From: Alexey Shvetsov Date: Thu, 26 Apr 2018 11:07:56 +0000 (+0300) Subject: New code dump X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=095bf17abe72a93d6f613cdbf23333e26bd77b3c;p=alexxy%2Fgromacs-fitng.git New code dump Signed-off-by: Alexey Shvetsov --- 095bf17abe72a93d6f613cdbf23333e26bd77b3c diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..00a70fb --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +*.config +*.creator +*.creator.user +*.files +*.includes +CMakeLists.txt.user diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 0000000..128bbdc --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,55 @@ +cmake_minimum_required(VERSION 2.8.8) + +project(gromacs-fitng 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) +option(GMX_OPENMP "Enable OpenMP-based multithreading" ON) +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 ${GMX_SUFFIX}) +endif() + +find_package(GROMACS 2016 REQUIRED) +gromacs_check_double(GMX_DOUBLE) +gromacs_check_compiler(CXX) +include(gmxManageOpenMP) + +add_definitions(${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() + +if(NOT GMX_OPENMP) + #Unset all OpenMP flags in case OpenMP was disabled either by the user + #or because it was only partially detected (e.g. only for C but not C++ compiler) + unset(OpenMP_C_FLAGS CACHE) + unset(OpenMP_CXX_FLAGS CACHE) +endif() + + +add_subdirectory(src) diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..8add30a --- /dev/null +++ b/COPYING @@ -0,0 +1,504 @@ + GNU LESSER GENERAL PUBLIC LICENSE + Version 2.1, February 1999 + + Copyright (C) 1991, 1999 Free Software Foundation, Inc. + 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + +[This is the first released version of the Lesser GPL. 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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. + +# This file should remain version-agnostic, with all things specific to a +# particular GROMACS version remaining in the package configuration files. +# This find module only provides some convenience functionality to manage the +# suffixes etc. +# That should allow using the same FindGROMACS.cmake file with multiple +# different GROMACS installations on the same machine. + +# Propagate all flags passed to parent find_package() to the config call below. +set(_gmx_find_args "") +if (GROMACS_FIND_VERSION) + 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) diff --git a/cmake/gmxManageOpenMP.cmake b/cmake/gmxManageOpenMP.cmake new file mode 100644 index 0000000..4aad27a --- /dev/null +++ b/cmake/gmxManageOpenMP.cmake @@ -0,0 +1,75 @@ +# +# This file is part of the GROMACS molecular simulation package. +# +# Copyright (c) 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. + +# Manage the OpenMP setup. This wrapper file checks for some known-bad compiler +# versions before trying to detect OpenMP with the standard find-package-module, +# and then does some additional tests for flags afterwards. + +if(GMX_OPENMP) + if(CMAKE_C_COMPILER_ID MATCHES "Cray" AND CMAKE_VERSION VERSION_LESS 3) + message(STATUS "OpenMP multithreading is not detected correctly for the Cray compiler with CMake before version 3.0 (see http://public.kitware.com/Bug/view.php?id=14567)") + set(GMX_OPENMP OFF CACHE BOOL + "OpenMP multithreading is not detected correctly for the Cray compiler with CMake before version 3.0 (see http://public.kitware.com/Bug/view.php?id=14567)" FORCE) + else() + # We should do OpenMP detection if we get here + # OpenMP check must come before other CFLAGS! + find_package(OpenMP) + if(OPENMP_FOUND) + # CMake on Windows doesn't support linker flags passed to target_link_libraries + # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed. + if(NOT (WIN32 AND NOT MINGW)) + if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE) + set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread") + set(OpenMP_SHARED_LINKER_FLAGS "") + else() + # Only set a linker flag if the user didn't set them manually + if(NOT DEFINED OpenMP_LINKER_FLAGS) + set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}") + endif() + if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS) + set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}") + endif() + endif() + endif() + if(MINGW) + #GCC Bug 48659 + set(OpenMP_C_FLAGS "${OpenMP_C_FLAGS} -mstackrealign") + endif() + else() + message(WARNING + "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.") + set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE) + endif() + endif() +endif() diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt new file mode 100644 index 0000000..c72f456 --- /dev/null +++ b/src/CMakeLists.txt @@ -0,0 +1,8 @@ +set(GROMACS_CXX_FLAGS "${GROMACS_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") +add_executable(fitng fitng.cpp) +include_directories( + ${GROMACS_INCLUDE_DIRS} + ${CMAKE_SOURCE_DIR}/include) +set_target_properties(fitng PROPERTIES + COMPILE_FLAGS "${GROMACS_CXX_FLAGS}") +target_link_libraries(fitng ${GROMACS_LIBRARIES}) diff --git a/src/fitng.cpp b/src/fitng.cpp new file mode 100644 index 0000000..ac6e380 --- /dev/null +++ b/src/fitng.cpp @@ -0,0 +1,443 @@ +/* + * This file is part of the GROMACS molecular simulation package. + * + * Copyright (c) 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. + */ +/*! \internal \file + * \brief + * Implements gmx::analysismodules::Freevolume. + * + * \author Titov Anatoly + * \ingroup module_trajectoryanalysis + */ + +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#define MAX_NTRICVEC 12 + +using namespace gmx; + +using gmx::RVec; + +struct node { + short int n; + RVec r; + bool yep; +}; + +void make_graph(int mgwi_natoms, rvec *mgwi_x, std::vector< std::vector< node > > &mgwi_graph) +{ + mgwi_graph.resize(mgwi_natoms); + for (int i = 0; i < mgwi_natoms; i++) { + mgwi_graph[i].resize(mgwi_natoms); + } + for (int i = 0; i < mgwi_natoms; i++) { + for (int j = 0; j < mgwi_natoms; j++) { + rvec_sub(mgwi_x[i], mgwi_x[j], mgwi_graph[i][j].r); + mgwi_graph[i][j].n = 0; + } + } +} + +void update_graph(std::vector< std::vector< node > > &ugwi_graph, rvec *ugwi_x, long double ugwi_epsi) { + rvec ugwi_temp; + int ugwi_for = ugwi_graph.size(); + for (int i = 0; i < ugwi_for; i++) { + for (int j = i; j < ugwi_for; j++) { + rvec_sub(ugwi_x[i], ugwi_x[j], ugwi_temp); + rvec_dec(ugwi_temp, ugwi_graph[i][j].r.as_vec()); + if (norm(ugwi_temp) <= ugwi_epsi) { + if (i == j) { + ugwi_graph[i][j].n++; + } + else { + ugwi_graph[i][j].n++; + ugwi_graph[j][i].n++; + } + } + } + } +} + +void check_domains(long double cd_delta, int cd_frames, std::vector< std::vector< std::vector< node > > > &cd_graph) { + int cd_for1 = cd_graph.size(), cd_for2 = cd_graph[1].size(); + for (int k = 0; k < cd_for1; k++) { + for (int i = 0; i < cd_for2; i++) { + for (int j = 0; j < cd_for2; j++) { + if (cd_graph[k][i][j].n >= cd_frames * cd_delta) { + cd_graph[k][i][j].yep = true; + } + else { + cd_graph[k][i][j].yep = false; + } + } + } + } +} + +void find_domain_sizes(std::vector< std::vector< std::vector< node > > > fds_graph, std::vector< std::vector< int > > &fds_domsizes) { + fds_domsizes.resize(fds_graph.size()); + int fds_for1 = fds_graph.size(), fds_for2 = fds_graph[1].size(); + for (int i = 0; i < fds_for1; i++) { + fds_domsizes[i].resize(fds_for2, 0); + for (int j = 0; j < fds_for2; j++) { + for (int k = 0; k < fds_for2; k++) { + if (fds_graph[i][j][k].yep) { + fds_domsizes[i][j]++; + } + } + } + } +} + +void get_maxsized_domain(std::vector< int > &gmd_max_d, std::vector< std::vector< std::vector< node > > > gmd_graph, std::vector< std::vector< int > > gmd_domsizes) { + int gmd_number1 = 0, gmd_number2 = 0; + int gmd_for1 = gmd_domsizes.size(), gmd_for2 = gmd_domsizes[0].size(), gmd_for3 = gmd_graph[1][1].size(); + for (int i = 0; i < gmd_for1; i++) { + for (int j = 0; j < gmd_for2; j++) { + if (gmd_domsizes[i][j] >= gmd_domsizes[gmd_number1][gmd_number2]) { + gmd_number1 = i; + gmd_number2 = j; + } + } + } + gmd_max_d.resize(0); + for (int i = 0; i < gmd_for3; i++) { + if (gmd_graph[gmd_number1][gmd_number2][i].yep) { + gmd_max_d.push_back(i); + } + } +} + +void delete_domain_from_graph(std::vector< std::vector< std::vector< node > > > &ddf_graph, std::vector< int > ddf_domain) { + int ddfg_for1 = ddf_domain.size(), ddfg_for2 = ddf_graph.size(), ddfg_for3 = ddf_graph[1].size(); + for (int i = 0; i < ddfg_for1; i++) { + for (int k = 0; k < ddfg_for2; k++) { + for (int j = 0; j < ddfg_for3; j++) { + if (ddf_graph[k][ddf_domain[i]][j].yep) { + ddf_graph[k][ddf_domain[i]][j].yep = false; + } + if (ddf_graph[k][j][ddf_domain[i]].yep) { + ddf_graph[k][j][ddf_domain[i]].yep = false; + } + } + } + } +} + +bool check_domsizes(std::vector< std::vector< int > > cd_domsizes, int cd_domain_min_size) { + int cd_for1 = cd_domsizes.size(), cd_for2 = cd_domsizes[0].size(); + for (int i = 0; i < cd_for1; i++) { + for (int j = 0; j < cd_for2; j++) { + if (cd_domsizes[i][j] >= cd_domain_min_size) { + return true; + } + } + } + return false; +} + +void print_domains(std::vector< std::vector< int > > pd_domains, std::vector< int > index, std::string fnNdx_) { + FILE *fpNdx_; + fpNdx_ = std::fopen(fnNdx_.c_str(), "w+"); + int write_count; + for (int i = 0; i < pd_domains.size(); i++) { + std::fprintf(fpNdx_, "[domain_%d]\n", i + 1); + write_count = 0; + for (int j = 0; j < pd_domains[i].size(); j++) { + write_count++; + if (write_count > 20) { + write_count -= 20; + std::fprintf(fpNdx_, "\n"); + } + std::fprintf(fpNdx_, "%5d ", index[pd_domains[i][j]] + 1); + } + std::fprintf(fpNdx_,"\n\n"); + } + std::fprintf(fpNdx_,"\n"); + std::fclose(fpNdx_); +} + + +/*! \brief + * Class used to compute free volume in a simulations box. + * + * Inherits TrajectoryAnalysisModule and all functions from there. + * Does not implement any new functionality. + * + * \ingroup module_trajectoryanalysis + */ +class Domains : public TrajectoryAnalysisModule +{ + public: + + Domains(); + virtual ~Domains(); + + //! Set the options and setting + virtual void initOptions(IOptionsContainer *options, + TrajectoryAnalysisSettings *settings); + + //! First routine called by the analysis framework + // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc); + virtual void initAnalysis(const TrajectoryAnalysisSettings &settings, + const TopologyInformation &top); + + virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings, + const t_trxframe &fr); + + //! Call for each frame of the trajectory + // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc); + virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, + TrajectoryAnalysisModuleData *pdata); + + //! Last routine called by the analysis framework + // virtual void finishAnalysis(t_pbc *pbc); + virtual void finishAnalysis(int nframes); + + //! Routine to write output, that is additional over the built-in + virtual void writeOutput(); + + private: + + std::string fnNdx_; + + std::vector< std::vector< std::vector< node > > > graph; + + std::vector< std::vector< int > > domains; + std::vector< std::vector< int > > domsizes; + + std::vector< int > index; + std::vector< int > numbers; + std::vector< std::vector < RVec > > trajectory; + Selection selec; + int frames = 0; + int domain_min_size = 5; // should be selectable + + real **w_rls; + int bone; + double delta = 0.90; //0.95 // should be selectable + double epsi = 0.15; //0.3 колебания внутри домена // should be selectable + + int domains_ePBC; + // Copy and assign disallowed by base. +}; + +Domains::Domains(): TrajectoryAnalysisModule() +{ +} + +Domains::~Domains() +{ +} + +void +Domains::initOptions(IOptionsContainer *options, + TrajectoryAnalysisSettings *settings) +{ + static const char *const desc[] = { + "[THISMODULE] to be done" + }; + // Add the descriptive text (program help text) to the options + settings->setHelpText(desc); + // Add option for selecting a subset of atoms + options->addOption(SelectionOption("select") + .store(&selec).required() + .description("Atoms that are considered as part of the excluded volume")); + // Add option for output file name + options->addOption(FileNameOption("on").filetype(eftIndex).outputFile() + .store(&fnNdx_).defaultBasename("domains") + .description("Index file from the domains")); + // Add option for etalon_frame constant + options->addOption(gmx::IntegerOption("dms") + .store(&domain_min_size) + .description("minimum domain size")); + // Add option for epsi constant + options->addOption(DoubleOption("epsilon") + .store(&epsi) + .description("thermal vibrations' constant")); + // Add option for delta constant + options->addOption(DoubleOption("delta") + .store(&delta) + .description("domain membership probability")); + // Control input settings + settings->setFlags(TrajectoryAnalysisSettings::efNoUserPBC); + settings->setPBC(true); +} + +void +Domains::initAnalysis(const TrajectoryAnalysisSettings &settings, + const TopologyInformation &top) +{ + domains_ePBC = top.ePBC(); +} + +void +Domains::initAfterFirstFrame(const TrajectoryAnalysisSettings &settings, + const t_trxframe &fr) +{ + t_pbc pbc; + t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL; + matrix boxx; + copy_mat(fr.box, boxx); + if (ppbc != NULL) { + set_pbc(ppbc, domains_ePBC, boxx); + } + ConstArrayRef< int > atomind = selec.atomIndices(); + index.resize(0); + for (ConstArrayRef::iterator ai = atomind.begin(); (ai < atomind.end()); ai++) { + index.push_back(*ai); + } + trajectory.resize(2); + trajectory[0].resize(selec.atomCount()); + + for (int i = 0; i < selec.atomCount(); i++) { + trajectory[0][i] = fr.x[index[i]]; + } + + bone = index.size() - domain_min_size + 1; + graph.resize(bone); + snew(w_rls, bone); + for (int i = 0; i < bone; i++) { + snew(w_rls[i], index.size()); + for (int j = 0; j < index.size(); j++) { + if (j >= i && j <= i + domain_min_size - 1) { + w_rls[i][j] = 1; + } else { + w_rls[i][j] = 0; + } + } + rvec *etalon; + snew(etalon, index.size()); + for (int j = 0; j < index.size(); j++) { + copy_rvec(trajectory[0][j].as_vec(), etalon[j]); + } + reset_x(index.size(), NULL, index.size(), NULL, etalon, w_rls[i]); + make_graph(index.size(), etalon, graph[i]); + sfree(etalon); + } + trajectory[1].resize(index.size()); +} + +void +Domains::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, + TrajectoryAnalysisModuleData *pdata) +{ + for (int i = 0; i < index.size(); i++) { + trajectory[1][i] = fr.x[index[i]]; + } + frames++; + + #pragma omp parallel + { + #pragma omp for schedule(dynamic) + for (int j = 0; j < bone; j++) { + rvec *etalon, *traj; + snew(etalon, index.size()); + for (int k = 0; k < index.size(); k++) { + copy_rvec(trajectory[0][k].as_vec(), etalon[k]); + } + snew(traj, index.size()); + for (int k = 0; k < index.size(); k++) { + copy_rvec(trajectory[1][k].as_vec(), traj[k]); + } + reset_x(index.size(), NULL, index.size(), NULL, etalon, w_rls[j]); + reset_x(index.size(), NULL, index.size(), NULL, traj, w_rls[j]); + do_fit(index.size(), w_rls[j], etalon, traj); + update_graph(graph[j], traj, epsi); + sfree(etalon); + sfree(traj); + } + } + std::cout << "frame: " << frames << " analyzed\n"; +} + +//domains -s '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Develop/samples/reca_rd/reca_rd.mono.xtc' -select 'name CA' +//domains -s '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.tpr' -f '/home/toluk/Develop/samples/banana_phone/pgk.md.non-sol.10th.xtc' -select 'name CA' +//domains -s '/home/toluk/Data/reca_rd/reca_rd.mono.tpr' -f '/home/toluk/Data/reca_rd/reca_rd.mono.xtc' - select 'name CA' + +void +Domains::finishAnalysis(int nframes) +{ + frames -= 1; + + std::cout << "final cheking\n"; + check_domains(delta, frames, graph); + + std::cout << "finding domains' sizes\n"; + find_domain_sizes(graph, domsizes); + + std::cout << "finding domains\n"; + std::vector< int > a; + a.resize(0); + while (check_domsizes(domsizes, domain_min_size)) { + domains.push_back(a); + get_maxsized_domain(domains.back(), graph, domsizes); + delete_domain_from_graph(graph, domains.back()); + domsizes.resize(0); + find_domain_sizes(graph, domsizes); + } + for (int i = 0; i < bone; i++) { + sfree(w_rls[i]); + } + sfree(w_rls); +} + +void +Domains::writeOutput() +{ + std::cout << "making output file\n"; + print_domains(domains, index, fnNdx_); // see function for details | numbers from index + std::cout << "\n END \n"; +} + + +/*! \brief + * The main function for the analysis template. + */ +int +main(int argc, char *argv[]) +{ + return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain(argc, argv); +}