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2020-04-16 13:03:33 +02:00
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/target
Cargo.lock

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Cargo.toml Normal file
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[package]
name = "xdrfile"
version = "0.1.0"
authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
license = "GNU"
edition = "2018"
description = "Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format."
build = "build.rs"
[dependencies]
failure = "0.1"
lazy-init = "0.3"
[dev-dependencies]
tempfile = "3.1.0"
[build-dependencies]
cc = { version = "1.0", features = ["parallel" ]}

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build.rs Normal file
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extern crate cc;
use std::fs;
fn main() {
// This builds gromacs' xdrfile library
let source_files: Vec<_> = fs::read_dir("external/xdrfile/src")
.unwrap()
.map(|f| f.unwrap())
.map(|f| f.path())
.collect();
cc::Build::new()
.files(source_files)
.include("external/xdrfile/include")
.warnings(false)
.compile("libxdrfile.a")
}

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Low-level C libraries for manipulating GROMACS XTC and TRR files.
This code is is taken from mdtraj library which is available at
https://github.com/mdtraj/mdtraj
and originally derived from xdrfile-1.1.4, available at
http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
These files are licensed under a BSD 2-clause license, and copyright
Erik Lindahl, David van der Spoel, Robert T. McGibbon.
Changes from upsteam's xdrfile-1.1.4 include:
- More descriptive error strings printed inside xdrfile.c
- Fix for a segfault on malformed xtc files inside xdrfile_decompress_coord_float (https://github.com/mdtraj/mdtraj/pull/607, https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-September/007942.html)
- Addition of read_xtc_nframes function in xdrfile_xtc.c
- Addition of read_trr_nframes function in xdrfile_trr.c
- Bugfix in do_trnheader to return the appropriate error code when reading magic, and properly check the value of the magic in xdrfile_trr.c
- Bugfix of float exception (divide by zero) in xdrfile.c, see https://github.com/SimTk/mdtraj/issues/616
- Implemented efficient seeking pattern inspired by xdrlib2 (part of MDAnalysis)

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external/xdrfile/include/ms_stdint.h vendored Normal file
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// ISO C9x compliant stdint.h for Microsoft Visual Studio
// Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
//
// Copyright (c) 2006-2013 Alexander Chemeris
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// 1. Redistributions of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the product nor the names of its contributors may
// be used to endorse or promote products derived from this software
// without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
// MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
// EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
///////////////////////////////////////////////////////////////////////////////
#ifndef _MSC_VER // [
#error "Use this header only with Microsoft Visual C++ compilers!"
#endif // _MSC_VER ]
#ifndef _MSC_STDINT_H_ // [
#define _MSC_STDINT_H_
#if _MSC_VER > 1000
#pragma once
#endif
#if _MSC_VER >= 1600 // [
#include <stdint.h>
#else // ] _MSC_VER >= 1600 [
#include <limits.h>
// For Visual Studio 6 in C++ mode and for many Visual Studio versions when
// compiling for ARM we should wrap <wchar.h> include with 'extern "C++" {}'
// or compiler give many errors like this:
// error C2733: second C linkage of overloaded function 'wmemchr' not allowed
#ifdef __cplusplus
extern "C" {
#endif
# include <wchar.h>
#ifdef __cplusplus
}
#endif
// Define _W64 macros to mark types changing their size, like intptr_t.
#ifndef _W64
# if !defined(__midl) && (defined(_X86_) || defined(_M_IX86)) && _MSC_VER >= 1300
# define _W64 __w64
# else
# define _W64
# endif
#endif
// 7.18.1 Integer types
// 7.18.1.1 Exact-width integer types
// Visual Studio 6 and Embedded Visual C++ 4 doesn't
// realize that, e.g. char has the same size as __int8
// so we give up on __intX for them.
#if (_MSC_VER < 1300)
typedef signed char int8_t;
typedef signed short int16_t;
typedef signed int int32_t;
typedef unsigned char uint8_t;
typedef unsigned short uint16_t;
typedef unsigned int uint32_t;
#else
typedef signed __int8 int8_t;
typedef signed __int16 int16_t;
typedef signed __int32 int32_t;
typedef unsigned __int8 uint8_t;
typedef unsigned __int16 uint16_t;
typedef unsigned __int32 uint32_t;
#endif
typedef signed __int64 int64_t;
typedef unsigned __int64 uint64_t;
// 7.18.1.2 Minimum-width integer types
typedef int8_t int_least8_t;
typedef int16_t int_least16_t;
typedef int32_t int_least32_t;
typedef int64_t int_least64_t;
typedef uint8_t uint_least8_t;
typedef uint16_t uint_least16_t;
typedef uint32_t uint_least32_t;
typedef uint64_t uint_least64_t;
// 7.18.1.3 Fastest minimum-width integer types
typedef int8_t int_fast8_t;
typedef int16_t int_fast16_t;
typedef int32_t int_fast32_t;
typedef int64_t int_fast64_t;
typedef uint8_t uint_fast8_t;
typedef uint16_t uint_fast16_t;
typedef uint32_t uint_fast32_t;
typedef uint64_t uint_fast64_t;
// 7.18.1.4 Integer types capable of holding object pointers
#ifdef _WIN64 // [
typedef signed __int64 intptr_t;
typedef unsigned __int64 uintptr_t;
#else // _WIN64 ][
typedef _W64 signed int intptr_t;
typedef _W64 unsigned int uintptr_t;
#endif // _WIN64 ]
// 7.18.1.5 Greatest-width integer types
typedef int64_t intmax_t;
typedef uint64_t uintmax_t;
// 7.18.2 Limits of specified-width integer types
#if !defined(__cplusplus) || defined(__STDC_LIMIT_MACROS) // [ See footnote 220 at page 257 and footnote 221 at page 259
// 7.18.2.1 Limits of exact-width integer types
#define INT8_MIN ((int8_t)_I8_MIN)
#define INT8_MAX _I8_MAX
#define INT16_MIN ((int16_t)_I16_MIN)
#define INT16_MAX _I16_MAX
#define INT32_MIN ((int32_t)_I32_MIN)
#define INT32_MAX _I32_MAX
#define INT64_MIN ((int64_t)_I64_MIN)
#define INT64_MAX _I64_MAX
#define UINT8_MAX _UI8_MAX
#define UINT16_MAX _UI16_MAX
#define UINT32_MAX _UI32_MAX
#define UINT64_MAX _UI64_MAX
// 7.18.2.2 Limits of minimum-width integer types
#define INT_LEAST8_MIN INT8_MIN
#define INT_LEAST8_MAX INT8_MAX
#define INT_LEAST16_MIN INT16_MIN
#define INT_LEAST16_MAX INT16_MAX
#define INT_LEAST32_MIN INT32_MIN
#define INT_LEAST32_MAX INT32_MAX
#define INT_LEAST64_MIN INT64_MIN
#define INT_LEAST64_MAX INT64_MAX
#define UINT_LEAST8_MAX UINT8_MAX
#define UINT_LEAST16_MAX UINT16_MAX
#define UINT_LEAST32_MAX UINT32_MAX
#define UINT_LEAST64_MAX UINT64_MAX
// 7.18.2.3 Limits of fastest minimum-width integer types
#define INT_FAST8_MIN INT8_MIN
#define INT_FAST8_MAX INT8_MAX
#define INT_FAST16_MIN INT16_MIN
#define INT_FAST16_MAX INT16_MAX
#define INT_FAST32_MIN INT32_MIN
#define INT_FAST32_MAX INT32_MAX
#define INT_FAST64_MIN INT64_MIN
#define INT_FAST64_MAX INT64_MAX
#define UINT_FAST8_MAX UINT8_MAX
#define UINT_FAST16_MAX UINT16_MAX
#define UINT_FAST32_MAX UINT32_MAX
#define UINT_FAST64_MAX UINT64_MAX
// 7.18.2.4 Limits of integer types capable of holding object pointers
#ifdef _WIN64 // [
# define INTPTR_MIN INT64_MIN
# define INTPTR_MAX INT64_MAX
# define UINTPTR_MAX UINT64_MAX
#else // _WIN64 ][
# define INTPTR_MIN INT32_MIN
# define INTPTR_MAX INT32_MAX
# define UINTPTR_MAX UINT32_MAX
#endif // _WIN64 ]
// 7.18.2.5 Limits of greatest-width integer types
#define INTMAX_MIN INT64_MIN
#define INTMAX_MAX INT64_MAX
#define UINTMAX_MAX UINT64_MAX
// 7.18.3 Limits of other integer types
#ifdef _WIN64 // [
# define PTRDIFF_MIN _I64_MIN
# define PTRDIFF_MAX _I64_MAX
#else // _WIN64 ][
# define PTRDIFF_MIN _I32_MIN
# define PTRDIFF_MAX _I32_MAX
#endif // _WIN64 ]
#define SIG_ATOMIC_MIN INT_MIN
#define SIG_ATOMIC_MAX INT_MAX
#ifndef SIZE_MAX // [
# ifdef _WIN64 // [
# define SIZE_MAX _UI64_MAX
# else // _WIN64 ][
# define SIZE_MAX _UI32_MAX
# endif // _WIN64 ]
#endif // SIZE_MAX ]
// WCHAR_MIN and WCHAR_MAX are also defined in <wchar.h>
#ifndef WCHAR_MIN // [
# define WCHAR_MIN 0
#endif // WCHAR_MIN ]
#ifndef WCHAR_MAX // [
# define WCHAR_MAX _UI16_MAX
#endif // WCHAR_MAX ]
#define WINT_MIN 0
#define WINT_MAX _UI16_MAX
#endif // __STDC_LIMIT_MACROS ]
// 7.18.4 Limits of other integer types
#if !defined(__cplusplus) || defined(__STDC_CONSTANT_MACROS) // [ See footnote 224 at page 260
// 7.18.4.1 Macros for minimum-width integer constants
#define INT8_C(val) val##i8
#define INT16_C(val) val##i16
#define INT32_C(val) val##i32
#define INT64_C(val) val##i64
#define UINT8_C(val) val##ui8
#define UINT16_C(val) val##ui16
#define UINT32_C(val) val##ui32
#define UINT64_C(val) val##ui64
// 7.18.4.2 Macros for greatest-width integer constants
// These #ifndef's are needed to prevent collisions with <boost/cstdint.hpp>.
// Check out Issue 9 for the details.
#ifndef INTMAX_C // [
# define INTMAX_C INT64_C
#endif // INTMAX_C ]
#ifndef UINTMAX_C // [
# define UINTMAX_C UINT64_C
#endif // UINTMAX_C ]
#endif // __STDC_CONSTANT_MACROS ]
#endif // _MSC_VER >= 1600 ]
#endif // _MSC_STDINT_H_ ]

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#ifndef _trr_header_h_
#define _trr_header_h_
typedef struct /* This struct describes the order and the */
/* sizes of the structs in a trjfile, sizes are given in bytes. */
{
int bDouble; /* Double precision? */
int ir_size; /* Backward compatibility */
int e_size; /* Backward compatibility */
int box_size; /* Non zero if a box is present */
int vir_size; /* Backward compatibility */
int pres_size; /* Backward compatibility */
int top_size; /* Backward compatibility */
int sym_size; /* Backward compatibility */
int x_size; /* Non zero if coordinates are present */
int v_size; /* Non zero if velocities are present */
int f_size; /* Non zero if forces are present */
int natoms; /* The total number of atoms */
int step; /* Current step number */
int nre; /* Backward compatibility */
float tf; /* Current time */
float lambdaf; /* Current value of lambda */
double td; /* Current time */
double lambdad; /* Current value of lambda */
} t_trnheader;
int do_trnheader(XDRFILE *xd, char bRead, t_trnheader *sh);
#endif

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#ifndef _xdr_seek_h
#define _xdr_seek_h
// for int64_t on older M$ Visual Studio
#if _MSC_VER && _MSVC_VER < 1600 && !__INTEL_COMPILER
#include "ms_stdint.h"
#else
#include <stdint.h>
#endif
#include "xdrfile.h"
int64_t xdr_tell(XDRFILE *xd);
int xdr_seek(XDRFILE *xd, int64_t pos, int whence);
int xdr_flush(XDRFILE* xd);
#endif

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/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
*
* $Id$
*
* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/*! \file xdrfile.h
* \brief Interface to read/write portabile binary files using XDR.
*
* This file provides an interface to read & write portably binary files,
* using XDR - the external data representation standard defined in RFC 1014.
*
* There are several advantages to the XDR approach:
*
* -# It is portable. And not just portable between big/small integer endian,
* but truly portable if you have system XDR routines. For example:
* - It doesn't matter if the character representation is ASCII or EBCDIC.
* - Some systems are small endian but use big endian order of the two
* dword in a double precision floating-point variable. The system XDR
* libraries will read/write this correctly.
* - Some systems (VAX...) don't use IEEE floating point. Their system
* XDR libraries will convert to/from this automatically.
* -# XDR libraries are required for NFS and lots of other network functions.
* This means there isn't a single Unix-like system that doesn't have them.
* -# There is NO extra metadata whatsoever, and we write plain XDR files.
* If you write a float, it will take exactly 4 bytes in the file.
* (All basic datatypes are 4 bytes, double fp 8 bytes).
* -# You can read/write the files by calling the system XDR routines directly
* too - you don't have to use the routines defined in this file.
* -# It is no problem if your system doesn't have XDR libraries (MS Windows).
* We have written our own versions of the necessary routines that work if
* your system uses ASCII for strings and IEEE floating-point. All types
* of byte and dword endian for integer and floating-point are supported.
* -# You can use these routines for any type of data, but since we designed
* them for Gromacs we also provide a special routine to write coordinates
* with (adjustable) lossy compression. The default precision will give you
* three decimals guaranteed accuracy, and reduces the filesize to 1/10th
* of normal binary data.
*
* We do not support getting or setting positions in XDR files, since it can
* break in horrible ways for large (64-bit) files, resulting in silent data
* corruption. Note that it works great to open/read/write 64-bit files if
* your system supports it; it is just the random access we cannot trust!
*
* We also provide wrapper routines so this module can be used from FORTRAN -
* see the file xdrfile_fortran.txt in the Gromacs distribution for
* documentation on the FORTRAN interface!
*/
#ifndef _XDRFILE_H_
#define _XDRFILE_H_
#ifdef __cplusplus
extern "C"
{
#endif
/*! \brief Abstract datatype for an portable binary file handle
*
* This datatype essentially works just like the standard FILE type in C.
* The actual contents is hidden in the implementation, so you can only
* define pointers to it, for use with the xdrfile routines.
*
* If you \a really need to see the definition it is in xdrfile.c, but you
* cannot access elements of the structure outside that file.
*
* \warning The implementation is completely different from the C standard
* library FILE, so don't even think about using an XDRFILE pointer as an
* argument to a routine that needs a standard FILE pointer.
*/
typedef struct XDRFILE XDRFILE;
enum { exdrOK, exdrHEADER, exdrSTRING, exdrDOUBLE,
exdrINT, exdrFLOAT, exdrUINT, exdr3DX, exdrCLOSE, exdrMAGIC,
exdrNOMEM, exdrENDOFFILE, exdrFILENOTFOUND, exdrNR };
extern char *exdr_message[exdrNR];
#define DIM 3
typedef float matrix[DIM][DIM];
typedef float rvec[DIM];
typedef int mybool;
/*! \brief Open a portable binary file, just like fopen()
*
* Use this routine much like calls to the standard library function
* fopen(). The only difference is that the returned pointer should only
* be used with routines defined in this header.
*
* \param path Full or relative path (including name) of the file
* \param mode "r" for reading, "w" for writing, "a" for append.
*
* \return Pointer to abstract xdr file datatype, or NULL if an error occurs.
*
*/
XDRFILE *
xdrfile_open (const char * path,
const char * mode);
/*! \brief Close a previously opened portable binary file, just like fclose()
*
* Use this routine much like calls to the standard library function
* fopen(). The only difference is that it is used for an XDRFILE handle
* instead of a FILE handle.
*
* \param xfp Pointer to an abstract XDRFILE datatype
*
* \return 0 on success, non-zero on error.
*/
int
xdrfile_close (XDRFILE * xfp);
/*! \brief Read one or more \a char type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of characters to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters read
*/
int
xdrfile_read_char(char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a characters type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of characters to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters written
*/
int
xdrfile_write_char(char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a unsigned \a char type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of unsigned characters to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned characters read
*/
int
xdrfile_read_uchar(unsigned char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a unsigned \a characters type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of unsigned characters to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned characters written
*/
int
xdrfile_write_uchar(unsigned char * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a short type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of shorts to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of shorts read
*/
int
xdrfile_read_short(short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a short type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of shorts to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of shorts written
*/
int
xdrfile_write_short(short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a unsigned \a short type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of unsigned shorts to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned shorts read
*/
int
xdrfile_read_ushort(unsigned short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a unsigned \a short type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of unsigned shorts to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned shorts written
*/
int
xdrfile_write_ushort(unsigned short * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a integer type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of integers to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of integers read
*
* The integer data type is assumed to be less than or equal to 32 bits.
*
* We do not provide any routines for reading/writing 64-bit integers, since
* - Not all XDR implementations support it
* - Not all machines have 64-bit integers
*
* Split your 64-bit data into two 32-bit integers for portability!
*/
int
xdrfile_read_int(int * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a integer type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of integers to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of integers written
*
* The integer data type is assumed to be less than or equal to 32 bits.
*
* We do not provide any routines for reading/writing 64-bit integers, since
* - Not all XDR implementations support it
* - Not all machines have 64-bit integers
*
* Split your 64-bit data into two 32-bit integers for portability!
*/
int
xdrfile_write_int(int * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a unsigned \a integers type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of unsigned integers to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned integers read
*
* The integer data type is assumed to be less than or equal to 32 bits.
*
* We do not provide any routines for reading/writing 64-bit integers, since
* - Not all XDR implementations support it
* - Not all machines have 64-bit integers
*
* Split your 64-bit data into two 32-bit integers for portability!
*/
int
xdrfile_read_uint(unsigned int * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a unsigned \a integer type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of unsigned integers to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of unsigned integers written
*
* The integer data type is assumed to be less than or equal to 32 bits.
*
* We do not provide any routines for reading/writing 64-bit integers, since
* - Not all XDR implementations support it
* - Not all machines have 64-bit integers
*
* Split your 64-bit data into two 32-bit integers for portability!
*/
int
xdrfile_write_uint(unsigned int * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a float type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of floats to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of floats read
*/
int
xdrfile_read_float(float * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a float type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of floats to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of floats written
*/
int
xdrfile_write_float(float * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read one or more \a double type variable(s)
*
* \param ptr Pointer to memory where data should be written
* \param ndata Number of doubles to read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of doubles read
*/
int
xdrfile_read_double(double * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Write one or more \a double type variable(s)
*
* \param ptr Pointer to memory where data should be read
* \param ndata Number of double to write.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of doubles written
*/
int
xdrfile_write_double(double * ptr,
int ndata,
XDRFILE * xfp);
/*! \brief Read a string (array of characters)
*
* \param ptr Pointer to memory where data should be written
* \param maxlen Maximum length of string. If no end-of-string is encountered,
* one byte less than this is read and end-of-string appended.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters read, including end-of-string
*/
int
xdrfile_read_string(char * ptr,
int maxlen,
XDRFILE * xfp);
/*! \brief Write a string (array of characters)
*
* \param ptr Pointer to memory where data should be read
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of characters written, including end-of-string
*/
int
xdrfile_write_string(char * ptr,
XDRFILE * xfp);
/*! \brief Read raw bytes from file (unknown datatype)
*
* \param ptr Pointer to memory where data should be written
* \param nbytes Number of bytes to read. No conversion whatsoever is done.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of bytes read from file
*/
int
xdrfile_read_opaque(char * ptr,
int nbytes,
XDRFILE * xfp);
/*! \brief Write raw bytes to file (unknown datatype)
*
* \param ptr Pointer to memory where data should be read
* \param nbytes Number of bytes to write. No conversion whatsoever is done.
* \param xfp Handle to portable binary file, created with xdrfile_open()
*
* \return Number of bytes written to file
*/
int
xdrfile_write_opaque(char * ptr,
int nbytes,
XDRFILE * xfp);
/*! \brief Compress coordiates in a float array to XDR file
*
* This routine will perform \a lossy compression on the three-dimensional
* coordinate data data specified and store it in the XDR file.
*
* The lossy part of the compression consists of multiplying each
* coordinate with the precision argument and then rounding to integers.
* We suggest a default value of 1000.0, which means you are guaranteed
* three decimals of accuracy. The only limitation is that scaled coordinates
* must still fit in an integer variable, so if the precision is 1000.0 the
* coordinate magnitudes must be less than +-2e6.
*
* \param ptr Pointer to coordinates to compress (length 3*ncoord)
* \param ncoord Number of coordinate triplets in data
* \param precision Scaling factor for lossy compression. If it is <=0,
* the default value of 1000.0 is used.
* \param xfp Handle to portably binary file
*
* \return Number of coordinate triplets written.
* IMPORTANT: Check that this is equal to ncoord - if it is
* negative, an error occured. This should not happen with
* normal data, but if your coordinates are NaN or very
* large (>1e6) it is not possible to use the compression.
*
* \warning The compression algorithm is not part of the XDR standard,
* and very complicated, so you will need this xdrfile module
* to read it later.
*/
int
xdrfile_compress_coord_float(float * ptr,
int ncoord,
float precision,
XDRFILE * xfp);
/*! \brief Decompress coordiates from XDR file to array of floats
*
* This routine will decompress three-dimensional coordinate data previously
* stored in an XDR file and store it in the specified array of floats.
*
* The precision used during the earlier compression is read from the file
* and returned - you cannot adjust the accuracy at this stage.
*
* \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
* \param ncoord Max number of coordinate triplets to read on input, actual
* number of coordinate triplets read on return. If this
* is smaller than the number of coordinates in the frame an
* error will occur.
* \param precision The precision used in the previous compression will be
* written to this variable on return.
* \param xfp Handle to portably binary file
*
* \return Number of coordinate triplets read. If this is negative,
* an error occured.
*
* \warning Since we cannot count on being able to set/get the
* position of large files (>2Gb), it is not possible to
* recover from errors by re-reading the frame if the
* storage area you provided was too small. To avoid this
* from happening, we recommend that you store the number of
* coordinates triplet as an integer either in a header or
* just before the compressed coordinate data, so you can
* read it first and allocated enough memory.
*/
int
xdrfile_decompress_coord_float(float * ptr,
int * ncoord,
float * precision,
XDRFILE * xfp);
/*! \brief Compress coordiates in a double array to XDR file
*
* This routine will perform \a lossy compression on the three-dimensional
* coordinate data data specified and store it in the XDR file. Double will
* NOT give you any extra precision since the coordinates are compressed. This
* routine just avoids allocating a temporary array of floats.
*
* The lossy part of the compression consists of multiplying each
* coordinate with the precision argument and then rounding to integers.
* We suggest a default value of 1000.0, which means you are guaranteed
* three decimals of accuracy. The only limitation is that scaled coordinates
* must still fit in an integer variable, so if the precision is 1000.0 the
* coordinate magnitudes must be less than +-2e6.
*
* \param ptr Pointer to coordinates to compress (length 3*ncoord)
* \param ncoord Number of coordinate triplets in data
* \param precision Scaling factor for lossy compression. If it is <=0, the
* default value of 1000.0 is used.
* \param xfp Handle to portably binary file
*
* \return Number of coordinate triplets written.
* IMPORTANT: Check that this is equal to ncoord - if it is
* negative, an error occured. This should not happen with
* normal data, but if your coordinates are NaN or very
* large (>1e6) it is not possible to use the compression.
*
* \warning The compression algorithm is not part of the XDR standard,
* and very complicated, so you will need this xdrfile module
* to read it later.
*/
int
xdrfile_compress_coord_double(double * ptr,
int ncoord,
double precision,
XDRFILE * xfp);
/*! \brief Decompress coordiates from XDR file to array of doubles
*
* This routine will decompress three-dimensional coordinate data previously
* stored in an XDR file and store it in the specified array of doubles.
* Double will NOT give you any extra precision since the coordinates are
* compressed. This routine just avoids allocating a temporary array of floats.
*
* The precision used during the earlier compression is read from the file
* and returned - you cannot adjust the accuracy at this stage.
*
* \param ptr Pointer to coordinates to compress (length>= 3*ncoord)
* \param ncoord Max number of coordinate triplets to read on input, actual
* number of coordinate triplets read on return. If this
* is smaller than the number of coordinates in the frame an
* error will occur.
* \param precision The precision used in the previous compression will be
* written to this variable on return.
* \param xfp Handle to portably binary file
*
* \return Number of coordinate triplets read. If this is negative,
* an error occured.
*
* \warning Since we cannot count on being able to set/get the
* position of large files (>2Gb), it is not possible to
* recover from errors by re-reading the frame if the
* storage area you provided was too small. To avoid this
* from happening, we recommend that you store the number of
* coordinates triplet as an integer either in a header or
* just before the compressed coordinate data, so you can
* read it first and allocated enough memory.
*/
int
xdrfile_decompress_coord_double(double * ptr,
int * ncoord,
double * precision,
XDRFILE * xfp);
#ifdef __cplusplus
}
#endif
#endif /* _XDRFILE_H_ */

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/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
*
* $Id$
*
* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#ifndef _xdrfile_trr_h
#define _xdrfile_trr_h
#ifdef __cplusplus
extern "C" {
#endif
#include "xdrfile.h"
/* All functions return exdrOK if successful.
* (error codes defined in xdrfile.h).
*/
/* This function returns the number of atoms in the xtc file in *natoms */
extern int read_trr_natoms(char *fn,int *natoms);
extern int read_trr_nframes(char* fn, unsigned long *nframes);
/* Read one frame of an open xtc file. If either of x,v,f,box are
NULL the arrays will be read from the file but not used. */
extern int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,
matrix box,rvec *x,rvec *v,rvec *f);
/* Write a frame to xtc file */
extern int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,
matrix box,rvec *x,rvec *v,rvec *f);
#ifdef __cplusplus
}
#endif
#endif

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/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
*
* $Id$
*
* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#ifndef _xdrfile_xtc_h
#define _xdrfile_xtc_h
#ifdef __cplusplus
extern "C" {
#endif
#include "xdrfile.h"
/* All functions return exdrOK if succesfull.
* (error codes defined in xdrfile.h).
*/
/* This function returns the number of atoms in the xtc file in *natoms */
extern int read_xtc_natoms(char *fn,int *natoms);
int read_xtc_nframes(char* fn, unsigned long *nframes);
/* Read one frame of an open xtc file */
extern int read_xtc(XDRFILE *xd,int natoms,int *step,float *time,
matrix box,rvec *x,float *prec);
/* Write a frame to xtc file */
extern int write_xtc(XDRFILE *xd,
int natoms,int step,float time,
matrix box,rvec *x,float prec);
#ifdef __cplusplus
}
#endif
#endif

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/* 64 bit fileseek operations */
#define _FILE_OFFSETS_BITS 64
#include "xdr_seek.h"
#include <stdio.h>
/// copied from xtcfile.c (version 1.1.4)
struct XDRFILE
{
FILE * fp; /**< pointer to standard C library file handle */
void * /*this used to be (XDR*) */ xdr; /**< pointer to corresponding XDR handle */
char mode; /**< r=read, w=write, a=append */
int * buf1; /**< Buffer for internal use */
int buf1size; /**< Current allocated length of buf1 */
int * buf2; /**< Buffer for internal use */
int buf2size; /**< Current allocated length of buf2 */
};
//// end of copied
int64_t xdr_tell(XDRFILE *xd)
{
FILE* fptr = xd->fp;
#ifndef _WIN32
// use posix 64 bit ftell version
return ftello(fptr);
#elif defined(_MSVC_VER) && !__INTEL_COMPILER
return _ftelli64(fptr);
#else
return ftell(fptr);
#endif
}
int xdr_seek(XDRFILE *xd, int64_t pos, int whence)
{
int result = 1;
FILE* fptr = xd->fp;
#ifndef _WIN32
// use posix 64 bit ftell version
result = fseeko(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#elif _MSVC_VER && !__INTEL_COMPILER
result = _fseeki64(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#else
result = fseek(fptr, pos, whence) < 0 ? exdrNR : exdrOK;
#endif
if (result != exdrOK)
return result;
return exdrOK;
}
int xdr_flush(XDRFILE* xdr)
{
return fflush(xdr->fp);
}

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/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
*
* $Id$
*
* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <stdlib.h>
#include <string.h>
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "xdrfile.h"
#include "xdrfile_trr.h"
#define BUFSIZE 128
#define GROMACS_MAGIC 1993
typedef struct /* This struct describes the order and the */
/* sizes of the structs in a trjfile, sizes are given in bytes. */
{
mybool bDouble; /* Double precision? */
int ir_size; /* Backward compatibility */
int e_size; /* Backward compatibility */
int box_size; /* Non zero if a box is present */
int vir_size; /* Backward compatibility */
int pres_size; /* Backward compatibility */
int top_size; /* Backward compatibility */
int sym_size; /* Backward compatibility */
int x_size; /* Non zero if coordinates are present */
int v_size; /* Non zero if velocities are present */
int f_size; /* Non zero if forces are present */
int natoms; /* The total number of atoms */
int step; /* Current step number */
int nre; /* Backward compatibility */
float tf; /* Current time */
float lambdaf; /* Current value of lambda */
double td; /* Current time */
double lambdad; /* Current value of lambda */
} t_trnheader;
static int nFloatSize(t_trnheader *sh,int *nflsz)
{
int nflsize=0;
if (sh->box_size)
nflsize = sh->box_size/(DIM*DIM);
else if (sh->x_size)
nflsize = sh->x_size/(sh->natoms*DIM);
else if (sh->v_size)
nflsize = sh->v_size/(sh->natoms*DIM);
else if (sh->f_size)
nflsize = sh->f_size/(sh->natoms*DIM);
else
return exdrHEADER;
if (((nflsize != sizeof(float)) && (nflsize != sizeof(double))))
return exdrHEADER;
*nflsz = nflsize;
return exdrOK;
}
extern int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh)
{
int magic=GROMACS_MAGIC;
int nflsz,slen,result;
char *version = "GMX_trn_file";
char buf[BUFSIZE];
if (xdrfile_read_int(&magic,1,xd) != 1) {
/* modification by RTM to return the right EOF code
this is what's happening in the XTC code */
if (bRead)
return exdrENDOFFILE;
else
return exdrINT;
}
if (magic != GROMACS_MAGIC)
return exdrMAGIC;
if (bRead)
{
if (xdrfile_read_int(&slen,1,xd) != 1)
return exdrINT;
if (slen != strlen(version)+1)
return exdrSTRING;
if (xdrfile_read_string(buf,BUFSIZE,xd) <= 0)
return exdrSTRING;
}
else
{
slen = strlen(version)+1;
if (xdrfile_read_int(&slen,1,xd) != 1)
return exdrINT;
if (xdrfile_write_string(version,xd) != (strlen(version)+1) )
return exdrSTRING;
}
if (xdrfile_read_int(&sh->ir_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->e_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->box_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->vir_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->pres_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->top_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->sym_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->x_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->v_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->f_size,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->natoms,1,xd) != 1)
return exdrINT;
if ((result = nFloatSize(sh,&nflsz)) != exdrOK)
return result;
sh->bDouble = (nflsz == sizeof(double));
if (xdrfile_read_int(&sh->step,1,xd) != 1)
return exdrINT;
if (xdrfile_read_int(&sh->nre,1,xd) != 1)
return exdrINT;
if (sh->bDouble)
{
if (xdrfile_read_double(&sh->td,1,xd) != 1)
return exdrDOUBLE;
sh->tf = sh->td;
if (xdrfile_read_double(&sh->lambdad,1,xd) != 1)
return exdrDOUBLE;
sh->lambdaf = sh->lambdad;
}
else
{
if (xdrfile_read_float(&sh->tf,1,xd) != 1)
return exdrFLOAT;
sh->td = sh->tf;
if (xdrfile_read_float(&sh->lambdaf,1,xd) != 1)
return exdrFLOAT;
sh->lambdad = sh->lambdaf;
}
return exdrOK;
}
static int do_htrn(XDRFILE *xd,mybool bRead,t_trnheader *sh,
matrix box,rvec *x,rvec *v,rvec *f)
{
double pvd[DIM*DIM];
double *dx=NULL;
float pvf[DIM*DIM];
float *fx=NULL;
int i,j;
if (sh->bDouble)
{
if (sh->box_size != 0)
{
if (!bRead)
{
for(i=0; (i<DIM); i++)
for(j=0; (j<DIM); j++)
if (NULL != box)
{
pvd[i*DIM+j] = box[i][j];
}
}
if (xdrfile_read_double(pvd,DIM*DIM,xd) == DIM*DIM)
{
for(i=0; (i<DIM); i++)
for(j=0; (j<DIM); j++)
if (NULL != box)
{
box[i][j] = pvd[i*DIM+j];
}
}
else
return exdrDOUBLE;
}
if (sh->vir_size != 0)
{
if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM)
return exdrDOUBLE;
}
if (sh->pres_size!= 0)
{
if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM)
return exdrDOUBLE;
}
if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
dx = (double *)calloc(sh->natoms*DIM,sizeof(dx[0]));
if (NULL == dx)
return exdrNOMEM;
}
if (sh->x_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
dx[i*DIM+j] = x[i][j];
}
}
if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
if (bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
x[i][j] = dx[i*DIM+j];
}
}
}
else
return exdrDOUBLE;
}
if (sh->v_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
dx[i*DIM+j] = v[i][j];
}
}
if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != v)
{
v[i][j] = dx[i*DIM+j];
}
}
else
return exdrDOUBLE;
}
if (sh->f_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
dx[i*DIM+j] = f[i][j];
}
}
if (xdrfile_read_double(dx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
for(i=0; (i<sh->natoms); i++)
{
for(j=0; (j<DIM); j++)
{
if (NULL != f)
{
f[i][j] = dx[i*DIM+j];
}
}
}
}
else
return exdrDOUBLE;
}
if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
free(dx);
}
}
else
/* Float */
{
if (sh->box_size != 0)
{
if (!bRead)
{
for(i=0; (i<DIM); i++)
for(j=0; (j<DIM); j++)
if (NULL != box)
{
pvf[i*DIM+j] = box[i][j];
}
}
if (xdrfile_read_float(pvf,DIM*DIM,xd) == DIM*DIM)
{
for(i=0; (i<DIM); i++)
{
for(j=0; (j<DIM); j++)
{
if (NULL != box)
{
box[i][j] = pvf[i*DIM+j];
}
}
}
}
else
return exdrFLOAT;
}
if (sh->vir_size != 0)
{
if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM)
return exdrFLOAT;
}
if (sh->pres_size!= 0)
{
if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM)
return exdrFLOAT;
}
if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
fx = (float *)calloc(sh->natoms*DIM,sizeof(fx[0]));
if (NULL == fx)
return exdrNOMEM;
}
if (sh->x_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
fx[i*DIM+j] = x[i][j];
}
}
if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
if (bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
x[i][j] = fx[i*DIM+j];
}
}
else
return exdrFLOAT;
}
if (sh->v_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
fx[i*DIM+j] = v[i][j];
}
}
if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != v)
v[i][j] = fx[i*DIM+j];
}
else
return exdrFLOAT;
}
if (sh->f_size != 0)
{
if (!bRead)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != x)
{
fx[i*DIM+j] = f[i][j];
}
}
if (xdrfile_read_float(fx,sh->natoms*DIM,xd) == sh->natoms*DIM)
{
for(i=0; (i<sh->natoms); i++)
for(j=0; (j<DIM); j++)
if (NULL != f)
f[i][j] = fx[i*DIM+j];
}
else
return exdrFLOAT;
}
if ((sh->x_size != 0) || (sh->v_size != 0) || (sh->f_size != 0)) {
free(fx);
}
}
return exdrOK;
}
static int do_trn(XDRFILE *xd,mybool bRead,int *step,float *t,float *lambda,
matrix box,int *natoms,rvec *x,rvec *v,rvec *f)
{
t_trnheader *sh;
int result;
sh = (t_trnheader *)calloc(1,sizeof(*sh));
if (!bRead) {
sh->box_size = (NULL != box) ? sizeof(matrix):0;
sh->x_size = ((NULL != x) ? (*natoms*sizeof(x[0])):0);
sh->v_size = ((NULL != v) ? (*natoms*sizeof(v[0])):0);
sh->f_size = ((NULL != f) ? (*natoms*sizeof(f[0])):0);
sh->natoms = *natoms;
sh->step = *step;
sh->nre = 0;
sh->td = *t;
sh->lambdad = *lambda;
sh->tf = *t;
sh->lambdaf = *lambda;
}
if ((result = do_trnheader(xd,bRead,sh)) != exdrOK)
return result;
if (bRead) {
*natoms = sh->natoms;
*step = sh->step;
*t = sh->td;
*lambda = sh->lambdad;
}
if ((result = do_htrn(xd,bRead,sh,box,x,v,f)) != exdrOK)
return result;
free(sh);
return exdrOK;
}
/************************************************************
*
* The following routines are the exported ones
*
************************************************************/
int read_trr_natoms(char *fn,int *natoms)
{
XDRFILE *xd;
t_trnheader sh;
int result;
xd = xdrfile_open(fn,"r");
if (NULL == xd)
return exdrFILENOTFOUND;
if ((result = do_trnheader(xd,1,&sh)) != exdrOK) {
xdrfile_close(xd);
return result;
}
xdrfile_close(xd);
*natoms = sh.natoms;
return exdrOK;
}
int read_trr_nframes(char *fn, unsigned long *nframes) {
XDRFILE *xd;
int result, step;
float time, lambda;
int natoms;
matrix box;
rvec *x;
*nframes = 0;
read_trr_natoms(fn, &natoms);
x = malloc(natoms * sizeof(*x));
xd = xdrfile_open(fn, "r");
if (NULL == xd)
return exdrFILENOTFOUND;
do {
result = read_trr(xd, natoms, &step, &time, &lambda,
box, x, NULL, NULL);
if (exdrENDOFFILE != result) {
(*nframes)++;
}
} while (result == exdrOK);
xdrfile_close(xd);
free(x);
return exdrOK;
}
int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,
matrix box,rvec *x,rvec *v,rvec *f)
{
return do_trn(xd,0,&step,&t,&lambda,box,&natoms,x,v,f);
}
int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,
matrix box,rvec *x,rvec *v,rvec *f)
{
return do_trn(xd,1,step,t,lambda,box,&natoms,x,v,f);
}

164
external/xdrfile/src/xdrfile_xtc.c vendored Normal file
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/* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
*
* $Id$
*
* Copyright (c) 2009-2014, Erik Lindahl & David van der Spoel
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
* SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
* CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <stdlib.h>
#include "xdrfile.h"
#include "xdrfile_xtc.h"
#define MAGIC 1995
enum { FALSE, TRUE };
static int xtc_header(XDRFILE *xd,int *natoms,int *step,float *time,mybool bRead)
{
int result,magic,n=1;
/* Note: read is same as write. He he he */
magic = MAGIC;
if ((result = xdrfile_write_int(&magic,n,xd)) != n)
{
if (bRead)
return exdrENDOFFILE;
else
return exdrINT;
}
if (magic != MAGIC)
return exdrMAGIC;
if ((result = xdrfile_write_int(natoms,n,xd)) != n)
return exdrINT;
if ((result = xdrfile_write_int(step,n,xd)) != n)
return exdrINT;
if ((result = xdrfile_write_float(time,n,xd)) != n)
return exdrFLOAT;
return exdrOK;
}
static int xtc_coord(XDRFILE *xd,int *natoms,matrix box,rvec *x,float *prec,
mybool bRead)
{
int i,j,result;
/* box */
result = xdrfile_read_float(box[0],DIM*DIM,xd);
if (DIM*DIM != result)
return exdrFLOAT;
else
{
if (bRead)
{
result = xdrfile_decompress_coord_float(x[0],natoms,prec,xd);
if (result != *natoms)
return exdr3DX;
}
else
{
result = xdrfile_compress_coord_float(x[0],*natoms,*prec,xd);
if (result != *natoms)
return exdr3DX;
}
}
return exdrOK;
}
int read_xtc_natoms(char *fn,int *natoms)
{
XDRFILE *xd;
int step,result;
float time;
xd = xdrfile_open(fn,"r");
if (NULL == xd)
return exdrFILENOTFOUND;
result = xtc_header(xd,natoms,&step,&time,TRUE);
xdrfile_close(xd);
return result;
}
int read_xtc_nframes(char* fn, unsigned long *nframes) {
XDRFILE *xd;
int result, step;
float time;
int natoms;
matrix box;
rvec *x;
float prec;
*nframes = 0;
read_xtc_natoms(fn, &natoms);
x = malloc(natoms * sizeof(*x));
xd = xdrfile_open(fn, "r");
if (NULL == xd)
return exdrFILENOTFOUND;
do {
result = read_xtc(xd, natoms, &step, &time, box, x, &prec);
if (exdrENDOFFILE != result) {
(*nframes)++;
}
} while (result == exdrOK);
xdrfile_close(xd);
free(x);
return exdrOK;
}
int read_xtc(XDRFILE *xd,
int natoms,int *step,float *time,
matrix box,rvec *x,float *prec)
/* Read subsequent frames */
{
int result;
if ((result = xtc_header(xd,&natoms,step,time,TRUE)) != exdrOK)
return result;
if ((result = xtc_coord(xd,&natoms,box,x,prec,1)) != exdrOK)
return result;
return exdrOK;
}
int write_xtc(XDRFILE *xd,
int natoms,int step,float time,
matrix box,rvec *x,float prec)
/* Write a frame to xtc file */
{
int result;
if ((result = xtc_header(xd,&natoms,&step,&time,FALSE)) != exdrOK)
return result;
if ((result = xtc_coord(xd,&natoms,box,x,&prec,0)) != exdrOK)
return result;
return exdrOK;
}

5
src/c_abi/mod.rs Normal file
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#[allow(non_upper_case_globals)]
pub mod xdrfile;
pub mod xdrfile_trr;
pub mod xdrfile_xtc;
pub mod xdr_seek;

160
src/c_abi/xdr_seek.rs Normal file
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use super::xdrfile::*;
pub const _STDINT_H: u32 = 1;
pub const _FEATURES_H: u32 = 1;
pub const _DEFAULT_SOURCE: u32 = 1;
pub const __USE_ISOC11: u32 = 1;
pub const __USE_ISOC99: u32 = 1;
pub const __USE_ISOC95: u32 = 1;
pub const __USE_POSIX_IMPLICITLY: u32 = 1;
pub const _POSIX_SOURCE: u32 = 1;
pub const _POSIX_C_SOURCE: u32 = 200809;
pub const __USE_POSIX: u32 = 1;
pub const __USE_POSIX2: u32 = 1;
pub const __USE_POSIX199309: u32 = 1;
pub const __USE_POSIX199506: u32 = 1;
pub const __USE_XOPEN2K: u32 = 1;
pub const __USE_XOPEN2K8: u32 = 1;
pub const _ATFILE_SOURCE: u32 = 1;
pub const __USE_MISC: u32 = 1;
pub const __USE_ATFILE: u32 = 1;
pub const __USE_FORTIFY_LEVEL: u32 = 0;
pub const _STDC_PREDEF_H: u32 = 1;
pub const __STDC_IEC_559__: u32 = 1;
pub const __STDC_IEC_559_COMPLEX__: u32 = 1;
pub const __STDC_ISO_10646__: u32 = 201605;
pub const __STDC_NO_THREADS__: u32 = 1;
pub const __GNU_LIBRARY__: u32 = 6;
pub const __GLIBC__: u32 = 2;
pub const __GLIBC_MINOR__: u32 = 24;
pub const _SYS_CDEFS_H: u32 = 1;
pub const __WORDSIZE: u32 = 64;
pub const __WORDSIZE_TIME64_COMPAT32: u32 = 1;
pub const __SYSCALL_WORDSIZE: u32 = 64;
pub const _BITS_WCHAR_H: u32 = 1;
pub const INT8_MIN: i32 = -128;
pub const INT16_MIN: i32 = -32768;
pub const INT32_MIN: i32 = -2147483648;
pub const INT8_MAX: u32 = 127;
pub const INT16_MAX: u32 = 32767;
pub const INT32_MAX: u32 = 2147483647;
pub const UINT8_MAX: u32 = 255;
pub const UINT16_MAX: u32 = 65535;
pub const UINT32_MAX: u32 = 4294967295;
pub const INT_LEAST8_MIN: i32 = -128;
pub const INT_LEAST16_MIN: i32 = -32768;
pub const INT_LEAST32_MIN: i32 = -2147483648;
pub const INT_LEAST8_MAX: u32 = 127;
pub const INT_LEAST16_MAX: u32 = 32767;
pub const INT_LEAST32_MAX: u32 = 2147483647;
pub const UINT_LEAST8_MAX: u32 = 255;
pub const UINT_LEAST16_MAX: u32 = 65535;
pub const UINT_LEAST32_MAX: u32 = 4294967295;
pub const INT_FAST8_MIN: i32 = -128;
pub const INT_FAST16_MIN: i64 = -9223372036854775808;
pub const INT_FAST32_MIN: i64 = -9223372036854775808;
pub const INT_FAST8_MAX: u32 = 127;
pub const INT_FAST16_MAX: u64 = 9223372036854775807;
pub const INT_FAST32_MAX: u64 = 9223372036854775807;
pub const UINT_FAST8_MAX: u32 = 255;
pub const UINT_FAST16_MAX: i32 = -1;
pub const UINT_FAST32_MAX: i32 = -1;
pub const INTPTR_MIN: i64 = -9223372036854775808;
pub const INTPTR_MAX: u64 = 9223372036854775807;
pub const UINTPTR_MAX: i32 = -1;
pub const PTRDIFF_MIN: i64 = -9223372036854775808;
pub const PTRDIFF_MAX: u64 = 9223372036854775807;
pub const SIG_ATOMIC_MIN: i32 = -2147483648;
pub const SIG_ATOMIC_MAX: u32 = 2147483647;
pub const SIZE_MAX: i32 = -1;
pub const WINT_MIN: u32 = 0;
pub const WINT_MAX: u32 = 4294967295;
pub const DIM: u32 = 3;
pub type int_least8_t = ::std::os::raw::c_schar;
pub type int_least16_t = ::std::os::raw::c_short;
pub type int_least32_t = ::std::os::raw::c_int;
pub type int_least64_t = ::std::os::raw::c_long;
pub type uint_least8_t = ::std::os::raw::c_uchar;
pub type uint_least16_t = ::std::os::raw::c_ushort;
pub type uint_least32_t = ::std::os::raw::c_uint;
pub type uint_least64_t = ::std::os::raw::c_ulong;
pub type int_fast8_t = ::std::os::raw::c_schar;
pub type int_fast16_t = ::std::os::raw::c_long;
pub type int_fast32_t = ::std::os::raw::c_long;
pub type int_fast64_t = ::std::os::raw::c_long;
pub type uint_fast8_t = ::std::os::raw::c_uchar;
pub type uint_fast16_t = ::std::os::raw::c_ulong;
pub type uint_fast32_t = ::std::os::raw::c_ulong;
pub type uint_fast64_t = ::std::os::raw::c_ulong;
pub type intmax_t = ::std::os::raw::c_long;
pub type uintmax_t = ::std::os::raw::c_ulong;
extern "C" {
pub fn xdr_tell(xd: *mut XDRFILE) -> i64;
}
extern "C" {
pub fn xdr_seek(
xd: *mut XDRFILE,
pos: i64,
whence: ::std::os::raw::c_int,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn xdr_flush(xd: *mut XDRFILE) -> ::std::os::raw::c_int;
}
#[cfg(test)]
mod tests {
use super::*;
use super::super::xdrfile_xtc::*;
use std::ffi::CString;
#[test]
fn test_xdr_tell() {
let path = CString::new("tests/1l2y.xtc").unwrap();
let num_atoms = 304;
let mut time: f32 = 2.0;
let mut step: i32 = 5;
let box_vec = [[0.0; 3]; 3];
let x_p = std::ptr::null_mut();
let mut prec: f32 = 0.0;
unsafe {
let mode = CString::new("r").unwrap();
let xdr = xdrfile_open(path.as_ptr(), mode.as_ptr());
assert!(!xdr.is_null());
let tell = xdr_tell(xdr);
assert!(tell == 0, "{}", tell);
read_xtc(xdr, num_atoms, &mut step, &mut time,
box_vec.as_ptr() as *mut Matrix,
x_p,
&mut prec);
let tell = xdr_tell(xdr);
assert!(tell > 0, "{}", tell);
}
}
#[test]
fn test_xdr_seek() {
let path = CString::new("tests/1l2y.xtc").unwrap();
unsafe {
let mode = CString::new("r").unwrap();
let xdr = xdrfile_open(path.as_ptr(), mode.as_ptr());
assert!(!xdr.is_null());
let tell = xdr_tell(xdr);
assert!(tell == 0, "{}", tell);
xdr_seek(xdr, 500, 0);
let tell = xdr_tell(xdr);
assert!(tell == 500, "{}", tell);
}
}
}

520
src/c_abi/xdrfile.rs Normal file
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pub const DIM: u32 = 3;
#[repr(C)]
#[derive(Debug, Copy, Clone)]
pub struct XDRFILE {
_unused: [u8; 0],
}
pub type BindgenTy1 = u32;
pub const exdrOK: BindgenTy1 = 0;
pub const exdrHEADER: BindgenTy1 = 1;
pub const exdrSTRING: BindgenTy1 = 2;
pub const exdrDOUBLE: BindgenTy1 = 3;
pub const exdrINT: BindgenTy1 = 4;
pub const exdrFLOAT: BindgenTy1 = 5;
pub const exdrUINT: BindgenTy1 = 6;
pub const exdr3DX: BindgenTy1 = 7;
pub const exdrCLOSE: BindgenTy1 = 8;
pub const exdrMAGIC: BindgenTy1 = 9;
pub const exdrNOMEM: BindgenTy1 = 10;
pub const exdrENDOFFILE: BindgenTy1 = 11;
pub const exdrFILENOTFOUND: BindgenTy1 = 12;
pub const exdrNR: BindgenTy1 = 13;
extern "C" {
pub static mut exdr_message: [*mut ::std::os::raw::c_char; 13usize];
}
pub type Matrix = [[::std::os::raw::c_float; 3usize]; 3usize];
pub type Rvec = [::std::os::raw::c_float; 3usize];
pub type Mybool = ::std::os::raw::c_int;
extern "C" {
#[doc = " \\brief Open a portable binary file, just like fopen()"]
#[doc = ""]
#[doc = " Use this routine much like calls to the standard library function"]
#[doc = " fopen(). The only difference is that the returned pointer should only"]
#[doc = " be used with routines defined in this header."]
#[doc = ""]
#[doc = " \\param path Full or relative path (including name) of the file"]
#[doc = " \\param mode \"r\" for reading, \"w\" for writing, \"a\" for append."]
#[doc = ""]
#[doc = " \\return Pointer to abstract xdr file datatype, or NULL if an error occurs."]
#[doc = ""]
pub fn xdrfile_open(
path: *const ::std::os::raw::c_char,
mode: *const ::std::os::raw::c_char,
) -> *mut XDRFILE;
}
extern "C" {
#[doc = " \\brief Close a previously opened portable binary file, just like fclose()"]
#[doc = ""]
#[doc = " Use this routine much like calls to the standard library function"]
#[doc = " fopen(). The only difference is that it is used for an XDRFILE handle"]
#[doc = " instead of a FILE handle."]
#[doc = ""]
#[doc = " \\param xfp Pointer to an abstract XDRFILE datatype"]
#[doc = ""]
#[doc = " \\return 0 on success, non-zero on error."]
pub fn xdrfile_close(xfp: *mut XDRFILE) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a char type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of characters to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of characters read"]
pub fn xdrfile_read_char(
ptr: *mut ::std::os::raw::c_char,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a characters type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of characters to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of characters written"]
pub fn xdrfile_write_char(
ptr: *mut ::std::os::raw::c_char,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a unsigned \\a char type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of unsigned characters to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned characters read"]
pub fn xdrfile_read_uchar(
ptr: *mut ::std::os::raw::c_uchar,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a unsigned \\a characters type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of unsigned characters to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned characters written"]
pub fn xdrfile_write_uchar(
ptr: *mut ::std::os::raw::c_uchar,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a short type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of shorts to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of shorts read"]
pub fn xdrfile_read_short(
ptr: *mut ::std::os::raw::c_short,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a short type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of shorts to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of shorts written"]
pub fn xdrfile_write_short(
ptr: *mut ::std::os::raw::c_short,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a unsigned \\a short type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of unsigned shorts to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned shorts read"]
pub fn xdrfile_read_ushort(
ptr: *mut ::std::os::raw::c_ushort,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a unsigned \\a short type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of unsigned shorts to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned shorts written"]
pub fn xdrfile_write_ushort(
ptr: *mut ::std::os::raw::c_ushort,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a integer type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of integers to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of integers read"]
#[doc = ""]
#[doc = " The integer data type is assumed to be less than or equal to 32 bits."]
#[doc = ""]
#[doc = " We do not provide any routines for reading/writing 64-bit integers, since"]
#[doc = " - Not all XDR implementations support it"]
#[doc = " - Not all machines have 64-bit integers"]
#[doc = ""]
#[doc = " Split your 64-bit data into two 32-bit integers for portability!"]
pub fn xdrfile_read_int(
ptr: *mut ::std::os::raw::c_int,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a integer type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of integers to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of integers written"]
#[doc = ""]
#[doc = " The integer data type is assumed to be less than or equal to 32 bits."]
#[doc = ""]
#[doc = " We do not provide any routines for reading/writing 64-bit integers, since"]
#[doc = " - Not all XDR implementations support it"]
#[doc = " - Not all machines have 64-bit integers"]
#[doc = ""]
#[doc = " Split your 64-bit data into two 32-bit integers for portability!"]
pub fn xdrfile_write_int(
ptr: *mut ::std::os::raw::c_int,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a unsigned \\a integers type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of unsigned integers to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned integers read"]
#[doc = ""]
#[doc = " The integer data type is assumed to be less than or equal to 32 bits."]
#[doc = ""]
#[doc = " We do not provide any routines for reading/writing 64-bit integers, since"]
#[doc = " - Not all XDR implementations support it"]
#[doc = " - Not all machines have 64-bit integers"]
#[doc = ""]
#[doc = " Split your 64-bit data into two 32-bit integers for portability!"]
pub fn xdrfile_read_uint(
ptr: *mut ::std::os::raw::c_uint,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a unsigned \\a integer type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of unsigned integers to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of unsigned integers written"]
#[doc = ""]
#[doc = " The integer data type is assumed to be less than or equal to 32 bits."]
#[doc = ""]
#[doc = " We do not provide any routines for reading/writing 64-bit integers, since"]
#[doc = " - Not all XDR implementations support it"]
#[doc = " - Not all machines have 64-bit integers"]
#[doc = ""]
#[doc = " Split your 64-bit data into two 32-bit integers for portability!"]
pub fn xdrfile_write_uint(
ptr: *mut ::std::os::raw::c_uint,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a float type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of floats to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of floats read"]
pub fn xdrfile_read_float(
ptr: *mut ::std::os::raw::c_float,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a float type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of floats to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of floats written"]
pub fn xdrfile_write_float(
ptr: *mut ::std::os::raw::c_float,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read one or more \\a double type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param ndata Number of doubles to read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of doubles read"]
pub fn xdrfile_read_double(
ptr: *mut ::std::os::raw::c_double,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write one or more \\a double type variable(s)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param ndata Number of double to write."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of doubles written"]
pub fn xdrfile_write_double(
ptr: *mut ::std::os::raw::c_double,
ndata: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read a string (array of characters)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param maxlen Maximum length of string. If no end-of-string is encountered,"]
#[doc = " one byte less than this is read and end-of-string appended."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of characters read, including end-of-string"]
pub fn xdrfile_read_string(
ptr: *mut ::std::os::raw::c_char,
maxlen: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write a string (array of characters)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of characters written, including end-of-string"]
pub fn xdrfile_write_string(
ptr: *mut ::std::os::raw::c_char,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Read raw bytes from file (unknown datatype)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be written"]
#[doc = " \\param nbytes Number of bytes to read. No conversion whatsoever is done."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of bytes read from file"]
pub fn xdrfile_read_opaque(
ptr: *mut ::std::os::raw::c_char,
nbytes: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Write raw bytes to file (unknown datatype)"]
#[doc = ""]
#[doc = " \\param ptr Pointer to memory where data should be read"]
#[doc = " \\param nbytes Number of bytes to write. No conversion whatsoever is done."]
#[doc = " \\param xfp Handle to portable binary file, created with xdrfile_open()"]
#[doc = ""]
#[doc = " \\return Number of bytes written to file"]
pub fn xdrfile_write_opaque(
ptr: *mut ::std::os::raw::c_char,
nbytes: ::std::os::raw::c_int,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Compress coordiates in a float array to XDR file"]
#[doc = ""]
#[doc = " This routine will perform \\a lossy compression on the three-dimensional"]
#[doc = " coordinate data data specified and store it in the XDR file."]
#[doc = ""]
#[doc = " The lossy part of the compression consists of multiplying each"]
#[doc = " coordinate with the precision argument and then rounding to integers."]
#[doc = " We suggest a default value of 1000.0, which means you are guaranteed"]
#[doc = " three decimals of accuracy. The only limitation is that scaled coordinates"]
#[doc = " must still fit in an integer variable, so if the precision is 1000.0 the"]
#[doc = " coordinate magnitudes must be less than +-2e6."]
#[doc = ""]
#[doc = " \\param ptr Pointer to coordinates to compress (length 3*ncoord)"]
#[doc = " \\param ncoord Number of coordinate triplets in data"]
#[doc = " \\param precision Scaling factor for lossy compression. If it is <=0,"]
#[doc = " the default value of 1000.0 is used."]
#[doc = " \\param xfp Handle to portably binary file"]
#[doc = ""]
#[doc = " \\return Number of coordinate triplets written."]
#[doc = " IMPORTANT: Check that this is equal to ncoord - if it is"]
#[doc = " negative, an error occured. This should not happen with"]
#[doc = "\t \t normal data, but if your coordinates are NaN or very"]
#[doc = " large (>1e6) it is not possible to use the compression."]
#[doc = ""]
#[doc = " \\warning The compression algorithm is not part of the XDR standard,"]
#[doc = " and very complicated, so you will need this xdrfile module"]
#[doc = " to read it later."]
pub fn xdrfile_compress_coord_float(
ptr: *mut ::std::os::raw::c_float,
ncoord: ::std::os::raw::c_int,
precision: ::std::os::raw::c_float,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Decompress coordiates from XDR file to array of floats"]
#[doc = ""]
#[doc = " This routine will decompress three-dimensional coordinate data previously"]
#[doc = " stored in an XDR file and store it in the specified array of floats."]
#[doc = ""]
#[doc = " The precision used during the earlier compression is read from the file"]
#[doc = " and returned - you cannot adjust the accuracy at this stage."]
#[doc = ""]
#[doc = " \\param ptr Pointer to coordinates to compress (length>= 3*ncoord)"]
#[doc = " \\param ncoord Max number of coordinate triplets to read on input, actual"]
#[doc = " number of coordinate triplets read on return. If this"]
#[doc = " is smaller than the number of coordinates in the frame an"]
#[doc = " error will occur."]
#[doc = " \\param precision The precision used in the previous compression will be"]
#[doc = " written to this variable on return."]
#[doc = " \\param xfp Handle to portably binary file"]
#[doc = ""]
#[doc = " \\return Number of coordinate triplets read. If this is negative,"]
#[doc = " an error occured."]
#[doc = ""]
#[doc = " \\warning Since we cannot count on being able to set/get the"]
#[doc = " position of large files (>2Gb), it is not possible to"]
#[doc = " recover from errors by re-reading the frame if the"]
#[doc = " storage area you provided was too small. To avoid this"]
#[doc = " from happening, we recommend that you store the number of"]
#[doc = " coordinates triplet as an integer either in a header or"]
#[doc = " just before the compressed coordinate data, so you can"]
#[doc = " read it first and allocated enough memory."]
pub fn xdrfile_decompress_coord_float(
ptr: *mut ::std::os::raw::c_float,
ncoord: *mut ::std::os::raw::c_int,
precision: *mut ::std::os::raw::c_float,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Compress coordiates in a double array to XDR file"]
#[doc = ""]
#[doc = " This routine will perform \\a lossy compression on the three-dimensional"]
#[doc = " coordinate data data specified and store it in the XDR file. Double will"]
#[doc = " NOT give you any extra precision since the coordinates are compressed. This"]
#[doc = " routine just avoids allocating a temporary array of floats."]
#[doc = ""]
#[doc = " The lossy part of the compression consists of multiplying each"]
#[doc = " coordinate with the precision argument and then rounding to integers."]
#[doc = " We suggest a default value of 1000.0, which means you are guaranteed"]
#[doc = " three decimals of accuracy. The only limitation is that scaled coordinates"]
#[doc = " must still fit in an integer variable, so if the precision is 1000.0 the"]
#[doc = " coordinate magnitudes must be less than +-2e6."]
#[doc = ""]
#[doc = " \\param ptr Pointer to coordinates to compress (length 3*ncoord)"]
#[doc = " \\param ncoord Number of coordinate triplets in data"]
#[doc = " \\param precision Scaling factor for lossy compression. If it is <=0, the"]
#[doc = " default value of 1000.0 is used."]
#[doc = " \\param xfp Handle to portably binary file"]
#[doc = ""]
#[doc = " \\return Number of coordinate triplets written."]
#[doc = " IMPORTANT: Check that this is equal to ncoord - if it is"]
#[doc = " negative, an error occured. This should not happen with"]
#[doc = " normal data, but if your coordinates are NaN or very"]
#[doc = " large (>1e6) it is not possible to use the compression."]
#[doc = ""]
#[doc = " \\warning The compression algorithm is not part of the XDR standard,"]
#[doc = " and very complicated, so you will need this xdrfile module"]
#[doc = " to read it later."]
pub fn xdrfile_compress_coord_double(
ptr: *mut ::std::os::raw::c_double,
ncoord: ::std::os::raw::c_int,
precision: ::std::os::raw::c_double,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}
extern "C" {
#[doc = " \\brief Decompress coordiates from XDR file to array of doubles"]
#[doc = ""]
#[doc = " This routine will decompress three-dimensional coordinate data previously"]
#[doc = " stored in an XDR file and store it in the specified array of doubles."]
#[doc = " Double will NOT give you any extra precision since the coordinates are"]
#[doc = " compressed. This routine just avoids allocating a temporary array of floats."]
#[doc = ""]
#[doc = " The precision used during the earlier compression is read from the file"]
#[doc = " and returned - you cannot adjust the accuracy at this stage."]
#[doc = ""]
#[doc = " \\param ptr Pointer to coordinates to compress (length>= 3*ncoord)"]
#[doc = " \\param ncoord Max number of coordinate triplets to read on input, actual"]
#[doc = " number of coordinate triplets read on return. If this"]
#[doc = " is smaller than the number of coordinates in the frame an"]
#[doc = " error will occur."]
#[doc = " \\param precision The precision used in the previous compression will be"]
#[doc = " written to this variable on return."]
#[doc = " \\param xfp Handle to portably binary file"]
#[doc = ""]
#[doc = " \\return Number of coordinate triplets read. If this is negative,"]
#[doc = " an error occured."]
#[doc = ""]
#[doc = " \\warning Since we cannot count on being able to set/get the"]
#[doc = " position of large files (>2Gb), it is not possible to"]
#[doc = " recover from errors by re-reading the frame if the"]
#[doc = " storage area you provided was too small. To avoid this"]
#[doc = " from happening, we recommend that you store the number of"]
#[doc = " coordinates triplet as an integer either in a header or"]
#[doc = " just before the compressed coordinate data, so you can"]
#[doc = " read it first and allocated enough memory."]
pub fn xdrfile_decompress_coord_double(
ptr: *mut ::std::os::raw::c_double,
ncoord: *mut ::std::os::raw::c_int,
precision: *mut ::std::os::raw::c_double,
xfp: *mut XDRFILE,
) -> ::std::os::raw::c_int;
}

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use super::xdrfile::*;
extern "C" {
pub fn read_trr_natoms(
fn_: *const ::std::os::raw::c_char,
natoms: *const ::std::os::raw::c_int,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn read_trr_nframes(
fn_: *const ::std::os::raw::c_char,
nframes: *const ::std::os::raw::c_ulong,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn read_trr(
xd: *mut XDRFILE,
natoms: ::std::os::raw::c_int,
step: *mut ::std::os::raw::c_int,
t: *mut ::std::os::raw::c_float,
lambda: *mut ::std::os::raw::c_float,
box_vec: *mut Matrix,
x: *mut Rvec,
v: *mut Rvec,
f: *mut Rvec,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn write_trr(
xd: *mut XDRFILE,
natoms: ::std::os::raw::c_int,
step: ::std::os::raw::c_int,
t: ::std::os::raw::c_float,
lambda: ::std::os::raw::c_float,
box_vec: *const Matrix,
x: *const Rvec,
v: *const Rvec,
f: *const Rvec,
) -> ::std::os::raw::c_int;
}
#[cfg(test)]
mod tests {
use super::*;
use std::ffi::CString;
use tempfile::NamedTempFile;
#[test]
fn test_read_trr_natoms() {
let path = CString::new("tests/1l2y.trr").unwrap();
let mut natoms = 0;
unsafe {
read_trr_natoms(path.as_ptr() as *const i8, &mut natoms);
}
assert!(natoms == 304);
}
#[test]
fn test_read_trr_nframes() {
let path = CString::new("tests/1l2y.trr").unwrap();
let mut nframes: u64 = 0;
unsafe {
let code = read_trr_nframes(path.as_ptr() as *const i8, &mut nframes);
assert!(code as u32 == exdrOK);
}
assert!(nframes == 38, "{:?}", nframes);
}
#[test]
fn test_read_write_trr() {
let tempfile = NamedTempFile::new().unwrap();
let tmp_path = CString::new(tempfile.path().to_str().unwrap()).unwrap();
// write atoms to tempfile
let natoms: i32 = 2;
let time: f32 = 2.0;
let lambda: f32 = 1.0;
let step: i32 = 5;
let box_vec: Matrix = [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]];
let x: Vec<Rvec> = vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]];
let v: Vec<Rvec> = vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]];
let f: Vec<Rvec> = vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]];
unsafe {
let mode = CString::new("w").unwrap();
let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
let write_code = write_trr(xdr, natoms, step, time, lambda,
box_vec.as_ptr() as *mut Matrix,
x.as_ptr() as *mut Rvec,
v.as_ptr() as *mut Rvec,
f.as_ptr() as *mut Rvec);
assert!(write_code as u32 == exdrOK);
xdrfile_close(xdr);
}
// read atoms from tempfile
let mut time2: f32 = 0.0;
let mut lambda2: f32 = 0.0;
let mut step2: i32 = 0;
let box_vec2: Matrix = [[0.0, 0.0, 0.0]; 3];
let x2: Vec<Rvec> = vec![[0.0, 0.0, 0.0]; 2];
let v2: Vec<Rvec> = vec![[0.0, 0.0, 0.0]; 2];
let f2: Vec<Rvec> = vec![[0.0, 0.0, 0.0]; 2];
unsafe {
let mode = CString::new("r").unwrap();
let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
let read_code = read_trr(xdr, natoms, &mut step2, &mut time2,
&mut lambda2, box_vec2.as_ptr() as *mut Matrix,
x2.as_ptr() as *mut Rvec,
v2.as_ptr() as *mut Rvec,
f2.as_ptr() as *mut Rvec);
assert!(read_code as u32 == exdrOK);
xdrfile_close(xdr);
}
// make sure everything is still the same
assert!(step2 == step);
assert!(time2 == time);
assert!(lambda == lambda2);
assert!(box_vec2 == box_vec);
assert!(x2 == x);
assert!(v2 == v);
assert!(f2 == f);
}
}

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use super::xdrfile::*;
extern "C" {
pub fn read_xtc_natoms(
fn_: *const ::std::os::raw::c_char,
natoms: *const ::std::os::raw::c_int,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn read_xtc_nframes(
fn_: *const ::std::os::raw::c_char,
nframes: *const ::std::os::raw::c_ulong,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn read_xtc(
xd: *mut XDRFILE,
natoms: ::std::os::raw::c_int,
step: *mut ::std::os::raw::c_int,
time: *mut ::std::os::raw::c_float,
box_vec: *mut Matrix,
x: *mut Rvec,
prec: *mut ::std::os::raw::c_float,
) -> ::std::os::raw::c_int;
}
extern "C" {
pub fn write_xtc(
xd: *mut XDRFILE,
natoms: ::std::os::raw::c_int,
step: ::std::os::raw::c_int,
time: ::std::os::raw::c_float,
box_vec: *mut Matrix,
x: *mut Rvec,
prec: ::std::os::raw::c_float,
) -> ::std::os::raw::c_int;
}
#[cfg(test)]
mod tests {
use super::*;
use std::ffi::CString;
use tempfile::NamedTempFile;
#[test]
fn test_read_xtc_natoms() {
let path = CString::new("tests/1l2y.xtc").unwrap();
let mut natoms = 0;
unsafe {
read_xtc_natoms(path.as_ptr() as *mut i8, &mut natoms);
}
assert!(natoms == 304);
}
#[test]
fn test_read_xtc_nframes() {
let path = CString::new("tests/1l2y.xtc").unwrap();
let mut nframes: u64 = 0;
unsafe {
let code = read_xtc_nframes(path.as_ptr() as *const i8, &mut nframes);
assert!(code as u32 == exdrOK);
}
assert!(nframes == 38, "{:?}", nframes);
}
#[test]
fn test_read_write_xtc() {
let tempfile = NamedTempFile::new().unwrap();
let tmp_path = CString::new(tempfile.path().to_str().unwrap()).unwrap();
// write atoms to tempfile
let natoms: i32 = 2;
let time: f32 = 2.0;
let step: i32 = 5;
let box_vec: Matrix = [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]];
let x: Vec<Rvec> = vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]];
unsafe {
let mode = CString::new("w").unwrap();
let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
let write_code = write_xtc(xdr, natoms, step, time,
box_vec.as_ptr() as *mut Matrix, x.as_ptr() as *mut Rvec,
1000.0);
assert!(write_code as u32 == exdrOK);
xdrfile_close(xdr);
}
// read atoms from tempfile
let mut time2: f32 = 0.0;
let mut step2: i32 = 0;
let box_vec2: Matrix = [[0.0, 0.0, 0.0]; 3];
let x2: Vec<Rvec> = vec![[0.0, 0.0, 0.0]; 2];
let mut prec: f32 = 0.0;
unsafe {
let mode = CString::new("r").unwrap();
let xdr = xdrfile_open(tmp_path.as_ptr(), mode.as_ptr());
let read_code = read_xtc(xdr, natoms, &mut step2, &mut time2,
box_vec2.as_ptr() as *mut Matrix, x2.as_ptr() as *mut Rvec,
&mut prec);
assert!(read_code as u32 == exdrOK);
xdrfile_close(xdr);
}
// make sure everything is still the same
assert!(step2 == step);
assert!(time2 == time);
assert!(box_vec2 == box_vec);
assert!(x2 == x);
}
}

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pub mod c_abi;

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