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* This file is part of the GROMACS molecular simulation package.
*
* Gromacs 4.0 Copyright (c) 1991-2003
* David van der Spoel, Erik Lindahl, University of Groningen.
* Copyright (c) 2012,2013, by the GROMACS development team, led by
* David van der Spoel, Berk Hess, Erik Lindahl, and including many
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#ifndef _GMX_FFT_H_
#define _GMX_FFT_H_
/*! \file gmx_fft.h
* \brief Fast Fourier Transforms.
*
* This file provides an abstract Gromacs interface to Fourier transforms,
* including multi-dimensional and real-to-complex transforms.
*
* Internally it is implemented as wrappers to external libraries such
* as FFTW or the Intel Math Kernel Library, but we also have a built-in
* version of FFTPACK in case the faster alternatives are unavailable.
*
* We also provide our own multi-dimensional transform setups even when
* the underlying library does not support it directly.
*
*/
#include <stdio.h>
#include "visibility.h"
#include "types/simple.h"
#include "gmxcomplex.h"
#ifdef __cplusplus
extern "C" {
#endif
#if 0
} /* fixes auto-indentation problems */
#endif
/*! \brief Datatype for FFT setup
*
* The gmx_fft_t type contains all the setup information, e.g. twiddle
* factors, necessary to perform an FFT. Internally it is mapped to
* whatever FFT library we are using, or the built-in FFTPACK if no fast
* external library is available.
*
* Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time, i.e.
* they should allocate one instance each when executing in parallel.
*/
typedef struct gmx_fft *
gmx_fft_t;
/*! \brief Specifier for FFT direction.
*
* The definition of the 1D forward transform from input x[] to output y[] is
* \f[
* y_{k} = \sum_{j=0}^{N-1} x_{j} \exp{-i 2 \pi j k /N}
* \f]
*
* while the corresponding backward transform is
*
* \f[
* y_{k} = \sum_{j=0}^{N-1} x_{j} \exp{i 2 \pi j k /N}
* \f]
*
* A forward-backward transform pair will this result in data scaled by N.
*
* For complex-to-complex transforms you can only use one of
* GMX_FFT_FORWARD or GMX_FFT_BACKWARD, and for real-complex transforms you
* can only use GMX_FFT_REAL_TO_COMPLEX or GMX_FFT_COMPLEX_TO_REAL.
*/
typedef enum gmx_fft_direction
{
GMX_FFT_FORWARD, /*!< Forward complex-to-complex transform */
GMX_FFT_BACKWARD, /*!< Backward complex-to-complex transform */
GMX_FFT_REAL_TO_COMPLEX, /*!< Real-to-complex valued fft */
GMX_FFT_COMPLEX_TO_REAL /*!< Complex-to-real valued fft */
} gmx_fft_direction;
/*! \brief Specifier for FFT flags.
*
* Some FFT libraries (FFTW, in particular) can do timings and other
* tricks to try and optimize the FFT for the current architecture. However,
* this can also lead to results that differ between consecutive runs with
* identical input.
* To avoid this, the conservative flag will attempt to disable such
* optimization, but there are no guarantees since we cannot control what
* the FFT libraries do internally.
*/
typedef int gmx_fft_flag;
static const int GMX_FFT_FLAG_NONE = 0;
static const int GMX_FFT_FLAG_CONSERVATIVE = (1<<0);
/*! \brief Setup a 1-dimensional complex-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_1d (gmx_fft_t * fft,
int nx,
gmx_fft_flag flags);
/*! \brief Setup multiple 1-dimensional complex-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform
* \param howmany Howmany 1D FFT
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_many_1d (gmx_fft_t * fft,
int nx,
int howmany,
gmx_fft_flag flags);
/*! \brief Setup a 1-dimensional real-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in real space
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
GMX_LIBMD_EXPORT
int
gmx_fft_init_1d_real (gmx_fft_t * fft,
int nx,
gmx_fft_flag flags);
/*! \brief Setup multiple 1-dimensional real-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in real space
* \param howmany Homany 1D FFTs
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_many_1d_real (gmx_fft_t * fft,
int nx,
int howmany,
gmx_fft_flag flags);
/*! \brief Setup a 2-dimensional complex-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in first dimension
* \param ny Length of transform in second dimension
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_2d (gmx_fft_t * fft,
int nx,
int ny,
gmx_fft_flag flags);
/*! \brief Setup a 2-dimensional real-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in first dimension
* \param ny Length of transform in second dimension
* \param flags FFT options
*
* The normal space is assumed to be real, while the values in
* frequency space are complex.
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
GMX_LIBMD_EXPORT
int
gmx_fft_init_2d_real (gmx_fft_t * fft,
int nx,
int ny,
gmx_fft_flag flags);
/*! \brief Setup a 3-dimensional complex-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in first dimension
* \param ny Length of transform in second dimension
* \param nz Length of transform in third dimension
* \param flags FFT options
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_3d (gmx_fft_t * fft,
int nx,
int ny,
int nz,
gmx_fft_flag flags);
/*! \brief Setup a 3-dimensional real-to-complex transform
*
* \param fft Pointer to opaque Gromacs FFT datatype
* \param nx Length of transform in first dimension
* \param ny Length of transform in second dimension
* \param nz Length of transform in third dimension
* \param flags FFT options
*
* The normal space is assumed to be real, while the values in
* frequency space are complex.
*
* \return status - 0 or a standard error message.
*
* \note Since some of the libraries (e.g. MKL) store work array data in their
* handles this datatype should only be used for one thread at a time,
* i.e. you should create one copy per thread when executing in parallel.
*/
int
gmx_fft_init_3d_real (gmx_fft_t * fft,
int nx,
int ny,
int nz,
gmx_fft_flag flags);
/*! \brief Perform a 1-dimensional complex-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d()
* \param dir Forward or Backward
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on your grid type.
*/
int
gmx_fft_1d (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform many 1-dimensional complex-to-complex transforms
*
* Performs many instances of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d()
* \param dir Forward or Backward
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on your grid type.
*/
int
gmx_fft_many_1d (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform a 1-dimensional real-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d_real()
* \param dir Real-to-complex or complex-to-real
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* If you are doing an in-place transform, the array must be padded up to
* an even integer length so n/2 complex numbers can fit. Out-of-place arrays
* should not be padded (although it doesn't matter in 1d).
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on transform direction.
*/
GMX_LIBMD_EXPORT
int
gmx_fft_1d_real (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform many 1-dimensional real-to-complex transforms
*
* Performs many instances of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d_real()
* \param dir Real-to-complex or complex-to-real
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* If you are doing an in-place transform, the array must be padded up to
* an even integer length so n/2 complex numbers can fit. Out-of-place arrays
* should not be padded (although it doesn't matter in 1d).
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on transform direction.
*/
int
gmx_fft_many_1d_real (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform a 2-dimensional complex-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d()
* \param dir Forward or Backward
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on your grid type.
*/
int
gmx_fft_2d (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform a 2-dimensional real-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d_real()
* \param dir Real-to-complex or complex-to-real
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note If you are doing an in-place transform, the last dimension of the
* array MUST be padded up to an even integer length so n/2 complex numbers can
* fit. Thus, if the real grid e.g. has dimension 5*3, you must allocate it as
* a 5*4 array, where the last element in the second dimension is padding.
* The complex data will be written to the same array, but since that dimension
* is 5*2 it will now fill the entire array. Reverse complex-to-real in-place
* transformation will produce the same sort of padded array.
*
* The padding does NOT apply to out-of-place transformation. In that case the
* input array will simply be 5*3 of real, while the output is 5*2 of complex.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on transform direction.
*/
GMX_LIBMD_EXPORT
int
gmx_fft_2d_real (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform a 3-dimensional complex-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d()
* \param dir Forward or Backward
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on your grid type.
*/
int
gmx_fft_3d (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Perform a 3-dimensional real-to-complex transform
*
* Performs an instance of a transform previously initiated.
*
* \param setup Setup returned from gmx_fft_init_1d_real()
* \param dir Real-to-complex or complex-to-real
* \param in_data Input grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* \param out_data Output grid data. This should be allocated with gmx_new()
* to make it 16-byte aligned for better performance.
* You can provide the same pointer for in_data and out_data
* to perform an in-place transform.
*
* \return 0 on success, or an error code.
*
* \note If you are doing an in-place transform, the last dimension of the
* array MUST be padded up to an even integer length so n/2 complex numbers can
* fit. Thus, if the real grid e.g. has dimension 7*5*3, you must allocate it as
* a 7*5*4 array, where the last element in the second dimension is padding.
* The complex data will be written to the same array, but since that dimension
* is 7*5*2 it will now fill the entire array. Reverse complex-to-real in-place
* transformation will produce the same sort of padded array.
*
* The padding does NOT apply to out-of-place transformation. In that case the
* input will simply be 7*5*3 of real, while the output is 7*5*2 of complex.
*
* \note Data pointers are declared as void, to avoid casting pointers
* depending on transform direction.
*/
int
gmx_fft_3d_real (gmx_fft_t setup,
enum gmx_fft_direction dir,
void * in_data,
void * out_data);
/*! \brief Release an FFT setup structure
*
* Destroy setup and release all allocated memory.
*
* \param setup Setup returned from gmx_fft_init_1d(), or one
* of the other initializers.
*
*/
GMX_LIBMD_EXPORT
void
gmx_fft_destroy (gmx_fft_t setup);
/*! \brief Release a many FFT setup structure
*
* Destroy setup and release all allocated memory.
*
* \param setup Setup returned from gmx_fft_init_1d(), or one
* of the other initializers.
*
*/
void
gmx_many_fft_destroy (gmx_fft_t setup);
/*! \brief Transpose 2d complex matrix, in-place or out-of-place.
*
* This routines works when the matrix is non-square, i.e. nx!=ny too,
* without allocating an entire matrix of work memory, which is important
* for huge FFT grids.
*
* \param in_data Input data, to be transposed
* \param out_data Output, transposed data. If this is identical to
* in_data, an in-place transpose is performed.
* \param nx Number of rows before transpose
* \param ny Number of columns before transpose
*
* \return GMX_SUCCESS, or an error code from gmx_errno.h
*/
int
gmx_fft_transpose_2d (t_complex * in_data,
t_complex * out_data,
int nx,
int ny);
/*! \brief Transpose 2d multi-element matrix
*
* This routine is very similar to gmx_fft_transpose_2d(), but it
* supports matrices with more than one data value for each position.
* It is extremely useful when transposing the x/y dimensions of a 3d
* matrix - in that case you just set nelem to nz, and the routine will do
* and x/y transpose where it moves entire columns of z data
*
* This routines works when the matrix is non-square, i.e. nx!=ny too,
* without allocating an entire matrix of work memory, which is important
* for huge FFT grid.
*
* For performance reasons you need to provide a \a small workarray
* with length at least 2*nelem (note that the type is char, not t_complex).
*
* \param in_data Input data, to be transposed
* \param out_data Output, transposed data. If this is identical to
* in_data, an in-place transpose is performed.
* \param nx Number of rows before transpose
* \param ny Number of columns before transpose
* \param nelem Number of t_complex values in each position. If this
* is 1 it is faster to use gmx_fft_transpose_2d() directly.
* \param work Work array of length 2*nelem, type t_complex.
*
* \return GMX_SUCCESS, or an error code from gmx_errno.h
*/
int
gmx_fft_transpose_2d_nelem(t_complex * in_data,
t_complex * out_data,
int nx,
int ny,
int nelem,
t_complex * work);
#ifdef __cplusplus
}
#endif
#endif /* _GMX_FFT_H_ */
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