From c1fc5aef12faefebebfd86125d463782ee560792 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 27 Jul 2016 14:08:32 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15370 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/fix_nh.txt | 30 +++++++++++++++++++++--------- doc/src/fix_nve_sphere.txt | 25 ++++++++++++++++++++----- 2 files changed, 41 insertions(+), 14 deletions(-) diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 94435a38f4..c03c82655a 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -56,8 +56,9 @@ keyword = {temp} or {iso} or {aniso} or {tri} or {x} or {y} or {z} or {xy} or {y {flip} value = {yes} or {no} = allow or disallow box flips when it becomes highly skewed {fixedpoint} values = x y z x,y,z = perform barostat dilation/contraction around this point (distance units) - {update} value = {dipole} update dipole orientation (only for sphere variants) :pre - + {update} value = {dipole} or {dipole/dlm} + dipole = update dipole orientation (only for sphere variants) + dipole/dlm = use DLM integrator to update dipole orientation (only for sphere variants) :pre :ule [Examples:] @@ -335,6 +336,13 @@ where a dipole moment is assigned to finite-size particles, e.g. spheroids via use of the "atom_style hybrid sphere dipole"_atom_style.html command. +The default dipole orientation integrator can be changed the +Dullweber-Leimkuhler-McLachlan integration scheme +"(Dullweber)"_#nh-Dullweber when using {update} with the value +{dipole/dlm}. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost. + :line NOTE: Using a barostat coupled to tilt dimensions {xy}, {xz}, {yz} can @@ -429,14 +437,14 @@ thermal degrees of freedom, and the bias is added back in. :line -These fixes can be used with either the {verlet} or {respa} +These fixes can be used with either the {verlet} or {respa} "integrators"_run_style.html. When using one of the barostat fixes with {respa}, LAMMPS uses an integrator constructed according to the following factorization of the Liouville propagator (for two rRESPA levels): -:c,image(Eqs/fix_nh1.jpg) - +:c,image(Eqs/fix_nh1.jpg) + This factorization differs somewhat from that of Tuckerman et al, in that the barostat is only updated at the outermost rRESPA level, whereas Tuckerman's factorization requires splitting the pressure into @@ -452,7 +460,7 @@ NOTE: This implementation has been shown to conserve linear momentum up to machine precision under NVT dynamics. Under NPT dynamics, for a system with zero initial total linear momentum, the total momentum fluctuates close to zero. It may occasionally undergo brief -excursions to non-negligible values, before returning close to zero. +excursions to non-negligible values, before returning close to zero. Over long simulations, this has the effect of causing the center-of-mass to undergo a slow random walk. This can be mitigated by resetting the momentum at infrequent intervals using the @@ -462,7 +470,7 @@ NOTE: This implementation has been shown to conserve linear momentum up to machine precision under NVT dynamics. Under NPT dynamics, for a system with zero initial total linear momentum, the total momentum fluctuates close to zero. It may occasionally undergo brief -excursions to non-negligible values, before returning close to zero. +excursions to non-negligible values, before returning close to zero. Over long simulations, this has the effect of causing the center-of-mass to undergo a slow random walk. This can be mitigated by resetting the momentum at infrequent intervals using the @@ -603,7 +611,7 @@ for 2D simulations. {scaleyz yes}, {scalexz yes}, and {scalexy yes} options can only be used if the 2nd dimension in the keyword is periodic, and if the tilt factor is not coupled to the barostat via keywords {tri}, {yz}, {xz}, and {xy}. - + These fixes can be used with dynamic groups as defined by the "group"_group.html command. Likewise they can be used with groups to which atoms are added or deleted over time, e.g. a deposition @@ -621,7 +629,7 @@ over time or the atom count becomes very small. The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and +scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and not coupled to barostat, otherwise no. :line @@ -638,3 +646,7 @@ Martyna, J Phys A: Math Gen, 39, 5629 (2006). :link(nh-Shinoda) [(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004). + +:link(nh-Dullweber) +[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997). diff --git a/doc/src/fix_nve_sphere.txt b/doc/src/fix_nve_sphere.txt index c797cc8ddb..37918c3431 100755 --- a/doc/src/fix_nve_sphere.txt +++ b/doc/src/fix_nve_sphere.txt @@ -16,15 +16,17 @@ fix ID group-ID nve/sphere :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l nve/sphere = style name of this fix command :l zero or more keyword/value pairs may be appended :l -keyword = {update} :l - {update} value = {dipole} - dipole = update orientation of dipole moment during integration :pre +keyword = {update} + {update} value = {dipole} or {dipole/dlm} + dipole = update orientation of dipole moment during integration + dipole/dlm = use DLM integrator to update dipole orientation :pre :ule [Examples:] fix 1 all nve/sphere -fix 1 all nve/sphere update dipole :pre +fix 1 all nve/sphere update dipole +fix 1 all nve/sphere update dipole/dlm :pre [Description:] @@ -43,6 +45,13 @@ where a dipole moment is assigned to finite-size particles, e.g. spheroids via use of the "atom_style hybrid sphere dipole"_atom_style.html command. +The default dipole orientation integrator can be changed the +Dullweber-Leimkuhler-McLachlan integration scheme +"(Dullweber)"_#nh-Dullweber when using {update} with the value +{dipole/dlm}. This integrator is symplectic and time-reversible, +giving better energy conservation and allows slightly longer timesteps +at only a small additional computational cost. + :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -78,7 +87,7 @@ commands"_Section_howto.html#howto_15. 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:] +[Restrictions:] This fix requires that atoms store torque and angular velocity (omega) and a radius as defined by the "atom_style sphere"_atom_style.html @@ -94,3 +103,9 @@ be point particles. "fix nve"_fix_nve.html, "fix nve/asphere"_fix_nve_asphere.html [Default:] none + +:line + +:link(nve-Dullweber) +[(Dullweber)] Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, +5840 (1997).