--- /dev/null
+cmake_minimum_required(VERSION 2.8.8)
+
+project(gromacs-rcore CXX)
+
+if (NOT CMAKE_BUILD_TYPE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
+endif()
+
+# CMake modules are in a subdirectory to keep this file cleaner
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
+
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+# In principle, this could be deduced from GROMACS_IS_DOUBLE returned by
+# find_package(GROMACS) based on the suffix alone, but it is clearer that the
+# user explicitly sets what they want to get, and then need to provide a suffix
+# to match.
+option(GMX_DOUBLE "Use double precision" OFF)
+set(GMX_SUFFIX "" CACHE STRING "Suffix for the GROMACS installation to use (empty for default)")
+
+# This does not allow for a non-suffixed double-precision libgromacs, but
+# that should be rare enough for demonstration purposes.
+if (GMX_DOUBLE AND NOT GMX_SUFFIX)
+ set(GROMACS_SUFFIX "_d")
+else()
+ set(GROMACS_SUFFIX ${GMX_SUFFIX})
+endif()
+
+find_package(GROMACS 2016 REQUIRED)
+gromacs_check_double(GMX_DOUBLE)
+gromacs_check_compiler(CXX)
+include_directories(
+ ${GROMACS_INCLUDE_DIRS}
+ ${CMAKE_SOURCE_DIR}/include)
+add_definitions(${GROMACS_DEFINITIONS})
+
+# Use static linking on MSVC
+if (CMAKE_GENERATOR MATCHES "Visual Studio")
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
+ set(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ string(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
+ set(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
+endif()
+
+add_subdirectory(src)
--- /dev/null
+ GNU LESSER GENERAL PUBLIC LICENSE
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--- /dev/null
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+ if (GROMACS_FIND_VERSION VERSION_LESS "5.1")
+ message(FATAL_ERROR
+ "This version of FindGROMACS.cmake requires GROMACS-provided "
+ "package configuration files, and only works to find "
+ "GROMACS 5.1 or later.")
+ endif()
+ list(APPEND _gmx_find_args ${GROMACS_FIND_VERSION})
+ if (GROMACS_FIND_VERSION_EXACT)
+ list(APPEND _gmx_find_args EXACT)
+ endif()
+endif()
+if (GROMACS_FIND_REQUIRED)
+ list(APPEND _gmx_find_args REQUIRED)
+endif()
+if (GROMACS_FIND_QUIETLY)
+ list(APPEND _gmx_find_args QUIET)
+endif()
+
+# Determine the actual name of the package configuration files.
+set(_gmx_pkg_name gromacs)
+if (DEFINED GROMACS_SUFFIX)
+ set(_gmx_pkg_name gromacs${GROMACS_SUFFIX})
+endif()
+# Delegate all the actual work to the package configuration files.
+# The CONFIGS option is not really necessary, but provides a bit better error
+# messages, since we actually know what the config file should be called.
+find_package(GROMACS ${_gmx_find_args} CONFIG
+ NAMES ${_gmx_pkg_name}
+ CONFIGS ${_gmx_pkg_name}-config.cmake)
+unset(_gmx_find_args)
+unset(_gmx_pkg_name)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MATH_VECTYPES_H
+#define GMX_MATH_VECTYPES_H
+
+#include <math.h> // since this file used from C source files TODO: replace with cmath
+
+#include "gromacs/utility/real.h"
+
+#define XX 0 /* Defines for indexing in */
+#define YY 1 /* vectors */
+#define ZZ 2
+#define DIM 3 /* Dimension of vectors */
+
+typedef real rvec[DIM];
+
+typedef double dvec[DIM];
+
+typedef real matrix[DIM][DIM];
+
+typedef real tensor[DIM][DIM];
+
+typedef int ivec[DIM];
+
+typedef int imatrix[DIM][DIM];
+
+#ifdef __cplusplus
+
+namespace gmx
+{
+
+/*! \brief
+ * C++ class for 3D vectors.
+ *
+ * \tparam ValueType Type
+ *
+ * This class provides a C++ version of rvec/dvec/ivec that can be put into STL
+ * containers etc. It is more or less a drop-in replacement for `rvec` and
+ * friends: it can be used in most contexts that accept the equivalent C type.
+ * However, there are two cases where explicit conversion is necessary:
+ * - An array of these objects needs to be converted with as_vec_array() (or
+ * convenience methods like as_rvec_array()).
+ * - Passing an RVec as a `const rvec &` parameter to a function needs an
+ * explicit call to as_vec(). The implicit conversion should work for this
+ * as well, but cppcheck parses the necessary implicit conversion operator
+ * incorrectly and MSVC fails to compile code that relies on the implicit
+ * conversion, so the explicit method is necessary.
+ *
+ * For the array conversion to work, the compiler should not add any extra
+ * alignment/padding in the layout of this class; that this actually works as
+ * intended is tested in the unit tests.
+ *
+ * \inpublicapi
+ */
+template <typename ValueType>
+class BasicVector
+{
+ public:
+ //! Underlying raw C array type (rvec/dvec/ivec).
+ typedef ValueType RawArray[DIM];
+
+ //! Constructs default (initialized to 0,0,0) vector.
+ BasicVector()
+ {
+ x_[XX] = 0;
+ x_[YY] = 0;
+ x_[ZZ] = 0;
+ }
+ //! Constructs a vector from given values.
+ BasicVector(ValueType x, ValueType y, ValueType z)
+ {
+ x_[XX] = x;
+ x_[YY] = y;
+ x_[ZZ] = z;
+ }
+ /*! \brief
+ * Constructs a vector from given values.
+ *
+ * This constructor is not explicit to support implicit conversions
+ * that allow, e.g., calling `std::vector<RVec>:``:push_back()` directly
+ * with an `rvec` parameter.
+ */
+ BasicVector(const RawArray x)
+ {
+ x_[XX] = x[XX];
+ x_[YY] = x[YY];
+ x_[ZZ] = x[ZZ];
+ }
+ //! Indexing operator to make the class work as the raw array.
+ ValueType &operator[](int i) { return x_[i]; }
+ //! Indexing operator to make the class work as the raw array.
+ ValueType operator[](int i) const { return x_[i]; }
+ // The conversion functions below could more accurately return
+ // RawArray &, but this fails with cppcheck and does not solve the
+ // issue with MSVC, so as_vec() should be used instead.
+ //! Makes BasicVector usable in contexts where a raw C array is expected.
+ operator ValueType *() { return x_; }
+ //! Makes BasicVector usable in contexts where a raw C array is expected.
+ operator const ValueType *() const { return x_; }
+ //! Allow inplace addition for BasicVector
+ BasicVector<ValueType> &operator+=(const BasicVector<ValueType> &right)
+ {
+ for (int i = 0; i < DIM; ++i)
+ {
+ this->x_[i] += right.x_[i];
+ }
+ return *this;
+ }
+ //! Allow inplace substraction for BasicVector
+ BasicVector<ValueType> &operator-=(const BasicVector<ValueType> &right)
+ {
+ for (int i = 0; i < DIM; ++i)
+ {
+ this->x_[i] -= right.x_[i];
+ }
+ return *this;
+ }
+ //! Allow vector addition
+ BasicVector<ValueType> operator+(const BasicVector<ValueType> &right) const
+ {
+ BasicVector<ValueType> temp;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp.x_[i] = this->x_[i] + right.x_[i];
+ }
+ return temp;
+ }
+ //! Allow vector substraction
+ BasicVector<ValueType> operator-(const BasicVector<ValueType> &right) const
+ {
+ BasicVector<ValueType> temp;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp.x_[i] = this->x_[i] - right.x_[i];
+ }
+ return temp;
+ }
+ //! Allow vector scalar multiplication (dot product)
+ ValueType dot(const BasicVector<ValueType> &right) const
+ {
+ ValueType temp = 0;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp += this->x_[i]*right.x_[i];
+ }
+ return temp;
+ }
+
+ //! Allow vector vector multiplication (cross product)
+ BasicVector<ValueType> cross(const BasicVector<ValueType> &right) const
+ {
+ BasicVector<ValueType> temp;
+ temp.x_[XX] = this->x_[YY]*right.x_[ZZ]-this->x_[ZZ]*right.x_[YY];
+ temp.x_[YY] = this->x_[ZZ]*right.x_[XX]-this->x_[XX]*right.x_[ZZ];
+ temp.x_[ZZ] = this->x_[XX]*right.x_[YY]-this->x_[YY]*right.x_[XX];
+ return temp;
+ }
+
+ //! Allow vector scaling (vector by scalar multiply)
+ BasicVector<ValueType> scale(const ValueType &right) const
+ {
+ BasicVector<ValueType> temp;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp.x_[i] = this->x_[i]*right;
+ }
+ return temp;
+ }
+
+ //! Return normalized to unit vector
+ BasicVector<ValueType> unitv() const
+ {
+ ValueType length;
+ BasicVector<ValueType> temp;
+ length = this->length();
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp.x_[i] = this->x_[i]/length;
+ }
+ return temp;
+ }
+
+ //! Length^2 of vector
+ ValueType sqlength() const
+ {
+ ValueType temp = 0;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp += this->x_[i]*this->x_[i];
+ }
+ return temp;
+ }
+
+ //! Length of vector
+ ValueType length() const
+ {
+ ValueType temp = 0;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp += this->x_[i]*this->x_[i];
+ }
+ return sqrt(temp);
+ }
+
+ //! cast to RVec
+ BasicVector<real> toRVec() const
+ {
+ BasicVector<real> temp;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp[i] = static_cast<real>(this->x_[i]);
+ }
+ return temp;
+ }
+
+ //! cast to DVec
+ BasicVector<double> toDVec() const
+ {
+ BasicVector<double> temp;
+ for (int i = 0; i < DIM; ++i)
+ {
+ temp[i] = static_cast<double>(this->x_[i]);
+ }
+ return temp;
+ }
+
+ //! Converts to a raw C array where implicit conversion does not work.
+ RawArray &as_vec() { return x_; }
+ //! Converts to a raw C array where implicit conversion does not work.
+ const RawArray &as_vec() const { return x_; }
+
+ private:
+ RawArray x_;
+};
+
+/*! \brief
+ * scale for gmx::BasicVector
+ */
+template <typename ValueType, typename BasicVector> static inline
+BasicVector scale(BasicVector v, ValueType s)
+{
+ BasicVector tmp;
+ tmp = v;
+ return tmp.scale(s);
+}
+
+/*! \brief
+ * unitv for gmx::BasicVector
+ */
+template <typename BasicVector> static inline
+BasicVector unitv(BasicVector v)
+{
+ return v.unitv();
+}
+
+/*! \brief
+ * norm for gmx::BasicVector
+ */
+template <typename ValueType> static inline
+ValueType length(BasicVector<ValueType> v)
+{
+ return v.length();
+}
+
+/*! \brief
+ * norm2 for gmx::BasicVector
+ */
+template <typename ValueType> static inline
+ValueType sqlength(BasicVector<ValueType> v)
+{
+ return v.sqlength();
+}
+
+/*! \brief
+ * cross product for gmx::BasicVector
+ */
+template <typename BasicVector> static inline
+BasicVector cross(BasicVector a, BasicVector b)
+{
+ return a.cross(b);
+}
+
+/*! \brief
+ * dot product for gmx::BasicVector
+ */
+template <typename ValueType> static inline
+ValueType dot(BasicVector<ValueType> a, BasicVector<ValueType> b)
+{
+ return a.dot(b);
+}
+
+/*! \brief
+ * Casts a gmx::BasicVector array into an equivalent raw C array.
+ */
+template <typename ValueType> static inline
+typename BasicVector<ValueType>::RawArray *
+as_vec_array(BasicVector<ValueType> *x)
+{
+ return reinterpret_cast<typename BasicVector<ValueType>::RawArray *>(x);
+}
+
+/*! \brief
+ * Casts a gmx::BasicVector array into an equivalent raw C array.
+ */
+template <typename ValueType> static inline
+const typename BasicVector<ValueType>::RawArray *
+as_vec_array(const BasicVector<ValueType> *x)
+{
+ return reinterpret_cast<const typename BasicVector<ValueType>::RawArray *>(x);
+}
+
+//! Shorthand for C++ `rvec`-equivalent type.
+typedef BasicVector<real> RVec;
+//! Shorthand for C++ `dvec`-equivalent type.
+typedef BasicVector<double> DVec;
+//! Shorthand for C++ `ivec`-equivalent type.
+typedef BasicVector<int> IVec;
+//! Casts a gmx::RVec array into an `rvec` array.
+static inline rvec *as_rvec_array(RVec *x)
+{
+ return as_vec_array(x);
+}
+//! Casts a gmx::DVec array into an `Dvec` array.
+static inline dvec *as_dvec_array(DVec *x)
+{
+ return as_vec_array(x);
+}
+//! Casts a gmx::IVec array into an `ivec` array.
+static inline ivec *as_ivec_array(IVec *x)
+{
+ return as_vec_array(x);
+}
+
+//! Casts a gmx::RVec array into an `rvec` array.
+static inline const rvec *as_rvec_array(const RVec *x)
+{
+ return as_vec_array(x);
+}
+//! Casts a gmx::DVec array into an `dvec` array.
+static inline const dvec *as_dvec_array(const DVec *x)
+{
+ return as_vec_array(x);
+}
+//! Casts a gmx::IVec array into an `ivec` array.
+static inline const ivec *as_ivec_array(const IVec *x)
+{
+ return as_vec_array(x);
+}
+
+
+} // namespace gmx
+
+#endif
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares OpenMP wrappers to avoid conditional compilation.
+ *
+ * This module defines wrappers for OpenMP API functions and enables compiling
+ * code without conditional compilation even when OpenMP is turned off in the
+ * build system.
+ * Therefore, OpenMP API functions should always be used through these wrappers
+ * and omp.h should never be directly included. Instead, this header should be
+ * used whenever OpenMP API functions are needed.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_OMP_H
+#define GMX_UTILITY_OMP_H
+
+#include <stdio.h>
+
+#if !GMX_NATIVE_WINDOWS
+/* Ugly hack because the openmp implementation below hacks into the SIMD
+ * settings to decide when to use _mm_pause(). This should eventually be
+ * changed into proper detection of the intrinsics uses, not SIMD.
+ */
+#if GMX_SIMD_X86_SSE2 || GMX_SIMD_X86_SSE4_1 || GMX_SIMD_X86_AVX_128_FMA || \
+ GMX_SIMD_X86_AVX_256 || GMX_SIMD_X86_AVX2_256
+# include <xmmintrin.h>
+#endif
+#else
+#include <windows.h>
+#endif
+
+#include "gromacs/utility/basedefinitions.h"
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif
+
+/*! \addtogroup module_utility
+ * \{
+ */
+
+/*! \brief
+ * Returns an integer equal to or greater than the number of threads
+ * that would be available if a parallel region without num_threads were
+ * defined at that point in the code.
+ *
+ * Acts as a wrapper for omp_get_max_threads().
+ */
+int gmx_omp_get_max_threads(void);
+
+/*! \brief
+ * Returns the number of processors available when the function is called.
+ *
+ * Acts as a wrapper around omp_get_num_procs().
+ */
+int gmx_omp_get_num_procs(void);
+
+/*! \brief
+ * Returns the thread number of the thread executing within its thread team.
+ *
+ * Acts as a wrapper for omp_get_thread_num().
+ */
+int gmx_omp_get_thread_num(void);
+
+/*! \brief
+ * Sets the number of threads in subsequent parallel regions, unless overridden
+ * by a num_threads clause.
+ *
+ * Acts as a wrapper for omp_set_num_threads().
+ */
+void gmx_omp_set_num_threads(int num_threads);
+
+/*! \brief
+ * Check for externally set thread affinity to avoid conflicts with \Gromacs
+ * internal setting.
+ *
+ * \param[out] message Receives the message to be shown to the user.
+ * \returns `true` if we can set thread affinity ourselves.
+ *
+ * While GNU OpenMP does not set affinity by default, the Intel OpenMP library
+ * does. This conflicts with the internal affinity (especially thread-MPI)
+ * setting, results in incorrectly locked threads, and causes dreadful performance.
+ *
+ * The KMP_AFFINITY environment variable is used by Intel, GOMP_CPU_AFFINITY
+ * by the GNU compilers (Intel also honors it well). If any of the variables
+ * is set, we should honor it and disable the internal pinning.
+ * When using Intel OpenMP, we will disable affinity if the user did not set it
+ * manually through one of the aforementioned environment variables.
+ *
+ * Note that the Intel OpenMP affinity disabling will only take effect if this
+ * function is called before the OpenMP library gets initialized, which happens
+ * when the first call is made into a compilation unit that contains OpenMP
+ * pragmas.
+ *
+ * If this function returns `false`, the caller is responsible to disable the
+ * pinning, show the message from \p *message to the user, and free the memory
+ * allocated for \p *message.
+ * If the return value is `true`, \p *message is NULL.
+ */
+gmx_bool gmx_omp_check_thread_affinity(char **message);
+
+/*! \brief
+ * Pause for use in a spin-wait loop.
+ */
+static gmx_inline void gmx_pause()
+{
+#ifndef _MSC_VER
+ /* Ugly hack because the openmp implementation below hacks into the SIMD
+ * settings to decide when to use _mm_pause(). This should eventually be
+ * changed into proper detection of the intrinsics uses, not SIMD.
+ */
+#if (GMX_SIMD_X86_SSE2 || GMX_SIMD_X86_SSE4_1 || GMX_SIMD_X86_AVX_128_FMA || \
+ GMX_SIMD_X86_AVX_256 || GMX_SIMD_X86_AVX2_256) && !defined(__MINGW32__)
+ /* Replace with tbb::internal::atomic_backoff when/if we use TBB */
+ _mm_pause();
+#elif defined __MIC__
+ _mm_delay_32(32);
+#else
+ /* No wait for unknown architecture */
+#endif
+#else
+ YieldProcessor();
+#endif
+}
+
+/*! \} */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
--- /dev/null
+#ifndef NEW_FIT_H
+#define NEW_FIT_H
+
+#include <iostream>
+#include <chrono>
+#include <omp.h>
+#include <thread>
+
+#include <gromacs/analysisdata/modules/plot.h>
+#include <gromacs/options/ioptionscontainer.h>
+#include <gromacs/pbcutil/pbc.h>
+#include <gromacs/math/functions.h>
+#include <gromacs/selection/selectionoption.h>
+#include <gromacs/utility/smalloc.h>
+#include <gromacs/trajectory/trajectoryframe.h>
+#include <gromacs/trajectoryanalysis/analysissettings.h>
+
+#include "gromacs/math/vectypes.h"
+
+using gmx::RVec;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+ void implement_fit(int if_size, std::vector< RVec > &if_frame, long double if_x, long double if_y, long double if_z, long double if_A, long double if_B, long double if_C);
+
+ long double F(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double Fx(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double Fy(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double Fz(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double FA(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double FB(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double FC(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C);
+
+ long double dist(std::vector< RVec > alfa, std::vector< RVec > beta, std::vector< std::pair< int, int > > cros);
+
+ void new_fit(std::vector< RVec > alfa, std::vector< RVec > &beta, std::vector< std::pair< int, int > > cros, int beta_size, long double prec);
+
+#endif // NEW_FIT_H
--- /dev/null
+add_executable(rcore new_fit.cpp rcore.cpp)
+set_target_properties(rcore PROPERTIES
+ COMPILE_FLAGS "${GROMACS_CXX_FLAGS}")
+target_link_libraries(rcore ${GROMACS_LIBRARIES})
--- /dev/null
+#include "new_fit.h"
+
+using gmx::RVec;
+
+void implement_fit(int if_size, std::vector< RVec > &if_frame, long double if_x, long double if_y, long double if_z, long double if_A, long double if_B, long double if_C) {
+ RVec if_step;
+ if_step[0] = if_x;
+ if_step[1] = if_y;
+ if_step[2] = if_z;
+ for (int i = 0; i < if_size; i++) {
+ if_frame[i] += if_step;
+ }
+
+ for (int i = 0; i < if_size; i++) {
+ if_step[0] = if_frame[i][0];
+ if_step[1] = if_frame[i][1];
+ if_step[2] = if_frame[i][2];
+
+ //if_frame[i][0] = if_step[0];
+ if_frame[i][1] = if_step[1] * cos(if_A) - if_step[2] * sin(if_A);
+ if_frame[i][2] = if_step[1] * sin(if_A) + if_step[2] * cos(if_A);
+ }
+ for (int i = 0; i < if_size; i++) {
+ if_step[0] = if_frame[i][0];
+ if_step[1] = if_frame[i][1];
+ if_step[2] = if_frame[i][2];
+
+ if_frame[i][0] = if_step[0] * cos(if_B) + if_step[2] * sin(if_B);
+ //if_frame[i][1] = if_step[1];
+ if_frame[i][2] = - if_step[0] * sin(if_B) + if_step[2] * cos(if_B);
+ }
+
+ for (int i = 0; i < if_size; i++) {
+ if_step[0] = if_frame[i][0];
+ if_step[1] = if_frame[i][1];
+ if_step[2] = if_frame[i][2];
+
+ if_frame[i][0] = if_step[0] * cos(if_C) - if_step[1] * sin(if_C);
+ if_frame[i][1] = if_step[0] * sin(if_C) + if_step[1] * cos(if_C);
+ //if_frame[i][2] = if_step[2];
+ }
+}
+
+long double F(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return gmx::square(aix + (biy + y)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) +
+ gmx::square(aiy - (biy + y)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) +
+ gmx::square(aiz + sin(B)*(bix + x) - cos(A)*cos(B)*(biz + z) - cos(B)*sin(A)*(biy + y)) ;
+}
+
+long double Fx(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*sin(B)*(aiz + sin(B)*(bix + x) - cos(A)*cos(B)*(biz + z) - cos(B)*sin(A)*(biy + y)) - 2*cos(B)*cos(C)*(aix + (biy + y)*(cos(A)*sin(C) -
+ cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) - 2*cos(B)*sin(C)*(aiy - (biy + y)*(cos(A)*cos(C) +
+ sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) ;
+}
+
+long double Fy(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B))*(aix + (biy + y)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) +
+ cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) - 2*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C))*(aiy - (biy + y)*(cos(A)*cos(C) +
+ sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) - 2*cos(B)*sin(A)*(aiz + sin(B)*(bix + x) -
+ cos(A)*cos(B)*(biz + z) - cos(B)*sin(A)*(biy + y)) ;
+}
+
+long double Fz(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C))*(aiy - (biy + y)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) -
+ cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) - 2*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B))*(aix + (biy + y)*(cos(A)*sin(C) -
+ cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) - 2*cos(A)*cos(B)*(aiz + sin(B)*(bix + x) -
+ cos(A)*cos(B)*(biz + z) - cos(B)*sin(A)*(biy + y)) ;
+}
+
+long double FA(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*((biy + y)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) + (biz + z)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)))*(aiy - (biy + y)*(cos(A)*cos(C) +
+ sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) - 2*(cos(A)*cos(B)*(biy + y) -
+ cos(B)*sin(A)*(biz + z))*(aiz + sin(B)*(bix + x) - cos(A)*cos(B)*(biz + z) - cos(B)*sin(A)*(biy + y)) - 2*((biy + y)*(sin(A)*sin(C) +
+ cos(A)*cos(C)*sin(B)) + (biz + z)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)))*(aix + (biy + y)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)) -
+ (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) ;
+}
+
+long double FB(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*(cos(B)*(bix + x) + sin(A)*sin(B)*(biy + y) + cos(A)*sin(B)*(biz + z))*(aiz + sin(B)*(bix + x) - cos(A)*cos(B)*(biz + z) -
+ cos(B)*sin(A)*(biy + y)) - 2*(cos(A)*cos(B)*cos(C)*(biz + z) - cos(C)*sin(B)*(bix + x) + cos(B)*cos(C)*sin(A)*(biy + y))*(aix + (biy + y)*(cos(A)*sin(C) -
+ cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) - 2*(cos(A)*cos(B)*sin(C)*(biz + z) -
+ sin(B)*sin(C)*(bix + x) + cos(B)*sin(A)*sin(C)*(biy + y))*(aiy - (biy + y)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)) +
+ (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) ;
+}
+
+long double FC(long double aix, long double aiy, long double aiz, long double bix, long double biy, long double biz, long double x, long double y, long double z, long double A, long double B, long double C) {
+ return 2*((biy + y)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)) - (biz + z)*(cos(C)*sin(A) - cos(A)*sin(B)*sin(C)) + cos(B)*sin(C)*(bix + x))*(aix +
+ (biy + y)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)) - (biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - cos(B)*cos(C)*(bix + x)) -
+ 2*((biz + z)*(sin(A)*sin(C) + cos(A)*cos(C)*sin(B)) - (biy + y)*(cos(A)*sin(C) - cos(C)*sin(A)*sin(B)) +
+ cos(B)*cos(C)*(bix + x))*(aiy - (biy + y)*(cos(A)*cos(C) + sin(A)*sin(B)*sin(C)) + (biz + z)*(cos(C)*sin(A) -
+ cos(A)*sin(B)*sin(C)) - cos(B)*sin(C)*(bix + x)) ;
+}
+
+long double dist(std::vector< RVec > alfa, std::vector< RVec > beta, std::vector< std::pair< int, int > > cros) {
+ long double temp = 0;
+ long double ax, ay, az, bx, by, bz;
+ int d_for = cros.size();
+ for (int i = 0; i < d_for/*cros.size()*/; i++) {
+ ax = alfa[cros[i].first][0];
+ ay = alfa[cros[i].first][1];
+ az = alfa[cros[i].first][2];
+ bx = beta[cros[i].second][0];
+ by = beta[cros[i].second][1];
+ bz = beta[cros[i].second][2];
+ temp += F(ax, ay, az, bx, by, bz, 0, 0, 0, 0, 0, 0);
+ }
+ return temp;
+}
+
+void new_fit(std::vector< RVec > alfa, std::vector< RVec > &beta, std::vector< std::pair< int, int > > cros, int beta_size, long double prec) {
+ long double ax, ay, az, bx, by, bz;
+ long double x1 = 0, y1 = 0, z1 = 0, A1 = 0, B1 = 0, C1 = 0;
+ long double x2 = 0, y2 = 0, z2 = 0, A2 = 0, B2 = 0, C2 = 0;
+ long double H1 = 0.00001, H2 = 0.00001, F1 = 0, F2 = 0;
+ int nf_for = cros.size();
+ do {
+ if (F1 > F2 || F1 == 0) {
+ F1 = F2;
+ }
+ F2 = 0;
+ for (int i = 0; i < nf_for/*cros.size()*/; i++) {
+ ax = alfa[cros[i].first][0];
+ ay = alfa[cros[i].first][1];
+ az = alfa[cros[i].first][2];
+ bx = beta[cros[i].second][0];
+ by = beta[cros[i].second][1];
+ bz = beta[cros[i].second][2];
+ x2 += Fx(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ y2 += Fy(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ z2 += Fz(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ A2 += FA(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ B2 += FB(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ C2 += FC(ax, ay, az, bx, by, bz, x1, y1, z1, A1, B1, C1);
+ }
+ if (std::max(std::fabs(H1*x2), std::max(std::fabs(H1*y2), std::fabs(H1*z2))) > 1) {
+ H1 = 1 / std::max(std::fabs(H1*x2), std::max(std::fabs(H1*y2), std::fabs(H1*z2)));
+ }
+ x2 = x1 - H1 * x2;
+ y2 = y1 - H1 * y2;
+ z2 = z1 - H1 * z2;
+ if (std::max(std::fabs(H2*A2), std::max(std::fabs(H2*B2), std::fabs(H2*C2))) > M_PI/90) {
+ H2 = M_PI/90 / std::max(std::fabs(H2*A2), std::max(std::fabs(H2*B2), std::fabs(H2*C2)));
+ }
+ A2 = A1 - H2 * A2;
+ if (std::fabs(A2) > M_PI / 2) {
+ A2 = 0;
+ }
+ B2 = B1 - H2 * B2;
+ if (std::fabs(B2) > M_PI / 2) {
+ B2 = 0;
+ }
+ C2 = C1 - H2 * C2;
+ if (std::fabs(C2) > M_PI / 2) {
+ C2 = 0;
+ }
+ for (int i = 0; i < nf_for/*cros.size()*/; i++) {
+ ax = alfa[cros[i].first][0];
+ ay = alfa[cros[i].first][1];
+ az = alfa[cros[i].first][2];
+ bx = beta[cros[i].second][0];
+ by = beta[cros[i].second][1];
+ bz = beta[cros[i].second][2];
+ F2 += F(ax, ay, az, bx, by, bz, x2, y2, z2, A2, B2, C2);
+ }
+ if (F2 > F1 && F1 != 0) {
+ H1 /= 10;
+ H2 /= 10;
+ } else {
+ x1 = x2;
+ y1 = y2;
+ z1 = z2;
+ A1 = A2;
+ B1 = B2;
+ C1 = C2;
+ x2 = 0;
+ y2 = 0;
+ z2 = 0;
+ A2 = 0;
+ B2 = 0;
+ C2 = 0;
+ }
+ } while (std::fabs(F1 - F2) > prec/*0.0000001*/);
+ implement_fit(beta_size, beta, x1, y1, z1, A1, B1, C1);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include <string>
+#include <vector>
+
+#include <gromacs/trajectoryanalysis.h>
+
+using namespace gmx;
+
+/*! \brief
+ * Template class to serve as a basis for user analysis tools.
+ */
+class AnalysisTemplate : public TrajectoryAnalysisModule
+{
+ public:
+ AnalysisTemplate();
+
+ virtual void initOptions(IOptionsContainer *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ class ModuleData;
+
+ std::string fnDist_;
+ double cutoff_;
+ Selection refsel_;
+ SelectionList sel_;
+
+ AnalysisNeighborhood nb_;
+
+ AnalysisData data_;
+ AnalysisDataAverageModulePointer avem_;
+};
+
+
+AnalysisTemplate::AnalysisTemplate()
+ : cutoff_(0.0)
+{
+ registerAnalysisDataset(&data_, "avedist");
+}
+
+
+void
+AnalysisTemplate::initOptions(IOptionsContainer *options,
+ TrajectoryAnalysisSettings *settings)
+{
+ static const char *const desc[] = {
+ "This is a template for writing your own analysis tools for",
+ "GROMACS. The advantage of using GROMACS for this is that you",
+ "have access to all information in the topology, and your",
+ "program will be able to handle all types of coordinates and",
+ "trajectory files supported by GROMACS. In addition,",
+ "you get a lot of functionality for free from the trajectory",
+ "analysis library, including support for flexible dynamic",
+ "selections. Go ahead an try it![PAR]",
+ "To get started with implementing your own analysis program,",
+ "follow the instructions in the README file provided.",
+ "This template implements a simple analysis programs that calculates",
+ "average distances from a reference group to one or more",
+ "analysis groups."
+ };
+
+ settings->setHelpText(desc);
+
+ options->addOption(FileNameOption("o")
+ .filetype(eftPlot).outputFile()
+ .store(&fnDist_).defaultBasename("avedist")
+ .description("Average distances from reference group"));
+
+ options->addOption(SelectionOption("reference")
+ .store(&refsel_).required()
+ .description("Reference group to calculate distances from"));
+ options->addOption(SelectionOption("select")
+ .storeVector(&sel_).required().multiValue()
+ .description("Groups to calculate distances to"));
+
+ options->addOption(DoubleOption("cutoff").store(&cutoff_)
+ .description("Cutoff for distance calculation (0 = no cutoff)"));
+
+ settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
+}
+
+
+void
+AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation & /*top*/)
+{
+ nb_.setCutoff(cutoff_);
+
+ data_.setColumnCount(0, sel_.size());
+
+ avem_.reset(new AnalysisDataAverageModule());
+ data_.addModule(avem_);
+
+ if (!fnDist_.empty())
+ {
+ AnalysisDataPlotModulePointer plotm(
+ new AnalysisDataPlotModule(settings.plotSettings()));
+ plotm->setFileName(fnDist_);
+ plotm->setTitle("Average distance");
+ plotm->setXAxisIsTime();
+ plotm->setYLabel("Distance (nm)");
+ data_.addModule(plotm);
+ }
+}
+
+
+void
+AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ AnalysisDataHandle dh = pdata->dataHandle(data_);
+ const Selection &refsel = pdata->parallelSelection(refsel_);
+
+ AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refsel);
+ dh.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ const Selection &sel = pdata->parallelSelection(sel_[g]);
+ int nr = sel.posCount();
+ real frave = 0.0;
+ for (int i = 0; i < nr; ++i)
+ {
+ SelectionPosition p = sel.position(i);
+ frave += nbsearch.minimumDistance(p.x());
+ }
+ frave /= nr;
+ dh.setPoint(g, frave);
+ }
+ dh.finishFrame();
+}
+
+
+void
+AnalysisTemplate::finishAnalysis(int /*nframes*/)
+{
+}
+
+
+void
+AnalysisTemplate::writeOutput()
+{
+ // We print out the average of the mean distances for each group.
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ fprintf(stderr, "Average mean distance for '%s': %.3f nm\n",
+ sel_[g].name(), avem_->average(0, g));
+ }
+}
+
+/*! \brief
+ * The main function for the analysis template.
+ */
+int
+main(int argc, char *argv[])
+{
+ return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<AnalysisTemplate>(argc, argv);
+}
biod.pnpi.spb.ru / alexxy / gromacs-rcore.git / commitdiff