Commit dc4c95d0 authored by Volker Springel's avatar Volker Springel
Browse files

Merge branch 'master' of gitlab.mpcdf.mpg.de:vrs/gadget4

parents 665abfe5 16dd051a
......@@ -51,7 +51,7 @@ GADGET-4 needs the following non-standard libraries for compilation:
libraries nowadays in any cases enable pinning by default.
6. **vectorclass** : This is a C++ library that the code utilizes when
explicit vectorization via the AVX instruction set is enabled in a
explicit vectorization via the AVX instruction set is enabled in
the SPH compute kernels. This is then implemented with the
vectorclass library by Agner Fog. For simplicity, the source code
of this library (which takes the form of C++ header files) is
......@@ -392,7 +392,7 @@ otherwise the simulation will restart from scratch, i.e. by reading in
the initial conditions again! Also note that upon restarting from
restart-files, the number of MPI ranks used for a simulation cannot be
changed; if this is attempted an error message is issued. Note that
restart files can not necessarily be transferred from on computer
restart files can not necessarily be transferred from one computer
system to another one, or reused when the compiler is changed, because
the layout and padding of structures stored in the binary restart
files may then be different. Hence, if you want to continue a
......
......@@ -159,7 +159,7 @@ the other dimensions should be set to zero.
In case periodic boundary conditions are used (i.e. `PERIODIC` is on),
one can stretch the x-dimension of the box relative to `BoxSize` by
the factor `1 / 2^LONG_X_BITS`. A setting equal to 2 like in this
example, would hence mean thet the boxsize in the x-direction will be
example, would hence mean that the boxsize in the x-direction will be
`BoxSize/4`.
-------
......@@ -393,7 +393,7 @@ in the way the force matching region is treated.
**NTAB** = 128
This can used define the size of the short-range lookup table. The
This can be used to define the size of the short-range lookup table. The
default should normally be sufficient to have negligible influence on
the obtained force accuracy.
......@@ -682,7 +682,7 @@ SPH viscosity options {#visc}
**TIMEDEP_ART_VISC**
Enables time dependent viscosity.
Enables-time dependent viscosity.
-------
......@@ -714,7 +714,7 @@ Note that metal-line cooling is not included in this module.
**STARFORMATION**
If this is enabled, the code can create new star particles out of SPH
particles. The default star formation model that is implement
particles. The default star formation model that is implemented
corresponds to a basic varient of the sub-resolution multi-phase model
described in Springel & Hernquist (2003,
<http://adsabs.harvard.edu/abs/2003MNRAS.339..289S>). By default, the
......@@ -1114,7 +1114,7 @@ particles are arranged in the order of the groups and subhalos.
**SUBFIND_HBT**
This enabled an implementation of the hierarchical bound tracing
This enables an implementation of the hierarchical bound tracing
algorithm, where subhalo candidates are identified with the help of a
substructure catalogue from a precious time instead of doing this with
density excursion sets. This option requires both `SUBFIND` and
......@@ -1382,7 +1382,7 @@ however.
Another issue with some MPI-libraries is that they may use quite a bit
of internal storage for carrying out MPI_Allgatherv. If this turns out
to be problem, one can set this option. The code will then replace all
to be a problem, one can set this option. The code will then replace all
uses of MPI_Allgatherv() with a simpler communication pattern that
uses hypercubes with MPI_Sendrecv as a work-around.
......
......@@ -54,7 +54,7 @@ an error message will be produced.
**SnapshotFileBase** snapshot
From this string, the name of the snapshot files is derived by adding
From this string, the name of the snapshot file is derived by adding
an underscore, and the number of the snapshot in a 3-digits format. If
`NumFilesPerSnapshot > 1` , each snapshot is distributed into several
files, with a group of processors writing their data to one of the
......@@ -75,7 +75,7 @@ this simple binary format (which has been available from GADGET-2
onwards). A value of 3 selects the use of HDF5 instead, which is the
strongly recommended format. This is because this data format allows a
simple browsing of its contents, access to individual data items is
easily possible though the name of the data set, conversions between
easily possible through the name of the data set, conversions between
endianness and single/double precision are automatically done if
needed, and pesky I/O errors (like reading too many items from a given
data set) are detected reliably. HDF5 output has been introduced for
......@@ -214,7 +214,7 @@ have a slightly different syntax or may not be available at all
The GADGET-4 code provides quite verbose output in its log-files, with
each timestep producing some entries. If you carry out a simulation
with a very large number of very short timesteps and you have a slow
or busy filesystems, this I/O can slow down the code if the filesystem
or busy filesystem, this I/O can slow down the code if the filesystem
buffers are flushed to disk after every output. With this parameter,
the flush operations are only carried out with a reduced frequency, in
the above example every 120 seconds. This should avoid any significant
......@@ -347,7 +347,7 @@ parameter has to be set to zero.
**OmegaBaryon** 0.04
Baryon density in units of the critical density at `z=0`. This is not
explicitly used in the time integration of GADGET-4, but the paramater
explicitly used in the time integration of GADGET-4, but the parameter
is relevant when initial conditions are created, or when dark
matter-only initial conditions are outfitted with gas particles upon
code start-up with the `GENERATE_GAS_IN_ICS` option.
......@@ -396,7 +396,7 @@ length unit to 1.0 kpc/h.
**UnitMass_in_g** 1.989e43
This sets the internal mass unit in g/h, where H_0 = 100 h
km/s/Mpc. The above choice is convenient for cosmology, it as sets the
km/s/Mpc. The above choice is convenient for cosmology, as it sets the
mass unit to 10^10 M_sun/h.
-------
......@@ -597,8 +597,8 @@ synchronization time, where `N` is the total particle number. Note
that the gravitational tree is always reconstructed in every step,
whereas the neighbor search tree is only reconstructed in case a
domain decomposition is done for the current step. Otherwise it
expands its nodes as needed to accomodate all the SPH particles that
where grouped into each node.
expands its nodes as needed to accommodate all the SPH particles that
were grouped into each node.
-------
......@@ -730,7 +730,7 @@ certain temperature if `InitGasTemp > 0` and if at the same time the
temperature of the gas particles in the initial conditions file was
found to be zero, otherwise the initial gas temperature is left at the
value stored in the IC file. If the temperature is set through this
paramater, and if it is below 10^4 K, a mean molecular weight
parameter, and if it is below 10^4 K, a mean molecular weight
corresponding to neutral gas of primordial abundance is assumed,
otherwise complete ionisation is assumed.
......@@ -1082,7 +1082,7 @@ formation model described in Springel & Hernquist (2003,
**MaxSfrTimescale** 1.5
Gas consumption time scale in internal time units at the threshold density for
star formation. This the parameter t_0^star in the above paper.
star formation. This sets the parameter t_0^star in the above paper.
-------
......
......@@ -84,7 +84,7 @@ the blocks may change from snapshot to snapshot. Also, a given
particle may not always be stored in the snapshot file with the same
sub-number among the files belonging to one set of snapshot files.
This is because particles may move around from one processor to
another during the coarse of a parallel simulation. In order to trace
another during the course of a parallel simulation. In order to trace
a particle between different outputs, one therefore has to resort to
the particle IDs, which are intended to be used to label particles
uniquely. (In fact, the uniqueness of the IDs in the initial
......@@ -116,7 +116,7 @@ particle number was stored as a 32-bit integer, such that simulations
exceeding particle numbers of a couple of billion needed as special
(and ugly) extension of the header, where the high-order bits in the
particle numbers where stored in a separate entry. In addition,
cosmological paramaters like `Omega0` and various flags informing
cosmological parameters like `Omega0` and various flags informing
about enabled/disabled code features were redundantly stored there as
well. Finally, the total header length was filled to a total length of
exactly 256 bytes, with a view to reserve the extra space for future
......
......@@ -39,8 +39,7 @@ During a run, the code outputs frequent log-message what is currently
done by GADGET-4. Usually, the corresponding lines begin with a
capitalized key-word that identifies the corresponding code part. For
example, lines beginning with "DOMAIN:" refer to information issued by
the domain decomposition, lines starting with "PM-PERIODIC:" will be
for identified with a the periodic FFT-based computation of the
the domain decomposition, lines starting with "PM-PERIODIC:" will be identified with the periodic FFT-based computation of the
long-range gravitational force. It can be useful to filter the file
with grep for one of these phrases to get a clearer picture of what is
happening in a particular code part.
......@@ -289,7 +288,7 @@ The values reported under grav-balance and hydro-balance inform about
the relative success of the domain decomposition to reach the desired
balance among multiple different quantities. The first number gives
the imbalance factor if only the current step would have to be
executed. This is however only the full story if a another domain
executed. This is however only the full story if another domain
decomposition will be carried out in the next step immediately. If
this is not the case, several steps need to be averaged appropriately,
and the relative slow-down of the residual imbalance in the present
......@@ -686,7 +685,7 @@ sfr.txt {#sfrlog}
=======
This is only present in simulations with cooling and star
formation. It can then be used to obtain simple global overview of the
formation. It can then be used to obtain a simple global overview of the
total star formation rate in the simulation.
......@@ -53,7 +53,7 @@ in a given FOF group is singled out as main subhalo in the group. To
organize the tree(s), a number of pointers for each subhalo need to be
defined.
Each halo must knows its __descendant__ in the subsequent group
Each halo must know its __descendant__ in the subsequent group
catalogue at later time, and the most important step in the merger
tree construction is determining this link. This can be accomplished
in two ways with GADGET-4. Either one enables `MERGERTREE` while a
......@@ -128,7 +128,7 @@ power spectra are measured in each case, one for the unmodified
periodic box, yielding a conventional measurement that extends up to
close to the Nyquist frequency of the employed Fourier mesh (which is
set by `PMGRID` ). The other two are extensions to smaller scales by
imposing periodicity on some inter devision of the box, with the box
imposing periodicity on some inter division of the box, with the box
folded on top of itself. The default value for this folding factor is
`POWERSPEC_FOLDFAC=16` but this value can be modified if desired by
overriding it with a configuration option.
......
......@@ -25,7 +25,7 @@ file `make-examples.sh`, with one line with a suitable call of `make`
for each of the examples. Copying the corresponding line and pasting
it as a command into the main directory of the code will then build
the executable for the example. Executing the full shell script will
compile all the examples at once (provided there are no complilation
compile all the examples at once (provided there are no compilation
problems, of course).
Below, we describe each of the examples and also give a few
......@@ -103,7 +103,7 @@ undergoes star formation.
Radiative cooling due to helium and hydrogen is included. Star
formation and feedback is modelled with a simple subgrid
treatment. The simulation in corresponds closely to the model of a
treatment. The simulation corresponds closely to the model of a
galaxy collisions considered in the code paper.
......@@ -179,8 +179,8 @@ high-resolution zone there are 140005 particles, surrounded by a
boundary region with two layers of different softening, the inner one
containing 39616 particles, and the outer one 96877 particles.
Not that while this simulation is a cosmological simulation in
comoving coordinates, it is unusual in that it doesn't use perdiodic
Note that while this simulation is a cosmological simulation in
comoving coordinates, it is unusual in that it doesn't use periodic
boundary conditions but rather follows a sphere of matter around the
origin with average density equal to the mean density. This technique
is not very commonly used any more.
......
......@@ -5,7 +5,7 @@ Guide to code changes
[TOC]
In the following, we give a set of assorted hints and recommendations
about modifying and/or extending the code. We also commment about some
about modifying and/or extending the code. We also comment about some
differences with respect to GADGET-2/3 in terms of code usage and its
architecture.
......@@ -90,7 +90,7 @@ n = get_particle_count();
~~~~~~~~~~~~~
- Avoid repetition of code, i.e. do not use cut & paste to implement
the same or similar functionality multiple times. This is always am
the same or similar functionality multiple times. This is always an
indication that a new function is in order here. Break up long
functions into smaller more manageable pieces.
......
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