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formatting corrections and minor tweaks to the Argon viscosity howto

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Axel Kohlmeyer
2022-07-01 09:26:23 -04:00
parent 0157a7d0d3
commit 957a8c85a9
1 changed files with 8 additions and 9 deletions
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15
doc/src/Howto_viscosity.rst
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@ -65,7 +65,7 @@ liquid Ar via the GK formalism:
.. code-block:: LAMMPS .. code-block:: LAMMPS
# Sample LAMMPS input script for viscosity of liquid Ar # Sample LAMMPS input script for viscosity of liquid Ar
units real units real
variable T equal 200.0 # run temperature variable T equal 200.0 # run temperature
@ -107,7 +107,7 @@ liquid Ar via the GK formalism:
# viscosity calculation, switch to NVE if desired # viscosity calculation, switch to NVE if desired
velocity all create $T 102486 mom yes rot yes dist gaussian velocity all create $T 102486 mom yes rot yes dist gaussian
#fix NVT all nvt temp $T $T 10 drag 0.2 fix NVT all nvt temp $T $T 10 drag 0.2
#unfix NVT #unfix NVT
#fix NVE all nve #fix NVE all nve
@ -121,12 +121,11 @@ liquid Ar via the GK formalism:
variable v11 equal trap(f_SS[3])*${scale} variable v11 equal trap(f_SS[3])*${scale}
variable v22 equal trap(f_SS[4])*${scale} variable v22 equal trap(f_SS[4])*${scale}
variable v33 equal trap(f_SS[5])*${scale} variable v33 equal trap(f_SS[5])*${scale}
compute msd all msd com yes thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33 c_msd[*]
run 100000 run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0 variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol variable ndens equal count(all)/vol
print "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3" print "average viscosity: $v [Pa.s] @ $T K, ${ndens} atoms/A^3"
The fifth method is related to the above Green-Kubo method, The fifth method is related to the above Green-Kubo method,
but uses the Einstein formulation, analogous to the Einstein but uses the Einstein formulation, analogous to the Einstein
@ -135,9 +134,9 @@ time-integrated momentum fluxes play the role of Cartesian
coordinates, whose mean-square displacement increases linearly coordinates, whose mean-square displacement increases linearly
with time at sufficiently long times. with time at sufficiently long times.
The sixth is periodic perturbation method. It is also a non-equilibrium MD method. The sixth is the periodic perturbation method, which is also a non-equilibrium MD method.
However, instead of measure the momentum flux in response of applied velocity gradient, However, instead of measuring the momentum flux in response to an applied velocity gradient,
it measures the velocity profile in response of applied stress. it measures the velocity profile in response to applied stress.
A cosine-shaped periodic acceleration is added to the system via the A cosine-shaped periodic acceleration is added to the system via the
:doc:`fix accelerate/cos <fix_accelerate_cos>` command, :doc:`fix accelerate/cos <fix_accelerate_cos>` command,
and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the