sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d4a4b4504660c7f3e2ec00634da0afd3b4481973e15c40033ea9cadd5b39df8e | C++ | 3,323 | 103 | /*
#################################################################################
#
# 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... |
cf82aff827335c7b41bebe3e04ed306a84425ef91e80be2db731e8b16c6660b3 | C++ | 3,327 | 86 | /* 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... |
fc26f64f9c61f71acb5d5167377790640d735b94af63b4d0f427b384a6ef235b | C++ | 3,329 | 90 | /* 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... |
621b9ac67f754f937ea7c68a477f314f43068027e57e6a4682c956bb949a7ad3 | C++ | 3,339 | 103 | /*
#################################################################################
#
# 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 ... |
edcf2d64193c2aad6e2dd4f781e0860cecafb01d787f9d4043d482e25a1382f7 | C++ | 3,354 | 114 | /*
Bayesian Functional GWAS --- MCMC (bfGWAS:MCMC)
Copyright (C) 2016 Jingjing Yang
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 yo... |
b58410f23bcec75ea42e687c9dfe18b72c08c055f57d3fbda47c8f84ea2f80c3 | C++ | 3,362 | 88 | #include "event_queue.hpp"
#include "util/debug.hpp"
#include "util/error.hpp"
namespace steps::dist::kproc {
void EventQueue::update(const KProcID id, const osh::Real time) {
// Remove previous event if it exists
auto timeit = kproc_to_event_time_.find(id.data());
if (timeit != kproc_to_event_time_.end(... |
ec5e3bff2eff16477a14b732ebcf5b34687c14c9e93a6e6e6ac51c7586cbf153 | C++ | 3,391 | 110 | /*
#################################################################################
#
# 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... |
fc53276c7689cf6c3bc1cc4c424b17a6f7a996ab620fa5c8dd1de72b48a92540 | C++ | 3,407 | 110 | /*
#################################################################################
#
# 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 ... |
9f8980d62d63ccb43a544c4f67fd386f66960bc892c6d1177048b906b7b1db38 | C++ | 3,410 | 102 | #include "efield.hpp"
#include "../mol_state.hpp"
#include "geom/dist/distmesh.hpp"
namespace steps::dist {
osh::Real OhmicCurrent::getReversalPotential(mesh::triangle_id_t triangle) const {
auto it = reversal_potentials.find(triangle);
if (it != reversal_potentials.end()) {
return it->second;
}
... |
de1ed1160d3416d530813d081378d5064997509cc694d92bc4d86ad3c7b22b08 | C++ | 3,411 | 119 | // `trimmed_filter_mex.cpp - MEX function wrapper for the trimmed_filter.cpp function (for compiling with MATLAB MEX command and running from MATLAB)
/*
% trimmed_filter - Trimmed filtering function.
%
% [y] = trimmed_filter(x, mode, wlen, alpha, weights)
%
% Inputs:
% x: Input signal (1D vector).
% mode: String... |
48725867cfbbef78d742a5f56ed02ec7e88b394dac3d3b347322d6128867ec71 | C++ | 3,416 | 136 | // ***************************************************************************
// bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ----------------... |
8a0beda4329c82d709fe2c36823da83407b973eb5a0a408cd1ce12f71cff514d | C++ | 3,416 | 124 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullRidge.cpp#3 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
*********************************************... |
82051121d458954c66c109d3caf3cfb3619b0a8e5be8ce35be5db24621f72e94 | C++ | 3,417 | 113 | /* 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... |
9296f21372acac3717be697247e5da0420a769cb5883094ffb9bcb80b103ecf5 | C++ | 3,421 | 112 | /*
#################################################################################
#
# 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... |
eb93678f75caeb011272ce3debd13fa3dc1f3648cb8a1bba234265b6ce0700da | C++ | 3,437 | 112 | /*
#################################################################################
#
# 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 ... |
1884025170a3716f2e5bcb21d850d359d9231e871535f1ce611f92744f4e5974 | C++ | 3,445 | 87 | #include "PointSource.h"
#include "Debug/Debug.h"
#include "Debug/Instrumentor.h"
#include "Design/DesignElement.h"
#include "Design/DesignSource.h"
#include "Random.h"
#include "Shader/Constants.h"
namespace rayx {
namespace {
/**
* get deviation from main ray according to specified distribution (uniform if
* har... |
2910bd708c5d362343b4493303eab67834620e3cf9f35d153e252b6252036d7f | C++ | 3,455 | 85 | /* 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... |
9350bec823c0701ca061fc4dd0e2cd9755a4260febd86392dbdc61887c7ebf1b | C++ | 3,484 | 117 | /* 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... |
44007ad6ca43b4b0f01a1ea0cd08c09563aae676c2a2bc89f87d1c8f2056ee25 | C++ | 3,492 | 116 | /*
#################################################################################
#
# 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... |
07af8d061855e88668ae11cdb2bec2cac7375a7edd8c972f662ff19b0b22c629 | C++ | 3,494 | 110 | /* 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... |
15aaf32a25a4fbf829b6d46131917cdc28950970c41ae4362b2cce8e45a479d6 | C++ | 3,494 | 97 | /* 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... |
1fb0ead8e70feed13d96ca418dfee218d5acc9ca7b8967dcbcb98e565a36719c | C++ | 3,498 | 171 | #include "iir_notch_filter.h"
//----------------------------------------------------------------------------------------
IIR_notch_filter::IIR_notch_filter(const double f0, const double fc, const double fs)
{
double alpha, w0;
a_cof = new double[3];
b_cof = new double[3];
//calculate b,a coefficients
w0... |
28282f555d42a118a6735f161b1ba78fcbe0d1810a6a337a399bd8471f79105e | C++ | 3,503 | 127 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <float.h>
#include <math.h>
union FloatBits
{
float f;
unsigned int ui;
};
unsigned short meshopt_quantizeHalf(float v)
{
FloatBits u = {v};
unsigned int ui = u.u... |
3828cfa3956ec7fc67782f8e52fec1d5655bfd07bccd3e9420307f349e12894b | C++ | 3,503 | 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... |
0fbc92e2b4ca3e0523094882bad4eeb732137fc6cd2155471e687f8f1bb7a40e | C++ | 3,504 | 117 | // [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <math.h>
using namespace Rcpp;
// declare K_Binary_SPA
double K_Binary_SPA(double x, arma::vec muhat, arma::vec G);
// declare K_Binary_SPA_alt (alternative way if not converge)
double K_Binary_SPA_alt... |
1fc892f4c03f1fb6304aa02f1bfc41b937cb9da976bb92dbb7f969bd2b4d2143 | C++ | 3,508 | 116 | /*
#################################################################################
#
# 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 ... |
ca85030c820c0d225841a3b22292eebf9d392a33690dfaf2350be3497019436a | C++ | 3,510 | 106 | /* 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... |
ac08f7b9f4181a86df2c6dd002e583e3117c52b0f8e907653a90a8e5893c64b7 | C++ | 3,523 | 158 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/RoadError.cpp#2 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
**********************************************... |
29aff2dc19a70be81a9ea93c82622b731294138ba34cd8abadec443aaab65984 | C++ | 3,529 | 134 | // ***************************************************************************
// SamSequence.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// --------------------------... |
32f5d80f678625c53036a46cabf3b9d8b283708cc0ef81139cf3adb73576f124 | C++ | 3,532 | 118 | /* 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... |
30e0da70fce2914a6054f3883d0caf7e77da96ba40a7663fbc2ed6314f4e80c3 | C++ | 3,534 | 113 | /* 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... |
623f5a07f1be3cdbea0ea835cfc0742e4412288c75772108751005991c930aed | C++ | 3,536 | 119 | /*
* 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... |
e38df5e3d9b25485fdc1313ef1bdd31c0688579c6ac369ef589004c9359a243c | C++ | 3,536 | 122 | /*
#################################################################################
#
# 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... |
7779ec329735ef4702a1e6edcad8776f2a3c575433c3c0811b1cfd50da60c09b | C++ | 3,549 | 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... |
10466366e9380fb8a77af4d6eb080ef7c7054f063e8ee03e909e2b1871551f43 | C++ | 3,552 | 124 | /* 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... |
c3cd01bb44a7a7e5ddeef35951e00fd3b683ffbc3c784e1785e3f163b424f85d | C++ | 3,552 | 107 | #include "steps/mpi/dist/tetopsplit/mol_state.hpp"
#include <iostream>
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
namespace osh = Omega_h;
TEST_CASE("MolState_Occupancy") {
size_t id = 3;
osh::Real n_molecules = 1;
int corr = 0;
osh::Real t ... |
f4ea5d84d830dd20418b6c4ed7a23a75d4ae64924b32142b06ec71fa6ba42318 | C++ | 3,552 | 122 | /*
#################################################################################
#
# 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 ... |
cd13d25328a3c7d64f5fe5d2cc4e418f323273d54a6e0394c6db4ab40d0859ac | C++ | 3,556 | 113 | /*
* 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... |
6e4c58966151af486973e8c2289ee0b874c3c961befe6ef963edd1cbe203125b | C++ | 3,557 | 101 | #include <cmath>
#include <iostream>
#include <random>
#include <vector>
#include <catch2/catch_test_macros.hpp>
#include "rng/small_binomial.hpp"
using namespace steps::rng;
// - - - One-Sample Kolmogorov-Smirnov Goodness of Fit - - -
// Measures discrepancy of empirical cdf w.r.t. theoretical one
// Significanc... |
324a4052bf3e8453b38547b2f67b50b5efe3cbbc5876a0ecab3f6b12b450ecda | C++ | 3,561 | 151 | /*
* 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... |
82905bf4db83ecfc7c0c6822792c07102fb53a2e9f81a215f35b80c7d3cd8f28 | C++ | 3,612 | 87 | /* 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... |
b2d3760795e385c57344c192a3bb6b19ecf24110f9e91661d9b75511fa8722ce | C++ | 3,615 | 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... |
9fffcb3b9ec4ee845e7057f629a8b512791c7f2d291c62a36c9e367052d45bd3 | C++ | 3,617 | 94 | /*
#################################################################################
#
# 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... |
0cb5ecd9daae0b3cabccb953b2303c03c1b829e96462a6eef7e71b2258f15046 | C++ | 3,633 | 94 | /*
#################################################################################
#
# 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 ... |
ac4284a5d8ca6caa45407964b4796df3f6be8b38996e85ad4a10e8f66fe764fd | C++ | 3,641 | 123 | // [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
#include <math.h>
using namespace Rcpp;
// declare K_Binary_SPA
double K_Binary_SPA(double x, arma::vec muhat, arma::vec G);
// declare K_Binary_SPA_alt (alternative way if not converge)
double K_Binary_SPA_alt... |
2b78f2d495ebd7381dc931e58f160202f76c80d684a46e5d36d69ec4a69be096 | C++ | 3,644 | 128 | /*
* 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... |
a1848b0aa0675ac03419f67e538ee6ba98c9114b499e622a1e3c0a5f09e143e8 | C++ | 3,648 | 111 | /*
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... |
07ba6f0d3f442e580accfa638dfb75029e0bdc4ff4a8a9f9ac1283fa1f48df92 | C++ | 3,670 | 94 | /*
#################################################################################
#
# 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... |
a4a6846c788b07a4ea71e07f19d267544fa3ee23cf45cc2a23c9b2acde410518 | C++ | 3,684 | 147 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullFacetSet.cpp#2 $$Change: 2066 $
** $DateTime: 2016/01/18 19:29:17 $$Author: bbarber $
**
******************************************... |
fca8fca69d545fd9a7edb579647fd5b9bb2449201edc709a506a229faa864f8f | C++ | 3,686 | 94 | /*
#################################################################################
#
# 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 ... |
ac62bc350ac5f87b7861a56ced9c69ac6cdfb9a76832e229dd87d1610da51831 | C++ | 3,700 | 114 | /* 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... |
7af8a7b91e2e41028a4b6aa476e93b1d96464e1e9f8d65d63abb5df1912231a1 | C++ | 3,706 | 104 | /* 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... |
07fca2db9934a3c254a3a55d4313020732c78626e3e24b6e11a798e7ae59fa36 | C++ | 3,727 | 116 | /*
#################################################################################
#
# 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... |
8de5c90be1f3aae225d2ec865fa1b0bf374fdc4558e55c0103e5d7e8816f04cd | C++ | 3,731 | 113 | #include "Debug/Debug.h"
#include <sstream>
#include <utility>
namespace rayx {
// The length of filename and line number is 30 characters.
// If it doesn't find, we insert "...".
// This is used to have a visually unified output that is easier to read.
constexpr int PREFIX_LEN = 30;
/**
* @param filename the fil... |
7de3939f4748ebc5cbc9ffe96f5877e2fa97f60b0868ac5f2176aa36254267d0 | C++ | 3,733 | 119 | /*
#################################################################################
#
# 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... |
80610dff0beb04b02abadbd7202b546aff6ca6ec950b91e53da231d8d5f4cc09 | C++ | 3,742 | 118 | /* 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... |
d7fec7742322871035c4a9d9e33fd90553b2a8a0f9e8042cac17e92af127855f | C++ | 3,743 | 116 | /*
#################################################################################
#
# 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 ... |
855c602eec0388a74c23f87cbad799898e99d9114537dc3b93c552496e79f987 | C++ | 3,749 | 119 | /*
#################################################################################
#
# 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 ... |
419bbe36606a62aabf459c6c7bb0cca5b9368c5a1b309e66be5a4bb9a3d66dd0 | C++ | 3,751 | 118 | /*
#################################################################################
#
# 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... |
adde7442a527ac2a15bd0f2526c86d1bb6f390ea6e6d34802f58f0548477bf60 | C++ | 3,756 | 138 | /* 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... |
d6941cfd9bfb228c53981faab011e9fc3e0379b877fc1231331db922d3971c6c | C++ | 3,759 | 113 | /* 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... |
8265e2cbbe481b2b6789046d0efdd1156b6a30811b257ddf32e39ded67e1bbec | C++ | 3,763 | 127 | /*
#################################################################################
#
# 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... |
d36e759faf27b666b0c1cfba92788d59d6856826c4ada8e6dadc0b8a19898c34 | C++ | 3,767 | 118 | /*
#################################################################################
#
# 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 ... |
783331f9812383de24fe2ae8171c24de83c7ffe0891298084de09f0acda0b397 | C++ | 3,779 | 127 | /*
#################################################################################
#
# 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 ... |
2d5fff304f9d9ec9fa5dec0e7695a8aaefb65e30dfc26eeeec89a69b3a31abed | C++ | 3,784 | 105 | /* 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... |
18ce87547bb09b1719ef170c447c523a4a227ed1110045598f8f256e743dfbb1 | C++ | 3,789 | 119 | /*
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... |
fda35bfb28a71caab0082f966e7608208aecf9756e4b5a2a2a884b6e157ef48e | C++ | 3,791 | 168 | /*
* Copyright (C) 2000-2007 Goncalo Abecasis
*
* 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 version.
*
* T... |
2d73731fc41ab6790a8777566625e0b4c28c43255e32f60feb32666e0a92977a | C++ | 3,795 | 156 | /*
* 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... |
64ba10ce7817ba513757e496e9c150fe12afc3a882406bbc89df828dc7c77bac | C++ | 3,800 | 112 | /* 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... |
8341042e6d37304e01b3ae612135cf04063968730fbe6a3d3240b47cadd9e954 | C++ | 3,813 | 148 | /*
* 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... |
bff37aecb10cefa33f3f6a217413c6ac98899c23e6de5282420c60e6baf786ec | C++ | 3,820 | 125 | // This file is part of meshoptimizer library; see meshoptimizer.h for version/license details
#include "meshoptimizer.h"
#include <assert.h>
#include <string.h>
meshopt_VertexCacheStatistics meshopt_analyzeVertexCache(const unsigned int* indices, size_t index_count, size_t vertex_count, unsigned int cache_size, unsi... |
17eda6770f4c453eedc379c7c5efcf6eef3bc99d6f4dfa4152fe7242ca423420 | C++ | 3,821 | 105 | /* 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... |
a2d79e2da95abfdcc0eb496bdf7485755293e2dc45d9c4cfff9da64f937ff2dc | C++ | 3,823 | 167 | /*
* 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... |
d97b79731f41a4c6d9e57cd4214b36776300926d5b948e78b78e45ec2ca8304d | C++ | 3,833 | 200 | // [[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
// declare K
double K(double x, arma::vec egvalues);
// declare K1 (first derivative)
double K1(double x, arma::vec egvalues, double q);
// declare K2 (second derivative)
double K2(double x, arma::vec egv... |
1607b82c0c4baad4703fbf646fdc1c816521e5bb6877bc2d62992a0cb208aebc | C++ | 3,835 | 121 | /*
* 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... |
e0cc60cdb8431c426f4d68c71f86a8b5bfccb5daacba0eb46708db4846b4a298 | C++ | 3,836 | 100 | /*
#################################################################################
#
# 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... |
4b3e0bd3187970a6e4c1d2b5280be1fd320f3f715e7289bc1a2a8d61e6134f81 | C++ | 3,840 | 93 | /* 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... |
64bfd873daee7e992133be7dba05971003a5ef407bc6a10c5c5644df6f850efe | C++ | 3,840 | 128 | /* 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... |
066d152a09de698704af5ad2b38b1e88f2357869b79ee9a331386104bedbbd85 | C++ | 3,846 | 128 | /*
#################################################################################
#
# 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... |
995f4971c5875174aa5da3edc76390e6bc3a16bd26d8cc132899485410104d22 | C++ | 3,849 | 124 | /* 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... |
b300b977a8605e4bd7b8b64a495bb98c3010f310f0d070d31a43c145089b58da | C++ | 3,852 | 100 | /*
#################################################################################
#
# 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 ... |
5ccc0813d45d5f18ff2952c14c5fca6008b201e288d611d19baa6ccc887200fa | C++ | 3,862 | 128 | /*
#################################################################################
#
# 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 ... |
233f75d978eb5e33e1c19c6c285954f52621e83d3f2d79fd65c9c4eff67d0bdd | C++ | 3,871 | 101 | #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 "model/complexreac.hpp"
#include "mpi/dist/tetopsplit/definition/fwd.hpp"
#include "util/vocabulary.hpp"
namespace steps::dist::kproc {
... |
26bbdeff79c426cb312feeff8a336685cf15cbaa3eb02df071bea368a720ef7b | C++ | 3,872 | 209 | // [[Rcpp::depends(RcppArmadillo)]]
#define ARMA_64BIT_WORD 1
#include <RcppArmadillo.h>
#include <Rcpp.h>
using namespace Rcpp;
// declare K
double K(double x, arma::vec egvalues);
// declare K1 (first derivative)
double K1(double x, arma::vec egvalues, double q);
// declare K2 (second derivative)
double K2(double ... |
7edb554230aa466149a902f34d19d42e6809e5035eee783408d668b22b14967d | C++ | 3,878 | 127 | /*
#################################################################################
#
# 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... |
d6442cccb9c124083cb18d603be56184fa2914b9e665cdebdff4c02b106db1a7 | C++ | 3,879 | 158 | /*
* 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... |
46e220508b7f07fbc448b2fec851b5941a20b8a1b5ee5b933b7b7995355d9b95 | C++ | 3,884 | 133 | /*
#################################################################################
#
# 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... |
f8f065972d3b51af99d937c3374ac1709d02933ab80f33d84dd3f3fe34303777 | C++ | 3,894 | 127 | /*
#################################################################################
#
# 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 ... |
b35d8d7f9ca3afc576793787678d7c19c5aaddfff763447c76c23f9227ad9059 | C++ | 3,897 | 110 | #include "Node.h"
#include <cassert>
#include "Beamline.h"
namespace rayx {
namespace {
std::string getNodeTypeString(const BeamlineNode* node) {
if (node->isSource()) return "Source";
if (node->isElement()) return "Element";
if (node->isGroup()) return "Group";
RAYX_EXIT << "error: unimpemented Bea... |
5b5ebe8e6242e1d4af56a400882670547385e06362b796abf9f1dd299c21af43 | C++ | 3,900 | 133 | /*
#################################################################################
#
# 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 ... |
142cbd20f4aa020dca960b0a32748a22f344e097182613f2571655a65696d2a4 | C++ | 3,923 | 122 | /* 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... |
da0309d8a7098b2345eec7a3acdbed320a2dd62dd5a4a00cc818ee28f84ba709 | C++ | 3,923 | 105 | /*
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... |
e536e4a11465812b588fc53679499cdde1b8ba8615bba0618838c2e817be4304 | C++ | 3,945 | 91 | /* 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... |
3a640df528ddd87e808e085c6798b8ed205f5793fd5bd792300ad4f01e8128eb | C++ | 3,962 | 133 | /*
* 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... |
0d56ecccccf7e1cae2c8bfacd2dbcd447661c413e65b448fdc1817821cc95053 | C++ | 3,963 | 118 | /* 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... |
17f92441efad045dbb39222135a081171204495e5e71679467d523c7d427de97 | C++ | 3,981 | 135 | // ***************************************************************************
// BamHeader_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 18 November 2012 (DB)
// -------------------------... |
45a4a639e8683da0cb8b0cae13f1b671e658689270cb974a71ad3e8bd35cb2b4 | C++ | 3,986 | 134 | /*
#################################################################################
#
# 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... |
a4f06c941257d1a57138b00c72193a18112dd341f1f07f915843365609d8b2aa | C++ | 3,995 | 117 | /*
#################################################################################
#
# 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... |
ae93c3ce3ab5f2fb962dcf10a9d9ce713bfaf4971f40e3877f3e138c7a6b15ef | C++ | 3,999 | 165 | /*
* 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... |
bc4ac5b38830a726ead4d9b40a32733bbaa7fbdc0578fc0d441a0e0168089ccb | C++ | 4,002 | 134 | /*
#################################################################################
#
# 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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