Merge pull request #2511 from samueljmcameron/fix_bd_sphere
Add USER-BROWNIAN package
This commit is contained in:
Axel Kohlmeyer
@ -124,7 +124,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
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USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
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USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
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USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
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USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
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USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
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USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
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USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
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set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
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set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
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@ -5,9 +5,9 @@
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set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
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set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
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GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
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GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
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PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
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PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
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USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
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USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
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USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
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USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
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USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
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USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
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USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
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USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
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foreach(PKG ${ALL_PACKAGES})
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foreach(PKG ${ALL_PACKAGES})
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@ -39,6 +39,9 @@ OPT.
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* :doc:`ave/time <fix_ave_time>`
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* :doc:`ave/time <fix_ave_time>`
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* :doc:`aveforce <fix_aveforce>`
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* :doc:`aveforce <fix_aveforce>`
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* :doc:`balance <fix_balance>`
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* :doc:`balance <fix_balance>`
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* :doc:`brownian <fix_brownian>`
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* :doc:`brownian/asphere <fix_brownian>`
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* :doc:`brownian/sphere <fix_brownian>`
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* :doc:`bocs <fix_bocs>`
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* :doc:`bocs <fix_bocs>`
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* :doc:`bond/break <fix_bond_break>`
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* :doc:`bond/break <fix_bond_break>`
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* :doc:`bond/create <fix_bond_create>`
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* :doc:`bond/create <fix_bond_create>`
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@ -69,6 +69,7 @@ page gives those details.
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* :ref:`USER-ATC <PKG-USER-ATC>`
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* :ref:`USER-ATC <PKG-USER-ATC>`
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* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
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* :ref:`USER-AWPMD <PKG-USER-AWPMD>`
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* :ref:`USER-BOCS <PKG-USER-BOCS>`
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* :ref:`USER-BOCS <PKG-USER-BOCS>`
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* :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
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* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
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* :ref:`USER-CGDNA <PKG-USER-CGDNA>`
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* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
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* :ref:`USER-CGSDK <PKG-USER-CGSDK>`
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* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
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* :ref:`USER-COLVARS <PKG-USER-COLVARS>`
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@ -1266,6 +1267,26 @@ Example inputs are in the examples/USER/bocs folder.
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----------
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----------
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.. _PKG-USER-BROWNIAN:
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USER-BROWNIAN package
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---------------------
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**Contents:**
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This package provides :doc:`fix brownian, fix brownian/sphere, and
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fix brownian/asphere <fix_brownian>` as well as
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:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
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Dynamics time integration of point, spherical and aspherical particles
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and also support self-propelled particles.
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**Authors:** Sam Cameron (University of Bristol),
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Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
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Example inputs are in the examples/USER/brownian folder.
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----------
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.. _PKG-USER-CGDNA:
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.. _PKG-USER-CGDNA:
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USER-CGDNA package
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USER-CGDNA package
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@ -39,6 +39,8 @@ package:
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
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| :ref:`USER-BOCS <PKG-USER-BOCS>` | BOCS bottom up coarse graining | :doc:`fix bocs <fix_bocs>` | USER/bocs | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>` | Brownian dynamics and self-propelled particles | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>` | USER/brownian | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
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| :ref:`USER-CGDNA <PKG-USER-CGDNA>` | coarse-grained DNA force fields | src/USER-CGDNA/README | USER/cgdna | no |
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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+------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
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| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
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| :ref:`USER-CGSDK <PKG-USER-CGSDK>` | SDK coarse-graining model | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cgsdk | no |
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@ -182,6 +182,9 @@ accelerated styles exist.
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* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
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* :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
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* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
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* :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
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* :doc:`balance <fix_balance>` - perform dynamic load-balancing
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* :doc:`balance <fix_balance>` - perform dynamic load-balancing
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* :doc:`brownian <fix_brownian>` - overdamped translational brownian motion
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* :doc:`brownian/asphere <fix_brownian>` - overdamped translational and rotational brownian motion for ellipsoids
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* :doc:`brownian/sphere <fix_brownian>` - overdamped translational and rotational brownian motion for spheres
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* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
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* :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
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* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
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* :doc:`bond/break <fix_bond_break>` - break bonds on the fly
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* :doc:`bond/create <fix_bond_create>` - create bonds on the fly
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* :doc:`bond/create <fix_bond_create>` - create bonds on the fly
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216
doc/src/fix_brownian.rst
Normal file
216
doc/src/fix_brownian.rst
Normal file
@ -0,0 +1,216 @@
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.. index:: fix brownian
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.. index:: fix brownian/sphere
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.. index:: fix brownian/asphere
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fix brownian command
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===========================
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fix brownian/sphere command
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===========================
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fix brownian/sphere command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID style_name temp seed keyword args
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
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* temp = temperature
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* seed = random number generator seed
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* one or more keyword/value pairs may be appended
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* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
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.. parsed-literal::
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*rng* value = *uniform* or *gaussian* or *none*
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*uniform* = use uniform random number generator
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*gaussian* = use gaussian random number generator
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*none* = turn off noise
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*dipole* value = *mux* and *muy* and *muz* for *brownian/asphere*
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*mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body
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*gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere*
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*gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor
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*gamma_r* values = *gr* for *brownian/sphere*
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*gr* = magnitude of the (isotropic) rotational friction tensor
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*gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere*
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*gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor
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*gamma_t* values = *gt* for *brownian* and *brownian/sphere*
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*gt* = magnitude of the (isotropic) translational friction tensor
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all brownian 1.0 12908410 gamma_t 1.0
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fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
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fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
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fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3 rng none
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fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
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fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
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Description
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"""""""""""
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Perform Brownian Dynamics time integration to update position, velocity,
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dipole orientation (for spheres) and quaternion orientation (for
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ellipsoids, with optional dipole update as well) of all particles in the
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fix group in each timestep. Brownian Dynamics uses Newton's laws of
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motion in the limit that inertial forces are negligible compared to
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viscous forces. The stochastic equation of motion for the center of mass
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positions is
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.. math::
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d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
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in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
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only depends on orientation and so the noise is still additive).
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The rotational motion for the spherical and ellipsoidal particles is not
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as simple an expression, but is chosen to replicate the Boltzmann
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distribution for the case of conservative torques (see :ref:`(Ilie)
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<Ilie1>` or :ref:`(Delong) <Delong1>`).
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For the style *brownian*, only the positions of the particles are
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updated. This is therefore suitable for point particle simulations.
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For the style *brownian/sphere*, the positions of the particles are
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updated, and a dipole slaved to the spherical orientation is also
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updated. This style therefore requires the hybrid atom style
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:doc:`atom_style dipole <atom_style>` and :doc:`atom_style sphere
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<atom_style>`.
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For the style *brownian/asphere*, the center of mass positions and the
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quaternions of ellipsoidal particles are updated. This fix style is
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suitable for equations of motion where the rotational and translational
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friction tensors can be diagonalized in a certain (body) reference frame.
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---------
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.. note::
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This integrator does not by default assume a relationship between the
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rotational and translational friction tensors, though such a relationship
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should exist in the case of no-slip boundary conditions between the particles and
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the surrounding (implicit) solvent. E.g. in the case of spherical particles,
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the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly
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accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
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:math:`\sigma` is the spherical diameter). A similar (though more complex)
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relationship holds for ellipsoids and rod-like particles.
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---------
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.. note::
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Temperature computation using the :doc:`compute temp <compute_temp>`
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will not correctly compute temperature of these overdamped dynamics
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since we are explicitly neglecting inertial effects.
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Furthermore, this time integrator does not add the stochastic terms or
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viscous terms to the force and/or torques. Rather, they are just added
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in to the equations of motion to update the degrees of freedom.
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---------
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If the *rng* keyword is used with the *uniform* value, then the noise
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is generated from a uniform distribution (see
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:ref:`(Dunweg) <Dunweg7>` for why this works). This is the same method
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of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
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If the *rng* keyword is used with the *gaussian* value, then the noise
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is generated from a gaussian distribution. Typically this added
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complexity is unnecessary, and one should be fine using the *uniform*
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value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
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If the *rng* keyword is used with the *none* value, then the noise
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terms are set to zero.
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The *gamma_t* keyword sets the (isotropic) translational viscous damping.
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Required for (and only compatible with) *brownian* and *brownian/sphere*.
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The units of *gamma_t* are mass/time.
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The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
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Required for (and only compatible with) *brownian/sphere*.
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The units of *gamma_r* are mass*length**2/time.
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The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
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the rotational and viscous damping tensors (having the same units as
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their isotropic counterparts). Required for (and only compatible with)
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*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen*
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must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen*
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must be inf (only diffusion in xy plane).
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If the *dipole* keyword is used, then the dipole moments of the particles
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are updated as described above. Only compatible with *brownian/asphere*
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(as *brownian/sphere* updates dipoles automatically).
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----------
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.. note::
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For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
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*gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
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*brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega)
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as defined by the :doc:`atom_style sphere <atom_style>` command.
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The style *brownian/asphere* fix requires that atoms store torque and quaternions
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as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
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If the *dipole* keyword is used, they must also store a dipole moment
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as defined by the :doc:`atom_style dipole <atom_style>` command.
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This fix is part of the USER-BROWNIAN package. It is only enabled if
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LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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Related commands
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""""""""""""""""
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:doc:`fix propel/self <fix_propel_self>`,
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:doc:`fix langevin <fix_langevin>`, :doc:`fix nve/sphere <fix_nve_sphere>`,
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Default
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"""""""
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The default for *rng* is *uniform*. The default for the rotational and translational friction
|
||||||
|
tensors are the identity tensor.
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
.. _Ilie1:
|
||||||
|
|
||||||
|
**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
|
||||||
|
|
||||||
|
.. _Delong1:
|
||||||
|
|
||||||
|
**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015)
|
||||||
|
|
||||||
|
.. _Dunweg7:
|
||||||
|
|
||||||
|
**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
|
||||||
@ -8,52 +8,121 @@ Syntax
|
|||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
fix ID group-ID propel/self mode magnitude keyword values ...
|
fix ID group-ID propel/self mode magnitude keyword values
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`fix <fix>` command
|
* ID, group-ID are documented in :doc:`fix <fix>` command
|
||||||
* propel/self = style name of this fix command
|
* propel/self = style name of this fix command
|
||||||
* mode = velocity or quat
|
* mode = *dipole* or *velocity* or *quat*
|
||||||
* magnitude = magnitude of the active force
|
* magnitude = magnitude of self-propulsion force
|
||||||
* one or more keyword/value pairs may be appended to args
|
* zero or one keyword/value pairs may be appended
|
||||||
* keyword = *types*
|
* keyword = *qvector*
|
||||||
|
|
||||||
|
.. parsed-literal::
|
||||||
|
|
||||||
|
*qvector* value = direction of force in ellipsoid frame
|
||||||
|
*sx*, *sy*, *sz* = components of *qvector*
|
||||||
|
|
||||||
*types* values = one or more atom types
|
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
.. code-block:: LAMMPS
|
||||||
|
|
||||||
fix active_group all propel/self velocity 1.0
|
fix active all propel/self dipole 40.0
|
||||||
fix constant_velocity all viscous 1.0
|
fix active all propel/self velocity 10.0
|
||||||
|
fix active all propel/self quat 15.7 qvector 1.0 0.0 0.0
|
||||||
fix active_group all propel/self quat 1.0
|
|
||||||
|
|
||||||
fix active all propel/self quat 1.0 types 1 2 4
|
|
||||||
|
|
||||||
Description
|
Description
|
||||||
"""""""""""
|
"""""""""""
|
||||||
|
|
||||||
Adds a force of a constant magnitude to each atom in the group. The nature in
|
Add a force to each atom in the group due to a self-propulsion force. The
|
||||||
which the force is added depends on the mode.
|
force is given by
|
||||||
|
|
||||||
For *mode* = *velocity*, the active force acts along the velocity vector of
|
.. math::
|
||||||
each atom. This can be interpreted as a velocity-dependent friction,
|
|
||||||
such as proposed by :ref:`(Erdmann) <Erdmann>`.
|
|
||||||
|
|
||||||
For *mode* = *quat* the force is applied along the axis obtained
|
F_i = f_P e_i
|
||||||
by rotating the x-axis along the atom's quaternion. In other words, the
|
|
||||||
force is along the x-axis in the atom's body frame. This mode requires
|
|
||||||
all atoms in the group to have a quaternion, so atom_style should
|
|
||||||
either be ellipsoid or body. In combination with Langevin thermostat
|
|
||||||
for translation and rotation in the overdamped regime, the quaternion
|
|
||||||
mode corresponds to the active Brownian particle model introduced by
|
|
||||||
:ref:`(Henkes) <Henkes>`, :ref:`(Bialke) <Bialke>` and :ref:`(Fily)
|
|
||||||
<Fily>`.
|
|
||||||
|
|
||||||
By default, this fix is applied to all atoms in the group. You can
|
where *i* is the particle the force is being applied to, :math:`f_P`
|
||||||
override this behavior by specifying the atom types the fix should work
|
is the magnitude of the force, and :math:`e_i` is the vector direction
|
||||||
on through the *types* keyword.
|
of the force. The specification of :math:`e_i` is based on which of the
|
||||||
|
three keywords (*dipole* or *velocity* or *quat*) one selects.
|
||||||
|
|
||||||
|
For mode *dipole*, :math:`e_i` is just equal to
|
||||||
|
the dipole vectors of the atoms in the group. Therefore, if the dipoles
|
||||||
|
are not unit vectors, the :math:`e_i` will not be unit vectors.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
If another command changes the magnitude of the dipole, this force will
|
||||||
|
change accordingly (since :math:`|e_i|` will change, which is physically
|
||||||
|
equivalent to re-scaling :math:`f_P` while keeping :math:`|e_i|` constant),
|
||||||
|
and no warning will be provided by LAMMPS. This is almost never what you
|
||||||
|
want, so ensure you are not changing dipole magnitudes with another LAMMPS
|
||||||
|
fix or pair style. Furthermore, self-propulsion forces (almost) always
|
||||||
|
set :math:`e_i` to be a unit vector for all times, so it's best to set
|
||||||
|
all the dipole magnitudes to 1.0 unless you have a good reason not to
|
||||||
|
(see the :doc:`set <set>` command on how to do this).
|
||||||
|
|
||||||
|
For mode *velocity*, :math:`e_i` points in the direction
|
||||||
|
of the current velocity (a unit-vector). This can be interpreted as a
|
||||||
|
velocity-dependent friction, as proposed by e.g. :ref:`(Erdmann) <Erdmann1>`.
|
||||||
|
|
||||||
|
For mode *quat*, :math:`e_i` points in the direction of a unit
|
||||||
|
vector, oriented in the coordinate frame of the ellipsoidal particles,
|
||||||
|
which defaults to point along the x-direction. This default behavior
|
||||||
|
can be changed by via the *quatvec* keyword.
|
||||||
|
|
||||||
|
The optional *quatvec* keyword specifies the direction of self-propulsion
|
||||||
|
via a unit vector (sx,sy,sz). The arguments *sx*, *sy*, and *sz*, are
|
||||||
|
defined within the coordinate frame of the atom's
|
||||||
|
ellipsoid. For instance, for an ellipsoid with long axis along
|
||||||
|
its x-direction, if one wanted the self-propulsion force to also
|
||||||
|
be along this axis, set *sx* equal to 1 and *sy*, *sz* both equal
|
||||||
|
to zero. This keyword may only be specified for mode *quat*.
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
In using keyword *quatvec*, the three arguments *sx*,
|
||||||
|
*sy*, and *sz* will be automatically normalized to components
|
||||||
|
of a unit vector internally to avoid users having to explicitly
|
||||||
|
do so themselves. Therefore, in mode *quat*, the vectors :math:`e_i`
|
||||||
|
will always be of unit length.
|
||||||
|
|
||||||
|
|
||||||
|
Along with adding a force contribution, this fix can also
|
||||||
|
contribute to the virial (pressure) of the system, defined as
|
||||||
|
:math:`f_P \sum_i <e_i . r_i>/(d V)`, where :math:`r_i` is the
|
||||||
|
*unwrapped* coordinate of particle i in the case of periodic
|
||||||
|
boundary conditions. See :ref:`(Winkler) <Winkler1>` for a
|
||||||
|
discussion of this active pressure contribution.
|
||||||
|
|
||||||
|
For modes *dipole* and *quat*, this fix is by default
|
||||||
|
included in pressure computations.
|
||||||
|
|
||||||
|
For mode *velocity*, this fix is by default not included
|
||||||
|
in pressure computations.
|
||||||
|
|
||||||
|
|
||||||
|
.. note::
|
||||||
|
|
||||||
|
In contrast to equilibrium systems, pressure of active systems
|
||||||
|
in general depends on the geometry of the container.
|
||||||
|
The active pressure contribution as calculated in this fix
|
||||||
|
is only valid for certain boundary conditions (spherical
|
||||||
|
walls, rectangular walls, or periodic boundary conditions).
|
||||||
|
For other geometries, the pressure must be measured via
|
||||||
|
explicit calculation of the force per unit area on a wall,
|
||||||
|
and so one must not calculate it using this fix.
|
||||||
|
(Use :doc:`fix_modify <fix_modify>` as described below
|
||||||
|
to turn off the virial contribution of this fix). Again,
|
||||||
|
see :ref:`(Winkler) <Winkler1>` for discussion of why this
|
||||||
|
is the case.
|
||||||
|
|
||||||
|
Furthermore, when dealing with active systems, the temperature
|
||||||
|
is no longer well defined. Therefore, one should ensure that
|
||||||
|
the *virial* flag is used in the
|
||||||
|
:doc:`compute pressure <compute_pressure>` command (turning
|
||||||
|
off temperature contributions).
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
@ -62,40 +131,48 @@ Restart, fix_modify, output, run start/stop, minimize info
|
|||||||
|
|
||||||
No information about this fix is written to :doc:`binary restart files <restart>`.
|
No information about this fix is written to :doc:`binary restart files <restart>`.
|
||||||
|
|
||||||
This fix is not imposed during minimization.
|
The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
|
||||||
|
fix to add the contribution due to the added forces on atoms to the
|
||||||
|
system's virial as part of :doc:`thermodynamic output <thermo_style>`.
|
||||||
|
The default is *virial yes* for keywords *dipole* and *quat*. The
|
||||||
|
default is *virial no* for keyword *velocity*.
|
||||||
|
|
||||||
|
|
||||||
|
No parameter of this fix can be used with the *start/stop* keywords of
|
||||||
|
the :doc:`run <run>` command.
|
||||||
|
|
||||||
|
|
||||||
Restrictions
|
Restrictions
|
||||||
""""""""""""
|
""""""""""""
|
||||||
|
|
||||||
In quat mode, this fix makes use of per-atom quaternions to take
|
With keyword *dipole*, this fix only works when the DIPOLE package is enabled.
|
||||||
into account the fact that the orientation can rotate and hence the
|
See the :doc:`Build package <Build_package>` doc page for more info.
|
||||||
direction of the active force can change. The quat mode
|
|
||||||
of this fix only works with atom_style ellipsoid.
|
This fix is part of the USER-BROWNIAN package. It is only enabled if
|
||||||
|
LAMMPS was built with that package. See the :doc:`Build package <Build_package>`
|
||||||
|
doc page for more info.
|
||||||
|
|
||||||
|
|
||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`fix setforce <fix_setforce>`, :doc:`fix addforce <fix_addforce>`
|
:doc:`fix efield <fix_efield>` , :doc:`fix setforce <fix_setforce>`,
|
||||||
|
:doc:`fix addforce <fix_addforce>`
|
||||||
.. _Erdmann:
|
|
||||||
|
|
||||||
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
|
|
||||||
Eur. Phys. J. B 15, 105-113, 2000.
|
|
||||||
|
|
||||||
.. _Henkes:
|
|
||||||
|
|
||||||
**(Henkes)** Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
|
|
||||||
|
|
||||||
.. _Bialke:
|
|
||||||
|
|
||||||
**(Bialke)** J. Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
|
|
||||||
|
|
||||||
.. _Fily:
|
|
||||||
|
|
||||||
**(Fily)** Y. Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012.
|
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|
||||||
types
|
none
|
||||||
|
|
||||||
|
----------
|
||||||
|
|
||||||
|
|
||||||
|
.. _Erdmann1:
|
||||||
|
|
||||||
|
**(Erdmann)** U. Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer,
|
||||||
|
Eur. Phys. J. B 15, 105-113, 2000.
|
||||||
|
|
||||||
|
|
||||||
|
.. _Winkler1:
|
||||||
|
|
||||||
|
**(Winkler)** Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
|
||||||
|
|||||||
@ -312,6 +312,7 @@ br
|
|||||||
Branduardi
|
Branduardi
|
||||||
Branicio
|
Branicio
|
||||||
brennan
|
brennan
|
||||||
|
Briels
|
||||||
Brien
|
Brien
|
||||||
Brilliantov
|
Brilliantov
|
||||||
Broadwell
|
Broadwell
|
||||||
@ -626,6 +627,7 @@ delflag
|
|||||||
Dellago
|
Dellago
|
||||||
delocalization
|
delocalization
|
||||||
delocalized
|
delocalized
|
||||||
|
Delong
|
||||||
delr
|
delr
|
||||||
deltaHf
|
deltaHf
|
||||||
Dendrimer
|
Dendrimer
|
||||||
@ -709,6 +711,7 @@ dodgerblue
|
|||||||
dof
|
dof
|
||||||
doi
|
doi
|
||||||
Donadio
|
Donadio
|
||||||
|
Donev
|
||||||
dotc
|
dotc
|
||||||
Doty
|
Doty
|
||||||
doxygen
|
doxygen
|
||||||
@ -1143,6 +1146,7 @@ GMock
|
|||||||
gneb
|
gneb
|
||||||
GNEB
|
GNEB
|
||||||
Goldfarb
|
Goldfarb
|
||||||
|
Gompper
|
||||||
Gonzalez-Melchor
|
Gonzalez-Melchor
|
||||||
googlemail
|
googlemail
|
||||||
googletest
|
googletest
|
||||||
@ -1321,6 +1325,7 @@ ijk
|
|||||||
ijkl
|
ijkl
|
||||||
ik
|
ik
|
||||||
Ikeshoji
|
Ikeshoji
|
||||||
|
Ilie
|
||||||
ilmenau
|
ilmenau
|
||||||
Ilmenau
|
Ilmenau
|
||||||
ilp
|
ilp
|
||||||
@ -3109,6 +3114,7 @@ Swinburne
|
|||||||
Swol
|
Swol
|
||||||
Swope
|
Swope
|
||||||
Sx
|
Sx
|
||||||
|
sx
|
||||||
sy
|
sy
|
||||||
Sy
|
Sy
|
||||||
symplectic
|
symplectic
|
||||||
@ -3118,6 +3124,7 @@ sysdim
|
|||||||
Syst
|
Syst
|
||||||
systemd
|
systemd
|
||||||
Sz
|
Sz
|
||||||
|
sz
|
||||||
Tabbernor
|
Tabbernor
|
||||||
tabinner
|
tabinner
|
||||||
Tadmor
|
Tadmor
|
||||||
@ -3358,6 +3365,7 @@ upenn
|
|||||||
upto
|
upto
|
||||||
Urbakh
|
Urbakh
|
||||||
Urbana
|
Urbana
|
||||||
|
Usabiaga
|
||||||
usec
|
usec
|
||||||
uSemiParallel
|
uSemiParallel
|
||||||
userguide
|
userguide
|
||||||
@ -3502,6 +3510,7 @@ Wikipedia
|
|||||||
Wildcard
|
Wildcard
|
||||||
wildcard
|
wildcard
|
||||||
wildcards
|
wildcards
|
||||||
|
Winkler
|
||||||
Wirnsberger
|
Wirnsberger
|
||||||
wirtes
|
wirtes
|
||||||
witin
|
witin
|
||||||
@ -3513,6 +3522,7 @@ Worley
|
|||||||
Wriggers
|
Wriggers
|
||||||
Wuppertal
|
Wuppertal
|
||||||
Wurtzite
|
Wurtzite
|
||||||
|
Wysocki
|
||||||
www
|
www
|
||||||
wx
|
wx
|
||||||
Wx
|
Wx
|
||||||
|
|||||||
53
examples/USER/brownian/2d_velocity/in2d.velocity
Normal file
53
examples/USER/brownian/2d_velocity/in2d.velocity
Normal file
@ -0,0 +1,53 @@
|
|||||||
|
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
|
||||||
|
|
||||||
|
variable gamma_t equal 1.0
|
||||||
|
variable temp equal 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp equal 4.0
|
||||||
|
variable params string ${gamma_t}_${temp}_${fp}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
|
||||||
|
fix vel all propel/self velocity ${fp}
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix_modify vel virial yes
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 500
|
||||||
|
run 5000
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
|
||||||
|
|
||||||
@ -0,0 +1,151 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
|
||||||
|
|
||||||
|
variable gamma_t equal 1.0
|
||||||
|
variable temp equal 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp equal 4.0
|
||||||
|
variable params string ${gamma_t}_${temp}_${fp}
|
||||||
|
variable params string 1_${temp}_${fp}
|
||||||
|
variable params string 1_1_${fp}
|
||||||
|
variable params string 1_1_4
|
||||||
|
|
||||||
|
units lj
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1024 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 1974019 gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 1974019 gamma_t 1
|
||||||
|
fix vel all propel/self velocity ${fp}
|
||||||
|
fix vel all propel/self velocity 4
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix_modify vel virial yes
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 500
|
||||||
|
run 5000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
|
||||||
|
Step Temp E_pair c_press
|
||||||
|
0 1 0 -0.18336111
|
||||||
|
500 2.0519273e+10 0 -0.048238222
|
||||||
|
1000 1.9821717e+10 0 -0.4711053
|
||||||
|
1500 1.9697609e+10 0 -0.13539588
|
||||||
|
2000 2.0209443e+10 0 0.0094958039
|
||||||
|
2500 1.9591299e+10 0 0.40117118
|
||||||
|
3000 2.089566e+10 0 -0.036548251
|
||||||
|
3500 1.978692e+10 0 0.28282578
|
||||||
|
4000 2.0657848e+10 0 0.17618064
|
||||||
|
4500 2.0837353e+10 0 -0.080724651
|
||||||
|
5000 2.0348316e+10 0 -0.17471195
|
||||||
|
Loop time of 0.575164 on 1 procs for 5000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 0.075 tau/day, 8693.168 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0036819 | 0.0036819 | 0.0036819 | 0.0 | 0.64
|
||||||
|
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.05
|
||||||
|
Modify | 0.51999 | 0.51999 | 0.51999 | 0.0 | 90.41
|
||||||
|
Other | | 0.05121 | | | 8.90
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 65.0000 ave 65 max 65 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 2.0328444e+10 0 0 0 0 0 -0.17471195
|
||||||
|
1000 197017.59 0 0.018147562 0.019839233 0 0.037986796 -0.71897807
|
||||||
|
2000 197030.23 0 0.03909867 0.041721342 0 0.080820011 -0.30051929
|
||||||
|
3000 201997.2 0 0.065694399 0.06235257 0 0.12804697 -0.85167039
|
||||||
|
4000 199927.76 0 0.085698715 0.080328815 0 0.16602753 0.18493117
|
||||||
|
5000 198665.7 0 0.10896054 0.097021266 0 0.2059818 -0.090735406
|
||||||
|
6000 199277.78 0 0.13081111 0.11724814 0 0.24805925 -0.18189034
|
||||||
|
7000 199850.54 0 0.14721838 0.13806858 0 0.28528696 0.11334674
|
||||||
|
8000 191577.11 0 0.16582149 0.15935853 0 0.32518002 -0.73284569
|
||||||
|
9000 197331.29 0 0.17995704 0.18652927 0 0.3664863 -0.015558407
|
||||||
|
10000 197048.17 0 0.2034106 0.20329856 0 0.40670916 0.36985211
|
||||||
|
11000 200105.54 0 0.21809835 0.21966463 0 0.43776298 0.36437
|
||||||
|
12000 203180.39 0 0.23810386 0.23666184 0 0.47476569 -0.072006034
|
||||||
|
Loop time of 1.37465 on 1 procs for 12000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 7542.303 tau/day, 8729.517 timesteps/s
|
||||||
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.01
|
||||||
|
Comm | 0.0024607 | 0.0024607 | 0.0024607 | 0.0 | 0.18
|
||||||
|
Output | 0.00068665 | 0.00068665 | 0.00068665 | 0.0 | 0.05
|
||||||
|
Modify | 1.2479 | 1.2479 | 1.2479 | 0.0 | 90.78
|
||||||
|
Other | | 0.1235 | | | 8.98
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
Total wall time: 0:00:01
|
||||||
@ -0,0 +1,151 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### 2d overdamped brownian dynamics with self-propulsion force in direction of velocity. #####
|
||||||
|
|
||||||
|
variable gamma_t equal 1.0
|
||||||
|
variable temp equal 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp equal 4.0
|
||||||
|
variable params string ${gamma_t}_${temp}_${fp}
|
||||||
|
variable params string 1_${temp}_${fp}
|
||||||
|
variable params string 1_1_${fp}
|
||||||
|
variable params string 1_1_4
|
||||||
|
|
||||||
|
units lj
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1024 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix step all brownian ${temp} ${seed} gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 ${seed} gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 1974019 gamma_t ${gamma_t}
|
||||||
|
fix step all brownian 1 1974019 gamma_t 1
|
||||||
|
fix vel all propel/self velocity ${fp}
|
||||||
|
fix vel all propel/self velocity 4
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix_modify vel virial yes
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 500
|
||||||
|
run 5000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.289 | 2.289 | 2.289 Mbytes
|
||||||
|
Step Temp E_pair c_press
|
||||||
|
0 1 0 -0.18336111
|
||||||
|
500 1.9862591e+10 0 -0.32013566
|
||||||
|
1000 2.0093184e+10 0 -0.36609742
|
||||||
|
1500 1.9562283e+10 0 -0.53349351
|
||||||
|
2000 1.9903977e+10 0 0.63783249
|
||||||
|
2500 2.0260128e+10 0 0.30046413
|
||||||
|
3000 1.9948065e+10 0 -0.63093105
|
||||||
|
3500 1.9507486e+10 0 0.48762848
|
||||||
|
4000 2.0049087e+10 0 0.40289309
|
||||||
|
4500 1.9975813e+10 0 0.57649363
|
||||||
|
5000 2.0129291e+10 0 -0.41288352
|
||||||
|
Loop time of 0.238949 on 4 procs for 5000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 0.181 tau/day, 20924.952 timesteps/s
|
||||||
|
92.6% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0080078 | 0.024718 | 0.031782 | 6.2 | 10.34
|
||||||
|
Output | 0.0001812 | 0.00029999 | 0.00063467 | 0.0 | 0.13
|
||||||
|
Modify | 0.13401 | 0.14401 | 0.15438 | 2.4 | 60.27
|
||||||
|
Other | | 0.06992 | | | 29.26
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 256 max 256 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 33.0000 ave 33 max 33 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 2.0109634e+10 0 0 0 0 0 -0.41288352
|
||||||
|
1000 195711.46 0 0.020076462 0.020523099 0 0.040599561 -0.32125126
|
||||||
|
2000 203263.85 0 0.039242992 0.039661282 0 0.078904274 0.11008705
|
||||||
|
3000 197417.54 0 0.064938128 0.057716419 0 0.12265455 0.16967601
|
||||||
|
4000 200505.97 0 0.086511225 0.074975267 0 0.16148649 0.31338473
|
||||||
|
5000 199373.77 0 0.10583263 0.098175658 0 0.20400829 0.34205791
|
||||||
|
6000 192881.14 0 0.12152088 0.11706037 0 0.23858125 -0.27870467
|
||||||
|
7000 203045.3 0 0.1383248 0.13629503 0 0.27461983 -0.046936646
|
||||||
|
8000 198544.08 0 0.16064738 0.1582206 0 0.31886798 -0.18803452
|
||||||
|
9000 205450.74 0 0.17926529 0.1829047 0 0.36216999 0.47191228
|
||||||
|
10000 200371.73 0 0.20084273 0.20365189 0 0.40449463 0.093098262
|
||||||
|
11000 202911.93 0 0.21569236 0.22221715 0 0.43790952 -0.38430031
|
||||||
|
12000 192590.04 0 0.24041439 0.24114487 0 0.48155926 -0.1677052
|
||||||
|
Loop time of 0.443026 on 4 procs for 12000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 23402.683 tau/day, 27086.439 timesteps/s
|
||||||
|
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 3.2663e-05 | 3.3855e-05 | 3.4809e-05 | 0.0 | 0.01
|
||||||
|
Comm | 0.0030291 | 0.0030628 | 0.0030825 | 0.0 | 0.69
|
||||||
|
Output | 0.00027895 | 0.00051624 | 0.001184 | 0.0 | 0.12
|
||||||
|
Modify | 0.31607 | 0.33372 | 0.37391 | 4.0 | 75.33
|
||||||
|
Other | | 0.1057 | | | 23.86
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 259 max 253 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 15
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
54
examples/USER/brownian/asphere/in2d.ellipsoid
Normal file
54
examples/USER/brownian/asphere/in2d.ellipsoid
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string inf
|
||||||
|
variable gamma_r_2 string inf
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string inf
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||||
|
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||||
|
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||||
|
dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
54
examples/USER/brownian/asphere/in3d.ellipsoid
Normal file
54
examples/USER/brownian/asphere/in3d.ellipsoid
Normal file
@ -0,0 +1,54 @@
|
|||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string 2.0
|
||||||
|
variable gamma_r_2 string 0.25
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string 9.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} &
|
||||||
|
gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} &
|
||||||
|
gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} &
|
||||||
|
dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string inf
|
||||||
|
variable gamma_r_2 string inf
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string inf
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.005 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for dipole/random
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for shape
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
set type * quat/random 198098
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for quat/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.114 | 5.114 | 5.114 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 34376.187 0 0.00034728749 0.00034318997 0 0.00069047747
|
||||||
|
200 36135.708 0 0.00067452936 0.0006818928 0 0.0013564222
|
||||||
|
300 34444.929 0 0.0010189319 0.00099849203 0 0.002017424
|
||||||
|
400 35668.312 0 0.0013648699 0.0013311884 0 0.0026960583
|
||||||
|
500 35388.615 0 0.0017330203 0.0016077184 0 0.0033407387
|
||||||
|
600 35180.065 0 0.002052223 0.0019394635 0 0.0039916865
|
||||||
|
700 34035.38 0 0.0024329956 0.0022664905 0 0.0046994861
|
||||||
|
800 34581.664 0 0.002783885 0.0025794872 0 0.0053633723
|
||||||
|
900 34579.945 0 0.003163442 0.0029351952 0 0.0060986372
|
||||||
|
1000 34158.066 0 0.0035589034 0.0032627605 0 0.0068216639
|
||||||
|
1100 33453.827 0 0.0038861895 0.003565372 0 0.0074515615
|
||||||
|
1200 33608.06 0 0.0041325698 0.0038943268 0 0.0080268966
|
||||||
|
1300 34381.633 0 0.004405682 0.0043294156 0 0.0087350976
|
||||||
|
1400 32925.746 0 0.0047383547 0.0046803517 0 0.0094187065
|
||||||
|
1500 34809.764 0 0.0051149571 0.0049309746 0 0.010045932
|
||||||
|
1600 33580.096 0 0.0054893472 0.0052465377 0 0.010735885
|
||||||
|
1700 34596.275 0 0.00581894 0.0056500316 0 0.011468972
|
||||||
|
1800 33926.736 0 0.0062129617 0.0059796125 0 0.012192574
|
||||||
|
1900 35577.131 0 0.0065668637 0.0062530163 0 0.01281988
|
||||||
|
2000 34224.967 0 0.0070005917 0.006598912 0 0.013599504
|
||||||
|
2100 33991.406 0 0.0073134826 0.0069119252 0 0.014225408
|
||||||
|
2200 34647.054 0 0.007659301 0.0073434715 0 0.015002772
|
||||||
|
2300 33956.835 0 0.007965191 0.0076318537 0 0.015597045
|
||||||
|
2400 35272.549 0 0.0082467116 0.007929202 0 0.016175914
|
||||||
|
2500 33901.494 0 0.0086251299 0.0082790757 0 0.016904206
|
||||||
|
2600 34138.227 0 0.0089419364 0.0086639744 0 0.017605911
|
||||||
|
2700 33691.013 0 0.0093083376 0.0090219118 0 0.018330249
|
||||||
|
2800 34716.817 0 0.0095840095 0.0094118945 0 0.018995904
|
||||||
|
2900 34473.982 0 0.0099773501 0.0098167668 0 0.019794117
|
||||||
|
3000 33406.776 0 0.010391969 0.010098625 0 0.020490594
|
||||||
|
Loop time of 3.67112 on 1 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 706.051 tau/day, 817.189 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.037973 | 0.037973 | 0.037973 | 0.0 | 1.03
|
||||||
|
Output | 0.0040674 | 0.0040674 | 0.0040674 | 0.0 | 0.11
|
||||||
|
Modify | 3.515 | 3.515 | 3.515 | 0.0 | 95.75
|
||||||
|
Other | | 0.1141 | | | 3.11
|
||||||
|
|
||||||
|
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 121.000 ave 121 max 121 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string inf
|
||||||
|
variable gamma_r_2 string inf
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string inf
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_${gamma_t_3}
|
||||||
|
variable params string gaussian_1.0_inf_inf_0.1_5.0_7.0_inf
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.007 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for dipole/random
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for shape
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
set type * quat/random 198098
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for quat/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng gaussian gamma_r_eigen inf inf 0.1 gamma_t_eigen 5.0 7.0 inf dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.102 | 5.102 | 5.102 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 33874.438 0 0.0003458147 0.00033165629 0 0.00067747099
|
||||||
|
200 34893.188 0 0.00066290209 0.00068146332 0 0.0013443654
|
||||||
|
300 34494.226 0 0.0010064902 0.0010276646 0 0.0020341548
|
||||||
|
400 34537.887 0 0.0013457339 0.0014057042 0 0.0027514381
|
||||||
|
500 34458.46 0 0.0017006949 0.0017120083 0 0.0034127033
|
||||||
|
600 33229.977 0 0.0020841613 0.0020485346 0 0.0041326959
|
||||||
|
700 33288.631 0 0.0024270272 0.0023673304 0 0.0047943576
|
||||||
|
800 35317.512 0 0.0027924435 0.0026950912 0 0.0054875347
|
||||||
|
900 33094.299 0 0.0031503627 0.0030789319 0 0.0062292946
|
||||||
|
1000 35801.751 0 0.003489398 0.0034594626 0 0.0069488607
|
||||||
|
1100 33427.701 0 0.0038547506 0.0038375809 0 0.0076923316
|
||||||
|
1200 34675.07 0 0.0041824195 0.0042017298 0 0.0083841493
|
||||||
|
1300 33080.294 0 0.0045258945 0.0045816356 0 0.0091075301
|
||||||
|
1400 34927.288 0 0.0048252992 0.0049215701 0 0.0097468693
|
||||||
|
1500 34338.558 0 0.0051959155 0.0053020102 0 0.010497926
|
||||||
|
1600 34686.248 0 0.0055111463 0.0056220225 0 0.011133169
|
||||||
|
1700 34336.158 0 0.0059240394 0.0059060319 0 0.011830071
|
||||||
|
1800 34315.859 0 0.0063027944 0.0063004467 0 0.012603241
|
||||||
|
1900 35096.721 0 0.0066098525 0.00672222 0 0.013332073
|
||||||
|
2000 33544.18 0 0.0069401261 0.007074124 0 0.01401425
|
||||||
|
2100 33863.219 0 0.0072726502 0.0074175954 0 0.014690246
|
||||||
|
2200 34705.892 0 0.0075586722 0.0077552683 0 0.015313941
|
||||||
|
2300 34025.357 0 0.0079046728 0.0081760519 0 0.016080725
|
||||||
|
2400 34741.849 0 0.008252969 0.0085203087 0 0.016773278
|
||||||
|
2500 34406.959 0 0.0085370091 0.0088556377 0 0.017392647
|
||||||
|
2600 34062.63 0 0.0088134153 0.0092536326 0 0.018067048
|
||||||
|
2700 34677.666 0 0.0090592854 0.0096225881 0 0.018681874
|
||||||
|
2800 33464.216 0 0.0093984162 0.0099647695 0 0.019363186
|
||||||
|
2900 32920.721 0 0.0098222985 0.010366517 0 0.020188816
|
||||||
|
3000 34539.66 0 0.010133317 0.01068102 0 0.020814337
|
||||||
|
Loop time of 1.12143 on 4 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 2311.341 tau/day, 2675.163 timesteps/s
|
||||||
|
96.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.036017 | 0.042828 | 0.051558 | 2.7 | 3.82
|
||||||
|
Output | 0.0012608 | 0.0025993 | 0.0063775 | 4.3 | 0.23
|
||||||
|
Modify | 0.9002 | 0.93095 | 0.99546 | 3.9 | 83.01
|
||||||
|
Other | | 0.1451 | | | 12.93
|
||||||
|
|
||||||
|
Nlocal: 900.000 ave 900 max 900 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 61.0000 ave 61 max 61 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string 2.0
|
||||||
|
variable gamma_r_2 string 0.25
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string 9.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.005 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for shape
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
set type * quat/random 198098
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for quat/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.219 | 5.219 | 5.219 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 45690.838 0 0.00029994317 0.00029953902 0.00030002809 0.00089951027
|
||||||
|
200 45571.166 0 0.00061376797 0.00060955238 0.00061153551 0.0018348559
|
||||||
|
300 44693.418 0 0.00093058034 0.00089383536 0.00091554588 0.0027399616
|
||||||
|
400 44831.846 0 0.001250227 0.0012230128 0.0012120517 0.0036852914
|
||||||
|
500 45028.015 0 0.0015448869 0.0015339549 0.0014978843 0.0045767262
|
||||||
|
600 45895.442 0 0.0018621952 0.0018169905 0.0018352784 0.0055144641
|
||||||
|
700 45858.744 0 0.0021617097 0.0021137714 0.0021360394 0.0064115206
|
||||||
|
800 45155.215 0 0.002428445 0.0024288837 0.0024516737 0.0073090023
|
||||||
|
900 45427.427 0 0.0027265978 0.0027662531 0.0027329878 0.0082258387
|
||||||
|
1000 45398.166 0 0.0030685345 0.0030805014 0.0029765916 0.0091256275
|
||||||
|
1100 44622.428 0 0.0033766954 0.0033976168 0.0032745406 0.010048853
|
||||||
|
1200 45500.277 0 0.0036410565 0.0036840528 0.0035831659 0.010908275
|
||||||
|
1300 45265.8 0 0.0039143146 0.0039419334 0.0038761633 0.011732411
|
||||||
|
1400 45482.435 0 0.0042006542 0.0043373651 0.004164002 0.012702021
|
||||||
|
1500 45126.629 0 0.0044647379 0.0046021855 0.004487041 0.013553965
|
||||||
|
1600 45178.172 0 0.0047726618 0.0049110287 0.0048012671 0.014484958
|
||||||
|
1700 44918.685 0 0.005104787 0.0052522662 0.0050844375 0.015441491
|
||||||
|
1800 44776.678 0 0.0054395368 0.0056092038 0.0054623875 0.016511128
|
||||||
|
1900 46035.987 0 0.0057735872 0.0059357043 0.0057296009 0.017438892
|
||||||
|
2000 45436.517 0 0.0060837459 0.0063485717 0.0059769119 0.018409229
|
||||||
|
2100 45871.502 0 0.0063736337 0.0066551978 0.0063077439 0.019336575
|
||||||
|
2200 45511.847 0 0.0066419141 0.0069700452 0.0065553318 0.020167291
|
||||||
|
2300 45597.047 0 0.0069251517 0.0073015716 0.0068945654 0.021121289
|
||||||
|
2400 44832.007 0 0.0071894253 0.0076238221 0.0071638554 0.021977103
|
||||||
|
2500 45668.42 0 0.0074351304 0.0079594991 0.0075390719 0.022933701
|
||||||
|
2600 45248.483 0 0.007781496 0.008293944 0.0077956068 0.023871047
|
||||||
|
2700 45308.515 0 0.0080302993 0.0086329679 0.0081457335 0.024809001
|
||||||
|
2800 45637.72 0 0.0083889026 0.0089173198 0.0086032427 0.025909465
|
||||||
|
2900 45909.343 0 0.0087169392 0.009181179 0.0088778569 0.026775975
|
||||||
|
3000 45213.613 0 0.0090508891 0.0094253485 0.0092660321 0.02774227
|
||||||
|
Loop time of 4.13937 on 1 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 626.183 tau/day, 724.749 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.24709 | 0.24709 | 0.24709 | 0.0 | 5.97
|
||||||
|
Output | 0.004636 | 0.004636 | 0.004636 | 0.0 | 0.11
|
||||||
|
Modify | 3.7604 | 3.7604 | 3.7604 | 0.0 | 90.85
|
||||||
|
Other | | 0.1272 | | | 3.07
|
||||||
|
|
||||||
|
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 817.000 ave 817 max 817 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:04
|
||||||
@ -0,0 +1,145 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting ellipsoids in 3D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_r_1 string 2.0
|
||||||
|
variable gamma_r_2 string 0.25
|
||||||
|
variable gamma_r_3 string 0.1
|
||||||
|
variable gamma_t_1 string 5.0
|
||||||
|
variable gamma_t_2 string 7.0
|
||||||
|
variable gamma_t_3 string 9.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_${temp}_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_${gamma_r_1}_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_${gamma_r_2}_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_${gamma_r_3}_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_${gamma_t_1}_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_${gamma_t_2}_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_${gamma_t_3}
|
||||||
|
variable params string uniform_1.0_2.0_0.25_0.1_5.0_7.0_9.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole ellipsoid
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
set type * shape 3.0 1.0 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for shape
|
||||||
|
set type * quat/random ${seed}
|
||||||
|
set type * quat/random 198098
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for quat/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/asphere ${temp} ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 ${seed} rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng ${rng} gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen ${gamma_r_1} ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 ${gamma_r_2} ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 ${gamma_r_3} gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen ${gamma_t_1} ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 ${gamma_t_2} ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 ${gamma_t_3} dipole 1.0 0.0 0.0
|
||||||
|
fix 1 all brownian/asphere 1.0 198098 rng uniform gamma_r_eigen 2.0 0.25 0.1 gamma_t_eigen 5.0 7.0 9.0 dipole 1.0 0.0 0.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.152 | 5.152 | 5.152 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 45236.508 0 0.00030817418 0.00030717742 0.0003019227 0.0009172743
|
||||||
|
200 45564.566 0 0.00062027526 0.00062110132 0.0006080391 0.0018494157
|
||||||
|
300 46232.801 0 0.00091155216 0.00094473459 0.00093009391 0.0027863807
|
||||||
|
400 45250.414 0 0.0011980791 0.0012538262 0.0012201461 0.0036720513
|
||||||
|
500 45217.133 0 0.0015186813 0.0015752994 0.001509437 0.0046034177
|
||||||
|
600 45531.276 0 0.0018194588 0.0019243758 0.0018209246 0.0055647592
|
||||||
|
700 44834.624 0 0.0021277747 0.0022417115 0.0021352036 0.0065046898
|
||||||
|
800 45413.998 0 0.0024558838 0.0025741787 0.0024088704 0.0074389329
|
||||||
|
900 45668.624 0 0.0027366171 0.002858242 0.0027580782 0.0083529374
|
||||||
|
1000 45809.223 0 0.0030331425 0.003186293 0.0030414906 0.0092609261
|
||||||
|
1100 45193.019 0 0.0033199824 0.0034668659 0.003298885 0.010085733
|
||||||
|
1200 44522.927 0 0.0036503132 0.0037490684 0.0036089852 0.011008367
|
||||||
|
1300 45214.567 0 0.0039958617 0.0040881934 0.0038709079 0.011954963
|
||||||
|
1400 45217.997 0 0.004276499 0.0044624985 0.0041104891 0.012849487
|
||||||
|
1500 45497.171 0 0.0045943272 0.0047116875 0.0044113504 0.013717365
|
||||||
|
1600 45905.187 0 0.0049004996 0.0049982014 0.0047394999 0.014638201
|
||||||
|
1700 45551.346 0 0.0051540939 0.0053187249 0.0050861052 0.015558924
|
||||||
|
1800 45347.782 0 0.0054101891 0.0056306 0.0053515873 0.016392376
|
||||||
|
1900 45107.895 0 0.005743705 0.0059584896 0.0056220384 0.017324233
|
||||||
|
2000 45043.389 0 0.0059803588 0.006230449 0.005911555 0.018122363
|
||||||
|
2100 45433.293 0 0.0062610364 0.0066140744 0.0062152977 0.019090408
|
||||||
|
2200 45804.217 0 0.0064995183 0.0068831274 0.0064971789 0.019879825
|
||||||
|
2300 45697.516 0 0.0067910846 0.0071845673 0.0068046192 0.020780271
|
||||||
|
2400 45447.422 0 0.0071022706 0.0074743709 0.0070983185 0.02167496
|
||||||
|
2500 45395.18 0 0.0073817023 0.0077467991 0.0074263196 0.022554821
|
||||||
|
2600 45943.044 0 0.0075953233 0.007997707 0.0076508583 0.023243889
|
||||||
|
2700 45859.978 0 0.0079082128 0.0082090043 0.0078853376 0.024002555
|
||||||
|
2800 45822.007 0 0.0082607534 0.0084510061 0.0081985549 0.024910314
|
||||||
|
2900 45438.456 0 0.0085958203 0.0088807705 0.0084755353 0.025952126
|
||||||
|
3000 45060.957 0 0.0089017992 0.0090966159 0.0086718875 0.026670303
|
||||||
|
Loop time of 1.23282 on 4 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 2102.502 tau/day, 2433.452 timesteps/s
|
||||||
|
97.9% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 8.5831e-06 | 8.5831e-06 | 8.5831e-06 | 0.0 | 0.00
|
||||||
|
Comm | 0.10931 | 0.11473 | 0.11748 | 0.9 | 9.31
|
||||||
|
Output | 0.001375 | 0.0018924 | 0.0034099 | 2.0 | 0.15
|
||||||
|
Modify | 0.97744 | 0.99158 | 1.0089 | 1.3 | 80.43
|
||||||
|
Other | | 0.1246 | | | 10.11
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1035 max 1016 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
43
examples/USER/brownian/point/in2d.point
Normal file
43
examples/USER/brownian/point/in2d.point
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
##### dynamics of non-interacting point particles in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
44
examples/USER/brownian/point/in3d.point
Normal file
44
examples/USER/brownian/point/in3d.point
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
|
||||||
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.1
Normal file
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.1
Normal file
@ -0,0 +1,119 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### dynamics of non-interacting point particles in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.003 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 1022861.2 0 0.010252464 0.0095481044 0 0.019800568
|
||||||
|
200 986781.19 0 0.020552091 0.019485252 0 0.040037343
|
||||||
|
300 1030219 0 0.030642552 0.028377678 0 0.05902023
|
||||||
|
400 1003322.5 0 0.040610693 0.038179284 0 0.078789978
|
||||||
|
500 989343.12 0 0.049978908 0.047445856 0 0.097424764
|
||||||
|
600 1029781.3 0 0.059551719 0.057941149 0 0.11749287
|
||||||
|
700 999447.72 0 0.06979546 0.067552325 0 0.13734778
|
||||||
|
800 995373.97 0 0.080049251 0.078006344 0 0.1580556
|
||||||
|
900 1011991.4 0 0.089753134 0.087065214 0 0.17681835
|
||||||
|
1000 1006017.1 0 0.10041092 0.097934217 0 0.19834514
|
||||||
|
1100 997762.63 0 0.11229742 0.10841547 0 0.22071289
|
||||||
|
1200 1011707.8 0 0.12006388 0.1190115 0 0.23907538
|
||||||
|
1300 1012099.1 0 0.13097486 0.12996632 0 0.26094117
|
||||||
|
1400 997602.43 0 0.14345778 0.13830585 0 0.28176362
|
||||||
|
1500 1005358.1 0 0.15441686 0.14927539 0 0.30369225
|
||||||
|
1600 1007081.8 0 0.16496828 0.15936363 0 0.3243319
|
||||||
|
1700 990284.9 0 0.1747286 0.16818246 0 0.34291106
|
||||||
|
1800 969006.97 0 0.18228778 0.17972813 0 0.3620159
|
||||||
|
1900 998066.69 0 0.19338277 0.19226121 0 0.38564397
|
||||||
|
2000 972300.66 0 0.20352485 0.20145928 0 0.40498413
|
||||||
|
2100 985025.88 0 0.21283854 0.21090075 0 0.42373929
|
||||||
|
2200 1010964.6 0 0.22279055 0.22110734 0 0.44389789
|
||||||
|
2300 975819.44 0 0.23128131 0.23226488 0 0.46354619
|
||||||
|
2400 977043.53 0 0.24284105 0.24301689 0 0.48585794
|
||||||
|
2500 969708.21 0 0.25415238 0.25354284 0 0.50769522
|
||||||
|
2600 981969.5 0 0.26457173 0.26318018 0 0.52775192
|
||||||
|
2700 987261.1 0 0.27497004 0.27761213 0 0.55258218
|
||||||
|
2800 1005751.1 0 0.28530448 0.28715428 0 0.57245876
|
||||||
|
2900 975930.11 0 0.29394811 0.29896948 0 0.59291759
|
||||||
|
3000 997388.08 0 0.30674701 0.31193573 0 0.61868274
|
||||||
|
Loop time of 1.501 on 1 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 1726.852 tau/day, 1998.672 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00059271 | 0.00059271 | 0.00059271 | 0.0 | 0.04
|
||||||
|
Comm | 0.0055437 | 0.0055437 | 0.0055437 | 0.0 | 0.37
|
||||||
|
Output | 0.0039999 | 0.0039999 | 0.0039999 | 0.0 | 0.27
|
||||||
|
Modify | 1.3852 | 1.3852 | 1.3852 | 0.0 | 92.28
|
||||||
|
Other | | 0.1057 | | | 7.04
|
||||||
|
|
||||||
|
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 21
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:01
|
||||||
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.4
Normal file
119
examples/USER/brownian/point/log.11May2021.in2d.point.g++.4
Normal file
@ -0,0 +1,119 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### dynamics of non-interacting point particles in 2D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.664 | 2.664 | 2.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 1017972.1 0 0.010094052 0.0097502899 0 0.019844342
|
||||||
|
200 1004552.1 0 0.020125116 0.01957629 0 0.039701406
|
||||||
|
300 1017712.9 0 0.030271373 0.029411656 0 0.059683029
|
||||||
|
400 1016693.8 0 0.040610061 0.038605869 0 0.07921593
|
||||||
|
500 999527.84 0 0.049451389 0.049042225 0 0.098493614
|
||||||
|
600 961157.92 0 0.059691948 0.059033176 0 0.11872512
|
||||||
|
700 1006804.9 0 0.071205977 0.069972106 0 0.14117808
|
||||||
|
800 1007321.8 0 0.081136977 0.079825976 0 0.16096295
|
||||||
|
900 1002801.7 0 0.091236148 0.090833816 0 0.18206996
|
||||||
|
1000 1010134.7 0 0.10091362 0.10023906 0 0.20115269
|
||||||
|
1100 990246.55 0 0.1118367 0.11141049 0 0.22324719
|
||||||
|
1200 1010555.5 0 0.12091736 0.12355456 0 0.24447192
|
||||||
|
1300 997117.19 0 0.13099592 0.13292775 0 0.26392367
|
||||||
|
1400 1020817.1 0 0.14167961 0.14172898 0 0.28340859
|
||||||
|
1500 1015048.1 0 0.15225884 0.15162948 0 0.30388833
|
||||||
|
1600 990291.98 0 0.16460973 0.16251919 0 0.32712891
|
||||||
|
1700 980848.58 0 0.17380313 0.17351201 0 0.34731513
|
||||||
|
1800 1000673.8 0 0.18383991 0.18175453 0 0.36559445
|
||||||
|
1900 1009388.9 0 0.19411523 0.19367453 0 0.38778976
|
||||||
|
2000 1005935.9 0 0.2015342 0.20585359 0 0.40738779
|
||||||
|
2100 985500.56 0 0.21161056 0.21238463 0 0.42399519
|
||||||
|
2200 997241.34 0 0.21841986 0.22117922 0 0.43959908
|
||||||
|
2300 1011672.3 0 0.22688099 0.23155741 0 0.4584384
|
||||||
|
2400 989837.68 0 0.23849839 0.24219 0 0.48068839
|
||||||
|
2500 1035706.8 0 0.24541408 0.24947563 0 0.49488971
|
||||||
|
2600 992370.08 0 0.25537803 0.25758332 0 0.51296135
|
||||||
|
2700 990586.56 0 0.26542605 0.26762286 0 0.53304892
|
||||||
|
2800 1002767.3 0 0.27570392 0.27874972 0 0.55445363
|
||||||
|
2900 995307.27 0 0.28580946 0.29115624 0 0.5769657
|
||||||
|
3000 1024317.7 0 0.29493208 0.30208924 0 0.59702132
|
||||||
|
Loop time of 0.413047 on 4 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 6275.312 tau/day, 7263.093 timesteps/s
|
||||||
|
98.0% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00016236 | 0.00016338 | 0.00016403 | 0.0 | 0.04
|
||||||
|
Comm | 0.0026367 | 0.0030084 | 0.0031497 | 0.4 | 0.73
|
||||||
|
Output | 0.0011849 | 0.0013574 | 0.0018065 | 0.7 | 0.33
|
||||||
|
Modify | 0.34447 | 0.35223 | 0.36357 | 1.2 | 85.28
|
||||||
|
Other | | 0.05629 | | | 13.63
|
||||||
|
|
||||||
|
Nlocal: 900.000 ave 906 max 891 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 22
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.1
Normal file
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.1
Normal file
@ -0,0 +1,119 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.694 | 2.694 | 2.694 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 1500286.3 0 0.0098123603 0.010352169 0.010242435 0.030406964
|
||||||
|
200 1488308 0 0.019934427 0.019968198 0.020471735 0.06037436
|
||||||
|
300 1484472.4 0 0.029397156 0.030749312 0.030121294 0.090267762
|
||||||
|
400 1517938.7 0 0.039217504 0.041440617 0.040512943 0.12117106
|
||||||
|
500 1492769.5 0 0.04890343 0.051561801 0.050614941 0.15108017
|
||||||
|
600 1510159.6 0 0.059770181 0.061650364 0.061298117 0.18271866
|
||||||
|
700 1485424.1 0 0.070537955 0.071144877 0.071141546 0.21282438
|
||||||
|
800 1496377.2 0 0.081291995 0.082546059 0.080653381 0.24449144
|
||||||
|
900 1484409.1 0 0.090940427 0.093298981 0.091328056 0.27556746
|
||||||
|
1000 1503322.4 0 0.10176921 0.10246052 0.10151773 0.30574747
|
||||||
|
1100 1503322.4 0 0.11295993 0.11052632 0.11053406 0.33402031
|
||||||
|
1200 1489236.2 0 0.12509723 0.11961982 0.12146498 0.36618203
|
||||||
|
1300 1476050.3 0 0.13449034 0.12941323 0.1309765 0.39488007
|
||||||
|
1400 1520818.7 0 0.14613571 0.13788044 0.14083944 0.42485558
|
||||||
|
1500 1498936.4 0 0.15752286 0.15057712 0.15063399 0.45873397
|
||||||
|
1600 1507524.1 0 0.16793678 0.16095681 0.16063531 0.4895289
|
||||||
|
1700 1480581.2 0 0.17748019 0.172614 0.16922383 0.51931802
|
||||||
|
1800 1505353.6 0 0.18850931 0.18304171 0.18063119 0.55218221
|
||||||
|
1900 1491234.7 0 0.19836402 0.19306339 0.1929707 0.58439811
|
||||||
|
2000 1519868.8 0 0.20698191 0.20211344 0.20328302 0.61237838
|
||||||
|
2100 1493919.5 0 0.21453524 0.21186097 0.21423293 0.64062914
|
||||||
|
2200 1517098.6 0 0.2257338 0.22381647 0.22474081 0.67429108
|
||||||
|
2300 1481270.7 0 0.23499747 0.23348379 0.23498244 0.70346369
|
||||||
|
2400 1495445.1 0 0.24535894 0.24290239 0.24229161 0.73055293
|
||||||
|
2500 1522839.3 0 0.25695938 0.25109669 0.25214541 0.76020148
|
||||||
|
2600 1518697.4 0 0.26680819 0.26120216 0.2604112 0.78842155
|
||||||
|
2700 1529283.1 0 0.27524422 0.26942681 0.27148042 0.81615146
|
||||||
|
2800 1500557.5 0 0.28436226 0.27957592 0.27935619 0.84329437
|
||||||
|
2900 1509711.1 0 0.2948528 0.28562401 0.29055956 0.87103637
|
||||||
|
3000 1522712.8 0 0.30347033 0.2975063 0.30121685 0.90219348
|
||||||
|
Loop time of 2.35056 on 1 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 1102.718 tau/day, 1276.293 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00077772 | 0.00077772 | 0.00077772 | 0.0 | 0.03
|
||||||
|
Comm | 0.010985 | 0.010985 | 0.010985 | 0.0 | 0.47
|
||||||
|
Output | 0.0045807 | 0.0045807 | 0.0045807 | 0.0 | 0.19
|
||||||
|
Modify | 2.2116 | 2.2116 | 2.2116 | 0.0 | 94.09
|
||||||
|
Other | | 0.1226 | | | 5.22
|
||||||
|
|
||||||
|
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 24
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:02
|
||||||
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.4
Normal file
119
examples/USER/brownian/point/log.11May2021.in3d.point.g++.4
Normal file
@ -0,0 +1,119 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of non-interacting point particles in 3D #####
|
||||||
|
|
||||||
|
variable rng string gaussian
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 5.0
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable params string ${rng}_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_${temp}_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_${gamma_t}
|
||||||
|
variable params string gaussian_5.0_1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass * 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian ${temp} ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 ${seed} rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng ${rng} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian 5.0 198098 rng gaussian gamma_t 1.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.672 | 2.672 | 2.672 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 1515328.2 0 0.010465453 0.010044629 0.0097242319 0.030234314
|
||||||
|
200 1510820.8 0 0.020658886 0.019954762 0.020008864 0.060622512
|
||||||
|
300 1482006.5 0 0.030402195 0.029802874 0.030047586 0.090252655
|
||||||
|
400 1492228.5 0 0.039622543 0.038899144 0.040381854 0.11890354
|
||||||
|
500 1494985.5 0 0.050523465 0.050022913 0.050186478 0.15073286
|
||||||
|
600 1516047.4 0 0.061111845 0.061433818 0.059195364 0.18174103
|
||||||
|
700 1510021.8 0 0.071636778 0.072829755 0.06946406 0.21393059
|
||||||
|
800 1505964.7 0 0.08240965 0.08433785 0.078799851 0.24554735
|
||||||
|
900 1491035.9 0 0.093659937 0.094517749 0.08812559 0.27630328
|
||||||
|
1000 1516599.6 0 0.10436496 0.10431759 0.097480868 0.30616342
|
||||||
|
1100 1495170.3 0 0.11468757 0.111397 0.1069763 0.33306087
|
||||||
|
1200 1500630.6 0 0.12360977 0.12264534 0.11583999 0.3620951
|
||||||
|
1300 1474889.5 0 0.13432447 0.13471694 0.12702491 0.39606632
|
||||||
|
1400 1487145.8 0 0.14573239 0.14431493 0.13669403 0.42674135
|
||||||
|
1500 1519496.7 0 0.15610742 0.15505416 0.14600182 0.4571634
|
||||||
|
1600 1525674.1 0 0.16728653 0.1649354 0.15562133 0.48784325
|
||||||
|
1700 1540725.4 0 0.17846447 0.17666562 0.16531781 0.52044791
|
||||||
|
1800 1512334.8 0 0.18872753 0.18538847 0.17450009 0.54861609
|
||||||
|
1900 1498371.4 0 0.19688928 0.19333299 0.18581712 0.5760394
|
||||||
|
2000 1546459.4 0 0.20955053 0.20243854 0.19613897 0.60812803
|
||||||
|
2100 1509712.9 0 0.21922567 0.20940597 0.20567239 0.63430404
|
||||||
|
2200 1509630.4 0 0.23067999 0.21856734 0.21619911 0.66544645
|
||||||
|
2300 1483929.1 0 0.24160803 0.231048 0.22617193 0.69882797
|
||||||
|
2400 1488492.1 0 0.25399491 0.24082678 0.23972356 0.73454526
|
||||||
|
2500 1508107.9 0 0.26608734 0.25316913 0.2486814 0.76793787
|
||||||
|
2600 1511952.1 0 0.27523956 0.2623673 0.25706539 0.79467225
|
||||||
|
2700 1488888.8 0 0.28518299 0.27425585 0.26728622 0.82672506
|
||||||
|
2800 1515428.4 0 0.29595429 0.28589969 0.27781327 0.85966725
|
||||||
|
2900 1504312.1 0 0.30393798 0.29533034 0.28725362 0.88652194
|
||||||
|
3000 1521521.3 0 0.31445132 0.30117607 0.29959324 0.91522062
|
||||||
|
Loop time of 0.708196 on 4 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 3660.004 tau/day, 4236.115 timesteps/s
|
||||||
|
97.2% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00020647 | 0.00021023 | 0.0002141 | 0.0 | 0.03
|
||||||
|
Comm | 0.0045607 | 0.0050649 | 0.0053098 | 0.4 | 0.72
|
||||||
|
Output | 0.0013759 | 0.002265 | 0.0037355 | 1.9 | 0.32
|
||||||
|
Modify | 0.57353 | 0.58931 | 0.6109 | 1.8 | 83.21
|
||||||
|
Other | | 0.1113 | | | 15.72
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1043 max 1001 min
|
||||||
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 25
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Total wall time: 0:00:00
|
||||||
45
examples/USER/brownian/sphere/in2d.sphere
Normal file
45
examples/USER/brownian/sphere/in2d.sphere
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
45
examples/USER/brownian/sphere/in3d.sphere
Normal file
45
examples/USER/brownian/sphere/in3d.sphere
Normal file
@ -0,0 +1,45 @@
|
|||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type &
|
||||||
|
# x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.1
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_5.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.005 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 20867.136 0 0.00040006704 0.00039570887 0 0.00079577592
|
||||||
|
200 20835.491 0 0.00077560901 0.00080455484 0 0.0015801638
|
||||||
|
300 20813.122 0 0.0011737739 0.0012172689 0 0.0023910428
|
||||||
|
400 21137.397 0 0.0015587675 0.0016096093 0 0.0031683768
|
||||||
|
500 21167.188 0 0.0019294105 0.0020251322 0 0.0039545428
|
||||||
|
600 21345.908 0 0.0023105313 0.0024111742 0 0.0047217054
|
||||||
|
700 21086.272 0 0.0027236116 0.0027846006 0 0.0055082122
|
||||||
|
800 20840.906 0 0.0031505299 0.0031810732 0 0.0063316031
|
||||||
|
900 20916.456 0 0.0035525852 0.0035981301 0 0.0071507153
|
||||||
|
1000 20752.249 0 0.0039147929 0.0039791172 0 0.0078939101
|
||||||
|
1100 20643.612 0 0.0042977921 0.0043701484 0 0.0086679405
|
||||||
|
1200 21085.63 0 0.0045584242 0.0047475091 0 0.0093059332
|
||||||
|
1300 20900.794 0 0.0049718803 0.0051481706 0 0.010120051
|
||||||
|
1400 20980.731 0 0.0054234603 0.0054230724 0 0.010846533
|
||||||
|
1500 20916.308 0 0.0058502946 0.0058114313 0 0.011661726
|
||||||
|
1600 20949.786 0 0.0062258463 0.006208129 0 0.012433975
|
||||||
|
1700 20531.205 0 0.0066276219 0.006595921 0 0.013223543
|
||||||
|
1800 21418.472 0 0.0070077409 0.007030461 0 0.014038202
|
||||||
|
1900 21291.928 0 0.0074052208 0.0074333041 0 0.014838525
|
||||||
|
2000 20893.895 0 0.0077407477 0.007901402 0 0.01564215
|
||||||
|
2100 21218.001 0 0.0080384756 0.0082611258 0 0.016299601
|
||||||
|
2200 21116.189 0 0.0084325164 0.008617977 0 0.017050493
|
||||||
|
2300 20718.83 0 0.0089455345 0.0091768161 0 0.018122351
|
||||||
|
2400 20719.164 0 0.0093666455 0.0095272546 0 0.0188939
|
||||||
|
2500 20991.382 0 0.009706795 0.0098256506 0 0.019532446
|
||||||
|
2600 20515.74 0 0.0099247069 0.010329841 0 0.020254548
|
||||||
|
2700 21001.55 0 0.010448354 0.010693502 0 0.021141855
|
||||||
|
2800 21363.824 0 0.010990971 0.011142092 0 0.022133063
|
||||||
|
2900 20497.025 0 0.011399704 0.011504868 0 0.022904573
|
||||||
|
3000 20726.572 0 0.011785354 0.01187482 0 0.023660175
|
||||||
|
Loop time of 1.76023 on 1 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 1472.538 tau/day, 1704.326 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.026518 | 0.026518 | 0.026518 | 0.0 | 1.51
|
||||||
|
Output | 0.0040107 | 0.0040107 | 0.0040107 | 0.0 | 0.23
|
||||||
|
Modify | 1.6194 | 1.6194 | 1.6194 | 0.0 | 92.00
|
||||||
|
Other | | 0.1103 | | | 6.27
|
||||||
|
|
||||||
|
Nlocal: 3600.00 ave 3600 max 3600 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 121.000 ave 121 max 121 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in2d.sphere.g++.4
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 2D #####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_5.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -30 30 -30 30 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-47.434165 -47.434165 -0.31622777) to (47.434165 47.434165 0.31622777)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
3600 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_2d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 0.99972222 0 0 0 0 0
|
||||||
|
100 21085.797 0 0.00042014118 0.00040399828 0 0.00082413946
|
||||||
|
200 20598.717 0 0.00081715618 0.00082613236 0 0.0016432885
|
||||||
|
300 21040.226 0 0.0012412527 0.0012520475 0 0.0024933002
|
||||||
|
400 21289.734 0 0.0016129899 0.001634482 0 0.003247472
|
||||||
|
500 20951.595 0 0.0020104279 0.0020197694 0 0.0040301973
|
||||||
|
600 20984.974 0 0.0023965593 0.0024277086 0 0.0048242679
|
||||||
|
700 21252.602 0 0.0028349303 0.0028407812 0 0.0056757114
|
||||||
|
800 20951.95 0 0.0032674595 0.0032573476 0 0.0065248071
|
||||||
|
900 20828.611 0 0.003647953 0.0036650963 0 0.0073130493
|
||||||
|
1000 21073.256 0 0.0040238604 0.0040103537 0 0.0080342142
|
||||||
|
1100 21104.396 0 0.0043694059 0.0044146515 0 0.0087840574
|
||||||
|
1200 20580.591 0 0.0047638237 0.0047646659 0 0.0095284896
|
||||||
|
1300 20667.623 0 0.0051512568 0.0051134445 0 0.010264701
|
||||||
|
1400 20466.72 0 0.0055921578 0.005517863 0 0.011110021
|
||||||
|
1500 20842.366 0 0.0059747304 0.0059374031 0 0.011912134
|
||||||
|
1600 20867.02 0 0.0065493697 0.0064163066 0 0.012965676
|
||||||
|
1700 21021.077 0 0.0070208005 0.0068164842 0 0.013837285
|
||||||
|
1800 21191.183 0 0.0073708939 0.0073226521 0 0.014693546
|
||||||
|
1900 20792.8 0 0.0076984189 0.0077400043 0 0.015438423
|
||||||
|
2000 21296.326 0 0.0081882545 0.0081503672 0 0.016338622
|
||||||
|
2100 21085.097 0 0.008596146 0.0086041272 0 0.017200273
|
||||||
|
2200 20506.523 0 0.0089905439 0.0091045462 0 0.01809509
|
||||||
|
2300 21068.555 0 0.0094163509 0.0094703314 0 0.018886682
|
||||||
|
2400 21128.867 0 0.0097349212 0.0098535832 0 0.019588504
|
||||||
|
2500 21009.514 0 0.010218059 0.010244621 0 0.020462679
|
||||||
|
2600 21177.52 0 0.01060437 0.010642719 0 0.021247089
|
||||||
|
2700 20832.56 0 0.011052623 0.011078899 0 0.022131522
|
||||||
|
2800 21298.053 0 0.011439708 0.011587702 0 0.023027411
|
||||||
|
2900 21002.28 0 0.011863624 0.01199682 0 0.023860443
|
||||||
|
3000 20737.939 0 0.012229608 0.012324579 0 0.024554186
|
||||||
|
Loop time of 0.492798 on 4 procs for 3000 steps with 3600 atoms
|
||||||
|
|
||||||
|
Performance: 5259.763 tau/day, 6087.689 timesteps/s
|
||||||
|
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.018005 | 0.021524 | 0.025207 | 2.2 | 4.37
|
||||||
|
Output | 0.0013187 | 0.0018334 | 0.0032332 | 1.9 | 0.37
|
||||||
|
Modify | 0.37545 | 0.38775 | 0.40664 | 1.9 | 78.68
|
||||||
|
Other | | 0.08169 | | | 16.58
|
||||||
|
|
||||||
|
Nlocal: 900.000 ave 900 max 900 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 61.0000 ave 61 max 61 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:00
|
||||||
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.1
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_5.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.005 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 32032.279 0 0.00040227568 0.00039159837 0.00040147813 0.0011953522
|
||||||
|
200 31673.093 0 0.00077657885 0.00077292327 0.00079963705 0.0023491392
|
||||||
|
300 31476.164 0 0.0011712083 0.0011606723 0.0012089537 0.0035408343
|
||||||
|
400 31911.374 0 0.0015803424 0.001562091 0.0016042321 0.0047466655
|
||||||
|
500 31182.011 0 0.0019677217 0.0019269105 0.0020015977 0.0058962298
|
||||||
|
600 31206.05 0 0.0023360975 0.0023134398 0.0024213372 0.0070708745
|
||||||
|
700 31278.057 0 0.0026966955 0.0027129858 0.0028721373 0.0082818187
|
||||||
|
800 31677.724 0 0.0031197964 0.003134834 0.0032726303 0.0095272607
|
||||||
|
900 31312.741 0 0.0035636612 0.0035573653 0.0037328373 0.010853864
|
||||||
|
1000 31426.075 0 0.0039774626 0.003952159 0.0041879386 0.01211756
|
||||||
|
1100 31361.699 0 0.0044256852 0.004320566 0.004638132 0.013384383
|
||||||
|
1200 31559.778 0 0.0048338539 0.0047210601 0.0050296056 0.01458452
|
||||||
|
1300 31716.797 0 0.0052239651 0.0050796723 0.0054794684 0.015783106
|
||||||
|
1400 31231.077 0 0.0055890568 0.005472377 0.0059264123 0.016987846
|
||||||
|
1500 31605.513 0 0.0059876582 0.0058974054 0.0063452478 0.018230311
|
||||||
|
1600 31551.402 0 0.006413094 0.0062665632 0.0067442106 0.019423868
|
||||||
|
1700 31725.868 0 0.0068244611 0.0067189707 0.0071424779 0.02068591
|
||||||
|
1800 31385.794 0 0.0071570297 0.0070502303 0.0075240296 0.02173129
|
||||||
|
1900 31754.094 0 0.0075638662 0.0074243015 0.0079935325 0.0229817
|
||||||
|
2000 31668.959 0 0.0080059944 0.0079019753 0.0084000614 0.024308031
|
||||||
|
2100 31781.994 0 0.0084108141 0.0082719077 0.0088004977 0.02548322
|
||||||
|
2200 31455.021 0 0.0088844434 0.0086931769 0.0091916929 0.026769313
|
||||||
|
2300 31273.079 0 0.0093155639 0.0091027782 0.0095364621 0.027954804
|
||||||
|
2400 31283.781 0 0.0098441686 0.0094496218 0.0099279073 0.029221698
|
||||||
|
2500 31758.315 0 0.010372129 0.0097843406 0.010334653 0.030491123
|
||||||
|
2600 31780.442 0 0.010770862 0.010313119 0.010637545 0.031721525
|
||||||
|
2700 31552.277 0 0.011268703 0.010693437 0.01110762 0.033069759
|
||||||
|
2800 31124.693 0 0.011661333 0.011100115 0.011480624 0.034242072
|
||||||
|
2900 31438.795 0 0.012068847 0.011346633 0.011842006 0.035257486
|
||||||
|
3000 31574.258 0 0.012482632 0.011691477 0.012210207 0.036384317
|
||||||
|
Loop time of 2.8531 on 1 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 908.486 tau/day, 1051.488 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 3.2425e-05 | 3.2425e-05 | 3.2425e-05 | 0.0 | 0.00
|
||||||
|
Comm | 0.13219 | 0.13219 | 0.13219 | 0.0 | 4.63
|
||||||
|
Output | 0.0045686 | 0.0045686 | 0.0045686 | 0.0 | 0.16
|
||||||
|
Modify | 2.5857 | 2.5857 | 2.5857 | 0.0 | 90.63
|
||||||
|
Other | | 0.1307 | | | 4.58
|
||||||
|
|
||||||
|
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4
Normal file
126
examples/USER/brownian/sphere/log.11May2021.in3d.sphere.g++.4
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
##### overdamped dynamics of a sphere (with dipole attached to it) in 3D#####
|
||||||
|
|
||||||
|
variable rng string uniform
|
||||||
|
variable seed string 198098
|
||||||
|
variable temp string 1.0
|
||||||
|
variable gamma_t string 5.0
|
||||||
|
variable gamma_r string 0.7
|
||||||
|
variable params string ${rng}_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_${temp}_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_${gamma_r}_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_${gamma_t}
|
||||||
|
variable params string uniform_1.0_0.7_5.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.006 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 198098 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
fix 1 all brownian/sphere ${temp} ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 ${seed} rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng ${rng} gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r ${gamma_r} gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t ${gamma_t}
|
||||||
|
fix 1 all brownian/sphere 1.0 198098 rng uniform gamma_r 0.7 gamma_t 5.0
|
||||||
|
|
||||||
|
#initialisation for the main run
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*]
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump_${params}_3d.lammpstrj id type # x y z xu yu zu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 3000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4]
|
||||||
|
0 1.4996338 0 0 0 0 0
|
||||||
|
100 30882.707 0 0.00040787161 0.00039391576 0.00040796913 0.0012097565
|
||||||
|
200 31370.751 0 0.00081742036 0.00078240455 0.0008195167 0.0024193416
|
||||||
|
300 31469.51 0 0.0012118299 0.0011819412 0.0012477119 0.003641483
|
||||||
|
400 31696.58 0 0.0015540547 0.0015849689 0.0015836091 0.0047226327
|
||||||
|
500 31488.269 0 0.0019638041 0.0019659637 0.0020547832 0.005984551
|
||||||
|
600 30942.589 0 0.0023273784 0.0023572171 0.0024715245 0.00715612
|
||||||
|
700 31228.473 0 0.0027821732 0.002735338 0.0028734675 0.0083909787
|
||||||
|
800 31426.92 0 0.0031663838 0.0031092782 0.0033231014 0.0095987634
|
||||||
|
900 31447.595 0 0.003539588 0.003564381 0.003753036 0.010857005
|
||||||
|
1000 31363.911 0 0.0039854308 0.003937555 0.0041203919 0.012043378
|
||||||
|
1100 31522.958 0 0.0043009285 0.0043676491 0.0044799414 0.013148519
|
||||||
|
1200 31403.033 0 0.0046361199 0.0047513598 0.0049014974 0.014288977
|
||||||
|
1300 31752.182 0 0.0049824718 0.0051327113 0.0053130614 0.015428244
|
||||||
|
1400 31336.955 0 0.0054251445 0.0055442325 0.0057472998 0.016716677
|
||||||
|
1500 31224.306 0 0.0059295596 0.0059920697 0.0061375228 0.018059152
|
||||||
|
1600 31744.535 0 0.0063845142 0.0063600989 0.0064833215 0.019227935
|
||||||
|
1700 31472.081 0 0.0068360092 0.0067985824 0.0069464303 0.020581022
|
||||||
|
1800 31577.334 0 0.0073001079 0.0071355564 0.0073400543 0.021775719
|
||||||
|
1900 31521.234 0 0.0077178677 0.0074371106 0.007708008 0.022862986
|
||||||
|
2000 31045.148 0 0.0080515968 0.0078583776 0.0081000219 0.024009996
|
||||||
|
2100 31289.809 0 0.0084280175 0.0082322226 0.0084475904 0.02510783
|
||||||
|
2200 31505.455 0 0.008802925 0.0085708943 0.0087648194 0.026138639
|
||||||
|
2300 31882.722 0 0.0092223105 0.0089242925 0.0092643028 0.027410906
|
||||||
|
2400 31028.15 0 0.0095737559 0.0093585981 0.0096771837 0.028609538
|
||||||
|
2500 31581.041 0 0.0099316284 0.009785264 0.010100235 0.029817127
|
||||||
|
2600 31272.119 0 0.010332986 0.01007291 0.010474606 0.030880502
|
||||||
|
2700 31537.8 0 0.010751592 0.010565273 0.01093107 0.032247935
|
||||||
|
2800 31060.697 0 0.011156729 0.011010751 0.011260025 0.033427506
|
||||||
|
2900 31541.612 0 0.011542003 0.011499419 0.011642873 0.034684295
|
||||||
|
3000 31305.382 0 0.011876832 0.011866445 0.012052577 0.035795854
|
||||||
|
Loop time of 1.00142 on 4 procs for 3000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 2588.329 tau/day, 2995.751 timesteps/s
|
||||||
|
95.2% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.084416 | 0.10685 | 0.12695 | 5.7 | 10.67
|
||||||
|
Output | 0.001471 | 0.0019466 | 0.0033245 | 1.8 | 0.19
|
||||||
|
Modify | 0.66585 | 0.70645 | 0.78995 | 6.0 | 70.54
|
||||||
|
Other | | 0.1862 | | | 18.59
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 353.000 ave 353 max 353 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:01
|
||||||
60
examples/USER/brownian/spherical_ABP/in2d.abp
Normal file
60
examples/USER/brownian/spherical_ABP/in2d.abp
Normal file
@ -0,0 +1,60 @@
|
|||||||
|
# 2D overdamped active brownian particle dynamics (ABP)
|
||||||
|
# with WCA potential
|
||||||
|
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
# more careful with neighbors since higher diffusion in abps
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
# WCA potential (purely repulsive)
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0 1.1224
|
||||||
|
pair_modify shift yes
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step pe ke c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 20000
|
||||||
67
examples/USER/brownian/spherical_ABP/in3d.ideal_abp
Normal file
67
examples/USER/brownian/spherical_ABP/in3d.ideal_abp
Normal file
@ -0,0 +1,67 @@
|
|||||||
|
# 3D overdamped active brownian dynamics with no interactions
|
||||||
|
|
||||||
|
variable gamma_t string 3.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
create_atoms 1 box
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||||
|
# brownian motion, which is
|
||||||
|
#
|
||||||
|
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||||
|
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||||
|
#
|
||||||
|
# with d being simulation dimension
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
|
||||||
|
# if you want to check that rotational diffusion is behaving as expected,
|
||||||
|
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||||
|
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||||
|
# being simulation dimension)
|
||||||
|
|
||||||
|
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type &
|
||||||
|
# x y xu yu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
#run 120000
|
||||||
@ -0,0 +1,221 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 2D overdamped active brownian particle dynamics (ABP)
|
||||||
|
# with WCA potential
|
||||||
|
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_1.0_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_1.0_1.0_${fp}
|
||||||
|
variable params string 1.0_1.0_1.0_4.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1024 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 1974019 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
1024 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
# more careful with neighbors since higher diffusion in abps
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
# WCA potential (purely repulsive)
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0 1.1224
|
||||||
|
pair_modify shift yes
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
fix activity all propel/self dipole 4.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step pe ke c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 1 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.1224
|
||||||
|
ghost atom cutoff = 2.1224
|
||||||
|
binsize = 1.0612, bins = 48 48 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/2d/newtoff
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes
|
||||||
|
Step PotEng KinEng c_press
|
||||||
|
0 0 0.99902344 -0.53979198
|
||||||
|
100 0 1.026585e+10 -0.5398101
|
||||||
|
200 0 1.0630628e+10 -0.53977393
|
||||||
|
300 0 1.03483e+10 -0.53977041
|
||||||
|
400 0 1.049279e+10 -0.53974314
|
||||||
|
500 0 1.0832067e+10 -0.53979451
|
||||||
|
600 0 1.0403632e+10 -0.53976233
|
||||||
|
700 0 1.0334726e+10 -0.53976174
|
||||||
|
800 0 1.0119596e+10 -0.53969338
|
||||||
|
900 0 1.0786136e+10 -0.53970415
|
||||||
|
1000 0 1.0539036e+10 -0.53974577
|
||||||
|
1100 0 1.0643695e+10 -0.53982431
|
||||||
|
1200 0 1.0234642e+10 -0.53976823
|
||||||
|
1300 0 1.036268e+10 -0.53981454
|
||||||
|
1400 0 1.0605702e+10 -0.53988117
|
||||||
|
1500 0 1.0517916e+10 -0.53989207
|
||||||
|
1600 0 1.0564482e+10 -0.53993016
|
||||||
|
1700 0 1.0460152e+10 -0.53984454
|
||||||
|
1800 0 1.0468566e+10 -0.53985574
|
||||||
|
1900 0 1.0474075e+10 -0.53985439
|
||||||
|
2000 0 1.0683568e+10 -0.53987349
|
||||||
|
2100 0 1.0269077e+10 -0.53990709
|
||||||
|
2200 0 1.0386943e+10 -0.53990068
|
||||||
|
2300 0 1.0406078e+10 -0.53978402
|
||||||
|
2400 0 1.0482072e+10 -0.53980757
|
||||||
|
2500 0 1.0442975e+10 -0.53982657
|
||||||
|
2600 0 1.0292103e+10 -0.53985533
|
||||||
|
2700 0 1.1106453e+10 -0.53991861
|
||||||
|
2800 0 1.0395289e+10 -0.53990138
|
||||||
|
2900 0 1.034021e+10 -0.53992375
|
||||||
|
3000 0 1.0434718e+10 -0.53995566
|
||||||
|
3100 0 1.0194094e+10 -0.53993997
|
||||||
|
3200 0 1.0411552e+10 -0.54000097
|
||||||
|
3300 0 1.0214175e+10 -0.53999884
|
||||||
|
3400 0 1.0434719e+10 -0.54000005
|
||||||
|
3500 0 1.0529638e+10 -0.53998281
|
||||||
|
3600 0 1.0406541e+10 -0.54000141
|
||||||
|
3700 0 1.0577151e+10 -0.54002354
|
||||||
|
3800 0 1.0488249e+10 -0.53996003
|
||||||
|
3900 0 1.0316153e+10 -0.54002024
|
||||||
|
4000 0 1.0491289e+10 -0.5400259
|
||||||
|
4100 0 1.0587981e+10 -0.5399811
|
||||||
|
4200 0 1.0332035e+10 -0.53997951
|
||||||
|
4300 0 1.0776469e+10 -0.53994151
|
||||||
|
4400 0 1.0982142e+10 -0.53983842
|
||||||
|
4500 0 1.0796919e+10 -0.5398414
|
||||||
|
4600 0 1.0324249e+10 -0.53979712
|
||||||
|
4700 0 1.0420899e+10 -0.53981967
|
||||||
|
4800 0 1.0274188e+10 -0.53976759
|
||||||
|
4900 0 1.0411535e+10 -0.5397757
|
||||||
|
5000 0 1.0399215e+10 -0.53980199
|
||||||
|
Loop time of 1.34285 on 1 procs for 5000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 0.032 tau/day, 3723.422 timesteps/s
|
||||||
|
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.25309 | 0.25309 | 0.25309 | 0.0 | 18.85
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.068734 | 0.068734 | 0.068734 | 0.0 | 5.12
|
||||||
|
Output | 0.0012887 | 0.0012887 | 0.0012887 | 0.0 | 0.10
|
||||||
|
Modify | 0.96552 | 0.96552 | 0.96552 | 0.0 | 71.90
|
||||||
|
Other | | 0.05422 | | | 4.04
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 201.000 ave 201 max 201 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2112.00 ave 2112 max 2112 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2112
|
||||||
|
Ave neighs/atom = 2.0625000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 20000
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes
|
||||||
|
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 1.0409381e+10 0 0 0 0 0 -0.53980199
|
||||||
|
1000 107022.73 0.0080050427 0.020451432 0.021388798 0 0.04184023 -0.54900967
|
||||||
|
2000 107475.82 0.017262846 0.040669645 0.044251149 0 0.084920794 -0.42740968
|
||||||
|
3000 105388.35 0.042257875 0.062828995 0.05845782 0 0.12128682 -0.31792184
|
||||||
|
4000 106238.38 0.052733384 0.079036841 0.079396453 0 0.15843329 -0.24243699
|
||||||
|
5000 102904.54 0.088524456 0.095977642 0.099533961 0 0.1955116 -0.093468615
|
||||||
|
6000 105274.15 0.065334999 0.11591691 0.11675531 0 0.23267222 -0.21904478
|
||||||
|
7000 108903.41 0.06724271 0.13694218 0.13914947 0 0.27609164 -0.15913012
|
||||||
|
8000 101451.44 0.097201152 0.15704893 0.16178845 0 0.31883738 -0.055786965
|
||||||
|
9000 106808.72 0.084301668 0.18029391 0.175753 0 0.3560469 0.014898739
|
||||||
|
10000 107381.19 0.088583354 0.2000753 0.19569789 0 0.39577319 0.19417596
|
||||||
|
11000 102105.78 0.081066654 0.22042599 0.21914042 0 0.43956641 0.060574143
|
||||||
|
12000 105384.94 0.098716908 0.24382064 0.24673594 0 0.49055657 0.17067875
|
||||||
|
13000 107479.53 0.099989043 0.26942088 0.27207566 0 0.54149654 0.25514896
|
||||||
|
14000 102938.12 0.093252916 0.28529564 0.28698837 0 0.57228401 0.19976355
|
||||||
|
15000 104408.02 0.11900926 0.31291315 0.31195058 0 0.62486373 0.36956014
|
||||||
|
16000 103447.68 0.09627777 0.34145225 0.33159885 0 0.6730511 0.29857404
|
||||||
|
17000 108400.05 0.11433561 0.36561966 0.36068301 0 0.72630267 0.41922801
|
||||||
|
18000 103363.68 0.11040153 0.38709746 0.39228677 0 0.77938423 0.38111686
|
||||||
|
19000 103310.43 0.10660536 0.41406235 0.40975085 0 0.8238132 0.36022184
|
||||||
|
20000 102692.1 0.13517651 0.43870812 0.44138776 0 0.88009588 0.51144366
|
||||||
|
Loop time of 5.66207 on 1 procs for 20000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 3051.889 tau/day, 3532.279 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 1.3123 | 1.3123 | 1.3123 | 0.0 | 23.18
|
||||||
|
Neigh | 0.011856 | 0.011856 | 0.011856 | 0.0 | 0.21
|
||||||
|
Comm | 0.2747 | 0.2747 | 0.2747 | 0.0 | 4.85
|
||||||
|
Output | 0.0011516 | 0.0011516 | 0.0011516 | 0.0 | 0.02
|
||||||
|
Modify | 3.8451 | 3.8451 | 3.8451 | 0.0 | 67.91
|
||||||
|
Other | | 0.2169 | | | 3.83
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 184.000 ave 184 max 184 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 2558.00 ave 2558 max 2558 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2558
|
||||||
|
Ave neighs/atom = 2.4980469
|
||||||
|
Neighbor list builds = 23
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:07
|
||||||
@ -0,0 +1,221 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 2D overdamped active brownian particle dynamics (ABP)
|
||||||
|
# with WCA potential
|
||||||
|
|
||||||
|
variable gamma_t string 1.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_1.0_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_1.0_1.0_${fp}
|
||||||
|
variable params string 1.0_1.0_1.0_4.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 2
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sq 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.5811388 1.5811388 1.5811388
|
||||||
|
region box block -16 16 -16 16 -0.2 0.2
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-25.298221 -25.298221 -0.31622777) to (25.298221 25.298221 0.31622777)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 1024 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 1974019 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
1024 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
# more careful with neighbors since higher diffusion in abps
|
||||||
|
neighbor 1.0 bin
|
||||||
|
neigh_modify every 1 delay 1 check yes
|
||||||
|
|
||||||
|
# WCA potential (purely repulsive)
|
||||||
|
pair_style lj/cut 2.5
|
||||||
|
pair_coeff * * 1.0 1.0 1.1224
|
||||||
|
pair_modify shift yes
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 1.0 gamma_r 1.0
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
fix activity all propel/self dipole 4.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step pe ke c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 1 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 2.1224
|
||||||
|
ghost atom cutoff = 2.1224
|
||||||
|
binsize = 1.0612, bins = 48 48 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton off
|
||||||
|
pair build: half/bin/newtoff
|
||||||
|
stencil: half/bin/2d/newtoff
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes
|
||||||
|
Step PotEng KinEng c_press
|
||||||
|
0 0 0.99902344 -0.53979198
|
||||||
|
100 0 1.0503521e+10 -0.53983092
|
||||||
|
200 0 1.0390343e+10 -0.5398287
|
||||||
|
300 0 1.0493441e+10 -0.53979247
|
||||||
|
400 0 1.0545991e+10 -0.53978678
|
||||||
|
500 0 1.0266398e+10 -0.53986297
|
||||||
|
600 0 1.0484775e+10 -0.53978746
|
||||||
|
700 0 1.0583596e+10 -0.53969114
|
||||||
|
800 0 1.0521919e+10 -0.53968754
|
||||||
|
900 0 1.0492019e+10 -0.53958643
|
||||||
|
1000 0 1.0298052e+10 -0.53949872
|
||||||
|
1100 0 1.0531424e+10 -0.53955431
|
||||||
|
1200 0 1.0635635e+10 -0.53960048
|
||||||
|
1300 0 1.0633405e+10 -0.53966331
|
||||||
|
1400 0 1.0195401e+10 -0.53968849
|
||||||
|
1500 0 1.0593758e+10 -0.53969763
|
||||||
|
1600 0 1.0425238e+10 -0.53971936
|
||||||
|
1700 0 1.0470017e+10 -0.53981957
|
||||||
|
1800 0 1.0545953e+10 -0.53987747
|
||||||
|
1900 0 1.0425015e+10 -0.53990412
|
||||||
|
2000 0 1.0655092e+10 -0.5399511
|
||||||
|
2100 0 1.0197224e+10 -0.53988687
|
||||||
|
2200 0 1.0448012e+10 -0.53986066
|
||||||
|
2300 0 1.0355268e+10 -0.53980415
|
||||||
|
2400 0 1.0246979e+10 -0.53979737
|
||||||
|
2500 0 1.0021539e+10 -0.5397919
|
||||||
|
2600 0 1.0200824e+10 -0.5397575
|
||||||
|
2700 0 1.0721591e+10 -0.53973512
|
||||||
|
2800 0 1.0354562e+10 -0.5397127
|
||||||
|
2900 0 1.0306795e+10 -0.5396946
|
||||||
|
3000 0 1.0301339e+10 -0.53968642
|
||||||
|
3100 0 1.0435826e+10 -0.53970945
|
||||||
|
3200 0 1.019524e+10 -0.53969746
|
||||||
|
3300 0 1.0550481e+10 -0.53967977
|
||||||
|
3400 0 1.0283446e+10 -0.53971102
|
||||||
|
3500 0 1.0956695e+10 -0.53976173
|
||||||
|
3600 0 1.0271033e+10 -0.53983632
|
||||||
|
3700 0 1.0389461e+10 -0.53977293
|
||||||
|
3800 0 1.0680515e+10 -0.53977425
|
||||||
|
3900 0 1.0072183e+10 -0.53982922
|
||||||
|
4000 0 1.0458036e+10 -0.53980042
|
||||||
|
4100 0 1.0588689e+10 -0.53971405
|
||||||
|
4200 0 1.0068308e+10 -0.5398033
|
||||||
|
4300 0 1.0502064e+10 -0.53981291
|
||||||
|
4400 0 1.0590544e+10 -0.5398346
|
||||||
|
4500 0 1.0411612e+10 -0.5397916
|
||||||
|
4600 0 1.0518596e+10 -0.53984868
|
||||||
|
4700 0 1.0386105e+10 -0.53977803
|
||||||
|
4800 0 1.029525e+10 -0.53970882
|
||||||
|
4900 0 1.0519112e+10 -0.53969616
|
||||||
|
5000 0 1.0335841e+10 -0.53976477
|
||||||
|
Loop time of 0.471663 on 4 procs for 5000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 0.092 tau/day, 10600.781 timesteps/s
|
||||||
|
95.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.067099 | 0.07105 | 0.077898 | 1.6 | 15.06
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.0581 | 0.066084 | 0.072322 | 2.0 | 14.01
|
||||||
|
Output | 0.0014644 | 0.002618 | 0.0037239 | 1.6 | 0.56
|
||||||
|
Modify | 0.24817 | 0.25719 | 0.26697 | 1.3 | 54.53
|
||||||
|
Other | | 0.07472 | | | 15.84
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 256 max 256 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 105.000 ave 105 max 105 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 544.000 ave 544 max 544 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2176
|
||||||
|
Ave neighs/atom = 2.1250000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
|
||||||
|
# MSD
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step temp epair c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 20000
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 5.427 | 5.427 | 5.427 Mbytes
|
||||||
|
Step Temp E_pair c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 1.0345945e+10 0 0 0 0 0 -0.53976477
|
||||||
|
1000 100114.28 0.0029703577 0.020320684 0.020950989 0 0.041271673 -0.43948247
|
||||||
|
2000 106825.83 0.020969054 0.039616412 0.039459167 0 0.079075578 -0.22765541
|
||||||
|
3000 105287.4 0.037343571 0.056828177 0.058639835 0 0.11546801 -0.11728136
|
||||||
|
4000 104522.23 0.052237136 0.080264931 0.080863543 0 0.16112847 0.033230576
|
||||||
|
5000 103277.94 0.053791862 0.099188864 0.10141444 0 0.20060331 0.073591503
|
||||||
|
6000 104252.87 0.073304776 0.11964238 0.1215576 0 0.24119999 0.22062305
|
||||||
|
7000 105184.19 0.089054043 0.13691291 0.14216478 0 0.27907769 0.29015692
|
||||||
|
8000 104211.82 0.072577918 0.15820522 0.15658491 0 0.31479013 0.25908291
|
||||||
|
9000 99242.172 0.071616004 0.17658708 0.17479704 0 0.35138412 0.26305532
|
||||||
|
10000 105070.83 0.077009979 0.20175025 0.19871513 0 0.40046538 0.34120567
|
||||||
|
11000 106421.07 0.098623061 0.22472634 0.22671582 0 0.45144216 0.44021335
|
||||||
|
12000 103209.85 0.12032847 0.25004966 0.25368441 0 0.50373406 0.57344873
|
||||||
|
13000 107156.89 0.1058386 0.27283231 0.2744873 0 0.54731961 0.47957408
|
||||||
|
14000 108119.3 0.1204768 0.29333677 0.30054535 0 0.59388213 0.51832639
|
||||||
|
15000 105477.62 0.12510026 0.32217621 0.32806599 0 0.6502422 0.50174158
|
||||||
|
16000 106676.27 0.10893618 0.34980866 0.36031184 0 0.7101205 0.44769198
|
||||||
|
17000 103048.41 0.10625673 0.3781797 0.37970499 0 0.75788468 0.42803898
|
||||||
|
18000 109454.8 0.10555778 0.40997694 0.41396777 0 0.82394471 0.41380982
|
||||||
|
19000 107459.73 0.11267582 0.43757738 0.43577856 0 0.87335594 0.4917748
|
||||||
|
20000 101991.9 0.084279008 0.45363612 0.46278076 0 0.91641688 0.41707912
|
||||||
|
Loop time of 1.80877 on 4 procs for 20000 steps with 1024 atoms
|
||||||
|
|
||||||
|
Performance: 9553.439 tau/day, 11057.221 timesteps/s
|
||||||
|
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.34461 | 0.36424 | 0.40948 | 4.4 | 20.14
|
||||||
|
Neigh | 0.0031493 | 0.003215 | 0.0032432 | 0.1 | 0.18
|
||||||
|
Comm | 0.19538 | 0.20419 | 0.2104 | 1.2 | 11.29
|
||||||
|
Output | 0.00054121 | 0.00087297 | 0.0018425 | 0.0 | 0.05
|
||||||
|
Modify | 0.98335 | 1.0156 | 1.0791 | 3.8 | 56.15
|
||||||
|
Other | | 0.2207 | | | 12.20
|
||||||
|
|
||||||
|
Nlocal: 256.000 ave 261 max 252 min
|
||||||
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||||
|
Nghost: 93.0000 ave 100 max 83 min
|
||||||
|
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||||
|
Neighs: 662.250 ave 693 max 635 min
|
||||||
|
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 2649
|
||||||
|
Ave neighs/atom = 2.5869141
|
||||||
|
Neighbor list builds = 23
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
@ -0,0 +1,210 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 3D overdamped active brownian dynamics with no interactions
|
||||||
|
|
||||||
|
variable gamma_t string 3.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_3.0_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_3.0_1.0_${fp}
|
||||||
|
variable params string 1.0_3.0_1.0_4.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.004 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 1974019 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
fix activity all propel/self dipole 4.0
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.362 | 4.362 | 4.362 Mbytes
|
||||||
|
Step KinEng PotEng c_press
|
||||||
|
0 1.4996338 0 0.068021726
|
||||||
|
100 5.184227e+09 0 0.06801544
|
||||||
|
200 5.2165482e+09 0 0.068010729
|
||||||
|
300 5.2782092e+09 0 0.068009058
|
||||||
|
400 5.3244927e+09 0 0.068003481
|
||||||
|
500 5.2376606e+09 0 0.067998237
|
||||||
|
600 5.2735634e+09 0 0.067998037
|
||||||
|
700 5.2692439e+09 0 0.068025402
|
||||||
|
800 5.2667984e+09 0 0.068030143
|
||||||
|
900 5.242057e+09 0 0.0680246
|
||||||
|
1000 5.2557468e+09 0 0.068028348
|
||||||
|
1100 5.2975687e+09 0 0.068029528
|
||||||
|
1200 5.2081927e+09 0 0.068017542
|
||||||
|
1300 5.2636873e+09 0 0.068012572
|
||||||
|
1400 5.2187907e+09 0 0.06802049
|
||||||
|
1500 5.2349541e+09 0 0.0680373
|
||||||
|
1600 5.216092e+09 0 0.068056885
|
||||||
|
1700 5.2598019e+09 0 0.068069504
|
||||||
|
1800 5.2569065e+09 0 0.068065306
|
||||||
|
1900 5.2072055e+09 0 0.068074863
|
||||||
|
2000 5.2092961e+09 0 0.068061619
|
||||||
|
2100 5.2918572e+09 0 0.068076418
|
||||||
|
2200 5.2680626e+09 0 0.068072149
|
||||||
|
2300 5.242958e+09 0 0.06806486
|
||||||
|
2400 5.2494099e+09 0 0.06805038
|
||||||
|
2500 5.2055798e+09 0 0.068072194
|
||||||
|
2600 5.2264829e+09 0 0.068069312
|
||||||
|
2700 5.3557342e+09 0 0.068064812
|
||||||
|
2800 5.2186177e+09 0 0.068042942
|
||||||
|
2900 5.2652497e+09 0 0.068044214
|
||||||
|
3000 5.1894899e+09 0 0.068044801
|
||||||
|
3100 5.241524e+09 0 0.068056675
|
||||||
|
3200 5.1915006e+09 0 0.06805641
|
||||||
|
3300 5.2367825e+09 0 0.068049946
|
||||||
|
3400 5.2288011e+09 0 0.068060182
|
||||||
|
3500 5.2704335e+09 0 0.068070881
|
||||||
|
3600 5.2886558e+09 0 0.068050439
|
||||||
|
3700 5.1976022e+09 0 0.068045927
|
||||||
|
3800 5.1525512e+09 0 0.068054494
|
||||||
|
3900 5.2212395e+09 0 0.068061432
|
||||||
|
4000 5.2309575e+09 0 0.068070842
|
||||||
|
4100 5.2260184e+09 0 0.068078378
|
||||||
|
4200 5.2829349e+09 0 0.068071652
|
||||||
|
4300 5.2204917e+09 0 0.068083072
|
||||||
|
4400 5.255242e+09 0 0.068066175
|
||||||
|
4500 5.2435681e+09 0 0.068050802
|
||||||
|
4600 5.2483356e+09 0 0.06805658
|
||||||
|
4700 5.2365098e+09 0 0.068041845
|
||||||
|
4800 5.2254325e+09 0 0.068038583
|
||||||
|
4900 5.1842852e+09 0 0.068028401
|
||||||
|
5000 5.2240722e+09 0 0.068031544
|
||||||
|
Loop time of 5.14275 on 1 procs for 5000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 0.008 tau/day, 972.242 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.26842 | 0.26842 | 0.26842 | 0.0 | 5.22
|
||||||
|
Output | 0.0035088 | 0.0035088 | 0.0035088 | 0.0 | 0.07
|
||||||
|
Modify | 4.6588 | 4.6588 | 4.6588 | 0.0 | 90.59
|
||||||
|
Other | | 0.212 | | | 4.12
|
||||||
|
|
||||||
|
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 817.000 ave 817 max 817 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||||
|
# brownian motion, which is
|
||||||
|
#
|
||||||
|
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||||
|
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||||
|
#
|
||||||
|
# with d being simulation dimension
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.737 | 4.737 | 4.737 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 5.2240722e+09 0 0 0 0 0 0.068031544
|
||||||
|
1000 52651.581 0 0.0066842466 0.0067977045 0.0066831353 0.020165086 0.060774985
|
||||||
|
2000 52835.806 0 0.013693443 0.014008773 0.013518945 0.041221161 0.094748037
|
||||||
|
3000 52097.629 0 0.020666918 0.021696789 0.020665685 0.063029392 0.10673866
|
||||||
|
4000 52579.452 0 0.028145318 0.028504548 0.02830967 0.084959536 0.13358122
|
||||||
|
5000 51255.456 0 0.035019271 0.034644123 0.03638843 0.10605182 0.13507609
|
||||||
|
6000 52730.035 0 0.041412307 0.042689213 0.043339117 0.12744064 0.16497663
|
||||||
|
7000 52247.642 0 0.048119396 0.050556395 0.050706527 0.14938232 0.16360301
|
||||||
|
8000 52169.849 0 0.055241196 0.058678631 0.059373122 0.17329295 0.1676169
|
||||||
|
9000 52520.526 0 0.063519587 0.066592779 0.066988842 0.19710121 0.17142694
|
||||||
|
10000 53519.297 0 0.07164814 0.074576535 0.075619236 0.22184391 0.15619444
|
||||||
|
11000 52937.293 0 0.077992504 0.083184462 0.082988794 0.24416576 0.15257327
|
||||||
|
12000 51762.283 0 0.085959749 0.090992292 0.08984213 0.26679417 0.15996211
|
||||||
|
Loop time of 11.6748 on 1 procs for 12000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 888.063 tau/day, 1027.851 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.0024164 | 0.0024164 | 0.0024164 | 0.0 | 0.02
|
||||||
|
Comm | 0.048127 | 0.048127 | 0.048127 | 0.0 | 0.41
|
||||||
|
Output | 0.0019393 | 0.0019393 | 0.0019393 | 0.0 | 0.02
|
||||||
|
Modify | 11.12 | 11.12 | 11.12 | 0.0 | 95.24
|
||||||
|
Other | | 0.5027 | | | 4.31
|
||||||
|
|
||||||
|
Nlocal: 4096.00 ave 4096 max 4096 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 75
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# if you want to check that rotational diffusion is behaving as expected,
|
||||||
|
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||||
|
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||||
|
# being simulation dimension)
|
||||||
|
|
||||||
|
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
#run 120000
|
||||||
|
Total wall time: 0:00:16
|
||||||
@ -0,0 +1,210 @@
|
|||||||
|
LAMMPS (8 Apr 2021)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# 3D overdamped active brownian dynamics with no interactions
|
||||||
|
|
||||||
|
variable gamma_t string 3.0
|
||||||
|
variable gamma_r string 1.0
|
||||||
|
variable temp string 1.0
|
||||||
|
variable seed equal 1974019
|
||||||
|
variable fp string 4.0
|
||||||
|
variable params string ${temp}_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_${gamma_t}_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_3.0_${gamma_r}_${fp}
|
||||||
|
variable params string 1.0_3.0_1.0_${fp}
|
||||||
|
variable params string 1.0_3.0_1.0_4.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:156)
|
||||||
|
dimension 3
|
||||||
|
newton off
|
||||||
|
|
||||||
|
lattice sc 0.4
|
||||||
|
Lattice spacing in x,y,z = 1.3572088 1.3572088 1.3572088
|
||||||
|
region box block -8 8 -8 8 -8 8
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (-10.857670 -10.857670 -10.857670) to (10.857670 10.857670 10.857670)
|
||||||
|
2 by 1 by 2 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 4096 atoms
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
mass * 1.0
|
||||||
|
set type * dipole/random ${seed} 1.0
|
||||||
|
set type * dipole/random 1974019 1.0
|
||||||
|
Setting atom values ...
|
||||||
|
4096 settings made for dipole/random
|
||||||
|
velocity all create 1.0 1 loop geom
|
||||||
|
|
||||||
|
pair_style none
|
||||||
|
|
||||||
|
# overdamped brownian dynamics time-step
|
||||||
|
fix step all brownian/sphere ${temp} ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 ${seed} gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t ${gamma_t} gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r ${gamma_r}
|
||||||
|
fix step all brownian/sphere 1.0 1974019 gamma_t 3.0 gamma_r 1.0
|
||||||
|
# self-propulsion force along the dipole direction
|
||||||
|
fix activity all propel/self dipole ${fp}
|
||||||
|
fix activity all propel/self dipole 4.0
|
||||||
|
|
||||||
|
compute press all pressure NULL virial
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_press
|
||||||
|
|
||||||
|
#equilibration
|
||||||
|
timestep 0.0000000001
|
||||||
|
thermo 100
|
||||||
|
run 5000
|
||||||
|
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2141)
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.319 | 4.319 | 4.319 Mbytes
|
||||||
|
Step KinEng PotEng c_press
|
||||||
|
0 1.4996338 0 0.068021726
|
||||||
|
100 5.2484581e+09 0 0.068010768
|
||||||
|
200 5.277936e+09 0 0.068024039
|
||||||
|
300 5.2651427e+09 0 0.068014821
|
||||||
|
400 5.2066432e+09 0 0.068027583
|
||||||
|
500 5.2250276e+09 0 0.068030242
|
||||||
|
600 5.239771e+09 0 0.068018406
|
||||||
|
700 5.1953674e+09 0 0.068017081
|
||||||
|
800 5.2097107e+09 0 0.068010167
|
||||||
|
900 5.2559863e+09 0 0.068012923
|
||||||
|
1000 5.2743197e+09 0 0.068017855
|
||||||
|
1100 5.1999741e+09 0 0.068014189
|
||||||
|
1200 5.3216344e+09 0 0.068005604
|
||||||
|
1300 5.2839264e+09 0 0.067982558
|
||||||
|
1400 5.2462761e+09 0 0.067977843
|
||||||
|
1500 5.2208208e+09 0 0.067979594
|
||||||
|
1600 5.2740284e+09 0 0.067972573
|
||||||
|
1700 5.1919692e+09 0 0.067974452
|
||||||
|
1800 5.2497614e+09 0 0.067966417
|
||||||
|
1900 5.2910442e+09 0 0.067976096
|
||||||
|
2000 5.27238e+09 0 0.067963979
|
||||||
|
2100 5.3305398e+09 0 0.06795661
|
||||||
|
2200 5.205471e+09 0 0.067970212
|
||||||
|
2300 5.1803713e+09 0 0.067931775
|
||||||
|
2400 5.2134311e+09 0 0.067941825
|
||||||
|
2500 5.2367424e+09 0 0.067963456
|
||||||
|
2600 5.2246738e+09 0 0.067957556
|
||||||
|
2700 5.2514573e+09 0 0.067960724
|
||||||
|
2800 5.2601577e+09 0 0.067965167
|
||||||
|
2900 5.2422855e+09 0 0.067956561
|
||||||
|
3000 5.1796674e+09 0 0.067946764
|
||||||
|
3100 5.2308189e+09 0 0.067946585
|
||||||
|
3200 5.1835395e+09 0 0.067951909
|
||||||
|
3300 5.2762112e+09 0 0.067963199
|
||||||
|
3400 5.3224133e+09 0 0.067944918
|
||||||
|
3500 5.2314242e+09 0 0.06795318
|
||||||
|
3600 5.2760337e+09 0 0.067958005
|
||||||
|
3700 5.2549349e+09 0 0.06795228
|
||||||
|
3800 5.3343065e+09 0 0.067944561
|
||||||
|
3900 5.2440993e+09 0 0.067947433
|
||||||
|
4000 5.2565026e+09 0 0.067962624
|
||||||
|
4100 5.1766738e+09 0 0.067949542
|
||||||
|
4200 5.2058437e+09 0 0.067959946
|
||||||
|
4300 5.2777775e+09 0 0.067945883
|
||||||
|
4400 5.2020331e+09 0 0.067953495
|
||||||
|
4500 5.1417619e+09 0 0.067944161
|
||||||
|
4600 5.2672994e+09 0 0.067936777
|
||||||
|
4700 5.222847e+09 0 0.067943025
|
||||||
|
4800 5.2467842e+09 0 0.06794191
|
||||||
|
4900 5.2784378e+09 0 0.067939495
|
||||||
|
5000 5.2563969e+09 0 0.067940246
|
||||||
|
Loop time of 1.55848 on 4 procs for 5000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 0.028 tau/day, 3208.260 timesteps/s
|
||||||
|
97.1% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Comm | 0.15304 | 0.15677 | 0.16459 | 1.2 | 10.06
|
||||||
|
Output | 0.0012078 | 0.0021182 | 0.0047011 | 3.2 | 0.14
|
||||||
|
Modify | 1.1966 | 1.2236 | 1.2761 | 2.8 | 78.51
|
||||||
|
Other | | 0.176 | | | 11.29
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1024 max 1024 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 353.000 ave 353 max 353 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 0
|
||||||
|
Dangerous builds = 0
|
||||||
|
reset_timestep 0
|
||||||
|
|
||||||
|
# MSD to demonstrate expected diffusive behaviour for ideal active
|
||||||
|
# brownian motion, which is
|
||||||
|
#
|
||||||
|
# MSD = (2*d*kb*T/gamma_t + 2*fp**2*gamma_r/(kb*T*gamma_t**2*(d-1)))*t
|
||||||
|
# + 2*fp**2*gamma_r**2/(gamma_t**2*(d-1)**2*(kb*T)**2)*(e^(-(d-1)*t*kb*T/gamma_r)-1)
|
||||||
|
#
|
||||||
|
# with d being simulation dimension
|
||||||
|
compute msd all msd
|
||||||
|
|
||||||
|
thermo_style custom step ke pe c_msd[*] c_press
|
||||||
|
|
||||||
|
|
||||||
|
timestep 0.00001
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# main run
|
||||||
|
run 12000
|
||||||
|
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:167)
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.694 | 4.694 | 4.694 Mbytes
|
||||||
|
Step KinEng PotEng c_msd[1] c_msd[2] c_msd[3] c_msd[4] c_press
|
||||||
|
0 5.2563969e+09 0 0 0 0 0 0.067940246
|
||||||
|
1000 52568.549 0 0.0067249858 0.0066478843 0.0066014231 0.019974293 0.066777589
|
||||||
|
2000 52836.937 0 0.013611101 0.013799663 0.013161144 0.040571907 0.066769693
|
||||||
|
3000 52129.467 0 0.020360834 0.02089829 0.01995025 0.061209374 0.060026879
|
||||||
|
4000 52075.177 0 0.027638751 0.028062314 0.026895904 0.082596969 0.078290387
|
||||||
|
5000 52203.996 0 0.034087112 0.034933104 0.033832559 0.10285278 0.083657551
|
||||||
|
6000 52986.764 0 0.041562413 0.042238976 0.040542538 0.12434393 0.11542014
|
||||||
|
7000 51941.229 0 0.049216989 0.049250201 0.047598008 0.1460652 0.13739893
|
||||||
|
8000 52618.713 0 0.057198947 0.057409217 0.05404895 0.16865711 0.13681938
|
||||||
|
9000 52501.332 0 0.066447829 0.065262287 0.062271789 0.19398191 0.14306596
|
||||||
|
10000 52545.628 0 0.073800792 0.072510553 0.070100713 0.21641206 0.14689578
|
||||||
|
11000 52416.561 0 0.081881868 0.080638809 0.078969817 0.24149049 0.15608324
|
||||||
|
12000 52271.578 0 0.090521937 0.088555992 0.08592156 0.26499949 0.1474981
|
||||||
|
Loop time of 3.13506 on 4 procs for 12000 steps with 4096 atoms
|
||||||
|
|
||||||
|
Performance: 3307.113 tau/day, 3827.677 timesteps/s
|
||||||
|
99.2% 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 | 0 | 0 | 0.0 | 0.00
|
||||||
|
Neigh | 0.00060225 | 0.00060934 | 0.00061345 | 0.0 | 0.02
|
||||||
|
Comm | 0.029197 | 0.029376 | 0.029582 | 0.1 | 0.94
|
||||||
|
Output | 0.00060606 | 0.00087148 | 0.0016448 | 0.0 | 0.03
|
||||||
|
Modify | 2.84 | 2.8773 | 2.8942 | 1.3 | 91.78
|
||||||
|
Other | | 0.2269 | | | 7.24
|
||||||
|
|
||||||
|
Nlocal: 1024.00 ave 1037 max 999 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Ave neighs/atom = 0.0000000
|
||||||
|
Neighbor list builds = 73
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
# if you want to check that rotational diffusion is behaving as expected,
|
||||||
|
# uncomment next three lines for dump output and then plot <e(t).e(0)>,
|
||||||
|
# which should decay exponentially with timescale (d-1)*D_r (with d
|
||||||
|
# being simulation dimension)
|
||||||
|
|
||||||
|
#dump 1 all custom 2000 dump_ideal_${params}_3d.lammpstrj id type # x y xu yu mux muy muz fx fy fz
|
||||||
|
#dump_modify 1 first yes sort id
|
||||||
|
|
||||||
|
#run 120000
|
||||||
|
Total wall time: 0:00:04
|
||||||
@ -1,54 +0,0 @@
|
|||||||
dimension 2
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
variable L equal 20
|
|
||||||
region total block -$L $L -$L $L -0.5 0.5
|
|
||||||
lattice hex 0.3
|
|
||||||
create_box 2 total
|
|
||||||
create_atoms 1 box
|
|
||||||
|
|
||||||
# Set random fraction to passive:
|
|
||||||
set type 1 type/fraction 2 0.5 1337
|
|
||||||
|
|
||||||
# Purely repulsive particles:
|
|
||||||
variable rc equal "2^(1.0/6.0)"
|
|
||||||
pair_style lj/cut ${rc}
|
|
||||||
pair_coeff * * 1.0 1.0
|
|
||||||
pair_modify shift yes
|
|
||||||
|
|
||||||
mass * 1.0
|
|
||||||
|
|
||||||
fix step all nve
|
|
||||||
fix temp all langevin 1.0 1.0 1.0 13
|
|
||||||
fix twod all enforce2d
|
|
||||||
|
|
||||||
neighbor 0.6 bin
|
|
||||||
|
|
||||||
dump traj all custom 250 2d_active.dump.bin id type x y z
|
|
||||||
|
|
||||||
thermo_style custom time step pe ke etotal temp
|
|
||||||
thermo 1000
|
|
||||||
run 5000
|
|
||||||
|
|
||||||
group one type 1
|
|
||||||
group two type 2
|
|
||||||
|
|
||||||
compute ke1 one ke
|
|
||||||
compute ke2 two ke
|
|
||||||
|
|
||||||
thermo_style custom step pe ke etotal temp c_ke1 c_ke2
|
|
||||||
|
|
||||||
fix active all propel/self velocity 1.0
|
|
||||||
|
|
||||||
# With active force there is more motion so increase bin size:
|
|
||||||
neighbor 1.0 bin
|
|
||||||
run 10000
|
|
||||||
|
|
||||||
# Only make type 1 active:
|
|
||||||
fix active all propel/self velocity 1.0 types 1
|
|
||||||
|
|
||||||
# With active force there is more motion so increase bin size:
|
|
||||||
neighbor 1.0 bin
|
|
||||||
run 10000
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,37 +0,0 @@
|
|||||||
dimension 2
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
variable L equal 20
|
|
||||||
region total block -$L $L -$L $L -0.5 0.5
|
|
||||||
lattice hex 0.3
|
|
||||||
create_box 2 total
|
|
||||||
create_atoms 1 box
|
|
||||||
|
|
||||||
# Set random fraction to passive:
|
|
||||||
set type 1 type/fraction 2 0.5 1337
|
|
||||||
|
|
||||||
# Purely repulsive particles:
|
|
||||||
variable rc equal "2^(1.0/6.0)"
|
|
||||||
pair_style lj/cut ${rc}
|
|
||||||
pair_coeff * * 1.0 1.0
|
|
||||||
pair_modify shift yes
|
|
||||||
|
|
||||||
mass * 1.0
|
|
||||||
|
|
||||||
fix step all nve
|
|
||||||
fix twod all enforce2d
|
|
||||||
|
|
||||||
neighbor 0.6 bin
|
|
||||||
|
|
||||||
dump traj all custom 250 2d_active.dump.bin id type x y z
|
|
||||||
|
|
||||||
thermo_style custom step pe ke etotal temp
|
|
||||||
thermo 1000
|
|
||||||
run 10000
|
|
||||||
|
|
||||||
fix active all propel/self velocity 1.0
|
|
||||||
fix fric all viscous 1.0
|
|
||||||
|
|
||||||
# With active force there is more motion so increase bin size:
|
|
||||||
neighbor 1.0 bin
|
|
||||||
run 10000
|
|
||||||
@ -1,40 +0,0 @@
|
|||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style ellipsoid
|
|
||||||
variable L equal 20
|
|
||||||
region total block -$L $L -$L $L -$L $L
|
|
||||||
lattice sc 0.1
|
|
||||||
create_box 2 total
|
|
||||||
create_atoms 1 box
|
|
||||||
|
|
||||||
# Set random fraction to passive:
|
|
||||||
set type 1 type/fraction 2 0.5 1337
|
|
||||||
|
|
||||||
# Purely repulsive particles:
|
|
||||||
variable rc equal "2^(1.0/6.0)"
|
|
||||||
pair_style lj/cut ${rc}
|
|
||||||
pair_coeff * * 1.0 1.0
|
|
||||||
pair_modify shift yes
|
|
||||||
|
|
||||||
# mass * 1.0
|
|
||||||
set type * shape 1.0 1.0 1.0
|
|
||||||
set type * density 1.9098593171027443
|
|
||||||
set type * quat 0 0 1 0
|
|
||||||
|
|
||||||
fix step all nve/asphere
|
|
||||||
fix temp all langevin 1.0 1.0 1.0 13 angmom 3.333333333
|
|
||||||
|
|
||||||
neighbor 0.6 bin
|
|
||||||
|
|
||||||
dump traj all custom 100 3d_active.dump.bin id type x y z fx fy fz
|
|
||||||
|
|
||||||
thermo_style custom step pe ke etotal temp
|
|
||||||
thermo 100
|
|
||||||
run 500
|
|
||||||
|
|
||||||
fix active all propel/self quat 1.0
|
|
||||||
|
|
||||||
# With active force there is more motion so increase bin size:
|
|
||||||
neighbor 1.0 bin
|
|
||||||
run 500
|
|
||||||
7
src/.gitignore
vendored
7
src/.gitignore
vendored
@ -27,6 +27,11 @@
|
|||||||
/*_ssa.h
|
/*_ssa.h
|
||||||
/*_ssa.cpp
|
/*_ssa.cpp
|
||||||
|
|
||||||
|
/fix_brownian*.cpp
|
||||||
|
/fix_brownian*.h
|
||||||
|
/fix_propel_self.cpp
|
||||||
|
/fix_propel_self.h
|
||||||
|
|
||||||
/kim_*.cpp
|
/kim_*.cpp
|
||||||
/kim_*.h
|
/kim_*.h
|
||||||
/pair_kim.cpp
|
/pair_kim.cpp
|
||||||
@ -700,8 +705,6 @@
|
|||||||
/fix_poems.h
|
/fix_poems.h
|
||||||
/fix_pour.cpp
|
/fix_pour.cpp
|
||||||
/fix_pour.h
|
/fix_pour.h
|
||||||
/fix_propel_self.cpp
|
|
||||||
/fix_propel_self.h
|
|
||||||
/fix_qeq_comb.cpp
|
/fix_qeq_comb.cpp
|
||||||
/fix_qeq_comb.h
|
/fix_qeq_comb.h
|
||||||
/fix_qeq_reax.cpp
|
/fix_qeq_reax.cpp
|
||||||
|
|||||||
13
src/Makefile
13
src/Makefile
@ -51,12 +51,13 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
|
|||||||
mliap molecule mpiio mscg opt peri plugin poems \
|
mliap molecule mpiio mscg opt peri plugin poems \
|
||||||
python qeq replica rigid shock snap spin srd voronoi
|
python qeq replica rigid shock snap spin srd voronoi
|
||||||
|
|
||||||
PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
|
PACKUSER = user-adios user-atc user-awpmd user-brownian user-bocs user-cgdna \
|
||||||
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
|
user-cgsdk user-colvars user-diffraction user-dpd user-drude \
|
||||||
user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \
|
user-eff user-fep user-h5md user-intel user-lb user-manifold \
|
||||||
user-mgpt user-misc user-mofff user-molfile \
|
user-meamc user-mesodpd user-mesont user-mgpt user-misc \
|
||||||
user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \
|
user-mofff \user-molfile user-netcdf user-omp user-phonon \
|
||||||
user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \
|
user-pace user-plumed user-ptm user-qmmm user-qtb user-quip \
|
||||||
|
user-reaction user-reaxc user-scafacos user-smd user-smtbq \
|
||||||
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
|
user-sdpd user-sph user-tally user-uef user-vtk user-yaff
|
||||||
|
|
||||||
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
|
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems python voronoi \
|
||||||
|
|||||||
136
src/USER-BROWNIAN/fix_brownian.cpp
Normal file
136
src/USER-BROWNIAN/fix_brownian.cpp
Normal file
@ -0,0 +1,136 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||||
|
|
||||||
|
Contributing author: Sam Cameron (University of Bristol)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_brownian.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "random_mars.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixBrownian::FixBrownian(LAMMPS *lmp, int narg, char **arg) : FixBrownianBase(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
if (dipole_flag || gamma_t_eigen_flag || gamma_r_eigen_flag || gamma_r_flag) {
|
||||||
|
error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
}
|
||||||
|
if (!gamma_t_flag) { error->all(FLERR, "Illegal fix brownian command."); }
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownian::init()
|
||||||
|
{
|
||||||
|
FixBrownianBase::init();
|
||||||
|
g1 /= gamma_t;
|
||||||
|
g2 *= sqrt(gamma_t);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownian::initial_integrate(int /*vflag */)
|
||||||
|
{
|
||||||
|
if (domain->dimension == 2) {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 1>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 1>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 1>();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 0>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 0>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 0>();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D> void FixBrownian::initial_integrate_templated()
|
||||||
|
{
|
||||||
|
double **x = atom->x;
|
||||||
|
double **v = atom->v;
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
double dx, dy, dz;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
if (Tp_2D) {
|
||||||
|
dz = 0;
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
|
||||||
|
} else {
|
||||||
|
dx = dt * g1 * f[i][0];
|
||||||
|
dy = dt * g1 * f[i][1];
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dz = dt * (g1 * f[i][2] + g2 * (rng->uniform() - 0.5));
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
|
||||||
|
dz = dt * (g1 * f[i][2] + g2 * rng->gaussian());
|
||||||
|
} else {
|
||||||
|
dx = dt * g1 * f[i][0];
|
||||||
|
dy = dt * g1 * f[i][1];
|
||||||
|
dz = dt * g1 * f[i][2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
x[i][0] += dx;
|
||||||
|
v[i][0] = dx / dt;
|
||||||
|
|
||||||
|
x[i][1] += dy;
|
||||||
|
v[i][1] = dy / dt;
|
||||||
|
|
||||||
|
x[i][2] += dz;
|
||||||
|
v[i][2] = dz / dt;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return;
|
||||||
|
}
|
||||||
61
src/USER-BROWNIAN/fix_brownian.h
Normal file
61
src/USER-BROWNIAN/fix_brownian.h
Normal file
@ -0,0 +1,61 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef FIX_CLASS
|
||||||
|
// clang-format off
|
||||||
|
FixStyle(brownian,FixBrownian);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_BROWNIAN_H
|
||||||
|
#define LMP_FIX_BROWNIAN_H
|
||||||
|
|
||||||
|
#include "fix_brownian_base.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixBrownian : public FixBrownianBase {
|
||||||
|
public:
|
||||||
|
FixBrownian(class LAMMPS *, int, char **);
|
||||||
|
virtual ~FixBrownian() {};
|
||||||
|
void init();
|
||||||
|
void initial_integrate(int);
|
||||||
|
|
||||||
|
private:
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
|
||||||
|
void initial_integrate_templated();
|
||||||
|
};
|
||||||
|
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal fix brownian command.
|
||||||
|
|
||||||
|
Wrong number/type of input arguments.
|
||||||
|
|
||||||
|
E: Fix brownian viscous drag coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian diffusion coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian seed must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
272
src/USER-BROWNIAN/fix_brownian_asphere.cpp
Normal file
272
src/USER-BROWNIAN/fix_brownian_asphere.cpp
Normal file
@ -0,0 +1,272 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||||
|
|
||||||
|
Contributing author: Sam Cameron (University of Bristol)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_brownian_asphere.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec_ellipsoid.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "random_mars.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixBrownianAsphere::FixBrownianAsphere(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
FixBrownianBase(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
if (!gamma_t_eigen_flag || !gamma_r_eigen_flag) {
|
||||||
|
error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
}
|
||||||
|
|
||||||
|
if (gamma_t_flag || gamma_r_flag) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
|
||||||
|
if (dipole_flag && !atom->mu_flag)
|
||||||
|
error->all(FLERR, "Fix brownian/asphere dipole requires atom attribute mu");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownianAsphere::init()
|
||||||
|
{
|
||||||
|
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||||
|
if (!avec) error->all(FLERR, "Compute brownian/asphere requires atom style ellipsoid");
|
||||||
|
|
||||||
|
// check that all particles are finite-size ellipsoids
|
||||||
|
// no point particles allowed, spherical is OK
|
||||||
|
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit)
|
||||||
|
if (ellipsoid[i] < 0) error->one(FLERR, "Fix brownian/asphere requires extended particles");
|
||||||
|
|
||||||
|
if (dipole_flag) {
|
||||||
|
|
||||||
|
double f_rot[3];
|
||||||
|
double *quat;
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||||
|
|
||||||
|
double Q[3][3];
|
||||||
|
double **mu = atom->mu;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
quat = bonus[ellipsoid[i]].quat;
|
||||||
|
MathExtra::quat_to_mat(quat, Q);
|
||||||
|
MathExtra::matvec(Q, dipole_body, f_rot);
|
||||||
|
|
||||||
|
mu[i][0] = f_rot[0];
|
||||||
|
mu[i][1] = f_rot[1];
|
||||||
|
mu[i][2] = f_rot[2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
FixBrownianBase::init();
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownianAsphere::initial_integrate(int /*vflag */)
|
||||||
|
{
|
||||||
|
if (domain->dimension == 2) {
|
||||||
|
if (dipole_flag) {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 1, 1>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 1, 1>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 1, 1>();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 0, 1>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 0, 1>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 0, 1>();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (dipole_flag) {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 1, 0>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 1, 0>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 1, 0>();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 0, 0>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 0, 0>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 0, 0>();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D>
|
||||||
|
void FixBrownianAsphere::initial_integrate_templated()
|
||||||
|
{
|
||||||
|
double **x = atom->x;
|
||||||
|
double **v = atom->v;
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||||
|
|
||||||
|
double **mu = atom->mu;
|
||||||
|
double **torque = atom->torque;
|
||||||
|
double qw[4];
|
||||||
|
double *quat;
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
|
||||||
|
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
// project dipole along x axis of quat
|
||||||
|
double f_rot[3];
|
||||||
|
double rotationmatrix_transpose[3][3];
|
||||||
|
double tmp[3];
|
||||||
|
double dv[3];
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
|
||||||
|
// update orientation first
|
||||||
|
|
||||||
|
quat = bonus[ellipsoid[i]].quat;
|
||||||
|
MathExtra::quat_to_mat_trans(quat, rotationmatrix_transpose);
|
||||||
|
|
||||||
|
// tmp holds angular velocity in body frame
|
||||||
|
MathExtra::matvec(rotationmatrix_transpose, torque[i], tmp);
|
||||||
|
|
||||||
|
if (Tp_2D) {
|
||||||
|
tmp[0] = tmp[1] = 0.0;
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * (rng->uniform() - 0.5) * g2;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * rng->gaussian() * g2;
|
||||||
|
} else {
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2];
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_r_inv[0] + gamma_r_invsqrt[0] * (rng->uniform() - 0.5) * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_r_inv[1] + gamma_r_invsqrt[1] * (rng->uniform() - 0.5) * g2;
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * (rng->uniform() - 0.5) * g2;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_r_inv[0] + gamma_r_invsqrt[0] * rng->gaussian() * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_r_inv[1] + gamma_r_invsqrt[1] * rng->gaussian() * g2;
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2] + gamma_r_invsqrt[2] * rng->gaussian() * g2;
|
||||||
|
} else {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_r_inv[0];
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_r_inv[1];
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_r_inv[2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// convert body frame angular velocity to quaternion
|
||||||
|
MathExtra::quatvec(quat, tmp, qw);
|
||||||
|
quat[0] = quat[0] + 0.5 * dt * qw[0];
|
||||||
|
quat[1] = quat[1] + 0.5 * dt * qw[1];
|
||||||
|
quat[2] = quat[2] + 0.5 * dt * qw[2];
|
||||||
|
quat[3] = quat[3] + 0.5 * dt * qw[3];
|
||||||
|
|
||||||
|
// normalisation introduces the stochastic drift term
|
||||||
|
// to recover the Boltzmann distribution for the case of conservative torques
|
||||||
|
MathExtra::qnormalize(quat);
|
||||||
|
|
||||||
|
// next, update centre of mass positions and velocities
|
||||||
|
|
||||||
|
// tmp now holds force in body frame
|
||||||
|
MathExtra::matvec(rotationmatrix_transpose, f[i], tmp);
|
||||||
|
// and then converts to gamma_t^{-1} * F (velocity) in body frame
|
||||||
|
|
||||||
|
if (Tp_2D) {
|
||||||
|
tmp[2] = 0.0;
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * (rng->uniform() - 0.5) * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * (rng->uniform() - 0.5) * g2;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * rng->gaussian() * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * rng->gaussian() * g2;
|
||||||
|
} else {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0];
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1];
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * (rng->uniform() - 0.5) * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * (rng->uniform() - 0.5) * g2;
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_t_inv[2] + gamma_t_invsqrt[2] * (rng->uniform() - 0.5) * g2;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0] + gamma_t_invsqrt[0] * rng->gaussian() * g2;
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1] + gamma_t_invsqrt[1] * rng->gaussian() * g2;
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_t_inv[2] + gamma_t_invsqrt[2] * rng->gaussian() * g2;
|
||||||
|
} else {
|
||||||
|
tmp[0] = g1 * tmp[0] * gamma_t_inv[0];
|
||||||
|
tmp[1] = g1 * tmp[1] * gamma_t_inv[1];
|
||||||
|
tmp[2] = g1 * tmp[2] * gamma_t_inv[2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// finally, convert this back to lab-frame velocity and store in dv
|
||||||
|
MathExtra::transpose_matvec(rotationmatrix_transpose, tmp, dv);
|
||||||
|
|
||||||
|
v[i][0] = dv[0];
|
||||||
|
v[i][1] = dv[1];
|
||||||
|
v[i][2] = dv[2];
|
||||||
|
|
||||||
|
x[i][0] += dv[0] * dt;
|
||||||
|
x[i][1] += dv[1] * dt;
|
||||||
|
x[i][2] += dv[2] * dt;
|
||||||
|
|
||||||
|
if (Tp_DIPOLE) {
|
||||||
|
MathExtra::quat_to_mat_trans(quat, rotationmatrix_transpose);
|
||||||
|
MathExtra::transpose_matvec(rotationmatrix_transpose, dipole_body, f_rot);
|
||||||
|
mu[i][0] = f_rot[0];
|
||||||
|
mu[i][1] = f_rot[1];
|
||||||
|
mu[i][2] = f_rot[2];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return;
|
||||||
|
}
|
||||||
81
src/USER-BROWNIAN/fix_brownian_asphere.h
Normal file
81
src/USER-BROWNIAN/fix_brownian_asphere.h
Normal file
@ -0,0 +1,81 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef FIX_CLASS
|
||||||
|
// clang-format off
|
||||||
|
FixStyle(brownian/asphere,FixBrownianAsphere);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_BROWNIAN_ASPHERE_H
|
||||||
|
#define LMP_FIX_BROWNIAN_ASPHERE_H
|
||||||
|
|
||||||
|
#include "fix_brownian_base.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixBrownianAsphere : public FixBrownianBase {
|
||||||
|
public:
|
||||||
|
FixBrownianAsphere(class LAMMPS *, int, char **);
|
||||||
|
virtual ~FixBrownianAsphere() {};
|
||||||
|
void initial_integrate(int);
|
||||||
|
void init();
|
||||||
|
|
||||||
|
protected:
|
||||||
|
class AtomVecEllipsoid *avec;
|
||||||
|
|
||||||
|
private:
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_DIPOLE, int Tp_2D>
|
||||||
|
void initial_integrate_templated();
|
||||||
|
};
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal fix brownian/asphere command.
|
||||||
|
|
||||||
|
Wrong number/type of input arguments.
|
||||||
|
|
||||||
|
E: Compute brownian/asphere requires atom style sphere
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Compute brownian/asphere requires atom style ellipsoid
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Compute brownian/asphere dipole requires atom attribute mu
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/asphere translational viscous drag coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/asphere rotational viscous drag coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/asphere translational diffusion coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/asphere rotational diffusion coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/asphere seed must be > 0.
|
||||||
|
|
||||||
|
*/
|
||||||
218
src/USER-BROWNIAN/fix_brownian_base.cpp
Normal file
218
src/USER-BROWNIAN/fix_brownian_base.cpp
Normal file
@ -0,0 +1,218 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||||
|
|
||||||
|
Contributing author: Sam Cameron (University of Bristol)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_brownian.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "random_mars.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixBrownianBase::FixBrownianBase(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
time_integrate = 1;
|
||||||
|
|
||||||
|
noise_flag = 1;
|
||||||
|
gaussian_noise_flag = 0;
|
||||||
|
gamma_t_flag = gamma_r_flag = 0;
|
||||||
|
gamma_t_eigen_flag = gamma_r_eigen_flag = 0;
|
||||||
|
dipole_flag = 0;
|
||||||
|
|
||||||
|
if (narg < 5) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
|
||||||
|
temp = utils::numeric(FLERR, arg[3], false, lmp);
|
||||||
|
if (temp <= 0) error->all(FLERR, "Fix brownian temp must be > 0.");
|
||||||
|
|
||||||
|
seed = utils::inumeric(FLERR, arg[4], false, lmp);
|
||||||
|
if (seed <= 0) error->all(FLERR, "Fix brownian seed must be > 0.");
|
||||||
|
|
||||||
|
int iarg = 5;
|
||||||
|
while (iarg < narg) {
|
||||||
|
if (strcmp(arg[iarg], "rng") == 0) {
|
||||||
|
if (narg == iarg + 1) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
if (strcmp(arg[iarg + 1], "uniform") == 0) {
|
||||||
|
noise_flag = 1;
|
||||||
|
} else if (strcmp(arg[iarg + 1], "gaussian") == 0) {
|
||||||
|
noise_flag = 1;
|
||||||
|
gaussian_noise_flag = 1;
|
||||||
|
} else if (strcmp(arg[iarg + 1], "none") == 0) {
|
||||||
|
noise_flag = 0;
|
||||||
|
} else {
|
||||||
|
error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
}
|
||||||
|
iarg = iarg + 2;
|
||||||
|
} else if (strcmp(arg[iarg], "dipole") == 0) {
|
||||||
|
if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
|
||||||
|
dipole_flag = 1;
|
||||||
|
dipole_body = new double[3];
|
||||||
|
|
||||||
|
dipole_body[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
|
dipole_body[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||||
|
dipole_body[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
|
||||||
|
iarg = iarg + 4;
|
||||||
|
|
||||||
|
} else if (strcmp(arg[iarg], "gamma_t_eigen") == 0) {
|
||||||
|
if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
|
||||||
|
gamma_t_eigen_flag = 1;
|
||||||
|
gamma_t_inv = new double[3];
|
||||||
|
gamma_t_invsqrt = new double[3];
|
||||||
|
gamma_t_inv[0] = 1. / utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
|
gamma_t_inv[1] = 1. / utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||||
|
|
||||||
|
if (domain->dimension == 2) {
|
||||||
|
if (strcmp(arg[iarg + 3], "inf") != 0) {
|
||||||
|
error->all(FLERR, "Fix brownian gamma_t_eigen third value must be inf for 2D system.");
|
||||||
|
}
|
||||||
|
gamma_t_inv[2] = 0;
|
||||||
|
} else {
|
||||||
|
gamma_t_inv[2] = 1.0 / utils::numeric(FLERR, arg[iarg + 3], false, lmp);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (gamma_t_inv[0] < 0 || gamma_t_inv[1] < 0 || gamma_t_inv[2] < 0)
|
||||||
|
error->all(FLERR, "Fix brownian gamma_t_eigen values must be > 0.");
|
||||||
|
|
||||||
|
gamma_t_invsqrt[0] = sqrt(gamma_t_inv[0]);
|
||||||
|
gamma_t_invsqrt[1] = sqrt(gamma_t_inv[1]);
|
||||||
|
gamma_t_invsqrt[2] = sqrt(gamma_t_inv[2]);
|
||||||
|
iarg = iarg + 4;
|
||||||
|
|
||||||
|
} else if (strcmp(arg[iarg], "gamma_r_eigen") == 0) {
|
||||||
|
if (narg == iarg + 3) error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
|
||||||
|
gamma_r_eigen_flag = 1;
|
||||||
|
gamma_r_inv = new double[3];
|
||||||
|
gamma_r_invsqrt = new double[3];
|
||||||
|
|
||||||
|
if (domain->dimension == 2) {
|
||||||
|
if (strcmp(arg[iarg + 1], "inf") != 0) {
|
||||||
|
error->all(FLERR, "Fix brownian gamma_r_eigen first value must be inf for 2D system.");
|
||||||
|
}
|
||||||
|
gamma_r_inv[0] = 0;
|
||||||
|
|
||||||
|
if (strcmp(arg[iarg + 2], "inf") != 0) {
|
||||||
|
error->all(FLERR, "Fix brownian gamma_r_eigen second value must be inf for 2D system.");
|
||||||
|
}
|
||||||
|
gamma_r_inv[1] = 0;
|
||||||
|
} else {
|
||||||
|
|
||||||
|
gamma_r_inv[0] = 1. / utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
|
gamma_r_inv[1] = 1. / utils::numeric(FLERR, arg[iarg + 2], false, lmp);
|
||||||
|
}
|
||||||
|
|
||||||
|
gamma_r_inv[2] = 1. / utils::numeric(FLERR, arg[iarg + 3], false, lmp);
|
||||||
|
|
||||||
|
if (gamma_r_inv[0] < 0 || gamma_r_inv[1] < 0 || gamma_r_inv[2] < 0)
|
||||||
|
error->all(FLERR, "Fix brownian gamma_r_eigen values must be > 0.");
|
||||||
|
|
||||||
|
gamma_r_invsqrt[0] = sqrt(gamma_r_inv[0]);
|
||||||
|
gamma_r_invsqrt[1] = sqrt(gamma_r_inv[1]);
|
||||||
|
gamma_r_invsqrt[2] = sqrt(gamma_r_inv[2]);
|
||||||
|
iarg = iarg + 4;
|
||||||
|
|
||||||
|
} else if (strcmp(arg[iarg], "gamma_t") == 0) {
|
||||||
|
if (narg == iarg + 1) { error->all(FLERR, "Illegal fix brownian command."); }
|
||||||
|
|
||||||
|
gamma_t_flag = 1;
|
||||||
|
gamma_t = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
|
if (gamma_t <= 0) error->all(FLERR, "Fix brownian gamma_t must be > 0.");
|
||||||
|
iarg = iarg + 2;
|
||||||
|
|
||||||
|
} else if (strcmp(arg[iarg], "gamma_r") == 0) {
|
||||||
|
if (narg == iarg + 1) { error->all(FLERR, "Illegal fix brownian command."); }
|
||||||
|
|
||||||
|
gamma_r_flag = 1;
|
||||||
|
gamma_r = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
||||||
|
if (gamma_r <= 0) error->all(FLERR, "Fix brownian gamma_r must be > 0.");
|
||||||
|
iarg = iarg + 2;
|
||||||
|
|
||||||
|
} else {
|
||||||
|
error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// initialize Marsaglia RNG with processor-unique seed
|
||||||
|
rng = new RanMars(lmp, seed + comm->me);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int FixBrownianBase::setmask()
|
||||||
|
{
|
||||||
|
int mask = 0;
|
||||||
|
mask |= INITIAL_INTEGRATE;
|
||||||
|
return mask;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixBrownianBase::~FixBrownianBase()
|
||||||
|
{
|
||||||
|
|
||||||
|
if (gamma_t_eigen_flag) {
|
||||||
|
delete[] gamma_t_inv;
|
||||||
|
delete[] gamma_t_invsqrt;
|
||||||
|
}
|
||||||
|
if (gamma_r_eigen_flag) {
|
||||||
|
delete[] gamma_r_inv;
|
||||||
|
delete[] gamma_r_invsqrt;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (dipole_flag) { delete[] dipole_body; }
|
||||||
|
delete rng;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownianBase::init()
|
||||||
|
{
|
||||||
|
dt = update->dt;
|
||||||
|
sqrtdt = sqrt(dt);
|
||||||
|
|
||||||
|
g1 = force->ftm2v;
|
||||||
|
if (noise_flag == 0) {
|
||||||
|
g2 = 0;
|
||||||
|
} else if (gaussian_noise_flag == 1) {
|
||||||
|
g2 = sqrt(2 * force->boltz * temp / dt / force->mvv2e);
|
||||||
|
} else {
|
||||||
|
g2 = sqrt(24 * force->boltz * temp / dt / force->mvv2e);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
void FixBrownianBase::reset_dt()
|
||||||
|
{
|
||||||
|
double sqrtdt_old = sqrtdt;
|
||||||
|
dt = update->dt;
|
||||||
|
sqrtdt = sqrt(dt);
|
||||||
|
g2 *= sqrtdt_old / sqrtdt;
|
||||||
|
}
|
||||||
88
src/USER-BROWNIAN/fix_brownian_base.h
Normal file
88
src/USER-BROWNIAN/fix_brownian_base.h
Normal file
@ -0,0 +1,88 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_BROWNIAN_BASE_H
|
||||||
|
#define LMP_FIX_BROWNIAN_BASE_H
|
||||||
|
|
||||||
|
#include "fix.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixBrownianBase : public Fix {
|
||||||
|
public:
|
||||||
|
FixBrownianBase(class LAMMPS *, int, char **);
|
||||||
|
virtual ~FixBrownianBase();
|
||||||
|
void init();
|
||||||
|
int setmask();
|
||||||
|
void reset_dt();
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int seed; // RNG seed
|
||||||
|
double dt, sqrtdt; // time step interval and its sqrt
|
||||||
|
int gamma_t_flag; // 0/1 if isotropic translational damping is unset/set
|
||||||
|
int gamma_r_flag; // 0/1 if isotropic rotational damping is unset/set
|
||||||
|
int gamma_t_eigen_flag; // 0/1 if anisotropic translational damping is unset/set
|
||||||
|
int gamma_r_eigen_flag; // 0/1 if anisotropic rotational damping is unset/set
|
||||||
|
|
||||||
|
double gamma_t, gamma_r; // translational and rotational (isotropic) damping params
|
||||||
|
double *gamma_t_inv; // anisotropic damping parameter eigenvalues
|
||||||
|
double *gamma_r_inv;
|
||||||
|
double *gamma_t_invsqrt;
|
||||||
|
double *gamma_r_invsqrt;
|
||||||
|
|
||||||
|
int dipole_flag; // set if dipole is used for asphere
|
||||||
|
double *dipole_body; // direction dipole is slaved to in body frame
|
||||||
|
|
||||||
|
int noise_flag; // 0/1 for noise off/on
|
||||||
|
int gaussian_noise_flag; // 0/1 for uniform/gaussian noise
|
||||||
|
|
||||||
|
double temp; // temperature
|
||||||
|
double g1, g2; // prefactors in time stepping
|
||||||
|
|
||||||
|
class RanMars *rng;
|
||||||
|
};
|
||||||
|
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal fix brownian command.
|
||||||
|
|
||||||
|
Wrong number/type of input arguments.
|
||||||
|
|
||||||
|
E: Fix brownian gamma_t_eigen values must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian gamma_r_eigen values must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian seed must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian temp must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian gamma_t must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian gamma_r must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
185
src/USER-BROWNIAN/fix_brownian_sphere.cpp
Normal file
185
src/USER-BROWNIAN/fix_brownian_sphere.cpp
Normal file
@ -0,0 +1,185 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Originally modified from USER-CGDNA/fix_nve_dotc_langevin.cpp.
|
||||||
|
|
||||||
|
Contributing author: Sam Cameron (University of Bristol)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_brownian_sphere.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "random_mars.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixBrownianSphere::FixBrownianSphere(LAMMPS *lmp, int narg, char **arg) :
|
||||||
|
FixBrownianBase(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
if (gamma_t_eigen_flag || gamma_r_eigen_flag) {
|
||||||
|
error->all(FLERR, "Illegal fix brownian command.");
|
||||||
|
}
|
||||||
|
|
||||||
|
if (!gamma_t_flag || !gamma_r_flag) { error->all(FLERR, "Illegal fix brownian command."); }
|
||||||
|
if (!atom->mu_flag) error->all(FLERR, "Fix brownian/sphere requires atom attribute mu");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownianSphere::init()
|
||||||
|
{
|
||||||
|
FixBrownianBase::init();
|
||||||
|
|
||||||
|
g3 = g1 / gamma_r;
|
||||||
|
g4 = g2 / sqrt(gamma_r);
|
||||||
|
g1 /= gamma_t;
|
||||||
|
g2 /= sqrt(gamma_t);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixBrownianSphere::initial_integrate(int /*vflag */)
|
||||||
|
{
|
||||||
|
if (domain->dimension == 2) {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 1>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 1>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 1>();
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (!noise_flag) {
|
||||||
|
initial_integrate_templated<0, 0, 0>();
|
||||||
|
} else if (gaussian_noise_flag) {
|
||||||
|
initial_integrate_templated<0, 1, 0>();
|
||||||
|
} else {
|
||||||
|
initial_integrate_templated<1, 0, 0>();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
return;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
|
||||||
|
void FixBrownianSphere::initial_integrate_templated()
|
||||||
|
{
|
||||||
|
double **x = atom->x;
|
||||||
|
double **v = atom->v;
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double wx, wy, wz;
|
||||||
|
double **torque = atom->torque;
|
||||||
|
double **mu = atom->mu;
|
||||||
|
double mux, muy, muz, mulen;
|
||||||
|
|
||||||
|
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
double dx, dy, dz;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
if (Tp_2D) {
|
||||||
|
dz = 0;
|
||||||
|
wx = wy = 0;
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
|
||||||
|
wz = (rng->uniform() - 0.5) * g4;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
|
||||||
|
wz = rng->gaussian() * g4;
|
||||||
|
} else {
|
||||||
|
dx = dt * g1 * f[i][0];
|
||||||
|
dy = dt * g1 * f[i][1];
|
||||||
|
wz = 0;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (Tp_UNIFORM) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * (rng->uniform() - 0.5));
|
||||||
|
dz = dt * (g1 * f[i][2] + g2 * (rng->uniform() - 0.5));
|
||||||
|
wx = (rng->uniform() - 0.5) * g4;
|
||||||
|
wy = (rng->uniform() - 0.5) * g4;
|
||||||
|
wz = (rng->uniform() - 0.5) * g4;
|
||||||
|
} else if (Tp_GAUSS) {
|
||||||
|
dx = dt * (g1 * f[i][0] + g2 * rng->gaussian());
|
||||||
|
dy = dt * (g1 * f[i][1] + g2 * rng->gaussian());
|
||||||
|
dz = dt * (g1 * f[i][2] + g2 * rng->gaussian());
|
||||||
|
wx = rng->gaussian() * g4;
|
||||||
|
wy = rng->gaussian() * g4;
|
||||||
|
wz = rng->gaussian() * g4;
|
||||||
|
} else {
|
||||||
|
dx = dt * g1 * f[i][0];
|
||||||
|
dy = dt * g1 * f[i][1];
|
||||||
|
dz = dt * g1 * f[i][2];
|
||||||
|
wx = wy = wz = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
x[i][0] += dx;
|
||||||
|
v[i][0] = dx / dt;
|
||||||
|
|
||||||
|
x[i][1] += dy;
|
||||||
|
v[i][1] = dy / dt;
|
||||||
|
|
||||||
|
x[i][2] += dz;
|
||||||
|
v[i][2] = dz / dt;
|
||||||
|
|
||||||
|
wx += g3 * torque[i][0];
|
||||||
|
wy += g3 * torque[i][1];
|
||||||
|
wz += g3 * torque[i][2];
|
||||||
|
|
||||||
|
// store length of dipole as we need to convert it to a unit vector and
|
||||||
|
// then back again
|
||||||
|
|
||||||
|
mulen = sqrt(mu[i][0] * mu[i][0] + mu[i][1] * mu[i][1] + mu[i][2] * mu[i][2]);
|
||||||
|
|
||||||
|
// unit vector at time t
|
||||||
|
mux = mu[i][0] / mulen;
|
||||||
|
muy = mu[i][1] / mulen;
|
||||||
|
muz = mu[i][2] / mulen;
|
||||||
|
|
||||||
|
// un-normalised unit vector at time t + dt
|
||||||
|
mu[i][0] = mux + (wy * muz - wz * muy) * dt;
|
||||||
|
mu[i][1] = muy + (wz * mux - wx * muz) * dt;
|
||||||
|
mu[i][2] = muz + (wx * muy - wy * mux) * dt;
|
||||||
|
|
||||||
|
// normalisation introduces the stochastic drift term due to changing from
|
||||||
|
// Stratonovich to Ito interpretation
|
||||||
|
MathExtra::norm3(mu[i]);
|
||||||
|
|
||||||
|
// multiply by original magnitude to obtain dipole of same length
|
||||||
|
mu[i][0] = mu[i][0] * mulen;
|
||||||
|
mu[i][1] = mu[i][1] * mulen;
|
||||||
|
mu[i][2] = mu[i][2] * mulen;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
75
src/USER-BROWNIAN/fix_brownian_sphere.h
Normal file
75
src/USER-BROWNIAN/fix_brownian_sphere.h
Normal file
@ -0,0 +1,75 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef FIX_CLASS
|
||||||
|
// clang-format off
|
||||||
|
FixStyle(brownian/sphere,FixBrownianSphere);
|
||||||
|
// clang-format on
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_FIX_BROWNIAN_SPHERE_H
|
||||||
|
#define LMP_FIX_BROWNIAN_SPHERE_H
|
||||||
|
|
||||||
|
#include "fix_brownian_base.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class FixBrownianSphere : public FixBrownianBase {
|
||||||
|
public:
|
||||||
|
FixBrownianSphere(class LAMMPS *, int, char **);
|
||||||
|
virtual ~FixBrownianSphere() {};
|
||||||
|
void init();
|
||||||
|
void initial_integrate(int);
|
||||||
|
|
||||||
|
private:
|
||||||
|
template <int Tp_UNIFORM, int Tp_GAUSS, int Tp_2D>
|
||||||
|
void initial_integrate_templated();
|
||||||
|
double g3, g4;
|
||||||
|
};
|
||||||
|
} // namespace LAMMPS_NS
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal fix brownian/sphere command.
|
||||||
|
|
||||||
|
Wrong number/type of input arguments.
|
||||||
|
|
||||||
|
E: Compute brownian/sphere requires atom style sphere
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Compute brownian/sphere requires atom attribute mu
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/sphere translational viscous drag coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/sphere rotational viscous drag coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/sphere translational diffusion coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/sphere rotational diffusion coefficient must be > 0.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix brownian/sphere seed must be > 0.
|
||||||
|
|
||||||
|
*/
|
||||||
303
src/USER-BROWNIAN/fix_propel_self.cpp
Normal file
303
src/USER-BROWNIAN/fix_propel_self.cpp
Normal file
@ -0,0 +1,303 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* -----------------------------------------------------------------------
|
||||||
|
Contributed by Stefan Paquay @ Brandeis University
|
||||||
|
|
||||||
|
Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions!
|
||||||
|
|
||||||
|
Current maintainer: Sam Cameron @ University of Bristol
|
||||||
|
----------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "fix_propel_self.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec_ellipsoid.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "update.h"
|
||||||
|
|
||||||
|
#include <cstring>
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace FixConst;
|
||||||
|
|
||||||
|
enum { DIPOLE, VELOCITY, QUAT };
|
||||||
|
|
||||||
|
#define TOL 1e-14
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
FixPropelSelf::FixPropelSelf(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||||
|
{
|
||||||
|
|
||||||
|
virial_global_flag = virial_peratom_flag = 1;
|
||||||
|
|
||||||
|
if (narg != 5 && narg != 9) error->all(FLERR, "Illegal fix propel/self command");
|
||||||
|
|
||||||
|
if (strcmp(arg[3], "velocity") == 0) {
|
||||||
|
mode = VELOCITY;
|
||||||
|
thermo_virial = 0;
|
||||||
|
} else if (strcmp(arg[3], "dipole") == 0) {
|
||||||
|
mode = DIPOLE;
|
||||||
|
thermo_virial = 1;
|
||||||
|
} else if (strcmp(arg[3], "quat") == 0) {
|
||||||
|
mode = QUAT;
|
||||||
|
thermo_virial = 1;
|
||||||
|
} else {
|
||||||
|
error->all(FLERR, "Illegal fix propel/self command");
|
||||||
|
}
|
||||||
|
|
||||||
|
magnitude = utils::numeric(FLERR, arg[4], false, lmp);
|
||||||
|
|
||||||
|
// check for keyword
|
||||||
|
|
||||||
|
if (narg == 9) {
|
||||||
|
if (mode != QUAT) { error->all(FLERR, "Illegal fix propel/self command"); }
|
||||||
|
if (strcmp(arg[5], "qvector") == 0) {
|
||||||
|
sx = utils::numeric(FLERR, arg[6], false, lmp);
|
||||||
|
sy = utils::numeric(FLERR, arg[7], false, lmp);
|
||||||
|
sz = utils::numeric(FLERR, arg[8], false, lmp);
|
||||||
|
double snorm = sqrt(sx * sx + sy * sy + sz * sz);
|
||||||
|
sx = sx / snorm;
|
||||||
|
sy = sy / snorm;
|
||||||
|
sz = sz / snorm;
|
||||||
|
} else {
|
||||||
|
error->all(FLERR, "Illegal fix propel/self command");
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
sx = 1.0;
|
||||||
|
sy = 0.0;
|
||||||
|
sz = 0.0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int FixPropelSelf::setmask()
|
||||||
|
{
|
||||||
|
int mask = 0;
|
||||||
|
mask |= POST_FORCE;
|
||||||
|
return mask;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::init()
|
||||||
|
{
|
||||||
|
if (mode == DIPOLE && !atom->mu_flag)
|
||||||
|
error->all(FLERR, "Fix propel/self requires atom attribute mu with option dipole");
|
||||||
|
|
||||||
|
if (mode == QUAT) {
|
||||||
|
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||||
|
if (!avec) error->all(FLERR, "Fix propel/self requires atom style ellipsoid with option quat");
|
||||||
|
|
||||||
|
// check that all particles are finite-size ellipsoids
|
||||||
|
// no point particles allowed, spherical is OK
|
||||||
|
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit)
|
||||||
|
if (ellipsoid[i] < 0)
|
||||||
|
error->one(FLERR, "Fix propel/self requires extended particles with option quat");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::setup(int vflag)
|
||||||
|
{
|
||||||
|
post_force(vflag);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::post_force(int vflag)
|
||||||
|
{
|
||||||
|
if (mode == DIPOLE)
|
||||||
|
post_force_dipole(vflag);
|
||||||
|
else if (mode == VELOCITY)
|
||||||
|
post_force_velocity(vflag);
|
||||||
|
else if (mode == QUAT)
|
||||||
|
post_force_quaternion(vflag);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::post_force_dipole(int vflag)
|
||||||
|
{
|
||||||
|
double **f = atom->f;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double **x = atom->x;
|
||||||
|
double **mu = atom->mu;
|
||||||
|
double fx, fy, fz;
|
||||||
|
|
||||||
|
// energy and virial setup
|
||||||
|
double vi[6];
|
||||||
|
if (vflag)
|
||||||
|
v_setup(vflag);
|
||||||
|
else
|
||||||
|
evflag = 0;
|
||||||
|
|
||||||
|
// if domain has PBC, need to unwrap for virial
|
||||||
|
double unwrap[3];
|
||||||
|
imageint *image = atom->image;
|
||||||
|
|
||||||
|
// Add the active force to the atom force:
|
||||||
|
for (int i = 0; i < nlocal; i++)
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
|
||||||
|
fx = magnitude * mu[i][0];
|
||||||
|
fy = magnitude * mu[i][1];
|
||||||
|
fz = magnitude * mu[i][2];
|
||||||
|
f[i][0] += fx;
|
||||||
|
f[i][1] += fy;
|
||||||
|
f[i][2] += fz;
|
||||||
|
|
||||||
|
if (evflag) {
|
||||||
|
domain->unmap(x[i], image[i], unwrap);
|
||||||
|
vi[0] = fx * unwrap[0];
|
||||||
|
vi[1] = fy * unwrap[1];
|
||||||
|
vi[2] = fz * unwrap[2];
|
||||||
|
vi[3] = fx * unwrap[1];
|
||||||
|
vi[4] = fx * unwrap[2];
|
||||||
|
vi[5] = fy * unwrap[2];
|
||||||
|
v_tally(i, vi);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::post_force_velocity(int vflag)
|
||||||
|
{
|
||||||
|
double **f = atom->f;
|
||||||
|
double **v = atom->v;
|
||||||
|
double **x = atom->x;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double nv2, fnorm, fx, fy, fz;
|
||||||
|
|
||||||
|
// energy and virial setup
|
||||||
|
double vi[6];
|
||||||
|
if (vflag)
|
||||||
|
v_setup(vflag);
|
||||||
|
else
|
||||||
|
evflag = 0;
|
||||||
|
|
||||||
|
// if domain has PBC, need to unwrap for virial
|
||||||
|
double unwrap[3];
|
||||||
|
imageint *image = atom->image;
|
||||||
|
|
||||||
|
// Add the active force to the atom force:
|
||||||
|
for (int i = 0; i < nlocal; ++i) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
|
||||||
|
nv2 = v[i][0] * v[i][0] + v[i][1] * v[i][1] + v[i][2] * v[i][2];
|
||||||
|
fnorm = 0.0;
|
||||||
|
|
||||||
|
if (nv2 > TOL) {
|
||||||
|
|
||||||
|
// Without this check you can run into numerical
|
||||||
|
// issues because fnorm will blow up.
|
||||||
|
|
||||||
|
fnorm = magnitude / sqrt(nv2);
|
||||||
|
}
|
||||||
|
fx = fnorm * v[i][0];
|
||||||
|
fy = fnorm * v[i][1];
|
||||||
|
fz = fnorm * v[i][2];
|
||||||
|
|
||||||
|
f[i][0] += fx;
|
||||||
|
f[i][1] += fy;
|
||||||
|
f[i][2] += fz;
|
||||||
|
|
||||||
|
if (evflag) {
|
||||||
|
domain->unmap(x[i], image[i], unwrap);
|
||||||
|
vi[0] = fx * unwrap[0];
|
||||||
|
vi[1] = fy * unwrap[1];
|
||||||
|
vi[2] = fz * unwrap[2];
|
||||||
|
vi[3] = fx * unwrap[1];
|
||||||
|
vi[4] = fx * unwrap[2];
|
||||||
|
vi[5] = fy * unwrap[2];
|
||||||
|
v_tally(i, vi);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void FixPropelSelf::post_force_quaternion(int vflag)
|
||||||
|
{
|
||||||
|
double **f = atom->f;
|
||||||
|
double **x = atom->x;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
|
||||||
|
// ellipsoidal properties
|
||||||
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||||
|
double f_act[3] = {sx, sy, sz};
|
||||||
|
double f_rot[3];
|
||||||
|
double *quat;
|
||||||
|
double Q[3][3];
|
||||||
|
double fx, fy, fz;
|
||||||
|
|
||||||
|
// energy and virial setup
|
||||||
|
double vi[6];
|
||||||
|
if (vflag)
|
||||||
|
v_setup(vflag);
|
||||||
|
else
|
||||||
|
evflag = 0;
|
||||||
|
|
||||||
|
// if domain has PBC, need to unwrap for virial
|
||||||
|
double unwrap[3];
|
||||||
|
imageint *image = atom->image;
|
||||||
|
|
||||||
|
// Add the active force to the atom force:
|
||||||
|
for (int i = 0; i < nlocal; ++i) {
|
||||||
|
if (mask[i] & groupbit) {
|
||||||
|
|
||||||
|
quat = bonus[ellipsoid[i]].quat;
|
||||||
|
MathExtra::quat_to_mat(quat, Q);
|
||||||
|
MathExtra::matvec(Q, f_act, f_rot);
|
||||||
|
|
||||||
|
fx = magnitude * f_rot[0];
|
||||||
|
fy = magnitude * f_rot[1];
|
||||||
|
fz = magnitude * f_rot[2];
|
||||||
|
|
||||||
|
f[i][0] += fx;
|
||||||
|
f[i][1] += fy;
|
||||||
|
f[i][2] += fz;
|
||||||
|
|
||||||
|
if (evflag) {
|
||||||
|
domain->unmap(x[i], image[i], unwrap);
|
||||||
|
vi[0] = fx * unwrap[0];
|
||||||
|
vi[1] = fy * unwrap[1];
|
||||||
|
vi[2] = fz * unwrap[2];
|
||||||
|
vi[3] = fx * unwrap[1];
|
||||||
|
vi[4] = fx * unwrap[2];
|
||||||
|
vi[5] = fy * unwrap[2];
|
||||||
|
v_tally(i, vi);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
@ -12,60 +12,57 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#ifdef FIX_CLASS
|
#ifdef FIX_CLASS
|
||||||
|
// clang-format off
|
||||||
FixStyle(propel/self,FixPropelSelf)
|
FixStyle(propel/self,FixPropelSelf);
|
||||||
|
// clang-format on
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_FIX_PROPEL_SELF_H
|
#ifndef LMP_FIX_PROPEL_SELF_H
|
||||||
#define LMP_FIX_PROPEL_SELF_H
|
#define LMP_FIX_PROPEL_SELF_H
|
||||||
|
|
||||||
#include "fix.h"
|
#include "fix.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class FixPropelSelf : public Fix {
|
class FixPropelSelf : public Fix {
|
||||||
public:
|
public:
|
||||||
|
|
||||||
FixPropelSelf(class LAMMPS *, int, char **);
|
FixPropelSelf(class LAMMPS *, int, char **);
|
||||||
virtual ~FixPropelSelf();
|
virtual ~FixPropelSelf() {};
|
||||||
virtual int setmask();
|
void init();
|
||||||
virtual void post_force(int);
|
void post_force(int);
|
||||||
|
void setup(int);
|
||||||
double memory_usage();
|
int setmask();
|
||||||
|
|
||||||
protected:
|
|
||||||
enum operation_modes {
|
|
||||||
VELOCITY = 0,
|
|
||||||
QUATERNION = 1
|
|
||||||
};
|
|
||||||
|
|
||||||
private:
|
private:
|
||||||
double magnitude;
|
double magnitude;
|
||||||
|
double sx, sy, sz;
|
||||||
int mode;
|
int mode;
|
||||||
|
|
||||||
// If 0, apply fix to everything in group. If > 0, apply only to those
|
void post_force_dipole(int);
|
||||||
// types i for which i <= n_types_filter _and_ apply_to_type[i] == 1:
|
void post_force_velocity(int);
|
||||||
int n_types_filter;
|
void post_force_quaternion(int);
|
||||||
int *apply_to_type; //< Specifies, per type, if the fix applies to it or not.
|
|
||||||
|
|
||||||
|
class AtomVecEllipsoid *avec;
|
||||||
int atoms_have_quaternion();
|
|
||||||
|
|
||||||
template <int filter_by_type> void post_force_velocity(int);
|
|
||||||
template <int filter_by_type> void post_force_quaternion(int);
|
|
||||||
};
|
};
|
||||||
}
|
} // namespace LAMMPS_NS
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
/* ERROR/WARNING messages:
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
E: Illegal ... command
|
E: Illegal fix propel/self command.
|
||||||
|
|
||||||
Self-explanatory. Check the input script syntax and compare to the
|
Wrong number/type of input arguments.
|
||||||
documentation for the command. You can use -echo screen as a
|
|
||||||
command-line option when running LAMMPS to see the offending line.
|
E: Fix propel/self requires atom attribute mu with option dipole.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix propel/self requires atom style ellipsoid with option quat.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
Fix propel/self requires extended particles with option quat.
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
*/
|
*/
|
||||||
@ -68,7 +68,6 @@ fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com
|
|||||||
fix orient/eco Adrian A. Schratt and Volker Mohles (Ruhr-Uni Bochum), volker.mohles at rub.de, 6 Jun 2020
|
fix orient/eco Adrian A. Schratt and Volker Mohles (Ruhr-Uni Bochum), volker.mohles at rub.de, 6 Jun 2020
|
||||||
fix pafi, Thomas Swinburne (CNRS), swinburne at cinam.univ-mrs.fr, 1st Sep 2020
|
fix pafi, Thomas Swinburne (CNRS), swinburne at cinam.univ-mrs.fr, 1st Sep 2020
|
||||||
fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
|
fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014
|
||||||
fix propel/self, Stefan Paquay (Brandeis U), stefanpaquay at gmail.com, 20 Jan 2020
|
|
||||||
fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017
|
fix rhok, Ulf Pedersen (Roskilde U), ulf at urp.dk, 25 Sep 2017
|
||||||
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
|
fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008
|
||||||
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
|
fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013
|
||||||
|
|||||||
@ -1,258 +0,0 @@
|
|||||||
/* ----------------------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://lammps.sandia.gov/, Sandia National Laboratories
|
|
||||||
Steve Plimpton, sjplimp@sandia.gov
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
/* -----------------------------------------------------------------------
|
|
||||||
Contributed by Stefan Paquay @ Brandeis University
|
|
||||||
|
|
||||||
Thanks to Liesbeth Janssen @ Eindhoven University for useful discussions!
|
|
||||||
----------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "fix_propel_self.h"
|
|
||||||
|
|
||||||
#include "atom.h"
|
|
||||||
#include "atom_vec_ellipsoid.h"
|
|
||||||
#include "error.h"
|
|
||||||
#include "math_const.h"
|
|
||||||
#include "math_extra.h"
|
|
||||||
|
|
||||||
#include <cctype>
|
|
||||||
#include <cmath>
|
|
||||||
#include <cstring>
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
using namespace FixConst;
|
|
||||||
using namespace MathConst;
|
|
||||||
|
|
||||||
#define PRINT_DEBUG_OUTPUT 0
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixPropelSelf::FixPropelSelf( LAMMPS *lmp, int narg, char **argv )
|
|
||||||
: Fix(lmp, narg, argv), magnitude(0.0),
|
|
||||||
mode(VELOCITY), n_types_filter(0), apply_to_type(nullptr)
|
|
||||||
{
|
|
||||||
if (narg < 5) error->all(FLERR, "Illegal fix propel/self command");
|
|
||||||
|
|
||||||
// The fix is to support the following cases:
|
|
||||||
// 1. Simple atoms, in which case the force points along the velocity
|
|
||||||
// 2. Aspherical particles with an orientation.
|
|
||||||
// The first argument (mode) is used to differentiate between these.
|
|
||||||
|
|
||||||
// args: fix ID all propel/self mode magnitude
|
|
||||||
// Optional args are
|
|
||||||
|
|
||||||
const char *mode_str = argv[3];
|
|
||||||
|
|
||||||
if (strcmp(mode_str, "velocity") == 0) {
|
|
||||||
mode = VELOCITY;
|
|
||||||
|
|
||||||
} else if (strcmp(mode_str, "quat") == 0) {
|
|
||||||
|
|
||||||
// This mode should only be supported if the atom style has
|
|
||||||
// a quaternion (and if all atoms in the group have it)
|
|
||||||
|
|
||||||
if (!atoms_have_quaternion()) {
|
|
||||||
error->all(FLERR, "All fix atoms need to be extended particles");
|
|
||||||
}
|
|
||||||
mode = QUATERNION;
|
|
||||||
|
|
||||||
} else {
|
|
||||||
char msg[2048];
|
|
||||||
sprintf(msg, "Illegal mode \"%s\" for fix propel/self", mode_str);
|
|
||||||
error->all(FLERR, msg);
|
|
||||||
}
|
|
||||||
|
|
||||||
magnitude = utils::numeric( FLERR, argv[4] ,false,lmp);
|
|
||||||
|
|
||||||
// Handle rest of args:
|
|
||||||
|
|
||||||
int iarg = 5;
|
|
||||||
while (iarg < narg) {
|
|
||||||
|
|
||||||
if (strcmp(argv[iarg],"types") == 0) {
|
|
||||||
|
|
||||||
apply_to_type = new int[atom->ntypes+1];
|
|
||||||
memset(apply_to_type, 0, atom->ntypes * sizeof(int));
|
|
||||||
|
|
||||||
// consume all following numerical arguments as types
|
|
||||||
|
|
||||||
iarg++;
|
|
||||||
int flag=0;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (isdigit(argv[iarg][0])) {
|
|
||||||
int thistype = utils::inumeric(FLERR,argv[iarg],false,lmp);
|
|
||||||
if ((thistype < 1) || (thistype > atom->ntypes))
|
|
||||||
error->all(FLERR,"Illegal atom type to types keyword");
|
|
||||||
apply_to_type[thistype] = 1;
|
|
||||||
flag = 1;
|
|
||||||
iarg++;
|
|
||||||
} else break;
|
|
||||||
}
|
|
||||||
if (!flag)
|
|
||||||
error->all(FLERR,"'types' keyword requires at least one type");
|
|
||||||
else
|
|
||||||
n_types_filter = 1;
|
|
||||||
|
|
||||||
} else {
|
|
||||||
error->all(FLERR,"Illegal fix propel/self command.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixPropelSelf::~FixPropelSelf()
|
|
||||||
{
|
|
||||||
delete[] apply_to_type;
|
|
||||||
}
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixPropelSelf::setmask()
|
|
||||||
{
|
|
||||||
int mask = 0;
|
|
||||||
mask |= POST_FORCE;
|
|
||||||
|
|
||||||
return mask;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixPropelSelf::memory_usage()
|
|
||||||
{
|
|
||||||
// magnitude + thermostat_orient + mode + n_types_filter + apply_to_type
|
|
||||||
double bytes = (double)sizeof(double) + 3*sizeof(int) + sizeof(int*);
|
|
||||||
bytes += (double)sizeof(int)*atom->ntypes*n_types_filter;
|
|
||||||
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixPropelSelf::post_force(int vflag )
|
|
||||||
{
|
|
||||||
switch(mode) {
|
|
||||||
case QUATERNION:
|
|
||||||
if (n_types_filter) post_force_quaternion<1>(vflag);
|
|
||||||
else post_force_quaternion<0>(vflag);
|
|
||||||
break;
|
|
||||||
case VELOCITY:
|
|
||||||
if (n_types_filter) post_force_velocity<1>(vflag);
|
|
||||||
else post_force_velocity<0>(vflag);
|
|
||||||
break;
|
|
||||||
default:
|
|
||||||
;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
template <int filter_by_type>
|
|
||||||
void FixPropelSelf::post_force_quaternion(int /* vflag */ )
|
|
||||||
{
|
|
||||||
double **f = atom->f;
|
|
||||||
|
|
||||||
int *mask = atom->mask;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
int *type = atom->type;
|
|
||||||
int* ellipsoid = atom->ellipsoid;
|
|
||||||
|
|
||||||
AtomVecEllipsoid *av = static_cast<AtomVecEllipsoid*>(atom->style_match("ellipsoid"));
|
|
||||||
AtomVecEllipsoid::Bonus *bonus = av->bonus;
|
|
||||||
|
|
||||||
// Add the active force to the atom force:
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; ++i) {
|
|
||||||
if (mask[i] & groupbit) {
|
|
||||||
if (filter_by_type && !apply_to_type[type[i]]) {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
|
|
||||||
double f_act[3] = { 1.0, 0.0, 0.0 };
|
|
||||||
double f_rot[3];
|
|
||||||
|
|
||||||
double *quat = bonus[ellipsoid[i]].quat;
|
|
||||||
|
|
||||||
double Q[3][3];
|
|
||||||
MathExtra::quat_to_mat( quat, Q );
|
|
||||||
MathExtra::matvec( Q, f_act, f_rot );
|
|
||||||
|
|
||||||
f[i][0] += magnitude * f_rot[0];
|
|
||||||
f[i][1] += magnitude * f_rot[1];
|
|
||||||
f[i][2] += magnitude * f_rot[2];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
template <int filter_by_type>
|
|
||||||
void FixPropelSelf::post_force_velocity(int /*vflag*/)
|
|
||||||
{
|
|
||||||
double **f = atom->f;
|
|
||||||
double **v = atom->v;
|
|
||||||
int *mask = atom->mask;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
int *type = atom->type;
|
|
||||||
|
|
||||||
// Add the active force to the atom force:
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; ++i) {
|
|
||||||
if (mask[i] & groupbit) {
|
|
||||||
if (filter_by_type && !apply_to_type[type[i]]) {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
|
|
||||||
const double *vi = v[i];
|
|
||||||
double f_act[3] = { vi[0], vi[1], vi[2] };
|
|
||||||
double nv2 = vi[0]*vi[0] + vi[1]*vi[1] + vi[2]*vi[2];
|
|
||||||
double fnorm = 0.0;
|
|
||||||
const double TOL = 1e-14;
|
|
||||||
|
|
||||||
if (nv2 > TOL) {
|
|
||||||
|
|
||||||
// Without this check you can run into numerical
|
|
||||||
// issues because fnorm will blow up.
|
|
||||||
|
|
||||||
fnorm = magnitude / sqrt(nv2);
|
|
||||||
}
|
|
||||||
|
|
||||||
f[i][0] += fnorm * f_act[0];
|
|
||||||
f[i][1] += fnorm * f_act[1];
|
|
||||||
f[i][2] += fnorm * f_act[2];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixPropelSelf::atoms_have_quaternion()
|
|
||||||
{
|
|
||||||
if (!atom->ellipsoid_flag) {
|
|
||||||
error->all(FLERR, "Mode 'quat' requires atom style ellipsoid");
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
int *mask = atom->mask;
|
|
||||||
int flag=0,flagall=0;
|
|
||||||
|
|
||||||
// Make sure all atoms have ellipsoid data:
|
|
||||||
|
|
||||||
for (int i = 0; i < atom->nlocal; ++i)
|
|
||||||
if (mask[i] & groupbit)
|
|
||||||
if (atom->ellipsoid[i] < 0) ++flag;
|
|
||||||
|
|
||||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
|
|
||||||
if (flagall > 0) return 0;
|
|
||||||
|
|
||||||
return 1;
|
|
||||||
}
|
|
||||||
@ -94,6 +94,7 @@ double RanMars::uniform()
|
|||||||
return uni;
|
return uni;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
gaussian RN
|
gaussian RN
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
86
unittest/force-styles/tests/data.brownian
Normal file
86
unittest/force-styles/tests/data.brownian
Normal file
@ -0,0 +1,86 @@
|
|||||||
|
LAMMPS data file via write_data, version 30 Nov 2020, timestep = 120000
|
||||||
|
|
||||||
|
32 atoms
|
||||||
|
1 atom types
|
||||||
|
|
||||||
|
-2.7144176165949063 2.7144176165949063 xlo xhi
|
||||||
|
-2.7144176165949063 2.7144176165949063 ylo yhi
|
||||||
|
-1.3572088082974532 1.3572088082974532 zlo zhi
|
||||||
|
|
||||||
|
Masses
|
||||||
|
|
||||||
|
1 1
|
||||||
|
|
||||||
|
Pair Coeffs # zero
|
||||||
|
|
||||||
|
1
|
||||||
|
|
||||||
|
Atoms # hybrid
|
||||||
|
|
||||||
|
1 1 0.8174385639059338 -1.5010271964354949 1.0637924298773633 0 0.6257069940596588 -0.111108944542851 -0.7721046302331049 1 1 -1 0 -1
|
||||||
|
2 1 -1.5885878110813303 2.2401728691740113 0.47068930278928994 0 -0.5102593570021903 0.8585717488647711 -0.049899305035241655 1 1 0 -1 -1
|
||||||
|
3 1 -1.1818944957014061 -2.6848623178033457 -1.1800939297629425 0 -0.004166477179696561 0.19766436575888424 0.9802609035236738 1 1 0 0 0
|
||||||
|
4 1 0.1720589621174558 1.3643946759490944 -1.1522506184595422 0 0.11721568749368932 0.2990753541702089 -0.9470028590945996 1 1 0 -1 0
|
||||||
|
5 1 -2.5038595242428823 -1.624930716630223 -1.1484315973168586 0 -0.3868419197154481 -0.6136739748888413 0.6883005024660352 1 1 0 0 0
|
||||||
|
6 1 -1.2345478646498314 -0.3224402671532977 0.5533955773621407 0 0.24969915142093102 -0.15640101573329426 -0.9556092590893315 1 1 0 0 -1
|
||||||
|
7 1 1.1946150666115714 0.4921384424233923 -0.516829526742452 0 0.0036359783326705107 -0.4590891155800383 -0.8883827798969893 1 1 0 0 -1
|
||||||
|
8 1 1.8342027600045443 1.516095010832566 0.043843911607852545 0 -0.8435468778359277 0.11782686457134713 -0.5239708912511688 1 1 0 -1 -1
|
||||||
|
9 1 -0.5406701027756321 2.23952568921304 0.5241488585364904 0 0.045872039042421424 0.13268297551853248 -0.9900964518882184 1 1 0 0 -1
|
||||||
|
10 1 -0.3972258497968314 0.7566024687022016 -0.2323435643206888 0 0.655171514572036 -0.43050189344470563 0.6208207520966965 1 1 0 0 -1
|
||||||
|
11 1 -0.7183933447005026 1.1587411649504586 0.20950093049531074 0 0.22933670283280452 -0.6843477395075139 -0.6921508854034168 1 1 0 0 -1
|
||||||
|
12 1 1.022524253197315 0.17877446802634833 0.29899480569943504 0 0.6711103355965887 -0.41621190608313047 -0.6134969981100816 1 1 0 0 -2
|
||||||
|
13 1 -1.4250800612966135 -2.4056565408365356 0.21801121763465003 0 -0.5029961497078136 0.46126362983367525 -0.7309108955076378 1 1 0 1 0
|
||||||
|
14 1 -1.7432369014700662 1.621196939810902 0.07955801420882219 0 -0.7988534279257005 0.3194109740977685 -0.5097154405325315 1 1 0 0 -1
|
||||||
|
15 1 -0.9908151496097626 -2.6488792381485773 -1.1948117198271224 0 0.5516163133238324 -0.6234158094772195 0.5541409309633126 1 1 0 1 0
|
||||||
|
16 1 2.6948716697156523 0.41280900513864877 0.1548529904178103 0 -0.8512724888069316 0.23988291811633639 0.4666811924605956 1 1 0 0 -1
|
||||||
|
17 1 -1.5494542712095147 -0.53420074244155 -0.6250925146711168 0 -0.07678144567993991 -0.03950496198488684 0.9962650087089635 1 1 0 0 0
|
||||||
|
18 1 -2.3151948315996678 -2.6221617748715036 -0.1899804833264763 0 -0.7569384929404162 -0.33315612552157964 -0.562184234866597 1 1 0 0 0
|
||||||
|
19 1 2.1590179665621467 1.6095466091914918 -1.2253859221608403 0 0.20879037375649698 -0.06905534931949565 0.9755193173674137 1 1 0 -1 0
|
||||||
|
20 1 2.202409043221526 0.14395355359028536 1.335860415061412 0 -0.14984238844204667 -0.9847320173066201 0.08860086183112265 1 1 0 -1 -1
|
||||||
|
21 1 -1.4500395490531754 -1.5281375693866057 0.00020797713894412338 0 -0.9915462127271186 0.08451237717795997 0.09845692525281326 1 1 0 0 0
|
||||||
|
22 1 -1.0657362106538344 0.6350242518491277 -0.7513800843604899 0 -0.6569043427466144 -0.07223746743273625 0.7505054515321944 1 1 0 -1 0
|
||||||
|
23 1 -0.5619632776222234 1.8699713384517294 -0.9467270322768698 0 0.7911745431454184 0.5177930983571434 -0.3254737310019788 1 1 0 0 0
|
||||||
|
24 1 -2.1040517028343215 -2.247249268720423 0.11322260281322279 0 -0.04193441020358475 0.2313330374822751 -0.9719704373128341 1 1 1 0 -1
|
||||||
|
25 1 -0.868354233492487 -0.14640654973697223 -0.9035771863161228 0 -0.15652971300701132 0.0848859275832726 -0.9840187133608133 1 1 0 0 0
|
||||||
|
26 1 -0.4652717213714348 0.12334049868763304 -0.3826888902964762 0 0.6487662426744875 0.7578954080882759 0.06853402632804934 1 1 -1 0 -1
|
||||||
|
27 1 -1.0478542019398558 2.3814414358320106 1.2039965288246885 0 0.10846325104076994 -0.6457073741173193 -0.7558423844851409 1 1 0 0 -1
|
||||||
|
28 1 2.500698605198214 -0.728008572758278 0.48410831318342695 0 -0.3622892345018212 0.911584495321123 0.19431988692415955 1 1 0 0 -1
|
||||||
|
29 1 -1.416084269787537 -1.7066588654378656 0.8328319180724224 0 -0.08971242415920104 -0.44687722085944426 0.8900856309526737 1 1 0 1 -1
|
||||||
|
30 1 -0.6370519124977301 0.47113373856505564 -0.08549434306971403 0 -0.6030496979424049 -0.7976847581640081 -0.0054852898193420265 1 1 0 0 0
|
||||||
|
31 1 0.8225325721319097 -0.441545584269452 0.3381678086542899 0 -0.6909877678544062 -0.7162885851668209 0.09729628685258002 1 1 0 0 0
|
||||||
|
32 1 2.1861742760925518 1.5740929150306235 -0.01693950575830974 0 0.890366016527044 0.3247001065794207 0.3190896385047258 1 1 0 0 0
|
||||||
|
|
||||||
|
Velocities
|
||||||
|
|
||||||
|
1 -524.6769664299819 215.42199277006424 -112.27005568908588 -462.03530876082846 -551.9512642384534 -196.46403300264745
|
||||||
|
2 391.3416799472542 48.7957761872576 -623.1311508507263 489.33832403519347 -260.3072072833973 -529.7105564646685
|
||||||
|
3 109.86388293585976 665.5499875054874 -583.4371492475789 -678.3137468561738 622.6210695594215 37.427168579931944
|
||||||
|
4 398.4814329387423 -117.47798197974335 -376.25882363220865 44.966011242133156 -720.7197483734453 654.1933839835833
|
||||||
|
5 584.5314601424474 159.82839534760055 -199.69054648577074 298.5492685852273 657.8565691587017 -616.4449676099423
|
||||||
|
6 609.4975570025578 738.2439586459146 284.06966373218285 143.74329023895925 256.75048911205783 -57.96098774586574
|
||||||
|
7 -27.968041606728725 752.3634409363073 223.6145040530379 -496.9033910070852 198.22198514310026 -81.32767873220877
|
||||||
|
8 -451.1189781565461 -759.642533657806 547.0603381420482 316.5054412546416 669.7302717449263 -447.9786170711034
|
||||||
|
9 -54.531235862640735 -115.1466962517251 -610.7279757582849 -731.9703465871636 -735.0301879611621 -584.8114323501295
|
||||||
|
10 748.6292469789635 701.8693636792311 -498.1997398935133 208.99011146198362 -538.4269075676226 130.16593091403558
|
||||||
|
11 -174.9453247974202 153.40962619436522 390.8158086666639 -381.20607659097726 548.6301954978544 225.4382939850729
|
||||||
|
12 -393.58450479962613 562.7494007708912 -512.2495061493412 425.83486537187855 260.1521699032197 -605.409242525273
|
||||||
|
13 294.0485676041469 -416.4803586200817 -678.9550420350499 284.48925268723156 -67.2753269810592 559.4386740115784
|
||||||
|
14 -764.1287373972617 733.8169442814999 720.6030317274988 357.0913464046234 521.8205481343224 173.7714175822938
|
||||||
|
15 -91.18940426263303 224.9036504882129 284.4326488075122 -207.62866349692237 501.5282881027212 445.99895870682315
|
||||||
|
16 179.07740801693492 -535.4403834538152 -318.55850921823156 266.7175735768374 444.97898080245074 -381.12832705309194
|
||||||
|
17 -428.2045641732463 -491.50884735767914 -270.6175162521197 727.5062118970601 128.20058511314278 270.88345291377027
|
||||||
|
18 395.0795674693432 306.1681692632796 -13.216405710204159 671.3857274637012 102.79070644890297 322.4136674209789
|
||||||
|
19 -203.6409986589429 -54.701509197392014 581.0635722032287 -186.75568274826543 476.4083542709755 -601.0363388843747
|
||||||
|
20 -115.92502268264624 -762.0000436955148 -223.1167962036293 489.85643882981896 -247.41158767130918 -365.8330907652003
|
||||||
|
21 658.7418242889948 586.715926671846 -624.8573383343708 -10.66175165422313 359.69577124554525 -340.2786090411881
|
||||||
|
22 56.13036471905219 261.41167548131494 373.8653013382346 673.5607754029996 -245.8613985477709 353.0482780954667
|
||||||
|
23 -252.99394908800596 -466.09490577221976 -670.846651689147 -616.9981712696467 -541.8114132827196 -369.70154580103025
|
||||||
|
24 -627.059810991902 278.53716543954556 457.18418082455213 -101.65170342061822 225.64771910612274 649.9004460194175
|
||||||
|
25 -542.388717452386 -105.31239543953356 69.1170307021082 -204.78231016519337 -522.3497436231834 -357.49930063072486
|
||||||
|
26 -213.4605252121538 -534.3449644895232 244.1099101456221 275.4530388773477 212.2684271906576 -165.97485643999994
|
||||||
|
27 595.2153731851414 626.5401264322599 -736.723964414168 -188.93350086112284 -459.44316502268424 -484.4606024327521
|
||||||
|
28 -400.55444615195614 606.638183855102 121.6628831751137 359.49918126198475 668.2849798601502 -135.04633035091715
|
||||||
|
29 -347.6624143232117 -365.7917228400548 -541.6372617049859 160.0398519292602 -624.5129134218859 -448.13097661684066
|
||||||
|
30 -104.98117502101249 500.1388613847156 731.4317325082025 -481.0858846642298 -574.8809141763269 122.21267028742885
|
||||||
|
31 754.8558584263326 -34.937336585228245 -726.0948084688208 -103.81133072710576 431.8053281041717 -479.89267857331
|
||||||
|
32 140.02839515740888 643.0847109951975 -535.5893264521633 -373.10470401809016 -661.5529040774077 37.5722333352976
|
||||||
80
unittest/force-styles/tests/fix-timestep-brownian.yaml
Normal file
80
unittest/force-styles/tests/fix-timestep-brownian.yaml
Normal file
@ -0,0 +1,80 @@
|
|||||||
|
---
|
||||||
|
lammps_version: 24 Aug 2020
|
||||||
|
date_generated: Tue Dec 08 12:28:40 2020
|
||||||
|
epsilon: 1e-12
|
||||||
|
prerequisites: ! |
|
||||||
|
atom hybrid dipole sphere
|
||||||
|
fix brownian/sphere
|
||||||
|
pre_commands: ! ""
|
||||||
|
post_commands: ! |
|
||||||
|
fix test solute brownian/sphere 1.0 1.0 1.0 1.0 1049270 dipole
|
||||||
|
fix_modify test virial yes
|
||||||
|
input_file: in.brownian
|
||||||
|
natoms: 32
|
||||||
|
run_pos: ! |2
|
||||||
|
1 0.8198132185477983 -1.5120221815010249 1.069236010215717
|
||||||
|
2 -1.583657719347759 2.2448791290372445 0.48185576252150486
|
||||||
|
3 -1.1880610036164596 -2.678219122115848 -1.1824396130063375
|
||||||
|
4 0.1908794667962731 1.3593710068293134 -1.1524405138570022
|
||||||
|
5 -2.502067366922716 -1.6291621715156412 -1.155308629818198
|
||||||
|
6 -1.214213515524568 -0.33667539680264325 0.5468489960944642
|
||||||
|
7 1.2020658999364164 0.5045561046001554 -0.5265404283266816
|
||||||
|
8 1.8138899397447894 1.5212405777462397 0.04943268689972926
|
||||||
|
9 -0.547736141448719 2.2385521615789026 0.5146647473679599
|
||||||
|
10 -0.38821952892982114 0.7570899758491753 -0.23554333362488367
|
||||||
|
11 -0.7101567507222957 1.1587573566149103 0.19674801175715137
|
||||||
|
12 1.0217947252204158 0.1732739652383159 0.3064332055619567
|
||||||
|
13 -1.43254480550968 -2.4145346257525504 0.22508495277327453
|
||||||
|
14 -1.7469141674373843 1.605802890508775 0.07604534549063337
|
||||||
|
15 -0.9840165887382163 -2.631709004347024 -1.1933270065258215
|
||||||
|
16 2.6947076505094056 0.4027838910781582 0.16197472527708037
|
||||||
|
17 -1.553343026077184 -0.5326249015108566 -0.6372569894483383
|
||||||
|
18 -2.32697929027452 -2.6229660088889384 -0.1908463010722981
|
||||||
|
19 2.161025566743724 1.613342829181601 -1.2185964188334404
|
||||||
|
20 2.200299550516107 0.13388691832171218 1.3492239308384593
|
||||||
|
21 -1.444652156145116 -1.5251851082502694 -0.01486082239207267
|
||||||
|
22 -1.069098522661769 0.6345737477571621 -0.7476592232484849
|
||||||
|
23 -0.5530156382651018 1.8581482829486815 -0.9359906503001887
|
||||||
|
24 -2.1057002294256346 -2.2411635326026076 0.1027461222133986
|
||||||
|
25 -0.846470575235486 -0.16100145290710122 -0.8945542130124591
|
||||||
|
26 -0.4600833044897612 0.1168099650353831 -0.3780372490219117
|
||||||
|
27 -1.0507601010756238 2.380597031527799 1.2042435415073673
|
||||||
|
28 2.4951223446270854 -0.7272384746662179 0.49148118274363145
|
||||||
|
29 -1.4227701815513125 -1.7103131555856865 0.8522428843219197
|
||||||
|
30 -0.6362527497446904 0.4809930863631752 -0.09023977411046079
|
||||||
|
31 0.8307577317570568 -0.43366523738108803 0.3435388363003548
|
||||||
|
32 2.193071783870056 1.5720818983016567 -0.002617308630618007
|
||||||
|
run_vel: ! |2
|
||||||
|
1 -199.33264006196603 -425.90458140644324 687.4446082626521
|
||||||
|
2 -437.96841023792416 91.79431782876951 428.57844526457393
|
||||||
|
3 256.4136360073004 753.6546188320922 -477.2093961250793
|
||||||
|
4 566.9823183079484 -598.4626629699561 -572.6010613373849
|
||||||
|
5 193.3673483203161 517.2757090545375 86.71381952181962
|
||||||
|
6 330.2395000638781 -14.096120493379578 -736.8264608358458
|
||||||
|
7 772.6058378438489 335.4342218605717 -492.47120565202727
|
||||||
|
8 -379.69346948872095 328.07026948905315 212.8907928502149
|
||||||
|
9 -32.22616772317161 520.1349898628745 -354.5179475075607
|
||||||
|
10 1.0828608441585152 -152.03654350035677 -287.63229160711455
|
||||||
|
11 -8.398427517515586 462.54972999070884 -696.8949630195855
|
||||||
|
12 -35.97938353895289 590.1362599649709 750.3193298672243
|
||||||
|
13 -738.0063700936831 2.1036698005985586 521.0581963709241
|
||||||
|
14 734.7145728536893 -576.3310076952716 -212.8973489276375
|
||||||
|
15 462.14962458969075 517.8011186395346 582.1970348843957
|
||||||
|
16 579.8864331189503 -723.7080269305067 -397.93358494791835
|
||||||
|
17 -74.75036331228799 -271.6937286797369 318.88308122021147
|
||||||
|
18 -390.80278885093725 -625.5459111419849 -678.090840223804
|
||||||
|
19 -598.6933260882906 41.7579655827356 750.013779723682
|
||||||
|
20 158.9763823000137 310.0053213378944 226.83667759758563
|
||||||
|
21 -578.1763126419472 755.241466585726 -387.1851268613029
|
||||||
|
22 -686.649568451259 496.2326396493665 -392.30182210275524
|
||||||
|
23 139.72339904857833 686.4901911325059 460.94182891802774
|
||||||
|
24 625.6387119562066 -178.79780516572728 194.63377933230842
|
||||||
|
25 761.5753760889415 -550.6374632586046 -355.3666363468769
|
||||||
|
26 -167.9925585211552 -748.0176849962858 537.6949353742531
|
||||||
|
27 -687.973065038564 -637.3675344653028 -231.07938308121751
|
||||||
|
28 -480.2313784604401 372.9809695991278 24.972745276651647
|
||||||
|
29 67.21410614540838 54.58636231646205 639.3712010004265
|
||||||
|
30 -469.9090654062959 715.7242943947524 -386.21519675922724
|
||||||
|
31 -380.59017466972404 487.7214660680053 177.24466119039292
|
||||||
|
32 138.31144158562722 31.005629253137737 621.8772779588675
|
||||||
|
...
|
||||||
16
unittest/force-styles/tests/in.brownian
Normal file
16
unittest/force-styles/tests/in.brownian
Normal file
@ -0,0 +1,16 @@
|
|||||||
|
variable newton_pair index on
|
||||||
|
variable newton_bond index on
|
||||||
|
variable units index lj
|
||||||
|
variable input_dir index .
|
||||||
|
variable data_file index ${input_dir}/data.brownian
|
||||||
|
variable pair_style index 'zero 8.0'
|
||||||
|
|
||||||
|
atom_style hybrid dipole sphere
|
||||||
|
atom_modify map array
|
||||||
|
neigh_modify delay 2 every 2 check no
|
||||||
|
units ${units}
|
||||||
|
timestep 0.00001
|
||||||
|
newton ${newton_pair} ${newton_bond}
|
||||||
|
|
||||||
|
pair_style ${pair_style}
|
||||||
|
read_data ${data_file}
|
||||||
Reference in New Issue
Block a user