diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 3d1ae19013..acb051aff9 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -730,6 +730,7 @@ KOKKOS, o = USER-OMP, t = OPT. "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, +"rigid/local"_compute_rigid_local.html, "slice"_compute_slice.html, "sna/atom"_compute_sna_atom.html, "snad/atom"_compute_sna_atom.html, diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt index 886ab9c620..8e76b85aa2 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/accelerate_gpu.txt @@ -44,10 +44,10 @@ NVIDIA support as well as more general OpenCL support, so that the same functionality can eventually be supported on a variety of GPU hardware. :l,ule -Here is a quick overview of how to use the GPU package: +Here is a quick overview of how to enable and use the GPU package: -build the library in lib/gpu for your GPU hardware wity desired precision -include the GPU package and build LAMMPS +build the library in lib/gpu for your GPU hardware with the desired precision settings +install the GPU package and build LAMMPS as usual use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU specify the # of GPUs per node use GPU styles in your input script :ul diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 3da2143411..e680abaa33 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -217,6 +217,7 @@ section of "this page"_Section_commands.html#cmd_5. "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/region"_compute_reduce.html - same as compute reduce, within a region +"rigid/local"_compute_rigid_local.html - extract rigid body attributes "slice"_compute_slice.html - extract values from global vector or array "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 0eade9b401..30389c3437 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -172,7 +172,11 @@ quatw,quati,quatj,quatk = unitless tqx,tqy,tqz = torque units inertiax,inertiay,inertiaz = mass*distance^2 units :ul -[Restrictions:] none +[Restrictions:] + +This compute is part of the RIGID package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/fix_addforce.txt b/doc/src/fix_addforce.txt index 9a9c71b300..495b527d39 100644 --- a/doc/src/fix_addforce.txt +++ b/doc/src/fix_addforce.txt @@ -138,6 +138,10 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force. +The "fix_modify"_fix_modify.html {respa} option is supported by +this fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar and a global 3-vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential diff --git a/doc/src/fix_addtorque.txt b/doc/src/fix_addtorque.txt index 3cda16af67..25c7855c7d 100644 --- a/doc/src/fix_addtorque.txt +++ b/doc/src/fix_addtorque.txt @@ -64,6 +64,10 @@ forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added forces. +The "fix_modify"_fix_modify.html {respa} option is supported by +this fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its torque. Default is the outermost level. + This fix computes a global scalar and a global 3-vector, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy discussed above. The vector is the diff --git a/doc/src/fix_aveforce.txt b/doc/src/fix_aveforce.txt index 00ba38aaf1..898c98f4f4 100644 --- a/doc/src/fix_aveforce.txt +++ b/doc/src/fix_aveforce.txt @@ -87,8 +87,11 @@ more instructions on how to use the accelerated styles effectively. [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. +files"_restart.html. + +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. This is the diff --git a/doc/src/fix_drag.txt b/doc/src/fix_drag.txt index 503563d975..44c0628183 100644 --- a/doc/src/fix_drag.txt +++ b/doc/src/fix_drag.txt @@ -40,8 +40,11 @@ in the simulation. [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. +files"_restart.html. + +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. This fix computes a global 3-vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. This is the diff --git a/doc/src/fix_efield.txt b/doc/src/fix_efield.txt index dd0857a07a..e9374a930f 100644 --- a/doc/src/fix_efield.txt +++ b/doc/src/fix_efield.txt @@ -124,6 +124,10 @@ can include the forces added by this fix in a consistent manner. I.e. there is a decrease in potential energy when atoms move in the direction of the added force due to the electric field. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix adding its forces. Default is the outermost level. + This fix computes a global scalar and a global 3-vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential diff --git a/doc/src/fix_gravity.txt b/doc/src/fix_gravity.txt index a1c1895a82..242eb7d942 100644 --- a/doc/src/fix_gravity.txt +++ b/doc/src/fix_gravity.txt @@ -120,6 +120,10 @@ fix to add the gravitational potential energy of the system to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. This scalar is the gravitational potential energy of the particles in the defined field, diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index c2428bdbbb..be13925897 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -174,6 +174,10 @@ the system's potential energy as part of "thermodynamic output"_thermo_style.html. The energy of each particle interacting with the indenter is K/3 (r - R)^3. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar energy and a global 3-vector of forces (on the indenter), which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar and vector values diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 8ddadfa24a..cfb1a35374 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -14,16 +14,18 @@ fix_modify fix-ID keyword value ... :pre fix-ID = ID of the fix to modify :ulb,l one or more keyword/value pairs may be appended :l -keyword = {temp} or {press} or {energy} :l +keyword = {temp} or {press} or {energy} or {respa} :l {temp} value = compute ID that calculates a temperature {press} value = compute ID that calculates a pressure - {energy} value = {yes} or {no} :pre + {energy} value = {yes} or {no} + {respa} value = {1} to {max respa level} or {0} (= outmost level) :pre :ule [Examples:] fix_modify 3 temp myTemp press myPress -fix_modify 1 energy yes :pre +fix_modify 1 energy yes +fix_modify tether respa 2 :pre [Description:] @@ -59,6 +61,17 @@ for a fix if you are using it when performing an "energy minimization"_minimize.html and if you want the energy and forces it produces to be part of the optimization criteria. +For fixes that set or modify forces, it may be possible to select at +which "r-RESPA"_run_style.html level the fix operates via the {respa} +keyword. The RESPA level at which the fix is active can be selected. +This is a number ranging from 1 to the number of levels. If the RESPA +level is larger than the current maximum, the outermost level will be +used, which is also the default setting. This default can be restored +using a value of {0} for the RESPA level. The affected fix has to be +programmed to support this feature; if not, {fix_modify} will report +an error. Active fixes with a custom RESPA level setting are reported +with their specified level at the beginning of a r-RESPA run. + [Restrictions:] none [Related commands:] @@ -69,4 +82,4 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html [Default:] The option defaults are temp = ID defined by fix, press = ID defined -by fix, energy = no. +by fix, energy = no, respa = 0. diff --git a/doc/src/fix_orient.txt b/doc/src/fix_orient.txt index 8de1174455..3c698e6508 100644 --- a/doc/src/fix_orient.txt +++ b/doc/src/fix_orient.txt @@ -130,6 +130,10 @@ fix to add the potential energy of atom interactions with the grain boundary driving force to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by these +fixes. This allows to set at which level of the "r-RESPA"_run_style.html +integrator a fix is adding its forces. Default is the outermost level. + This fix calculates a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the potential energy change due to this fix. The scalar value calculated diff --git a/doc/src/fix_qeq_comb.txt b/doc/src/fix_qeq_comb.txt index a697008fab..7c71aab1d7 100644 --- a/doc/src/fix_qeq_comb.txt +++ b/doc/src/fix_qeq_comb.txt @@ -85,8 +85,12 @@ more instructions on how to use the accelerated styles effectively. [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. +files"_restart.html. + +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is performing charge equilibration. Default is +the outermost level. This fix produces a per-atom vector which can be accessed by various "output commands"_Section_howto.html#howto_15. The vector stores the diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index cb0248d48b..9655b7cb72 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -163,6 +163,10 @@ fix to add the potential energy associated with this fix to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + NOTE: If you want the fictitious potential energy associated with the added forces to be included in the total potential energy of the system (the quantity being minimized), you MUST enable the diff --git a/doc/src/fix_setforce.txt b/doc/src/fix_setforce.txt index 0b151cbabd..072c09a293 100644 --- a/doc/src/fix_setforce.txt +++ b/doc/src/fix_setforce.txt @@ -93,8 +93,14 @@ more instructions on how to use the accelerated styles effectively. [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. +files"_restart.html. + +The "fix_modify"_fix_modify.html {respa} option is supported by +this fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is setting the forces to the desired values; on all +other levels, the force is set to 0.0 for the atoms in the fix group, +so that setforce values are not counted multiple times. Default is to +to override forces at the outermost level. This fix computes a global 3-vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. This is the diff --git a/doc/src/fix_shardlow.txt b/doc/src/fix_shardlow.txt index 485f0a4b6f..1e1f019390 100644 --- a/doc/src/fix_shardlow.txt +++ b/doc/src/fix_shardlow.txt @@ -69,6 +69,9 @@ lengths to be larger than twice the cutoff+skin. Generally, the domain decomposition is dependent on the number of processors requested. +This fix also requires "atom_style dpd"_atom_style.html to be used +due to shared data structures. + [Related commands:] "pair_style dpd/fdt"_pair_dpd_fdt.html, "fix eos/cv"_fix_eos_cv.html diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index d58a24eb13..01ec79e71e 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -101,8 +101,9 @@ See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion. -None of the "fix_modify"_fix_modify.html options are relevant to this -fix. +The "fix_modify"_fix_modify.html {respa} option is supported by +this fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. This fix computes a vector list of 7 quantities, which can be accessed by various "output commands"_Section_howto.html#howto_15. The diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 232d35ba41..6674f3351c 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -104,6 +104,10 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy stored in the spring to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the spring energy = 0.5 * K * r^2. diff --git a/doc/src/fix_spring_chunk.txt b/doc/src/fix_spring_chunk.txt index 295961bce3..299300e8c6 100644 --- a/doc/src/fix_spring_chunk.txt +++ b/doc/src/fix_spring_chunk.txt @@ -55,6 +55,10 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy stored in all the springs to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is the energy of all the springs, i.e. 0.5 * K * r^2 per-spring. diff --git a/doc/src/fix_spring_rg.txt b/doc/src/fix_spring_rg.txt index 768ed0cc4a..bff6b38e7e 100644 --- a/doc/src/fix_spring_rg.txt +++ b/doc/src/fix_spring_rg.txt @@ -56,6 +56,10 @@ 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. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + [Restrictions:] none [Related commands:] diff --git a/doc/src/fix_spring_self.txt b/doc/src/fix_spring_self.txt index 113ad966b6..829c27448b 100644 --- a/doc/src/fix_spring_self.txt +++ b/doc/src/fix_spring_self.txt @@ -52,6 +52,10 @@ The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the energy stored in the per-atom springs to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by +this fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar is an energy which is the sum of the spring energy for each atom, where the diff --git a/doc/src/fix_viscous.txt b/doc/src/fix_viscous.txt index 3993b897a1..4a7abc385a 100644 --- a/doc/src/fix_viscous.txt +++ b/doc/src/fix_viscous.txt @@ -86,6 +86,10 @@ by this fix for access by various "output 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. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is modifying forces. Default is the outermost level. + The forces due to this fix are imposed during an energy minimization, invoked by the "minimize"_minimize.html command. This fix should only be used with damped dynamics minimizers that allow for diff --git a/doc/src/fix_wall.txt b/doc/src/fix_wall.txt index 7403311f30..024719f057 100644 --- a/doc/src/fix_wall.txt +++ b/doc/src/fix_wall.txt @@ -251,6 +251,10 @@ fix to add the energy of interaction between atoms and each wall to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar energy and a global vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. Note that the scalar energy is diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt index b5d1c089d4..56616a4f40 100644 --- a/doc/src/fix_wall_region.txt +++ b/doc/src/fix_wall_region.txt @@ -177,6 +177,10 @@ fix to add the energy of interaction between atoms and the wall to the system's potential energy as part of "thermodynamic output"_thermo_style.html. +The "fix_modify"_fix_modify.html {respa} option is supported by this +fix. This allows to set at which level of the "r-RESPA"_run_style.html +integrator the fix is adding its forces. Default is the outermost level. + This fix computes a global scalar energy and a global 3-length vector of forces, which can be accessed by various "output commands"_Section_howto.html#howto_15. The scalar energy is the sum diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 07d5f3d5bb..aa61fc7860 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -122,6 +122,10 @@ Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html to be used in order to properly account for the particle internal energies and temperatures. +Pair style {dpd/fdt} currently also requires +"atom_style dpd"_atom_style.html to be used in conjunction with +"fix shardlow"_fix_shardlow.html due to shared data structures. + [Related commands:] "pair_coeff"_pair_coeff.html, "fix shardlow"_fix_shardlow.html diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index 980ed51a52..5f0e3d9c24 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -223,7 +223,7 @@ pair/local"_compute_pair_local.html command, as {p1}, {p2}, ..., :line -[Restrictions:] none +[Restrictions:] All the granular pair styles are part of the GRANULAR package. It is only enabled if LAMMPS was built with that package. See the "Making diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 9fc2465203..cc38f7ed25 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -155,6 +155,9 @@ computed where dihedral forces are, pair forces are computed at the outermost level, and kspace forces are computed where pair forces are. The inner, middle, outer forces have no defaults. +For fixes that support it, the rRESPA level at which a given fix is +active, can be selected through the "fix_modify"_fix_modify.html command. + The {inner} and {middle} keywords take additional arguments for cutoffs that are used by the pairwise force computations. If the 2 cutoffs for {inner} are 5.0 and 6.0, this means that all pairs up to diff --git a/doc/src/timer.txt b/doc/src/timer.txt index f3c4b7223a..e68d982d31 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -12,17 +12,20 @@ timer command :h3 timer args :pre -{args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} :l +{args} = one or more of {off} or {loop} or {normal} or {full} or {sync} or {nosync} or {timeout} or {every} :l {off} = do not collect or print any timing information {loop} = collect only the total time for the simulation loop {normal} = collect timer information broken down by sections (default) {full} = like {normal} but also include CPU and thread utilzation {sync} = explicitly synchronize MPI tasks between sections - {nosync} = do not synchronize MPI tasks between sections (default) :pre + {nosync} = do not synchronize MPI tasks between sections (default) + {timeout} value = set walltime limit to {value} + {every} value = perform timeout check every {value} steps :pre [Examples:] timer full sync +timer timeout 2:00:00 every 100 timer loop :pre [Description:] @@ -50,8 +53,27 @@ call which meaures load imbalance more accuractly, though it can also slow down the simulation. Using the {nosync} setting (which is the default) turns off this synchronization. -Multiple keywords can be specified. For keywords that are mutually -exclusive, the last one specified takes effect. +With the {timeout} keyword a walltime limit can be imposed that affects +"run"_run.html and "minimize"_minimize.html commands. If the time +limit it reached, ongoing calculations will be stopped on the next +step that is a multiple of the value specified with {every}. All +follwing run or minimize commands will be skipped until the timeout +is reset or turned off by a new {timer} command. The timeout value +can be "off" or "unlimited" to turn the timeout off, otherwise a +single number is interpreted as seconds, two numbers separated by +a colon (MM:SS) as minutes and seconds and three numbers separated +by colons as hours, minutes and seconds, respectively. + +The {every} keyword sets how frequent during a run or minimization +the wall clock will be checked. This check count applies to the outer +iterations or time steps during minimizations or r-RESPA runs, respectively. +Checking for timeout very often, can slow a calculation down, checking +too infrequent makes the timeout measurement less accurate and the run +will be stopped later than desired. + +Multiple keywords can be specified with the {timer} command. For +keywords that are mutually exclusive, the last one specified takes +effect. NOTE: Using the {full} and {sync} options provides the most detailed and accurate timing information, but can also have a negative @@ -71,3 +93,5 @@ can just use the {loop} or {off} setting. [Default:] timer normal nosync +timer timeout off +timer every 10 :pre