Daniel Eisenstein & Lehman Garrison
https://github.com/abacusorg/zeldovich-PLT
This code generates Zel'dovich approximation (ZA) initial conditions (i.e. first-order Lagrangian perturbation theory) for cosmological N-body simulations, optionally applying particle linear theory (PLT) corrections. This code does not provide second-order ICs (2LPT), but one can use these ICs with the config-space 2LPT detailed in Garrison et al. (2016). This is the primary IC generator used by the Abacus N-body code.
If you do not intend to use the config-space 2LPT, then it's better to use a Fourier-space 2LPT code (e.g. 2LPTic) than to rely on ZA, even with PLT corrections.
This code supports two types of PLT corrections: (1) PLT eigenmodes, and (2) rescaling. Both corrections are most important on small scales (where "small" is defined by the mean interparticle separation, i.e. kNyquist).
-
PLT eigenmodes (
ZD_qPLT) initializes the simulation in the correct eigenmodes for a particle lattice. This eliminates transients that arise due to the common assumption that the particle system obeys the continuum modes. -
Rescaling (
ZD_qPLT_rescaleandZD_PLT_target_z) increases the amplitude of initial power on small scales to exactly cancel out future (unavoidable) under-growth. This requires (1).
This code does not presently support glass initial conditions, only particle lattices.
The code uses double precision internally, but you can set output format to single or double precision (see the ICFormat option).
The code can run small problems in memory, but it has an efficient scheme for buffering state on disk to support massive problems (100s of billions of particles). Setup the build with meson setup build -DDISK=true to turn this on.
zeldovich-PLT uses the Meson build system. Meson has a two-step build process, a lot like CMake. You setup a build directory, and then compile in that build directory:
$ meson setup build
$ meson compile -C build # equivalent to "cd build; meson compile"The zeldovich executable will be written to build/zeldovich (you can run meson install if you want to, but usually it's fine to run out of the build directory).
To build in out-of-core mode, use meson setup build -DDISK=true. The state will be buffered in the InitialConditionsDirectory. This allows one to generate much larger ICs than fit in memory.
Run with ./build/zeldovich <param_file>. An example parameter file (example.par) is provided, and all of the options are detailed in the "Parameter file options" section below.
Meson itself can be obtained via pip. You probably want ninja too: pip install meson ninja.
zeldovich-PLT is a C++11 code. It requires FFTW 3 and GSL, and the ParseHeader library needs flex and Bison >= 3.0. The code has been tested with the GNU and Intel C++ compilers.
This code supports generating phase-matched ICs with different particle densities. Simply increase the particle number NP while holding other parameters fixed. If desired, the ZD_k_cutoff parameter may be utilized to limit the oversampled ICs to the same modes as the original ICs without including new power past the original kNyquist. Otherwise, each set of ICs will include power out to their respective kNyquist spheres.
For example, to generate 1283 oversampled initial conditions that sample the same modes as 643 initial conditions, invoke the code twice: once with NP = 643 to generate the nominal resolution, then again with NP = 1283 to generate the oversampled resolution. The second invocation can include ZD_k_cutoff = 2 if one does not want new power.
If ZD_Version=1, then ZD_NumBlock also affects the IC phases. This is not the case in version 2 or later. But if using ZD_Version = 1, then one must take care to not change ZD_NumBlock between invocations.
ZD_Version=1 also only supported the flavor of oversampling that used ZD_k_cutoff (i.e. no new power). Since version 2, ZD_k_cutoff is optional when oversampling.
This code doesn't support true zoom-in/zoom-out simulations where the box size can be changed, a la Panphasia.
If you use this code, please cite Garrison et al. (2016).
We're doing four big [z][y][x] transform. But we don't store the
data that way. Instead, we block the z & y directions. So for a
PPD^3 problem (PPD = particles per dimension), we have NB blocks of P=PPD/NB two-d information. Each
block contains the full PPD x-dimension for all four problems.
We require that NB divides PPD evenly, just for sanity.
This is done so that we first operate on a y row of blocks, so we can do the x-z FFT. Then we operate on a z column of blocks, so that we can do the y FFT and output ordered in z.
We also store the four transforms packed into two complex transforms. We store these two arrays interleaved at the block level.
We order the full array as:
double complex data[zblock=0..NB-1][yblock=0..NB-1][arr=0..1][zresidual=0..P-1][yresidual=0..P-1][x=0..PPD-1]where
z = zblock*P+zresidual
zblock = floor(z/P)
zresidual = z-P*floor(z/P)and the same for y.
Each block is 4*P*P*PPD = 4*PPD^3/NB^2 numbers. For 4096 and 64, that's
a total array of 256 Gdoubles = 2 TB. Each slab is 32 GB and each
block is 512 MB. Each skewer of X's is 4096 complex doubles, which is
64 KB, so memory movements are efficient.
The concept is that 2/NB of the problem has to fit into memory at one time.
The coefficient is 2 because we have to construct the conjugate wavenumber
simultaneously so as to enforce the correct (anti-)Hermitian structure.
One can refer to the array as [z][y][x], but of course the intent is
that one operates the outer loop by block, so that one can load a big
chunk from disk.
We're going to load the 4 real FFTs into 2 complex FFTs. This will allow us to do the iFFTs as a simple cubic approach. We'll have
Re A = density
Im A = q_x
Re B = q_y
Im B = q_zSo Ahat = D + iF, and Bhat = G + iH, where
D(k) = D(-k)^* = delta(k)
F(k) = F(-k)^* = delta(k)*i k_x/k^2
G(k) = G(-k)^* = delta(k)*i k_y/k^2
H(k) = H(-k)^* = delta(k)*i k_z/k^2In detail, we treat k_x/k^2 as j/n^2, where n^2 = (j^2+l^2+m^2)*(2*pi/L)
for integral triples (j,l,m). We must wrap 0..N-1 to -N/2+1..N/2 for this
computation. In this language, -k means (j,l,m) -> (N-j,N-l,N-m).
delta(k) is a complex Gaussian with variance in Re(delta) and Im(delta)
of P_theory/Volume_box. This is the correct normalization if the iFFT
is in the FFTW convention (no prefactor of 1/N).
We will force delta(k) to be 0 at k=0 and also if j=N/2, l=N/2, or m=N/2.
The latter avoids bookkeeping about Nyquist aliasing and can't matter
physically.
In regards to Nyquist aliasing, if we set k and -k each time we
generate a delta, it doesn't matter if we do an element more than
once. It just overwrites both elements with a different random
number. That avoids some Nyquist bookkeeping.
We must load k and -k at the same time (or play horrid tricks to
reset and resynchronize the random number generator). There is no
avoiding having two slabs in memory for this. Given that our first
sweep is in Y slabs, it is probably easiest to split the half-space
on y=0.
We use a Permuted Congruential Generator (PCG; http://www.pcg-random.org/) to generate the random numbers used in the Gaussian random field. PCG offers many of the nice properties of a linear congruential generator (LCG), such as speed, known period, and the ability to fast-forward, without the associated statistical issues of an LCG. See O'Neill (2014) for the details.
We use PCG64, which yields 64-bit output from 128-bit internal state. Thus, we easily probe the high-density tails of the Gaussian distribution (which 32-bit generators have to treat carefully).
We use PCG's fast-forward, or jump-ahead ability to support changing the number of particles (and thus changing the size of the Fourier cube) while keeping the modes fixed. Logically, we are generating a large cube of white noise suitable for a huge PPD (65536, in this case) and then only using the corners of the space that our actual PPD requires. But PCG's fast-forward ability lets us skip the regions of Fourier space that are not sampled in O(log N) time, where N is the number of samples being skipped. This is what allows our efficient up- and down-sampling.
Since we need a consistent mapping of random numbers to Fourier element, we use the "deterministic" version of Box-Muller instead of the more common rejection sampling method. This means we need to use expensive trig functions, but in practice there was no performance hit from this change. The FFTs, IO, and memory movement dominate the runtime.
PCG's fast-forward also helps with the parallelization of the RNG. Logically, we imagine the entire PPD^3 Fourier cube being filled with a single stream of random numbers from the PCG with the specified seed, but in practice many planes are filled in parallel by separate threads. So we assign each particle plane a single RNG whose state has been fast-forwarded from the initial state, and each thread uses that plane's RNG when operating on it.
Version 1 of the code used GSL's Mersenne Twister (which does not support jump-ahead). This is actually our only GSL dependency, so the code could be compiled without GSL if one didn't care about Version 1 support.
This code supports particle linear theory (PLT) corrections to the initial conditions—essentially discreteness corrections. These are described in the Overview above.
The PLT eigenmode features of this code are developed and tested in Garrison et al. (2016) based on the work of Marcos, et al. (2006).
Nominally, this code only produces ZA displacements, from which velocities can be computed in config space later. However, using the PLT eigenmodes requires computing the velocities in Fourier space, so we have to do that here. Thus, we require four complex FFTs instead of two, doubling the overall memory usage.
We provide a precompted set of 1283 numerical eigenmodes with this code. The code does linear interpolation if a finer FFT mesh is being used.
ZD_Seed: integer
The random number seed. This variable determines the output phases.
If ZD_Version=1, ZD_NumBlock also affects
the output phases. This is not the case in version 2.
In the past, a seed of 0 used the current time. This is no longer the case.
ZD_NumBlock: integer
This is the number of blocks to break the FFT
into, per linear dimension. This must be an even number; moreover,
it must divide PPD = NP^(1/3) evenly. The default is 2, but you
may need a higher number.
This is a key tuning parameter for the code. The full problem
requires 32*NP bytes (or 64*NP if ZD_qPLT is being used), which may exceed the amount of RAM.
The zeldovich code holds 2/NumBlock of the full volume in memory,
by splitting the problem in 2 dimensions into NumBlock^2 parts.
Each block therefore is 32*NP/NumBlock^2 bytes. It
is important that these blocks be larger than the latency of the
disk, so sizes of order 100 MB are useful. We are holding
2*NumBlock such blocks in memory.
Hence, for a computer with M bytes of available memory and a
problem of NP particles, we need NumBlock > 64*NP/M
(preferably to be the next larger even number that divides evenly
into NP^(1/3)) and we prefer that 32*NP/NumBlock^2 is
larger than the latency.
For example, for a 4096^3 simulation, 32*NP is 2 TB. If we use
NumBlock of 128, then we will need 32 GB of RAM and each block saved
to disk will be 128 MB. For a 2048^3 simulation, 32*NP is 256 GB
and NumBlock of 16 will require 32 GB of RAM and each block will
be 1024 MB. For a 8192^3 simulation, 32*NP is 16 TB and NumBlock
of 256 will require 128 GB of RAM and a block size of 256 MB.
If ZD_Version=1, then if ZD_k_cutoff != 1, then the actual ZD_NumBlock
will be ZD_NumBlock*ZD_k_cutoff. See ZD_k_cutoff for details.
If ZD_Version=1, both this variable and ZD_Seed affect the output phases.
This is not the case since version 2.
If the -DDISK flag is not set, then blocks are stored in memory, not disk.
So NumBlock matters less in that case.
ZD_Version: integer
The version of the algorithm for generating modes from random numbers.
The current version is 2, which is the default. New ICs should
always use ZD_Version=2, but ZD_Version=1 is available for backwards
compatibility.
If ZD_Version=1, then the output phases depend on both ZD_Seed
and ZD_NumBlock.
ZD_Pk_filename: string
The file name of the input power spectrum.
This can be a CAMB power spectrum.
ZD_Pk_scale: double
This is the quantity by which to multiply the
wavenumbers in the input file to place them in the units that will be used
in the zeldovich code, in which the fundamental wavenumber is 2*pi divided
by BoxSize. Default value is 1.0.
As a common example, one might need to convert between Mpc^-1 and
h Mpc^-1 units. The zeldovich code does not use the hMpc value,
so it doesn't know what the units of BoxSize are. If BoxSize is in
h^-1 Mpc units, so that hMpc=1, and if the P(k) file had k
in h Mpc^-1 units, then all is well: use the value of 1.0.
However, if BoxSize were in Mpc units and the input power were in
h Mpc^-1 units, then we want to convert the wavenumbers to
Mpc^-1 units. That means multiplying by h, so we should use
ZD_Pk_scale = h.
ZD_Pk_norm: double
The scale at which to normalize the input
P(k), in the same units as BoxSize. For example, if BoxSize is
given in h^-1 Mpc, then one might choose 8 to select sigma_8.
If this value is 0, then the power spectrum will not be renormalized
(but ZD_Pk_scale will be applied to the wavevectors, so beware that
the power isn't thrown off, as it does have units of volume). The
default is 0, but we recommend controlling the normalization.
ZD_Pk_sigma: double
The amplitude to use to normalize the
fluctuations of the density field, with a tophat of radius ZD_Pk_norm.
This must be scaled to the initial redshift by the growth function;
the zeldovich code does not know about cosmology. The default is 0,
but one almost certainly wants to change this!
Note that using this parameter means that the choice of unit of power in the input power spectrum file is irrelevant (but we do care about the unit of wavenumber, see above).
ZD_Pk_smooth: double
The length scale by which to smooth the input
power spectrum before generating the density field. This is applied as
a Gaussian smoothing as exp(-r^2/2a^2) on the density field, which is
exp(-k^2 a^2) on the power spectrum. Smoothing the power spectrum
is useful for testing, as it reduces grid artifacts. The smooth occurs
after the power spectrum has been normalized. Default is 0.
ZD_qPk_fix_to_mean: integer
Fix the amplitude of the modes to sqrt(P(k)). The phases are unchanged.
That is, running with this option off then on will produce ICs with identical phases
but different mode amplitudes. This is useful for producing "paired and fixed" sims,
as suggested by Angulo & Pontzen (2016). Default is 0.
ZD_qoneslab: integer
If > 0, output only one PPD slab. For debugging only.
The default is -1.
ZD_qonemode: integer
If > 0, zero out all modes except the one with the wavevector specified in ZD_one_mode.
ZD_one_mode: three ints
This is the one wavevector that will be inserted into the box if ZD_qonemode > 0.
This is useful for automatically iterating through a series of wavevectors, for examining isotropy or Nyquist effects, for example.
Each component can be an integer in the range [-ppd/2,ppd/2].
ZD_qPLT: integer
If > 0, turn on particle linear theory corrections.
This tweaks the displacements and velocities, mostly near k_Nyquist, to ensure everything starts in the growing mode.
The output format should include velocities if you turn this on, either in the RVZel or RVdoubleZel format.
ZD_PLT_filename: string
The file containing the PLT eigenmodes; i.e. the true growing modes for the grid.
This file usually contains something like a 1283 grid,
and the code linearly interpolates the eigenmodes and eigenvalues to finer meshes as needed.
This parameter should be eigmodes128 to use the file of that name included in this repository.
ZD_qPLT_rescale: integer
If > 0, increase the amplitude of the displacements on small scales (near k_Nyquist)
to preemptively compensate for unavoidable future mode "under-growth" that occurs due
to the discrete particle nature of the simulations.
ZD_PLT_target_z: double
If ZD_qPLT_rescale > 0, then increase the initial displacements such that they will match the linear theory prediction
at this redshift. Recall that modes on the grid (mostly) grow more slowly than linear theory, which is why we (mostly) increase the initial displacements.
This redshift should be in a quasi-linear regime where linear theory is still mostly valid, e.g. z~5.
ZD_k_cutoff: double
The wavenumber above which not to generate any power, expressed such that k_max = k_Nyquist / k_cutoff, e.g. ZD_k_cutoff = 2 means we null out modes above half-Nyquist. Fractional numbers like 1.5 are allowed. This is useful for doing convergence tests, e.g. run once with PPD=64 and ZD_k_cutoff = 1, and again with PPD=128 and ZD_k_cutoff = 2. This will produce two boxes with the exact same modes (although the PLT corrections will be slightly different), but the second box's modes are oversampled by a factor of two.
If ZD_Version=1, then to keep the random number generation synchronized between the two boxes (fixed number of particle planes per block), ZD_NumBlock is increased by a factor of ZD_k_cutoff. So do not change ZD_NumBlock between invocations in version 1! Version 2 does not suffer from this limitation.
ZD_qdensity: integer
Set to 1 to output the density field in addition to the displacements. Set to 2 to output just density, and not displacements (this saves memory).
BoxSize: double
This is the box size, probably in Mpc or h-1Mpc. The zeldovich code only cares about the units to the extent that they should match the units in the power spectrum file. See ZD_Pk_scale for further discussion.
NP: long long int
Number of particles. This must be a perfect cube for the zeldovich code to work.
CPD: integer
Cells per dimension. Zeldovich will output CPD slabs, each with CPD^2 cells. These slabs are only defined by the
initial grid position; we do not guarantee that the initial displacement may not have
taken the particle out of the slab. Usually the deviations will be small enough that
particles move by at most 1 slab.
InitialConditionsDirectory: string
The location to write the output. In addition,
the zeldovich code will use this for the swap space for the block transpose.
This will generate files of the name zeldovich.%d.%d, which should be automatically
deleted after the code has finished.
InitialRedshift: double
The output redshift. This is only used for determining rescaling amplitude; i.e. this option has no effect if ZD_qPLT_rescale is not set. This code does not compute growth functions; ZD_Pk_sigma controls the power spectrum normalization.
ICFormat: string
Valid options are: RVZel, RVdoubleZel, or Zeldovich.
One should use one the RV options if ZD_qPLT is set, because the velocities have been explicitly computed in Fourier space.
All displacements are comoving displacements in the same units as BoxSize, and the velocities are comoving redshift-space displacements (same units as BoxSize).
To get to proper velocities from comoving redshift-space displacements, multiply by a*H(z).
The comoving positions of the initial lattice (in unit-box units where the domain is [0,1)) are simply given by
x = i/PPD
y = j/PPD
z = k/PPDThus, the global, absolute positions of the particles can be formed by adding the displacements (which this code outputs) to this lattice.
RVZel
Single-precision output of the displacement and velocity, and particle lattice location.
class RVZelParticle {
public:
unsigned short i,j,k;
float displ[3];
float vel[3];
};RVdoubleZel
Double-precision output of the displacement and velocity, and particle lattice location.
class RVdoubleZelParticle {
public:
unsigned short i,j,k;
double displ[3];
double vel[3];
};Zeldovich
Double-precision output of the displacement and particle lattice location.
class ZelParticle {
public:
unsigned short i,j,k;
double displ[3];
};If you use this code, please cite Garrison et al. (2016).