git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15201 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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,

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

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

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:]
 

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

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

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

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

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

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,

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

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.

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

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

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

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

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

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

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.

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.

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:]

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

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

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

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

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

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

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

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