diff --git a/doc/src/fix_deform.rst b/doc/src/fix_deform.rst index 2c76463369..c5832d1729 100644 --- a/doc/src/fix_deform.rst +++ b/doc/src/fix_deform.rst @@ -4,9 +4,6 @@ fix deform command ================== -:doc:`fix deform/pressure ` command -======================================================== - Accelerator Variants: *deform/kk* Syntax @@ -14,12 +11,11 @@ Syntax .. code-block:: LAMMPS - fix ID group-ID fix_style N parameter style args ... keyword value ... + fix ID group-ID deform N parameter style args ... keyword value ... * ID, group-ID are documented in :doc:`fix ` command -* fix_style = *deform* or *deform/pressure* * N = perform box deformation every this many timesteps -* one or more parameter/style/args sequences of arguments may be appended +* one or more parameter/args sequences may be appended .. parsed-literal:: @@ -46,12 +42,6 @@ Syntax *variable* values = v_name1 v_name2 v_name1 = variable with name1 for box length change as function of time v_name2 = variable with name2 for change rate as function of time - *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure ` command) - target = target pressure (pressure units) - gain = proportional gain constant (1/(time * pressure) or 1/time units) - *pressure/mean* values = target gain (ONLY available in :doc:`fix deform/pressure ` command) - target = target pressure (pressure units) - gain = proportional gain constant (1/(time * pressure) or 1/time units) *xy*, *xz*, *yz* args = style value style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* @@ -64,8 +54,6 @@ Syntax effectively an engineering shear strain rate *erate* value = R R = engineering shear strain rate (1/time units) - *erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure ` command) - R = engineering shear strain rate (1/time units) *trate* value = R R = true shear strain rate (1/time units) *wiggle* values = A Tp @@ -74,9 +62,6 @@ Syntax *variable* values = v_name1 v_name2 v_name1 = variable with name1 for tilt change as function of time v_name2 = variable with name2 for change rate as function of time - *pressure* values = target gain (ONLY available in :doc:`fix deform/pressure ` command) - target = target pressure (pressure units) - gain = proportional gain constant (1/(time * pressure) or 1/time units) * zero or more keyword/value pairs may be appended * keyword = *remap* or *flip* or *units* or *couple* or *vol/balance/p* or *max/rate* or *normalize/pressure* @@ -92,15 +77,6 @@ Syntax *units* value = *lattice* or *box* lattice = distances are defined in lattice units box = distances are defined in simulation box units - *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* (ONLY available in :doc:`fix deform/pressure ` command) - couple pressure values of various dimensions - *vol/balance/p* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure ` command) - Modifies the behavior of the *volume* option to try and balance pressures - *max/rate* value = *rate* (ONLY available in :doc:`fix deform/pressure ` command) - rate = maximum strain rate for pressure control - *normalize/pressure* value = *yes* or *no* (ONLY available in :doc:`fix deform/pressure ` command) - Modifies pressure controls such that the deviation in pressure is normalized by the target pressure - Examples """""""" @@ -112,8 +88,6 @@ Examples fix 1 all deform 1 xy erate 0.001 remap v fix 1 all deform 10 y delta -0.5 0.5 xz vel 1.0 -See examples for :doc:`fix deform/pressure ` on its doc page - Description """"""""""" @@ -123,17 +97,13 @@ run. Orthogonal simulation boxes have 3 adjustable parameters adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be adjusted independently and simultaneously. -The fix deform command allows use of all the arguments listed above, -except those flagged as available ONLY for the :doc:`fix -deform/pressure ` command, which are -pressure-based controls. The fix deform/pressure command allows use -of all the arguments listed above. - -The rest of this doc page explains the options common to both -commands. The :doc:`fix deform/pressure ` doc -page explains the options available ONLY with the fix deform/pressure -command. Note that a simulation can define only a single deformation -command: fix deform or fix deform/pressure. +The :doc:`fix deform/pressure ` command extends +this command with additional keywords and arguments. The rest of this +page explains the options common to both commands. The :doc:`fix +deform/pressure ` page explains the options +available ONLY with the fix deform/pressure command. Note that a +simulation can define only a single deformation command: fix deform or +fix deform/pressure. Both these fixes can be used to perform non-equilibrium MD (NEMD) simulations of a continuously strained system. See the :doc:`fix diff --git a/doc/src/fix_deform_pressure.rst b/doc/src/fix_deform_pressure.rst index 25ad5bfeca..d99a7611c4 100644 --- a/doc/src/fix_deform_pressure.rst +++ b/doc/src/fix_deform_pressure.rst @@ -13,29 +13,66 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * deform/pressure = style name of this fix command * N = perform box deformation every this many timesteps -* one or more parameter/arg sequences may be appended +* one or more parameter/args sequences may be appended .. parsed-literal:: parameter = *x* or *y* or *z* or *xy* or *xz* or *yz* or *box* *x*, *y*, *z* args = style value(s) style = *final* or *delta* or *scale* or *vel* or *erate* or *trate* or *volume* or *wiggle* or *variable* or *pressure* or *pressure/mean* + *final* values = lo hi + lo hi = box boundaries at end of run (distance units) + *delta* values = dlo dhi + dlo dhi = change in box boundaries at end of run (distance units) + *scale* values = factor + factor = multiplicative factor for change in box length at end of run + *vel* value = V + V = change box length at this velocity (distance/time units), + effectively an engineering strain rate + *erate* value = R + R = engineering strain rate (1/time units) + *trate* value = R + R = true strain rate (1/time units) + *volume* value = none = adjust this dim to preserve volume of system + *wiggle* values = A Tp + A = amplitude of oscillation (distance units) + Tp = period of oscillation (time units) + *variable* values = v_name1 v_name2 + v_name1 = variable with name1 for box length change as function of time + v_name2 = variable with name2 for change rate as function of time *pressure* values = target gain target = target pressure (pressure units) gain = proportional gain constant (1/(time * pressure) or 1/time units) *pressure/mean* values = target gain target = target pressure (pressure units) gain = proportional gain constant (1/(time * pressure) or 1/time units) - NOTE: All other styles are documented by the :doc:`fix deform ` command *xy*, *xz*, *yz* args = style value style = *final* or *delta* or *vel* or *erate* or *trate* or *wiggle* or *variable* or *pressure* or *erate/rescale* + *final* value = tilt + tilt = tilt factor at end of run (distance units) + *delta* value = dtilt + dtilt = change in tilt factor at end of run (distance units) + *vel* value = V + V = change tilt factor at this velocity (distance/time units), + effectively an engineering shear strain rate + *erate* value = R + R = engineering shear strain rate (1/time units) + *erate/rescale* value = R + R = engineering shear strain rate (1/time units) + *trate* value = R + R = true shear strain rate (1/time units) + *wiggle* values = A Tp + A = amplitude of oscillation (distance units) + Tp = period of oscillation (time units) + *variable* values = v_name1 v_name2 + v_name1 = variable with name1 for tilt change as function of time + v_name2 = variable with name2 for change rate as function of time *pressure* values = target gain target = target pressure (pressure units) gain = proportional gain constant (1/(time * pressure) or 1/time units) *erate/rescale* value = R R = engineering shear strain rate (1/time units) - NOTE: All other styles are documented by the :doc:`fix deform ` command *box* = style value style = *volume* or *pressure* @@ -49,6 +86,15 @@ Syntax .. parsed-literal:: + *remap* value = *x* or *v* or *none* + x = remap coords of atoms in group into deforming box + v = remap velocities of atoms in group when they cross periodic boundaries + none = no remapping of x or v + *flip* value = *yes* or *no* + allow or disallow box flips when it becomes highly skewed + *units* value = *lattice* or *box* + lattice = distances are defined in lattice units + box = distances are defined in simulation box units *couple* value = *none* or *xyz* or *xy* or *yz* or *xz* couple pressure values of various dimensions *vol/balance/p* value = *yes* or *no* @@ -57,7 +103,6 @@ Syntax rate = maximum strain rate for pressure control *normalize/pressure* value = *yes* or *no* Modifies pressure controls such that the deviation in pressure is normalized by the target pressure - NOTE: All other keywords are documented by the :doc:`fix deform ` command Examples """""""" @@ -79,7 +124,7 @@ pressure-based controls implemented by this command. All arguments described on the :doc:`fix deform ` doc page also apply to this fix unless otherwise noted below. The rest of this -doc page explains the arguments specific to this fix. Note that a +page explains the arguments specific to this fix only. Note that a simulation can define only a single deformation command: fix deform or fix deform/pressure.