git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15202 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_commands.html

@@ -923,35 +923,35 @@ KOKKOS, o = USER-OMP, t = OPT.</p>
 <td><a class="reference internal" href="compute_rdf.html"><span class="doc">rdf</span></a></td>
 <td><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce</span></a></td>
 <td><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce/region</span></a></td>
-<td><a class="reference internal" href="compute_slice.html"><span class="doc">slice</span></a></td>
+<td><a class="reference internal" href="compute_rigid_local.html"><span class="doc">rigid/local</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_sna_atom.html"><span class="doc">sna/atom</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_slice.html"><span class="doc">slice</span></a></td>
+<td><a class="reference internal" href="compute_sna_atom.html"><span class="doc">sna/atom</span></a></td>
 <td><a class="reference internal" href="compute_sna_atom.html"><span class="doc">snad/atom</span></a></td>
 <td><a class="reference internal" href="compute_sna_atom.html"><span class="doc">snav/atom</span></a></td>
 <td><a class="reference internal" href="compute_stress_atom.html"><span class="doc">stress/atom</span></a></td>
 <td><a class="reference internal" href="compute_temp.html"><span class="doc">temp (k)</span></a></td>
-<td><a class="reference internal" href="compute_temp_asphere.html"><span class="doc">temp/asphere</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_temp_body.html"><span class="doc">temp/body</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_temp_asphere.html"><span class="doc">temp/asphere</span></a></td>
+<td><a class="reference internal" href="compute_temp_body.html"><span class="doc">temp/body</span></a></td>
 <td><a class="reference internal" href="compute_temp_chunk.html"><span class="doc">temp/chunk</span></a></td>
 <td><a class="reference internal" href="compute_temp_com.html"><span class="doc">temp/com</span></a></td>
 <td><a class="reference internal" href="compute_temp_deform.html"><span class="doc">temp/deform</span></a></td>
 <td><a class="reference internal" href="compute_temp_partial.html"><span class="doc">temp/partial</span></a></td>
-<td><a class="reference internal" href="compute_temp_profile.html"><span class="doc">temp/profile</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">temp/ramp</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="compute_temp_profile.html"><span class="doc">temp/profile</span></a></td>
+<td><a class="reference internal" href="compute_temp_ramp.html"><span class="doc">temp/ramp</span></a></td>
 <td><a class="reference internal" href="compute_temp_region.html"><span class="doc">temp/region</span></a></td>
 <td><a class="reference internal" href="compute_temp_sphere.html"><span class="doc">temp/sphere</span></a></td>
 <td><a class="reference internal" href="compute_ti.html"><span class="doc">ti</span></a></td>
 <td><a class="reference internal" href="compute_torque_chunk.html"><span class="doc">torque/chunk</span></a></td>
-<td><a class="reference internal" href="compute_vacf.html"><span class="doc">vacf</span></a></td>
 </tr>
-<tr class="row-odd"><td><a class="reference internal" href="compute_vcm_chunk.html"><span class="doc">vcm/chunk</span></a></td>
+<tr class="row-odd"><td><a class="reference internal" href="compute_vacf.html"><span class="doc">vacf</span></a></td>
+<td><a class="reference internal" href="compute_vcm_chunk.html"><span class="doc">vcm/chunk</span></a></td>
 <td><a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">voronoi/atom</span></a></td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
-<td>&nbsp;</td>
 </tr>
 </tbody>
 </table>

doc/html/_sources/Section_commands.txt

@@ -543,15 +543,15 @@ KOKKOS, o = USER-OMP, t = OPT.
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
 | :doc:`pair/local <compute_pair_local>`         | :doc:`pe <compute_pe>`                         | :doc:`pe/atom <compute_pe_atom>`                 | :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure <compute_pressure>`                 | :doc:`property/atom <compute_property_atom>`             |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
-| :doc:`property/local <compute_property_local>` | :doc:`property/chunk <compute_property_chunk>` | :doc:`rdf <compute_rdf>`                         | :doc:`reduce <compute_reduce>`                   | :doc:`reduce/region <compute_reduce>`              | :doc:`slice <compute_slice>`                             |
+| :doc:`property/local <compute_property_local>` | :doc:`property/chunk <compute_property_chunk>` | :doc:`rdf <compute_rdf>`                         | :doc:`reduce <compute_reduce>`                   | :doc:`reduce/region <compute_reduce>`              | :doc:`rigid/local <compute_rigid_local>`                 |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
-| :doc:`sna/atom <compute_sna_atom>`             | :doc:`snad/atom <compute_sna_atom>`            | :doc:`snav/atom <compute_sna_atom>`              | :doc:`stress/atom <compute_stress_atom>`         | :doc:`temp (k) <compute_temp>`                     | :doc:`temp/asphere <compute_temp_asphere>`               |
+| :doc:`slice <compute_slice>`                   | :doc:`sna/atom <compute_sna_atom>`             | :doc:`snad/atom <compute_sna_atom>`              | :doc:`snav/atom <compute_sna_atom>`              | :doc:`stress/atom <compute_stress_atom>`           | :doc:`temp (k) <compute_temp>`                           |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
-| :doc:`temp/body <compute_temp_body>`           | :doc:`temp/chunk <compute_temp_chunk>`         | :doc:`temp/com <compute_temp_com>`               | :doc:`temp/deform <compute_temp_deform>`         | :doc:`temp/partial <compute_temp_partial>`         | :doc:`temp/profile <compute_temp_profile>`               |
+| :doc:`temp/asphere <compute_temp_asphere>`     | :doc:`temp/body <compute_temp_body>`           | :doc:`temp/chunk <compute_temp_chunk>`           | :doc:`temp/com <compute_temp_com>`               | :doc:`temp/deform <compute_temp_deform>`           | :doc:`temp/partial <compute_temp_partial>`               |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
-| :doc:`temp/ramp <compute_temp_ramp>`           | :doc:`temp/region <compute_temp_region>`       | :doc:`temp/sphere <compute_temp_sphere>`         | :doc:`ti <compute_ti>`                           | :doc:`torque/chunk <compute_torque_chunk>`         | :doc:`vacf <compute_vacf>`                               |
+| :doc:`temp/profile <compute_temp_profile>`     | :doc:`temp/ramp <compute_temp_ramp>`           | :doc:`temp/region <compute_temp_region>`         | :doc:`temp/sphere <compute_temp_sphere>`         | :doc:`ti <compute_ti>`                             | :doc:`torque/chunk <compute_torque_chunk>`               |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
-| :doc:`vcm/chunk <compute_vcm_chunk>`           | :doc:`voronoi/atom <compute_voronoi_atom>`     |                                                  |                                                  |                                                    |                                                          |
+| :doc:`vacf <compute_vacf>`                     | :doc:`vcm/chunk <compute_vcm_chunk>`           | :doc:`voronoi/atom <compute_voronoi_atom>`       |                                                  |                                                    |                                                          |
 +------------------------------------------------+------------------------------------------------+--------------------------------------------------+--------------------------------------------------+----------------------------------------------------+----------------------------------------------------------+
 
 These are additional compute styles in USER packages, which can be

doc/html/_sources/accelerate_gpu.txt

@@ -29,10 +29,10 @@ long-range Coulombics.  It has the following general features:
   NVIDIA support as well as more general OpenCL support, so that the
   same functionality can eventually be supported on a variety of GPU
   hardware.
-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
+* build the library in lib/gpu for your GPU hardware with the desired precision settings
-* include the GPU package and build LAMMPS
+* 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

doc/html/_sources/compute.txt

@@ -222,6 +222,7 @@ section of :ref:`this page <cmd_5>`.
 * :doc:`rdf <compute_rdf>` - radial distribution function g(r) histogram of group of atoms
 * :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
 * :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
+* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
 * :doc:`slice <compute_slice>` - extract values from global vector or array
 * :doc:`sna/atom <compute_sna_atom>` - calculate bispectrum coefficients for each atom
 * :doc:`snad/atom <compute_sna_atom>` - derivative of bispectrum coefficients for each atom

doc/html/_sources/compute_rigid_local.txt

@@ -159,7 +159,10 @@ corresponding attribute is in:
 
 Restrictions
 """"""""""""
- none
+
+
+This compute is part of the RIGID package.  It is only enabled if
+LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.
 
 Related commands
 """"""""""""""""

doc/html/_sources/fix_addforce.txt

@@ -149,6 +149,10 @@ 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 :doc:`fix_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  The scalar is the potential
 energy discussed above.  The vector is the total force on the group of

doc/html/_sources/fix_addtorque.txt

@@ -65,6 +65,10 @@ 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 :doc:`fix_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.
 The scalar is the potential energy discussed above.  The vector is the

doc/html/_sources/fix_aveforce.txt

@@ -97,8 +97,11 @@ 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 :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files <restart>`.
-are relevant to this fix.
+
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  This is the

doc/html/_sources/fix_drag.txt

@@ -41,8 +41,11 @@ in the simulation.
 Restart, fix_modify, output, run start/stop, minimize info
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files <restart>`.
-are relevant to this fix.
+
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  This is the

doc/html/_sources/fix_efield.txt

@@ -133,6 +133,10 @@ 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 :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  The scalar is the potential
 energy discussed above.  The vector is the total force added to the

doc/html/_sources/fix_gravity.txt

@@ -128,6 +128,10 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the gravitational potential energy of the system to the
 system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 This fix computes a global scalar which can be accessed by various
 :ref:`output commands <howto_15>`.  This scalar is the
 gravitational potential energy of the particles in the defined field,

doc/html/_sources/fix_indent.txt

@@ -187,6 +187,10 @@ fix to add the energy of interaction between atoms and the indenter to
 the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  The energy of each particle interacting
 with the indenter is K/3 (r - R)^3.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  The scalar and vector values
 calculated by this fix are "extensive".

doc/html/_sources/fix_modify.txt

@@ -12,12 +12,13 @@ Syntax
 
 * fix-ID = ID of the fix to modify
 * one or more keyword/value pairs may be appended
-* keyword = *temp* or *press* or *energy*
+* keyword = *temp* or *press* or *energy* or *respa*
 .. parsed-literal::
 
      *temp* value = compute ID that calculates a temperature
      *press* value = compute ID that calculates a pressure
      *energy* value = *yes* or *no*
+     *respa* value = *1* to *max respa level* or *0* (= outmost level)
 
 
 
@@ -28,6 +29,7 @@ Examples
 
    fix_modify 3 temp myTemp press myPress
    fix_modify 1 energy yes
+   fix_modify tether respa 2
 
 Description
 """""""""""
@@ -63,6 +65,17 @@ fix-ID of the appropriate fix.  Note that you must use this setting
 for a fix if you are using it when performing an :doc:`energy minimization <minimize>` 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 :doc:`r-RESPA <run_style>` 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
@@ -76,7 +89,7 @@ Default
 """""""
 
 The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no.
+by fix, energy = no, respa = 0.
 
 
 .. _lws: http://lammps.sandia.gov

doc/html/_sources/fix_orient.txt

@@ -134,6 +134,10 @@ fix to add the potential energy of atom interactions with the grain
 boundary driving force to the system's potential energy as part of
 :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by these
+fixes. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator a fix is adding its forces. Default is the outermost level.
+
 This fix calculates a global scalar which can be accessed by various
 :ref:`output commands <howto_15>`.  The scalar is the
 potential energy change due to this fix.  The scalar value calculated

doc/html/_sources/fix_qeq_comb.txt

@@ -94,8 +94,12 @@ 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 :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files <restart>`.
-are relevant to this fix.
+
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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
 :ref:`output commands <howto_15>`.  The vector stores the

doc/html/_sources/fix_restrain.txt

@@ -180,6 +180,10 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the potential energy associated with this fix to the
 system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 .. note::
 
    If you want the fictitious potential energy associated with the

doc/html/_sources/fix_setforce.txt

@@ -102,8 +102,14 @@ 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 :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files <restart>`.
-are relevant to this fix.
+
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  This is the

doc/html/_sources/fix_shardlow.txt

@@ -70,6 +70,9 @@ 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 :doc:`atom_style dpd <atom_style>` to be used
+due to shared data structures.
+
 Related commands
 """"""""""""""""
 

doc/html/_sources/fix_smd.txt

@@ -108,8 +108,9 @@ See the :doc:`read_restart <read_restart>` 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 :doc:`fix_modify <fix_modify>` options are relevant to this
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
-fix.
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  The

doc/html/_sources/fix_spring.txt

@@ -111,6 +111,10 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the energy stored in the spring to the system's potential
 energy as part of :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 This fix computes a global scalar which can be accessed by various
 :ref:`output commands <howto_15>`.  The scalar is the
 spring energy = 0.5 * K * r^2.

doc/html/_sources/fix_spring_chunk.txt

@@ -57,6 +57,10 @@ The :doc:`fix_modify <fix_modify>` *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 :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 This fix computes a global scalar which can be accessed by various
 :ref:`output commands <howto_15>`.  The scalar is the
 energy of all the springs, i.e. 0.5 * K * r^2 per-spring.

doc/html/_sources/fix_spring_rg.txt

@@ -61,6 +61,10 @@ by this fix for access by various :ref:`output commands <howto_15>`.  No paramet
 be used with the *start/stop* keywords of the :doc:`run <run>` command.
 This fix is not invoked during :doc:`energy minimization <minimize>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 Restrictions
 """"""""""""
  none

doc/html/_sources/fix_spring_self.txt

@@ -54,6 +54,10 @@ The :doc:`fix_modify <fix_modify>` *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 :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
+this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+integrator the fix is adding its forces. Default is the outermost level.
+
 This fix computes a global scalar which can be accessed by various
 :ref:`output commands <howto_15>`.  The scalar is an
 energy which is the sum of the spring energy for each atom, where the

doc/html/_sources/fix_viscous.txt

@@ -92,6 +92,10 @@ are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various :ref:`output commands <howto_15>`.  No parameter of this fix can
 be used with the *start/stop* keywords of the :doc:`run <run>` command.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :doc:`minimize <minimize>` command.  This fix should only
 be used with damped dynamics minimizers that allow for

doc/html/_sources/fix_wall.txt

@@ -289,6 +289,10 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the energy of interaction between atoms and each wall to
 the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  Note that the scalar energy is
 the sum of interactions with all defined walls.  If you want the

doc/html/_sources/fix_wall_region.txt

@@ -190,6 +190,10 @@ The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
 fix to add the energy of interaction between atoms and the wall to the
 system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+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 :ref:`output commands <howto_15>`.  The scalar energy is the sum
 of energy interactions for all particles interacting with the wall

doc/html/_sources/pair_dpd_fdt.txt

@@ -135,6 +135,10 @@ Pair style *dpd/fdt/energy* requires :doc:`atom_style dpd <atom_style>`
 to be used in order to properly account for the particle internal
 energies and temperatures.
 
+Pair style *dpd/fdt* currently also requires
+:doc:`atom_style dpd <atom_style>` to be used in conjunction with
+:doc:`fix shardlow <fix_shardlow>` due to shared data structures.
+
 Related commands
 """"""""""""""""
 

doc/html/_sources/pair_gran.txt

@@ -246,7 +246,7 @@ These extra quantites can be accessed by the :doc:`compute pair/local <compute_p
 
 Restrictions
 """"""""""""
- none
+
 
 All the granular pair styles are part of the GRANULAR package.  It is
 only enabled if LAMMPS was built with that package.  See the :ref:`Making LAMMPS <start_3>` section for more info.

doc/html/_sources/run_style.txt

@@ -170,6 +170,9 @@ 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 :doc:`fix_modify <fix_modify>` 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/html/_sources/timer.txt

@@ -10,7 +10,7 @@ Syntax
 
    timer args
 
-* *args* = one or more of *off* or *loop* or *normal* or *full* or *sync* or *nosync*
+* *args* = one or more of *off* or *loop* or *normal* or *full* or *sync* or *nosync* or *timeout* or *every*
 .. parsed-literal::
 
      *off* = do not collect or print any timing information
@@ -19,6 +19,8 @@ Syntax
      *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)
+     *timeout* elapse = set walltime limit to *elapse*
+     *every* Ncheck = perform timeout check every *Ncheck* steps
 
 Examples
 """"""""
@@ -26,19 +28,19 @@ Examples
 .. parsed-literal::
 
    timer full sync
+   timer timeout 2:00:00 every 100
    timer loop
 
 Description
 """""""""""
 
-Select the level of detail LAMMPS performs its CPU timings.
+Select the level of detail at which LAMMPS performs its CPU timings.
 
 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
-valuable information for determining performance and load imbalance
+information for determining performance and load imbalance problems.
-problems.  This can be done at different levels of detail and
+This can be done at different levels of detail and accuracy.  For more
-accuracy.  For more information about the timing output, see this
+information about the timing output, see this :ref:`discussion of screen output <start_8>`.
-:ref:`discussion of screen output <start_8>`.
 
 The *off* setting will turn all time measurements off. The *loop*
 setting will only measure the total time for a run and not collect any
@@ -54,8 +56,29 @@ 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
+With the *timeout* keyword a walltime limit can be imposed that
-exclusive, the last one specified takes effect.
+affects the :doc:`run <run>` and :doc:`minimize <minimize>` commands.  If
+the time limit is reached, the run or energy minimization will exit on
+the next step or iteration that is a multiple of the *Ncheck* value
+specified with the *every* keyword.  All subsequent run or minimize
+commands in the input script will be skipped until the timeout is
+reset or turned off by a new *timer* command.  The timeout *elapse*
+value can be specified as *off* or *unlimited* to impose no timeout
+condition (which is the default).  The *elapse* setting can be
+specified as a single number for seconds, two numbers separated by a
+colon (MM:SS) for minutes and seconds, or as three numbers separated
+by colons for hours, minutes, and seconds.
+
+The *every* keyword sets how frequently during a run or energy
+minimization the wall clock will be checked.  This check count applies
+to the outer iterations or time steps during minimizations or :doc:`r-RESPA runs <run_style>`, respectively.  Checking for timeout too often,
+can slow a calculation down.  Checking too infrequently can make the
+timeout measurement less accurate, with the run being 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::
 
@@ -80,7 +103,11 @@ Related commands
 Default
 """""""
 
-timer normal nosync
+.. parsed-literal::
+
+   timer normal nosync
+   timer timeout off
+   timer every 10
 
 
 .. _lws: http://lammps.sandia.gov

doc/html/accelerate_gpu.html

@@ -154,10 +154,10 @@ NVIDIA support as well as more general OpenCL support, so that the
 same functionality can eventually be supported on a variety of GPU
 hardware.</li>
 </ul>
-<p>Here is a quick overview of how to use the GPU package:</p>
+<p>Here is a quick overview of how to enable and use the GPU package:</p>
 <ul class="simple">
-<li>build the library in lib/gpu for your GPU hardware wity desired precision</li>
+<li>build the library in lib/gpu for your GPU hardware with the desired precision settings</li>
-<li>include the GPU package and build LAMMPS</li>
+<li>install the GPU package and build LAMMPS as usual</li>
 <li>use the mpirun command to set the number of MPI tasks/node which determines the number of MPI tasks/GPU</li>
 <li>specify the # of GPUs per node</li>
 <li>use GPU styles in your input script</li>

doc/html/compute.html

@@ -323,6 +323,7 @@ section of <a class="reference internal" href="Section_commands.html#cmd-5"><spa
 <li><a class="reference internal" href="compute_rdf.html"><span class="doc">rdf</span></a> - radial distribution function g(r) histogram of group of atoms</li>
 <li><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce</span></a> - combine per-atom quantities into a single global value</li>
 <li><a class="reference internal" href="compute_reduce.html"><span class="doc">reduce/region</span></a> - same as compute reduce, within a region</li>
+<li><a class="reference internal" href="compute_rigid_local.html"><span class="doc">rigid/local</span></a> - extract rigid body attributes</li>
 <li><a class="reference internal" href="compute_slice.html"><span class="doc">slice</span></a> - extract values from global vector or array</li>
 <li><a class="reference internal" href="compute_sna_atom.html"><span class="doc">sna/atom</span></a> - calculate bispectrum coefficients for each atom</li>
 <li><a class="reference internal" href="compute_sna_atom.html"><span class="doc">snad/atom</span></a> - derivative of bispectrum coefficients for each atom</li>

doc/html/compute_rigid_local.html

@@ -252,8 +252,8 @@ corresponding attribute is in:</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
-<blockquote>
+<p>This compute is part of the RIGID package.  It is only enabled if
-<div>none</div></blockquote>
+LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/fix_addforce.html

@@ -243,6 +243,9 @@ needed so that the <a class="reference internal" href="minimize.html"><span clas
 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.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by
+this fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar and a global 3-vector of forces,
 which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the potential
 energy discussed above.  The vector is the total force on the group of

doc/html/fix_addtorque.html

@@ -178,6 +178,9 @@ needed so that the <a class="reference internal" href="minimize.html"><span clas
 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.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by
+this fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its torque. Default is the outermost level.</p>
 <p>This fix computes a global scalar and a global 3-vector, which can be
 accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.
 The scalar is the potential energy discussed above.  The vector is the

doc/html/fix_aveforce.html

@@ -201,8 +201,10 @@ more instructions on how to use the accelerated styles effectively.</p>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
 <h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
-<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
+<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
-are relevant to this fix.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global 3-vector of forces, which can be accessed
 by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  This is the
 total force on the group of atoms before the forces on individual

doc/html/fix_drag.html

@@ -159,8 +159,10 @@ in the simulation.</p>
 </div>
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
 <h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
-<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
+<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
-are relevant to this fix.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global 3-vector of forces, which can be accessed
 by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  This is the
 total force on the group of atoms by the drag force.  The vector

doc/html/fix_efield.html

@@ -231,6 +231,9 @@ quantity but is needed so that the <a class="reference internal" href="minimize.
 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.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar and a global 3-vector of forces,
 which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the potential
 energy discussed above.  The vector is the total force added to the

doc/html/fix_gravity.html

@@ -228,6 +228,9 @@ more instructions on how to use the accelerated styles effectively.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the gravitational potential energy of the system to the
 system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  This scalar is the
 gravitational potential energy of the particles in the defined field,

doc/html/fix_indent.html

@@ -283,6 +283,9 @@ fix 1 all indent $k sphere ...
 fix to add the energy of interaction between atoms and the indenter to
 the system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.  The energy of each particle interacting
 with the indenter is K/3 (r - R)^3.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar energy and a global 3-vector of
 forces (on the indenter), which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar and vector values
 calculated by this fix are &#8220;extensive&#8221;.</p>

doc/html/fix_modify.html

@@ -134,18 +134,20 @@
 <ul class="simple">
 <li>fix-ID = ID of the fix to modify</li>
 <li>one or more keyword/value pairs may be appended</li>
-<li>keyword = <em>temp</em> or <em>press</em> or <em>energy</em></li>
+<li>keyword = <em>temp</em> or <em>press</em> or <em>energy</em> or <em>respa</em></li>
 </ul>
 <pre class="literal-block">
 <em>temp</em> value = compute ID that calculates a temperature
 <em>press</em> value = compute ID that calculates a pressure
 <em>energy</em> value = <em>yes</em> or <em>no</em>
+<em>respa</em> value = <em>1</em> to <em>max respa level</em> or <em>0</em> (= outmost level)
 </pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix_modify</span> <span class="mi">3</span> <span class="n">temp</span> <span class="n">myTemp</span> <span class="n">press</span> <span class="n">myPress</span>
 <span class="n">fix_modify</span> <span class="mi">1</span> <span class="n">energy</span> <span class="n">yes</span>
+<span class="n">fix_modify</span> <span class="n">tether</span> <span class="n">respa</span> <span class="mi">2</span>
 </pre></div>
 </div>
 </div>
@@ -178,6 +180,16 @@ the keyword f_ID in the thermo_style custom command, where ID is the
 fix-ID of the appropriate fix.  Note that you must use this setting
 for a fix if you are using it when performing an <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a> and if you want the energy and forces it
 produces to be part of the optimization criteria.</p>
+<p>For fixes that set or modify forces, it may be possible to select at
+which <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a> level the fix operates via the <em>respa</em>
+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 <em>0</em> for the RESPA level. The affected fix has to be
+programmed to support this feature; if not, <em>fix_modify</em> 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.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
@@ -191,7 +203,7 @@ produces to be part of the optimization criteria.</p>
 <div class="section" id="default">
 <h2>Default</h2>
 <p>The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no.</p>
+by fix, energy = no, respa = 0.</p>
 </div>
 </div>
 

doc/html/fix_orient.html

@@ -240,6 +240,9 @@ writing the orientation files is given in <a class="reference internal" href="#w
 fix to add the potential energy of atom interactions with the grain
 boundary driving force to the system&#8217;s potential energy as part of
 <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by these
+fixes. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator a fix is adding its forces. Default is the outermost level.</p>
 <p>This fix calculates a global scalar which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the
 potential energy change due to this fix.  The scalar value calculated

doc/html/fix_qeq_comb.html

@@ -199,8 +199,11 @@ more instructions on how to use the accelerated styles effectively.</p>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
 <h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
-<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
+<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
-are relevant to this fix.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is performing charge equilibration. Default is
+the outermost level.</p>
 <p>This fix produces a per-atom vector which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The vector stores the
 gradient of the charge on each atom.  The per-atom values be accessed

doc/html/fix_restrain.html

@@ -267,6 +267,9 @@ current dihedral angle phi is equal to phi0.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the potential energy associated with this fix to the
 system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If you want the fictitious potential energy associated with the

doc/html/fix_setforce.html

@@ -204,8 +204,13 @@ more instructions on how to use the accelerated styles effectively.</p>
 <hr class="docutils" />
 <div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
 <h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
-<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.  None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
+<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
-are relevant to this fix.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by
+this fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+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.</p>
 <p>This fix computes a global 3-vector of forces, which can be accessed
 by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  This is the
 total force on the group of atoms before the forces on individual

doc/html/fix_shardlow.html

@@ -180,6 +180,8 @@ integration, e.g. <a class="reference internal" href="fix_nve.html"><span class=
 lengths to be larger than twice the cutoff+skin.  Generally, the
 domain decomposition is dependent on the number of processors
 requested.</p>
+<p>This fix also requires <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a> to be used
+due to shared data structures.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/fix_smd.html

@@ -220,8 +220,9 @@ distance and the running PMF to <a class="reference internal" href="restart.html
 See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> 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.</p>
-<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by
-fix.</p>
+this fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a vector list of 7 quantities, which can be accessed
 by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The
 quantities in the vector are in this order: the x-, y-, and

doc/html/fix_spring.html

@@ -222,6 +222,9 @@ way, as explained on the <a class="reference internal" href="fix_rigid.html"><sp
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy stored in the spring to the system&#8217;s potential
 energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the
 spring energy = 0.5 * K * r^2.</p>

doc/html/fix_spring_chunk.html

@@ -173,6 +173,9 @@ atom.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy stored in all the springs to the system&#8217;s potential
 energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is the
 energy of all the springs, i.e. 0.5 * K * r^2 per-spring.</p>

doc/html/fix_spring_rg.html

@@ -174,6 +174,9 @@ are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
 be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.
 This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 </div>
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>

doc/html/fix_spring_self.html

@@ -171,6 +171,9 @@ operation of the fix continues in an uninterrupted fashion.</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy stored in the per-atom springs to the system&#8217;s
 potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by
+this fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar which can be accessed by various
 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar is an
 energy which is the sum of the spring energy for each atom, where the

doc/html/fix_viscous.html

@@ -202,6 +202,9 @@ easily be used as a thermostat.</p>
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  No parameter of this fix can
 be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is modifying forces. Default is the outermost level.</p>
 <p>The forces due to this fix are imposed during an energy minimization,
 invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.  This fix should only
 be used with damped dynamics minimizers that allow for

doc/html/fix_wall.html

@@ -362,6 +362,9 @@ perturbation on the particles:</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy of interaction between atoms and each wall to
 the system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar energy and a global vector of
 forces, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  Note that the scalar energy is
 the sum of interactions with all defined walls.  If you want the

doc/html/fix_wall_region.html

@@ -287,6 +287,9 @@ region surface (r &gt; 0).</p>
 <p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
 fix to add the energy of interaction between atoms and the wall to the
 system&#8217;s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
+<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
+fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
+integrator the fix is adding its forces. Default is the outermost level.</p>
 <p>This fix computes a global scalar energy and a global 3-length vector
 of forces, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.  The scalar energy is the sum
 of energy interactions for all particles interacting with the wall

doc/html/pair_dpd_fdt.html

@@ -235,6 +235,9 @@ stored by ghost atoms.</p>
 <p>Pair style <em>dpd/fdt/energy</em> requires <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
 to be used in order to properly account for the particle internal
 energies and temperatures.</p>
+<p>Pair style <em>dpd/fdt</em> currently also requires
+<a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a> to be used in conjunction with
+<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a> due to shared data structures.</p>
 </div>
 <div class="section" id="related-commands">
 <h2>Related commands</h2>

doc/html/pair_gran.html

@@ -332,8 +332,6 @@ tangential direction.</p>
 <hr class="docutils" />
 <div class="section" id="restrictions">
 <h2>Restrictions</h2>
-<blockquote>
-<div>none</div></blockquote>
 <p>All the granular pair styles are part of the GRANULAR package.  It is
 only enabled if LAMMPS was built with that package.  See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
 <p>These pair styles require that atoms store torque and angular velocity

doc/html/run_style.html

@@ -267,6 +267,8 @@ forces are computed where angle forces are, improper forces are
 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.</p>
+<p>For fixes that support it, the rRESPA level at which a given fix is
+active, can be selected through the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command.</p>
 <p>The <em>inner</em> and <em>middle</em> keywords take additional arguments for
 cutoffs that are used by the pairwise force computations.  If the 2
 cutoffs for <em>inner</em> are 5.0 and 6.0, this means that all pairs up to

doc/html/timer.html

@@ -132,7 +132,7 @@
 </pre></div>
 </div>
 <ul class="simple">
-<li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em></li>
+<li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em> or <em>timeout</em> or <em>every</em></li>
 </ul>
 <pre class="literal-block">
 <em>off</em> = do not collect or print any timing information
@@ -141,24 +141,26 @@
 <em>full</em> = like <em>normal</em> but also include CPU and thread utilzation
 <em>sync</em> = explicitly synchronize MPI tasks between sections
 <em>nosync</em> = do not synchronize MPI tasks between sections (default)
+<em>timeout</em> elapse = set walltime limit to <em>elapse</em>
+<em>every</em> Ncheck = perform timeout check every <em>Ncheck</em> steps
 </pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timer</span> <span class="n">full</span> <span class="n">sync</span>
+<span class="n">timer</span> <span class="n">timeout</span> <span class="mi">2</span><span class="p">:</span><span class="mi">00</span><span class="p">:</span><span class="mi">00</span> <span class="n">every</span> <span class="mi">100</span>
 <span class="n">timer</span> <span class="n">loop</span>
 </pre></div>
 </div>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
-<p>Select the level of detail LAMMPS performs its CPU timings.</p>
+<p>Select the level of detail at which LAMMPS performs its CPU timings.</p>
 <p>During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
-valuable information for determining performance and load imbalance
+information for determining performance and load imbalance problems.
-problems.  This can be done at different levels of detail and
+This can be done at different levels of detail and accuracy.  For more
-accuracy.  For more information about the timing output, see this
+information about the timing output, see this <a class="reference internal" href="Section_start.html#start-8"><span class="std std-ref">discussion of screen output</span></a>.</p>
-<a class="reference internal" href="Section_start.html#start-8"><span class="std std-ref">discussion of screen output</span></a>.</p>
 <p>The <em>off</em> setting will turn all time measurements off. The <em>loop</em>
 setting will only measure the total time for a run and not collect any
 detailed per section information.  With the <em>normal</em> setting, timing
@@ -171,8 +173,27 @@ utilization and thread utilization, when multi-threading is enabled.</p>
 call which meaures load imbalance more accuractly, though it can also
 slow down the simulation.  Using the <em>nosync</em> setting (which is the
 default) turns off this synchronization.</p>
-<p>Multiple keywords can be specified.  For keywords that are mutually
+<p>With the <em>timeout</em> keyword a walltime limit can be imposed that
-exclusive, the last one specified takes effect.</p>
+affects the <a class="reference internal" href="run.html"><span class="doc">run</span></a> and <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> commands.  If
+the time limit is reached, the run or energy minimization will exit on
+the next step or iteration that is a multiple of the <em>Ncheck</em> value
+specified with the <em>every</em> keyword.  All subsequent run or minimize
+commands in the input script will be skipped until the timeout is
+reset or turned off by a new <em>timer</em> command.  The timeout <em>elapse</em>
+value can be specified as <em>off</em> or <em>unlimited</em> to impose no timeout
+condition (which is the default).  The <em>elapse</em> setting can be
+specified as a single number for seconds, two numbers separated by a
+colon (MM:SS) for minutes and seconds, or as three numbers separated
+by colons for hours, minutes, and seconds.</p>
+<p>The <em>every</em> keyword sets how frequently during a run or energy
+minimization the wall clock will be checked.  This check count applies
+to the outer iterations or time steps during minimizations or <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA runs</span></a>, respectively.  Checking for timeout too often,
+can slow a calculation down.  Checking too infrequently can make the
+timeout measurement less accurate, with the run being stopped later
+than desired.</p>
+<p>Multiple keywords can be specified with the <em>timer</em> command.  For
+keywords that are mutually exclusive, the last one specified takes
+effect.</p>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Using the <em>full</em> and <em>sync</em> options provides the most detailed
@@ -196,7 +217,11 @@ can just use the <em>loop</em> or <em>off</em> setting.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<p>timer normal nosync</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timer</span> <span class="n">normal</span> <span class="n">nosync</span>
+<span class="n">timer</span> <span class="n">timeout</span> <span class="n">off</span>
+<span class="n">timer</span> <span class="n">every</span> <span class="mi">10</span>
+</pre></div>
+</div>
 </div>
 </div>
 

doc/src/timer.txt

@@ -19,8 +19,8 @@ timer args :pre
   {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)
-  {timeout} value = set walltime limit to {value}
+  {timeout} elapse = set walltime limit to {elapse}
-  {every} value = perform timeout check every {value} steps :pre
+  {every} Ncheck = perform timeout check every {Ncheck} steps :pre
 
 [Examples:]
 
@@ -30,14 +30,14 @@ timer loop :pre
 
 [Description:]
 
-Select the level of detail LAMMPS performs its CPU timings.
+Select the level of detail at which LAMMPS performs its CPU timings.
 
 During a simulation run LAMMPS collects information about how much
 time is spent in different sections of the code and thus can provide
-valuable information for determining performance and load imbalance
+information for determining performance and load imbalance problems.
-problems.  This can be done at different levels of detail and
+This can be done at different levels of detail and accuracy.  For more
-accuracy.  For more information about the timing output, see this
+information about the timing output, see this "discussion of screen
-"discussion of screen output"_Section_start.html#start_8.
+output"_Section_start.html#start_8.
 
 The {off} setting will turn all time measurements off. The {loop}
 setting will only measure the total time for a run and not collect any
@@ -53,23 +53,26 @@ 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.
 
-With the {timeout} keyword a walltime limit can be imposed that affects
+With the {timeout} keyword a walltime limit can be imposed that
-"run"_run.html  and "minimize"_minimize.html commands. If the time
+affects the "run"_run.html and "minimize"_minimize.html commands.  If
-limit it reached, ongoing calculations will be stopped on the next
+the time limit is reached, the run or energy minimization will exit on
-step that is a multiple of the value specified with {every}. All
+the next step or iteration that is a multiple of the {Ncheck} value
-follwing run or minimize commands will be skipped until the timeout
+specified with the {every} keyword.  All subsequent run or minimize
-is reset or turned off by a new {timer} command. The timeout value
+commands in the input script will be skipped until the timeout is
-can be "off" or "unlimited" to turn the timeout off, otherwise a
+reset or turned off by a new {timer} command.  The timeout {elapse}
-single number is interpreted as seconds, two numbers separated by
+value can be specified as {off} or {unlimited} to impose no timeout
-a colon (MM:SS) as minutes and seconds and three numbers separated
+condition (which is the default).  The {elapse} setting can be
-by colons as hours, minutes and seconds, respectively.
+specified as a single number for seconds, two numbers separated by a
+colon (MM:SS) for minutes and seconds, or as three numbers separated
+by colons for hours, minutes, and seconds.
 
-The {every} keyword sets how frequent during a run or minimization
+The {every} keyword sets how frequently during a run or energy
-the wall clock will be checked. This check count applies to the outer
+minimization the wall clock will be checked.  This check count applies
-iterations or time steps during minimizations or r-RESPA runs, respectively.
+to the outer iterations or time steps during minimizations or "r-RESPA
-Checking for timeout very often, can slow a calculation down, checking
+runs"_run_style.html, respectively.  Checking for timeout too often,
-too infrequent makes the timeout measurement less accurate and the run
+can slow a calculation down.  Checking too infrequently can make the
-will be stopped later than desired.
+timeout measurement less accurate, with the run being stopped later
+than desired.
 
 Multiple keywords can be specified with the {timer} command.  For
 keywords that are mutually exclusive, the last one specified takes