diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index f787801c36..10139d907c 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -24,6 +24,11 @@ by subtracting out the streaming velocity of the shearing atoms. The velocity profile or other properties of the fluid can be monitored via the "fix ave/chunk"_fix_ave_chunk.html command. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermostatting generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. + As discussed in the previous section on non-orthogonal simulation boxes, the amount of tilt or skew that can be applied is limited by LAMMPS for computational efficiency to be 1/2 of the parallel box @@ -46,3 +51,9 @@ An alternative method for calculating viscosities is provided via the NEMD simulations can also be used to measure transport properties of a fluid through a pore or channel. Simulations of steady-state flow can be performed using the "fix flow/gauss"_fix_flow_gauss.html command. + +:line + +:link(Daivis-nemd) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index 0e2feb1869..9f7e2f3000 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -43,6 +43,11 @@ nvt/asphere"_fix_nvt_asphere.html thermostat not only translation velocities but also rotational velocities for spherical and aspherical particles. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermostatting generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. + DPD thermostatting alters pairwise interactions in a manner analogous to the per-particle thermostatting of "fix langevin"_fix_langevin.html. @@ -87,3 +92,9 @@ specify them explicitly via the "thermo_style custom"_thermo_style.html command. Or you can use the "thermo_modify"_thermo_modify.html command to re-define what temperature compute is used for default thermodynamic output. + +:line + +:link(Daivis-thermostat) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index 8bcab6dd24..b4e441557d 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -37,6 +37,11 @@ used to shear the fluid in between them, again with some kind of thermostat that modifies only the thermal (non-shearing) components of velocity to prevent the fluid from heating up. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermostatting generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. + In both cases, the velocity profile setup in the fluid by this procedure can be monitored by the "fix ave/chunk"_fix_ave_chunk.html command, which determines grad(Vstream) in the equation above. @@ -131,3 +136,9 @@ mean-square-displacement formulation for self-diffusivity. The time-integrated momentum fluxes play the role of Cartesian coordinates, whose mean-square displacement increases linearly with time at sufficiently long times. + +:line + +:link(Daivis-viscosity) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 29ebeaeef3..d41607e2ed 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -221,8 +221,8 @@ This equation only applies when the box dimensions are equal to those of the reference dimensions. If this is not the case, then the converged stress tensor will not equal that specified by the user. We can resolve this problem by periodically resetting the reference -dimensions. The keyword {nreset_ref} controls how often this is done. -If this keyword is not used, or is given a value of zero, then the +dimensions. The keyword {nreset} controls how often this is done. If +this keyword is not used, or is given a value of zero, then the reference dimensions are set to those of the initial simulation domain and are never changed. A value of {nstep} means that every {nstep} minimization steps, the reference dimensions are set to those of the diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 97a864a231..7a350e48b5 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -63,6 +63,11 @@ implemented in LAMMPS, they are coupled to a Nose/Hoover chain thermostat in a velocity Verlet formulation, closely following the implementation used for the "fix nvt"_fix_nh.html command. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermostatting generally, for both simple and complex fluids, +e.g. molecular systems. The latter can be tricky to do correctly. + Additional parameters affecting the thermostat are specified by keywords and values documented with the "fix nvt"_fix_nh.html command. See, for example, discussion of the {temp} and {drag} @@ -177,3 +182,7 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. :link(Daivis) [(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). + +:link(Daivis-sllod) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_shake.txt b/doc/src/fix_shake.txt index 77bb5794f6..5c11f96b98 100644 --- a/doc/src/fix_shake.txt +++ b/doc/src/fix_shake.txt @@ -214,8 +214,10 @@ which can lead to poor energy conservation. You can test for this in your system by running a constant NVE simulation with a particular set of SHAKE parameters and monitoring the energy versus time. -SHAKE or RATTLE should not be used to constrain an angle at 180 degrees -(e.g. linear CO2 molecule). This causes numeric difficulties. +SHAKE or RATTLE should not be used to constrain an angle at 180 +degrees (e.g. linear CO2 molecule). This causes numeric difficulties. +You can use "fix rigid or fix rigid/small"_fix_rigid.html instead to +make a linear molecule rigid. [Related commands:] none diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 910fc7f821..73858fc249 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -216,10 +216,10 @@ The "fix box/relax"_fix_box_relax.html command can be used to apply an external pressure to the simulation box and allow it to shrink/expand during the minimization. -Only a few other fixes (typically those that apply force constraints) -are invoked during minimization. See the doc pages for individual -"fix"_fix.html commands to see which ones are relevant. Current -examples of fixes that can be used include: +Only a few other fixes (typically those that add forces) are invoked +during minimization. See the doc pages for individual "fix"_fix.html +commands to see which ones are relevant. Current examples of fixes +that can be used include: "fix addforce"_fix_addforce.html "fix addtorque"_fix_addtorque.html @@ -242,6 +242,11 @@ you MUST enable the "fix_modify"_fix_modify.html {energy} option for that fix. The doc pages for individual "fix"_fix.html commands specify if this should be done. +NOTE: The minimizers in LAMMPS do not allow for bonds (or angles, etc) +to be held fixed while atom coordinates are being relaxed, e.g. via +"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. See more +info in the Restrictions section below. + :line [Restrictions:]