From 055b20301e77fc2c25e05c43e149ad32f5d05e70 Mon Sep 17 00:00:00 2001 From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa> Date: Mon, 9 May 2016 16:56:43 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14948 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_angle.rst | 60 -------------- doc/compute_dihedral.rst | 59 -------------- doc/compute_improper.rst | 59 -------------- doc/fix_shardlow.rst | 115 --------------------------- doc/fix_smd.rst | 168 --------------------------------------- 5 files changed, 461 deletions(-) delete mode 100644 doc/compute_angle.rst delete mode 100644 doc/compute_dihedral.rst delete mode 100644 doc/compute_improper.rst delete mode 100644 doc/fix_shardlow.rst delete mode 100644 doc/fix_smd.rst diff --git a/doc/compute_angle.rst b/doc/compute_angle.rst deleted file mode 100644 index 91df79f906..0000000000 --- a/doc/compute_angle.rst +++ /dev/null @@ -1,60 +0,0 @@ -.. index:: compute angle - -compute angle command -===================== - -Syntax -"""""" - -.. parsed-literal:: - - compute ID group-ID angle - -* ID, group-ID are documented in :doc:`compute <compute>` command -* angle = style name of this compute command - -Examples -"""""""" - -.. parsed-literal:: - - compute 1 all angle - -Description -""""""""""" - -Define a computation that extracts the angle energy calculated by each -of the angle sub-styles used in the "angle_style -hybrid" angle_hybrid.html command. These values are made accessible -for output or further processing by other commands. The group -specified for this command is ignored. - -This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total -energy contributed by one or more of the hybrid sub-styles. - -**Output info:** - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -:doc:`units <units>`. - -Restrictions -"""""""""""" - none - -Related commands -"""""""""""""""" - -:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` - -**Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/compute_dihedral.rst b/doc/compute_dihedral.rst deleted file mode 100644 index 8c0281e409..0000000000 --- a/doc/compute_dihedral.rst +++ /dev/null @@ -1,59 +0,0 @@ -.. index:: compute dihedral - -compute dihedral command -======================== - -Syntax -"""""" - -.. parsed-literal:: - - compute ID group-ID dihedral - -* ID, group-ID are documented in :doc:`compute <compute>` command -* dihedral = style name of this compute command - -Examples -"""""""" - -.. parsed-literal:: - - compute 1 all dihedral - -Description -""""""""""" - -Define a computation that extracts the dihedral energy calculated by -each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid <dihedral_hybrid>` command. These values are made -accessible for output or further processing by other commands. The -group specified for this command is ignored. - -This compute is useful when using :doc:`dihedral_style hybrid <dihedral_hybrid>` if you want to know the portion of the -total energy contributed by one or more of the hybrid sub-styles. - -**Output info:** - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command. which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -:doc:`units <units>`. - -Restrictions -"""""""""""" - none - -Related commands -"""""""""""""""" - -:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` - -**Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/compute_improper.rst b/doc/compute_improper.rst deleted file mode 100644 index ade78d6cb7..0000000000 --- a/doc/compute_improper.rst +++ /dev/null @@ -1,59 +0,0 @@ -.. index:: compute improper - -compute improper command -======================== - -Syntax -"""""" - -.. parsed-literal:: - - compute ID group-ID improper - -* ID, group-ID are documented in :doc:`compute <compute>` command -* improper = style name of this compute command - -Examples -"""""""" - -.. parsed-literal:: - - compute 1 all improper - -Description -""""""""""" - -Define a computation that extracts the improper energy calculated by -each of the improper sub-styles used in the :doc:`improper_style hybrid <improper_hybrid>` command. These values are made -accessible for output or further processing by other commands. The -group specified for this command is ignored. - -This compute is useful when using :doc:`improper_style hybrid <improper_hybrid>` if you want to know the portion of the -total energy contributed by one or more of the hybrid sub-styles. - -**Output info:** - -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command. which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output -options. - -The vector values are "extensive" and will be in energy -:doc:`units <units>`. - -Restrictions -"""""""""""" - none - -Related commands -"""""""""""""""" - -:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>` - -**Default:** none - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/fix_shardlow.rst b/doc/fix_shardlow.rst deleted file mode 100644 index 560aaf5fa4..0000000000 --- a/doc/fix_shardlow.rst +++ /dev/null @@ -1,115 +0,0 @@ -.. index:: fix shardlow - -fix shardlow command -==================== - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID shardlow - -* ID, group-ID are documented in :doc:`fix <fix>` command -* shardlow = style name of this fix command - -Examples -"""""""" - -.. parsed-literal:: - - fix 1 all shardlow - -Description -""""""""""" - -Specifies that the Shardlow splitting algorithm (SSA) is to be used to -integrate the DPD equations of motion. The SSA splits the integration -into a stochastic and deterministic integration step. The fix -*shardlow* performs the stochastic integration step and must be used -in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nph>`). The stochastic -integration of the dissipative and random forces is performed prior to -the deterministic integration of the conservative force. Further -details regarding the method are provided in :ref:`(Lisal) <Lisal>` and -:ref:`(Larentzos) <Larentzos>`. - -The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the -fluctuation-dissipation theorem parameter(s) sigma (and kappa, if -necessary). - -Note that numerous variants of DPD can be specified by choosing an -appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command. DPD under isothermal conditions can -be specified by using fix *shardlow*, fix *nve* and pair_style -*dpd/fdt*. DPD under isoenergetic conditions can be specified by -using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*. DPD -under isobaric conditions can be specified by using fix shardlow, fix -*nph* and pair_style *dpd/fdt*. DPD under isoenthalpic conditions can -be specified by using fix shardlow, fix *nph* and pair_style -*dpd/fdt/energy*. Examples of each DPD variant are provided in the -examples/USER/dpd directory. - - ----------- - - -Restrictions -"""""""""""" - - -This fix is only available if LAMMPS is built with the USER-DPD -package. See the :ref:`Making LAMMPS <start_3>` section -for more info. - -This fix is currently limited to orthogonal simulation cell -geometries. - -This fix must be used with an additional fix that specifies time -integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`. - -The Shardlow splitting algorithm requires the sizes of the sub-domain -lengths to be larger than twice the cutoff+skin. Generally, the -domain decomposition is dependant on the number of processors -requested. - -Related commands -"""""""""""""""" - -:doc:`pair_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>` - -**Default:** none - - ----------- - - -.. _Lisal: - - - -**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative -particle dynamics as isothermal, isobaric, isoenergetic, and -isoenthalpic conditions using Shardlow-like splitting algorithms.", -J. Chem. Phys., 135, 204105 (2011). - -.. _Larentzos: - - - -**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and -W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic -Dissipative Particle Dynamics Using Shardlow-Like Splitting -Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014). - -.. _Larentzos: - - - -**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and -W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative -Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research -Laboratory, Aberdeen Proving Ground, MD (2014). - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm diff --git a/doc/fix_smd.rst b/doc/fix_smd.rst deleted file mode 100644 index 62d215a648..0000000000 --- a/doc/fix_smd.rst +++ /dev/null @@ -1,168 +0,0 @@ -.. index:: fix smd - -fix smd command -=============== - -Syntax -"""""" - -.. parsed-literal:: - - fix ID group-ID smd type values keyword values - -* ID, group-ID are documented in :doc:`fix <fix>` command -* smd = style name of this fix command -* mode = *cvel* or *cfor* to select constant velocity or constant force SMD -.. parsed-literal:: - - *cvel* values = K vel - K = spring constant (force/distance units) - vel = velocity of pulling (distance/time units) - *cfor* values = force - force = pulling force (force units) - -* keyword = *tether* or *couple* -.. parsed-literal:: - - *tether* values = x y z R0 - x,y,z = point to which spring is tethered - R0 = distance of end of spring from tether point (distance units) - *couple* values = group-ID2 x y z R0 - group-ID2 = 2nd group to couple to fix group with a spring - x,y,z = direction of spring, automatically computed with 'auto' - R0 = distance of end of spring (distance units) - - - -Examples -"""""""" - -.. parsed-literal:: - - fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0 - fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0 - fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0 - fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0 - -Description -""""""""""" - -This fix implements several options of steered MD (SMD) as reviewed in -:ref:`(Izrailev) <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) <Park>` based on Jarzynski's -equality :ref:`(Jarzynski) <Jarzynski>`. This fix borrows a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce <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 -can then be used in either constant velocity (*cvel*) mode or in -constant force (*cfor*) mode to induce transitions in your systems. -When running in *tether* style, you may need some way to fix some -other part of the system (e.g. via :doc:`fix spring/self <fix_spring_self>`) - -The *tether* style attaches a spring between a point at a distance of -R0 away from a fixed point *x,y,z* and the center of mass of the fix -group of atoms. A restoring force of magnitude K (R - R0) Mi / M is -applied to each atom in the group where *K* is the spring constant, Mi -is the mass of the atom, and M is the total mass of all atoms in the -group. Note that *K* thus represents the total force on the group of -atoms, not a per-atom force. - -In *cvel* mode the distance R is incremented or decremented -monotonously according to the pulling (or pushing) velocity. -In *cfor* mode a constant force is added and the actual distance -in direction of the spring is recorded. - -The *couple* style links two groups of atoms together. The first -group is the fix group; the second is specified by group-ID2. The -groups are coupled together by a spring that is at equilibrium when -the two groups are displaced by a vector in direction *x,y,z* with -respect to each other and at a distance R0 from that displacement. -Note that *x,y,z* only provides a direction and will be internally -normalized. But since it represents the *absolute* displacement of -group-ID2 relative to the fix group, (1,1,0) is a different spring -than (-1,-1,0). For each vector component, the displacement can be -described with the *auto* parameter. In this case the direction is -recomputed in every step, which can be useful for steering a local -process where the whole object undergoes some other change. When the -relative positions and distance between the two groups are not in -equilibrium, the same spring force described above is applied to atoms -in each of the two groups. - -For both the *tether* and *couple* styles, any of the x,y,z values can -be specified as NULL which means do not include that dimension in the -distance calculation or force application. - -For constant velocity pulling (*cvel* mode), the running integral -over the pulling force in direction of the spring is recorded and -can then later be used to compute the potential of mean force (PMF) -by averaging over multiple independent trajectories along the same -pulling path. - -Restart, fix_modify, output, run start/stop, minimize info -"""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -The fix stores the direction of the spring, current pulling target -distance and the running PMF to :doc:`binary restart files <restart>`. -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. - -This fix computes a vector list of 7 quantities, which can be accessed -by various :ref:`output commands <howto_15>`. 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 2nd 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 <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`. - -Restrictions -"""""""""""" - - -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info. - -Related commands -"""""""""""""""" - -:doc:`fix drag <fix_drag>`, :doc:`fix spring <fix_spring>`, -:doc:`fix spring/self <fix_spring_self>`, -:doc:`fix spring/rg <fix_spring_rg>` - -**Default:** none - - ----------- - - -.. _Israilev: - - - -**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, -Wriggers, Schulten. Computational Molecular Dynamics: Challenges, -Methods, Ideas, volume 4 of Lecture Notes in Computational Science and -Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998. - -**(Park)** -Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004) - -**(Jarzynski)** -Jarzynski, Phys. Rev. Lett. 78, 2690 (1997) - - -.. _lws: http://lammps.sandia.gov -.. _ld: Manual.html -.. _lc: Section_commands.html#comm -- GitLab