instead
of a ``ctypes`` pointer.
.. versionchanged:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:return: requested data
@ -356,13 +356,13 @@ class numpy_wrapper:
def fix_external_set_energy_peratom(self, fix_id, eatom):
"""Set the per-atom energy contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This function is an alternative to
:py:meth:`lammps.fix_external_set_energy_peratom() <lammps.lammps.fix_external_set_energy_peratom()>`
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy
@ -383,13 +383,13 @@ class numpy_wrapper:
def fix_external_set_virial_peratom(self, fix_id, vatom):
"""Set the per-atom virial contribution for a fix external instance with the given ID.
.. versionadded:: 28Jul2021
This function is an alternative to
:py:meth:`lammps.fix_external_set_virial_peratom() <lammps.lammps.fix_external_set_virial_peratom()>`
method. It behaves the same as the original method, but accepts a NumPy array
instead of a list as argument.
.. versionadded:: 28Jul2021
:param fix_id: Fix-ID of a fix external instance
:type: string
:param eatom: per-atom potential energy

8
src/.gitignore vendored
View File

@ -1058,6 +1058,10 @@
/pair_adp.h
/pair_agni.cpp
/pair_agni.h
/pair_aip_water_2dm.cpp
/pair_aip_water_2dm.h
/pair_aip_water_2dm_opt.cpp
/pair_aip_water_2dm_opt.h
/pair_airebo.cpp
/pair_airebo.h
/pair_airebo_morse.cpp
@ -1549,6 +1553,10 @@
/fix_langevin_drude.h
/fix_mol_swap.cpp
/fix_mol_swap.h
/fix_pimd.cpp
/fix_pimd.h
/fix_pimd_langevin.cpp
/fix_pimd_langevin.h
/fix_alchemy.cpp
/fix_alchemy.h
/fix_pimd_nvt.cpp

8
src/BPM/bond_bpm.cpp
View File

@ -187,10 +187,12 @@ void BondBPM::settings(int narg, char **arg)
iarg++;
}
} else if (strcmp(arg[iarg], "overlay/pair") == 0) {
overlay_flag = 1;
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for overlay/pair");
overlay_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg++;
} else if (strcmp(arg[iarg], "break/no") == 0) {
break_flag = 0;
} else if (strcmp(arg[iarg], "break") == 0) {
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for break");
break_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
iarg++;
} else {
leftover_iarg.push_back(iarg);

30
src/BPM/bond_bpm_rotational.cpp
View File

@ -50,6 +50,7 @@ BondBPMRotational::BondBPMRotational(LAMMPS *_lmp) :
{
partial_flag = 1;
smooth_flag = 1;
normalize_flag = 0;
single_extra = 7;
svector = new double[7];
@ -203,6 +204,13 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
double Ts[3], Tb[3], Tt[3], Tbp[3], Ttp[3], Tsp[3], T_rot[3], Ttmp[3];
double **quat = atom->quat;
double r0_mag_inv = 1.0 / r0_mag;
double Kr_type = Kr[type];
double Ks_type = Ks[type];
if (normalize_flag) {
Kr_type *= r0_mag_inv;
Ks_type *= r0_mag_inv;
}
q1[0] = quat[i1][0];
q1[1] = quat[i1][1];
@ -217,26 +225,26 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
// Calculate normal forces, rb = bond vector in particle 1's frame
MathExtra::qconjugate(q2, q2inv);
MathExtra::quatrotvec(q2inv, r, rb);
Fr = Kr[type] * (r_mag - r0_mag);
Fr = Kr_type * (r_mag - r0_mag);
MathExtra::scale3(Fr * r_mag_inv, rb, F_rot);
// Calculate forces due to tangential displacements (no rotation)
r0_dot_rb = MathExtra::dot3(r0, rb);
c = r0_dot_rb * r_mag_inv / r0_mag;
c = r0_dot_rb * r_mag_inv * r0_mag_inv;
gamma = acos_limit(c);
MathExtra::cross3(rb, r0, rb_x_r0);
MathExtra::cross3(rb, rb_x_r0, s);
MathExtra::norm3(s);
MathExtra::scale3(Ks[type] * r_mag * gamma, s, Fs);
MathExtra::scale3(Ks_type * r_mag * gamma, s, Fs);
// Calculate torque due to tangential displacements
MathExtra::cross3(r0, rb, t);
MathExtra::norm3(t);
MathExtra::scale3(0.5 * r_mag * Ks[type] * r_mag * gamma, t, Ts);
MathExtra::scale3(0.5 * r_mag * Ks_type * r_mag * gamma, t, Ts);
// Relative rotation force/torque
// Use representation of X'Y'Z' rotations from Wang, Mora 2009
@ -316,12 +324,12 @@ double BondBPMRotational::elastic_forces(int i1, int i2, int type, double r_mag,
Ttp[1] = 0.0;
Ttp[2] = Kt[type] * psi;
Fsp[0] = -0.5 * Ks[type] * r_mag * theta * cos_phi;
Fsp[1] = -0.5 * Ks[type] * r_mag * theta * sin_phi;
Fsp[0] = -0.5 * Ks_type * r_mag * theta * cos_phi;
Fsp[1] = -0.5 * Ks_type * r_mag * theta * sin_phi;
Fsp[2] = 0.0;
Tsp[0] = 0.25 * Ks[type] * r_mag * r_mag * theta * sin_phi;
Tsp[1] = -0.25 * Ks[type] * r_mag * r_mag * theta * cos_phi;
Tsp[0] = 0.25 * Ks_type * r_mag * r_mag * theta * sin_phi;
Tsp[1] = -0.25 * Ks_type * r_mag * r_mag * theta * cos_phi;
Tsp[2] = 0.0;
// Rotate forces/torques back to 1st particle's frame
@ -667,6 +675,10 @@ void BondBPMRotational::settings(int narg, char **arg)
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth");
smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else if (strcmp(arg[iarg], "normalize") == 0) {
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for normalize");
normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else {
error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]);
}
@ -793,7 +805,7 @@ double BondBPMRotational::single(int type, double rsq, int i, int j, double &ffo
double breaking = elastic_forces(i, j, type, r_mag, r0_mag, r_mag_inv, rhat, r, r0, force1on2,
torque1on2, torque2on1);
damping_forces(i, j, type, rhat, r, force1on2, torque1on2, torque2on1);
fforce = MathExtra::dot3(force1on2, r);
fforce = MathExtra::dot3(force1on2, rhat);
fforce *= -1;
double smooth = 1.0;

2
src/BPM/bond_bpm_rotational.h
View File

@ -41,7 +41,7 @@ class BondBPMRotational : public BondBPM {
protected:
double *Kr, *Ks, *Kt, *Kb, *gnorm, *gslide, *groll, *gtwist;
double *Fcr, *Fcs, *Tct, *Tcb;
int smooth_flag;
int smooth_flag, normalize_flag;
double elastic_forces(int, int, int, double, double, double, double *, double *, double *,
double *, double *, double *);

16
src/BPM/bond_bpm_spring.cpp
View File

@ -37,6 +37,7 @@ BondBPMSpring::BondBPMSpring(LAMMPS *_lmp) :
{
partial_flag = 1;
smooth_flag = 1;
normalize_flag = 0;
single_extra = 1;
svector = new double[1];
@ -190,7 +191,10 @@ void BondBPMSpring::compute(int eflag, int vflag)
}
rinv = 1.0 / r;
fbond = k[type] * (r0 - r);
if (normalize_flag)
fbond = -k[type] * e;
else
fbond = k[type] * (r0 - r);
delvx = v[i1][0] - v[i2][0];
delvy = v[i1][1] - v[i2][1];
@ -302,6 +306,10 @@ void BondBPMSpring::settings(int narg, char **arg)
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for smooth");
smooth_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else if (strcmp(arg[iarg], "normalize") == 0) {
if (iarg + 1 > narg) error->all(FLERR, "Illegal bond bpm command, missing option for normalize");
normalize_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
i += 1;
} else {
error->all(FLERR, "Illegal bond bpm command, invalid argument {}", arg[iarg]);
}
@ -376,7 +384,11 @@ double BondBPMSpring::single(int type, double rsq, int i, int j, double &fforce)
double r = sqrt(rsq);
double rinv = 1.0 / r;
fforce = k[type] * (r0 - r);
if (normalize_flag)
fforce = k[type] * (r0 - r) / r0;
else
fforce = k[type] * (r0 - r);
double **x = atom->x;
double **v = atom->v;

2
src/BPM/bond_bpm_spring.h
View File

@ -40,7 +40,7 @@ class BondBPMSpring : public BondBPM {
protected:
double *k, *ecrit, *gamma;
int smooth_flag;
int smooth_flag, normalize_flag;
void allocate();
void store_data();

3
src/DIFFRACTION/compute_xrd.cpp
View File

@ -90,8 +90,7 @@ ComputeXRD::ComputeXRD(LAMMPS *lmp, int narg, char **arg) :
ztype[i] = j;
}
}
if (ztype[i] == XRDmaxType + 1)
error->all(FLERR,"Compute XRD: Invalid ASF atom type");
if (ztype[i] == XRDmaxType + 1) error->all(FLERR,"Compute XRD: Invalid ASF atom type {}", arg[iarg]);
iarg++;
}

492
src/EXTRA-COMPUTE/compute_stress_mop.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,15 +13,21 @@
/*------------------------------------------------------------------------
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
Support for bonds and angles added by : Evangelos Voyiatzis (NovaMechanics)
--------------------------------------------------------------------------*/
#include "compute_stress_mop.h"
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "molecule.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "pair.h"
@ -33,40 +38,52 @@
using namespace LAMMPS_NS;
enum{X,Y,Z};
enum{TOTAL,CONF,KIN};
#define BIG 1000000000
enum { X, Y, Z };
enum { TOTAL, CONF, KIN, PAIR, BOND, ANGLE };
// clang-format off
/* ---------------------------------------------------------------------- */
ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 6) error->all(FLERR,"Illegal compute stress/mop command");
if (narg < 6) utils::missing_cmd_args(FLERR, "compute stress/mop", error);
MPI_Comm_rank(world,&me);
bondflag = 0;
angleflag = 0;
// set compute mode and direction of plane(s) for pressure calculation
if (strcmp(arg[3],"x")==0) {
if (strcmp(arg[3],"x") == 0) {
dir = X;
} else if (strcmp(arg[3],"y")==0) {
} else if (strcmp(arg[3],"y") == 0) {
dir = Y;
} else if (strcmp(arg[3],"z")==0) {
} else if (strcmp(arg[3],"z") == 0) {
dir = Z;
} else error->all(FLERR,"Illegal compute stress/mop command");
// Position of the plane
if (strcmp(arg[4],"lower")==0) {
if (strcmp(arg[4],"lower") == 0) {
pos = domain->boxlo[dir];
} else if (strcmp(arg[4],"upper")==0) {
} else if (strcmp(arg[4],"upper") == 0) {
pos = domain->boxhi[dir];
} else if (strcmp(arg[4],"center")==0) {
} else if (strcmp(arg[4],"center") == 0) {
pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
} else pos = utils::numeric(FLERR,arg[4],false,lmp);
// plane inside the box
if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir])) {
error->warning(FLERR, "The specified initial plane lies outside of the simulation box");
double dx[3] = {0.0, 0.0, 0.0};
dx[dir] = pos - 0.5*(domain->boxhi[dir] + domain->boxlo[dir]);
domain->minimum_image(dx[0], dx[1], dx[2]);
pos = 0.5*(domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir]))
error->all(FLERR, "Plane for compute stress/mop is out of bounds");
}
if (pos < (domain->boxlo[dir]+domain->prd_half[dir])) {
pos1 = pos + domain->prd[dir];
} else {
@ -96,34 +113,53 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = TOTAL;
nvalues++;
}
} else if (strcmp(arg[iarg],"pair") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = PAIR;
nvalues++;
}
} else if (strcmp(arg[iarg],"bond") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = BOND;
nvalues++;
}
} else if (strcmp(arg[iarg],"angle") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = ANGLE;
nvalues++;
}
} else error->all(FLERR, "Illegal compute stress/mop command"); //break;
iarg++;
}
// Error check
// Error checks
// 3D only
if (domain->dimension < 3)
error->all(FLERR, "Compute stress/mop incompatible with simulation dimension");
if (domain->dimension != 3)
error->all(FLERR, "Compute stress/mop requires a 3d system");
// orthogonal simulation box
if (domain->triclinic != 0)
error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box");
// plane inside the box
if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
error->all(FLERR, "Plane for compute stress/mop is out of bounds");
error->all(FLERR, "Compute stress/mop is incompatible with triclinic simulation box");
// Initialize some variables
values_local = values_global = vector = nullptr;
bond_local = nullptr;
bond_global = nullptr;
angle_local = nullptr;
angle_global = nullptr;
// this fix produces a global vector
memory->create(vector,nvalues,"stress/mop:vector");
memory->create(values_local,nvalues,"stress/mop/spatial:values_local");
memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
memory->create(values_local,nvalues,"stress/mop:values_local");
memory->create(values_global,nvalues,"stress/mop:values_global");
memory->create(bond_local,nvalues,"stress/mop:bond_local");
memory->create(bond_global,nvalues,"stress/mop:bond_global");
memory->create(angle_local,nvalues,"stress/mop:angle_local");
memory->create(angle_global,nvalues,"stress/mop:angle_global");
size_vector = nvalues;
vector_flag = 1;
@ -135,11 +171,14 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
ComputeStressMop::~ComputeStressMop()
{
delete [] which;
delete[] which;
memory->destroy(values_local);
memory->destroy(values_global);
memory->destroy(bond_local);
memory->destroy(bond_global);
memory->destroy(angle_local);
memory->destroy(angle_global);
memory->destroy(vector);
}
@ -169,31 +208,39 @@ void ComputeStressMop::init()
// Compute stress/mop requires fixed simulation box
if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
error->all(FLERR, "Compute stress/mop requires a fixed simulation box");
error->all(FLERR, "Compute stress/mop requires a fixed size simulation box");
// This compute requires a pair style with pair_single method implemented
if (force->pair == nullptr)
if (!force->pair)
error->all(FLERR,"No pair style is defined for compute stress/mop");
if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute stress/mop");
// Warnings
// Errors
if (me==0) {
if (comm->me == 0) {
//Compute stress/mop only accounts for pair interactions.
// issue a warning if any intramolecular potential or Kspace is defined.
// issue an error for unimplemented intramolecular potentials or Kspace.
if (force->bond!=nullptr)
error->warning(FLERR,"compute stress/mop does not account for bond potentials");
if (force->angle!=nullptr)
error->warning(FLERR,"compute stress/mop does not account for angle potentials");
if (force->dihedral!=nullptr)
error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
if (force->improper!=nullptr)
error->warning(FLERR,"compute stress/mop does not account for improper potentials");
if (force->kspace!=nullptr)
if (force->bond) bondflag = 1;
if (force->angle) {
if (force->angle->born_matrix_enable == 0) {
if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
error->all(FLERR,"compute stress/mop does not account for angle potentials");
} else {
angleflag = 1;
}
}
if (force->dihedral) {
if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
}
if (force->improper) {
if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
error->all(FLERR,"compute stress/mop does not account for improper potentials");
}
if (force->kspace)
error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
}
@ -221,14 +268,31 @@ void ComputeStressMop::compute_vector()
compute_pairs();
// sum pressure contributions over all procs
MPI_Allreduce(values_local,values_global,nvalues,
MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(values_local,values_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
int m;
for (m=0; m<nvalues; m++) {
vector[m] = values_global[m];
if (bondflag) {
//Compute bond contribution on separate procs
compute_bonds();
} else {
for (int i=0; i<nvalues; i++) bond_local[i] = 0.0;
}
// sum bond contribution over all procs
MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
if (angleflag) {
//Compute angle contribution on separate procs
compute_angles();
} else {
for (int i=0; i<nvalues; i++) angle_local[i] = 0.0;
}
// sum angle contribution over all procs
MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
for (int m=0; m<nvalues; m++) {
vector[m] = values_global[m] + bond_global[m] + angle_global[m];
}
}
@ -280,8 +344,8 @@ void ComputeStressMop::compute_pairs()
double xj[3];
m = 0;
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL) {
while (m < nvalues) {
if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
//Compute configurational contribution to pressure
for (ii = 0; ii < inum; ii++) {
@ -316,47 +380,34 @@ void ComputeStressMop::compute_pairs()
if (newton_pair || j < nlocal) {
//check if ij pair is across plane, add contribution to pressure
if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
}
else if (((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1))) {
} else if (((xi[dir] < pos) && (xj[dir] > pos)) || ((xi[dir] < pos1) && (xj[dir] > pos1))) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
}
} else {
if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
}
}
}
}
}
// Compute kinetic contribution to pressure
// counts local particles transfers across the plane
if (which[m] == KIN || which[m] == TOTAL) {
if ((which[m] == KIN) || (which[m] == TOTAL)) {
double sgn;
for (int i = 0; i < nlocal; i++) {
@ -383,13 +434,13 @@ void ComputeStressMop::compute_pairs()
//coordinates at t-dt (based on Velocity-Verlet alg.)
if (rmass) {
xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v;
xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v;
xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/rmass[i]*dt*dt*ftm2v;
xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/rmass[i]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/rmass[i]*dt*dt*ftm2v;
} else {
xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/mass[itype]*dt*dt*ftm2v;
xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/mass[itype]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/mass[itype]*dt*dt*ftm2v;
}
// because LAMMPS does not put atoms back in the box
@ -399,21 +450,21 @@ void ComputeStressMop::compute_pairs()
double pos_temp = pos+copysign(1.0,domain->prd_half[dir]-pos)*domain->prd[dir];
if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)) {
if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)) < 0) {
//sgn = copysign(1.0,vi[dir]-vcm[dir]);
// sgn = copysign(1.0,vi[dir]-vcm[dir]);
sgn = copysign(1.0,vi[dir]);
//approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
// approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
double vcross[3];
if (rmass) {
vcross[0] = vi[0]-fi[0]/rmass[i]/2*ftm2v*dt;
vcross[1] = vi[1]-fi[1]/rmass[i]/2*ftm2v*dt;
vcross[2] = vi[2]-fi[2]/rmass[i]/2*ftm2v*dt;
vcross[0] = vi[0]-fi[0]/rmass[i]/2.0*ftm2v*dt;
vcross[1] = vi[1]-fi[1]/rmass[i]/2.0*ftm2v*dt;
vcross[2] = vi[2]-fi[2]/rmass[i]/2.0*ftm2v*dt;
} else {
vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
vcross[0] = vi[0]-fi[0]/mass[itype]/2.0*ftm2v*dt;
vcross[1] = vi[1]-fi[1]/mass[itype]/2.0*ftm2v*dt;
vcross[2] = vi[2]-fi[2]/mass[itype]/2.0*ftm2v*dt;
}
values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
@ -423,7 +474,288 @@ void ComputeStressMop::compute_pairs()
}
}
}
m+=3;
m += 3;
}
}
/*------------------------------------------------------------------------
* compute bond contribution to pressure of local proc
*-------------------------------------------------------------------------*/
void ComputeStressMop::compute_bonds()
{
int i, nb, atom1, atom2, imol, iatom, btype;
tagint tagprev;
double rsq, fpair;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Bond *bond = force->bond;
double dx[3] = {0.0, 0.0, 0.0};
double x_bond_1[3] = {0.0, 0.0, 0.0};
double x_bond_2[3] = {0.0, 0.0, 0.0};
double local_contribution[3] = {0.0, 0.0, 0.0};
// initialization
for (int i = 0; i < nvalues; i++) bond_local[i] = 0.0;
// loop over all bonded atoms in the current proc
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & groupbit)) continue;
if (molecular == 1)
nb = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
nb = onemols[imol]->num_bond[iatom];
}
for (i = 0; i < nb; i++) {
if (molecular == 1) {
btype = bond_type[atom1][i];
atom2 = atom->map(bond_atom[atom1][i]);
} else {
tagprev = tag[atom1] - iatom - 1;
btype = onemols[imol]->bond_type[iatom][i];
atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
}
if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype <= 0) continue;
// minimum image of atom1 with respect to the plane of interest
dx[0] = x[atom1][0];
dx[1] = x[atom1][1];
dx[2] = x[atom1][2];
dx[dir] -= pos;
domain->minimum_image(dx[0], dx[1], dx[2]);
x_bond_1[0] = dx[0];
x_bond_1[1] = dx[1];
x_bond_1[2] = dx[2];
x_bond_1[dir] += pos;
// minimum image of atom2 with respect to atom1
dx[0] = x[atom2][0] - x_bond_1[0];
dx[1] = x[atom2][1] - x_bond_1[1];
dx[2] = x[atom2][2] - x_bond_1[2];
domain->minimum_image(dx[0], dx[1], dx[2]);
x_bond_2[0] = x_bond_1[0] + dx[0];
x_bond_2[1] = x_bond_1[1] + dx[1];
x_bond_2[2] = x_bond_1[2] + dx[2];
// check if the bond vector crosses the plane of interest
double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
if ((tau <= 1) && (tau >= 0)) {
dx[0] = x_bond_1[0] - x_bond_2[0];
dx[1] = x_bond_1[1] - x_bond_2[1];
dx[2] = x_bond_1[2] - x_bond_2[2];
rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
bond->single(btype, rsq, atom1, atom2, fpair);
double sgn = copysign(1.0, x_bond_1[dir] - pos);
local_contribution[0] += sgn*fpair*dx[0]/area*nktv2p;
local_contribution[1] += sgn*fpair*dx[1]/area*nktv2p;
local_contribution[2] += sgn*fpair*dx[2]/area*nktv2p;
}
}
}
// loop over the keywords and if necessary add the bond contribution
int m = 0;
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) {
bond_local[m] = local_contribution[0];
bond_local[m+1] = local_contribution[1];
bond_local[m+2] = local_contribution[2];
}
m += 3;
}
}
/*------------------------------------------------------------------------
compute angle contribution to pressure of local proc
-------------------------------------------------------------------------*/
void ComputeStressMop::compute_angles()
{
int na, atom1, atom2, atom3, imol, iatom, atype;
tagint tagprev;
double r1, r2, cos_theta;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_angle = atom->num_angle;
tagint **angle_atom1 = atom->angle_atom1;
tagint **angle_atom2 = atom->angle_atom2;
tagint **angle_atom3 = atom->angle_atom3;
int **angle_type = atom->angle_type;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int molecular = atom->molecular;
// loop over all atoms and their angles
Angle *angle = force->angle;
double duang, du2ang;
double dx[3] = {0.0, 0.0, 0.0};
double dx_left[3] = {0.0, 0.0, 0.0};
double dx_right[3] = {0.0, 0.0, 0.0};
double x_angle_left[3] = {0.0, 0.0, 0.0};
double x_angle_middle[3] = {0.0, 0.0, 0.0};
double x_angle_right[3] = {0.0, 0.0, 0.0};
double dcos_theta[3] = {0.0, 0.0, 0.0};
double local_contribution[3] = {0.0, 0.0, 0.0};
// initialization
for (int i = 0; i < nvalues; i++) angle_local[i] = 0.0;
for (atom2 = 0; atom2 < nlocal; atom2++) {
if (!(mask[atom2] & groupbit)) continue;
if (molecular == 1)
na = num_angle[atom2];
else {
if (molindex[atom2] < 0) continue;
imol = molindex[atom2];
iatom = molatom[atom2];
na = onemols[imol]->num_angle[iatom];
}
for (int i = 0; i < na; i++) {
if (molecular == 1) {
if (tag[atom2] != angle_atom2[atom2][i]) continue;
atype = angle_type[atom2][i];
atom1 = atom->map(angle_atom1[atom2][i]);
atom3 = atom->map(angle_atom3[atom2][i]);
} else {
if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue;
atype = onemols[imol]->angle_type[atom2][i];
tagprev = tag[atom2] - iatom - 1;
atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i] + tagprev);
atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i] + tagprev);
}
if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
if (atype <= 0) continue;
// minimum image of atom1 with respect to the plane of interest
dx[0] = x[atom1][0];
dx[1] = x[atom1][1];
dx[2] = x[atom1][2];
dx[dir] -= pos;
domain->minimum_image(dx[0], dx[1], dx[2]);
x_angle_left[0] = dx[0];
x_angle_left[1] = dx[1];
x_angle_left[2] = dx[2];
x_angle_left[dir] += pos;
// minimum image of atom2 with respect to atom1
dx_left[0] = x[atom2][0] - x_angle_left[0];
dx_left[1] = x[atom2][1] - x_angle_left[1];
dx_left[2] = x[atom2][2] - x_angle_left[2];
domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]);
x_angle_middle[0] = x_angle_left[0] + dx_left[0];
x_angle_middle[1] = x_angle_left[1] + dx_left[1];
x_angle_middle[2] = x_angle_left[2] + dx_left[2];
// minimum image of atom3 with respect to atom2
dx_right[0] = x[atom3][0] - x_angle_middle[0];
dx_right[1] = x[atom3][1] - x_angle_middle[1];
dx_right[2] = x[atom3][2] - x_angle_middle[2];
domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]);
x_angle_right[0] = x_angle_middle[0] + dx_right[0];
x_angle_right[1] = x_angle_middle[1] + dx_right[1];
x_angle_right[2] = x_angle_middle[2] + dx_right[2];
// check if any bond vector crosses the plane of interest
double tau_right = (x_angle_right[dir] - pos) / (x_angle_right[dir] - x_angle_middle[dir]);
double tau_left = (x_angle_middle[dir] - pos) / (x_angle_middle[dir] - x_angle_left[dir]);
bool right_cross = ((tau_right >=0) && (tau_right <= 1));
bool left_cross = ((tau_left >=0) && (tau_left <= 1));
// no bonds crossing the plane
if (!right_cross && !left_cross) continue;
// compute the cos(theta) of the angle
r1 = sqrt(dx_left[0]*dx_left[0] + dx_left[1]*dx_left[1] + dx_left[2]*dx_left[2]);
r2 = sqrt(dx_right[0]*dx_right[0] + dx_right[1]*dx_right[1] + dx_right[2]*dx_right[2]);
cos_theta = -(dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
if (cos_theta > 1.0) cos_theta = 1.0;
if (cos_theta < -1.0) cos_theta = -1.0;
// The method returns derivative with regards to cos(theta)
angle->born_matrix(atype, atom1, atom2, atom3, duang, du2ang);
// only right bond crossing the plane
if (right_cross && !left_cross)
{
double sgn = copysign(1.0, x_angle_right[dir] - pos);
dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
}
// only left bond crossing the plane
if (!right_cross && left_cross)
{
double sgn = copysign(1.0, x_angle_left[dir] - pos);
dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
}
// both bonds crossing the plane
if (right_cross && left_cross)
{
// due to right bond
double sgn = copysign(1.0, x_angle_middle[dir] - pos);
dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
// due to left bond
dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
}
// final contribution of the given angle term
local_contribution[0] += duang*dcos_theta[0]/area*nktv2p;
local_contribution[1] += duang*dcos_theta[1]/area*nktv2p;
local_contribution[2] += duang*dcos_theta[2]/area*nktv2p;
}
}
// loop over the keywords and if necessary add the angle contribution
int m = 0;
while (m < nvalues) {
if (which[m] == CONF || which[m] == TOTAL || which[m] == ANGLE) {
angle_local[m] = local_contribution[0];
angle_local[m+1] = local_contribution[1];
angle_local[m+2] = local_contribution[2];
}
m += 3;
}
}

8
src/EXTRA-COMPUTE/compute_stress_mop.h
View File

@ -38,11 +38,17 @@ class ComputeStressMop : public Compute {
private:
void compute_pairs();
void compute_bonds();
void compute_angles();
int me, nvalues, dir;
int nvalues, dir;
int *which;
int bondflag, angleflag;
double *values_local, *values_global;
double *bond_local, *bond_global;
double *angle_local, *angle_global;
double pos, pos1, dt, nktv2p, ftm2v;
double area;
class NeighList *list;

249
src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -14,47 +13,51 @@
/*------------------------------------------------------------------------
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
Support for bonds added by : Evangelos Voyiatzis (NovaMechanics)
--------------------------------------------------------------------------*/
#include "compute_stress_mop_profile.h"
#include "atom.h"
#include "update.h"
#include "atom_vec.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "neigh_list.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "molecule.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "pair.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
enum{X,Y,Z};
enum{LOWER,CENTER,UPPER,COORD};
enum{TOTAL,CONF,KIN};
#define BIG 1000000000
enum { X, Y, Z };
enum { LOWER, CENTER, UPPER, COORD };
enum { TOTAL, CONF, KIN, PAIR, BOND };
// clang-format off
/* ---------------------------------------------------------------------- */
ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command");
if (narg < 7) utils::missing_cmd_args(FLERR, "compute stress/mop/profile", error);
MPI_Comm_rank(world,&me);
bondflag = 0;
// set compute mode and direction of plane(s) for pressure calculation
if (strcmp(arg[3],"x")==0) {
if (strcmp(arg[3],"x") == 0) {
dir = X;
} else if (strcmp(arg[3],"y")==0) {
} else if (strcmp(arg[3],"y") == 0) {
dir = Y;
} else if (strcmp(arg[3],"z")==0) {
} else if (strcmp(arg[3],"z") == 0) {
dir = Z;
} else error->all(FLERR,"Illegal compute stress/mop/profile command");
@ -64,8 +67,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD)
origin = utils::numeric(FLERR,arg[4],false,lmp);
if (originflag == COORD) origin = utils::numeric(FLERR,arg[4],false,lmp);
delta = utils::numeric(FLERR,arg[5],false,lmp);
invdelta = 1.0/delta;
@ -92,6 +94,16 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
which[nvalues] = TOTAL;
nvalues++;
}
} else if (strcmp(arg[iarg],"pair") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = PAIR;
nvalues++;
}
} else if (strcmp(arg[iarg],"bond") == 0) {
for (i=0; i<3; i++) {
which[nvalues] = BOND;
nvalues++;
}
} else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
iarg++;
@ -114,6 +126,9 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
nbins = 0;
coord = coordp = nullptr;
values_local = values_global = array = nullptr;
bond_local = nullptr;
bond_global = nullptr;
local_contribution = nullptr;
// bin setup
@ -133,13 +148,15 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
ComputeStressMopProfile::~ComputeStressMopProfile()
{
delete [] which;
delete[] which;
memory->destroy(coord);
memory->destroy(coordp);
memory->destroy(values_local);
memory->destroy(values_global);
memory->destroy(bond_local);
memory->destroy(bond_global);
memory->destroy(local_contribution);
memory->destroy(array);
}
@ -147,7 +164,6 @@ ComputeStressMopProfile::~ComputeStressMopProfile()
void ComputeStressMopProfile::init()
{
// conversion constants
nktv2p = force->nktv2p;
@ -173,27 +189,30 @@ void ComputeStressMopProfile::init()
//This compute requires a pair style with pair_single method implemented
if (force->pair == nullptr)
if (!force->pair)
error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute stress/mop/profile");
// Warnings
// Errors
if (me==0) {
if (comm->me == 0) {
//Compute stress/mop/profile only accounts for pair interactions.
// issue a warning if any intramolecular potential or Kspace is defined.
// issue an error if any intramolecular potential or Kspace is defined.
if (force->bond!=nullptr)
error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials");
if (force->angle!=nullptr)
error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials");
if (force->dihedral!=nullptr)
error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
if (force->improper!=nullptr)
error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials");
if (force->kspace!=nullptr)
if (force->bond) bondflag = 1;
if (force->angle)
if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
if (force->dihedral)
if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
if (force->improper)
if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
if (force->kspace)
error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
}
@ -222,17 +241,29 @@ void ComputeStressMopProfile::compute_array()
compute_pairs();
// sum pressure contributions over all procs
MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
int ibin,m,mo;
for (ibin=0; ibin<nbins; ibin++) {
if (bondflag) {
//Compute bond contribution on separate procs
compute_bonds();
} else {
for (int m = 0; m < nbins; m++) {
for (int i = 0; i < nvalues; i++) {
bond_local[m][i] = 0.0;
}
}
}
// sum bond contribution over all procs
MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
for (int ibin=0; ibin<nbins; ibin++) {
array[ibin][0] = coord[ibin][0];
mo=1;
m = 0;
while (m<nvalues) {
array[ibin][m+mo] = values_global[ibin][m];
int mo = 1;
int m = 0;
while (m < nvalues) {
array[ibin][m+mo] = values_global[ibin][m] + bond_global[ibin][m];
m++;
}
}
@ -289,8 +320,8 @@ void ComputeStressMopProfile::compute_pairs()
double xj[3];
m = 0;
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL) {
while (m < nvalues) {
if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
// Compute configurational contribution to pressure
@ -377,7 +408,7 @@ void ComputeStressMopProfile::compute_pairs()
// compute kinetic contribution to pressure
// counts local particles transfers across the plane
if (which[m] == KIN || which[m] == TOTAL) {
if ((which[m] == KIN) || (which[m] == TOTAL)) {
double sgn;
@ -415,7 +446,7 @@ void ComputeStressMopProfile::compute_pairs()
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
}
for (ibin=0;ibin<nbins;ibin++) {
for (ibin = 0; ibin < nbins; ibin++) {
pos = coord[ibin][0];
pos1 = coordp[ibin][0];
@ -452,6 +483,129 @@ void ComputeStressMopProfile::compute_pairs()
}
}
/*------------------------------------------------------------------------
compute bond contribution to pressure of local proc
-------------------------------------------------------------------------*/
void ComputeStressMopProfile::compute_bonds()
{
int i, nb, atom1, atom2, imol, iatom, btype;
tagint tagprev;
double rsq, fpair;
double **x = atom->x;
tagint *tag = atom->tag;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int **bond_type = atom->bond_type;
int *mask = atom->mask;
int *molindex = atom->molindex;
int *molatom = atom->molatom;
Molecule **onemols = atom->avec->onemols;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
int molecular = atom->molecular;
Bond *bond = force->bond;
double dx[3] = {0.0, 0.0, 0.0};
double x_bond_1[3] = {0.0, 0.0, 0.0};
double x_bond_2[3] = {0.0, 0.0, 0.0};
// initialization
for (int m = 0; m < nbins; m++) {
for (int i = 0; i < nvalues; i++) {
bond_local[m][i] = 0.0;
}
local_contribution[m][0] = 0.0;
local_contribution[m][1] = 0.0;
local_contribution[m][2] = 0.0;
}
// loop over all bonded atoms in the current proc
for (atom1 = 0; atom1 < nlocal; atom1++) {
if (!(mask[atom1] & groupbit)) continue;
if (molecular == 1)
nb = num_bond[atom1];
else {
if (molindex[atom1] < 0) continue;
imol = molindex[atom1];
iatom = molatom[atom1];
nb = onemols[imol]->num_bond[iatom];
}
for (i = 0; i < nb; i++) {
if (molecular == 1) {
btype = bond_type[atom1][i];
atom2 = atom->map(bond_atom[atom1][i]);
} else {
tagprev = tag[atom1] - iatom - 1;
btype = onemols[imol]->bond_type[iatom][i];
atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
}
if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
if (btype <= 0) continue;
for (int ibin = 0; ibin<nbins; ibin++) {
double pos = coord[ibin][0];
// minimum image of atom1 with respect to the plane of interest
dx[0] = x[atom1][0];
dx[1] = x[atom1][1];
dx[2] = x[atom1][2];
dx[dir] -= pos;
domain->minimum_image(dx[0], dx[1], dx[2]);
x_bond_1[0] = dx[0];
x_bond_1[1] = dx[1];
x_bond_1[2] = dx[2];
x_bond_1[dir] += pos;
// minimum image of atom2 with respect to atom1
dx[0] = x[atom2][0] - x_bond_1[0];
dx[1] = x[atom2][1] - x_bond_1[1];
dx[2] = x[atom2][2] - x_bond_1[2];
domain->minimum_image(dx[0], dx[1], dx[2]);
x_bond_2[0] = x_bond_1[0] + dx[0];
x_bond_2[1] = x_bond_1[1] + dx[1];
x_bond_2[2] = x_bond_1[2] + dx[2];
// check if the bond vector crosses the plane of interest
double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
if ((tau <= 1) && (tau >= 0)) {
dx[0] = x_bond_1[0] - x_bond_2[0];
dx[1] = x_bond_1[1] - x_bond_2[1];
dx[2] = x_bond_1[2] - x_bond_2[2];
rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
bond->single(btype, rsq, atom1, atom2, fpair);
double sgn = copysign(1.0, x_bond_1[dir] - pos);
local_contribution[ibin][0] += sgn*fpair*dx[0]/area*nktv2p;
local_contribution[ibin][1] += sgn*fpair*dx[1]/area*nktv2p;
local_contribution[ibin][2] += sgn*fpair*dx[2]/area*nktv2p;
}
}
}
}
// loop over the keywords and if necessary add the bond contribution
int m = 0;
while (m < nvalues) {
if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == BOND)) {
for (int ibin = 0; ibin < nbins; ibin++) {
bond_local[ibin][m] = local_contribution[ibin][0];
bond_local[ibin][m+1] = local_contribution[ibin][1];
bond_local[ibin][m+2] = local_contribution[ibin][2];
}
}
m += 3;
}
}
/* ----------------------------------------------------------------------
setup 1d bins and their extent and coordinates
called at init()
@ -492,6 +646,9 @@ void ComputeStressMopProfile::setup_bins()
memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
memory->create(bond_local,nbins,nvalues,"stress/mop/profile:bond_local");
memory->create(bond_global,nbins,nvalues,"stress/mop/profile:bond_global");
memory->create(local_contribution,nbins,3,"stress/mop/profile:local_contribution");
// set bin coordinates
for (i = 0; i < nbins; i++) {

7
src/EXTRA-COMPUTE/compute_stress_mop_profile.h
View File

@ -38,16 +38,21 @@ class ComputeStressMopProfile : public Compute {
private:
void compute_pairs();
void compute_bonds();
void setup_bins();
int me, nvalues, dir;
int nvalues, dir;
int *which;
int bondflag;
int originflag;
double origin, delta, offset, invdelta;
int nbins;
double **coord, **coordp;
double **values_local, **values_global;
double **bond_local, **bond_global;
double **local_contribution;
double dt, nktv2p, ftm2v;
double area;

36
src/EXTRA-DUMP/dump_yaml.cpp
View File

@ -60,21 +60,29 @@ void DumpYAML::write_header(bigint ndump)
std::string thermo_data;
if (thermo) {
Thermo *th = output->thermo;
thermo_data += "thermo:\n - keywords: [ ";
for (int i = 0; i < th->nfield; ++i) thermo_data += fmt::format("{}, ", th->keyword[i]);
thermo_data += "]\n - data: [ ";
// output thermo data only on timesteps where it was computed
if (update->ntimestep == *th->get_timestep()) {
int nfield = *th->get_nfield();
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
for (int i = 0; i < th->nfield; ++i) {
th->call_vfunc(i);
if (th->vtype[i] == Thermo::FLOAT)
thermo_data += fmt::format("{}, ", th->dvalue);
else if (th->vtype[i] == Thermo::INT)
thermo_data += fmt::format("{}, ", th->ivalue);
else if (th->vtype[i] == Thermo::BIGINT)
thermo_data += fmt::format("{}, ", th->bivalue);
thermo_data += "thermo:\n - keywords: [ ";
for (int i = 0; i < nfield; ++i) thermo_data += fmt::format("{}, ", keywords[i]);
thermo_data += "]\n - data: [ ";
for (int i = 0; i < nfield; ++i) {
if (fields[i].type == multitype::DOUBLE)
thermo_data += fmt::format("{}, ", fields[i].data.d);
else if (fields[i].type == multitype::INT)
thermo_data += fmt::format("{}, ", fields[i].data.i);
else if (fields[i].type == multitype::BIGINT)
thermo_data += fmt::format("{}, ", fields[i].data.b);
else
thermo_data += ", ";
}
thermo_data += "]\n";
MPI_Barrier(world);
}
thermo_data += "]\n";
MPI_Barrier(world);
}
if (comm->me == 0) {
@ -85,7 +93,7 @@ void DumpYAML::write_header(bigint ndump)
fmt::print(fp, "natoms: {}\n", ndump);
fputs("boundary: [ ", fp);
for (const auto bflag : boundary) {
for (const auto &bflag : boundary) {
if (bflag == ' ') continue;
fmt::print(fp, "{}, ", bflag);
}

3
src/EXTRA-FIX/fix_electron_stopping.cpp
View File

@ -175,7 +175,8 @@ void FixElectronStopping::post_force(int /*vflag*/)
if (energy < Ecut) continue;
if (energy < elstop_ranges[0][0]) continue;
if (energy > elstop_ranges[0][table_entries - 1])
error->one(FLERR, "Atom kinetic energy too high for fix electron/stopping");
error->one(FLERR, "Fix electron/stopping: kinetic energy too high for atom {}: {} vs {}",
atom->tag[i], energy, elstop_ranges[0][table_entries - 1]);
if (region) {
// Only apply in the given region

46
src/GRANULAR/gran_sub_mod_normal.cpp
View File

@ -150,6 +150,7 @@ GranSubModNormalHertzMaterial::GranSubModNormalHertzMaterial(GranularModel *gm,
material_properties = 1;
num_coeffs = 3;
contact_radius_flag = 1;
mixed_coefficients = 0;
}
/* ---------------------------------------------------------------------- */
@ -159,10 +160,12 @@ void GranSubModNormalHertzMaterial::coeffs_to_local()
Emod = coeffs[0];
damp = coeffs[1];
poiss = coeffs[2];
if (gm->contact_type == PAIR) {
k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
if (!mixed_coefficients) {
if (gm->contact_type == PAIR) {
k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
}
}
if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal Hertz material normal model");
@ -175,6 +178,10 @@ void GranSubModNormalHertzMaterial::mix_coeffs(double *icoeffs, double *jcoeffs)
coeffs[0] = mix_stiffnessE(icoeffs[0], jcoeffs[0], icoeffs[2], jcoeffs[2]);
coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
k = FOURTHIRDS * coeffs[0];
mixed_coefficients = 1;
coeffs_to_local();
}
@ -188,6 +195,7 @@ GranSubModNormalDMT::GranSubModNormalDMT(GranularModel *gm, LAMMPS *lmp) : GranS
cohesive_flag = 1;
num_coeffs = 4;
contact_radius_flag = 1;
mixed_coefficients = 0;
}
/* ---------------------------------------------------------------------- */
@ -198,10 +206,13 @@ void GranSubModNormalDMT::coeffs_to_local()
damp = coeffs[1];
poiss = coeffs[2];
cohesion = coeffs[3];
if (gm->contact_type == PAIR) {
k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
if (!mixed_coefficients) {
if (gm->contact_type == PAIR) {
k = FOURTHIRDS * mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
k = FOURTHIRDS * mix_stiffnessE_wall(Emod, poiss);
}
}
if (Emod < 0.0 || damp < 0.0) error->all(FLERR, "Illegal DMT normal model");
@ -215,6 +226,10 @@ void GranSubModNormalDMT::mix_coeffs(double *icoeffs, double *jcoeffs)
coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
k = FOURTHIRDS * coeffs[0];
mixed_coefficients = 1;
coeffs_to_local();
}
@ -246,6 +261,7 @@ GranSubModNormalJKR::GranSubModNormalJKR(GranularModel *gm, LAMMPS *lmp) : GranS
beyond_contact = 1;
num_coeffs = 4;
contact_radius_flag = 1;
mixed_coefficients = 0;
}
/* ---------------------------------------------------------------------- */
@ -257,10 +273,12 @@ void GranSubModNormalJKR::coeffs_to_local()
poiss = coeffs[2];
cohesion = coeffs[3];
if (gm->contact_type == PAIR) {
Emix = mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
Emix = mix_stiffnessE_wall(Emod, poiss);
if (!mixed_coefficients) {
if (gm->contact_type == PAIR) {
Emix = mix_stiffnessE(Emod, Emod, poiss, poiss);
} else {
Emix = mix_stiffnessE_wall(Emod, poiss);
}
}
k = FOURTHIRDS * Emix;
@ -276,6 +294,10 @@ void GranSubModNormalJKR::mix_coeffs(double *icoeffs, double *jcoeffs)
coeffs[1] = mix_geom(icoeffs[1], jcoeffs[1]);
coeffs[2] = mix_geom(icoeffs[2], jcoeffs[2]);
coeffs[3] = mix_geom(icoeffs[3], jcoeffs[3]);
Emix = coeffs[0];
mixed_coefficients = 1;
coeffs_to_local();
}

5
src/GRANULAR/gran_sub_mod_normal.h
View File

@ -29,6 +29,7 @@ GranSubModStyle(jkr,GranSubModNormalJKR,NORMAL);
namespace LAMMPS_NS {
namespace Granular_NS {
class GranSubModNormal : public GranSubMod {
public:
GranSubModNormal(class GranularModel *, class LAMMPS *);
@ -92,6 +93,8 @@ namespace Granular_NS {
GranSubModNormalHertzMaterial(class GranularModel *, class LAMMPS *);
void coeffs_to_local() override;
void mix_coeffs(double *, double *) override;
private:
int mixed_coefficients;
};
/* ---------------------------------------------------------------------- */
@ -107,6 +110,7 @@ namespace Granular_NS {
protected:
double k, cohesion;
double F_pulloff, Fne;
int mixed_coefficients;
};
/* ---------------------------------------------------------------------- */
@ -125,6 +129,7 @@ namespace Granular_NS {
protected:
double k, cohesion;
double Emix, F_pulloff, Fne;
int mixed_coefficients;
};
} // namespace Granular_NS

72
src/INTERLAYER/pair_aip_water_2dm.cpp Normal file
View File

@ -0,0 +1,72 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
------------------------------------------------------------------------- */
#include "pair_aip_water_2dm.h"
#include "citeme.h"
#include "error.h"
#include "force.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
static const char cite_aip_water[] =
"aip/water/2dm potential doi/10.1021/acs.jpcc.2c08464\n"
"@Article{Feng2023\n"
" author = {Z. Feng, Y. Yao, J. Liu, B. Wu, Z. Liu, and W. Ouyang},\n"
" title = {Registry-Dependent Potential for Interfaces of Water with Graphene},\n"
" journal = {J. Phys. Chem. C},\n"
" volume = 127,\n"
" pages = {8704-8713}\n"
" year = 2023,\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairAIPWATER2DM::PairAIPWATER2DM(LAMMPS *lmp) : PairILPGrapheneHBN(lmp), PairILPTMD(lmp)
{
variant = AIP_WATER_2DM;
single_enable = 0;
// for TMD, each atom have six neighbors
Nnei = 6;
if (lmp->citeme) lmp->citeme->add(cite_aip_water);
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairAIPWATER2DM::settings(int narg, char **arg)
{
if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command");
if (!utils::strmatch(force->pair_style, "^hybrid/overlay"))
error->all(FLERR, "Pair style aip/water/2dm must be used as sub-style with hybrid/overlay");
cut_global = utils::numeric(FLERR, arg[0], false, lmp);
if (narg == 2) tap_flag = utils::numeric(FLERR, arg[1], false, lmp);
}

39
src/INTERLAYER/pair_aip_water_2dm.h Normal file
View File

@ -0,0 +1,39 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(aip/water/2dm,PairAIPWATER2DM);
// clang-format on
#else
#ifndef LMP_PAIR_AIP_WATER_2DM_H
#define LMP_PAIR_AIP_WATER_2DM_H
#include "pair_ilp_tmd.h"
namespace LAMMPS_NS {
class PairAIPWATER2DM : virtual public PairILPTMD {
public:
PairAIPWATER2DM(class LAMMPS *);
protected:
void settings(int, char **) override;
};
} // namespace LAMMPS_NS
#endif
#endif

2
src/INTERLAYER/pair_coul_shield.cpp
View File

@ -11,7 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wengen Ouyang (Tel Aviv University)
Contributing author: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
This is a Coulomb potential described in

13
src/INTERLAYER/pair_ilp_graphene_hbn.cpp
View File

@ -11,13 +11,11 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wengen Ouyang (Tel Aviv University)
Contributing author: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017)]
The definition of normals are the same as that in
[Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)]
[Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
------------------------------------------------------------------------- */
#include "pair_ilp_graphene_hbn.h"
@ -59,6 +57,7 @@ static const char cite_ilp[] =
static std::map<int, std::string> variant_map = {
{PairILPGrapheneHBN::ILP_GrhBN, "ilp/graphene/hbn"},
{PairILPGrapheneHBN::ILP_TMD, "ilp/tmd"},
{PairILPGrapheneHBN::AIP_WATER_2DM, "aip/water/2dm"},
{PairILPGrapheneHBN::SAIP_METAL, "saip/metal"}};
/* ---------------------------------------------------------------------- */
@ -632,7 +631,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
void PairILPGrapheneHBN::ILP_neigh()
{
int i, j, ii, jj, n, allnum, jnum, itype, jtype;
int i, j, ii, jj, n, inum, jnum, itype, jtype;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
int *ilist, *jlist, *numneigh, **firstneigh;
int *neighptr;
@ -649,7 +648,7 @@ void PairILPGrapheneHBN::ILP_neigh()
(int **) memory->smalloc(maxlocal * sizeof(int *), "ILPGrapheneHBN:firstneigh");
}
allnum = list->inum + list->gnum;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -659,7 +658,7 @@ void PairILPGrapheneHBN::ILP_neigh()
ipage->reset();
for (ii = 0; ii < allnum; ii++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
n = 0;

2
src/INTERLAYER/pair_ilp_graphene_hbn.h
View File

@ -39,7 +39,7 @@ class PairILPGrapheneHBN : public Pair {
static constexpr int NPARAMS_PER_LINE = 13;
enum { ILP_GrhBN, ILP_TMD, SAIP_METAL }; // for telling class variants apart in shared code
enum { ILP_GrhBN, ILP_TMD, SAIP_METAL, AIP_WATER_2DM }; // for telling class variants apart in shared code
protected:
int me;

183
src/INTERLAYER/pair_ilp_tmd.cpp
View File

@ -15,7 +15,7 @@
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Ouyang et al, J. Chem. Theory Comput. 17, 7237 (2021).]
[Ouyang et al., J. Chem. Theory Comput. 17, 7237 (2021).]
------------------------------------------------------------------------- */
#include "pair_ilp_tmd.h"
@ -35,10 +35,6 @@
using namespace LAMMPS_NS;
using namespace InterLayer;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
static const char cite_ilp_tmd[] =
"ilp/tmd potential doi:10.1021/acs.jctc.1c00782\n"
"@Article{Ouyang2021\n"
@ -232,7 +228,7 @@ void PairILPTMD::calc_FRep(int eflag, int /* vflag */)
void PairILPTMD::ILP_neigh()
{
int i, j, l, ii, jj, ll, n, allnum, jnum, itype, jtype, ltype, imol, jmol, count;
int i, j, l, ii, jj, ll, n, inum, jnum, itype, jtype, ltype, imol, jmol, count;
double xtmp, ytmp, ztmp, delx, dely, delz, deljx, deljy, deljz, rsq, rsqlj;
int *ilist, *jlist, *numneigh, **firstneigh;
int *neighsort;
@ -249,7 +245,7 @@ void PairILPTMD::ILP_neigh()
ILP_firstneigh = (int **) memory->smalloc(maxlocal * sizeof(int *), "ILPTMD:firstneigh");
}
allnum = list->inum + list->gnum;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
@ -259,7 +255,7 @@ void PairILPTMD::ILP_neigh()
ipage->reset();
for (ii = 0; ii < allnum; ii++) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
//initialize varibles
@ -288,21 +284,21 @@ void PairILPTMD::ILP_neigh()
delz = ztmp - x[j][2];
rsq = delx * delx + dely * dely + delz * delz;
// check if the atom i is TMD, i.e., Mo/S/W/Se
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
// check if the atom i is a TMD atom, i.e., Mo/S/W/Se
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
strcmp(elements[itype], "Te") == 0) {
if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol && type[i] == type[j]) {
neighptr[n++] = j;
}
} else { // atom i is C, B, N or H.
} else { // atom i can be P, C, B, N or H.
if (rsq != 0 && rsq < cutILPsq[itype][jtype] && imol == jmol) { neighptr[n++] = j; }
}
} // loop over jj
// if atom i is Mo/W/S/Se/Te, then sorting the orders of neighbors
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
strcmp(elements[itype], "Te") == 0) {
// initialize neighsort
for (ll = 0; ll < n; ll++) {
@ -336,9 +332,6 @@ void PairILPTMD::ILP_neigh()
}
} // end of idenfying the first neighbor
} else if (n > Nnei) {
fprintf(screen, "Molecule ID = %d\n", imol);
fprintf(screen, "Atom Type = %d\n", type[i]);
fprintf(screen, "Neinum = %d\n", n);
error->one(FLERR,
"There are too many neighbors for TMD atoms, please check your configuration");
}
@ -367,11 +360,11 @@ void PairILPTMD::ILP_neigh()
ll++;
}
} // end of sorting the order of neighbors
} else { // for B/N/C/H atoms
} else { // for P/B/N/C/H atoms
if (n > 3)
error->one(
FLERR,
"There are too many neighbors for B/N/C/H atoms, please check your configuration");
"There are too many neighbors for P/B/N/C/H atoms, please check your configuration");
for (ll = 0; ll < n; ll++) { neighsort[ll] = neighptr[ll]; }
}
@ -390,12 +383,14 @@ void PairILPTMD::calc_normal()
{
int i, j, ii, jj, inum, jnum;
int cont, id, ip, m, k, itype;
double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
int *ilist, *jlist;
int iH1,iH2,jH1,jH2;
double Nave[3], dni[3], dpvdri[3][3];
double nn, xtp, ytp, ztp, delx, dely, delz, nn2;
double **x = atom->x;
int *type = atom->type;
tagint *tag = atom->tag;
memory->destroy(dnn);
memory->destroy(vect);
@ -479,9 +474,60 @@ void PairILPTMD::calc_normal()
for (m = 0; m < Nnei; m++) { dnormal[i][id][m][ip] = 0.0; }
}
}
// for hydrogen in water molecule
if (strcmp(elements[itype], "Hw") == 0) {
if(cont == 0) {
jH1 = atom->map(tag[i] - 1);
jH2 = atom->map(tag[i] - 2);
iH1 = map[type[jH1]];
iH2 = map[type[jH2]];
if (strcmp(elements[iH1], "Ow") == 0 ) {
vect[0][0] = x[jH1][0] - xtp;
vect[0][1] = x[jH1][1] - ytp;
vect[0][2] = x[jH1][2] - ztp;
} else if (strcmp(elements[iH2], "Ow") == 0 ) {
vect[0][0] = x[jH2][0] - xtp;
vect[0][1] = x[jH2][1] - ytp;
vect[0][2] = x[jH2][2] - ztp;
} else {
error->one(FLERR, "The order of atoms in water molecule should be O H H !");
}
}
Nave[0] = vect[0][0];
Nave[1] = vect[0][1];
Nave[2] = vect[0][2];
// the magnitude of the normal vector
nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
nn = sqrt(nn2);
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = Nave[0] / nn;
normal[i][1] = Nave[1] / nn;
normal[i][2] = Nave[2] / nn;
// Calculte dNave/dri, defined as dpvdri
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
if (ip == id) { dpvdri[id][ip] = -1.0;}
else {dpvdri[id][ip] = 0.0;}
}
}
// derivatives of nn, dnn:3x1 vector
dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
// derivatives of unit vector ni respect to ri, the result is 3x3 matrix
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
dnormal[i][id][0][ip] = -dnormdri[i][id][ip];
}
}
}
}
//############################ For the edge atoms of TMD ################################
else if (cont < Nnei) {
else if (cont > 1 && cont < Nnei) {
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0) {
// derivatives of Ni[l] respect to the cont neighbors
@ -557,8 +603,7 @@ void PairILPTMD::calc_normal()
for (m = 0; m < cont; m++) {
for (id = 0; id < 3; id++) {
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
Nave[2] * dNave[2][m][id]) /
nn;
Nave[2] * dNave[2][m][id]) / nn;
}
}
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
@ -589,12 +634,99 @@ void PairILPTMD::calc_normal()
}
}
} // for TMD
//############################ For Oxygen in the water molecule #######################
else if (strcmp(elements[itype], "Ow") == 0) {
if(cont == 0) {
jH1 = atom->map(tag[i] + 1);
jH2 = atom->map(tag[i] + 2);
iH1 = map[type[jH1]];
iH2 = map[type[jH2]];
if (strcmp(elements[iH1], "Hw") == 0 && strcmp(elements[iH2], "Hw") == 0) {
vect[0][0] = x[jH1][0] - xtp;
vect[0][1] = x[jH1][1] - ytp;
vect[0][2] = x[jH1][2] - ztp;
vect[1][0] = x[jH2][0] - xtp;
vect[1][1] = x[jH2][1] - ytp;
vect[1][2] = x[jH2][2] - ztp;
cont = 2;
} else {
error->one(FLERR, "The order of atoms in water molecule should be O H H !");
}
}
if (cont == 2) {
Nave[0] = (vect[0][0] + vect[1][0])/cont;
Nave[1] = (vect[0][1] + vect[1][1])/cont;
Nave[2] = (vect[0][2] + vect[1][2])/cont;
// the magnitude of the normal vector
nn2 = Nave[0] * Nave[0] + Nave[1] * Nave[1] + Nave[2] * Nave[2];
nn = sqrt(nn2);
if (nn == 0) error->one(FLERR, "The magnitude of the normal vector is zero");
// the unit normal vector
normal[i][0] = Nave[0] / nn;
normal[i][1] = Nave[1] / nn;
normal[i][2] = Nave[2] / nn;
// derivatives of non-normalized normal vector, dNave:3xcontx3 array
// dNave[id][m][ip]: the derivatve of the id component of Nave
// respect to the ip component of atom m
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
for (m = 0; m < cont; m++) {
if (ip == id) { dNave[id][m][ip] = 0.5;}
else {dNave[id][m][ip] = 0.0;}
}
}
}
// derivatives of nn, dnn:contx3 vector
// dnn[m][id]: the derivative of nn respect to r[m][id], m=0,...Nnei-1; id=0,1,2
// r[m][id]: the id's component of atom m
for (m = 0; m < cont; m++) {
for (id = 0; id < 3; id++) {
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
Nave[2] * dNave[2][m][id]) / nn;
}
}
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.
// for atom m, which is a neighbor atom of atom i, m = 0,...,Nnei-1
for (m = 0; m < cont; m++) {
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormal[i][id][m][ip] = dNave[id][m][ip] / nn - Nave[id] * dnn[m][ip] / nn2;
}
}
}
// Calculte dNave/dri, defined as dpvdri
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dpvdri[id][ip] = 0.0;
for (k = 0; k < cont; k++) { dpvdri[id][ip] -= dNave[id][k][ip]; }
}
}
// derivatives of nn, dnn:3x1 vector
dni[0] = (Nave[0] * dpvdri[0][0] + Nave[1] * dpvdri[1][0] + Nave[2] * dpvdri[2][0]) / nn;
dni[1] = (Nave[0] * dpvdri[0][1] + Nave[1] * dpvdri[1][1] + Nave[2] * dpvdri[2][1]) / nn;
dni[2] = (Nave[0] * dpvdri[0][2] + Nave[1] * dpvdri[1][2] + Nave[2] * dpvdri[2][2]) / nn;
// derivatives of unit vector ni respect to ri, the result is 3x3 matrix
for (id = 0; id < 3; id++) {
for (ip = 0; ip < 3; ip++) {
dnormdri[i][id][ip] = dpvdri[id][ip] / nn - Nave[id] * dni[ip] / nn2;
}
}
}
else if (cont >= 3) {
error->one(FLERR,
"There are too many neighbors for calculating normals of water molecules");
}
}
//############################ For the edge & bulk atoms of GrhBN ################################
else {
if (cont == 2) {
for (ip = 0; ip < 3; ip++) {
pvet[0][ip] = vect[0][modulo(ip + 1, 3)] * vect[1][modulo(ip + 2, 3)] -
vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
vect[0][modulo(ip + 2, 3)] * vect[1][modulo(ip + 1, 3)];
}
// dpvet1[k][l][ip]: the derivatve of the k (=0,...cont-1)th Nik respect to the ip component of atom l
// derivatives respect to atom l
@ -657,8 +789,7 @@ void PairILPTMD::calc_normal()
for (m = 0; m < cont; m++) {
for (id = 0; id < 3; id++) {
dnn[m][id] = (Nave[0] * dNave[0][m][id] + Nave[1] * dNave[1][m][id] +
Nave[2] * dNave[2][m][id]) /
nn;
Nave[2] * dNave[2][m][id]) / nn;
}
}
// dnormal[i][id][m][ip]: the derivative of normal[i][id] respect to r[m][ip], id,ip=0,1,2.

2
src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
View File

@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Wengen Ouyang (Tel Aviv University)
Contributing author: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
based on previous versions by Jaap Kroes

2
src/INTERLAYER/pair_saip_metal.cpp
View File

@ -15,7 +15,7 @@
e-mail: w.g.ouyang at gmail dot com
This is a full version of the potential described in
[Ouyang et al, J. Chem. Theory Comput. 17, 7215-7223 (2021)]
[Ouyang et al., J. Chem. Theory Comput. 17, 7215-7223 (2021)]
------------------------------------------------------------------------- */
#include "pair_saip_metal.h"

4
src/KOKKOS/comm_kokkos.cpp
View File

@ -980,9 +980,9 @@ void CommKokkos::borders()
} else {
atomKK->sync(Host,ALL_MASK);
k_sendlist.sync<LMPHostType>();
CommBrick::borders();
k_sendlist.modify<LMPHostType>();
atomKK->modified(Host,ALL_MASK);
atomKK->modified(Host,ALL_MASK); // needed here for atom map
CommBrick::borders();
}
if (comm->nprocs == 1 && !ghost_velocity && !forward_comm_classic)

2
src/MANYBODY/pair_tersoff.cpp
View File

@ -14,7 +14,7 @@
/* ----------------------------------------------------------------------
Contributing author: Aidan Thompson (SNL) - original Tersoff implementation
Wengen Ouyang (TAU) - Shift addition
Wengen Ouyang (WHU) - Shift addition
------------------------------------------------------------------------- */
#include "pair_tersoff.h"

71
src/NETCDF/dump_netcdf.cpp
View File

@ -195,6 +195,7 @@ DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
type_nc_real = NC_FLOAT;
thermo = false;
thermo_warn = true;
thermovar = nullptr;
framei = 0;
@ -223,7 +224,7 @@ void DumpNetCDF::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -321,8 +322,11 @@ void DumpNetCDF::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
NCERRX( nc_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
NCERRX( nc_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
}
}
@ -433,21 +437,17 @@ void DumpNetCDF::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
#else
NCERRX( nc_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims,
&thermovar[i]), th->keyword[i].c_str() );
#endif
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( nc_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
}
@ -606,19 +606,30 @@ void DumpNetCDF::write()
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
th->call_vfunc(i);
// will output current thermo data only on timesteps where it was computed.
// warn (once) about using cached copy from old timestep.
if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
thermo_warn = false;
if (comm->me == 0) {
error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
" Dump netcdf always stores thermo data from last thermo output",
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start,
&th->dvalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i].c_str() );
if (fields[i].type == multitype::DOUBLE) {
NCERRX( nc_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( nc_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( nc_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}
}

1
src/NETCDF/dump_netcdf.h
View File

@ -65,6 +65,7 @@ class DumpNetCDF : public DumpCustom {
int type_nc_real; // netcdf type to use for real variables: float or double
bool thermo; // write thermo output to netcdf file
bool thermo_warn; // warn (once) that thermo output is on incompatible step
bigint n_buffer; // size of buffer
bigint *int_buffer; // buffer for passing data to netcdf

69
src/NETCDF/dump_netcdf_mpiio.cpp
View File

@ -192,6 +192,7 @@ DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
type_nc_real = NC_FLOAT;
thermo = false;
thermo_warn = true;
thermovar = nullptr;
framei = 0;
@ -220,7 +221,7 @@ void DumpNetCDFMPIIO::openfile()
if (thermo && !singlefile_opened) {
delete[] thermovar;
thermovar = new int[output->thermo->nfield];
thermovar = new int[*output->thermo->get_nfield()];
}
// now the computes and fixes have been initialized, so we can query
@ -319,8 +320,11 @@ void DumpNetCDFMPIIO::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
NCERRX( ncmpi_inq_varid(ncid, th->keyword[i].c_str(), &thermovar[i]), th->keyword[i].c_str() );
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
NCERRX( ncmpi_inq_varid(ncid, keywords[i].c_str(), &thermovar[i]), keywords[i].c_str() );
}
}
@ -423,17 +427,17 @@ void DumpNetCDFMPIIO::openfile()
// perframe variables
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
#if defined(LAMMPS_SMALLBIG) || defined(LAMMPS_BIGBIG)
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
#else
NCERRX( ncmpi_def_var(ncid, th->keyword[i].c_str(), NC_LONG, 1, dims, &thermovar[i]), th->keyword[i].c_str() );
#endif
const auto &fields = th->get_fields();
const auto &keywords = th->get_keywords();
const int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (fields[i].type == multitype::DOUBLE) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), type_nc_real, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT, 1, dims, &thermovar[i]), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( ncmpi_def_var(ncid, keywords[i].c_str(), NC_INT64, 1, dims, &thermovar[i]), keywords[i].c_str() );
}
}
}
@ -595,25 +599,36 @@ void DumpNetCDFMPIIO::write()
if (thermo) {
Thermo *th = output->thermo;
for (int i = 0; i < th->nfield; i++) {
th->call_vfunc(i);
// will output current thermo data only on timesteps where it was computed.
// warn (once) about using cached copy from old timestep.
if (thermo_warn && (update->ntimestep != *th->get_timestep())) {
thermo_warn = false;
if (comm->me == 0) {
error->warning(FLERR, "Dump {} output on incompatible timestep with thermo output: {} vs {} \n"
" Dump netcdf/mpiio always stores thermo data from last thermo output",
id, *th->get_timestep(), update->ntimestep);
}
}
const auto &keywords = th->get_keywords();
const auto &fields = th->get_fields();
int nfield = *th->get_nfield();
for (int i = 0; i < nfield; i++) {
if (filewriter) {
if (th->vtype[i] == Thermo::FLOAT) {
NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start,
&th->dvalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::INT) {
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &th->ivalue),
th->keyword[i].c_str() );
} else if (th->vtype[i] == Thermo::BIGINT) {
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &th->bivalue),
th->keyword[i].c_str() );
if (fields[i].type == multitype::DOUBLE) {
NCERRX( ncmpi_put_var1_double(ncid, thermovar[i], start, &fields[i].data.d), keywords[i].c_str() );
} else if (fields[i].type == multitype::INT) {
NCERRX( ncmpi_put_var1_int(ncid, thermovar[i], start, &fields[i].data.i), keywords[i].c_str() );
} else if (fields[i].type == multitype::BIGINT) {
NCERRX( ncmpi_put_var1_bigint(ncid, thermovar[i], start, &fields[i].data.b), keywords[i].c_str() );
}
}
}
}
// write timestep header
// write timestep header
write_time_and_cell();

1
src/NETCDF/dump_netcdf_mpiio.h
View File

@ -62,6 +62,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
int type_nc_real; // netcdf type to use for real variables: float or double
bool thermo; // write thermo output to netcdf file
bool thermo_warn; // warn (once) that thermo output is on incompatible step
bigint n_buffer; // size of buffer
bigint *int_buffer; // buffer for passing data to netcdf

63
src/OPT/pair_aip_water_2dm_opt.cpp Normal file
View File

@ -0,0 +1,63 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This is an optimized version of aip/water/2dm based on the contribution of:
author: Wengen Ouyang (Wuhan University)
e-mail: w.g.ouyang at gmail dot com
Optimizations are done by:
author1: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
e-mail: sunrise_duan at 126 dot com
author2: Ping Gao (National Supercomputing Center in Wuxi, China)
e-mail: qdgaoping at gmail dot com
Optimizations are described in:
Gao, Ping and Duan, Xiaohui, et al.:
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
DOI: 10.1145/3458817.3476137
Potential is described by:
[Feng and Ouyang et al, J. Phys. Chem. C 127, 8704-8713 (2023).]
*/
#include "pair_aip_water_2dm_opt.h"
#include "atom.h"
#include "memory.h"
#include <cstring>
using namespace LAMMPS_NS;
PairAIPWATER2DMOpt::PairAIPWATER2DMOpt(LAMMPS *lmp) :
PairILPGrapheneHBN(lmp), PairILPTMD(lmp), PairAIPWATER2DM(lmp), PairILPGrapheneHBNOpt(lmp)
{
}
void PairAIPWATER2DMOpt::coeff(int narg, char **args)
{
PairILPTMD::coeff(narg, args);
memory->create(special_type, atom->ntypes + 1, "PairAIPWATER2DMOpt:check_sublayer");
for (int i = 1; i <= atom->ntypes; i++) {
int itype = map[i];
if (strcmp(elements[itype], "Mo") == 0 || strcmp(elements[itype], "W") == 0 ||
strcmp(elements[itype], "S") == 0 || strcmp(elements[itype], "Se") == 0 ||
strcmp(elements[itype], "Te") == 0) {
special_type[i] = TMD_METAL;
} else if (strcmp(elements[itype], "Hw") == 0 || strcmp(elements[itype], "Ow") == 0) {
special_type[i] = WATER;
} else {
special_type[i] = NOT_SPECIAL;
}
}
}

38
src/OPT/pair_aip_water_2dm_opt.h Normal file
View File

@ -0,0 +1,38 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
// clang-format off
PairStyle(aip/water/2dm/opt,PairAIPWATER2DMOpt);
// clang-format on
#else
#ifndef LMP_PAIR_AIP_WATER_2DM_OPT_H
#define LMP_PAIR_AIP_WATER_2DM_OPT_H
#include "pair_ilp_graphene_hbn_opt.h"
#include "pair_aip_water_2dm.h"
namespace LAMMPS_NS {
class PairAIPWATER2DMOpt : public PairAIPWATER2DM, public PairILPGrapheneHBNOpt {
public:
PairAIPWATER2DMOpt(class LAMMPS *);
void coeff(int narg, char **args) override;
protected:
};
} // namespace LAMMPS_NS
#endif
#endif

113
src/OPT/pair_ilp_graphene_hbn_opt.cpp
View File

@ -11,12 +11,24 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Optimization author1: Ping Gao (National Supercomputing Center in Wuxi, China)
This is an optimized version of ilp/graphene/hbn based on the contirubtion of:
author: Wengen Ouyang (Wuhan University, China)
e-mail: w.g.ouyang at gmail dot com
Optimizations are done by:
author1: Ping Gao (National Supercomputing Center in Wuxi, China) implements the base ILP potential.
e-mail: qdgaoping at gmail dot com
Optimization author2: Xiaohui Duan (National Supercomputing Center in Wuxi, China)
author2: Xiaohui Duan (Shandong University, China) adjusts the framework to adopt SAIP, TMD, WATER2DM, etc.
e-mail: sunrise_duan at 126 dot com
Provides some bugfixes and performance optimizations in this potential.
Optimizations are described in:
Gao, Ping and Duan, Xiaohui, et al:
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
DOI: 10.1145/3458817.3476137
Potential is described by:
[Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020)]
*/
#include "pair_ilp_graphene_hbn_opt.h"
@ -28,19 +40,21 @@
#include "interlayer_taper.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "neighbor.h"
#include "pointers.h"
#include <cmath>
#include <utility>
#include <cstring>
using namespace LAMMPS_NS;
using namespace InterLayer;
static const char cite_ilp_cur[] =
"ilp/graphene/hbn/opt potential: doi:10.1145/3458817.3476137\n"
"ilp/graphene/hbn/opt potential doi:10.1145/3458817.3476137\n"
"@inproceedings{gao2021lmff\n"
" author = {Gao, Ping and Duan, Xiaohui and others},\n"
" title = {{LMFF}: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
" author = {Gao, Ping and Duan, Xiaohui and Others},\n"
" title = {LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous "
"Many-Core Processors},\n"
" year = {2021},\n"
" isbn = {9781450384421},\n"
@ -50,14 +64,12 @@ static const char cite_ilp_cur[] =
" doi = {10.1145/3458817.3476137},\n"
" booktitle = {Proceedings of the International Conference for High Performance Computing, "
"Networking, Storage and Analysis},\n"
" pages = {42},\n"
" articleno = {42},\n"
" numpages = {14},\n"
" location = {St.~Louis, Missouri},\n"
" location = {St. Louis, Missouri},\n"
" series = {SC'21},\n"
"}\n\n";
static bool check_vdw(tagint itag, tagint jtag, double *xi, double *xj);
/* ---------------------------------------------------------------------- */
PairILPGrapheneHBNOpt::PairILPGrapheneHBNOpt(LAMMPS *lmp) :
@ -168,6 +180,36 @@ void PairILPGrapheneHBNOpt::compute(int eflag, int vflag)
}
}
}
} else if (variant == AIP_WATER_2DM) {
if (eflag_global || eflag_atom) {
if (vflag_either) {
if (tap_flag) {
eval<6, 1, 1, 1, AIP_WATER_2DM>();
} else {
eval<6, 1, 1, 0, AIP_WATER_2DM>();
}
} else {
if (tap_flag) {
eval<6, 1, 0, 1, AIP_WATER_2DM>();
} else {
eval<6, 1, 0, 0, AIP_WATER_2DM>();
}
}
} else {
if (vflag_either) {
if (tap_flag) {
eval<6, 0, 1, 1, AIP_WATER_2DM>();
} else {
eval<6, 0, 1, 0, AIP_WATER_2DM>();
}
} else {
if (tap_flag) {
eval<6, 0, 0, 1, AIP_WATER_2DM>();
} else {
eval<6, 0, 0, 0, AIP_WATER_2DM>();
}
}
}
} else if (variant == SAIP_METAL) {
if (eflag_global || eflag_atom) {
if (vflag_either) {
@ -255,7 +297,7 @@ void PairILPGrapheneHBNOpt::eval()
rsq = delx * delx + dely * dely + delz * delz;
if (rsq != 0 && rsq < cutILPsq[itype_map][jtype]) {
if (VARIANT == ILP_TMD && special_type[itype] && itype != type[j]) continue;
if ((VARIANT == ILP_TMD || VARIANT == AIP_WATER_2DM) && special_type[itype] == TMD_METAL && itype != type[j]) continue;
if (ILP_nneigh >= MAX_NNEIGH) {
error->one(FLERR, "There are too many neighbors for calculating normals");
}
@ -269,7 +311,8 @@ void PairILPGrapheneHBNOpt::eval()
dproddni[2] = 0.0;
double norm[3], dnormdxi[3][3], dnormdxk[MAX_NNEIGH][3][3];
calc_normal<MAX_NNEIGH>(i, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
calc_atom_normal<MAX_NNEIGH>(i, itype, ILP_neigh, ILP_nneigh, norm, dnormdxi, dnormdxk);
for (jj = 0; jj < jnum_inter; jj++) {
j = jlist_inter[jj];
@ -298,7 +341,7 @@ void PairILPGrapheneHBNOpt::eval()
Tap = 1.0;
dTap = 0.0;
}
if (VARIANT != SAIP_METAL || !special_type[itype]) {
if (VARIANT != SAIP_METAL || special_type[itype] != SAIP_BNCH) {
// Calculate the transverse distance
prodnorm1 = norm[0] * delx + norm[1] * dely + norm[2] * delz;
rhosq1 = rsq - prodnorm1 * prodnorm1; // rho_ij
@ -310,7 +353,7 @@ void PairILPGrapheneHBNOpt::eval()
frho1 = exp1 * p.C;
Erep = 0.5 * p.epsilon + frho1;
if (VARIANT == SAIP_METAL && special_type[jtype]) { Erep += 0.5 * p.epsilon + p.C; }
if (VARIANT == SAIP_METAL && special_type[jtype] == SAIP_BNCH) { Erep += 0.5 * p.epsilon + p.C; }
Vilp = exp0 * Erep;
// derivatives
@ -428,6 +471,18 @@ inline void deriv_normal(double dndr[3][3], double *del, double *n, double rnnor
dndr[1][2] = (del[1] * n[0] * n[1] + del[0] * (n[0] * n[0] + n[2] * n[2])) * rnnorm;
dndr[2][2] = (del[1] * n[0] * n[2] - del[0] * n[1] * n[2]) * rnnorm;
}
inline void deriv_hat(double dnhatdn[3][3], double *n, double rnnorm, double factor){
double cfactor = rnnorm * factor;
dnhatdn[0][0] = (n[1]*n[1]+n[2]*n[2])*cfactor;
dnhatdn[1][0] = -n[1]*n[0]*cfactor;
dnhatdn[2][0] = -n[2]*n[0]*cfactor;
dnhatdn[0][1] = -n[0]*n[1]*cfactor;
dnhatdn[1][1] = (n[0]*n[0]+n[2]*n[2])*cfactor;
dnhatdn[2][1] = -n[2]*n[1]*cfactor;
dnhatdn[0][2] = -n[0]*n[2]*cfactor;
dnhatdn[1][2] = -n[1]*n[2]*cfactor;
dnhatdn[2][2] = (n[0]*n[0]+n[1]*n[1])*cfactor;
}
inline double normalize_factor(double *n)
{
double nnorm = sqrt(n[0] * n[0] + n[1] * n[1] + n[2] * n[2]);
@ -441,7 +496,7 @@ inline double normalize_factor(double *n)
Yet another normal calculation method for simpiler code.
*/
template <int MAX_NNEIGH>
void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, double *n,
void PairILPGrapheneHBNOpt::calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *n,
double (*dnormdri)[3], double (*dnormdrk)[3][3])
{
double **x = atom->x;
@ -475,6 +530,32 @@ void PairILPGrapheneHBNOpt::calc_normal(int i, int *ILP_neigh, int nneigh, doubl
vet[jj][2] = x[j][2] - x[i][2];
}
//specialize for AIP_WATER_2DM for hydrogen has special normal vector rule
if (variant == AIP_WATER_2DM && special_type[itype] == WATER) {
if (nneigh == 1){
n[0] = vet[0][0];
n[1] = vet[0][1];
n[2] = vet[0][2];
double rnnorm = normalize_factor(n);
deriv_hat(dnormdri, n, rnnorm, -1.0);
deriv_hat(dnormdrk[0], n, rnnorm, 1.0);
} else if (nneigh == 2){
n[0] = (vet[0][0] + vet[1][0])*0.5;
n[1] = (vet[0][1] + vet[1][1])*0.5;
n[2] = (vet[0][2] + vet[1][2])*0.5;
double rnnorm = normalize_factor(n);
deriv_hat(dnormdri, n, rnnorm, -1.0);
deriv_hat(dnormdrk[0], n, rnnorm, 0.5);
deriv_hat(dnormdrk[1], n, rnnorm, 0.5);
} else {
error->one(FLERR, "malformed water");
}
return;
}
if (nneigh <= 1) {
n[0] = 0.0;
n[1] = 0.0;

10
src/OPT/pair_ilp_graphene_hbn_opt.h
View File

@ -35,7 +35,7 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
protected:
void update_internal_list();
template <int MAX_NNEIGH>
void calc_normal(int i, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
void calc_atom_normal(int i, int itype, int *ILP_neigh, int nneigh, double *normal, double (*dnormdri)[3],
double (*dnormdrk)[3][3]);
template <int MAX_NNEIGH, int EFLAG, int VFLAG_EITHER, int TAP_FLAG, int VARIANT = ILP_GrhBN>
void eval();
@ -44,6 +44,14 @@ class PairILPGrapheneHBNOpt : virtual public PairILPGrapheneHBN {
int *special_type;
int *num_intra, *num_inter, *num_vdw;
int inum_max, jnum_max;
enum special_type_const {
NOT_SPECIAL = 0,
TMD_METAL,
SAIP_BNCH,
WATER,
};
};
} // namespace LAMMPS_NS

2
src/OPT/pair_ilp_tmd_opt.cpp
View File

@ -23,7 +23,7 @@
e-mail: qdgaoping at gmail dot com
Optimizations are described in:
Gao, Ping and Duan, Xiaohui, et al:
Gao, Ping and Duan, Xiaohui, et al.:
LMFF: Efficient and Scalable Layered Materials Force Field on Heterogeneous Many-Core Processors
DOI: 10.1145/3458817.3476137

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