forked from lijiext/lammps
first commit: added SDPD
This commit is contained in:
Morteza Jalalvand
parent
fb4df86d3d
commit
ba6f6f73f1
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@ -171,8 +171,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
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USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
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USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
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USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
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USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
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USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
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USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD
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USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
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set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
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set(OTHER_PACKAGES CORESHELL QEQ)
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foreach(PKG ${DEFAULT_PACKAGES})
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -61,6 +61,7 @@ set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
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set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
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set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
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set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
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set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
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set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
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set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
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set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
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USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
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USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
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USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
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USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
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USER-UEF USER-VTK)
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set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
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@ -94,6 +94,7 @@ OPT.
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"lineforce"_fix_lineforce.html,
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"manifoldforce"_fix_manifoldforce.html,
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"meso"_fix_meso.html,
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"meso/move"_fix_meso_move.html,
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"meso/stationary"_fix_meso_stationary.html,
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"momentum (k)"_fix_momentum.html,
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"move"_fix_move.html,
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@ -172,6 +173,7 @@ OPT.
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"restrain"_fix_restrain.html,
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"rhok"_fix_rhok.html,
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"rigid (o)"_fix_rigid.html,
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"rigid/meso"_fix_rigid_meso.html,
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"rigid/nph (o)"_fix_rigid.html,
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"rigid/nph/small"_fix_rigid.html,
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"rigid/npt (o)"_fix_rigid.html,
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@ -198,6 +198,7 @@ OPT.
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"reax/c (ko)"_pair_reaxc.html,
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"rebo (io)"_pair_airebo.html,
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"resquared (go)"_pair_resquared.html,
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"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
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"smd/hertz"_pair_smd_hertz.html,
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"smd/tlsph"_pair_smd_tlsph.html,
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"smd/tri_surface"_pair_smd_triangulated_surface.html,
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@ -95,6 +95,7 @@ as contained in the file name.
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"USER-QUIP"_#PKG-USER-QUIP,
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"USER-REAXC"_#PKG-USER-REAXC,
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"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
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"USER-SDPD"_#PKG-USER-SDPD,
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"USER-SMD"_#PKG-USER-SMD,
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"USER-SMTBQ"_#PKG-USER-SMTBQ,
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"USER-SPH"_#PKG-USER-SPH,
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@ -1916,6 +1917,31 @@ examples/USER/scafacos :ul
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:line
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USER-SDPD package :link(PKG-USER-SDPD),h4
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[Contents:]
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A pair style for smoothed dissipative particle dynamics (SDPD), which
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is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
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where thermal fluctuations are important (see the
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"USER-SPH package"_#PKG-USER-SPH).
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Also two fixes for moving and rigid body integration of SPH/SDPD particles
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(particles of atom_style meso).
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[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
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Sciences, Iran).
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[Supporting info:]
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src/USER-SDPD: filenames -> commands
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src/USER-SDPD/README
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"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
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"fix meso/move"_fix_meso_move.html
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"fix rigid/meso"_fix_rigid_meso.html
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examples/USER/sdpd :ul
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:line
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USER-SMD package :link(PKG-USER-SMD),h4
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[Contents:]
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@ -68,6 +68,7 @@ Package, Description, Doc page, Example, Library
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"USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
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"USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no
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"USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext
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"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal, USER/sdpd, no
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"USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext
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"USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no
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"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
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@ -237,6 +237,7 @@ accelerated styles exist.
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"lineforce"_fix_lineforce.html - constrain atoms to move in a line
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"manifoldforce"_fix_manifoldforce.html -
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"meso"_fix_meso.html -
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"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
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"meso/stationary"_fix_meso_stationary.html -
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"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
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"move"_fix_move.html - move atoms in a prescribed fashion
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@ -331,6 +332,7 @@ accelerated styles exist.
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"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
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"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
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"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
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"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
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"rx"_fix_rx.html -
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"saed/vtk"_fix_saed_vtk.html -
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"setforce"_fix_setforce.html - set the force on each atom
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@ -0,0 +1,233 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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fix meso/move command :h3
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[Syntax:]
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fix ID group-ID meso/move style args keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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meso/move = style name of this fix command :l
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style = {linear} or {wiggle} or {rotate} or {variable} :l
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{linear} args = Vx Vy Vz
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Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
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{wiggle} args = Ax Ay Az period
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Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
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period = period of oscillation (time units)
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{rotate} args = Px Py Pz Rx Ry Rz period
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Px,Py,Pz = origin point of axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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period = period of rotation (time units)
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{variable} args = v_dx v_dy v_dz v_vx v_vy v_vz
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v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
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v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {units} :l
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{units} value = {box} or {lattice} :pre
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:ule
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[Examples:]
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fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box
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fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
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fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL :pre
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[Description:]
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Perform updates of position, velocity, internal energy and local
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density for mesoscopic particles in the group each timestep using the
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specified settings or formulas, without regard to forces on the
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particles. This can be useful for boundary, solid bodies or other
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particles, whose movement can influence nearby particles.
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The operation of this fix is exactly like that described by the
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"fix move"_fix_move.html command, except that particles' density,
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internal energy and extrapolated velocity are also updated.
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NOTE: The particles affected by this fix should not be time integrated
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by other fixes (e.g. "fix meso"_fix_meso.html, "fix
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meso/stationary"_fix_meso_stationary.html), since that will change their
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positions and velocities twice.
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NOTE: As particles move due to this fix, they will pass thru periodic
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boundaries and be remapped to the other side of the simulation box,
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just as they would during normal time integration (e.g. via the "fix
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meso"_fix_meso.html command). It is up to you to decide whether periodic
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boundaries are appropriate with the kind of particle motion you are
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prescribing with this fix.
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NOTE: As dicsussed below, particles are moved relative to their initial
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position at the time the fix is specified. These initial coordinates
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are stored by the fix in "unwrapped" form, by using the image flags
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associated with each particle. See the "dump custom"_dump.html command
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for a discussion of "unwrapped" coordinates. See the Atoms section of
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the "read_data"_read_data.html command for a discussion of image flags
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and how they are set for each particle. You can reset the image flags
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(e.g. to 0) before invoking this fix by using the "set image"_set.html
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command.
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:line
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The {linear} style moves particles at a constant velocity, so that their
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position {X} = (x,y,z) as a function of time is given in vector
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notation as
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X(t) = X0 + V * delta :pre
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where {X0} = (x0,y0,z0) is their position at the time the fix is
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specified, {V} is the specified velocity vector with components
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(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was
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specified. This style also sets the velocity of each particle to V =
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(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
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then the position and velocity of that component is time integrated
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the same as the "fix meso"_fix_meso.html command would perform, using
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the corresponding force component on the particle.
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Note that the {linear} style is identical to using the {variable}
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style with an "equal-style variable"_variable.html that uses the
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vdisplace() function. E.g.
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variable V equal 10.0
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variable x equal vdisplace(0.0,$V)
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fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre
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The {wiggle} style moves particles in an oscillatory fashion, so that
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their position {X} = (x,y,z) as a function of time is given in vector
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notation as
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X(t) = X0 + A sin(omega*delta) :pre
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where {X0} = (x0,y0,z0) is their position at the time the fix is
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specified, {A} is the specified amplitude vector with components
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(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time
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elapsed since the fix was specified. This style also sets the
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velocity of each particle to the time derivative of this expression.
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If any of the amplitude components is specified as NULL, then the
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position and velocity of that component is time integrated the same as
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the "fix meso"_fix_meso.html command would perform, using the
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corresponding force component on the particle.
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Note that the {wiggle} style is identical to using the {variable}
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style with "equal-style variables"_variable.html that use the
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swiggle() and cwiggle() functions. E.g.
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variable A equal 10.0
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variable T equal 5.0
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variable omega equal 2.0*PI/$T
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variable x equal swiggle(0.0,$A,$T)
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variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
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fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
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The {rotate} style rotates particles around a rotation axis {R} =
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(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of
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the rotation is also specified. The direction of rotation for the
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particles around the rotation axis is consistent with the right-hand
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rule: if your right-hand thumb points along {R}, then your fingers wrap
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around the axis in the direction of rotation.
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This style also sets the velocity of each particle to (omega cross
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Rperp) where omega is its angular velocity around the rotation axis and
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Rperp is a perpendicular vector from the rotation axis to the particle.
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The {variable} style allows the position and velocity components of
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each particle to be set by formulas specified via the
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"variable"_variable.html command. Each of the 6 variables is
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specified as an argument to the fix as v_name, where name is the
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variable name that is defined elsewhere in the input script.
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Each variable must be of either the {equal} or {atom} style.
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{Equal}-style variables compute a single numeric quantity, that can be
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a function of the timestep as well as of other simulation values.
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{Atom}-style variables compute a numeric quantity for each particle, that
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can be a function per-atom quantities, such as the particle's position, as
|
||||
well as of the timestep and other simulation values. Note that this
|
||||
fix stores the original coordinates of each particle (see note below) so
|
||||
that per-atom quantity can be used in an atom-style variable formula.
|
||||
See the "variable"_variable.html command for details.
|
||||
|
||||
The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable}
|
||||
style are used to calculate a displacement from the particle's original
|
||||
position at the time the fix was specified. The second 3 variables
|
||||
(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
|
||||
particle.
|
||||
|
||||
Any of the 6 variables can be specified as NULL. If both the
|
||||
displacement and velocity variables for a particular x,y,z component
|
||||
are specified as NULL, then the position and velocity of that
|
||||
component is time integrated the same as the "fix meso"_fix_meso.html
|
||||
command would perform, using the corresponding force component on the
|
||||
particle. If only the velocity variable for a component is specified as
|
||||
NULL, then the displacement variable will be used to set the position
|
||||
of the particle, and its velocity component will not be changed. If only
|
||||
the displacement variable for a component is specified as NULL, then
|
||||
the velocity variable will be used to set the velocity of the particle,
|
||||
and the position of the particle will be time integrated using that
|
||||
velocity.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
to define the {linear} velocity and {wiggle} amplitude and {rotate}
|
||||
origin. This setting is ignored for the {variable} style. A {box}
|
||||
value selects standard units as defined by the "units"_units.html
|
||||
command, e.g. velocity in Angstroms/fmsec and amplitude and position
|
||||
in Angstroms for units = real. A {lattice} value means the velocity
|
||||
units are in lattice spacings per time and the amplitude and position
|
||||
are in lattice spacings. The "lattice"_lattice.html command must have
|
||||
been previously used to define the lattice spacing. Each of these 3
|
||||
quantities may be dependent on the x,y,z dimension, since the lattice
|
||||
spacings can be different in x,y,z.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
This fix writes the original coordinates of moving particles to "binary
|
||||
restart files"_restart.html, as well as the initial timestep, so that
|
||||
the motion can be continuous in a restarted simulation. See the
|
||||
"read_restart"_read_restart.html command for info on how to re-specify
|
||||
a fix in an input script that reads a restart file, so that the
|
||||
operation of the fix continues in an uninterrupted fashion.
|
||||
|
||||
NOTE: Because the move positions are a function of the current
|
||||
timestep and the initial timestep, you cannot reset the timestep to a
|
||||
different value after reading a restart file, if you expect a fix move
|
||||
command to work in an uninterrupted fashion.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix.
|
||||
|
||||
This fix produces a per-atom array which can be accessed by various
|
||||
"output commands"_Howto_output.html. The number of columns for each
|
||||
atom is 3, and the columns store the original unwrapped x,y,z coords
|
||||
of each particle. The per-atom values can be accessed on any timestep.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-SDPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
This fix requires that atoms store density and internal energy as
|
||||
defined by the "atom_style meso"_atom_style.html command.
|
||||
|
||||
All particles in the group must be mesoscopic SPH/SDPD particles.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix move"_fix_move.html, "fix meso"_fix_meso.html,
|
||||
"displace_atoms"_displace_atoms.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option default is units = lattice.
|
||||
|
|
@ -0,0 +1,349 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
fix rigid/meso command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID rigid/meso bodystyle args keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
rigid/meso = style name of this fix command :l
|
||||
bodystyle = {single} or {molecule} or {group} :l
|
||||
{single} args = none
|
||||
{molecule} args = none
|
||||
{custom} args = {i_propname} or {v_varname}
|
||||
i_propname = an integer property defined via fix property/atom
|
||||
v_varname = an atom-style or atomfile-style variable
|
||||
{group} args = N groupID1 groupID2 ...
|
||||
N = # of groups
|
||||
groupID1, groupID2, ... = list of N group IDs :pre
|
||||
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {reinit} or {force} or {torque} or {infile} :l
|
||||
{reinit} = {yes} or {no}
|
||||
{force} values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass force is active
|
||||
{torque} values = M xflag yflag zflag
|
||||
M = which rigid body from 1-Nbody (see asterisk form below)
|
||||
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
|
||||
{infile} filename
|
||||
filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 ellipsoid rigid/meso single
|
||||
fix 1 rods rigid/meso molecule
|
||||
fix 1 spheres rigid/meso single force 1 off off on
|
||||
fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on
|
||||
fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Treat one or more sets of mesoscopic SPH/SDPD particles as independent
|
||||
rigid bodies. This means that each timestep the total force and torque
|
||||
on each rigid body is computed as the sum of the forces and torques on
|
||||
its constituent particles. The coordinates and velocities of the
|
||||
particles in each body are then updated so that the body moves and
|
||||
rotates as a single entity using the methods described in the paper by
|
||||
"(Miller)"_#Miller. Density and internal energy of the particles will
|
||||
also be updated. This is implemented by creating internal data structures
|
||||
for each rigid body and performing time integration on these data
|
||||
structures. Positions and velocities of the constituent particles are
|
||||
regenerated from the rigid body data structures in every time step. This
|
||||
restricts which operations and fixes can be applied to rigid bodies. See
|
||||
below for a detailed discussion.
|
||||
|
||||
The operation of this fix is exactly like that described by the
|
||||
"fix rigid/nve"_fix_rigid.html command, except that particles' density,
|
||||
internal energy and extrapolated velocity are also updated.
|
||||
|
||||
NOTE: You should not update the particles in rigid bodies via other
|
||||
time-integration fixes (e.g. "fix meso"_fix_meso.html,
|
||||
"fix meso/stationary"_fix_meso_stationary.html), or you will have conflicting
|
||||
updates to positions and velocities resulting in unphysical behavior in most
|
||||
cases. When performing a hybrid simulation with some atoms in rigid bodies,
|
||||
and some not, a separate time integration fix like "fix meso"_fix_meso.html
|
||||
should be used for the non-rigid particles.
|
||||
|
||||
NOTE: These fixes are overkill if you simply want to hold a collection
|
||||
of particles stationary or have them move with a constant velocity. To
|
||||
hold particles stationary use "fix
|
||||
meso/stationary"_fix_meso_stationary.html instead. If you would like to
|
||||
move particles with a constant velocity use "fix
|
||||
meso/move"_fix_meso_move.html.
|
||||
|
||||
IMPORTANT NOTE: The aggregate properties of each rigid body are
|
||||
calculated at the start of a simulation run and are maintained in
|
||||
internal data structures. The properties include the position and
|
||||
velocity of the center-of-mass of the body, its moments of inertia, and
|
||||
its angular momentum. This is done using the properties of the
|
||||
constituent particles of the body at that point in time (or see the {infile}
|
||||
keyword option). Thereafter, changing these properties of individual
|
||||
particles in the body will have no effect on a rigid body's dynamics, unless
|
||||
they effect any computation of per-particle forces or torques. If the
|
||||
keyword {reinit} is set to {yes} (the default), the rigid body data
|
||||
structures will be recreated at the beginning of each {run} command;
|
||||
if the keyword {reinit} is set to {no}, the rigid body data structures
|
||||
will be built only at the very first {run} command and maintained for
|
||||
as long as the rigid fix is defined. For example, you might think you
|
||||
could displace the particles in a body or add a large velocity to each particle
|
||||
in a body to make it move in a desired direction before a 2nd run is
|
||||
performed, using the "set"_set.html or
|
||||
"displace_atoms"_displace_atoms.html or "velocity"_velocity.html
|
||||
commands. But these commands will not affect the internal attributes
|
||||
of the body unless {reinit} is set to {yes}. With {reinit} set to {no}
|
||||
(or using the {infile} option, which implies {reinit} {no}) the position
|
||||
and velocity of individual particles in the body will be reset when time
|
||||
integration starts again.
|
||||
|
||||
:line
|
||||
|
||||
Each rigid body must have two or more particles. A particle can belong
|
||||
to at most one rigid body. Which particles are in which bodies can be
|
||||
defined via several options.
|
||||
|
||||
For bodystyle {single} the entire fix group of particles is treated as
|
||||
one rigid body.
|
||||
|
||||
For bodystyle {molecule}, particles are grouped into rigid bodies by their
|
||||
respective molecule IDs: each set of particles in the fix group with the
|
||||
same molecule ID is treated as a different rigid body. Note that particles
|
||||
with a molecule ID = 0 will be treated as a single rigid body. For a
|
||||
system with solvent (typically this is particles with molecule ID = 0)
|
||||
surrounding rigid bodies, this may not be what you want. Thus you
|
||||
should be careful to use a fix group that only includes particles you
|
||||
want to be part of rigid bodies.
|
||||
|
||||
Bodystyle {custom} is similar to bodystyle {molecule} except that it
|
||||
is more flexible in using other per-atom properties to define the sets
|
||||
of particles that form rigid bodies. An integer vector defined by the
|
||||
"fix property/atom"_fix_property_atom.html command can be used. Or an
|
||||
"atom-style or atomfile-style variable"_variable.html can be used; the
|
||||
floating-point value produced by the variable is rounded to an
|
||||
integer. As with bondstyle {molecule}, each set of particles in the fix
|
||||
groups with the same integer value is treated as a different rigid
|
||||
body. Since fix property/atom vectors and atom-style variables
|
||||
produce values for all particles, you should be careful to use a fix group
|
||||
that only includes particles you want to be part of rigid bodies.
|
||||
|
||||
For bodystyle {group}, each of the listed groups is treated as a
|
||||
separate rigid body. Only particles that are also in the fix group are
|
||||
included in each rigid body.
|
||||
|
||||
NOTE: To compute the initial center-of-mass position and other
|
||||
properties of each rigid body, the image flags for each particle in the
|
||||
body are used to "unwrap" the particle coordinates. Thus you must
|
||||
insure that these image flags are consistent so that the unwrapping
|
||||
creates a valid rigid body (one where the particles are close together)
|
||||
, particularly if the particles in a single rigid body straddle a
|
||||
periodic boundary. This means the input data file or restart file must
|
||||
define the image flags for each particle consistently or that you have
|
||||
used the "set"_set.html command to specify them correctly. If a
|
||||
dimension is non-periodic then the image flag of each particle must be
|
||||
0 in that dimension, else an error is generated.
|
||||
|
||||
By default, each rigid body is acted on by other particles which induce
|
||||
an external force and torque on its center of mass, causing it to
|
||||
translate and rotate. Components of the external center-of-mass force
|
||||
and torque can be turned off by the {force} and {torque} keywords.
|
||||
This may be useful if you wish a body to rotate but not translate, or
|
||||
vice versa, or if you wish it to rotate or translate continuously
|
||||
unaffected by interactions with other particles. Note that if you
|
||||
expect a rigid body not to move or rotate by using these keywords, you
|
||||
must insure its initial center-of-mass translational or angular
|
||||
velocity is 0.0. Otherwise the initial translational or angular
|
||||
momentum the body has will persist.
|
||||
|
||||
An xflag, yflag, or zflag set to {off} means turn off the component of
|
||||
force or torque in that dimension. A setting of {on} means turn on
|
||||
the component, which is the default. Which rigid body(s) the settings
|
||||
apply to is determined by the first argument of the {force} and
|
||||
{torque} keywords. It can be an integer M from 1 to Nbody, where
|
||||
Nbody is the number of rigid bodies defined. A wild-card asterisk can
|
||||
be used in place of, or in conjunction with, the M argument to set the
|
||||
flags for multiple rigid bodies. This takes the form "*" or "*n" or
|
||||
"n*" or "m*n". If N = the number of rigid bodies, then an asterisk
|
||||
with no numeric values means all bodies from 1 to N. A leading
|
||||
asterisk means all bodies from 1 to n (inclusive). A trailing
|
||||
asterisk means all bodies from n to N (inclusive). A middle asterisk
|
||||
means all bodies from m to n (inclusive). Note that you can use the
|
||||
{force} or {torque} keywords as many times as you like. If a
|
||||
particular rigid body has its component flags set multiple times, the
|
||||
settings from the final keyword are used.
|
||||
|
||||
For computational efficiency, you should typically define one fix
|
||||
rigid/meso command which includes all the desired rigid bodies. LAMMPS
|
||||
will allow multiple rigid/meso fixes to be defined, but it is more
|
||||
expensive.
|
||||
|
||||
:line
|
||||
|
||||
The keyword/value option pairs are used in the following ways.
|
||||
|
||||
The {reinit} keyword determines, whether the rigid body properties
|
||||
are re-initialized between run commands. With the option {yes} (the
|
||||
default) this is done, with the option {no} this is not done. Turning
|
||||
off the re-initialization can be helpful to protect rigid bodies against
|
||||
unphysical manipulations between runs or when properties cannot be
|
||||
easily re-computed (e.g. when read from a file). When using the {infile}
|
||||
keyword, the {reinit} option is automatically set to {no}.
|
||||
|
||||
:line
|
||||
|
||||
The {infile} keyword allows a file of rigid body attributes to be read
|
||||
in from a file, rather then having LAMMPS compute them. There are 5
|
||||
such attributes: the total mass of the rigid body, its center-of-mass
|
||||
position, its 6 moments of inertia, its center-of-mass velocity, and
|
||||
the 3 image flags of the center-of-mass position. For rigid bodies
|
||||
consisting of point particles or non-overlapping finite-size
|
||||
particles, LAMMPS can compute these values accurately. However, for
|
||||
rigid bodies consisting of finite-size particles which overlap each
|
||||
other, LAMMPS will ignore the overlaps when computing these 4
|
||||
attributes. The amount of error this induces depends on the amount of
|
||||
overlap. To avoid this issue, the values can be pre-computed
|
||||
(e.g. using Monte Carlo integration).
|
||||
|
||||
The format of the file is as follows. Note that the file does not
|
||||
have to list attributes for every rigid body integrated by fix rigid.
|
||||
Only bodies which the file specifies will have their computed
|
||||
attributes overridden. The file can contain initial blank lines or
|
||||
comment lines starting with "#" which are ignored. The first
|
||||
non-blank, non-comment line should list N = the number of lines to
|
||||
follow. The N successive lines contain the following information:
|
||||
|
||||
ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
|
||||
ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm
|
||||
...
|
||||
IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre
|
||||
|
||||
The rigid body IDs are all positive integers. For the {single}
|
||||
bodystyle, only an ID of 1 can be used. For the {group} bodystyle,
|
||||
IDs from 1 to Ng can be used where Ng is the number of specified
|
||||
groups. For the {molecule} bodystyle, use the molecule ID for the
|
||||
atoms in a specific rigid body as the rigid body ID.
|
||||
|
||||
The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
|
||||
self-explanatory. The center-of-mass should be consistent with what
|
||||
is calculated for the position of the rigid body with all its atoms
|
||||
unwrapped by their respective image flags. If this produces a
|
||||
center-of-mass that is outside the simulation box, LAMMPS wraps it
|
||||
back into the box.
|
||||
|
||||
The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
|
||||
values consistent with the current orientation of the rigid body
|
||||
around its center of mass. The values are with respect to the
|
||||
simulation box XYZ axes, not with respect to the principal axes of the
|
||||
rigid body itself. LAMMPS performs the latter calculation internally.
|
||||
|
||||
The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
|
||||
The (lx,ly,lz) values are the angular momentum of the body. The
|
||||
(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
|
||||
wish the body to have no initial motion.
|
||||
|
||||
The (ixcm,iycm,izcm) values are the image flags of the center of mass
|
||||
of the body. For periodic dimensions, they specify which image of the
|
||||
simulation box the body is considered to be in. An image of 0 means
|
||||
it is inside the box as defined. A value of 2 means add 2 box lengths
|
||||
to get the true value. A value of -1 means subtract 1 box length to
|
||||
get the true value. LAMMPS updates these flags as the rigid bodies
|
||||
cross periodic boundaries during the simulation.
|
||||
|
||||
NOTE: If you use the {infile} keyword and write restart
|
||||
files during a simulation, then each time a restart file is written,
|
||||
the fix also write an auxiliary restart file with the name
|
||||
rfile.rigid, where "rfile" is the name of the restart file,
|
||||
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
|
||||
file is in the same format described above. Thus it can be used in a
|
||||
new input script that restarts the run and re-specifies a rigid fix
|
||||
using an {infile} keyword and the appropriate filename. Note that the
|
||||
auxiliary file will contain one line for every rigid body, even if the
|
||||
original file only listed a subset of the rigid bodies.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information is written to "binary restart files"_restart.html.
|
||||
If the {infile} keyword is used, an auxiliary file is written out
|
||||
with rigid body information each time a restart file is written, as
|
||||
explained above for the {infile} keyword.
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various "output commands"_Howto_output.html.
|
||||
|
||||
The number of rows in the array is equal to the number of rigid
|
||||
bodies. The number of columns is 28. Thus for each rigid body, 28
|
||||
values are stored: the xyz coords of the center of mass (COM), the xyz
|
||||
components of the COM velocity, the xyz components of the force acting
|
||||
on the COM, the components of the 4-vector quaternion representing the
|
||||
orientation of the rigid body, the xyz components of the angular momentum
|
||||
of the body around its COM, the xyz components of the torque acting on the
|
||||
COM, the 3 principal components of the moment of inertia and the xyz image
|
||||
flags of the COM.
|
||||
|
||||
The center of mass (COM) for each body is similar to unwrapped
|
||||
coordinates written to a dump file. It will always be inside (or
|
||||
slightly outside) the simulation box. The image flags have the same
|
||||
meaning as image flags for particle positions (see the "dump" command).
|
||||
This means you can calculate the unwrapped COM by applying the image
|
||||
flags to the COM, the same as when unwrapped coordinates are written
|
||||
to a dump file.
|
||||
|
||||
The force and torque values in the array are not affected by the
|
||||
{force} and {torque} keywords in the fix rigid command; they reflect
|
||||
values before any changes are made by those keywords.
|
||||
|
||||
The ordering of the rigid bodies (by row in the array) is as follows.
|
||||
For the {single} keyword there is just one rigid body. For the
|
||||
{molecule} keyword, the bodies are ordered by ascending molecule ID.
|
||||
For the {group} keyword, the list of group IDs determines the ordering
|
||||
of bodies.
|
||||
|
||||
The array values calculated by this fix are "intensive", meaning they
|
||||
are independent of the number of particles in the simulation.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command.
|
||||
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-SDPD package and also depends on the RIGID
|
||||
package. It is only enabled if LAMMPS was built with both packages. See
|
||||
the "Build package"_Build_package.html doc page for more info.
|
||||
|
||||
This fix requires that atoms store density and internal energy as
|
||||
defined by the "atom_style meso"_atom_style.html command.
|
||||
|
||||
All particles in the group must be mesoscopic SPH/SDPD particles.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix meso/move"_fix_meso_move.html, "fix rigid"_fix_rigid.html,
|
||||
"neigh_modify exclude"_neigh_modify.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are force * on on on and torque * on on on,
|
||||
meaning all rigid bodies are acted on by center-of-mass force and
|
||||
torque. Also reinit = yes.
|
||||
|
||||
:line
|
||||
|
||||
:link(Miller)
|
||||
[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
|
||||
J Chem Phys, 116, 8649 (2002).
|
||||
|
|
@ -73,6 +73,7 @@ Fixes :h1
|
|||
fix_lineforce
|
||||
fix_manifoldforce
|
||||
fix_meso
|
||||
fix_meso_move
|
||||
fix_meso_stationary
|
||||
fix_momentum
|
||||
fix_move
|
||||
|
|
@ -137,6 +138,7 @@ Fixes :h1
|
|||
fix_restrain
|
||||
fix_rhok
|
||||
fix_rigid
|
||||
fix_rigid_meso
|
||||
fix_rx
|
||||
fix_saed_vtk
|
||||
fix_setforce
|
||||
|
|
|
|||
|
|
@ -293,6 +293,7 @@ fix_lb_viscous.html
|
|||
fix_lineforce.html
|
||||
fix_manifoldforce.html
|
||||
fix_meso.html
|
||||
fix_meso_move.html
|
||||
fix_meso_stationary.html
|
||||
fix_momentum.html
|
||||
fix_move.html
|
||||
|
|
@ -356,6 +357,7 @@ fix_reaxc_species.html
|
|||
fix_recenter.html
|
||||
fix_restrain.html
|
||||
fix_rigid.html
|
||||
fix_rigid_meso.html
|
||||
fix_rhok.html
|
||||
fix_rx.html
|
||||
fix_saed_vtk.html
|
||||
|
|
@ -615,6 +617,7 @@ pair_reax.html
|
|||
pair_reaxc.html
|
||||
pair_resquared.html
|
||||
pair_sdk.html
|
||||
pair_sdpd_taitwater_isothermal.html
|
||||
pair_smd_hertz.html
|
||||
pair_smd_tlsph.html
|
||||
pair_smd_triangulated_surface.html
|
||||
|
|
|
|||
|
|
@ -0,0 +1,108 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style sdpd/taitwater/isothermal command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style sdpd/taitwater/isothermal temperature viscosity seed
|
||||
:pre
|
||||
|
||||
temperature = temperature of the fluid (temperature units)
|
||||
viscosity = dynamic viscosity of the fluid (mass*distance/time units)
|
||||
seed = random number generator seed (positive integer, optional) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style sdpd/taitwater/isothermal 300. 1. 28681
|
||||
pair_coeff * * 1000.0 1430.0 2.4 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The sdpd/taitwater/isothermal style computes forces between mesoscopic
|
||||
particles according to the Smoothed Dissipative Particle Dynamics model
|
||||
described in this paper by "(Español and Revenga)"_#Español_Revenga under
|
||||
the following assumptions:
|
||||
|
||||
:olb
|
||||
The temperature is constant and uniform. :l
|
||||
The shear viscosity is constant and uniform. :l
|
||||
The volume viscosity is negligible before the shear viscosity. :l
|
||||
The Boltzmann constant is negligible before the heat capacity of a
|
||||
single mesoscopic particle of fluid. :ole,l
|
||||
|
||||
The third assumption is true for water in nearly incompressible flows.
|
||||
The fourth holds true for water for any reasonable size one can
|
||||
imagine for a mesoscopic particle.
|
||||
|
||||
The pressure forces between particles will be computed according to
|
||||
Tait's equation of state:
|
||||
|
||||
:c,image(Eqs/pair_sph_tait.jpg)
|
||||
|
||||
where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the
|
||||
reference density and c_0 the reference speed of sound.
|
||||
|
||||
The laminar viscosity and the random forces will be computed according
|
||||
to formulas described in "(Español and Revenga)"_#Español_Revenga.
|
||||
|
||||
IMPORTANT NOTE: Similar to "brownian"_pair_brownian.html and
|
||||
"dpd"_pair_dpd.html styles, the "newton"_newton.html setting for
|
||||
pairwise interactions needs to be on when running LAMMPS in parallel
|
||||
if you want to ensure linear momentum conservation. Otherwise random
|
||||
forces generated for pairs straddling processor boundary will not be
|
||||
equal and opposite.
|
||||
|
||||
NOTE: The actual random seed used will be a mix of what you specify
|
||||
and other parameters like the MPI ranks. This is to ensure that
|
||||
different MPI tasks have distinct seeds.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
above.
|
||||
|
||||
rho0 reference density (mass/volume units)
|
||||
c0 reference soundspeed (distance/time units)
|
||||
h kernel function cutoff (distance units) :ul
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This style does not support mixing. Thus, coefficients for all
|
||||
I,J pairs must be specified explicitly.
|
||||
|
||||
This style does not support the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options.
|
||||
|
||||
This style does not write information to "binary restart
|
||||
files"_restart.html. Thus, you need to re-specify the pair_style and
|
||||
pair_coeff commands in an input script that reads a restart file.
|
||||
|
||||
This style can only be used via the {pair} keyword of the "run_style
|
||||
respa"_run_style.html command. It does not support the {inner},
|
||||
{middle}, {outer} keywords.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This pair style is part of the USER-SDPD package. It is only enabled
|
||||
if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair coeff"_pair_coeff.html, "pair sph/rhosum"_pair_sph_rhosum.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default seed is 0 (before mixing).
|
||||
|
||||
:line
|
||||
|
||||
:link(Español_Revenga)
|
||||
[(Español and Revenga)] Español, Revenga, Physical Review E, 67, 026705 (2003).
|
||||
|
|
@ -268,6 +268,7 @@ pair"_Commands_pair.html doc page are followed by one or more of
|
|||
"reax/c"_pair_reaxc.html - ReaxFF potential in C
|
||||
"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
|
||||
"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
|
||||
"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
|
||||
"smd/hertz"_pair_smd_hertz.html -
|
||||
"smd/tlsph"_pair_smd_tlsph.html -
|
||||
"smd/tri_surface"_pair_smd_triangulated_surface.html -
|
||||
|
|
|
|||
|
|
@ -86,6 +86,7 @@ Pair Styles :h1
|
|||
pair_reaxc
|
||||
pair_resquared
|
||||
pair_sdk
|
||||
pair_sdpd_taitwater_isothermal
|
||||
pair_smd_hertz
|
||||
pair_smd_tlsph
|
||||
pair_smd_triangulated_surface
|
||||
|
|
|
|||
|
|
@ -0,0 +1,61 @@
|
|||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable Lf equal $R*3
|
||||
variable Lb equal $R*4
|
||||
variable wall_velocity equal 0.01 # micrometers/microsecond
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
create_box 4 box
|
||||
lattice sq $a
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
set region sphere type 2
|
||||
|
||||
region upper_wall block INF INF +${Lf} INF INF INF units box
|
||||
set region upper_wall type 3
|
||||
|
||||
region lower_wall block INF INF INF -${Lf} INF INF units box
|
||||
set region lower_wall type 4
|
||||
|
||||
group fluid type 1
|
||||
group sphere type 2
|
||||
group upper_wall type 3
|
||||
group lower_wall type 4
|
||||
|
||||
mass * ${mass}
|
||||
set group all meso/rho ${rho_0}
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,247 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable a equal 0.5/5
|
||||
variable Lf equal $R*3
|
||||
variable Lf equal 0.5*3
|
||||
variable Lb equal $R*4
|
||||
variable Lb equal 0.5*4
|
||||
variable wall_velocity equal 0.01 # micrometers/microsecond
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.5
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
variable skin equal 0.2*0.45
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -2 2 0 ${a} units box
|
||||
region box block -2 2 -2 2 0 0.1 units box
|
||||
create_box 4 box
|
||||
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
lattice sq $a
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 1600 atoms
|
||||
Time spent = 0.00169706 secs
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
region sphere sphere 0 0 0 0.5 units box
|
||||
set region sphere type 2
|
||||
81 settings made for type
|
||||
|
||||
region upper_wall block INF INF +${Lf} INF INF INF units box
|
||||
region upper_wall block INF INF +1.5 INF INF INF units box
|
||||
set region upper_wall type 3
|
||||
200 settings made for type
|
||||
|
||||
region lower_wall block INF INF INF -${Lf} INF INF units box
|
||||
region lower_wall block INF INF INF -1.5 INF INF units box
|
||||
set region lower_wall type 4
|
||||
240 settings made for type
|
||||
|
||||
group fluid type 1
|
||||
1079 atoms in group fluid
|
||||
group sphere type 2
|
||||
81 atoms in group sphere
|
||||
group upper_wall type 3
|
||||
200 atoms in group upper_wall
|
||||
group lower_wall type 4
|
||||
240 atoms in group lower_wall
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
1600 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 100 ${h}
|
||||
pair_coeff * * 1 100 0.45
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
1 rigid bodies with 81 atoms
|
||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.09 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
timestep 0.001
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.54
|
||||
ghost atom cutoff = 0.54
|
||||
binsize = 0.27, bins = 15 15 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes
|
||||
Step Time Nbuild Ndanger
|
||||
0 0 0 0
|
||||
100 0.1 0 0
|
||||
200 0.2 0 0
|
||||
300 0.3 0 0
|
||||
400 0.4 0 0
|
||||
500 0.5 1 0
|
||||
600 0.6 1 0
|
||||
700 0.7 2 0
|
||||
800 0.8 2 0
|
||||
900 0.9 2 0
|
||||
1000 1 3 0
|
||||
1100 1.1 3 0
|
||||
1200 1.2 3 0
|
||||
1300 1.3 4 0
|
||||
1400 1.4 4 0
|
||||
1500 1.5 4 0
|
||||
1600 1.6 5 0
|
||||
1700 1.7 5 0
|
||||
1800 1.8 5 0
|
||||
1900 1.9 6 0
|
||||
2000 2 6 0
|
||||
2100 2.1 6 0
|
||||
2200 2.2 7 0
|
||||
2300 2.3 7 0
|
||||
2400 2.4 7 0
|
||||
2500 2.5 8 0
|
||||
2600 2.6 8 0
|
||||
2700 2.7 8 0
|
||||
2800 2.8 9 0
|
||||
2900 2.9 9 0
|
||||
3000 3 9 0
|
||||
3100 3.1 10 0
|
||||
3200 3.2 10 0
|
||||
3300 3.3 10 0
|
||||
3400 3.4 11 0
|
||||
3500 3.5 11 0
|
||||
3600 3.6 11 0
|
||||
3700 3.7 12 0
|
||||
3800 3.8 12 0
|
||||
3900 3.9 12 0
|
||||
4000 4 13 0
|
||||
4100 4.1 13 0
|
||||
4200 4.2 14 0
|
||||
4300 4.3 14 0
|
||||
4400 4.4 14 0
|
||||
4500 4.5 15 0
|
||||
4600 4.6 15 0
|
||||
4700 4.7 15 0
|
||||
4800 4.8 16 0
|
||||
4900 4.9 16 0
|
||||
5000 5 16 0
|
||||
5100 5.1 17 0
|
||||
5200 5.2 17 0
|
||||
5300 5.3 17 0
|
||||
5400 5.4 17 0
|
||||
5500 5.5 18 0
|
||||
5600 5.6 18 0
|
||||
5700 5.7 19 0
|
||||
5800 5.8 19 0
|
||||
5900 5.9 19 0
|
||||
6000 6 20 0
|
||||
6100 6.1 20 0
|
||||
6200 6.2 21 0
|
||||
6300 6.3 21 0
|
||||
6400 6.4 21 0
|
||||
6500 6.5 22 0
|
||||
6600 6.6 22 0
|
||||
6700 6.7 22 0
|
||||
6800 6.8 23 0
|
||||
6900 6.9 23 0
|
||||
7000 7 23 0
|
||||
7100 7.1 24 0
|
||||
7200 7.2 24 0
|
||||
7300 7.3 25 0
|
||||
7400 7.4 25 0
|
||||
7500 7.5 25 0
|
||||
7600 7.6 26 0
|
||||
7700 7.7 26 0
|
||||
7800 7.8 26 0
|
||||
7900 7.9 27 0
|
||||
8000 8 27 0
|
||||
8100 8.1 27 0
|
||||
8200 8.2 28 0
|
||||
8300 8.3 28 0
|
||||
8400 8.4 28 0
|
||||
8500 8.5 29 0
|
||||
8600 8.6 29 0
|
||||
8700 8.7 30 0
|
||||
8800 8.8 30 0
|
||||
8900 8.9 30 0
|
||||
9000 9 31 0
|
||||
9100 9.1 31 0
|
||||
9200 9.2 31 0
|
||||
9300 9.3 32 0
|
||||
9400 9.4 32 0
|
||||
9500 9.5 32 0
|
||||
9600 9.6 33 0
|
||||
9700 9.7 33 0
|
||||
9800 9.8 33 0
|
||||
9900 9.9 34 0
|
||||
10000 10 34 0
|
||||
Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
|
||||
|
||||
Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 143.08 | 143.08 | 143.08 | 0.0 | 99.22
|
||||
Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02
|
||||
Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17
|
||||
Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08
|
||||
Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43
|
||||
Other | | 0.117 | | | 0.08
|
||||
|
||||
Nlocal: 1600 ave 1600 max 1600 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 993 ave 993 max 993 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 73236 ave 73236 max 73236 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 73236
|
||||
Ave neighs/atom = 45.7725
|
||||
Neighbor list builds = 34
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:24
|
||||
|
|
@ -0,0 +1,247 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable a equal 0.5/5
|
||||
variable Lf equal $R*3
|
||||
variable Lf equal 0.5*3
|
||||
variable Lb equal $R*4
|
||||
variable Lb equal 0.5*4
|
||||
variable wall_velocity equal 0.01 # micrometers/microsecond
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.5
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
variable skin equal 0.2*0.45
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
||||
region box block -2 2 -2 2 0 ${a} units box
|
||||
region box block -2 2 -2 2 0 0.1 units box
|
||||
create_box 4 box
|
||||
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq $a
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 1600 atoms
|
||||
Time spent = 0.000589566 secs
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
region sphere sphere 0 0 0 0.5 units box
|
||||
set region sphere type 2
|
||||
81 settings made for type
|
||||
|
||||
region upper_wall block INF INF +${Lf} INF INF INF units box
|
||||
region upper_wall block INF INF +1.5 INF INF INF units box
|
||||
set region upper_wall type 3
|
||||
200 settings made for type
|
||||
|
||||
region lower_wall block INF INF INF -${Lf} INF INF units box
|
||||
region lower_wall block INF INF INF -1.5 INF INF units box
|
||||
set region lower_wall type 4
|
||||
240 settings made for type
|
||||
|
||||
group fluid type 1
|
||||
1079 atoms in group fluid
|
||||
group sphere type 2
|
||||
81 atoms in group sphere
|
||||
group upper_wall type 3
|
||||
200 atoms in group upper_wall
|
||||
group lower_wall type 4
|
||||
240 atoms in group lower_wall
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
1600 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 100 ${h}
|
||||
pair_coeff * * 1 100 0.45
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
1 rigid bodies with 81 atoms
|
||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.09 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
timestep 0.001
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.54
|
||||
ghost atom cutoff = 0.54
|
||||
binsize = 0.27, bins = 15 15 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes
|
||||
Step Time Nbuild Ndanger
|
||||
0 0 0 0
|
||||
100 0.1 0 0
|
||||
200 0.2 0 0
|
||||
300 0.3 0 0
|
||||
400 0.4 1 0
|
||||
500 0.5 1 0
|
||||
600 0.6 1 0
|
||||
700 0.7 2 0
|
||||
800 0.8 2 0
|
||||
900 0.9 2 0
|
||||
1000 1 3 0
|
||||
1100 1.1 3 0
|
||||
1200 1.2 4 0
|
||||
1300 1.3 4 0
|
||||
1400 1.4 4 0
|
||||
1500 1.5 4 0
|
||||
1600 1.6 5 0
|
||||
1700 1.7 5 0
|
||||
1800 1.8 5 0
|
||||
1900 1.9 6 0
|
||||
2000 2 6 0
|
||||
2100 2.1 6 0
|
||||
2200 2.2 6 0
|
||||
2300 2.3 7 0
|
||||
2400 2.4 7 0
|
||||
2500 2.5 7 0
|
||||
2600 2.6 8 0
|
||||
2700 2.7 8 0
|
||||
2800 2.8 8 0
|
||||
2900 2.9 9 0
|
||||
3000 3 9 0
|
||||
3100 3.1 9 0
|
||||
3200 3.2 10 0
|
||||
3300 3.3 10 0
|
||||
3400 3.4 10 0
|
||||
3500 3.5 11 0
|
||||
3600 3.6 11 0
|
||||
3700 3.7 11 0
|
||||
3800 3.8 12 0
|
||||
3900 3.9 12 0
|
||||
4000 4 12 0
|
||||
4100 4.1 13 0
|
||||
4200 4.2 13 0
|
||||
4300 4.3 13 0
|
||||
4400 4.4 14 0
|
||||
4500 4.5 14 0
|
||||
4600 4.6 15 0
|
||||
4700 4.7 15 0
|
||||
4800 4.8 15 0
|
||||
4900 4.9 16 0
|
||||
5000 5 16 0
|
||||
5100 5.1 17 0
|
||||
5200 5.2 17 0
|
||||
5300 5.3 17 0
|
||||
5400 5.4 17 0
|
||||
5500 5.5 18 0
|
||||
5600 5.6 18 0
|
||||
5700 5.7 18 0
|
||||
5800 5.8 19 0
|
||||
5900 5.9 19 0
|
||||
6000 6 20 0
|
||||
6100 6.1 20 0
|
||||
6200 6.2 20 0
|
||||
6300 6.3 21 0
|
||||
6400 6.4 21 0
|
||||
6500 6.5 21 0
|
||||
6600 6.6 22 0
|
||||
6700 6.7 22 0
|
||||
6800 6.8 22 0
|
||||
6900 6.9 23 0
|
||||
7000 7 23 0
|
||||
7100 7.1 23 0
|
||||
7200 7.2 24 0
|
||||
7300 7.3 24 0
|
||||
7400 7.4 25 0
|
||||
7500 7.5 25 0
|
||||
7600 7.6 25 0
|
||||
7700 7.7 25 0
|
||||
7800 7.8 26 0
|
||||
7900 7.9 26 0
|
||||
8000 8 26 0
|
||||
8100 8.1 27 0
|
||||
8200 8.2 27 0
|
||||
8300 8.3 27 0
|
||||
8400 8.4 28 0
|
||||
8500 8.5 28 0
|
||||
8600 8.6 28 0
|
||||
8700 8.7 29 0
|
||||
8800 8.8 29 0
|
||||
8900 8.9 29 0
|
||||
9000 9 30 0
|
||||
9100 9.1 30 0
|
||||
9200 9.2 31 0
|
||||
9300 9.3 31 0
|
||||
9400 9.4 31 0
|
||||
9500 9.5 32 0
|
||||
9600 9.6 32 0
|
||||
9700 9.7 32 0
|
||||
9800 9.8 32 0
|
||||
9900 9.9 33 0
|
||||
10000 10 33 0
|
||||
Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms
|
||||
|
||||
Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
|
||||
94.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86
|
||||
Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02
|
||||
Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51
|
||||
Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20
|
||||
Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09
|
||||
Other | | 0.2038 | | | 0.32
|
||||
|
||||
Nlocal: 400 ave 411 max 388 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 552.25 ave 567 max 539 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 18298.8 ave 18781 max 17829 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 73195
|
||||
Ave neighs/atom = 45.7469
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:03
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable L equal $R*3
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
create_box 2 box
|
||||
lattice sq $a
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
set region sphere type 2
|
||||
|
||||
group fluid type 1
|
||||
group sphere type 2
|
||||
|
||||
mass * ${mass}
|
||||
set group all meso/rho ${rho_0}
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
|
|
@ -0,0 +1,226 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable a equal 0.5/5
|
||||
variable L equal $R*3
|
||||
variable L equal 0.5*3
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.5
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
variable skin equal 0.2*0.45
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
region box block -1.5 $L -$L $L 0 $a units box
|
||||
region box block -1.5 1.5 -$L $L 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 $L 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 1.5 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
lattice sq $a
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 900 atoms
|
||||
Time spent = 0.0015769 secs
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
region sphere sphere 0 0 0 0.5 units box
|
||||
set region sphere type 2
|
||||
81 settings made for type
|
||||
|
||||
group fluid type 1
|
||||
819 atoms in group fluid
|
||||
group sphere type 2
|
||||
81 atoms in group sphere
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
900 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 100 ${h}
|
||||
pair_coeff * * 1 100 0.45
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
1 rigid bodies with 81 atoms
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.09 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
timestep 0.001
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.54
|
||||
ghost atom cutoff = 0.54
|
||||
binsize = 0.27, bins = 12 12 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes
|
||||
Step Time Nbuild Ndanger
|
||||
0 0 0 0
|
||||
100 0.1 0 0
|
||||
200 0.2 0 0
|
||||
300 0.3 0 0
|
||||
400 0.4 1 0
|
||||
500 0.5 1 0
|
||||
600 0.6 1 0
|
||||
700 0.7 2 0
|
||||
800 0.8 2 0
|
||||
900 0.9 2 0
|
||||
1000 1 3 0
|
||||
1100 1.1 3 0
|
||||
1200 1.2 3 0
|
||||
1300 1.3 4 0
|
||||
1400 1.4 4 0
|
||||
1500 1.5 4 0
|
||||
1600 1.6 5 0
|
||||
1700 1.7 5 0
|
||||
1800 1.8 6 0
|
||||
1900 1.9 6 0
|
||||
2000 2 6 0
|
||||
2100 2.1 7 0
|
||||
2200 2.2 7 0
|
||||
2300 2.3 7 0
|
||||
2400 2.4 7 0
|
||||
2500 2.5 8 0
|
||||
2600 2.6 8 0
|
||||
2700 2.7 8 0
|
||||
2800 2.8 9 0
|
||||
2900 2.9 9 0
|
||||
3000 3 10 0
|
||||
3100 3.1 10 0
|
||||
3200 3.2 10 0
|
||||
3300 3.3 11 0
|
||||
3400 3.4 11 0
|
||||
3500 3.5 11 0
|
||||
3600 3.6 12 0
|
||||
3700 3.7 12 0
|
||||
3800 3.8 12 0
|
||||
3900 3.9 13 0
|
||||
4000 4 13 0
|
||||
4100 4.1 13 0
|
||||
4200 4.2 14 0
|
||||
4300 4.3 14 0
|
||||
4400 4.4 14 0
|
||||
4500 4.5 15 0
|
||||
4600 4.6 15 0
|
||||
4700 4.7 15 0
|
||||
4800 4.8 16 0
|
||||
4900 4.9 16 0
|
||||
5000 5 17 0
|
||||
5100 5.1 17 0
|
||||
5200 5.2 17 0
|
||||
5300 5.3 17 0
|
||||
5400 5.4 18 0
|
||||
5500 5.5 18 0
|
||||
5600 5.6 18 0
|
||||
5700 5.7 19 0
|
||||
5800 5.8 19 0
|
||||
5900 5.9 19 0
|
||||
6000 6 19 0
|
||||
6100 6.1 20 0
|
||||
6200 6.2 20 0
|
||||
6300 6.3 20 0
|
||||
6400 6.4 21 0
|
||||
6500 6.5 21 0
|
||||
6600 6.6 21 0
|
||||
6700 6.7 21 0
|
||||
6800 6.8 22 0
|
||||
6900 6.9 22 0
|
||||
7000 7 22 0
|
||||
7100 7.1 23 0
|
||||
7200 7.2 23 0
|
||||
7300 7.3 23 0
|
||||
7400 7.4 24 0
|
||||
7500 7.5 24 0
|
||||
7600 7.6 24 0
|
||||
7700 7.7 25 0
|
||||
7800 7.8 25 0
|
||||
7900 7.9 26 0
|
||||
8000 8 26 0
|
||||
8100 8.1 26 0
|
||||
8200 8.2 26 0
|
||||
8300 8.3 27 0
|
||||
8400 8.4 27 0
|
||||
8500 8.5 27 0
|
||||
8600 8.6 28 0
|
||||
8700 8.7 28 0
|
||||
8800 8.8 28 0
|
||||
8900 8.9 29 0
|
||||
9000 9 29 0
|
||||
9100 9.1 29 0
|
||||
9200 9.2 30 0
|
||||
9300 9.3 30 0
|
||||
9400 9.4 30 0
|
||||
9500 9.5 30 0
|
||||
9600 9.6 31 0
|
||||
9700 9.7 31 0
|
||||
9800 9.8 32 0
|
||||
9900 9.9 32 0
|
||||
10000 10 32 0
|
||||
Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
|
||||
|
||||
Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 80.306 | 80.306 | 80.306 | 0.0 | 99.21
|
||||
Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02
|
||||
Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21
|
||||
Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09
|
||||
Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39
|
||||
Other | | 0.067 | | | 0.08
|
||||
|
||||
Nlocal: 900 ave 900 max 900 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 762 ave 762 max 762 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 40697 ave 40697 max 40697 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 40697
|
||||
Ave neighs/atom = 45.2189
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:20
|
||||
|
|
@ -0,0 +1,226 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 2
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable R equal 0.5 # radius of sphere micrometers
|
||||
variable a equal $R/5 # lattice spacing micrometers
|
||||
variable a equal 0.5/5
|
||||
variable L equal $R*3
|
||||
variable L equal 0.5*3
|
||||
variable T equal 300.
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.5 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.5
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
variable skin equal 0.2*0.45
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
region box block -1.5 $L -$L $L 0 $a units box
|
||||
region box block -1.5 1.5 -$L $L 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 $L 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 1.5 0 $a units box
|
||||
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
|
||||
create_box 2 box
|
||||
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
lattice sq $a
|
||||
lattice sq 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 900 atoms
|
||||
Time spent = 0.0010246 secs
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
region sphere sphere 0 0 0 0.5 units box
|
||||
set region sphere type 2
|
||||
81 settings made for type
|
||||
|
||||
group fluid type 1
|
||||
819 atoms in group fluid
|
||||
group sphere type 2
|
||||
81 atoms in group sphere
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
900 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 100 ${h}
|
||||
pair_coeff * * 1 100 0.45
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
1 rigid bodies with 81 atoms
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.09 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
timestep 0.001
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.54
|
||||
ghost atom cutoff = 0.54
|
||||
binsize = 0.27, bins = 12 12 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes
|
||||
Step Time Nbuild Ndanger
|
||||
0 0 0 0
|
||||
100 0.1 0 0
|
||||
200 0.2 0 0
|
||||
300 0.3 0 0
|
||||
400 0.4 1 0
|
||||
500 0.5 1 0
|
||||
600 0.6 1 0
|
||||
700 0.7 2 0
|
||||
800 0.8 2 0
|
||||
900 0.9 2 0
|
||||
1000 1 3 0
|
||||
1100 1.1 3 0
|
||||
1200 1.2 3 0
|
||||
1300 1.3 4 0
|
||||
1400 1.4 4 0
|
||||
1500 1.5 5 0
|
||||
1600 1.6 5 0
|
||||
1700 1.7 5 0
|
||||
1800 1.8 6 0
|
||||
1900 1.9 6 0
|
||||
2000 2 6 0
|
||||
2100 2.1 7 0
|
||||
2200 2.2 7 0
|
||||
2300 2.3 7 0
|
||||
2400 2.4 8 0
|
||||
2500 2.5 8 0
|
||||
2600 2.6 8 0
|
||||
2700 2.7 9 0
|
||||
2800 2.8 9 0
|
||||
2900 2.9 9 0
|
||||
3000 3 9 0
|
||||
3100 3.1 10 0
|
||||
3200 3.2 10 0
|
||||
3300 3.3 10 0
|
||||
3400 3.4 11 0
|
||||
3500 3.5 11 0
|
||||
3600 3.6 11 0
|
||||
3700 3.7 12 0
|
||||
3800 3.8 12 0
|
||||
3900 3.9 12 0
|
||||
4000 4 13 0
|
||||
4100 4.1 13 0
|
||||
4200 4.2 13 0
|
||||
4300 4.3 14 0
|
||||
4400 4.4 14 0
|
||||
4500 4.5 15 0
|
||||
4600 4.6 15 0
|
||||
4700 4.7 15 0
|
||||
4800 4.8 16 0
|
||||
4900 4.9 16 0
|
||||
5000 5 16 0
|
||||
5100 5.1 16 0
|
||||
5200 5.2 17 0
|
||||
5300 5.3 17 0
|
||||
5400 5.4 18 0
|
||||
5500 5.5 18 0
|
||||
5600 5.6 19 0
|
||||
5700 5.7 19 0
|
||||
5800 5.8 19 0
|
||||
5900 5.9 20 0
|
||||
6000 6 20 0
|
||||
6100 6.1 20 0
|
||||
6200 6.2 21 0
|
||||
6300 6.3 21 0
|
||||
6400 6.4 21 0
|
||||
6500 6.5 22 0
|
||||
6600 6.6 22 0
|
||||
6700 6.7 22 0
|
||||
6800 6.8 23 0
|
||||
6900 6.9 23 0
|
||||
7000 7 23 0
|
||||
7100 7.1 24 0
|
||||
7200 7.2 24 0
|
||||
7300 7.3 24 0
|
||||
7400 7.4 25 0
|
||||
7500 7.5 25 0
|
||||
7600 7.6 25 0
|
||||
7700 7.7 26 0
|
||||
7800 7.8 26 0
|
||||
7900 7.9 26 0
|
||||
8000 8 27 0
|
||||
8100 8.1 27 0
|
||||
8200 8.2 27 0
|
||||
8300 8.3 28 0
|
||||
8400 8.4 28 0
|
||||
8500 8.5 28 0
|
||||
8600 8.6 28 0
|
||||
8700 8.7 29 0
|
||||
8800 8.8 29 0
|
||||
8900 8.9 29 0
|
||||
9000 9 30 0
|
||||
9100 9.1 30 0
|
||||
9200 9.2 31 0
|
||||
9300 9.3 31 0
|
||||
9400 9.4 31 0
|
||||
9500 9.5 31 0
|
||||
9600 9.6 32 0
|
||||
9700 9.7 32 0
|
||||
9800 9.8 32 0
|
||||
9900 9.9 33 0
|
||||
10000 10 33 0
|
||||
Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms
|
||||
|
||||
Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s
|
||||
48.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 56.528 | 57.936 | 58.729 | 11.0 | 83.95
|
||||
Neigh | 0.013157 | 0.013382 | 0.013551 | 0.1 | 0.02
|
||||
Comm | 8.9594 | 9.7555 | 11.113 | 26.7 | 14.14
|
||||
Output | 0.14644 | 0.15009 | 0.15809 | 1.2 | 0.22
|
||||
Modify | 0.72913 | 0.91574 | 1.0524 | 12.4 | 1.33
|
||||
Other | | 0.2389 | | | 0.35
|
||||
|
||||
Nlocal: 225 ave 229 max 223 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 442 ave 444 max 439 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 10188.8 ave 10437 max 9932 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 40755
|
||||
Ave neighs/atom = 45.2833
|
||||
Neighbor list builds = 33
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:09
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
Smoothed Dissipative Particle Dynamics examples
|
||||
|
||||
equipartition-verification:
|
||||
This example verifies the equipartition theorem.
|
||||
It simulates a periodic box of water with no solid bodies.
|
||||
If equipartition theorem holds true, the average of each component of
|
||||
translational kinetic energy should be equal to k_B T, and therefore
|
||||
vx_sq_check, vy_sq_check, and vz_sq_check should fluctuate near 1.
|
||||
|
||||
2d-diffusion:
|
||||
This example demonstrates the free diffusion of a disk in 2D.
|
||||
The 3D simulation is similar but takes much longer to complete.
|
||||
As with other statistical experiments you need an ensemble to
|
||||
extract meaningful average quantities.
|
||||
For a more realistic simulation you should increase the resolution
|
||||
of the disk/sphere which also necessitates reduction of timestep.
|
||||
|
||||
2d-diffusion-in-shear-flow:
|
||||
This example demonstrates the diffusion of a disk in shear flow in 2D.
|
||||
The 3D simulation is similar but takes much longer to complete.
|
||||
As with other statistical experiments you need an ensemble to
|
||||
extract meaningful average quantities.
|
||||
For a more realistic simulation you should increase the resolution
|
||||
of the disk/sphere which also necessitates reduction of timestep.
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
create_box 1 box
|
||||
lattice sc $a
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
mass * ${mass}
|
||||
set group all meso/rho ${rho_0}
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
timestep ${dt}
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
|
|
@ -0,0 +1,146 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable L equal 0.1*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.0
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
variable skin equal 0.1*0.4
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
region box block -1 $L -$L $L -$L $L units box
|
||||
region box block -1 1 -$L $L -$L $L units box
|
||||
region box block -1 1 -1 $L -$L $L units box
|
||||
region box block -1 1 -1 1 -$L $L units box
|
||||
region box block -1 1 -1 1 -1 $L units box
|
||||
region box block -1 1 -1 1 -1 1 units box
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
lattice sc $a
|
||||
lattice sc 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
Time spent = 0.00285411 secs
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
8000 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 10 ${h}
|
||||
pair_coeff * * 1 10 0.4
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.04 bin
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.44
|
||||
ghost atom cutoff = 0.44
|
||||
binsize = 0.22, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
|
||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
0 0 0 0 0
|
||||
10 0.005 0.70973271 0.71495693 0.71910087
|
||||
20 0.01 0.90418096 0.88845437 0.89659567
|
||||
30 0.015 0.9590736 0.97880338 0.9619016
|
||||
40 0.02 0.98533774 0.96057682 0.95600448
|
||||
50 0.025 0.96433662 0.96650071 0.95509683
|
||||
60 0.03 0.96598029 0.96373656 0.96734888
|
||||
70 0.035 0.95433045 0.98004764 0.96255924
|
||||
80 0.04 0.97872906 0.95987289 0.96623598
|
||||
90 0.045 0.99913888 0.99255731 0.95616142
|
||||
100 0.05 0.98872675 0.97141018 0.95338841
|
||||
110 0.055 0.97794592 0.97389258 0.98473719
|
||||
120 0.06 0.98389266 0.96716284 0.95504862
|
||||
130 0.065 0.98572886 0.96680923 0.95599065
|
||||
140 0.07 0.97602684 0.97580081 0.9886878
|
||||
150 0.075 0.99172003 0.95027467 0.96028033
|
||||
160 0.08 0.96793247 0.94590928 0.95644301
|
||||
170 0.085 0.94167619 0.98048861 0.93439426
|
||||
180 0.09 0.97277934 0.97383622 0.96900866
|
||||
190 0.095 0.96647288 1.0027643 0.96230782
|
||||
200 0.1 0.94864291 0.95902585 0.96398175
|
||||
Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
|
||||
|
||||
Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19
|
||||
Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01
|
||||
Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07
|
||||
Other | | 0.02811 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8000 max 8000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 16389 ave 16389 max 16389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1456000
|
||||
Ave neighs/atom = 182
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:00
|
||||
|
|
@ -0,0 +1,146 @@
|
|||
LAMMPS (24 Oct 2018)
|
||||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable L equal 0.1*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.0
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*$a*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*$a*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*${rho_0}
|
||||
variable mass equal 0.1*0.1*0.1*1
|
||||
variable dt equal 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
variable skin equal 0.1*0.4
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
region box block -1 $L -$L $L -$L $L units box
|
||||
region box block -1 1 -$L $L -$L $L units box
|
||||
region box block -1 1 -1 $L -$L $L units box
|
||||
region box block -1 1 -1 1 -$L $L units box
|
||||
region box block -1 1 -1 1 -1 $L units box
|
||||
region box block -1 1 -1 1 -1 1 units box
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
lattice sc $a
|
||||
lattice sc 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
Time spent = 0.00252754 secs
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
8000 settings made for meso/rho
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
||||
pair_style sdpd/taitwater/isothermal 300 1 76787
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
pair_coeff * * 1 ${c_0} ${h}
|
||||
pair_coeff * * 1 10 ${h}
|
||||
pair_coeff * * 1 10 0.4
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.04 bin
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.44
|
||||
ghost atom cutoff = 0.44
|
||||
binsize = 0.22, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
|
||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
0 0 0 0 0
|
||||
10 0.005 0.71224819 0.71470372 0.7008956
|
||||
20 0.01 0.90627589 0.90683966 0.90116506
|
||||
30 0.015 0.938505 0.95884272 0.93337542
|
||||
40 0.02 0.94394649 0.93668038 0.96468004
|
||||
50 0.025 0.97152309 0.97546161 0.95107762
|
||||
60 0.03 0.94710871 0.95678322 0.97285504
|
||||
70 0.035 0.96253148 0.95838642 0.95450883
|
||||
80 0.04 0.97581495 0.95278681 0.95099478
|
||||
90 0.045 0.96251614 0.9740684 0.96081505
|
||||
100 0.05 0.94191275 0.97137523 0.94084858
|
||||
110 0.055 0.953406 0.95739684 0.98574522
|
||||
120 0.06 0.99001614 0.99608287 0.9839996
|
||||
130 0.065 0.96575225 0.94309655 0.92847798
|
||||
140 0.07 0.97642687 0.97458638 0.94696406
|
||||
150 0.075 0.99316381 0.96876814 0.95440106
|
||||
160 0.08 0.94589744 0.95264791 0.95495169
|
||||
170 0.085 0.97599092 0.95336014 0.97687718
|
||||
180 0.09 0.97214242 0.9726305 0.9726035
|
||||
190 0.095 0.97577583 0.96523645 0.9756968
|
||||
200 0.1 0.96386053 0.97268854 0.94582436
|
||||
Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
|
||||
|
||||
Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
|
||||
73.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10
|
||||
Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08
|
||||
Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10
|
||||
Other | | 0.1226 | | | 0.38
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8469 ave 8469 max 8469 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 364000 ave 376628 max 351184 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1456000
|
||||
Ave neighs/atom = 182
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:32
|
||||
|
|
@ -107,6 +107,7 @@ fi
|
|||
|
||||
if (test $1 = "RIGID") then
|
||||
depend USER-OMP
|
||||
depend USER-SDPD
|
||||
fi
|
||||
|
||||
if (test $1 = "SNAP") then
|
||||
|
|
|
|||
|
|
@ -0,0 +1,37 @@
|
|||
# Install/Uninstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
|
||||
mode=$1
|
||||
|
||||
# enforce using portable C locale
|
||||
LC_ALL=C
|
||||
export LC_ALL
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
# package files without dependencies
|
||||
action pair_sdpd_taitwater_isothermal.h
|
||||
action pair_sdpd_taitwater_isothermal.cpp
|
||||
action fix_meso_move.h
|
||||
action fix_meso_move.cpp
|
||||
|
||||
# package files with dependencies
|
||||
action fix_rigid_meso.h fix_rigid.h
|
||||
action fix_rigid_meso.cpp fix_rigid.h
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
This package implements the Smoothed Dissipative Particle Dynamics (SDPD)
|
||||
method for modelling fluids at mesoscale and diffusion of colloids.
|
||||
Currently it adds pair style sdpd/taitwater/isothermal for modelling water
|
||||
at isothermal conditions using the Tait equation of state.
|
||||
It also adds fix meso/move command to move mesoscopic SPH/SDPD particles with
|
||||
prescribed velocity and fix rigid/meso command to integrate rigid bodies
|
||||
composed of mesoscopic SPH/SDPD particles.
|
||||
|
||||
Creator of this package is:
|
||||
|
||||
Morteza Jalalvand
|
||||
Institute for Advanced Studies in Basic Sciences
|
||||
jalalvand.m AT gmail DOT com
|
||||
|
|
@ -0,0 +1,998 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author:
|
||||
Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "math.h"
|
||||
#include "fix_meso_move.h"
|
||||
#include "atom.h"
|
||||
#include "group.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "force.h"
|
||||
#include "domain.h"
|
||||
#include "lattice.h"
|
||||
#include "comm.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{LINEAR,WIGGLE,ROTATE,VARIABLE};
|
||||
enum{EQUAL,ATOM};
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMesoMove::FixMesoMove (LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
xvarstr(NULL), yvarstr(NULL), zvarstr(NULL),
|
||||
vxvarstr(NULL), vyvarstr(NULL), vzvarstr(NULL),
|
||||
xoriginal(NULL), displace(NULL), velocity(NULL) {
|
||||
if ((atom->e_flag != 1) || (atom->rho_flag != 1))
|
||||
error->all(FLERR,
|
||||
"fix meso/move command requires atom_style with both energy and density");
|
||||
|
||||
if (narg < 4) error->all(FLERR,"Illegal fix meso/move command");
|
||||
|
||||
restart_global = 1;
|
||||
restart_peratom = 1;
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 3;
|
||||
peratom_freq = 1;
|
||||
time_integrate = 1;
|
||||
create_attribute = 1;
|
||||
displaceflag = 0;
|
||||
velocityflag = 0;
|
||||
maxatom = 0;
|
||||
|
||||
// parse args
|
||||
|
||||
int iarg;
|
||||
|
||||
if (strcmp(arg[3],"linear") == 0) {
|
||||
if (narg < 7) error->all(FLERR,"Illegal fix meso/move command");
|
||||
iarg = 7;
|
||||
mstyle = LINEAR;
|
||||
if (strcmp(arg[4],"NULL") == 0) vxflag = 0;
|
||||
else {
|
||||
vxflag = 1;
|
||||
vx = force->numeric(FLERR,arg[4]);
|
||||
}
|
||||
if (strcmp(arg[5],"NULL") == 0) vyflag = 0;
|
||||
else {
|
||||
vyflag = 1;
|
||||
vy = force->numeric(FLERR,arg[5]);
|
||||
}
|
||||
if (strcmp(arg[6],"NULL") == 0) vzflag = 0;
|
||||
else {
|
||||
vzflag = 1;
|
||||
vz = force->numeric(FLERR,arg[6]);
|
||||
}
|
||||
|
||||
} else if (strcmp(arg[3],"wiggle") == 0) {
|
||||
if (narg < 8) error->all(FLERR,"Illegal fix meso/move command");
|
||||
iarg = 8;
|
||||
mstyle = WIGGLE;
|
||||
if (strcmp(arg[4],"NULL") == 0) axflag = 0;
|
||||
else {
|
||||
axflag = 1;
|
||||
ax = force->numeric(FLERR,arg[4]);
|
||||
}
|
||||
if (strcmp(arg[5],"NULL") == 0) ayflag = 0;
|
||||
else {
|
||||
ayflag = 1;
|
||||
ay = force->numeric(FLERR,arg[5]);
|
||||
}
|
||||
if (strcmp(arg[6],"NULL") == 0) azflag = 0;
|
||||
else {
|
||||
azflag = 1;
|
||||
az = force->numeric(FLERR,arg[6]);
|
||||
}
|
||||
period = force->numeric(FLERR,arg[7]);
|
||||
if (period <= 0.0) error->all(FLERR,"Illegal fix meso/move command");
|
||||
|
||||
} else if (strcmp(arg[3],"rotate") == 0) {
|
||||
if (narg < 11) error->all(FLERR,"Illegal fix meso/move command");
|
||||
iarg = 11;
|
||||
mstyle = ROTATE;
|
||||
point[0] = force->numeric(FLERR,arg[4]);
|
||||
point[1] = force->numeric(FLERR,arg[5]);
|
||||
point[2] = force->numeric(FLERR,arg[6]);
|
||||
axis[0] = force->numeric(FLERR,arg[7]);
|
||||
axis[1] = force->numeric(FLERR,arg[8]);
|
||||
axis[2] = force->numeric(FLERR,arg[9]);
|
||||
period = force->numeric(FLERR,arg[10]);
|
||||
if (period <= 0.0) error->all(FLERR,"Illegal fix meso/move command");
|
||||
|
||||
} else if (strcmp(arg[3],"variable") == 0) {
|
||||
if (narg < 10) error->all(FLERR,"Illegal fix meso/move command");
|
||||
iarg = 10;
|
||||
mstyle = VARIABLE;
|
||||
if (strcmp(arg[4],"NULL") == 0) xvarstr = NULL;
|
||||
else if (strstr(arg[4],"v_") == arg[4]) {
|
||||
int n = strlen(&arg[4][2]) + 1;
|
||||
xvarstr = new char[n];
|
||||
strcpy(xvarstr,&arg[4][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[5],"NULL") == 0) yvarstr = NULL;
|
||||
else if (strstr(arg[5],"v_") == arg[5]) {
|
||||
int n = strlen(&arg[5][2]) + 1;
|
||||
yvarstr = new char[n];
|
||||
strcpy(yvarstr,&arg[5][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[6],"NULL") == 0) zvarstr = NULL;
|
||||
else if (strstr(arg[6],"v_") == arg[6]) {
|
||||
int n = strlen(&arg[6][2]) + 1;
|
||||
zvarstr = new char[n];
|
||||
strcpy(zvarstr,&arg[6][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[7],"NULL") == 0) vxvarstr = NULL;
|
||||
else if (strstr(arg[7],"v_") == arg[7]) {
|
||||
int n = strlen(&arg[7][2]) + 1;
|
||||
vxvarstr = new char[n];
|
||||
strcpy(vxvarstr,&arg[7][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[8],"NULL") == 0) vyvarstr = NULL;
|
||||
else if (strstr(arg[8],"v_") == arg[8]) {
|
||||
int n = strlen(&arg[8][2]) + 1;
|
||||
vyvarstr = new char[n];
|
||||
strcpy(vyvarstr,&arg[8][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[9],"NULL") == 0) vzvarstr = NULL;
|
||||
else if (strstr(arg[9],"v_") == arg[9]) {
|
||||
int n = strlen(&arg[9][2]) + 1;
|
||||
vzvarstr = new char[n];
|
||||
strcpy(vzvarstr,&arg[9][2]);
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
|
||||
// optional args
|
||||
|
||||
int scaleflag = 1;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"units") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix meso/move command");
|
||||
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
|
||||
else error->all(FLERR,"Illegal fix meso/move command");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal fix meso/move command");
|
||||
}
|
||||
|
||||
// error checks and warnings
|
||||
|
||||
if (domain->dimension == 2) {
|
||||
if (mstyle == LINEAR && vzflag && vz != 0.0)
|
||||
error->all(FLERR,"Fix meso/move cannot set linear z motion for 2d problem");
|
||||
if (mstyle == WIGGLE && azflag && az != 0.0)
|
||||
error->all(FLERR,"Fix meso/move cannot set wiggle z motion for 2d problem");
|
||||
if (mstyle == ROTATE && (axis[0] != 0.0 || axis[1] != 0.0))
|
||||
error->all(FLERR, "Fix meso/move cannot rotate aroung non z-axis for 2d problem");
|
||||
if (mstyle == VARIABLE && (zvarstr || vzvarstr))
|
||||
error->all(FLERR, "Fix meso/move cannot define z or vz variable for 2d problem");
|
||||
}
|
||||
|
||||
// setup scaling and apply scaling factors to velocity & amplitude
|
||||
|
||||
if ((mstyle == LINEAR || mstyle == WIGGLE || mstyle == ROTATE) &&
|
||||
scaleflag) {
|
||||
double xscale = domain->lattice->xlattice;
|
||||
double yscale = domain->lattice->ylattice;
|
||||
double zscale = domain->lattice->zlattice;
|
||||
|
||||
if (mstyle == LINEAR) {
|
||||
if (vxflag) vx *= xscale;
|
||||
if (vyflag) vy *= yscale;
|
||||
if (vzflag) vz *= zscale;
|
||||
} else if (mstyle == WIGGLE) {
|
||||
if (axflag) ax *= xscale;
|
||||
if (ayflag) ay *= yscale;
|
||||
if (azflag) az *= zscale;
|
||||
} else if (mstyle == ROTATE) {
|
||||
point[0] *= xscale;
|
||||
point[1] *= yscale;
|
||||
point[2] *= zscale;
|
||||
}
|
||||
}
|
||||
|
||||
// set omega_rotate from period
|
||||
|
||||
if (mstyle == WIGGLE || mstyle == ROTATE) omega_rotate = MY_2PI / period;
|
||||
|
||||
// runit = unit vector along rotation axis
|
||||
|
||||
if (mstyle == ROTATE) {
|
||||
double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]);
|
||||
if (len == 0.0)
|
||||
error->all(FLERR,"Zero length rotation vector with fix meso/move");
|
||||
runit[0] = axis[0]/len;
|
||||
runit[1] = axis[1]/len;
|
||||
runit[2] = axis[2]/len;
|
||||
}
|
||||
|
||||
// perform initial allocation of atom-based array
|
||||
// register with Atom class
|
||||
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(0);
|
||||
atom->add_callback(1);
|
||||
|
||||
displace = velocity = NULL;
|
||||
|
||||
// xoriginal = initial unwrapped positions of atoms
|
||||
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
|
||||
}
|
||||
|
||||
time_origin = update->ntimestep;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMesoMove::~FixMesoMove () {
|
||||
// unregister callbacks to this fix from Atom class
|
||||
|
||||
atom->delete_callback(id,0);
|
||||
atom->delete_callback(id,1);
|
||||
|
||||
// delete locally stored arrays
|
||||
|
||||
memory->destroy(xoriginal);
|
||||
memory->destroy(displace);
|
||||
memory->destroy(velocity);
|
||||
|
||||
delete [] xvarstr;
|
||||
delete [] yvarstr;
|
||||
delete [] zvarstr;
|
||||
delete [] vxvarstr;
|
||||
delete [] vyvarstr;
|
||||
delete [] vzvarstr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::setmask () {
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
mask |= PRE_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::init () {
|
||||
dt = update->dt;
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
|
||||
// set indices and style of all variables
|
||||
|
||||
displaceflag = velocityflag = 0;
|
||||
|
||||
if (mstyle == VARIABLE) {
|
||||
if (xvarstr) {
|
||||
xvar = input->variable->find(xvarstr);
|
||||
if (xvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(xvar)) xvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(xvar)) xvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
if (yvarstr) {
|
||||
yvar = input->variable->find(yvarstr);
|
||||
if (yvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(yvar)) yvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(yvar)) yvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
if (zvarstr) {
|
||||
zvar = input->variable->find(zvarstr);
|
||||
if (zvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(zvar)) zvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(zvar)) zvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
if (vxvarstr) {
|
||||
vxvar = input->variable->find(vxvarstr);
|
||||
if (vxvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(vxvar)) vxvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(vxvar)) vxvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
if (vyvarstr) {
|
||||
vyvar = input->variable->find(vyvarstr);
|
||||
if (vyvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(vyvar)) vyvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(vyvar)) vyvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
if (vzvarstr) {
|
||||
vzvar = input->variable->find(vzvarstr);
|
||||
if (vzvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist");
|
||||
if (input->variable->equalstyle(vzvar)) vzvarstyle = EQUAL;
|
||||
else if (input->variable->atomstyle(vzvar)) vzvarstyle = ATOM;
|
||||
else error->all(FLERR,"Variable for fix meso/move is invalid style");
|
||||
}
|
||||
|
||||
if (xvarstr && xvarstyle == ATOM) displaceflag = 1;
|
||||
if (yvarstr && yvarstyle == ATOM) displaceflag = 1;
|
||||
if (zvarstr && zvarstyle == ATOM) displaceflag = 1;
|
||||
if (vxvarstr && vxvarstyle == ATOM) velocityflag = 1;
|
||||
if (vyvarstr && vyvarstyle == ATOM) velocityflag = 1;
|
||||
if (vzvarstr && vzvarstyle == ATOM) velocityflag = 1;
|
||||
}
|
||||
|
||||
maxatom = atom->nmax;
|
||||
memory->destroy(displace);
|
||||
memory->destroy(velocity);
|
||||
if (displaceflag) memory->create(displace,maxatom,3,"move:displace");
|
||||
else displace = NULL;
|
||||
if (velocityflag) memory->create(velocity,maxatom,3,"move:velocity");
|
||||
else velocity = NULL;
|
||||
}
|
||||
|
||||
void FixMesoMove::setup_pre_force (int /*vflag*/) {
|
||||
// set vest equal to v
|
||||
double **v = atom->v;
|
||||
double **vest = atom->vest;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
vest[i][0] = v[i][0];
|
||||
vest[i][1] = v[i][1];
|
||||
vest[i][2] = v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set x,v of particles
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::initial_integrate (int /*vflag*/) {
|
||||
double ddotr,dx,dy,dz;
|
||||
double dtfm;
|
||||
double xold[3],a[3],b[3],c[3],d[3],disp[3],disp_next[3];
|
||||
|
||||
double delta = (update->ntimestep - time_origin) * dt;
|
||||
double delta_next = (update->ntimestep - time_origin + 1) * dt;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **vest = atom->vest;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int rmass_flag = atom->rmass_flag;
|
||||
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
// for linear: X = X0 + V*dt
|
||||
|
||||
if (mstyle == LINEAR) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
xold[0] = x[i][0];
|
||||
xold[1] = x[i][1];
|
||||
xold[2] = x[i][2];
|
||||
|
||||
e[i] += dtf * de[i]; // half-step update of particle internal energy
|
||||
rho[i] += dtf * drho[i]; // ... and density
|
||||
|
||||
if (vxflag) {
|
||||
vest[i][0] = v[i][0] = vx;
|
||||
x[i][0] = xoriginal[i][0] + vx*delta;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
}
|
||||
|
||||
if (vyflag) {
|
||||
vest[i][1] = v[i][1] = vy;
|
||||
x[i][1] = xoriginal[i][1] + vy*delta;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
}
|
||||
|
||||
if (vzflag) {
|
||||
vest[i][2] = v[i][2] = vz;
|
||||
x[i][2] = xoriginal[i][2] + vz*delta;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
|
||||
domain->remap_near(x[i],xold);
|
||||
}
|
||||
}
|
||||
|
||||
// for wiggle: X = X0 + A sin(w*dt)
|
||||
|
||||
} else if (mstyle == WIGGLE) {
|
||||
double arg = omega_rotate * delta;
|
||||
double arg_next = omega_rotate * delta_next;
|
||||
double sine = sin(arg);
|
||||
double cosine = cos(arg);
|
||||
double cosine_next = cos(arg_next);
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
xold[0] = x[i][0];
|
||||
xold[1] = x[i][1];
|
||||
xold[2] = x[i][2];
|
||||
|
||||
e[i] += dtf * de[i]; // half-step update of particle internal energy
|
||||
rho[i] += dtf * drho[i]; // ... and density
|
||||
|
||||
if (axflag) {
|
||||
v[i][0] = ax*omega_rotate*cosine;
|
||||
vest[i][0] = ax*omega_rotate*cosine_next;
|
||||
x[i][0] = xoriginal[i][0] + ax*sine;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
}
|
||||
|
||||
if (ayflag) {
|
||||
v[i][1] = ay*omega_rotate*cosine;
|
||||
vest[i][1] = ay*omega_rotate*cosine_next;
|
||||
x[i][1] = xoriginal[i][1] + ay*sine;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
}
|
||||
|
||||
if (azflag) {
|
||||
v[i][2] = az*omega_rotate*cosine;
|
||||
vest[i][2] = az*omega_rotate*cosine_next;
|
||||
x[i][2] = xoriginal[i][2] + az*sine;
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
|
||||
domain->remap_near(x[i],xold);
|
||||
}
|
||||
}
|
||||
|
||||
// for rotate by right-hand rule around omega:
|
||||
// P = point = vector = point of rotation
|
||||
// R = vector = axis of rotation
|
||||
// w = omega of rotation (from period)
|
||||
// X0 = xoriginal = initial coord of atom
|
||||
// R0 = runit = unit vector for R
|
||||
// D = X0 - P = vector from P to X0
|
||||
// C = (D dot R0) R0 = projection of atom coord onto R line
|
||||
// A = D - C = vector from R line to X0
|
||||
// B = R0 cross A = vector perp to A in plane of rotation
|
||||
// A,B define plane of circular rotation around R line
|
||||
// X = P + C + A cos(w*dt) + B sin(w*dt)
|
||||
// V = w R0 cross (A cos(w*dt) + B sin(w*dt))
|
||||
|
||||
} else if (mstyle == ROTATE) {
|
||||
double arg = omega_rotate * delta;
|
||||
double arg_next = omega_rotate * delta_next;
|
||||
double sine = sin(arg);
|
||||
double cosine = cos(arg);
|
||||
double sine_next = sin(arg_next);
|
||||
double cosine_next = cos(arg_next);
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
xold[0] = x[i][0];
|
||||
xold[1] = x[i][1];
|
||||
xold[2] = x[i][2];
|
||||
|
||||
e[i] += dtf * de[i]; // half-step update of particle internal energy
|
||||
rho[i] += dtf * drho[i]; // ... and density
|
||||
|
||||
d[0] = xoriginal[i][0] - point[0];
|
||||
d[1] = xoriginal[i][1] - point[1];
|
||||
d[2] = xoriginal[i][2] - point[2];
|
||||
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
|
||||
c[0] = ddotr*runit[0];
|
||||
c[1] = ddotr*runit[1];
|
||||
c[2] = ddotr*runit[2];
|
||||
a[0] = d[0] - c[0];
|
||||
a[1] = d[1] - c[1];
|
||||
a[2] = d[2] - c[2];
|
||||
b[0] = runit[1]*a[2] - runit[2]*a[1];
|
||||
b[1] = runit[2]*a[0] - runit[0]*a[2];
|
||||
b[2] = runit[0]*a[1] - runit[1]*a[0];
|
||||
disp[0] = a[0]*cosine + b[0]*sine;
|
||||
disp[1] = a[1]*cosine + b[1]*sine;
|
||||
disp[2] = a[2]*cosine + b[2]*sine;
|
||||
disp_next[0] = a[0]*cosine_next + b[0]*sine_next;
|
||||
disp_next[1] = a[1]*cosine_next + b[1]*sine_next;
|
||||
disp_next[2] = a[2]*cosine_next + b[2]*sine_next;
|
||||
|
||||
x[i][0] = point[0] + c[0] + disp[0];
|
||||
x[i][1] = point[1] + c[1] + disp[1];
|
||||
x[i][2] = point[2] + c[2] + disp[2];
|
||||
v[i][0] = omega_rotate * (runit[1]*disp[2] - runit[2]*disp[1]);
|
||||
v[i][1] = omega_rotate * (runit[2]*disp[0] - runit[0]*disp[2]);
|
||||
v[i][2] = omega_rotate * (runit[0]*disp[1] - runit[1]*disp[0]);
|
||||
vest[i][0] = omega_rotate * (runit[1]*disp_next[2] - runit[2]*disp_next[1]);
|
||||
vest[i][1] = omega_rotate * (runit[2]*disp_next[0] - runit[0]*disp_next[2]);
|
||||
vest[i][2] = omega_rotate * (runit[0]*disp_next[1] - runit[1]*disp_next[0]);
|
||||
|
||||
domain->remap_near(x[i],xold);
|
||||
}
|
||||
}
|
||||
|
||||
// for variable: compute x,v from variables
|
||||
|
||||
} else if (mstyle == VARIABLE) {
|
||||
|
||||
// reallocate displace and velocity arrays as necessary
|
||||
|
||||
if ((displaceflag || velocityflag) && atom->nmax > maxatom) {
|
||||
maxatom = atom->nmax;
|
||||
if (displaceflag) {
|
||||
memory->destroy(displace);
|
||||
memory->create(displace,maxatom,3,"move:displace");
|
||||
}
|
||||
if (velocityflag) {
|
||||
memory->destroy(velocity);
|
||||
memory->create(velocity,maxatom,3,"move:velocity");
|
||||
}
|
||||
}
|
||||
|
||||
// pre-compute variable values, wrap with clear/add
|
||||
|
||||
modify->clearstep_compute();
|
||||
|
||||
if (xvarstr) {
|
||||
if (xvarstyle == EQUAL) dx = input->variable->compute_equal(xvar);
|
||||
else input->variable->compute_atom(xvar,igroup,&displace[0][0],3,0);
|
||||
}
|
||||
if (yvarstr) {
|
||||
if (yvarstyle == EQUAL) dy = input->variable->compute_equal(yvar);
|
||||
else input->variable->compute_atom(yvar,igroup,&displace[0][1],3,0);
|
||||
}
|
||||
if (zvarstr) {
|
||||
if (zvarstyle == EQUAL) dz = input->variable->compute_equal(zvar);
|
||||
else input->variable->compute_atom(zvar,igroup,&displace[0][2],3,0);
|
||||
}
|
||||
if (vxvarstr) {
|
||||
if (vxvarstyle == EQUAL) vx = input->variable->compute_equal(vxvar);
|
||||
else input->variable->compute_atom(vxvar,igroup,&velocity[0][0],3,0);
|
||||
}
|
||||
if (vyvarstr) {
|
||||
if (vyvarstyle == EQUAL) vy = input->variable->compute_equal(vyvar);
|
||||
else input->variable->compute_atom(vyvar,igroup,&velocity[0][1],3,0);
|
||||
}
|
||||
if (vzvarstr) {
|
||||
if (vzvarstyle == EQUAL) vz = input->variable->compute_equal(vzvar);
|
||||
else input->variable->compute_atom(vzvar,igroup,&velocity[0][2],3,0);
|
||||
}
|
||||
|
||||
modify->addstep_compute(update->ntimestep + 1);
|
||||
|
||||
// update x,v
|
||||
// vest (velocity in next step) could be different from v in the next
|
||||
// step, but this is the best we could do
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
xold[0] = x[i][0];
|
||||
xold[1] = x[i][1];
|
||||
xold[2] = x[i][2];
|
||||
|
||||
if (xvarstr && vxvarstr) {
|
||||
if (vxvarstyle == EQUAL) {
|
||||
vest[i][0] = 2*vx - v[i][0];
|
||||
v[i][0] = vx;
|
||||
}
|
||||
else {
|
||||
vest[i][0] = 2*velocity[i][0] - v[i][0];
|
||||
v[i][0] = velocity[i][0];
|
||||
}
|
||||
if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
|
||||
else x[i][0] = xoriginal[i][0] + displace[i][0];
|
||||
} else if (xvarstr) {
|
||||
if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx;
|
||||
else x[i][0] = xoriginal[i][0] + displace[i][0];
|
||||
} else if (vxvarstr) {
|
||||
if (vxvarstyle == EQUAL) {
|
||||
vest[i][0] = 2*vx - v[i][0];
|
||||
v[i][0] = vx;
|
||||
}
|
||||
else {
|
||||
vest[i][0] = 2*velocity[i][0] - v[i][0];
|
||||
v[i][0] = velocity[i][0];
|
||||
}
|
||||
x[i][0] += dtv * v[i][0];
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
}
|
||||
|
||||
if (yvarstr && vyvarstr) {
|
||||
if (vyvarstyle == EQUAL) {
|
||||
vest[i][1] = 2*vy - v[i][1];
|
||||
v[i][1] = vy;
|
||||
}
|
||||
else {
|
||||
vest[i][1] = 2*velocity[i][1] - v[i][1];
|
||||
v[i][1] = velocity[i][1];
|
||||
}
|
||||
if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
|
||||
else x[i][1] = xoriginal[i][1] + displace[i][1];
|
||||
} else if (yvarstr) {
|
||||
if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy;
|
||||
else x[i][1] = xoriginal[i][1] + displace[i][1];
|
||||
} else if (vyvarstr) {
|
||||
if (vyvarstyle == EQUAL) {
|
||||
vest[i][1] = 2*vy - v[i][1];
|
||||
v[i][1] = vy;
|
||||
}
|
||||
else {
|
||||
vest[i][1] = 2*velocity[i][1] - v[i][1];
|
||||
v[i][1] = velocity[i][1];
|
||||
}
|
||||
x[i][1] += dtv * v[i][1];
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
}
|
||||
|
||||
if (zvarstr && vzvarstr) {
|
||||
if (vzvarstyle == EQUAL) {
|
||||
vest[i][2] = 2*vz - v[i][2];
|
||||
v[i][2] = vz;
|
||||
}
|
||||
else {
|
||||
vest[i][2] = 2*velocity[i][2] - v[i][2];
|
||||
v[i][2] = velocity[i][2];
|
||||
}
|
||||
if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
|
||||
else x[i][2] = xoriginal[i][2] + displace[i][2];
|
||||
} else if (zvarstr) {
|
||||
if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz;
|
||||
else x[i][2] = xoriginal[i][2] + displace[i][2];
|
||||
} else if (vzvarstr) {
|
||||
if (vzvarstyle == EQUAL) {
|
||||
vest[i][2] = 2*vz - v[i][2];
|
||||
v[i][2] = vz;
|
||||
}
|
||||
else {
|
||||
vest[i][2] = 2*velocity[i][2] - v[i][2];
|
||||
v[i][2] = velocity[i][2];
|
||||
}
|
||||
x[i][2] += dtv * v[i][2];
|
||||
} else {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
|
||||
domain->remap_near(x[i],xold);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
final NVE of particles with NULL components
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::final_integrate () {
|
||||
double dtfm;
|
||||
|
||||
int xflag = 1;
|
||||
if (mstyle == LINEAR && vxflag) xflag = 0;
|
||||
else if (mstyle == WIGGLE && axflag) xflag = 0;
|
||||
else if (mstyle == ROTATE) xflag = 0;
|
||||
else if (mstyle == VARIABLE && (xvarstr || vxvarstr)) xflag = 0;
|
||||
|
||||
int yflag = 1;
|
||||
if (mstyle == LINEAR && vyflag) yflag = 0;
|
||||
else if (mstyle == WIGGLE && ayflag) yflag = 0;
|
||||
else if (mstyle == ROTATE) yflag = 0;
|
||||
else if (mstyle == VARIABLE && (yvarstr || vyvarstr)) yflag = 0;
|
||||
|
||||
int zflag = 1;
|
||||
if (mstyle == LINEAR && vzflag) zflag = 0;
|
||||
else if (mstyle == WIGGLE && azflag) zflag = 0;
|
||||
else if (mstyle == ROTATE) zflag = 0;
|
||||
else if (mstyle == VARIABLE && (zvarstr || vzvarstr)) zflag = 0;
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int rmass_flag = atom->rmass_flag;
|
||||
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
e[i] += dtf * de[i];
|
||||
rho[i] += dtf * drho[i];
|
||||
|
||||
if (xflag) {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
}
|
||||
|
||||
if (yflag) {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
}
|
||||
|
||||
if (zflag) {
|
||||
dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixMesoMove::memory_usage () {
|
||||
double bytes = atom->nmax*3 * sizeof(double);
|
||||
if (displaceflag) bytes += atom->nmax*3 * sizeof(double);
|
||||
if (velocityflag) bytes += atom->nmax*3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack entire state of Fix into one write
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::write_restart (FILE *fp) {
|
||||
int n = 0;
|
||||
double list[1];
|
||||
list[n++] = time_origin;
|
||||
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::restart (char *buf) {
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
|
||||
time_origin = static_cast<int> (list[n++]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::grow_arrays (int nmax) {
|
||||
memory->grow(xoriginal,nmax,3,"move:xoriginal");
|
||||
array_atom = xoriginal;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
copy values within local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::copy_arrays (int i, int j, int /*delflag*/) {
|
||||
xoriginal[j][0] = xoriginal[i][0];
|
||||
xoriginal[j][1] = xoriginal[i][1];
|
||||
xoriginal[j][2] = xoriginal[i][2];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
initialize one atom's array values, called when atom is created
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::set_arrays (int i) {
|
||||
double **x = atom->x;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
|
||||
// particle not in group
|
||||
|
||||
if (!(mask[i] & groupbit)) {
|
||||
xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
|
||||
return;
|
||||
}
|
||||
|
||||
// current time still equal fix creation time
|
||||
|
||||
if (update->ntimestep == time_origin) {
|
||||
domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
return;
|
||||
}
|
||||
|
||||
// backup particle to time_origin
|
||||
|
||||
if (mstyle == VARIABLE)
|
||||
error->all(FLERR,"Cannot add atoms to fix meso/move variable");
|
||||
|
||||
domain->unmap(x[i],image[i],xoriginal[i]);
|
||||
double delta = (update->ntimestep - time_origin) * update->dt;
|
||||
|
||||
if (mstyle == LINEAR) {
|
||||
if (vxflag) xoriginal[i][0] -= vx * delta;
|
||||
if (vyflag) xoriginal[i][1] -= vy * delta;
|
||||
if (vzflag) xoriginal[i][2] -= vz * delta;
|
||||
} else if (mstyle == WIGGLE) {
|
||||
double arg = omega_rotate * delta;
|
||||
double sine = sin(arg);
|
||||
if (axflag) xoriginal[i][0] -= ax*sine;
|
||||
if (ayflag) xoriginal[i][1] -= ay*sine;
|
||||
if (azflag) xoriginal[i][2] -= az*sine;
|
||||
} else if (mstyle == ROTATE) {
|
||||
double a[3],b[3],c[3],d[3],disp[3],ddotr;
|
||||
double arg = - omega_rotate * delta;
|
||||
double sine = sin(arg);
|
||||
double cosine = cos(arg);
|
||||
d[0] = x[i][0] - point[0];
|
||||
d[1] = x[i][1] - point[1];
|
||||
d[2] = x[i][2] - point[2];
|
||||
ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2];
|
||||
c[0] = ddotr*runit[0];
|
||||
c[1] = ddotr*runit[1];
|
||||
c[2] = ddotr*runit[2];
|
||||
|
||||
a[0] = d[0] - c[0];
|
||||
a[1] = d[1] - c[1];
|
||||
a[2] = d[2] - c[2];
|
||||
b[0] = runit[1]*a[2] - runit[2]*a[1];
|
||||
b[1] = runit[2]*a[0] - runit[0]*a[2];
|
||||
b[2] = runit[0]*a[1] - runit[1]*a[0];
|
||||
disp[0] = a[0]*cosine + b[0]*sine;
|
||||
disp[1] = a[1]*cosine + b[1]*sine;
|
||||
disp[2] = a[2]*cosine + b[2]*sine;
|
||||
|
||||
xoriginal[i][0] = point[0] + c[0] + disp[0];
|
||||
xoriginal[i][1] = point[1] + c[1] + disp[1];
|
||||
xoriginal[i][2] = point[2] + c[2] + disp[2];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based array for exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::pack_exchange (int i, double *buf) {
|
||||
buf[0] = xoriginal[i][0];
|
||||
buf[1] = xoriginal[i][1];
|
||||
buf[2] = xoriginal[i][2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values in local atom-based array from exchange with another proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::unpack_exchange (int nlocal, double *buf) {
|
||||
xoriginal[nlocal][0] = buf[0];
|
||||
xoriginal[nlocal][1] = buf[1];
|
||||
xoriginal[nlocal][2] = buf[2];
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack values in local atom-based arrays for restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::pack_restart (int i, double *buf) {
|
||||
buf[0] = 4;
|
||||
buf[1] = xoriginal[i][0];
|
||||
buf[2] = xoriginal[i][1];
|
||||
buf[3] = xoriginal[i][2];
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack values from atom->extra array to restart the fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::unpack_restart (int nlocal, int nth) {
|
||||
double **extra = atom->extra;
|
||||
|
||||
// skip to Nth set of extra values
|
||||
|
||||
int m = 0;
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
|
||||
m++;
|
||||
|
||||
xoriginal[nlocal][0] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][1] = extra[nlocal][m++];
|
||||
xoriginal[nlocal][2] = extra[nlocal][m++];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
maxsize of any atom's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::maxsize_restart () {
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
size of atom nlocal's restart data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoMove::size_restart (int nlocal) {
|
||||
return 4;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoMove::reset_dt () {
|
||||
error->all(FLERR,"Resetting timestep size is not allowed with fix meso/move");
|
||||
}
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
/* -*- 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
|
||||
|
||||
FixStyle(meso/move,FixMesoMove)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MESO_MOVE_H
|
||||
#define LMP_FIX_MESO_MOVE_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixMesoMove : public Fix {
|
||||
public:
|
||||
FixMesoMove (class LAMMPS *, int, char **);
|
||||
~FixMesoMove ();
|
||||
int setmask ();
|
||||
void init ();
|
||||
void setup_pre_force (int);
|
||||
void initial_integrate (int);
|
||||
void final_integrate ();
|
||||
|
||||
double memory_usage ();
|
||||
void write_restart (FILE *);
|
||||
void restart (char *);
|
||||
void grow_arrays (int);
|
||||
void copy_arrays (int, int, int);
|
||||
void set_arrays (int);
|
||||
int pack_exchange (int, double *);
|
||||
int unpack_exchange (int, double *);
|
||||
int pack_restart (int, double *);
|
||||
void unpack_restart (int, int);
|
||||
int maxsize_restart ();
|
||||
int size_restart (int);
|
||||
|
||||
void reset_dt ();
|
||||
|
||||
private:
|
||||
char *xvarstr,*yvarstr,*zvarstr,*vxvarstr,*vyvarstr,*vzvarstr;
|
||||
int mstyle;
|
||||
int vxflag,vyflag,vzflag,axflag,ayflag,azflag;
|
||||
double vx,vy,vz,ax,ay,az;
|
||||
double period,omega_rotate;
|
||||
double point[3],axis[3],runit[3];
|
||||
double dt,dtv,dtf;
|
||||
int xvar,yvar,zvar,vxvar,vyvar,vzvar;
|
||||
int xvarstyle,yvarstyle,zvarstyle,vxvarstyle,vyvarstyle,vzvarstyle;
|
||||
int time_origin;
|
||||
|
||||
double **xoriginal; // original coords of atoms
|
||||
int displaceflag,velocityflag;
|
||||
int maxatom;
|
||||
double **displace,**velocity;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix meso/move cannot set linear z motion for 2d problem
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix meso/move cannot set wiggle z motion for 2d problem
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix meso/move cannot rotate aroung non z-axis for 2d problem
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix meso/move cannot define z or vz variable for 2d problem
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Fix meso/move does not update angular momentum
|
||||
|
||||
Atoms store this quantity, but fix meso/move does not (yet) update it.
|
||||
|
||||
W: Fix meso/move does not update quaternions
|
||||
|
||||
Atoms store this quantity, but fix meso/move does not (yet) update it.
|
||||
|
||||
E: Zero length rotation vector with fix meso/move
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable name for fix meso/move does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable for fix meso/move is invalid style
|
||||
|
||||
Only equal-style variables can be used.
|
||||
|
||||
E: Cannot add atoms to fix meso/move variable
|
||||
|
||||
Atoms can not be added afterwards to this fix option.
|
||||
|
||||
E: Resetting timestep size is not allowed with fix meso/move
|
||||
|
||||
This is because fix meso/move is moving atoms based on elapsed time.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,500 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Tony Sheh (U Michigan), Trung Dac Nguyen (U Michigan)
|
||||
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
|
||||
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author:
|
||||
Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com
|
||||
|
||||
This is an extension of fix/rigid/nve to SPH/SDPD particles
|
||||
You can see the original copyright notice of fix/rigid authors above
|
||||
Note that the Kamberaj paper was related to the nvt variant
|
||||
and all codes relevant to that has been removed
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include "fix_rigid_meso.h"
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "compute.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "group.h"
|
||||
#include "force.h"
|
||||
#include "output.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRigidMeso::FixRigidMeso (LAMMPS *lmp, int narg, char **arg) :
|
||||
FixRigid (lmp, narg, arg) {
|
||||
scalar_flag = 0;
|
||||
size_array_cols = 28;
|
||||
if ((atom->e_flag != 1) || (atom->rho_flag != 1))
|
||||
error->all (FLERR, "fix rigid/meso command requires atom_style with"
|
||||
" both energy and density");
|
||||
|
||||
if (langflag || tstat_flag)
|
||||
error->all (FLERR,"Can not use thermostat with fix rigid/meso");
|
||||
|
||||
if (pstat_flag)
|
||||
error->all (FLERR,"Can not use barostat with fix rigid/meso");
|
||||
|
||||
// memory allocation and initialization
|
||||
|
||||
memory->create(conjqm,nbody,4,"rigid_nh:conjqm");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixRigidMeso::~FixRigidMeso () {
|
||||
memory->destroy(conjqm);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixRigidMeso::setmask () {
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
mask |= PRE_NEIGHBOR;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidMeso::setup (int vflag) {
|
||||
FixRigid::setup(vflag);
|
||||
|
||||
double mbody[3];
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
angmom[ibody],mbody);
|
||||
MathExtra::quatvec (quat[ibody],mbody,conjqm[ibody]);
|
||||
conjqm[ibody][0] *= 2.0;
|
||||
conjqm[ibody][1] *= 2.0;
|
||||
conjqm[ibody][2] *= 2.0;
|
||||
conjqm[ibody][3] *= 2.0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
perform preforce velocity Verlet integration
|
||||
see Kamberaj paper for step references
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidMeso::initial_integrate (int vflag) {
|
||||
double dtfm,mbody[3],tbody[3],fquat[4];
|
||||
double dtf2 = dtf * 2.0;
|
||||
|
||||
// update xcm, vcm, quat, conjqm and angmom
|
||||
|
||||
for (int ibody = 0; ibody < nbody; ibody++) {
|
||||
|
||||
// step 1.1 - update vcm by 1/2 step
|
||||
|
||||
dtfm = dtf / masstotal[ibody];
|
||||
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
|
||||
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
|
||||
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
|
||||
|
||||
// step 1.2 - update xcm by full step
|
||||
|
||||
xcm[ibody][0] += dtv * vcm[ibody][0];
|
||||
xcm[ibody][1] += dtv * vcm[ibody][1];
|
||||
xcm[ibody][2] += dtv * vcm[ibody][2];
|
||||
|
||||
// step 1.3 - apply torque (body coords) to quaternion momentum
|
||||
|
||||
torque[ibody][0] *= tflag[ibody][0];
|
||||
torque[ibody][1] *= tflag[ibody][1];
|
||||
torque[ibody][2] *= tflag[ibody][2];
|
||||
|
||||
MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
torque[ibody],tbody);
|
||||
MathExtra::quatvec (quat[ibody],tbody,fquat);
|
||||
|
||||
conjqm[ibody][0] += dtf2 * fquat[0];
|
||||
conjqm[ibody][1] += dtf2 * fquat[1];
|
||||
conjqm[ibody][2] += dtf2 * fquat[2];
|
||||
conjqm[ibody][3] += dtf2 * fquat[3];
|
||||
|
||||
// step 1.4 to 1.13 - use no_squish rotate to update p and q
|
||||
|
||||
MathExtra::no_squish_rotate (3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
MathExtra::no_squish_rotate (2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
MathExtra::no_squish_rotate (1,conjqm[ibody],quat[ibody],inertia[ibody],dtv);
|
||||
MathExtra::no_squish_rotate (2,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
MathExtra::no_squish_rotate (3,conjqm[ibody],quat[ibody],inertia[ibody],dtq);
|
||||
|
||||
// update exyz_space
|
||||
// transform p back to angmom
|
||||
// update angular velocity
|
||||
|
||||
MathExtra::q_to_exyz (quat[ibody],ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody]);
|
||||
MathExtra::invquatvec (quat[ibody],conjqm[ibody],mbody);
|
||||
MathExtra::matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
mbody,angmom[ibody]);
|
||||
|
||||
angmom[ibody][0] *= 0.5;
|
||||
angmom[ibody][1] *= 0.5;
|
||||
angmom[ibody][2] *= 0.5;
|
||||
|
||||
MathExtra::angmom_to_omega (angmom[ibody],ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],inertia[ibody],omega[ibody]);
|
||||
}
|
||||
|
||||
// virial setup before call to set_xv
|
||||
|
||||
if (vflag) v_setup(vflag);
|
||||
else evflag = 0;
|
||||
|
||||
// set coords/orient and velocity/rotation of atoms in rigid bodies
|
||||
// from quarternion and omega
|
||||
|
||||
set_xv();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidMeso::final_integrate () {
|
||||
int i,ibody;
|
||||
double dtfm,xy,xz,yz;
|
||||
double mbody[3],tbody[3],fquat[4];
|
||||
|
||||
double dtf2 = dtf * 2.0;
|
||||
|
||||
// late calculation of forces and torques (if requested)
|
||||
|
||||
if (!earlyflag) compute_forces_and_torques();
|
||||
|
||||
// update vcm and angmom
|
||||
// fflag,tflag = 0 for some dimensions in 2d
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++) {
|
||||
|
||||
// update vcm by 1/2 step
|
||||
|
||||
dtfm = dtf / masstotal[ibody];
|
||||
|
||||
vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0];
|
||||
vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1];
|
||||
vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2];
|
||||
|
||||
// update conjqm, then transform to angmom, set velocity again
|
||||
// virial is already setup from initial_integrate
|
||||
|
||||
torque[ibody][0] *= tflag[ibody][0];
|
||||
torque[ibody][1] *= tflag[ibody][1];
|
||||
torque[ibody][2] *= tflag[ibody][2];
|
||||
|
||||
MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],torque[ibody],tbody);
|
||||
MathExtra::quatvec (quat[ibody],tbody,fquat);
|
||||
|
||||
conjqm[ibody][0] += dtf2 * fquat[0];
|
||||
conjqm[ibody][1] += dtf2 * fquat[1];
|
||||
conjqm[ibody][2] += dtf2 * fquat[2];
|
||||
conjqm[ibody][3] += dtf2 * fquat[3];
|
||||
|
||||
MathExtra::invquatvec (quat[ibody],conjqm[ibody],mbody);
|
||||
MathExtra::matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody],
|
||||
mbody,angmom[ibody]);
|
||||
|
||||
angmom[ibody][0] *= 0.5;
|
||||
angmom[ibody][1] *= 0.5;
|
||||
angmom[ibody][2] *= 0.5;
|
||||
|
||||
MathExtra::angmom_to_omega (angmom[ibody],ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],inertia[ibody],omega[ibody]);
|
||||
}
|
||||
|
||||
// set velocity/rotation of atoms in rigid bodies
|
||||
// virial is already setup from initial_integrate
|
||||
|
||||
set_v();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set space-frame coords and velocity of each atom in each rigid body
|
||||
set orientation and rotation of extended particles
|
||||
x = Q displace + Xcm, mapped back to periodic box
|
||||
v = Vcm + (W cross (x - Xcm))
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidMeso::set_xv () {
|
||||
int ibody;
|
||||
int xbox,ybox,zbox;
|
||||
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
|
||||
double xy,xz,yz;
|
||||
double ione[3],exone[3],eyone[3],ezone[3],vr[6],p[3][3];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **vest = atom->vest;
|
||||
double **f = atom->f;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
if (triclinic) {
|
||||
xy = domain->xy;
|
||||
xz = domain->xz;
|
||||
yz = domain->yz;
|
||||
}
|
||||
|
||||
// set x and v of each atom
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (body[i] < 0) continue;
|
||||
|
||||
// half-step update of particle internal energy and density
|
||||
e[i] += dtf * de[i];
|
||||
rho[i] += dtf * drho[i];
|
||||
|
||||
ibody = body[i];
|
||||
|
||||
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
|
||||
|
||||
// save old positions and velocities for virial
|
||||
|
||||
if (evflag) {
|
||||
if (triclinic == 0) {
|
||||
x0 = x[i][0] + xbox*xprd;
|
||||
x1 = x[i][1] + ybox*yprd;
|
||||
x2 = x[i][2] + zbox*zprd;
|
||||
} else {
|
||||
x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
|
||||
x1 = x[i][1] + ybox*yprd + zbox*yz;
|
||||
x2 = x[i][2] + zbox*zprd;
|
||||
}
|
||||
}
|
||||
|
||||
v0 = v[i][0];
|
||||
v1 = v[i][1];
|
||||
v2 = v[i][2];
|
||||
|
||||
// x = displacement from center-of-mass, based on body orientation
|
||||
// v = vcm + omega around center-of-mass
|
||||
// vest = 2*v - v_old
|
||||
|
||||
MathExtra::matvec (ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],displace[i],x[i]);
|
||||
|
||||
v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] +
|
||||
vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] +
|
||||
vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] +
|
||||
vcm[ibody][2];
|
||||
|
||||
vest[i][0] = 2*v[i][0] - v0;
|
||||
vest[i][1] = 2*v[i][1] - v1;
|
||||
vest[i][2] = 2*v[i][2] - v2;
|
||||
|
||||
// add center of mass to displacement
|
||||
// map back into periodic box via xbox,ybox,zbox
|
||||
// for triclinic, add in box tilt factors as well
|
||||
|
||||
if (triclinic == 0) {
|
||||
x[i][0] += xcm[ibody][0] - xbox*xprd;
|
||||
x[i][1] += xcm[ibody][1] - ybox*yprd;
|
||||
x[i][2] += xcm[ibody][2] - zbox*zprd;
|
||||
} else {
|
||||
x[i][0] += xcm[ibody][0] - xbox*xprd - ybox*xy - zbox*xz;
|
||||
x[i][1] += xcm[ibody][1] - ybox*yprd - zbox*yz;
|
||||
x[i][2] += xcm[ibody][2] - zbox*zprd;
|
||||
}
|
||||
|
||||
// virial = unwrapped coords dotted into body constraint force
|
||||
// body constraint force = implied force due to v change minus f external
|
||||
// assume f does not include forces internal to body
|
||||
// 1/2 factor b/c final_integrate contributes other half
|
||||
// assume per-atom contribution is due to constraint force on that atom
|
||||
|
||||
if (evflag) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
|
||||
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
|
||||
fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
|
||||
|
||||
vr[0] = 0.5*x0*fc0;
|
||||
vr[1] = 0.5*x1*fc1;
|
||||
vr[2] = 0.5*x2*fc2;
|
||||
vr[3] = 0.5*x0*fc1;
|
||||
vr[4] = 0.5*x0*fc2;
|
||||
vr[5] = 0.5*x1*fc2;
|
||||
|
||||
v_tally(1,&i,1.0,vr);
|
||||
}
|
||||
}
|
||||
|
||||
// set orientation, omega, angmom of each extended particle
|
||||
|
||||
if (extended) {
|
||||
// TBD
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set space-frame velocity of each atom in a rigid body
|
||||
set omega and angmom of extended particles
|
||||
v = Vcm + (W cross (x - Xcm))
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixRigidMeso::set_v () {
|
||||
int xbox,ybox,zbox;
|
||||
double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone;
|
||||
double xy,xz,yz;
|
||||
double ione[3],exone[3],eyone[3],ezone[3],delta[3],vr[6];
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
if (triclinic) {
|
||||
xy = domain->xy;
|
||||
xz = domain->xz;
|
||||
yz = domain->yz;
|
||||
}
|
||||
|
||||
// set v of each atom
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (body[i] < 0) continue;
|
||||
|
||||
// half-step update of particle internal energy and density
|
||||
e[i] += dtf * de[i];
|
||||
rho[i] += dtf * drho[i];
|
||||
|
||||
const int ibody = body[i];
|
||||
|
||||
MathExtra::matvec (ex_space[ibody],ey_space[ibody],
|
||||
ez_space[ibody],displace[i],delta);
|
||||
|
||||
// save old velocities for virial
|
||||
|
||||
if (evflag) {
|
||||
v0 = v[i][0];
|
||||
v1 = v[i][1];
|
||||
v2 = v[i][2];
|
||||
}
|
||||
|
||||
v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] +
|
||||
vcm[ibody][0];
|
||||
v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] +
|
||||
vcm[ibody][1];
|
||||
v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] +
|
||||
vcm[ibody][2];
|
||||
|
||||
// virial = unwrapped coords dotted into body constraint force
|
||||
// body constraint force = implied force due to v change minus f external
|
||||
// assume f does not include forces internal to body
|
||||
// 1/2 factor b/c initial_integrate contributes other half
|
||||
// assume per-atom contribution is due to constraint force on that atom
|
||||
|
||||
if (evflag) {
|
||||
if (rmass) massone = rmass[i];
|
||||
else massone = mass[type[i]];
|
||||
fc0 = massone*(v[i][0] - v0)/dtf - f[i][0];
|
||||
fc1 = massone*(v[i][1] - v1)/dtf - f[i][1];
|
||||
fc2 = massone*(v[i][2] - v2)/dtf - f[i][2];
|
||||
|
||||
xbox = (xcmimage[i] & IMGMASK) - IMGMAX;
|
||||
ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX;
|
||||
|
||||
if (triclinic == 0) {
|
||||
x0 = x[i][0] + xbox*xprd;
|
||||
x1 = x[i][1] + ybox*yprd;
|
||||
x2 = x[i][2] + zbox*zprd;
|
||||
} else {
|
||||
x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz;
|
||||
x1 = x[i][1] + ybox*yprd + zbox*yz;
|
||||
x2 = x[i][2] + zbox*zprd;
|
||||
}
|
||||
|
||||
vr[0] = 0.5*x0*fc0;
|
||||
vr[1] = 0.5*x1*fc1;
|
||||
vr[2] = 0.5*x2*fc2;
|
||||
vr[3] = 0.5*x0*fc1;
|
||||
vr[4] = 0.5*x0*fc2;
|
||||
vr[5] = 0.5*x1*fc2;
|
||||
|
||||
v_tally(1,&i,1.0,vr);
|
||||
}
|
||||
}
|
||||
|
||||
// set omega, angmom of each extended particle
|
||||
|
||||
if (extended) {
|
||||
// TBD
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return attributes of a rigid body
|
||||
19 values per body
|
||||
xcm = 0,1,2; vcm = 3,4,5; fcm = 6,7,8;
|
||||
quat = 9,10,11,12; omega = 13,14,15; torque = 16,17,18;
|
||||
inertia = 19,20,21; angmom = 22,23,24;
|
||||
image = 25,26,27
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixRigidMeso::compute_array (int i, int j) {
|
||||
if (j < 3) return xcm[i][j];
|
||||
if (j < 6) return vcm[i][j-3];
|
||||
if (j < 9) return fcm[i][j-6];
|
||||
if (j < 13) return quat[i][j-9];
|
||||
if (j < 16) return omega[i][j-13];
|
||||
if (j < 19) return torque[i][j-16];
|
||||
if (j < 22) return inertia[i][j-19];
|
||||
if (j < 25) return angmom[i][j-22];
|
||||
if (j == 25) return (imagebody[i] & IMGMASK) - IMGMAX;
|
||||
if (j == 26) return (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
return (imagebody[i] >> IMG2BITS) - IMGMAX;
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
/* -*- 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
|
||||
|
||||
FixStyle(rigid/meso,FixRigidMeso)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_RIGID_MESO_H
|
||||
#define LMP_FIX_RIGID_MESO_H
|
||||
|
||||
#include "fix_rigid.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixRigidMeso : public FixRigid {
|
||||
public:
|
||||
FixRigidMeso (class LAMMPS *, int, char **);
|
||||
~FixRigidMeso ();
|
||||
int setmask ();
|
||||
void setup (int);
|
||||
void initial_integrate (int);
|
||||
void final_integrate ();
|
||||
double compute_scalar () {}
|
||||
double compute_array (int, int);
|
||||
|
||||
protected:
|
||||
void set_xv ();
|
||||
void set_v ();
|
||||
double **conjqm; // conjugate quaternion momentum
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: fix rigid/meso command requires atom_style with both energy and density
|
||||
|
||||
You should use atom_style meso with this fix
|
||||
|
||||
E: Can not use thermostat with fix rigid/meso
|
||||
|
||||
Self-explanatory
|
||||
|
||||
E: Can not use barostat with fix rigid/meso
|
||||
|
||||
Self-explanatory
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,321 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author:
|
||||
Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com
|
||||
|
||||
references: Espanol and Revenga, Phys Rev E 67, 026705 (2003)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include "pair_sdpd_taitwater_isothermal.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#ifndef USE_ZEST
|
||||
#include "random_mars.h"
|
||||
#endif
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
static const double sqrt_2_inv = std::sqrt(0.5);
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSDPDTaitwaterIsothermal::PairSDPDTaitwaterIsothermal (LAMMPS *lmp)
|
||||
: Pair (lmp) {
|
||||
restartinfo = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSDPDTaitwaterIsothermal::~PairSDPDTaitwaterIsothermal () {
|
||||
if (allocated) {
|
||||
memory->destroy (setflag);
|
||||
memory->destroy (cutsq);
|
||||
|
||||
memory->destroy (cut);
|
||||
memory->destroy (rho0);
|
||||
memory->destroy (soundspeed);
|
||||
memory->destroy (B);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSDPDTaitwaterIsothermal::compute (int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc;
|
||||
double h, ih, ihsq, velx, vely, velz;
|
||||
double rsq, tmp, wfd, delVdotDelR, deltaE;
|
||||
double prefactor, wiener[3][3], f_random[3];
|
||||
|
||||
if (eflag || vflag) ev_setup (eflag, vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **v = atom->vest;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *de = atom->de;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
int dimension = domain->dimension;
|
||||
double dtinv = 1.0 / update->dt;
|
||||
double kBoltzmann = force->boltz;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
// compute pressure of atom i with Tait EOS
|
||||
tmp = rho[i] / rho0[itype];
|
||||
fi = tmp * tmp * tmp;
|
||||
fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
double r = sqrt (rsq);
|
||||
wfd = h - r;
|
||||
if (dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// (1) using delV . delX instead of delV . (delX/r) and
|
||||
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
// compute pressure of atom j with Tait EOS
|
||||
tmp = rho[j] / rho0[jtype];
|
||||
fj = tmp * tmp * tmp;
|
||||
fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]);
|
||||
|
||||
velx=vxtmp - v[j][0];
|
||||
vely=vytmp - v[j][1];
|
||||
velz=vztmp - v[j][2];
|
||||
|
||||
// dot product of velocity delta and distance vector
|
||||
delVdotDelR = delx * velx + dely * vely + delz * velz;
|
||||
|
||||
// Espanol Viscosity (Espanol, 2003)
|
||||
|
||||
fvisc = (5. / 3.) * viscosity * imass * jmass * wfd / (rho[i]*rho[j]);
|
||||
|
||||
// total pair force
|
||||
fpair = -imass * jmass * (fi + fj) * wfd;
|
||||
|
||||
// random force calculation
|
||||
// independent increments of a Wiener process matrix
|
||||
#ifdef USE_ZEST
|
||||
wiener[0][0] = gaussian (generator);
|
||||
wiener[1][1] = gaussian (generator);
|
||||
wiener[2][2] = gaussian (generator);
|
||||
|
||||
wiener[0][1] = wiener[1][0] = sqrt_2_inv * gaussian (generator);
|
||||
wiener[0][2] = wiener[2][0] = sqrt_2_inv * gaussian (generator);
|
||||
wiener[1][2] = wiener[2][1] = sqrt_2_inv * gaussian (generator);
|
||||
#else
|
||||
wiener[0][0] = random->gaussian ();
|
||||
wiener[1][1] = random->gaussian ();
|
||||
wiener[2][2] = random->gaussian ();
|
||||
|
||||
wiener[0][1] = wiener[1][0] = sqrt_2_inv * random->gaussian ();
|
||||
wiener[0][2] = wiener[2][0] = sqrt_2_inv * random->gaussian ();
|
||||
wiener[1][2] = wiener[2][1] = sqrt_2_inv * random->gaussian ();
|
||||
#endif
|
||||
|
||||
prefactor = sqrt (-4. * kBoltzmann*temperature * fvisc * dtinv) / r;
|
||||
|
||||
f_random[0] = prefactor * (wiener[0][0]*delx + wiener[0][1]*dely + wiener[0][2]*delz);
|
||||
f_random[1] = prefactor * (wiener[1][0]*delx + wiener[1][1]*dely + wiener[1][2]*delz);
|
||||
f_random[2] = prefactor * (wiener[2][0]*delx + wiener[2][1]*dely + wiener[2][2]*delz);
|
||||
|
||||
f[i][0] += delx * fpair + (velx + delx * delVdotDelR / rsq) * fvisc + f_random[0];
|
||||
f[i][1] += dely * fpair + (vely + dely * delVdotDelR / rsq) * fvisc + f_random[1];
|
||||
f[i][2] += delz * fpair + (velz + delz * delVdotDelR / rsq) * fvisc + f_random[2];
|
||||
|
||||
// and change in density
|
||||
drho[i] += jmass * delVdotDelR * wfd;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair + (velx + delx * delVdotDelR / rsq) * fvisc + f_random[0];
|
||||
f[j][1] -= dely * fpair + (vely + dely * delVdotDelR / rsq) * fvisc + f_random[1];
|
||||
f[j][2] -= delz * fpair + (velz + delz * delVdotDelR / rsq) * fvisc + f_random[2];
|
||||
drho[j] += imass * delVdotDelR * wfd;
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally (i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute ();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSDPDTaitwaterIsothermal::allocate () {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create (setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create (cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create (rho0, n + 1, "pair:rho0");
|
||||
memory->create (soundspeed, n + 1, "pair:soundspeed");
|
||||
memory->create (B, n + 1, "pair:B");
|
||||
memory->create (cut, n + 1, n + 1, "pair:cut");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) {
|
||||
if (narg != 2 && narg != 3) error->all (FLERR, "Illegal number of setting "
|
||||
"arguments for pair_style sdpd/taitwater/morris/isothermal");
|
||||
|
||||
temperature = force->numeric (FLERR, arg[0]);
|
||||
viscosity = force->numeric (FLERR, arg[1]);
|
||||
|
||||
if (temperature <= 0) error->all (FLERR, "Temperature must be positive");
|
||||
if (viscosity <= 0) error->all (FLERR, "Viscosity must be positive");
|
||||
|
||||
// seed is immune to underflow/overflow because it is unsigned
|
||||
seed = comm->nprocs + comm->me + atom->nlocal;
|
||||
if (narg == 3) seed += force->inumeric (FLERR, arg[2]);
|
||||
#ifdef USE_ZEST
|
||||
generator.seed (seed);
|
||||
#else
|
||||
random = new RanMars (lmp, seed);
|
||||
#endif
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) {
|
||||
if (narg != 5) error->all (FLERR, "Incorrect args for pair_style "
|
||||
"sph/taitwater/morris coefficients");
|
||||
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds (FLERR, arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds (FLERR, arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double rho0_one = force->numeric (FLERR,arg[2]);
|
||||
double soundspeed_one = force->numeric (FLERR,arg[3]);
|
||||
double cut_one = force->numeric (FLERR,arg[4]);
|
||||
double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
|
||||
|
||||
if (rho0_one <= 0) error->all (FLERR, "Density must be positive");
|
||||
if (soundspeed_one <= 0) error->all (FLERR, "Sound speed must be positive");
|
||||
if (cut_one <= 0) error->all (FLERR, "Cutoff must be positive");
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
rho0[i] = rho0_one;
|
||||
soundspeed[i] = soundspeed_one;
|
||||
B[i] = B_one;
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
cut[i][j] = cut_one;
|
||||
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSDPDTaitwaterIsothermal::init_one (int i, int j) {
|
||||
if (setflag[i][j] == 0)
|
||||
error->all(FLERR,"Not all pair sph/taitwater/morris coeffs are not set");
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSDPDTaitwaterIsothermal::single (int /*i*/, int /*j*/, int /*itype*/,
|
||||
int /*jtype*/, double /*rsq*/, double /*factor_coul*/,
|
||||
double /*factor_lj*/, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
|
@ -0,0 +1,60 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(sdpd/taitwater/isothermal,PairSDPDTaitwaterIsothermal)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_SDPD_TAITWATER_MORRIS_ISOTHERMAL_H
|
||||
#define LMP_PAIR_SDPD_TAITWATER_MORRIS_ISOTHERMAL_H
|
||||
|
||||
#include "pair.h"
|
||||
#ifdef USE_ZEST
|
||||
#include <random>
|
||||
#include "zest.hpp"
|
||||
#endif
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSDPDTaitwaterIsothermal : public Pair {
|
||||
public:
|
||||
PairSDPDTaitwaterIsothermal (class LAMMPS *);
|
||||
virtual ~PairSDPDTaitwaterIsothermal ();
|
||||
virtual void compute (int, int);
|
||||
void settings (int, char **);
|
||||
void coeff (int, char **);
|
||||
virtual double init_one (int, int);
|
||||
virtual double single (int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double viscosity, temperature;
|
||||
double *rho0, *soundspeed, *B;
|
||||
double **cut;
|
||||
|
||||
void allocate ();
|
||||
|
||||
unsigned int seed;
|
||||
#ifdef USE_ZEST
|
||||
std::mt19937_64 generator;
|
||||
Ziggurat<zest::StandardNormal,std::mt19937_64> gaussian;
|
||||
#else
|
||||
class RanMars *random;
|
||||
#endif
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue