For styles xy and yz and xz, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. +
In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat is applied. The optional drag keyword will damp these diff -Naur lammps-10May08/doc/fix_nph.txt lammps-14May08/doc/fix_nph.txt --- lammps-10May08/doc/fix_nph.txt 2008-04-10 14:53:47.000000000 -0600 +++ lammps-14May08/doc/fix_nph.txt 2008-05-13 15:46:42.000000000 -0600 @@ -104,6 +104,10 @@ pressure components must be specified as NULL when using style {aniso}. +For styles {xy} and {yz} and {xz}, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. + In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat is applied. The optional {drag} keyword will damp these diff -Naur lammps-10May08/doc/fix_npt.html lammps-14May08/doc/fix_npt.html --- lammps-10May08/doc/fix_npt.html 2008-04-10 14:53:47.000000000 -0600 +++ lammps-14May08/doc/fix_npt.html 2008-05-13 15:46:42.000000000 -0600 @@ -124,6 +124,10 @@ pressure components must be specified as NULL when using style aniso.
+For styles xy and yz and xz, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. +
In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional drag keyword will diff -Naur lammps-10May08/doc/fix_npt.txt lammps-14May08/doc/fix_npt.txt --- lammps-10May08/doc/fix_npt.txt 2008-04-10 14:53:47.000000000 -0600 +++ lammps-14May08/doc/fix_npt.txt 2008-05-13 15:46:42.000000000 -0600 @@ -113,6 +113,10 @@ pressure components must be specified as NULL when using style {aniso}. +For styles {xy} and {yz} and {xz}, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. + In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional {drag} keyword will diff -Naur lammps-10May08/doc/fix_npt_asphere.html lammps-14May08/doc/fix_npt_asphere.html --- lammps-10May08/doc/fix_npt_asphere.html 2008-03-19 16:51:12.000000000 -0600 +++ lammps-14May08/doc/fix_npt_asphere.html 2008-05-13 15:46:42.000000000 -0600 @@ -111,6 +111,10 @@ pressure components must be specified as NULL when using style aniso.
+For styles xy and yz and xz, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. +
In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional drag keyword will diff -Naur lammps-10May08/doc/fix_npt_asphere.txt lammps-14May08/doc/fix_npt_asphere.txt --- lammps-10May08/doc/fix_npt_asphere.txt 2008-03-19 16:51:12.000000000 -0600 +++ lammps-14May08/doc/fix_npt_asphere.txt 2008-05-13 15:46:42.000000000 -0600 @@ -100,6 +100,10 @@ pressure components must be specified as NULL when using style {aniso}. +For styles {xy} and {yz} and {xz}, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. + In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional {drag} keyword will diff -Naur lammps-10May08/doc/fix_npt_sphere.html lammps-14May08/doc/fix_npt_sphere.html --- lammps-10May08/doc/fix_npt_sphere.html 2008-03-19 16:51:12.000000000 -0600 +++ lammps-14May08/doc/fix_npt_sphere.html 2008-05-13 15:46:42.000000000 -0600 @@ -113,6 +113,10 @@ pressure components must be specified as NULL when using style aniso.
+For styles xy and yz and xz, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. +
In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional drag keyword will diff -Naur lammps-10May08/doc/fix_npt_sphere.txt lammps-14May08/doc/fix_npt_sphere.txt --- lammps-10May08/doc/fix_npt_sphere.txt 2008-03-19 16:51:12.000000000 -0600 +++ lammps-14May08/doc/fix_npt_sphere.txt 2008-05-13 15:46:42.000000000 -0600 @@ -102,6 +102,10 @@ pressure components must be specified as NULL when using style {aniso}. +For styles {xy} and {yz} and {xz}, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. + In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat and thermostat is applied. The optional {drag} keyword will diff -Naur lammps-10May08/doc/fix_press_berendsen.html lammps-14May08/doc/fix_press_berendsen.html --- lammps-10May08/doc/fix_press_berendsen.html 2008-04-10 14:53:47.000000000 -0600 +++ lammps-14May08/doc/fix_press_berendsen.html 2008-05-13 15:46:42.000000000 -0600 @@ -105,6 +105,10 @@ pressure components must be specified as NULL when using style aniso.
+For styles xy and yz and xz, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. +
In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat is applied. The optional drag keyword will damp these diff -Naur lammps-10May08/doc/fix_press_berendsen.txt lammps-14May08/doc/fix_press_berendsen.txt --- lammps-10May08/doc/fix_press_berendsen.txt 2008-04-10 14:53:47.000000000 -0600 +++ lammps-14May08/doc/fix_press_berendsen.txt 2008-05-13 15:46:42.000000000 -0600 @@ -96,6 +96,10 @@ pressure components must be specified as NULL when using style {aniso}. +For styles {xy} and {yz} and {xz}, the starting and stopping pressures +must be the same for the two coupled dimensions and cannot be +specified as NULL. + In some cases (e.g. for solids) the pressure (volume) and/or temperature of the system can oscillate undesirably when a Nose/Hoover barostat is applied. The optional {drag} keyword will damp these diff -Naur lammps-10May08/doc/fix_thermal_conductivity.html lammps-14May08/doc/fix_thermal_conductivity.html --- lammps-10May08/doc/fix_thermal_conductivity.html 1969-12-31 17:00:00.000000000 -0700 +++ lammps-14May08/doc/fix_thermal_conductivity.html 2008-05-14 15:40:50.000000000 -0600 @@ -0,0 +1,154 @@ + +
Syntax: +
+fix ID group-ID thermal/conductivity N edim Nbin keyword value ... ++
swap value = Nswap = number of swaps to perform every N steps ++ +
Examples: +
+fix 1 all thermal/conductivity 100 z 20 +fix 1 all thermal/conductivity 50 z 20 swap 2 ++
Description: +
+Use the Muller-Plathe algorithm described in this +paper to exchange kinetic energy between two particles +in different regions of the simulation box every N steps. This +induces a temperature gradient in the system. As described below this +enables a thermal conductivity of the fluid to be calculated. This +algorithm is sometimes called a reverse non-equilibrium MD (reverse +NEMD) approach to computing thermal conductivity. This is because the +usual NEMD approach is to impose a temperature gradient on the system +and measure the response as the resulting heat flux. In the +Muller-Plathe method, the heat flux is imposed, and the temperature +gradient is the system's response. +
+The simulation box is divided into Nbin layers in the edim +direction. Every N steps, Nswap pairs of atoms are chosen in the +following manner. Only atoms in the fix group are considered. The +hottest Nswap atoms in the bottom layer are selected. Similarly, the +coldest Nswap atoms in the middle later are selected. The two sets of +Nswap atoms are paired up and their velocities are exchanged. This +effectively swaps their kinetic energies, assuming their masses are +the same. Over time, this induces a temperature gradient in the +system which can be measured using commands such as the following, +which writes the temperature profile (assuming z = edim) to the file +tmp.profile: +
+compute ke all ke/atom +variable temp atom c_ke/1.5 +fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp & + file tmp.profile units reduced ++
Note that by default, Nswap = 1, though this can be changed by the +optional swap keyword. Setting this parameter appropriately, in +conjunction with the swap rate N, allows the heat flux to be adjusted +across a wide range of values, and the kinetic energy to be exchanged +in large chunks or more smoothly. +
+As described below, the total kinetic energy transferred by these +swaps is computed by the fix and can be output. Dividing this +quantity by time and the cross-sectional area of the simulation box +yields a heat flux. The ratio of heat flux to the slope of the +temperature profile is the thermal conductivity of the fluid, +in appopriate units. See the Muller-Plathe paper for +details. +
+IMPORTANT NOTE: After equilibration, if the temperature gradient you +observe is not linear, then you are likely swapping energy too +frequently and are not in a regime of linear response. In this case +you cannot accurately infer a thermal conductivity and should try +increasing the Nevery parameter. +
+Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +
+The cummulative kinetic energy transferred between the bottom and +middle of the simulation box (in the edim direction) is stored as a +scalar quantity by this fix. This quantity is zeroed when the fix is +defined and accumlates thereafter, once every N steps. The units of +the quantity are energy; see the units command for +details. This quantity can be accessed by various output +commands, such as thermo_style +custom. The scalar value calculated by this fix is +"intensive", meaning it is independent of the number of atoms in the +simulation. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
+Restrictions: +
+LAMMPS does not check, but the masses of all exchanged atom pairs +should be the same to use this fix in a way that conserves both +momentum and kinetic energy. Thus you should not need to thermostat +the system. If you do use a thermostat, you may want to apply it only +to the non-swapped dimensions (other than vdim). +
+LAMMPS does not check, but you should not use this fix to swap the +kinetic energy of atoms that are in constrained molecules, e.g. via +fix shake or fix rigid. This is +because application of the constraints will alter the amount of +transferred momentum. You should, however, be able to use flexible +molecules. See the Zhang paper for a discussion and results +of this idea. +
+When running a simulation with large, massive particles or molecules +in a background solvent, you may want to only exchange kinetic energy +bewteen solvent particles. +
+Related commands: +
+fix ave/spatial, fix +viscosity +
+Default: +
+The option defaults are swap = 1. +
+(Muller-Plathe) Muller-Plathe and Reith, Computational and +Theoretical Polymer Science, 9, 203-209 (1999). +
+ + +(Zhang) Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, +109, 15060-15067 (2005). +
+ diff -Naur lammps-10May08/doc/fix_thermal_conductivity.txt lammps-14May08/doc/fix_thermal_conductivity.txt --- lammps-10May08/doc/fix_thermal_conductivity.txt 1969-12-31 17:00:00.000000000 -0700 +++ lammps-14May08/doc/fix_thermal_conductivity.txt 2008-05-14 15:40:50.000000000 -0600 @@ -0,0 +1,140 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix thermal/conductivity command :h3 + +[Syntax:] + +fix ID group-ID thermal/conductivity N edim Nbin keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +thermal/conductivity = style name of this fix command :l +N = perform kinetic energy exchange every N steps :l +edim = {x} or {y} or {z} = direction of kinetic energy transfer :l +Nbin = # of layers in edim direction :l + +zero or more keyword/value pairs may be appended :l +keyword = {swap} :l + {swap} value = Nswap = number of swaps to perform every N steps :pre +:ule + +[Examples:] + +fix 1 all thermal/conductivity 100 z 20 +fix 1 all thermal/conductivity 50 z 20 swap 2 :pre + +[Description:] + +Use the Muller-Plathe algorithm described in "this +paper"_#Muller-Plathe to exchange kinetic energy between two particles +in different regions of the simulation box every N steps. This +induces a temperature gradient in the system. As described below this +enables a thermal conductivity of the fluid to be calculated. This +algorithm is sometimes called a reverse non-equilibrium MD (reverse +NEMD) approach to computing thermal conductivity. This is because the +usual NEMD approach is to impose a temperature gradient on the system +and measure the response as the resulting heat flux. In the +Muller-Plathe method, the heat flux is imposed, and the temperature +gradient is the system's response. + +The simulation box is divided into {Nbin} layers in the {edim} +direction. Every N steps, Nswap pairs of atoms are chosen in the +following manner. Only atoms in the fix group are considered. The +hottest Nswap atoms in the bottom layer are selected. Similarly, the +coldest Nswap atoms in the middle later are selected. The two sets of +Nswap atoms are paired up and their velocities are exchanged. This +effectively swaps their kinetic energies, assuming their masses are +the same. Over time, this induces a temperature gradient in the +system which can be measured using commands such as the following, +which writes the temperature profile (assuming z = edim) to the file +tmp.profile: + +compute ke all ke/atom +variable temp atom c_ke[]/1.5 +fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp & + file tmp.profile units reduced :pre + +Note that by default, Nswap = 1, though this can be changed by the +optional {swap} keyword. Setting this parameter appropriately, in +conjunction with the swap rate N, allows the heat flux to be adjusted +across a wide range of values, and the kinetic energy to be exchanged +in large chunks or more smoothly. + +As described below, the total kinetic energy transferred by these +swaps is computed by the fix and can be output. Dividing this +quantity by time and the cross-sectional area of the simulation box +yields a heat flux. The ratio of heat flux to the slope of the +temperature profile is the thermal conductivity of the fluid, +in appopriate units. See the "Muller-Plathe paper"_#Muller-Plathe for +details. + +IMPORTANT NOTE: After equilibration, if the temperature gradient you +observe is not linear, then you are likely swapping energy too +frequently and are not in a regime of linear response. In this case +you cannot accurately infer a thermal conductivity and should try +increasing the Nevery parameter. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. + +The cummulative kinetic energy transferred between the bottom and +middle of the simulation box (in the {edim} direction) is stored as a +scalar quantity by this fix. This quantity is zeroed when the fix is +defined and accumlates thereafter, once every N steps. The units of +the quantity are energy; see the "units"_units.html command for +details. This quantity can be accessed by various "output +commands"_Section_howto.html#4_15, such as "thermo_style +custom"_thermo_style.html. The scalar value calculated by this fix is +"intensive", meaning it is independent of the number of atoms in the +simulation. + +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:] + +LAMMPS does not check, but the masses of all exchanged atom pairs +should be the same to use this fix in a way that conserves both +momentum and kinetic energy. Thus you should not need to thermostat +the system. If you do use a thermostat, you may want to apply it only +to the non-swapped dimensions (other than {vdim}). + +LAMMPS does not check, but you should not use this fix to swap the +kinetic energy of atoms that are in constrained molecules, e.g. via +"fix shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is +because application of the constraints will alter the amount of +transferred momentum. You should, however, be able to use flexible +molecules. See the "Zhang paper"_#Zhang for a discussion and results +of this idea. + +When running a simulation with large, massive particles or molecules +in a background solvent, you may want to only exchange kinetic energy +bewteen solvent particles. + +[Related commands:] + +"fix ave/spatial"_fix_ave_spatial.html, "fix +viscosity"_fix_viscosity.html + +[Default:] + +The option defaults are swap = 1. + +:line + +:link(Muller-Plathe) +[(Muller-Plathe)] Muller-Plathe and Reith, Computational and +Theoretical Polymer Science, 9, 203-209 (1999). + +:link(Zhang) +[(Zhang)] Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, +109, 15060-15067 (2005). diff -Naur lammps-10May08/doc/fix_viscosity.html lammps-14May08/doc/fix_viscosity.html --- lammps-10May08/doc/fix_viscosity.html 2008-03-28 09:45:51.000000000 -0600 +++ lammps-14May08/doc/fix_viscosity.html 2008-05-14 15:40:02.000000000 -0600 @@ -70,8 +70,8 @@ measured using commands such as the following, which writes the profile to the file tmp.profile: -fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & - file tmp.profile units reduced +fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & + file tmp.profile units reducedNote that by default, Nswap = 1 and vtarget = INF, though this can be changed by the optional swap and vtarget keywords. When vtarget = @@ -144,8 +144,7 @@
Related commands:
-fix ave/spatial, fix -nvt/sllod +
Default:
diff -Naur lammps-10May08/doc/fix_viscosity.txt lammps-14May08/doc/fix_viscosity.txt --- lammps-10May08/doc/fix_viscosity.txt 2008-03-28 09:45:51.000000000 -0600 +++ lammps-14May08/doc/fix_viscosity.txt 2008-05-14 15:40:02.000000000 -0600 @@ -59,8 +59,8 @@ measured using commands such as the following, which writes the profile to the file tmp.profile: -fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & - file tmp.profile units reduced :pre +fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx & + file tmp.profile units reduced :pre Note that by default, Nswap = 1 and vtarget = INF, though this can be changed by the optional {swap} and {vtarget} keywords. When vtarget = @@ -133,8 +133,7 @@ [Related commands:] -"fix ave/spatial"_fix_ave_spatial.html, "fix -nvt/sllod"_fix_nvt_sllod.html +"fix ave/spatial"_fix_ave_spatial.html [Default:] diff -Naur lammps-10May08/doc/fix_wall_reflect.html lammps-14May08/doc/fix_wall_reflect.html --- lammps-10May08/doc/fix_wall_reflect.html 2007-10-10 16:28:11.000000000 -0600 +++ lammps-14May08/doc/fix_wall_reflect.html 2008-05-13 15:49:52.000000000 -0600 @@ -35,6 +35,14 @@ put back inside the box by the same delta and the sign of the corresponding component of its velocity is flipped. +When used in conjunction with fix nve and run_style +verlet, the resultant time-integration algorithm is +equivalent to the primitive splitting algorithm (PSA) described by +Bond. Because each reflection event divides +the corresponding timestep asymmetrically, energy conservation is only +satisfied to O(dt), rather than to O(dt^2) as it would be for +velocity-Verlet integration without reflective walls. +
IMPORTANT NOTE: This fix performs its operations at the same point in the timestep as other time integration fixes, such as fix nve, fix nvt, or fix npt. @@ -69,4 +77,8 @@
Default: none
+ + +(Bond) Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007). +