Merge pull request #399 from rbberger/docs_spelling_fixes
Correct spelling errors in documentation
This commit is contained in:
sjplimp
@ -85,7 +85,7 @@ Kappa = 3.45
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(4) in.mp
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dQ = 15087 / 100 / 18.82^2 / 2
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15087 = cummulative delta energy, tallied by fix thermal/conductivity
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15087 = cumulative delta energy, tallied by fix thermal/conductivity
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100 = 20,000 steps at 0.005 tau timestep = run time in tau
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xy box area = 18.82^2
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divide by 2 since energy flux goes in 2 directions due to periodic z
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@ -93,7 +93,7 @@ peri: Peridynamic model of cylinder impacted by indenter
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pour: pouring of granular particles into a 3d box, then chute flow
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prd: parallel replica dynamics of vacancy diffusion in bulk Si
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python: use of PYTHON package to invoke Python code from input script
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qeq: use of QEQ pacakge for charge equilibration
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qeq: use of QEQ package for charge equilibration
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reax: RDX and TATB models using the ReaxFF
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rigid: rigid bodies modeled as independent or coupled
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shear: sideways shear applied to 2d solid, with and without a void
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@ -65,7 +65,7 @@ elastic:
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in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms
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in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation
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in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field
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in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field
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in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
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in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
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in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
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in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
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@ -146,7 +146,7 @@ elastic:
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in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms
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in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation
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in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field
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in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field
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in.cnt_electrostatic2 - Mechanical response of CNT with self-consistent charge density and electric field
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in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
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in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
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in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at 40.
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# temperature is initially 20 everywhere and the left boundary BC is fixed at 40.
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# The result should show heat diffusing through the FEM to the MD and back out
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# to the FEM on the right. Insufficient time is captured to reach the linear
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# steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests thermostats applied in all atom simulations. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into an MD region at a fixed temperature at one end. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing the boundaries should be observed,
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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# AtC Thermal Coupling
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# This benchmark tests thermostats applied in all atom simulations. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -1,6 +1,6 @@
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#AtC Thermal Coupling
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# This benchmark tests heat conducting into and out of the MD region. The
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# temperature is intially 20 everywhere and the left boundary BC is fixed at
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# temperature is initially 20 everywhere and the left boundary BC is fixed at
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# 40.# The result should show heat diffusing through the FEM to the MD and back
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# out # to the FEM on the right. Insufficient time is captured to reach the
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# linear # steady state, but heat crossing both boundaries should be observed.
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@ -67,7 +67,7 @@ timestep 0.0006
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particles specified through FluidAtoms
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# (however, this fix does not explicity apply a force back on to these
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the viscous_lb fix).
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# Use the standard LB integration scheme, a fluid density = 1.0,
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# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
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@ -61,7 +61,7 @@ group FluidAtoms type 2
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particles specified through FluidAtoms
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# (however, this fix does not explicity apply a force back on to these
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the viscous_lb fix).
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# Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid
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# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
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@ -61,7 +61,7 @@ group FluidAtoms type 2
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particles specified through FluidAtoms
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# (however, this fix does not explicity apply a force back on to these
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the rigid_pc_sphere
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# fix).
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# Use the LB integration scheme of Ollila et. al. (for stability reasons,
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@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box
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#----------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# All of the particles in the simulation apply a force to the fluid.
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# (however, this fix does not explicity apply a force back on to these
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the viscous_lb fix.
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# Use the standard LB integration scheme, a fluid density = 1.0,
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# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
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@ -54,7 +54,7 @@ velocity all set 0.0 0.0 0.0 units box
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#----------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# All of the particles in the simulation apply a force to the fluid.
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# (however, this fix does not explicity apply a force back on to these
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# (however, this fix does not explicitly apply a force back on to these
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# particles...this is accomplished through the use of the rigid_pc_sphere
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# fix).
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# Use the LB integration scheme of Ollila et. al. (for stability reasons,
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File diff suppressed because it is too large
Load Diff
@ -1,107 +1,107 @@
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#===========================================================================#
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# polymer test #
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# #
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# Run consists of a lone 32-bead coarse-grained polymer #
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# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
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# #
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# Here, gamma (used in the calculation of the monomer-fluid interaction #
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# force) is set by the user (gamma = 0.03 for this simulation...this #
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# value has been calibrated a priori through simulations of the drag #
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# force acting on a single particle of the same radius). #
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# Sample output from this run can be found in the file: #
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# 'dump.polymer.lammpstrj' #
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# and viewed using, e.g., the VMD software. #
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# #
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#===========================================================================#
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units nano
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dimension 3
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boundary p p p
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atom_style hybrid molecular
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special_bonds fene
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read_data data.polymer
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#----------------------------------------------------------------------------
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# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
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# to ensure that the particles belonging to a given processor remain inside
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# that processors lattice-Boltzmann grid.
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#----------------------------------------------------------------------------
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neighbor 0.5 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude type 2 2
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neigh_modify exclude type 2 1
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#----------------------------------------------------------------------------
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# Implement a hard-sphere interaction between the particles at the center of
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# each monomer (use a truncated and shifted Lennard-Jones potential).
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#----------------------------------------------------------------------------
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bond_style fene
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bond_coeff 1 60.0 2.25 4.14195 1.5
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pair_style lj/cut 1.68369
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pair_coeff 1 1 4.14195 1.5 1.68369
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pair_coeff 1 2 4.14195 1.5 1.68369
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pair_coeff 2 2 0 1.0
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mass * 0.000000771064
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timestep 0.00003
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#----------------------------------------------------------------------------
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# ForceAtoms are the particles at the center of each monomer which
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# do not interact with the fluid, but are used to implement the hard-sphere
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# interactions.
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# FluidAtoms are the particles representing the surface of the monomer
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# which do interact with the fluid. Monomer surface is shell of radius 0.7
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#----------------------------------------------------------------------------
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group ForceAtoms type 1
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group FluidAtoms type 2
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particles specified through FluidAtoms
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# (however, this fix does not explicity apply a force back on to these
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# particles. This is accomplished through the use of the lb/viscous
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# fix).
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# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
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# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
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# dm=0.0000166368.
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# Use the default method to calculate the interaction force between the
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# particles and the fluid. This calculation requires the surface area
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# of the composite object represented by each particle node. By default
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# this area is assumed equal to dx*dx; however, since this is not the case
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# here, it is input through the setArea keyword (i.e. particles of type 2
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# correspond to a surface area of 0.2025=4 Pi R^2/N ).
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# Use the trilinear interpolation stencil to distribute the force from
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# a given particle onto the fluid mesh (results in a smaller hydrodynamic
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# radius than if the Peskin stencil is used).
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# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
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# seed=15003). This enables the particles to undergo Brownian motion in
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# the fluid.
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#----------------------------------------------------------------------------
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fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
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#----------------------------------------------------------------------------
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# Apply the force from the fluid to the particles, and integrate their
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# motion, constraining them to move and rotate together as a single rigid
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# spherical object.
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# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
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# shell) should move and rotate together, this fix is applied to all of
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# the atoms in the system. However, since the central atoms should not
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# feel a force due to the fluid, they are excluded from the fluid force
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# calculation.
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#----------------------------------------------------------------------------
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fix 2 FluidAtoms lb/viscous
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fix 3 all rigid molecule
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#----------------------------------------------------------------------------
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# To ensure that numerical errors do not lead to a buildup of momentum in the
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# system, the momentum_lb fix is used every 10000 timesteps to zero out the
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# total (particle plus fluid) momentum in the system.
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#----------------------------------------------------------------------------
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fix 4 all lb/momentum 10000 linear 1 1 1
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#----------------------------------------------------------------------------
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# Write position and velocity coordinates into a file every 2000 time steps.
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#----------------------------------------------------------------------------
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dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
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run 2000001
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#===========================================================================#
|
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# polymer test #
|
||||
# #
|
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# Run consists of a lone 32-bead coarse-grained polymer #
|
||||
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# Here, gamma (used in the calculation of the monomer-fluid interaction #
|
||||
# force) is set by the user (gamma = 0.03 for this simulation...this #
|
||||
# value has been calibrated a priori through simulations of the drag #
|
||||
# force acting on a single particle of the same radius). #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# 'dump.polymer.lammpstrj' #
|
||||
# and viewed using, e.g., the VMD software. #
|
||||
# #
|
||||
#===========================================================================#
|
||||
|
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units nano
|
||||
dimension 3
|
||||
boundary p p p
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||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data data.polymer
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each monomer (use a truncated and shifted Lennard-Jones potential).
|
||||
#----------------------------------------------------------------------------
|
||||
bond_style fene
|
||||
bond_coeff 1 60.0 2.25 4.14195 1.5
|
||||
pair_style lj/cut 1.68369
|
||||
pair_coeff 1 1 4.14195 1.5 1.68369
|
||||
pair_coeff 1 2 4.14195 1.5 1.68369
|
||||
pair_coeff 2 2 0 1.0
|
||||
|
||||
mass * 0.000000771064
|
||||
timestep 0.00003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each monomer which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the monomer
|
||||
# which do interact with the fluid. Monomer surface is shell of radius 0.7
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
group FluidAtoms type 2
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicitly apply a force back on to these
|
||||
# particles. This is accomplished through the use of the lb/viscous
|
||||
# fix).
|
||||
# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
|
||||
# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
|
||||
# dm=0.0000166368.
|
||||
# Use the default method to calculate the interaction force between the
|
||||
# particles and the fluid. This calculation requires the surface area
|
||||
# of the composite object represented by each particle node. By default
|
||||
# this area is assumed equal to dx*dx; however, since this is not the case
|
||||
# here, it is input through the setArea keyword (i.e. particles of type 2
|
||||
# correspond to a surface area of 0.2025=4 Pi R^2/N ).
|
||||
# Use the trilinear interpolation stencil to distribute the force from
|
||||
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
|
||||
# radius than if the Peskin stencil is used).
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=15003). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object.
|
||||
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
|
||||
# shell) should move and rotate together, this fix is applied to all of
|
||||
# the atoms in the system. However, since the central atoms should not
|
||||
# feel a force due to the fluid, they are excluded from the fluid force
|
||||
# calculation.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 FluidAtoms lb/viscous
|
||||
fix 3 all rigid molecule
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# To ensure that numerical errors do not lead to a buildup of momentum in the
|
||||
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
|
||||
# total (particle plus fluid) momentum in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 4 all lb/momentum 10000 linear 1 1 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Write position and velocity coordinates into a file every 2000 time steps.
|
||||
#----------------------------------------------------------------------------
|
||||
|
||||
dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
|
||||
run 2000001
|
||||
|
||||
@ -1,105 +1,105 @@
|
||||
#===========================================================================#
|
||||
# polymer test #
|
||||
# #
|
||||
# Run consists of a lone 32-bead coarse-grained polymer #
|
||||
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# Here, gamma (used in the calculation of the monomer-fluid interaction #
|
||||
# force) is set by the user (gamma = 0.03 for this simulation...this #
|
||||
# value has been calibrated a priori through simulations of the drag #
|
||||
# force acting on a single particle of the same radius). #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# 'dump.polymer.lammpstrj' #
|
||||
# and viewed using, e.g., the VMD software. #
|
||||
# #
|
||||
# Santtu Ollila #
|
||||
# santtu.ollila@aalto.fi #
|
||||
# Aalto University #
|
||||
# August 14, 2013 #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data data.polymer
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each monomer (use a truncated and shifted Lennard-Jones potential).
|
||||
#----------------------------------------------------------------------------
|
||||
bond_style fene
|
||||
bond_coeff 1 60.0 2.25 4.14195 1.5
|
||||
pair_style lj/cut 1.68369
|
||||
pair_coeff 1 1 4.14195 1.5 1.68369
|
||||
pair_coeff 1 2 4.14195 1.5 1.68369
|
||||
pair_coeff 2 2 0 1.0
|
||||
|
||||
mass * 0.000000771064
|
||||
timestep 0.00003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each monomer which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the monomer
|
||||
# which do interact with the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
group FluidAtoms type 2
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicity apply a force back on to these
|
||||
# particles. This is accomplished through the use of the rigid_pc_sphere
|
||||
# fix).
|
||||
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
|
||||
# this integration scheme should be used when a large user set value for
|
||||
# gamma is specified), a fluid viscosity = 0.023333333,
|
||||
# fluid density= 0.0000166368,
|
||||
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=15003). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object.
|
||||
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
|
||||
# shell) should move and rotate together, this fix is applied to all of
|
||||
# the atoms in the system. However, since the central atoms should not
|
||||
# feel a force due to the fluid, they are excluded from the force
|
||||
# calculation through the use of the 'innerNodes' keyword.
|
||||
# NOTE: This fix should only be used when the user specifies a value for
|
||||
# gamma (through the setGamma keyword) in the lb_fluid fix.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# To ensure that numerical errors do not lead to a buildup of momentum in the
|
||||
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
|
||||
# total (particle plus fluid) momentum in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 3 all lb/momentum 10000 linear 1 1 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Write position and velocity coordinates into a file every 2000 time steps.
|
||||
#----------------------------------------------------------------------------
|
||||
|
||||
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
|
||||
run 2000001
|
||||
#===========================================================================#
|
||||
# polymer test #
|
||||
# #
|
||||
# Run consists of a lone 32-bead coarse-grained polymer #
|
||||
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
|
||||
# #
|
||||
# Here, gamma (used in the calculation of the monomer-fluid interaction #
|
||||
# force) is set by the user (gamma = 0.03 for this simulation...this #
|
||||
# value has been calibrated a priori through simulations of the drag #
|
||||
# force acting on a single particle of the same radius). #
|
||||
# Sample output from this run can be found in the file: #
|
||||
# 'dump.polymer.lammpstrj' #
|
||||
# and viewed using, e.g., the VMD software. #
|
||||
# #
|
||||
# Santtu Ollila #
|
||||
# santtu.ollila@aalto.fi #
|
||||
# Aalto University #
|
||||
# August 14, 2013 #
|
||||
#===========================================================================#
|
||||
|
||||
units nano
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style hybrid molecular
|
||||
special_bonds fene
|
||||
read_data data.polymer
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
|
||||
# to ensure that the particles belonging to a given processor remain inside
|
||||
# that processors lattice-Boltzmann grid.
|
||||
#----------------------------------------------------------------------------
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude type 2 2
|
||||
neigh_modify exclude type 2 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Implement a hard-sphere interaction between the particles at the center of
|
||||
# each monomer (use a truncated and shifted Lennard-Jones potential).
|
||||
#----------------------------------------------------------------------------
|
||||
bond_style fene
|
||||
bond_coeff 1 60.0 2.25 4.14195 1.5
|
||||
pair_style lj/cut 1.68369
|
||||
pair_coeff 1 1 4.14195 1.5 1.68369
|
||||
pair_coeff 1 2 4.14195 1.5 1.68369
|
||||
pair_coeff 2 2 0 1.0
|
||||
|
||||
mass * 0.000000771064
|
||||
timestep 0.00003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# ForceAtoms are the particles at the center of each monomer which
|
||||
# do not interact with the fluid, but are used to implement the hard-sphere
|
||||
# interactions.
|
||||
# FluidAtoms are the particles representing the surface of the monomer
|
||||
# which do interact with the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
group ForceAtoms type 1
|
||||
group FluidAtoms type 2
|
||||
|
||||
#---------------------------------------------------------------------------
|
||||
# Create a lattice-Boltzmann fluid covering the simulation domain.
|
||||
# This fluid feels a force due to the particles specified through FluidAtoms
|
||||
# (however, this fix does not explicitly apply a force back on to these
|
||||
# particles. This is accomplished through the use of the rigid_pc_sphere
|
||||
# fix).
|
||||
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
|
||||
# this integration scheme should be used when a large user set value for
|
||||
# gamma is specified), a fluid viscosity = 0.023333333,
|
||||
# fluid density= 0.0000166368,
|
||||
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
|
||||
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
|
||||
# seed=15003). This enables the particles to undergo Brownian motion in
|
||||
# the fluid.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Apply the force from the fluid to the particles, and integrate their
|
||||
# motion, constraining them to move and rotate together as a single rigid
|
||||
# spherical object.
|
||||
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
|
||||
# shell) should move and rotate together, this fix is applied to all of
|
||||
# the atoms in the system. However, since the central atoms should not
|
||||
# feel a force due to the fluid, they are excluded from the force
|
||||
# calculation through the use of the 'innerNodes' keyword.
|
||||
# NOTE: This fix should only be used when the user specifies a value for
|
||||
# gamma (through the setGamma keyword) in the lb_fluid fix.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# To ensure that numerical errors do not lead to a buildup of momentum in the
|
||||
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
|
||||
# total (particle plus fluid) momentum in the system.
|
||||
#----------------------------------------------------------------------------
|
||||
fix 3 all lb/momentum 10000 linear 1 1 1
|
||||
|
||||
#----------------------------------------------------------------------------
|
||||
# Write position and velocity coordinates into a file every 2000 time steps.
|
||||
#----------------------------------------------------------------------------
|
||||
|
||||
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
|
||||
run 2000001
|
||||
|
||||
@ -24,7 +24,7 @@ pair_coeff 1 1 dpd 60.0 4.5 1.0
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0
|
||||
|
||||
# auto normalization of thermo quantites is turned off by pair srp
|
||||
# auto normalization of thermo quantities is turned off by pair srp
|
||||
# just divide by natoms
|
||||
variable natoms equal count(all)
|
||||
variable nPotEng equal c_thermo_pe/v_natoms
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
This directory illustrates the usage of fix-phonon to calculate the dynamical
|
||||
matrix as well as phonon dispersion curve for FCC Cu based on EAM potentail.
|
||||
matrix as well as phonon dispersion curve for FCC Cu based on EAM potential.
|
||||
|
||||
The files under this directory:
|
||||
|
||||
|
||||
@ -1,5 +1,5 @@
|
||||
This directory illustrates the usage of fix-phonon to calculate the dynamical
|
||||
matrix as well as phonon dispersion curve for Graphene based on a Tersoff potentail.
|
||||
matrix as well as phonon dispersion curve for Graphene based on a Tersoff potential.
|
||||
|
||||
The files under this directory:
|
||||
|
||||
|
||||
@ -3,4 +3,4 @@ Examples and tests for USER-TALLY compute styles.
|
||||
The examples in this directory show where and how compute tally styles
|
||||
are equivalent to other facilities in LAMMPS and thus they can also be
|
||||
used to validate their correct function. Various columns should have
|
||||
equivalent or idential output as indicated in the input.
|
||||
equivalent or identical output as indicated in the input.
|
||||
|
||||
@ -24,7 +24,7 @@ times; the G-K and Einstein systems need to run longer to generate good statisti
|
||||
|
||||
The scripts were all run on a single processor. They all run in a
|
||||
minute or so and produce the accompanying log files and profile files
|
||||
(for velocity or momemtum flux).
|
||||
(for velocity or momentum flux).
|
||||
|
||||
See the Movies page of the LAMMPS web site
|
||||
(http://lammps.sandia.gov/movies.html), for animations of the NEMD
|
||||
@ -74,7 +74,7 @@ eta = 0.997 = running average output as last log file column
|
||||
|
||||
eta is computed directly within the script, by performing a time
|
||||
integration of the formula discussed in Section 6.21 of the manual,
|
||||
analagous to the formula for thermal conductivity given on the compute
|
||||
analogous to the formula for thermal conductivity given on the compute
|
||||
heat/flux doc page - the resulting value prints at the end of the run
|
||||
and is in the log file
|
||||
|
||||
@ -84,7 +84,7 @@ eta = 1.07
|
||||
|
||||
eta is computed directly within the script, by performing a time
|
||||
integration of the formula discussed in Section 6.21 of the manual,
|
||||
analagous to the formula for thermal conductivity given on the compute
|
||||
analogous to the formula for thermal conductivity given on the compute
|
||||
heat/flux doc page - the resulting value prints at the end of the run
|
||||
and is in the log file
|
||||
|
||||
|
||||
@ -130,7 +130,7 @@ lmp_kokkos_omp -k on t 1 -sf kk -pk kokkos neigh half < in.lj
|
||||
mpirun -np 2 lmp_kokkos_omp -k on t 4 -sf kk < in.lj # 2 MPI, 4 thread/MPI
|
||||
|
||||
Note that when running with just 1 thread/MPI, "-pk kokkos neigh half"
|
||||
was speficied to use half neighbor lists which are faster when running
|
||||
was specified to use half neighbor lists which are faster when running
|
||||
on just 1 thread.
|
||||
|
||||
** KOKKOS package for CUDA
|
||||
|
||||
Reference in New Issue
Block a user