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

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sjplimp 2016-06-17 23:24:05 +00:00
parent d89ee2a40d
commit b161fbb52a
60 changed files with 320 additions and 92 deletions
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18
doc/html/Section_commands.html
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@ -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>

10
doc/html/_sources/Section_commands.txt
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@ -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

6
doc/html/_sources/accelerate_gpu.txt
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@ -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
* 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

1
doc/html/_sources/compute.txt
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@ -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

5
doc/html/_sources/compute_rigid_local.txt
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@ -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
""""""""""""""""

4
doc/html/_sources/fix_addforce.txt
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@ -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

4
doc/html/_sources/fix_addtorque.txt
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@ -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

7
doc/html/_sources/fix_aveforce.txt
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@ -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
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
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

7
doc/html/_sources/fix_drag.txt
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@ -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
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
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

4
doc/html/_sources/fix_efield.txt
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@ -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

4
doc/html/_sources/fix_gravity.txt
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@ -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,

4
doc/html/_sources/fix_indent.txt
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@ -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".

17
doc/html/_sources/fix_modify.txt
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@ -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

4
doc/html/_sources/fix_orient.txt
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@ -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

8
doc/html/_sources/fix_qeq_comb.txt
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@ -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
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
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

4
doc/html/_sources/fix_restrain.txt
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@ -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

10
doc/html/_sources/fix_setforce.txt
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@ -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
are relevant to this fix.
No information about this fix is written to :doc:`binary restart files <restart>`.
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

3
doc/html/_sources/fix_shardlow.txt
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@ -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
""""""""""""""""

5
doc/html/_sources/fix_smd.txt
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@ -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
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 vector list of 7 quantities, which can be accessed
by various :ref:`output commands <howto_15>`. The

4
doc/html/_sources/fix_spring.txt
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@ -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.

4
doc/html/_sources/fix_spring_chunk.txt
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@ -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.

4
doc/html/_sources/fix_spring_rg.txt
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@ -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

4
doc/html/_sources/fix_spring_self.txt
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@ -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

4
doc/html/_sources/fix_viscous.txt
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@ -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

4
doc/html/_sources/fix_wall.txt
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@ -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

4
doc/html/_sources/fix_wall_region.txt
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@ -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

4
doc/html/_sources/pair_dpd_fdt.txt
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@ -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
""""""""""""""""

2
doc/html/_sources/pair_gran.txt
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@ -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.

3
doc/html/_sources/run_style.txt
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@ -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

45
doc/html/_sources/timer.txt
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@ -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
problems. This can be done at different levels of detail and
accuracy. For more information about the timing output, see this
:ref:`discussion of screen output <start_8>`.
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
information about the timing output, see this :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
exclusive, the last one specified takes effect.
With the *timeout* keyword a walltime limit can be imposed that
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

6
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@ -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>include the GPU package and build LAMMPS</li>
<li>build the library in lib/gpu for your GPU hardware with the desired precision settings</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>

1
doc/html/compute.html
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@ -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>

4
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@ -252,8 +252,8 @@ corresponding attribute is in:</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
<p>This compute is part of the RIGID 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>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

3
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@ -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

3
doc/html/fix_addtorque.html
View File

@ -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

6
doc/html/fix_aveforce.html
View File

@ -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
are relevant to this fix.</p>
<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>
<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

6
doc/html/fix_drag.html
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@ -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
are relevant to this fix.</p>
<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>
<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

3
doc/html/fix_efield.html
View File

@ -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

3
doc/html/fix_gravity.html
View File

@ -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,

3
doc/html/fix_indent.html
View File

@ -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>

16
doc/html/fix_modify.html
View File

@ -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>

3
doc/html/fix_orient.html
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@ -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

7
doc/html/fix_qeq_comb.html
View File

@ -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
are relevant to this fix.</p>
<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>
<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

3
doc/html/fix_restrain.html
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@ -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

9
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@ -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
are relevant to this fix.</p>
<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>
<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

2
doc/html/fix_shardlow.html
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@ -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>

5
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@ -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
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 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

3
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@ -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>

3
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@ -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>

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@ -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>

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@ -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

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@ -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

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@ -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

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@ -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

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@ -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>

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@ -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

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@ -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

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43
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@ -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
problems. This can be done at different levels of detail and
accuracy. For more 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>
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
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>
<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
exclusive, the last one specified takes effect.</p>
<p>With the <em>timeout</em> keyword a walltime limit can be imposed that
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>

49
doc/src/timer.txt
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@ -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}
{every} value = perform timeout check every {value} steps :pre
{timeout} elapse = set walltime limit to {elapse}
{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
problems. This can be done at different levels of detail and
accuracy. For more information about the timing output, see this
"discussion of screen output"_Section_start.html#start_8.
information for determining performance and load imbalance problems.
This can be done at different levels of detail and accuracy. For more
information about the timing output, see this "discussion of screen
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
"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.
With the {timeout} keyword a walltime limit can be imposed that
affects the "run"_run.html and "minimize"_minimize.html 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 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.
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 "r-RESPA
runs"_run_style.html, 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