HAVE_DOT = @DOXYGEN_DOT_FOUND@
DOT_PATH = @DOXYGEN_DOT_PATH@
+MACRO_EXPANSION = YES
+EXPAND_ONLY_PREDEF = YES
+PREDEFINED = F77_FUNC(name,NAME)=name
+
ENABLED_SECTIONS = libapi internal
INTERNAL_DOCS = YES
HIDE_UNDOC_CLASSES = YES
add_subdirectory(gmxpreprocess)
add_subdirectory(analysisdata)
add_subdirectory(commandline)
+add_subdirectory(linearalgebra)
add_subdirectory(options)
add_subdirectory(selection)
add_subdirectory(trajectoryanalysis)
file(GLOB GMX_PPC_ALTIVEC_SRC nonbonded/nb_kernel_ppc_altivec/*.c)
endif(GMX_PPC_ALTIVEC)
-if(NOT GMX_EXTERNAL_BLAS)
- file(GLOB BLAS_SOURCES gmx_blas/*.c)
-endif(NOT GMX_EXTERNAL_BLAS)
-
-if(NOT GMX_EXTERNAL_LAPACK)
- file(GLOB LAPACK_SOURCES gmx_lapack/*.c)
-endif(NOT GMX_EXTERNAL_LAPACK)
-
# This would be the standard way to include thread_mpi, but we want libgmx
# to link the functions directly
#if(GMX_THREAD_MPI)
file(GLOB THREAD_MPI_SOURCES ${THREAD_MPI_SRC})
set(GMX_SSEKERNEL_ASM_SRC ${GMX_SSEKERNEL_ASM_SRC} PARENT_SCOPE)
-set(GMXLIB_SOURCES ${GMXLIB_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES}
+set(GMXLIB_SOURCES ${GMXLIB_SOURCES}
${GMX_SSEKERNEL_C_SRC} ${FORTRAN_SOURCES}
${GMX_BLUEGENE_C_SRC} ${GMX_PPC_ALTIVEC_SRC} ${THREAD_MPI_SOURCES}
PARENT_SCOPE)
--- /dev/null
+file(GLOB LINEARALGEBRA_SOURCES *.c)
+
+if (NOT GMX_EXTERNAL_BLAS)
+ file(GLOB BLAS_SOURCES gmx_blas/*.c)
+endif (NOT GMX_EXTERNAL_BLAS)
+
+if (NOT GMX_EXTERNAL_LAPACK)
+ file(GLOB LAPACK_SOURCES gmx_lapack/*.c)
+endif (NOT GMX_EXTERNAL_LAPACK)
+
+set(LINEARALGEBRA_SOURCES
+ ${LINEARALGEBRA_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES})
+
+set(LIBGROMACS_SOURCES
+ ${LIBGROMACS_SOURCES} ${LINEARALGEBRA_SOURCES} PARENT_SCOPE)
+
+set(LINEARALGEBRA_PUBLIC_HEADERS
+ eigensolver.h
+ matrix.h
+ mtxio.h
+ sparsematrix.h)
+install(FILES ${LINEARALGEBRA_PUBLIC_HEADERS}
+ DESTINATION ${INCL_INSTALL_DIR}/gromacs/linearalgebra
+ COMPONENT development)
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
-
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "types/simple.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
-
-#include "sparsematrix.h"
#include "eigensolver.h"
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
-#endif
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/legacyheaders/smalloc.h"
+
+#include "gromacs/linearalgebra/sparsematrix.h"
#include "gmx_lapack.h"
#include "gmx_arpack.h"
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
+#ifndef GMX_LINEARALGEBRA_EIGENSOLVER_H
+#define GMX_LINEARALGEBRA_EIGENSOLVER_H
-#ifndef _EIGENSOLVER_H
-#define _EIGENSOLVER_H
+#include "../legacyheaders/types/simple.h"
-#include "types/simple.h"
#include "sparsematrix.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
/** Calculate eigenvalues/vectors a matrix stored in linear memory (not sparse).
*
real * eigenvectors,
int maxiter);
+#ifdef __cplusplus
+}
+#endif
#endif
* Rice University
* Houston, Texas
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
#include <math.h>
#include <string.h>
-#include "types/simple.h"
-#include "gmx_lapack.h"
-#include "gmx_blas.h"
-#include "gmx_arpack.h"
-
-
-/* Default Fortran name mangling */
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
-#endif
-
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gmx_arpack.h"
+#include "gmx_blas.h"
+#include "gmx_lapack.h"
static void
F77_FUNC(dstqrb,DSTQRB)(int * n,
* Rice University
* Houston, Texas
*/
-
-#ifndef _GMX_ARPACK_H
-#define _GMX_ARPACK_H
-
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*! \file
- * \brief Selected routines from ARPACK
+/*! \internal \file
+ * \brief
+ * Selected routines from ARPACK
*
* This file contains a subset of ARPACK functions to perform
* diagonalization and SVD for sparse matrices in Gromacs.
* from ARPACK. The code is essentially the same, but the routines
* have been made thread-safe by using extra workspace arrays.
*/
+#ifndef GMX_ARPACK_H
+#define GMX_ARPACK_H
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
#ifndef F77_FUNC
#define F77_FUNC(name,NAME) name ## _
#endif
+#ifdef __cplusplus
+extern "C" {
+#endif
/*! \brief Implicitly Restarted Arnoldi Iteration, double precision.
*
* And Hey:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
-
-#ifndef _GMX_BLAS_H_
-#define _GMX_BLAS_H_
-
-#include "types/simple.h"
-
-/* Suppress Cygwin compiler warnings from using newlib version of
- * ctype.h */
-#ifdef GMX_CYGWIN
-#undef toupper
-#endif
-
-
-/** @file
- *
- * @brief Header definitions for the standard BLAS library.
+/*! \internal \file
+ * \brief
+ * Header definitions for the standard BLAS library.
*
* This is the subset of BLAS routines used for the
* linear algebra operations in Gromacs.
* at http://www.netlib.org/blas , so there is no point in repeating
* it here.
*/
+#ifndef GMX_BLAS_H
+#define GMX_BLAS_H
+
+/*! \cond */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+#ifndef F77_FUNC
+#define F77_FUNC(name,NAME) name ## _
+#endif
+#include "gromacs/utility/gmx_header_config.h"
+
+/* Suppress Cygwin compiler warnings from using newlib version of
+ * ctype.h */
+#ifdef GMX_CYGWIN
+#undef toupper
+#endif
#ifdef __cplusplus
extern "C" {
}
#endif
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
-#endif
-
-
/* Double precision versions */
double
F77_FUNC(dasum,DASUM)(int *n, double *dx, int *incx);
}
#endif
+/*! \endcond */
-
-#endif /* _BLAS_H_ */
+#endif /* GMX_BLAS_H */
#include <math.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
double
F77_FUNC(dasum,DASUM)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dcopy,DCOPY)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
double
F77_FUNC(ddot,DDOT)(int *n_arg,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dgemm,DGEMM)(const char *transa,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dgemv,DGEMV)(const char *trans,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dger,DGER)(int *m__,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
double
F77_FUNC(dnrm2,DNRM2)(int * n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(drot,DROT)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dscal,DSCAL)(int * n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dswap,DSWAP)(int *n__,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dsymv,DSYMV)(const char *uplo,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dsyr2,DSYR2)(const char * uplo,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dsyr2k,DSYR2K)(const char *uplo,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dtrmm,DTRMM)(const char *side,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dtrmv,DTRMV)(const char *uplo,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(dtrsm,DTRSM)(const char * side,
#include <math.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
int
F77_FUNC(idamax,IDAMAX)(int *n__,
#include <math.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
int
F77_FUNC(isamax,ISAMAX)(int *n__,
#include <math.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
float
F77_FUNC(sasum,SASUM)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(scopy,SCOPY)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
float
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(sgemm,SGEMM)(const char *transa,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(sgemv,SGEMV)(const char *trans,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(sger,SGER)(int *m__,
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
float
F77_FUNC(snrm2,SNRM2)(int * n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(srot,SROT)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(sscal,SSCAL)(int *n__,
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(sswap,SSWAP)(int *n__,
#include <ctype.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(ssymv,SSYMV)(const char *uplo,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(ssyr2,SSYR2)(const char * uplo,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(ssyr2k,SSYR2K)(const char *uplo,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(strmm,STRMM)(const char *side,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(strmv,STRMV)(const char *uplo,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
+#include "../gmx_blas.h"
void
F77_FUNC(strsm,STRSM)(const char * side,
* And Hey:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
-
-#ifndef _GMX_LAPACK_H_
-#define _GMX_LAPACK_H_
-
-
-/** @file
- *
- * @brief Header definitions for the standard LAPACK library.
+/*! \internal \file
+ * \brief
+ * Header definitions for the standard LAPACK library.
*
* This is the subset of LAPACK routines used for the
* linear algebra operations in Gromacs. Most of the execution time
* at http://www.netlib.org/lapack , so there is no point in repeating
* it here.
*/
+#ifndef GMX_LAPACK_H
+#define GMX_LAPACK_H
+/*! \cond */
-
-#ifdef __cplusplus
-extern "C" {
+#ifdef HAVE_CONFIG_H
+#include "config.h"
#endif
-#if 0
-}
+#ifndef F77_FUNC
+#define F77_FUNC(name,NAME) name ## _
#endif
-
-#include "types/simple.h"
+#include "gromacs/utility/gmx_header_config.h"
/* Suppress Cygwin compiler warnings from using newlib version of
* ctype.h */
#undef toupper
#endif
-#ifndef F77_FUNC
-#define F77_FUNC(name,NAME) name ## _
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+}
#endif
-
-
/* Double precision */
}
#endif
+/*! \endcond */
-
-#endif /* _LAPACK_H_ */
+#endif /* GMX_LAPACK_H */
#include <ctype.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <ctype.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dgebd2,DGEBD2)(int *m,
-#include "gmx_lapack.h"
-#include "gmx_blas.h"
+#include "../gmx_lapack.h"
+#include "../gmx_blas.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dgelq2,DGELQ2)(int *m,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dgetrs,DGETRS)(const char *trans,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include<ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlaebz,DLAEBZ)(int *ijob,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
#include<math.h>
#include<ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
double
#include <math.h>
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
double
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
double
F77_FUNC(dlansy,DLANSY)(const char *norm, const char *uplo, int *n, double *a, int
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void F77_FUNC(dlar1vx,DLAR1VX)(int *n,
#include <math.h>
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlarft,DLARFT)(const char *direct,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlarnv,DLARNV)(int *idist,
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlaruv,DLARUV)(int *iseed, int *n, double *x)
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlas2,DLAS2)(double *f,
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd0,DLASD0)(int *n,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd1,DLASD1)(int *nl,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd3,DLASD3)(int *nl,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd5,DLASD5)(int *i__,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd6,DLASD6)(int *icompq,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasd8,DLASD8)(int *icompq,
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasda,DLASDA)(int *icompq,
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasdt,DLASDT)(int *n,
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasq4,DLASQ4)(int *i0,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasq5,DLASQ5)(int *i0,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasr,DLASR)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlasrt,DLASRT)(const char *id,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void F77_FUNC(dlasrt2,DLASRT2)(const char *id,
int *n,
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dlassq,DLASSQ)(int *n,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
void
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dorg2r,DORG2R)(int *m,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dorgl2,DORGL2)(int *m,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#define DORGLQ_BLOCKSIZE 32
#define DORGLQ_MINBLOCKSIZE 2
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dorm2l,DORM2L)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dorm2r,DORM2R)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dorml2,DORML2)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* Normally, DSTEVR is the LAPACK wrapper which calls one
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include <types/simple.h>
+
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(dsytd2,DSYTD2)(const char * uplo,
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(ilasrt2,ILASRT2)(const char *id,
#include <ctype.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <ctype.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sgebd2,SGEBD2)(int *m,
-#include "gmx_lapack.h"
-#include "gmx_blas.h"
+#include "../gmx_lapack.h"
+#include "../gmx_blas.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sgelq2,SGELQ2)(int *m,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sgetrs,SGETRS)(const char *trans,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include<ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slaebz,SLAEBZ)(int *ijob,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
#include<math.h>
#include<ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
float
#include <math.h>
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
float
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
float
F77_FUNC(slansy,SLANSY)(const char *norm, const char *uplo, int *n, float *a, int
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void F77_FUNC(slar1vx,SLAR1VX)(int *n,
#include <math.h>
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slarft,SLARFT)(const char *direct,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slarnv,SLARNV)(int *idist,
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slaruv,SLARUV)(int *iseed, int *n, float *x)
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slas2,SLAS2)(float *f,
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd0,SLASD0)(int *n,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd1,SLASD1)(int *nl,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd3,SLASD3)(int *nl,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd5,SLASD5)(int *i__,
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd6,SLASD6)(int *icompq,
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasd8,SLASD8)(int *icompq,
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasda,SLASDA)(int *icompq,
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasdt,SLASDT)(int *n,
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasq4,SLASQ4)(int *i0,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasq5,SLASQ5)(int *i0,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasr,SLASR)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slasrt,SLASRT)(const char *id,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void F77_FUNC(slasrt2,SLASRT2)(const char *id,
int *n,
#include <math.h>
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(slassq,SLASSQ)(int *n,
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* LAPACK */
void
#include <ctype.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sorg2r,SORG2R)(int *m,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sorgl2,SORGL2)(int *m,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#define SORGLQ_BLOCKSIZE 32
#define SORGLQ_MINBLOCKSIZE 2
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sorm2l,SORM2L)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sorm2r,SORM2R)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <ctype.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(sorml2,SORML2)(const char *side,
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
#include <math.h>
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
-#include "gmx_lapack.h"
+#include "../gmx_lapack.h"
/* Normally, SSTEVR is the LAPACK wrapper which calls one
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include <types/simple.h>
+
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <types/simple.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
void
F77_FUNC(ssytd2,SSYTD2)(const char * uplo,
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
void
#include <math.h>
-#include "gmx_blas.h"
-#include "gmx_lapack.h"
+#include "../gmx_blas.h"
+#include "../gmx_lapack.h"
#include "lapack_limits.h"
#include <types/simple.h>
* And Hey:
* Groningen Machine for Chemical Simulation
*/
+#include "matrix.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include <stdlib.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "gmx_fatal.h"
-#include "gmx_matrix.h"
+#include <stdio.h>
+
+#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/legacyheaders/smalloc.h"
+#include "gromacs/legacyheaders/vec.h"
+
#include "gmx_lapack.h"
double **alloc_matrix(int n,int m)
* And Hey:
* Groningen Machine for Chemical Simulation
*/
+#ifndef GMX_LINEARALGEBRA_MATRIX_H
+#define GMX_LINEARALGEBRA_MATRIX_H
-#ifndef _gmx_matrix_h
-#define _gmx_matrix_h
-
#include <stdio.h>
-
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
double **alloc_matrix(int n,int m);
void free_matrix(double **a,int n);
* If fp is not NULL debug information will be written to it.
*/
+#ifdef __cplusplus
+}
+#endif
+
#endif
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
+#include "mtxio.h"
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
* in normal mode analysis.
*/
-#include "xdrf.h"
-#include "smalloc.h"
-#include "gmxfio.h"
-#include "copyrite.h"
-#include "gmx_fatal.h"
-#include "mtxio.h"
-#include "gmxfio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/legacyheaders/gmxfio.h"
+#include "gromacs/legacyheaders/smalloc.h"
+#include "gromacs/legacyheaders/xdrf.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
/* Just a number to identify our file type */
* in normal mode analysis.
*/
-#ifndef _MTXIO_H_
-#define _MTXIO_H_
+#ifndef GMX_LINEARALGEBRA_MTXIO_H
+#define GMX_LINEARALGEBRA_MTXIO_H
+
+#include "../legacyheaders/types/simple.h"
-#include "types/simple.h"
#include "sparsematrix.h"
#ifdef __cplusplus
* This routine will autodetect the matrix format stored in the file
* (sparse or full) and set either the full or sparse matrix arguments (ptr to ptr)
* to a newly allocated matrix structure. Note that the full storage
- * structure is simply nrow*ncol floating-point elements. The sparse
+ * structure is simply nrow*ncol floating-point elements. The sparse
* matrix structure should be freed with gmx_sparsematrix_destroy() when you are done.
*
* To determine the format you should set *full_matrix and *sparse_matrix to NULL
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "sparsematrix.h"
+#include <assert.h>
#include <stdlib.h>
#include <stdio.h>
-#include <assert.h>
-#include "smalloc.h"
-
-#include "sparsematrix.h"
+#include "gromacs/legacyheaders/smalloc.h"
* And Hey:
* Green Red Orange Magenta Azure Cyan Skyblue
*/
-#ifndef _SPARSEMATRIX_H_
-#define _SPARSEMATRIX_H_
+#ifndef GMX_LINEARALGEBRA_SPARSEMATRIX_H
+#define GMX_LINEARALGEBRA_SPARSEMATRIX_H
-#include "typedefs.h"
-#include "types/simple.h"
+#include <stdio.h>
+
+#include "../legacyheaders/types/simple.h"
#ifdef __cplusplus
extern "C" {
#endif
+typedef struct
+gmx_sparsematrix_entry
+{
+ int col;
+ real value;
+} gmx_sparsematrix_entry_t;
+
/*! \brief Sparse matrix storage format
*
* This structure specifies a storage format for a sparse matrix.
*
* In other words: Not perfect, but it works.
*/
-
-typedef struct
-gmx_sparsematrix_entry
-{
- int col;
- real value;
-} gmx_sparsematrix_entry_t;
-
typedef struct
gmx_sparsematrix
{
- gmx_bool compressed_symmetric; /*!< Store half elements and assume symmetry. */
- int nrow; /*!< Number of rows in matrix */
- int * ndata; /*!< Number of entries on each row (list) */
- int * nalloc; /*!< Allocated entry list length for each row */
- gmx_sparsematrix_entry_t ** data; /*!< data[i] is a list with entries on row i */
+ gmx_bool compressed_symmetric; /**< Store half elements and assume symmetry. */
+ int nrow; /**< Number of rows in matrix */
+ int * ndata; /**< Number of entries on each row (list) */
+ int * nalloc; /**< Allocated entry list length for each row */
+ gmx_sparsematrix_entry_t ** data; /**< data[i] is a list with entries on row i */
}
gmx_sparsematrix_t;
-/*! \Allocate a new sparse matrix structure
+/*! \brief Allocate a new sparse matrix structure
*
* The number of rows is used to allocate the index array entry. Obviously you
* can reallocate these later yourself if necessary - this is a
#include "domdec.h"
#include "partdec.h"
#include "trnio.h"
-#include "sparsematrix.h"
-#include "mtxio.h"
#include "mdatoms.h"
#include "ns.h"
#include "gmx_wallcycle.h"
#include "gmxfio.h"
#include "pme.h"
+#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+
typedef struct {
t_state s;
rvec *f;
#include "gmxcpp.h"
#include "checkpoint.h"
#include "mtop_util.h"
-#include "sparsematrix.h"
-#include "mtxio.h"
+
+#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
static void list_tpx(const char *fn, gmx_bool bShowNumbers,const char *mdpfn,
add_library(gmxana
autocorr.c expfit.c polynomials.c levenmar.c
anadih.c pp2shift.c dlist.c
- eigio.c cmat.c
- eigensolver.c nsc.c
+ eigio.c cmat.c nsc.c
hxprops.c fitahx.c
geminate.c nsfactor.c
gmx_analyze.c gmx_anaeig.c gmx_angle.c gmx_bond.c
#include "statutil.h"
#include "txtdump.h"
#include "gstat.h"
-#include "gmx_matrix.h"
#include "gmx_statistics.h"
#include "xvgr.h"
#include "gmx_ana.h"
#include "geminate.h"
+#include "gromacs/linearalgebra/matrix.h"
+
/* must correspond to char *avbar_opt[] declared in main() */
enum { avbarSEL, avbarNONE, avbarSTDDEV, avbarERROR, avbar90, avbarNR };
#include "xvgr.h"
#include "futil.h"
#include "matio.h"
-#include "eigensolver.h"
#include "cmat.h"
#include "do_fit.h"
#include "trnio.h"
#include "viewit.h"
#include "gmx_ana.h"
+#include "gromacs/linearalgebra/eigensolver.h"
+
/* print to two file pointers at once (i.e. stderr and log) */
static inline
void lo_ffprintf(FILE *fp1, FILE *fp2, const char *buf)
#include "txtdump.h"
#include "matio.h"
#include "eigio.h"
-#include "eigensolver.h"
#include "physics.h"
#include "gmx_ana.h"
#include "string2.h"
+#include "gromacs/linearalgebra/eigensolver.h"
+
/* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
char *
gmx_ctime_r(const time_t *clock,char *buf, int n);
#include "xvgr.h"
#include "gstat.h"
#include "txtdump.h"
-#include "eigensolver.h"
#include "eigio.h"
-#include "mtxio.h"
#include "mtop_util.h"
-#include "sparsematrix.h"
#include "physics.h"
#include "main.h"
#include "gmx_ana.h"
+#include "gromacs/linearalgebra/eigensolver.h"
+#include "gromacs/linearalgebra/mtxio.h"
+#include "gromacs/linearalgebra/sparsematrix.h"
+
static double cv_corr(double nu,double T)
{
double x = PLANCK*nu/(BOLTZ*T);
#include "princ.h"
#include "rmpbc.h"
#include "confio.h"
-#include "eigensolver.h"
#include "gmx_ana.h"
+#include "gromacs/linearalgebra/eigensolver.h"
static real find_pdb_bfac(t_atoms *atoms,t_resinfo *ri,char *atomnm)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff