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add missinng portions of a couple doc pages

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Steve Plimpton
2022-08-04 08:49:38 -06:00
parent 883a25bbd8
commit 53f49a160f
4 changed files with 128 additions and 91 deletions
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6
doc/src/Howto_amoeba.rst
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@ -2,9 +2,9 @@ AMOEBA and HIPPO force fields
============================= =============================
The AMOEBA and HIPPO polarizable force fields were developed by Jay The AMOEBA and HIPPO polarizable force fields were developed by Jay
Ponder's group at the U Washington at St Louis. Their implementation Ponder's group at the U Washington at St Louis. The LAMMPS
in LAMMPS was done using F90 code provided by the Ponder group from implementation was done using F90 code provided by the Ponder group
their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_. from their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren) version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)

25
doc/src/Packages_details.rst
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@ -157,14 +157,28 @@ AMOEBA package
**Contents:** **Contents:**
TODO Implementation of the AMOEBA and HIPPO polarized force fields
orginally developed by Jay Ponder's group at the U Washington at St
Louis. The LAMMPS implementation was done using F90 code provided by
the Ponder group from their `Tinker MD code
<https://dasher.wustl.edu/tinker/>`_.
**Authors:** Josh Rackers and Steve Plimpton (Sandia), Trung Nguyen (U
Chicago)
**Supporting info:** **Supporting info:**
* src/AMOEBA: filenames -> commands * src/AMOEBA: filenames -> commands
* :doc:`AMOEBA and HIPPO howto <Howto_amoeba>` * :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
* :doc:`pair_style amoeba <pair_amoeba>`
* :doc:`pair_style hippo <pair_amoeba>`
* :doc:`atom_style amoeba <atom_style>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* tools/tinker/tinker2lmp.py
* examples/amoeba * examples/amoeba
* TODO
---------- ----------
@ -200,9 +214,10 @@ ATC package
**Contents:** **Contents:**
ATC stands for atoms-to-continuum. This package implements a :doc:`fix atc <fix_atc>` command to either couple molecular dynamics with ATC stands for atoms-to-continuum. This package implements a
continuum finite element equations or perform on-the-fly conversion of :doc:`fix atc <fix_atc>` command to either couple molecular dynamics
atomic information to continuum fields. with continuum finite element equations or perform on-the-fly
conversion of atomic information to continuum fields.
**Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). **Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).

175
doc/src/fix_ave_chunk.rst
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@ -17,12 +17,12 @@ Syntax
* Nfreq = calculate averages every this many timesteps * Nfreq = calculate averages every this many timesteps
* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command * chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
* one or more input values can be listed * one or more input values can be listed
* value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name * value = vx, vy, vz, fx, fy, fz, density/mass, density/number, mass, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
.. parsed-literal:: .. parsed-literal::
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) vx,vy,vz,fx,fy,fz,mass = atom attribute (velocity, force component, mass)
density/number, density/mass = number or mass density density/number, density/mass = number or mass density (per volume)
temp = temperature temp = temperature
c_ID = per-atom vector calculated by a compute with ID c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below) c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
@ -99,29 +99,33 @@ averages can be used by other :doc:`output commands <Howto_output>` such
as :doc:`thermo_style custom <thermo_style>`, and can also be written to as :doc:`thermo_style custom <thermo_style>`, and can also be written to
a file. a file.
In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
to a single chunk (or no chunk). The ID for this command is specified chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
as chunkID. For example, a single chunk could be the atoms in a single chunk (or no chunk). The ID for this command is specified as
molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` page and the :doc:`Howto chunk <Howto_chunk>` page for details of how chunks can be chunkID. For example, a single chunk could be the atoms in a molecule
defined and examples of how they can be used to measure properties of or atoms in a spatial bin. See the :doc:`compute chunk/atom
a system. <compute_chunk_atom>` page and the :doc:`Howto chunk <Howto_chunk>`
page for details of how chunks can be defined and examples of how they
can be used to measure properties of a system.
Note that only atoms in the specified group contribute to the summing Note that only atoms in the specified group contribute to the summing
and averaging calculations. The :doc:`compute chunk/atom <compute_chunk_atom>` command defines its own group as and averaging calculations. The :doc:`compute chunk/atom
well as an optional region. Atoms will have a chunk ID = 0, meaning <compute_chunk_atom>` command defines its own group as well as an
they belong to no chunk, if they are not in that group or region. optional region. Atoms will have a chunk ID = 0, meaning they belong
Thus you can specify the "all" group for this command if you simply to no chunk, if they are not in that group or region. Thus you can
want to use the chunk definitions provided by chunkID. specify the "all" group for this command if you simply want to use the
chunk definitions provided by chunkID.
Each specified per-atom value can be an atom attribute (position, Each specified per-atom value can be an atom attribute (position,
velocity, force component), a mass or number density, or the result of velocity, force component), a number or mass density, a mass or
a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation of an temperature, or the result of a :doc:`compute <compute>` or :doc:`fix
atom-style :doc:`variable <variable>`. In the latter cases, the <fix>` or the evaluation of an atom-style :doc:`variable <variable>`.
compute, fix, or variable must produce a per-atom quantity, not a In the latter cases, the compute, fix, or variable must produce a
global quantity. Note that the :doc:`compute property/atom <compute_property_atom>` command provides access to per-atom quantity, not a global quantity. Note that the :doc:`compute
any attribute defined and stored by atoms. If you wish to property/atom <compute_property_atom>` command provides access to any
time-average global quantities from a compute, fix, or variable, then attribute defined and stored by atoms. If you wish to time-average
see the :doc:`fix ave/time <fix_ave_time>` command. global quantities from a compute, fix, or variable, then see the
:doc:`fix ave/time <fix_ave_time>` command.
The per-atom values of each input vector are summed and averaged The per-atom values of each input vector are summed and averaged
independently of the per-atom values in other input vectors. independently of the per-atom values in other input vectors.
@ -145,8 +149,9 @@ means all indices from m to n (inclusive).
Using a wildcard is the same as if the individual columns of the array Using a wildcard is the same as if the individual columns of the array
had been listed one by one. E.g. these 2 fix ave/chunk commands are had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the :doc:`compute property/atom <compute_property_atom>` command creates, in this equivalent, since the :doc:`compute property/atom
case, a per-atom array with 3 columns: <compute_property_atom>` command creates, in this case, a per-atom
array with 3 columns:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -194,28 +199,31 @@ discussed below.
.. note:: .. note::
To perform per-chunk averaging within a *Nfreq* time window, the To perform per-chunk averaging within a *Nfreq* time window, the
number of chunks *Nchunk* defined by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant. If number of chunks *Nchunk* defined by the :doc:`compute chunk/atom
the *ave* keyword is set to *running* or *window* then *Nchunk* must <compute_chunk_atom>` command must remain constant. If the *ave*
remain constant for the duration of the simulation. This fix forces keyword is set to *running* or *window* then *Nchunk* must remain
the chunk/atom compute specified by chunkID to hold *Nchunk* constant constant for the duration of the simulation. This fix forces the
for the appropriate time windows, by not allowing it to re-calculate chunk/atom compute specified by chunkID to hold *Nchunk* constant
*Nchunk*, which can also affect how it assigns chunk IDs to atoms. for the appropriate time windows, by not allowing it to
This is particularly important to understand if the chunks defined by re-calculate *Nchunk*, which can also affect how it assigns chunk
the :doc:`compute chunk/atom <compute_chunk_atom>` command are spatial IDs to atoms. This is particularly important to understand if the
bins. If its *units* keyword is set to *box* or *lattice*, then the chunks defined by the :doc:`compute chunk/atom
number of bins *Nchunk* and size of each bin will be fixed over the <compute_chunk_atom>` command are spatial bins. If its *units*
*Nfreq* time window, which can affect which atoms are discarded if the keyword is set to *box* or *lattice*, then the number of bins
*Nchunk* and size of each bin will be fixed over the *Nfreq* time
window, which can affect which atoms are discarded if the
simulation box size changes. If its *units* keyword is set to simulation box size changes. If its *units* keyword is set to
*reduced*, then the number of bins *Nchunk* will still be fixed, but *reduced*, then the number of bins *Nchunk* will still be fixed,
the size of each bin can vary at each timestep if the simulation box but the size of each bin can vary at each timestep if the
size changes, e.g. for an NPT simulation. simulation box size changes, e.g. for an NPT simulation.
---------- ----------
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. The atom attribute values (vx,vy,vz,fx,fy,fz,mass) are
As noted above, any other atom attributes can be used as input values self-explanatory. As noted above, any other atom attributes can be
to this fix by using the :doc:`compute property/atom <compute_property_atom>` command and then specifying used as input values to this fix by using the :doc:`compute
an input value from that compute. property/atom <compute_property_atom>` command and then specifying an
input value from that compute.
The *density/number* value means the number density is computed for The *density/number* value means the number density is computed for
each chunk, i.e. number/volume. The *density/mass* value means the each chunk, i.e. number/volume. The *density/mass* value means the
@ -243,12 +251,13 @@ Note that currently this temperature only includes translational
degrees of freedom for each atom. No rotational degrees of freedom degrees of freedom for each atom. No rotational degrees of freedom
are included for finite-size particles. Also no degrees of freedom are included for finite-size particles. Also no degrees of freedom
are subtracted for any velocity bias or constraints that are applied, are subtracted for any velocity bias or constraints that are applied,
such as :doc:`compute temp/partial <compute_temp_partial>`, or :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. This is because such as :doc:`compute temp/partial <compute_temp_partial>`, or
those degrees of freedom (e.g. a constrained bond) could apply to sets :doc:`fix shake <fix_shake>` or :doc:`fix rigid <fix_rigid>`. This is
of atoms that are both included and excluded from a specific chunk, because those degrees of freedom (e.g. a constrained bond) could apply
and hence the concept is somewhat ill-defined. In some cases, you can to sets of atoms that are both included and excluded from a specific
use the *adof* and *cdof* keywords to adjust the calculated degrees of chunk, and hence the concept is somewhat ill-defined. In some cases,
freedom appropriately, as explained below. you can use the *adof* and *cdof* keywords to adjust the calculated
degrees of freedom appropriately, as explained below.
Also note that a bias can be subtracted from atom velocities before Also note that a bias can be subtracted from atom velocities before
they are used in the above formula for KE, by using the *bias* they are used in the above formula for KE, by using the *bias*
@ -256,22 +265,22 @@ keyword. This allows, for example, a thermal temperature to be
computed after removal of a flow velocity profile. computed after removal of a flow velocity profile.
Note that the per-chunk temperature calculated by this fix and the Note that the per-chunk temperature calculated by this fix and the
:doc:`compute temp/chunk <compute_temp_chunk>` command can be different. :doc:`compute temp/chunk <compute_temp_chunk>` command can be
The compute calculates the temperature for each chunk for a single different. The compute calculates the temperature for each chunk for
snapshot. This fix can do that but can also time average those values a single snapshot. This fix can do that but can also time average
over many snapshots, or it can compute a temperature as if the atoms those values over many snapshots, or it can compute a temperature as
in the chunk on different timesteps were collected together as one set if the atoms in the chunk on different timesteps were collected
of atoms to calculate their temperature. The compute allows the together as one set of atoms to calculate their temperature. The
center-of-mass velocity of each chunk to be subtracted before compute allows the center-of-mass velocity of each chunk to be
calculating the temperature; this fix does not. subtracted before calculating the temperature; this fix does not.
If a value begins with "c\_", a compute ID must follow which has been If a value begins with "c\_", a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array bracketed integer is appended, the Ith column of the per-atom array
calculated by the compute is used. Users can also write code for calculated by the compute is used. Users can also write code for
their own compute styles and :doc:`add them to LAMMPS <Modify>`. their own compute styles and :doc:`add them to LAMMPS <Modify>`. See
See the discussion above for how I can be specified with a wildcard the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values. asterisk to effectively specify multiple values.
If a value begins with "f\_", a fix ID must follow which has been If a value begins with "f\_", a fix ID must follow which has been
@ -307,9 +316,10 @@ atoms in the chunk. The averaged output value for the chunk on the
average over atoms across the entire *Nfreq* timescale. For the average over atoms across the entire *Nfreq* timescale. For the
*density/number* and *density/mass* values, the volume (bin volume or *density/number* and *density/mass* values, the volume (bin volume or
system volume) used in the final normalization will be the volume at system volume) used in the final normalization will be the volume at
the final *Nfreq* timestep. For the *temp* values, degrees of freedom and the final *Nfreq* timestep. For the *temp* values, degrees of freedom
kinetic energy are summed separately across the entire *Nfreq* timescale, and and kinetic energy are summed separately across the entire *Nfreq*
the output value is calculated by dividing those two sums. timescale, and the output value is calculated by dividing those two
sums.
If the *norm* setting is *sample*, the chunk value is summed over If the *norm* setting is *sample*, the chunk value is summed over
atoms for each sample, as is the count, and an "average sample value" atoms for each sample, as is the count, and an "average sample value"
@ -431,44 +441,50 @@ the first of each section of output. In the third line the values are
replaced with the appropriate value names, e.g. fx or c_myCompute[2]. replaced with the appropriate value names, e.g. fx or c_myCompute[2].
The words in parenthesis only appear with corresponding columns if the The words in parenthesis only appear with corresponding columns if the
chunk style specified for the :doc:`compute chunk/atom <compute_chunk_atom>` command supports them. The OrigID chunk style specified for the :doc:`compute chunk/atom
column is only used if the *compress* keyword was set to *yes* for the <compute_chunk_atom>` command supports them. The OrigID column is
:doc:`compute chunk/atom <compute_chunk_atom>` command. This means that only used if the *compress* keyword was set to *yes* for the
the original chunk IDs (e.g. molecule IDs) will have been compressed :doc:`compute chunk/atom <compute_chunk_atom>` command. This means
to remove chunk IDs with no atoms assigned to them. Thus a compressed that the original chunk IDs (e.g. molecule IDs) will have been
chunk ID of 3 may correspond to an original chunk ID or molecule ID of compressed to remove chunk IDs with no atoms assigned to them. Thus a
compressed chunk ID of 3 may correspond to an original chunk ID or
molecule ID of
415. The OrigID column will list 415 for the third chunk. 415. The OrigID column will list 415 for the third chunk.
The CoordN columns only appear if a *binning* style was used in the The CoordN columns only appear if a *binning* style was used in the
:doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*, :doc:`compute chunk/atom <compute_chunk_atom>` command. For *bin/1d*,
*bin/2d*, and *bin/3d* styles the column values are the center point *bin/2d*, and *bin/3d* styles the column values are the center point
of the bin in the corresponding dimension. Just Coord1 is used for of the bin in the corresponding dimension. Just Coord1 is used for
*bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\ . *bin/1d*, Coord2 is added for *bin/2d*, Coord3 is added for *bin/3d*\
For *bin/sphere*, just Coord1 is used, and it is the radial . For *bin/sphere*, just Coord1 is used, and it is the radial
coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1 coordinate. For *bin/cylinder*, Coord1 and Coord2 are used. Coord1
is the radial coordinate (away from the cylinder axis), and coord2 is is the radial coordinate (away from the cylinder axis), and coord2 is
the coordinate along the cylinder axis. the coordinate along the cylinder axis.
Note that if the value of the *units* keyword used in the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or *lattice*, the Note that if the value of the *units* keyword used in the
coordinate values will be in distance :doc:`units <units>`. If the :doc:`compute chunk/atom command <compute_chunk_atom>` is *box* or
value of the *units* keyword is *reduced*, the coordinate values will *lattice*, the coordinate values will be in distance :doc:`units
be in unitless reduced units (0-1). This is not true for the Coord1 value <units>`. If the value of the *units* keyword is *reduced*, the
of style *bin/sphere* or *bin/cylinder* which both represent radial coordinate values will be in unitless reduced units (0-1). This is
dimensions. Those values are always in distance :doc:`units <units>`. not true for the Coord1 value of style *bin/sphere* or *bin/cylinder*
which both represent radial dimensions. Those values are always in
distance :doc:`units <units>`.
---------- ----------
Restart, fix_modify, output, run start/stop, minimize info Restart, fix_modify, output, run start/stop, minimize info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options No information about this fix is written to :doc:`binary restart files
are relevant to this fix. <restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix.
This fix computes a global array of values which can be accessed by This fix computes a global array of values which can be accessed by
various :doc:`output commands <Howto_output>`. The values can only be various :doc:`output commands <Howto_output>`. The values can only be
accessed on timesteps that are multiples of *Nfreq* since that is when accessed on timesteps that are multiples of *Nfreq* since that is when
averaging is performed. The global array has # of rows = the number averaging is performed. The global array has # of rows = the number
of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The # of columns = of chunks *Nchunk* as calculated by the specified :doc:`compute
chunk/atom <compute_chunk_atom>` command. The # of columns =
M+1+Nvalues, where M = 1 to 4, depending on whether the optional M+1+Nvalues, where M = 1 to 4, depending on whether the optional
columns for OrigID and CoordN are used, as explained above. Following columns for OrigID and CoordN are used, as explained above. Following
the optional columns, the next column contains the count of atoms in the optional columns, the next column contains the count of atoms in
@ -483,7 +499,8 @@ since they are typically already normalized by the count of atoms in
each chunk. each chunk.
No parameter of this fix can be used with the *start/stop* keywords of 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>`. the :doc:`run <run>` command. This fix is not invoked during
:doc:`energy minimization <minimize>`.
Restrictions Restrictions
"""""""""""" """"""""""""

13
src/fix_ave_chunk.cpp
View File

@ -107,6 +107,9 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = ArgInfo::F; which[nvalues] = ArgInfo::F;
argindex[nvalues++] = 2; argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"mass") == 0) {
which[nvalues] = ArgInfo::MASS;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"density/number") == 0) { } else if (strcmp(arg[iarg],"density/number") == 0) {
densityflag = 1; densityflag = 1;
which[nvalues] = ArgInfo::DENSITY_NUMBER; which[nvalues] = ArgInfo::DENSITY_NUMBER;
@ -115,9 +118,6 @@ FixAveChunk::FixAveChunk(LAMMPS *lmp, int narg, char **arg) :
densityflag = 1; densityflag = 1;
which[nvalues] = ArgInfo::DENSITY_MASS; which[nvalues] = ArgInfo::DENSITY_MASS;
argindex[nvalues++] = 0; argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"mass") == 0) {
which[nvalues] = ArgInfo::MASS;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"temp") == 0) { } else if (strcmp(arg[iarg],"temp") == 0) {
which[nvalues] = ArgInfo::TEMPERATURE; which[nvalues] = ArgInfo::TEMPERATURE;
argindex[nvalues++] = 0; argindex[nvalues++] = 0;
@ -632,7 +632,12 @@ void FixAveChunk::end_of_step()
if (which[m] == ArgInfo::V) attribute = atom->v; if (which[m] == ArgInfo::V) attribute = atom->v;
else attribute = atom->f; else attribute = atom->f;
for (i = 0; i < nlocal; i++) for (i = 0; i < nlocalThe *temp* value means the temperature is computed for each chunk, by
the formula KE = DOF/2 k T, where KE = total kinetic energy of the
chunk of atoms (sum of 1/2 m v\^2), DOF = the total number of degrees
of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
temperature.
; i++)
if (mask[i] & groupbit && ichunk[i] > 0) { if (mask[i] & groupbit && ichunk[i] > 0) {
index = ichunk[i]-1; index = ichunk[i]-1;
values_one[index][m] += attribute[i][j]; values_one[index][m] += attribute[i][j];