diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 4aca227246..0137066ff7 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -122,8 +122,8 @@ No information about this fix is written to :doc:`binary restart files `. The :doc:`fix_modify ` *energy* option is supported by -this fix to add the global potential "energy" inferred by the added -force to the global potential energy of the system as part of +this fix to add the potential energy inferred by the added force to +the global potential energy of the system as part of :doc:`thermodynamic output `. The default setting for this fix is :doc:`fix_modify energy no `. Note that this energy is a fictitious quantity but is needed so that the @@ -133,21 +133,23 @@ potential energy when atoms move in the direction of the added force. The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to -the global pressure of the system as part of :doc:`thermodynamic -output `. The default setting for this fix is -:doc:`fix_modify virial no `. +both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial no `. The :doc:`fix_modify ` *respa* option is supported by this -fix. This allows to set at which level of the :doc:`r-RESPA ` -integrator the fix is adding its forces. Default is the outermost -level. +fix. This allows to set at which level of the :doc:`r-RESPA +` 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 :doc:`output commands `. -The scalar is the potential energy discussed above. The vector is the -total force on the group of atoms before the forces on individual -atoms are changed by the fix. The scalar and vector values calculated -by this fix are "extensive". +which can be accessed by various :doc:`output commands +`. The scalar is the potential energy discussed above. +The vector is the total force on the group of atoms before the forces +on individual atoms are changed by the fix. The scalar and vector +values calculated by this fix are "extensive". No parameter of this fix can be used with the *start/stop* keywords of the :doc:`run ` command. diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst index 5344f29459..3bcc6bdaa5 100644 --- a/doc/src/fix_client_md.rst +++ b/doc/src/fix_client_md.rst @@ -80,10 +80,11 @@ the global potential energy of the system as part of this fix is :doc:`fix_modify energy yes `. The :doc:`fix_modify ` *virial* option is supported by -this fix to add the contribution computed by the external program to -the global pressure of the system as part of :doc:`thermodynamic -output `. The default setting for this fix is -:doc:`fix_modify virial yes `. +this fix to add the contribution computed by the server application to +the global pressure of the system via the :doc:`compute pressure +` command. This can be accessed by +:doc:`thermodynamic output `. The default setting for +this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the potential diff --git a/doc/src/fix_cmap.rst b/doc/src/fix_cmap.rst index 83e4b6d9b8..94f8a903e9 100644 --- a/doc/src/fix_cmap.rst +++ b/doc/src/fix_cmap.rst @@ -109,10 +109,12 @@ default setting for this fix is :doc:`fix_modify energy yes `. The :doc:`fix_modify ` *virial* option is supported by -this fix to add the contribution due to the CMAP interactions between -atoms to the global prsesure of the system as part of -:doc:`thermodynamic output `. The default setting for -this fix is :doc:`fix_modify virial yes `. +this fix to add the contribution due to the CMAP interactions to both +the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the potential diff --git a/doc/src/fix_efield.rst b/doc/src/fix_efield.rst index fdfc8b427b..2feaa61db7 100644 --- a/doc/src/fix_efield.rst +++ b/doc/src/fix_efield.rst @@ -133,8 +133,11 @@ due to the electric field. The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the added forces on atoms to -the system's virial as part of :doc:`thermodynamic output -`. The default is *virial no* +both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` :doc:`compute stress/atom +` commands. The former can be accessed by +:doc:`thermodynamic output `. The default setting for +this fix is :doc:`fix_modify virial no `. The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index cdb87c68a9..481df30628 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -167,9 +167,11 @@ potential energy when atoms move in the direction of the added force. The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution computed by the external program to -the global pressure of the system as part of :doc:`thermodynamic -output `. The default setting for this fix is -:doc:`fix_modify virial yes `. +both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` :doc:`compute stress/atom +` commands. The former can be accessed by +:doc:`thermodynamic output `. The default setting for +this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the potential diff --git a/doc/src/fix_latte.rst b/doc/src/fix_latte.rst index 563656be5f..58a8ddbe20 100644 --- a/doc/src/fix_latte.rst +++ b/doc/src/fix_latte.rst @@ -116,6 +116,13 @@ potential energy of the system as part of :doc:`thermodynamic output `. The default setting for this fix is :doc:`fix_modify energy yes `. +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution compute by LATTE to the global +pressure of the system via the :doc:`compute pressure +` command. This can be accessed by +:doc:`thermodynamic output `. The default setting for +this fix is :doc:`fix_modify virial yes `. + The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution computed by LATTE to the global pressure of the system as part of :doc:`thermodynamic output diff --git a/doc/src/fix_lb_rigid_pc_sphere.rst b/doc/src/fix_lb_rigid_pc_sphere.rst index 66b5f5f8d5..b6a19c98d5 100644 --- a/doc/src/fix_lb_rigid_pc_sphere.rst +++ b/doc/src/fix_lb_rigid_pc_sphere.rst @@ -50,7 +50,8 @@ This fix is based on the :doc:`fix rigid ` command, and was created to be used in place of that fix, to integrate the equations of motion of spherical rigid bodies when a lattice-Boltzmann fluid is present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in :ref:`Mackay et al. ` to update the positions, velocities, and orientations of +The fix uses the integration algorithm described in :ref:`Mackay et +al. ` to update the positions, velocities, and orientations of a set of spherical rigid bodies experiencing velocity dependent hydrodynamic forces. The spherical bodies are assumed to rotate as solid, uniform density spheres, with moments of inertia calculated @@ -88,9 +89,18 @@ Restart, fix_modify, output, run start/stop, minimize info No information about the *rigid* and *rigid/nve* fixes are written to :doc:`binary restart files `. +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution due to the added forces on atoms to +both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial yes `. + Similar to the :doc:`fix rigid ` command: The rigid fix -computes a global scalar which can be accessed by various :doc:`output commands `. The scalar value calculated by these -fixes is "intensive". The scalar is the current temperature of the +computes a global scalar which can be accessed by various :doc:`output +commands `. The scalar value calculated by these fixes +is "intensive". The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid bodies and their translational and rotational degrees of freedom. The translational energy of a rigid body is 1/2 m v\^2, where m = total @@ -130,7 +140,8 @@ Restrictions """""""""""" This fix is part of the USER-LB package. It is only enabled if LAMMPS -was built with that package. See the :doc:`Build package ` doc page for more info. +was built with that package. See the :doc:`Build package +` doc page for more info. Can only be used if a lattice-Boltzmann fluid has been created via the :doc:`fix lb/fluid ` command, and must come after this diff --git a/doc/src/fix_plumed.rst b/doc/src/fix_plumed.rst index 67118b6bfa..bd2c05adfe 100644 --- a/doc/src/fix_plumed.rst +++ b/doc/src/fix_plumed.rst @@ -95,6 +95,13 @@ PLUMED to the global potential energy of the system as part of :doc:`thermodynamic output `. The default setting for this fix is :doc:`fix_modify energy yes `. +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution from the biasing force to the global +pressure of the system via the :doc:`compute pressure +` command. This can be accessed by +:doc:`thermodynamic output `. The default setting for +this fix is :doc:`fix_modify virial yes `. + This fix computes a global scalar which can be accessed by various :doc:`output commands `. The scalar is the PLUMED energy mentioned above. The scalar value calculated by this fix is diff --git a/doc/src/fix_poems.rst b/doc/src/fix_poems.rst index 0f173fcc4e..b782b7809e 100644 --- a/doc/src/fix_poems.rst +++ b/doc/src/fix_poems.rst @@ -39,14 +39,15 @@ useful for treating a large biomolecule as a collection of connected, coarse-grained particles. The coupling, associated motion constraints, and time integration is -performed by the software package `Parallelizable Open source Efficient Multibody Software (POEMS)` which computes the -constrained rigid-body motion of articulated (jointed) multibody -systems :ref:`(Anderson) `. POEMS was written and is distributed -by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, -and other members of his group at Rensselaer Polytechnic Institute -(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For -copyright information on POEMS and other details, please refer to the -documents in the poems directory distributed with LAMMPS. +performed by the software package `Parallelizable Open source +Efficient Multibody Software (POEMS)` which computes the constrained +rigid-body motion of articulated (jointed) multibody systems +:ref:`(Anderson) `. POEMS was written and is distributed by +Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee, and +other members of his group at Rensselaer Polytechnic Institute (RPI). +Rudranarayan developed the LAMMPS/POEMS interface. For copyright +information on POEMS and other details, please refer to the documents +in the poems directory distributed with LAMMPS. This fix updates the positions and velocities of the rigid atoms with a constant-energy time integration, so you should not update the same @@ -107,7 +108,16 @@ off, and there is only a single fix poems defined. Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. +No information about this fix is written to :doc:`binary restart files +`. + +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution due to the added forces and torques +on atoms to both the global pressure and per-atom stress of the system +via the :doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial yes `. The :doc:`fix_modify ` *bodyforces* option is supported by this fix style to set whether per-body forces and torques are computed @@ -115,16 +125,18 @@ early or late in a timestep, i.e. at the post-force stage or at the final-integrate stage, respectively. No global or per-atom quantities are stored by this fix for access by -various :doc:`output commands `. No parameter of this fix -can be used with the *start/stop* keywords of the :doc:`run ` -command. This fix is not invoked during :doc:`energy minimization `. +various :doc:`output commands `. No parameter of this +fix can be used with the *start/stop* keywords of the :doc:`run ` +command. This fix is not invoked during :doc:`energy minimization +`. Restrictions """""""""""" -This fix is part of the :ref:`POEMS ` package. It is only enabled if LAMMPS -was built with that package, which also requires the POEMS library be -built and linked with LAMMPS. See the :doc:`Build package ` doc page for more info. +This fix is part of the :ref:`POEMS ` package. It is only +enabled if LAMMPS was built with that package, which also requires the +POEMS library be built and linked with LAMMPS. See the :doc:`Build +package ` doc page for more info. Related commands """""""""""""""" diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 116edd8c7e..8e8f3e0988 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -191,22 +191,29 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -The :doc:`fix_modify ` *virial* option is supported by this -fix to add the contribution due to keeping the constraints to the -system's virial as part of :doc:`thermodynamic output `. -The default is *virial yes* +No information about these fixes is written to :doc:`binary restart +files `. -No information about these fixes is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to these fixes. No global or per-atom quantities are -stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used -with the *start/stop* keywords of the :doc:`run ` command. These -fixes are not invoked during :doc:`energy minimization `. +The :doc:`fix_modify ` *virial* option is supported by +these fixes to add the contribution due to the added forces on atoms +to both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial yes `. + +No global or per-atom quantities are stored by these fixes for access +by various :doc:`output commands `. No parameter of +these fixes can be used with the *start/stop* keywords of the +:doc:`run ` command. These fixes are not invoked during +:doc:`energy minimization `. Restrictions """""""""""" These fixes are part of the RIGID package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. For computational efficiency, there can only be one shake or rattle fix defined in a simulation. diff --git a/doc/src/fix_smd.rst b/doc/src/fix_smd.rst index 8cbae29adf..8bf7c25478 100644 --- a/doc/src/fix_smd.rst +++ b/doc/src/fix_smd.rst @@ -48,10 +48,12 @@ Description """"""""""" This fix implements several options of steered MD (SMD) as reviewed in -:ref:`(Izrailev) `, which allows to induce conformational changes -in systems and to compute the potential of mean force (PMF) along the -assumed reaction coordinate :ref:`(Park) ` based on Jarzynski's -equality :ref:`(Jarzynski) `. This fix borrows a lot from :doc:`fix spring ` and :doc:`fix setforce `. +:ref:`(Izrailev) `, which allows to induce conformational +changes in systems and to compute the potential of mean force (PMF) +along the assumed reaction coordinate :ref:`(Park) ` based on +Jarzynski's equality :ref:`(Jarzynski) `. This fix borrows +a lot from :doc:`fix spring ` and :doc:`fix setforce +`. You can apply a moving spring force to a group of atoms (\ *tether* style) or between two groups of atoms (\ *couple* style). The spring @@ -108,30 +110,36 @@ See the :doc:`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. -The :doc:`fix_modify ` *virial* option is supported by this -fix to add the contribution due to the added forces on atoms to the -system's virial as part of :doc:`thermodynamic output `. -The default is *virial no* +The :doc:`fix_modify ` *virial* option is supported by +this fix to add the contribution due to the added forces on atoms to +both the global pressure and per-atom stress of the system via the +:doc:`compute pressure ` and :doc:`compute +stress/atom ` commands. The former can be +accessed by :doc:`thermodynamic output `. The default +setting for this fix is :doc:`fix_modify virial no `. -The :doc:`fix_modify ` *respa* option is supported by -this fix. This allows to set at which level of the :doc:`r-RESPA ` -integrator the fix is adding its forces. Default is the outermost level. +The :doc:`fix_modify ` *respa* option is supported by this +fix. This allows to set at which level of the :doc:`r-RESPA +` 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 :doc:`output commands `. The quantities in the -vector are in this order: the x-, y-, and z-component of the pulling -force, the total force in direction of the pull, the equilibrium -distance of the spring, the distance between the two reference points, -and finally the accumulated PMF (the sum of pulling forces times -displacement). +by various :doc:`output commands `. The quantities in +the vector are in this order: the x-, y-, and z-component of the +pulling force, the total force in direction of the pull, the +equilibrium distance of the spring, the distance between the two +reference points, and finally the accumulated PMF (the sum of pulling +forces times displacement). The force is the total force on the group of atoms by the spring. In the case of the *couple* style, it is the force on the fix group -(group-ID) or the negative of the force on the second group (group-ID2). -The vector values calculated by this fix are "extensive". +(group-ID) or the negative of the force on the second group +(group-ID2). The vector values calculated by this fix are +"extensive". No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 0bd7f241dd..cda9d4f8fa 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -342,8 +342,12 @@ for this fix is :doc:`fix_modify energy no `. The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms -and each wall to the system's virial as part of :doc:`thermodynamic -output `. The default is *virial no* +and all the specified walls to both the global pressure and per-atom +stress of the system via the :doc:`compute pressure +` :doc:`compute stress/atom ` +commands. The former can be accessed by :doc:`thermodynamic output +`. The default setting for this fix is :doc:`fix_modify +virial no `. The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA diff --git a/doc/src/fix_wall_ees.rst b/doc/src/fix_wall_ees.rst index c3e8a9affb..fde9fe7234 100644 --- a/doc/src/fix_wall_ees.rst +++ b/doc/src/fix_wall_ees.rst @@ -134,11 +134,6 @@ system as part of :doc:`thermodynamic output `. The default settings for thes fixes are :doc:`fix_modify energy no `. -The :doc:`fix_modify ` *virial* option is supported by -these rixes to add the contribution due to the interaction between -atoms and each wall to the system's virial as part of -:doc:`thermodynamic output `. The default is *virial no* - The :doc:`fix_modify ` *respa* option is supported by these fixes. This allows to set at which level of the :doc:`r-RESPA ` integrator the fix is adding its forces. Default is the diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 12bbaea454..1d06062fdd 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -202,8 +202,12 @@ this fix is :doc:`fix_modify energy no `. The :doc:`fix_modify ` *virial* option is supported by this fix to add the contribution due to the interaction between atoms -and each wall to the system's virial as part of :doc:`thermodynamic -output `. The default is *virial no* +and the region wall to both the global pressure and per-atom stress of +the system via the :doc:`compute pressure ` +:doc:`compute stress/atom ` commands. The former +can be accessed by :doc:`thermodynamic output `. The +default setting for this fix is :doc:`fix_modify virial no +`. The :doc:`fix_modify ` *respa* option is supported by this fix. This allows to set at which level of the :doc:`r-RESPA `