sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5d97beeec7747989d209a1e1d5222681245ffc105dbba7b7bcd13487ab24ba40 | C++ | 4,785 | 129 | #include "Locate.h"
#include <algorithm>
#include <filesystem>
#include <iostream>
#include <vector>
#if defined(_WIN32)
#include <windows.h>
#elif defined(__APPLE__)
#include <cassert>
#else
#include <limits.h>
#include <unistd.h>
#endif
#include <Debug/Debug.h>
namespace rayx {
// Adds a new lookup path where th... |
092b2b5b1fbdd71ed8caa393d6227dff6a1f85f3aa22d63387246e639858d37b | C++ | 4,799 | 145 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
3bb2a5e2c7315e7789312103e882b27c17cca332a1e39290520a93aa39b5308c | C++ | 4,803 | 166 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
37a8ed18920682a5ae47be3f1b586ad46824caa7bd12f5c527d891276c310cc7 | C++ | 4,810 | 144 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
d710bb238c4dbb8905726b03810dd2c0c944e920796c3340551991d830449af8 | C++ | 4,819 | 166 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
0fbaca4d764f29a053b8b8a0e43890e603e9f553ff00ce7eefa732a0d49dfb3f | C++ | 4,820 | 166 | #include <cmath>
#include <limits>
#include <steps/solver/efield/bdsystem.hpp>
#include <steps/solver/efield/bdsystem_lapack.hpp>
#include <steps/solver/efield/linsystem.hpp>
#include <catch2/catch_template_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
#include "lapack_common.hpp"
us... |
d963522dccc2cd284445c82cfebc0ac00a5042f56c3628114e3a3425e270c49f | C++ | 4,826 | 163 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
8fa5827776a02f7b225c29912480a17fdbd04580c5ffd1be7da25a18286a0d7a | C++ | 4,836 | 142 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
e50f840ee83fee2a9207f6264ade550c7a760e81e5fca7f0cf115a9e3d63316a | C++ | 4,842 | 163 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
2e0935fc30538ee9fcaca4ba243979dbd2635361d59103d8c225c6dce3bd64d2 | C++ | 4,844 | 77 | #include "setupTests.h"
// in this module tests mostly compare rayx's output with RAY-UI.
// The output of Ray-UI is mostly generated using RawRaysOutgoing.
TEST_F(TestSuite, ImagePlane) { traceRmlAndCompareAgainstRayUi("ImagePlane"); }
TEST_F(TestSuite, ImagePlaneRectangle) { loadBeamline("ImagePlaneRectangle"); } ... |
7f2c11e9e25de02639da9eb0e87bc461c4808ede55891e2ba6a5902efd865146 | C++ | 4,849 | 186 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
7ec965b173e214abf689839a5446431eada28d7146f6c6d5d34840b337286816 | C++ | 4,852 | 142 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
578fc2fb4bb7c15dd964e7619b6d3a6e9ac784b729249c7f292958c9ee067500 | C++ | 4,864 | 126 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later v... |
cb3d1a1f613c8a95e5cb8a96f570e93b1ffa5cb4bcd7745801c1e2e96818042a | C++ | 4,865 | 166 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
6164ea6edfef6feec09a6b9d4963bcda8748660b4ece91569e8790016e416163 | C++ | 4,873 | 128 | /*
* Track time and memory usage for a region.
* Print summary with min/max/avg across mpi ranks
*
*/
#include "region_tracker.hpp"
#include <array>
#include <iomanip>
#include <utility>
#include "peak_rss.hpp"
namespace steps::util {
#ifdef STEPS_USE_MPI
void RegionTracker::init(MPI_Comm comm) {
comm_ = ... |
493bef7784d210875a35fbcfdc68d9378fe0e48249d5d173ea814197165f8498 | C++ | 4,874 | 149 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
69dfd41f74df930f361458cc31a34b24057addbe0243a0f2ee54a00654c9ee23 | C++ | 4,877 | 159 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
0557e9d6c6778aa1f48fe242f77ae6297d53cf867c0d81d598375f8d3503ac1e | C++ | 4,881 | 166 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
6db47bea477a68d9622069c2685faecd1e5919ae1ac14b0e2a00725f58eb82ad | C++ | 4,886 | 161 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
df32830ac528858110439862327d047cb695d698e8156be982636ca2156f98d5 | C++ | 4,887 | 143 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
6afb6d238941d6299fd1239bfd77911f6c269cb29289b58ac99227a716e97254 | C++ | 4,898 | 162 | #//! user_eg3_r.cpp -- Invoke rbox and qhull from C++
#include "libqhullcpp/RboxPoints.h"
#include "libqhullcpp/QhullError.h"
#include "libqhullcpp/QhullQh.h"
#include "libqhullcpp/QhullFacet.h"
#include "libqhullcpp/QhullFacetList.h"
#include "libqhullcpp/QhullLinkedList.h"
#include "libqhullcpp/QhullVertex.h"
#inclu... |
58ff8fe754f3344cd859f4523e80fa69438dd3b262e1c7e7820bb3c040518fa9 | C++ | 4,914 | 121 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
3e29c09a9824d3c656c0a0b2e1a3e6dd7fc1a6119b6b65e744b67ddfa2f63f81 | C++ | 4,924 | 163 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
c63d43518e75a09dc91c43428b073bd755a0d790e0296c11bb716363e20e10b1 | C++ | 4,932 | 148 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
17e6af4038438dac3ffe171af2109619a324ef45257fc513c6ae6a027d390021 | C++ | 4,941 | 143 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
75837c3ae9ea1807250d19c67c93d213353dc8b00941c4108fca38c41904172c | C++ | 4,944 | 135 | #include "compdef.hpp"
#include <cassert>
#include "diffdef.hpp"
#include "reacdef.hpp"
namespace steps::dist {
Compdef::Compdef(const Statedef& statedef,
model::compartment_id t_model_compartment,
container::compartment_id t_container_compartment)
: pStatedef(statedef)
, m... |
09b8c145f2eb0297d869b6c94b61f5191243f079815f6870e1f625d4d613416c | C++ | 4,969 | 141 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
dfea7dd208634d25fe0a16474fed8e969036ee775be065cd9508d05d18555e98 | C++ | 5,004 | 145 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
967fd984ad27612b7399d4b37a74d076e570cc23c7a6af13fe4ef0cd4659521d | C++ | 5,005 | 155 | // ***************************************************************************
// BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 25 October 2011 (DB)
// ---------... |
8d93604757c35736af1716c7d3414f565cb9d726d6756716ebc67e068e5a017a | C++ | 5,020 | 145 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
f141985a1f29008a62ee6465e703f384d77cb0b152d17f38f68d71e40ade969d | C++ | 5,021 | 134 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
31be96f1d7296acbad9a8dfbda41fb273d25826c6aad2d2dea4c1bfec6b5e400 | C++ | 5,030 | 205 | // ***************************************************************************
// TcpSocketEngine_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 8 December 2011 (DB)
// --------------------... |
893443baf3fc0058b0b34b346246059551dbb10438b808dbe9b032d28cd55ace | C++ | 5,037 | 100 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
75cc4dc4891d4c36be3f6a2e47d4134f3062ad58c18237f2a484f55c45a77533 | C++ | 5,063 | 149 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
a242ab436914195f28a41822b6468b4f694233d0f7fe72daf4595292a9238063 | C++ | 5,077 | 165 |
#include "patchdef.hpp"
#include "geom/dist/distpatch.hpp"
#include "model/ghkcurr.hpp"
#include "model/spec.hpp"
#include "model/sreac.hpp"
#include "model/vdepsreac.hpp"
#include "sreacdef.hpp"
#include "statedef.hpp"
#include "util/vocabulary.hpp"
#include <optional>
namespace steps::dist {
//-------------------... |
d7cb63c11eaf61c4965bdf6f9af605c1682c4a60c06feeb74bd38072acda2832 | C++ | 5,088 | 208 | /*
* Copyright (C) 2010-2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any la... |
24c74870efda189219a87cad7e570c8a2435e351f28efcd71236d92570fdc879 | C++ | 5,095 | 136 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
b0fafc387f4a46319e76f178dbbba41e75632c3545bda1d907bf9d643be7659f | C++ | 5,100 | 241 | // A filter for moving averaging, median, trimmed mean, and weighted median filtering
/*
% Revision History:
% 2008: First release
% 2023: Renamed from deprecated version TrimmedFilter.cpp
%
% Reza Sameni, 2022-2023 The Open-Source Electrophysiological Toolbox
% https://github.com/alphanumericslab/OSET
... |
349e35a03f6ac34158bfb530702df87bc2b1e554ed4192611b170fd4903756ed | C++ | 5,103 | 187 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullHyperplane.cpp#3 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
****************************************... |
678c668c0e957616bb8253c23122cdba7cd1235f395ae3b6bdd256e186af01a9 | C++ | 5,116 | 187 | // ***************************************************************************
// SamReadGroup.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// -------------------------... |
963010a7b0c89a86ad2aeb7e55796fdf9fe3e4fc27556436453d0d8e67b1183f | C++ | 5,127 | 168 | // B_matrix.cpp
//
// Jim Bagrow
// Last Modified: 2007-04-23
#include <iostream>
#include <fstream>
#include <string>
#include <vector> // this code makes heavy use of the
#include <queue> // STL, since I suck at actual C
#include <map>
using namespace std;
vector<vector<int> > readEdgeList(string fN){
// ... |
dbae257027ba800bb5998e9644a3f761cbbab62a2e350733afa1cdc3b5fac389 | C++ | 5,140 | 121 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
1fbce68487570b38657c58dc81fee96a4ae0f46dcb36589f10fd1cc3d4896d8d | C++ | 5,142 | 162 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
32de9424c61531b2ad4d7e1511c66802c19d8f17b254fdff930a7858c556b38c | C++ | 5,144 | 141 | /*
*! @title Axi lite object
*! @file AxiLite.cpp
*! @author Romain Beaubois
*! @date 10 Aug 2022
*! @copyright
*! SPDX-FileCopyrightText: © 2021 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*!
*! @brief
*! Axi lite object
*! * Store pointer to bas... |
c23ece68662f206ef35822256cf99ac376df355dbd64e7964840a2423d36347f | C++ | 5,169 | 167 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
a9e87efc983277c67a653511cf60e21388a58543c52a21f8a09e6ffcb0fe8217 | C++ | 5,192 | 169 | // This file is part of gltfpack; see gltfpack.h for version/license details
#ifdef WITH_LIBWEBP
#include "gltfpack.h"
#include "webp/decode.h"
#include "webp/encode.h"
#ifndef WITH_LIBWEBP_BASIS
#include "imageio/image_dec.h"
#endif
#include <atomic>
#include <memory>
#include <thread>
static int writeWebP(const u... |
79dc0ab2555062dd8cf5b4a7102d1da68fb4ad0aa60867c4da4480f558f61375 | C++ | 5,195 | 237 | #include "iir_filter.h"
//----------------------------------------------------------------------------------------
IIR_filter::IIR_filter(): b(NULL), a(NULL), M(0), N(0)
{
}
//----------------------------------------------------------------------------------------
IIR_filter::IIR_filter(const double *b_arg, con... |
d42ca7a99b8b4e233f63458d21d1c655f21570d4b3a6ba07c3d876546ae47c83 | C++ | 5,198 | 143 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
e6d2508c0e29f5c16eb44f0b06f195723462e8cab19b379e89ef339946d27933 | C++ | 5,214 | 143 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
1ae7065d5b4320231df356c4c85c04e00b91dc15d65ed4881ac4b498f55f56a1 | C++ | 5,239 | 157 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
970a1ba9bd7f979da63bb0b668ef40e421b74e308dd03fce81097bd64edc421a | C++ | 5,266 | 137 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
2a770629e650de59b9d9ee7cd8f5977b79e7cb5b98c4853f468194f62b87bde2 | C++ | 5,274 | 208 | // ***************************************************************************
// bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 24 July 2013
// -------------... |
c5b5b6acfac4aefb9b6071ac21d5a9e3e00e2de352ac074f0e1a574f7c2f5041 | C++ | 5,275 | 123 | #include "SimpleUndulatorSource.h"
#include "Design/DesignSource.h"
#include "Shader/Utils.h"
namespace rayx {
namespace {
double calcUndulatorSigma(const SigmaType sigmaType, const double photonWaveLength, const double undulatorLength) {
double undulatorSigma;
if (sigmaType == SigmaType::ST_STANDARD) {
... |
f18701e78db2307e61dcec89c510d5bb820307f7474a1fcd7524c45fd92f5696 | C++ | 5,276 | 184 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullVertex_test.cpp#3 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
*****************************************... |
3e38a662812b9d002eb575cc48b56b340e099698543b69b8555c5ed40574b8c3 | C++ | 5,299 | 186 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
c47fd2fb1a23655f4e2329d3256d581a64cadcba99d4792c4ddbec469f1f5fa8 | C++ | 5,300 | 161 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullVertexSet.cpp#3 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
*****************************************... |
8c7cb2630cc18ea559e5433884de538134b57efa266492ba9e9f575b1ae3820e | C++ | 5,307 | 174 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
0ab9bddd8e8cf3debd70013f64fdcb88ec820d8d8835bc2fa70f075f0e87562b | C++ | 5,309 | 178 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
cd62a55dc1c25a3692ba49984423d82498aede0eb82adef011a4e703b3d15235 | C++ | 5,309 | 166 | #include "compdef.hpp"
#include <cassert>
#include <memory>
#include "diffdef.hpp"
#include "geom/dist/distcomp.hpp"
#include "model/diff.hpp"
#include "model/reac.hpp"
#include "model/spec.hpp"
#include "mpi/dist/tetopsplit/definition/fwd.hpp"
#include "reacdef.hpp"
#include "statedef.hpp"
#include "util/vocabulary.... |
fac5d1b7d5ba120a35f6ad318e8610849f26b64ebfc374049d039460bc894c73 | C++ | 5,309 | 147 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
8cabb2fbad6a16126fedf2d65c0596d1caddaa526924262adcc3bb0757553cad | C++ | 5,314 | 242 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
46789ae171311c78efd49873b517bd442365e88e8a5f54d75dc3d904176dd676 | C++ | 5,315 | 186 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
1078512dff563c79fb3398b99d4752330fcf706a6bd0272b0e188e4849858551 | C++ | 5,341 | 180 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
f57a6368af6323e63143ace8a4fd52d815983c4ae9016ebd9712b6601446d0f4 | C++ | 5,343 | 144 | #include "reactions.hpp"
#include <Omega_h_map.hpp>
#include <Omega_h_mark.hpp>
#include "geom/dist/distmesh.hpp"
#include "kproc_state.hpp"
#include "math/constants.hpp"
#include "util/vocabulary.hpp"
namespace steps::dist::kproc {
Reactions::Reactions(const Statedef& statedef, DistMesh& mesh, MolState& mol_state)... |
af6c7d93cc79f3978eddb24fec2f6c34d9d7cf83926829cfadee169e344410ff | C++ | 5,357 | 180 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
9c3eb4956991eb85b95ae8c255a6ad144135bc9d479ab0ff15a6b996e65ace33 | C++ | 5,369 | 167 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any l... |
e628cbfc077365b3fa36ef35d475a8747e72b41efb12434330c004c903b50ad1 | C++ | 5,386 | 220 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
a19a0888d74dc5b4bb10d637304984805457a0ba765e2685eba9f165fd9108f1 | C++ | 5,400 | 175 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
adeb42cfc0fd47afb3ab785b570c2e8d419b9c910706275438427205fef52f3b | C++ | 5,481 | 156 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
71ccd018a17bcc024ea170be588bc9b67a2864c95821afe70acb4029e42f6c6f | C++ | 5,496 | 153 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
317c19a21f0f59a6d4669bdd6ad6f2b9c0d34f364ce08df88fe61e4e4d287f8e | C++ | 5,501 | 143 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
6295c8f9e5c9c592c02489bcbe0e66add15a0faa9ca7e5eee674fc193d9656c6 | C++ | 5,528 | 206 | // This file is part of gltfpack; see gltfpack.h for version/license details
#include "gltfpack.h"
#include <math.h>
#include <string.h>
void markScenes(cgltf_data* data, std::vector<NodeInfo>& nodes)
{
for (size_t i = 0; i < nodes.size(); ++i)
nodes[i].scene = -1;
for (size_t i = 0; i < data->scenes_count; ++i)... |
036b0f875c51a086a6f66f4fff4818cded51e84a7bfa6490fd6fff54b2f8d32c | C++ | 5,538 | 192 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <stdint.h>
// allocator cache requires std::atomic and thread_local for thread safety; if these are not available, meshopt_setAllocatorCache is not supported
#if !defi... |
cd1340f1122be260c644330003c43b5e61d6be3d77717a8d5b13854ae07abec9 | C++ | 5,559 | 166 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
0f5213c38abb65b9bb1bc88dd60d2b76f836241a6b0027d61fb8097f8df6a2a0 | C++ | 5,570 | 172 | /*
*! @title Main application for bioemus
*! @file bioemus.cpp
*! @author Romain Beaubois
*! @date 10 Aug 2022
*! @copyright
*! SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*!
*! @brief
*!
*! @details
*! > **10 Aug 2022** : fil... |
9b84e6d91be09da2f97c46aa374589a402296ae1129b363b8b9ed7a0d01eb2a0 | C++ | 5,606 | 203 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullPoint.cpp#3 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
*********************************************... |
4fac59bcaade4b804fafec178595a914545efda4b87d47573856b72360ed8397 | C++ | 5,607 | 230 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later v... |
8694a1a558a4ed5c75217804a78dda4172b15a46782ecd322518d57cad7216a8 | C++ | 5,615 | 165 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later v... |
fa80970b0dbc4e98864d334b188b7f3d34a0369e2148a664ef3494414591a5a9 | C++ | 5,633 | 176 | #include <Rcpp.h>
#include <algorithm>
#include <vector>
using namespace std;
using namespace Rcpp;
//' Find index of matched donor units
//'
//' @param d Numeric vector with values from donor cases.
//' @param t Numeric vector with values from target cases.
//' @param k Integer, number of unique donors from whi... |
2dc1ce36c459be8a11bee28654d22361ceb5d1a82b42cdd70edb33d3cab1c31e | C++ | 5,653 | 185 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
71be8f5f87a0eb0e98a373d7afba6b9ce0d1dd7be7fb81fc74011ff0662a572e | C++ | 5,661 | 175 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
fbb75e80483c26e37b23e1d44689c4fc14a99a17aa13b98448e65bc80143c716 | C++ | 5,667 | 193 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
1975925c74a540004d0cd2d3f51720f57b05cb90a0c41af668bda8edb88838d2 | C++ | 5,669 | 186 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
bd7f0e3853a5a6eb51ae80498a53f08c2478d8fdfb4a4ac9a8f9d32d2db9855a | C++ | 5,685 | 186 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
2f940cf6557f5298f027acde584bfa23ebd5ead559708c4ea13f22db640e28d9 | C++ | 5,687 | 190 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
475bde321a0a4480bbd4e656e30badbeaa1a3f72d56740b1f743f254cb5c3dde | C++ | 5,688 | 127 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
ce86d59cc681b1892db2c286d3737380d5cadca59e78b6afcf3f4d2900c06084 | C++ | 5,692 | 196 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/qhulltest/QhullFacetList_test.cpp#3 $$Change: 2062 $
** $DateTime: 2016/01/17 13:13:18 $$Author: bbarber $
**
**************************************... |
886742d22987f64b0596c91d8e183b648c71e5a7a49162b153edd91a9a09c90b | C++ | 5,698 | 173 | #include "Rays.h"
#include <algorithm>
#include <bitset>
#include <unordered_map>
#include "Debug/Instrumentor.h"
namespace rayx {
Rays Rays::copy() const {
RAYX_PROFILE_FUNCTION_STDOUT();
return *this;
}
RayAttrMask Rays::attrMask() const {
RayAttrMask mask = RayAttrMask::None;
#define X(type, name, ... |
1f05d93e416c4e0fc8192b249c7dfb13aea6ca3a222e9a8196528d674f03141a | C++ | 5,703 | 190 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
318e675e5c14eea99e0ac4fc5f75be9557ccdda41d5aa345c6120c6833cde9e3 | C++ | 5,722 | 149 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
88c84909bf263480931c916376d3e979414685122bc02d20229de82715030f33 | C++ | 5,744 | 165 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
0613aecdfb33da3c7def17af1c0bfbc529c1abc71f0cccc89ef13ecd0028aab9 | C++ | 5,746 | 251 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later v... |
afdad61e3098c1471202576551832a2c1de4aa4e873930af4f56e23c55c9b043 | C++ | 5,757 | 178 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
38a5cc41abb6502f826db063358005f6d96b14ddba9cc4d49a934ed20cba17ff | C++ | 5,773 | 178 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
1564bfcf93924e898493c901d62fef01fa48dabdc4ba9449127238622cf7baca | C++ | 5,776 | 204 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for deta... |
6e8693a1f573545a306eb37049858392ebc2a06d75b3d02586cbe5d0de68bad2 | C++ | 5,792 | 204 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
851603aacde5fd37bee36cafca6b3eb11a318fbf884988f738227d51ba17f376 | C++ | 5,810 | 208 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
ddc84a437555c867655588c4a4a2989a05d34807759cbad5075ca735ec4df50b | C++ | 5,824 | 193 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later v... |
ff4111f8371f16359b07f87b3eab1ca3c651044ee1f4166fb25599ea556b4564 | C++ | 5,892 | 136 | #ifndef NO_H5
#include "H5Writer.h"
#include <highfive/highfive.hpp>
#include "Debug/Debug.h"
#include "Debug/Instrumentor.h"
// declare user types for HighFive
namespace {
inline HighFive::DataType highfive_create_type_EventType() {
return HighFive::EnumType<rayx::EventType>({
{"HitElement", rayx::Even... |
064f894b74f944fd340be8949702e0786e0fbfbdc237022e53817a75975cdac8 | C++ | 5,905 | 201 | /*
#################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for ... |
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