ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'github/develop' into general-triclinic

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-04-02 09:41:21 -04:00
parent 1bdcf7e42e a017a775bd
commit ed0cff92de
37 changed files with 457 additions and 373 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
doc/src/Fortran.rst
View File

@ -1255,8 +1255,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
three elements of the global vector calculated by fix recenter into the
variables *dx*, *dy*, and *dz*, respectively.
If asked for per-atom or local data, :f:func:`extract_compute` returns a
pointer to actual LAMMPS data. The pointer so returned will have the
If asked for per-atom or local data, :f:func:`extract_fix` returns a
pointer to actual LAMMPS data. The pointer returned will have the
appropriate size to match the internal data, and will be
type/kind/rank-checked at the time of the assignment. For example,

28
doc/src/fix_ave_chunk.rst
View File

@ -31,7 +31,7 @@ Syntax
v_name = per-atom vector calculated by an atom-style variable with name
* zero or more keyword/arg pairs may be appended
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *append* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -51,6 +51,8 @@ Syntax
dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
*file* arg = filename
filename = file to write results to
*append* arg = filename
filename = file to append results to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -433,15 +435,21 @@ molecule.
----------
The *file* keyword allows a filename to be specified. Every
:math:`N_\text{freq}` timesteps, a section of chunk info will be written to a
text file in the following format. A line with the timestep and number of
chunks is written. Then one line per chunk is written, containing the chunk
ID :math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of atoms
in the chunk, and one or more calculated values. More explanation of the
optional values is given below. The number of values in each line
corresponds to the number of values specified in the fix ave/chunk
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every :math:`N_\text{freq}`
timesteps, a section of chunk info will be written to a text file in the
following format. A line with the timestep and number of chunks is
written. Then one line per chunk is written, containing the chunk ID
:math:`(1-N_\text{chunk}),` an optional original ID value, optional
coordinate values for chunks that represent spatial bins, the number of
atoms in the chunk, and one or more calculated values. More explanation
of the optional values is given below. The number of values in each
line corresponds to the number of values specified in the fix ave/chunk
command. The number of atoms and the value(s) are summed or average
quantities, as explained above.

36
doc/src/fix_ave_histo.rst
View File

@ -35,7 +35,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
* keyword = *mode* or *kind* or *file* or *append* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
*kind* arg = *global* or *peratom* or *local*
*file* arg = filename
filename = name of file to output histogram(s) to
*append* arg = filename
filename = name of file to append histogram(s) to
*ave* args = *one* or *running* or *window*
one = output a new average value every Nfreq steps
running = output cumulative average of all previous Nfreq steps
@ -317,19 +319,25 @@ on. The default is step 0. Often input values can be 0.0 at time 0,
so setting *start* to a larger value can avoid including a 0.0 in
a running or windowed histogram.
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one histogram is written to the file. This includes a leading
line that contains the timestep, number of bins, the total count of
values contributing to the histogram, the count of values that were
not histogrammed (see the *beyond* keyword), the minimum value
encountered, and the maximum value encountered. The min/max values
include values that were not histogrammed. Following the leading
line, one line per bin is written into the file. Each line contains
the bin #, the coordinate for the center of the bin (between *lo* and
*hi*\ ), the count of values in the bin, and the normalized count. The
normalized count is the bin count divided by the total count (not
including values not histogrammed), so that the normalized values sum
to 1.0 across all bins.
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
histogram is written to the file. This includes a leading line that
contains the timestep, number of bins, the total count of values
contributing to the histogram, the count of values that were not
histogrammed (see the *beyond* keyword), the minimum value encountered,
and the maximum value encountered. The min/max values include values
that were not histogrammed. Following the leading line, one line per
bin is written into the file. Each line contains the bin #, the
coordinate for the center of the bin (between *lo* and *hi*\ ), the
count of values in the bin, and the normalized count. The normalized
count is the bin count divided by the total count (not including values
not histogrammed), so that the normalized values sum to 1.0 across all
bins.
The *overwrite* keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of

29
doc/src/fix_ave_time.rst
View File

@ -28,7 +28,7 @@ Syntax
v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
* keyword = *mode* or *file* or *append* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
.. parsed-literal::
@ -45,6 +45,8 @@ Syntax
M = value # from 1 to Nvalues
*file* arg = filename
filename = name of file to output time averages to
*append* arg = filename
filename = name of file to append time averages to
*overwrite* arg = none = overwrite output file with only latest output
*format* arg = string
string = C-style format string
@ -270,16 +272,21 @@ are effectively constant or are simply current values (e.g., they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output).
The *file* keyword allows a filename to be specified. Every *Nfreq*
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For *mode* =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For *mode* = vector, an array
of numbers is written each time output is performed. The number of rows
is the length of the input vectors, and the number of columns is the
number of values. Thus the file ends up to be a series of these array
sections.
.. versionadded:: TBD
new keyword *append*
The *file* or *append* keywords allow a filename to be specified. If
*file* is used, then the filename is overwritten if it already exists.
If *append* is used, then the filename is appended to if it already
exists, or created if it does not exist. Every *Nfreq* steps, one
quantity or vector of quantities is written to the file for each input
value specified in the fix ave/time command. For *mode* = scalar, this
means a single line is written each time output is performed. Thus the
file ends up to be a series of lines, i.e. one column of numbers for
each input value. For *mode* = vector, an array of numbers is written
each time output is performed. The number of rows is the length of the
input vectors, and the number of columns is the number of values. Thus
the file ends up to be a series of these array sections.
.. versionadded:: 4May2022

29
doc/src/fix_electrode.rst
View File

@ -255,23 +255,24 @@ and the fix will issue an error in that case.
.. versionadded:: TBD
The keyword *qtotal* causes *fix electrode/conp* and *fix electrode/thermo*
to add an overall potential to all electrodes so that the total charge on
the electrodes is a specified amount (which may be an equal-style variable).
For example, if a user wanted to simulate a solution of excess cations
such that the total electrolyte charge is +2, setting *qtotal -2* would cause
the total electrode charge to be -2, so that the simulation box remains overall
electroneutral. Since *fix electrode/conq* constrains the total charges of
individual electrodes, and since *symm on* constrains the total charge of all
electrodes to be zero, either option is incompatible with the *qtotal* keyword
(even if *qtotal* is set to zero).
The keyword *qtotal* causes *fix electrode/conp* and *fix
electrode/thermo* to add an overall potential to all electrodes so that
the total charge on the electrodes is a specified amount (which may be
an equal-style variable). For example, if a user wanted to simulate a
solution of excess cations such that the total electrolyte charge is +2,
setting *qtotal -2* would cause the total electrode charge to be -2, so
that the simulation box remains overall electroneutral. Since *fix
electrode/conq* constrains the total charges of individual electrodes,
and since *symm on* constrains the total charge of all electrodes to be
zero, either option is incompatible with the *qtotal* keyword (even if
*qtotal* is set to zero).
.. versionadded:: TBD
The keyword *eta* takes the name of a custom double vector defined via fix
property/atom. The values will be used instead of the standard eta value. The
property/atom fix must be for vector of double values and use the *ghost on*
option.
The keyword *eta* takes the name of a custom double vector defined via
fix property/atom. The values will be used instead of the standard eta
value. The property/atom fix must be for vector of double values and
use the *ghost on* option.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

26
doc/src/processors.rst
View File

@ -159,17 +159,17 @@ surface-to-volume ratio of each processor's subdomain.
for most MPI implementations, but some MPIs provide options for this
ordering, e.g. via environment variable settings.
The *numa* style operates similar to the *twolevel* keyword except
that it auto-detects which cores are running on which nodes.
It will also subdivide the cores into numa domains. Currently, the
number of numa domains is not autodetected and must be specified using
the *numa_nodes* keyword; otherwise, the default value is used. The
*numa* style uses a different algorithm than the *twolevel* keyword for
doing the two-level factorization of the simulation box into a 3d
processor grid to minimize off-node communication and communication
across numa domains. It does its own MPI-based mapping of nodes and
cores to the regular 3d grid. Thus it may produce a different layout
of the processors than the *twolevel* options.
The *numa* style operates similar to the *twolevel* keyword except that
it auto-detects which cores are running on which nodes. It will also
subdivide the cores into numa domains. Currently, the number of numa
domains is not auto-detected and must be specified using the
*numa_nodes* keyword; otherwise, the default value is used. The *numa*
style uses a different algorithm than the *twolevel* keyword for doing
the two-level factorization of the simulation box into a 3d processor
grid to minimize off-node communication and communication across numa
domains. It does its own MPI-based mapping of nodes and cores to the
regular 3d grid. Thus it may produce a different layout of the
processors than the *twolevel* options.
The *numa* style will give an error if the number of MPI processes is
not divisible by the number of cores used per node, or any of the Px
@ -182,7 +182,7 @@ or Py or Pz values is greater than 1.
is because it auto-detects which processes are running on which nodes.
However, it assumes that the lowest ranks are in the first numa
domain, and so forth. MPI rank orderings that do not preserve this
property might result in more intranode communication between CPUs.
property might result in more intra-node communication between CPUs.
The *custom* style uses the file *infile* to define both the 3d
factorization and the mapping of processors to the grid.
@ -213,7 +213,7 @@ any order, but no processor ID should appear more than once.
----------
The *numa_nodes* keyword is used to specifiy the number of numa domains
The *numa_nodes* keyword is used to specify the number of numa domains
per node. It is currently only used by the *numa* style for two-level
factorization to reduce the amount of MPI communications between CPUs.
A good setting for this will typically be equal to the number of CPU