From 983e8bb110a6faeab4675137ccccb51e3f986739 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 11:36:37 -0600 Subject: [PATCH 1/8] doc page clarifications --- doc/src/fix_shake.txt | 6 ++++-- doc/src/minimize.txt | 13 +++++++++---- 2 files changed, 13 insertions(+), 6 deletions(-) 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:] From 7f328d3f79bba1b3ce517084d556fccefc3e5bc4 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 11:49:46 -0600 Subject: [PATCH 2/8] cite a good book on SLLOD thermostatting for molecular systems --- doc/src/Howto_nemd.txt | 11 +++++++++++ doc/src/Howto_thermostat.txt | 11 +++++++++++ doc/src/Howto_viscosity.txt | 11 +++++++++++ doc/src/fix_nvt_sllod.txt | 9 +++++++++ 4 files changed, 42 insertions(+) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index f787801c36..0a76859dcf 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)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +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(Daivis2) +[(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..6a0095e741 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)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +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(Daivis2) +[(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..adfabf8279 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)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +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(Daivis2) +[(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_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 97a864a231..67c4d76417 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)"_#Daivis2 discusses +use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating +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(Daivis2) +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). From c3ece2f0861b48d39b4f3da2350f2f969f11d40d Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Tue, 11 Sep 2018 12:44:35 -0600 Subject: [PATCH 3/8] typo in fix relax/box doc page --- doc/src/fix_box_relax.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From e14db00d522bbc7802a648c1844c44ded1417fa1 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Fri, 14 Sep 2018 17:31:33 -0600 Subject: [PATCH 4/8] doc link adjustments --- doc/src/Howto_nemd.txt | 10 +++++----- doc/src/Howto_thermostat.txt | 10 +++++----- doc/src/Howto_viscosity.txt | 10 +++++----- doc/src/fix_nvt_sllod.txt | 10 +++++----- 4 files changed, 20 insertions(+), 20 deletions(-) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index 0a76859dcf..3387611d4e 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -24,10 +24,10 @@ 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)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-nemd +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating 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 @@ -54,6 +54,6 @@ using the "fix flow/gauss"_fix_flow_gauss.html command. :line -:link(Daivis2) +: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 6a0095e741..ccc9674641 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -43,10 +43,10 @@ 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)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating 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 @@ -95,6 +95,6 @@ temperature compute is used for default thermodynamic output. :line -:link(Daivis2) +: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 adfabf8279..0b3892c1ad 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -37,10 +37,10 @@ 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)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-viscosity +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating 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 @@ -139,6 +139,6 @@ with time at sufficiently long times. :line -:link(Daivis2) +: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_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 67c4d76417..fbc3143af3 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -63,10 +63,10 @@ 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)"_#Daivis2 discusses -use of the SLLOD method and non-equilibrium MD (NEMD) thermosttating -generally, for both simple and complex fluids, e.g. molecular systems. -The latter can be tricky to do correctly. +NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-sllod +discusses use of the SLLOD method and non-equilibrium MD (NEMD) +thermosttating 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 @@ -183,6 +183,6 @@ 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(Daivis2) +:link(Daivis-sllod) [(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). From 8fa80081df3513dfd20fb6ab92471b6a451bc55a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:08:22 -0400 Subject: [PATCH 5/8] fix typo --- doc/src/Howto_nemd.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_nemd.txt b/doc/src/Howto_nemd.txt index 3387611d4e..10139d907c 100644 --- a/doc/src/Howto_nemd.txt +++ b/doc/src/Howto_nemd.txt @@ -26,7 +26,7 @@ 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) -thermosttating generally, for both simple and complex fluids, +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 From 39ee7876c48dcdf1367b05f7f184f2f88048618a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:09:23 -0400 Subject: [PATCH 6/8] fix typo --- doc/src/Howto_thermostat.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_thermostat.txt b/doc/src/Howto_thermostat.txt index ccc9674641..9f7e2f3000 100644 --- a/doc/src/Howto_thermostat.txt +++ b/doc/src/Howto_thermostat.txt @@ -45,7 +45,7 @@ particles. NOTE: A recent (2017) book by "(Daivis and Todd)"_#Daivis-thermostat discusses use of the SLLOD method and non-equilibrium MD (NEMD) -thermosttating generally, for both simple and complex fluids, +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 From 494b1492720bf34c7dee6b9ade18c570c38dcf48 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:10:56 -0400 Subject: [PATCH 7/8] fix typo --- doc/src/Howto_viscosity.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_viscosity.txt b/doc/src/Howto_viscosity.txt index 0b3892c1ad..b4e441557d 100644 --- a/doc/src/Howto_viscosity.txt +++ b/doc/src/Howto_viscosity.txt @@ -39,7 +39,7 @@ 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) -thermosttating generally, for both simple and complex fluids, +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 From 5f6b5c5400019d1b4e09f0138eb0aac4b789d5fe Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 17 Sep 2018 05:11:59 -0400 Subject: [PATCH 8/8] fix typo --- doc/src/fix_nvt_sllod.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index fbc3143af3..7a350e48b5 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -65,7 +65,7 @@ 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) -thermosttating generally, for both simple and complex fluids, +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