sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
6071b51e8a73699cb4f2a83774b83683c5babdd2a28da2922e64542a0ed5bdc5 | C | 22,228 | 691 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
b4788a25192fcaf9ede37c3f14566bd219bf4bde1af196541b06f4d444359dc3 | C | 22,257 | 632 | #include "li_rudy_2011.h"
// TODO: Move this to a function and remember that each cell must have this variables ...
// Do the same for the GPU code ...
//real ical, camkactive;
//real qtr1,qtr2;
//real qrel1, qrel2, qup2;
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_... |
61720e130c83614cba0e4cc70849c96a68afe377c003cdd012a110fc1ad62b39 | C | 22,488 | 699 | //========================================================================
// GLFW 3.4 GLX - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'a... |
2990b6920ad1c5047a3f9345f7cc24f938d7e17cda4a913c488533eacb9c1680 | C | 22,541 | 803 | #include <stdlib.h>
#include <assert.h>
#if defined(WIN32) || defined(_WIN32)
#include <io.h> // for open(2)
#else
#include <unistd.h>
#endif
#include <fcntl.h>
#include <stdio.h>
#define __STDC_FORMAT_MACROS
#include <inttypes.h>
#define __STDC_LIMIT_MACROS
#include "kthread.h"
#include "bseq.h"
#include "minimap.h"
#... |
4e1a4fd50e96fbf29792928a90bf35adf14e95d07fb5e03e7516c82dd7a22cf1 | C | 22,613 | 897 | #include <stdio.h>
#include "mixed_tentusscher_myo_epi_2004.h"
GET_CELL_MODEL_DATA(init_cell_model_data)
{
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu)
{
log_... |
1359e8b0960e46000d39ba662c849e07e56d20d95e1c824a4e91971162108332 | C | 22,778 | 681 | #include "trovato_2019.h"
#include <stdlib.h>
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
log_info("Using Trova... |
3a3f627b303a5503e45bfa3fd88eaa9d84017b27fbb8d6b2794572fad2eca04f | C | 22,864 | 679 | // Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// physical constants
real R=8314.0;
real T=310.0;
real F=96485.0;
// cell geometry
real L=0.01;
real rad=0.0011;
re... |
78a7b9ff9aeab2181281185f93accea5117e9b58f4a7b55a48587e44fbd8e123 | C | 22,886 | 476 | //
// Created by sachetto on 21/08/2020.
//
struct gpu_persistent_data {
int *d_col, *d_row;
float *d_val, *d_x;
float *d_r, *d_p, *d_Ax, *d_rw, *d_v, *d_t;
int N, nz;
/* Get handle to the CUBLAS context */
cublasHandle_t cublasHandle;
cublasStatus_t cublasStatus;
/* Get handle to th... |
d4a046a7a4e18479aec6dcac50b89df6974d499a5bbba346dd0190678363dfef | C | 22,982 | 942 | //========================================================================
// GLFW 3.4 X11 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2017 Camilla Löwy <[email protected]>
//
// This software is provided 'a... |
220f235d8aeae4f5c324d28262522e89a139d8dad7cb5f73182f6d772dc4b19d | C | 23,012 | 707 | /*
Copyright (C) 2017-2021 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without ... |
51914776cbecb28565624e09edc9618e0c619ff79dcde9fb645f2661ede095ec | C | 23,037 | 699 | // Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Current multipliers
//real INa_Multiplier = 1;
//real ICaL_Multiplier = 1;
//real Ito_Multiplier = 1;
//real INaL... |
086bce58b3ac8931d83466f9a0910a230149cd1b0107958cdfdfa4489f71a5a5 | C | 23,265 | 353 | #include <stdlib.h>
#include "bondarenko_2004.h"
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
uint32_t num_cells = solver->original_num_cells;
solver->sv = MALLOC_ARRAY_OF_TYPE(real, NEQ*num_cells);
if(solver->adaptive) {
solver->ode_dt = (real*)malloc(num_cells*sizeof(rea... |
0a36f84932b1fa0f631d6f444c377d363f42de850260dc67c99a30348c9347c1 | C | 23,271 | 633 | #include "gui_draw.h"
#include "gui.h"
#include <float.h>
void set_camera_params(Camera3D *camera, bool set_mode) {
camera->position = (Vector3){0.1f, 0.1f, 12.0f};
camera->target = (Vector3){0.f, 0.f, 0.f};
camera->up = (Vector3){0.0f, 1.0f, 0.0f};
camera->fovy = 45.0f;
if(set_mode) {
cam... |
349c1f51dcdad4736d9025437ca9ef9c3383c8261475800ff3f346aead7874ed | C | 23,334 | 710 | // Avoid NaN errors
if (v >= 100.0) v = 100.0;
if (v <= -100.0) v = -100.0;
// Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Current multipliers
//real INa_Multip... |
7e00e226bf789fc122c5c9bc09797775d983bea03a105fde6f7a967fc4d9ea41 | C | 23,366 | 682 | #include "ToRORd_Land_mixed_endo_mid_epi.h"
#include <stdlib.h>
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
log... |
05d2f94a2520d7bee1bcc66053efdd89fe31bceda7ac5923da52826b65e3096f | C | 23,386 | 636 | //========================================================================
// GLFW 3.4 Win32 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided ... |
1252f5a3fb9d90592a371d04897f55a3fa7456c19b5539ec56f556875f2eb0e4 | C | 23,433 | 834 | /*
Copyright (c) 2013-2020 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this lis... |
ff5eb04af18dd676fbb3a04b93918c9100ac31c2400b2d9d9b189586e23d82b1 | C | 23,700 | 689 | /* File: coremodule.c
* This file is auto-generated with f2py (version:2).
* f2py is a Fortran to Python Interface Generator (FPIG), Second Edition,
* written by Pearu Peterson <[email protected]>.
* Generation date: Fri Apr 23 04:18:04 2021
* Do not edit this file directly unless you know what you are doing!!!
*... |
85fab14afc2f66c8d95d2e1f83508ecce7eab11969f675e06784fd2460cb64c7 | C | 24,044 | 692 | #include <stdarg.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <stdio.h>
#include "kalloc.h"
#include "mmpriv.h"
static char mm_rg_id[256];
static inline void str_enlarge(kstring_t *s, int l)
{
if (s->l + l + 1 > s->m) {
s->m = s->l + l + 1;
kroundup32(s->m);
s->s = (char*)realloc(s->... |
fd015c14ba650df9dad90f74829013fad81b43a63099b6c7e2b53efe37f90b22 | C | 24,133 | 735 | // Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// physical constants
real R=8314.0;
real T=310.0;
real F=96485.0;
// cell geometry
real L=0.01;
real rad=0.0011;
re... |
8a54c234a938ae0b2b9acfe48a56e6288597a52a6873231a540298a1ff054652 | C | 24,306 | 755 | // Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Current multipliers
//real INa_Multiplier = 1;
//real ICaL_Multiplier = 1;
//real Ito_Multiplier = 1;
//real INaL... |
cd45931c59fcbaaa78f52b5a3451aa87ca7a0b9fe7d005dd756130977b883333 | C | 24,354 | 629 | //
// EIF_normalization_default.c
// Exponential Integrate-and-Fire Network Simulation for normalization and selective spatial attention
//
// Created by Deying Song on 2022/6/29.
// Revised for improved robustness and clarity
//
/*
* MATLAB Usage Instructions:
*
* To compile this MEX file:
* >> mex -DDEBUG=0... |
7c5e0daf5c03bc7e25afc2e962694a021add3c3ebcf388d9687560a5633d798b | C | 24,421 | 644 | /* The sor06.C main program */
// $Id: sor06.C,v 1.13 2010-10-20 15:38:28 mette Exp $
#include "sor06.h"
#include "tools.h"
#include "arteries.h"
#include "junction.h"
extern "C" void impedance_init_driver_(int *tmstps);
#include <cstdio>
#include <cstdlib>
#include <cmath>
#include <ctime>
#include <cstring>
usi... |
d02a894c92975bd9a93170d0e41ce56af50a9eed89036ca6fc681f8089322b66 | C | 24,603 | 766 | // Avoid NaN errors
if (v >= 100.0) v = 100.0;
if (v <= -100.0) v = -100.0;
// Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Current multipliers
//real INa_Multip... |
569a81fd9665baf3cfc0661286c40ff166feee826545ddf3c30596c74eb3b0cc | C | 24,635 | 897 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mech_api.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if ... |
0daba89af25b4ffb536156d399e2c99fa7035b34884f4b60bc21997ee53d2617 | C | 24,822 | 692 | /*****************************************************************
Copyright (C) 2001-2012 Leo Breiman, Adele Cutler and Merck & Co., Inc.
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 R_Free Software Foundation; either ver... |
18065003687ebd64371d73aec5f276853514d7ba161f3987043296f086cbb293 | C | 24,956 | 758 | /*
* Copyright (c) 2017-2023 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
cc7927ca65c2b662861955172515e3601d2630d82f8fe179ba730ecb4d089920 | C | 25,058 | 897 | /* Created by Language version: 7.7.0 */
/* VECTORIZED */
#define NRN_VECTORIZED 1
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "mech_api.h"
#undef PI
#define nil 0
#include "md1redef.h"
#include "section.h"
#include "nrniv_mf.h"
#include "md2redef.h"
#if METHOD3
extern int _method3;
#endif
#if ... |
2cfdefb01a02ae0249982ce0f9a6a6dbbffa992e83a7e5bb31989f8f1b073479 | C | 25,107 | 844 | /*
* Copyright (c) 2014-2022 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
423d0007f82fa31ebd6c049b215d24ab695f9b52a3a56d3b2b3064be9a6423f5 | C | 25,190 | 655 |
/******************************************************************************
*
* This file is part of meryl, a genomic k-kmer counter with nice features.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* 'Celera Assembler' r4587 (http://... |
88f8ccb8211cb2684ce1acb873fafe7ca5ca865fed991e8decc772f6db0d4a9f | C | 25,469 | 756 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2016 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is... |
941b21f41660866204c5e801e36567c24808029644835dd566f6bc8aefbb0db2 | C | 25,644 | 526 | #include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <errno.h>
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "ketopt.h"
#ifdef __linux__
#include <sys/resource.h>
#include <sys/time.h>
void liftrlimit()
{
struct rlimit r;
getrlimit(RLIMIT_AS, &r);
r.rlim_cur = r.rlim_max;
setrl... |
4082a821bd8e164a000f0c8d2fe15fd6ac059b6a4c7636bf8c32ee196531c64b | C | 26,051 | 763 | #include "lbfgsb.h"
static integer c__1 = 1;
int lnsrlb(integer *n, double *l, double *u,
integer *nbd, double *x, double *f, double *fold,
double *gd, double *gdold, double *g, double *d__,
double *r__, double *t, double *z__, double *stp,
double *dnorm, double *dtd, double *xstep, double *
stpmx, integer ... |
5d3a51e88d70d348ce9b466cf0c37c51b7be875df84d9a253871576c9b43eaa5 | C | 26,122 | 705 | /* vi: set sw=4 ts=4: */
/* Small bzip2 deflate implementation, by Rob Landley ([email protected]).
Based on bzip2 decompression code by Julian R Seward ([email protected]),
which also acknowledges contributions by Mike Burrows, David Wheeler,
Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
Robert Sedgewi... |
7aa19be2a403f4b0bd5499472f121c3852056731e3c089419c5e0fd8f837ce7c | C | 26,338 | 753 | //========================================================================
// GLFW 3.4 Win32 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided ... |
73c2b0acc91fed94e44887d8bd29b07c713709df622fb249c3939c4add6be7dc | C | 26,524 | 983 | /* elf.c -- Get debug data from an ELF file for backtraces.
Copyright (C) 2012-2016 Free Software Foundation, Inc.
Written by Ian Lance Taylor, Google.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
(1) Redistrib... |
af3156d069ab731a857eda5efd29cb89745541b551bb43c94b886fd3990f6c0d | C | 26,716 | 874 | /* ----------
* pg_lzcompress.c -
*
* This is an implementation of LZ compression for PostgreSQL.
* It uses a simple history table and generates 2-3 byte tags
* capable of backward copy information for 3-273 bytes with
* a max offset of 4095.
*
* Entry routines:
*
* int32
* pglz_compress(const char ... |
396d61ee30ea738a4b97e06d45894e73d42eae02f64576dcc88efe754b903096 | C | 26,749 | 757 | #include "ToRORd_dynCl_mixed_endo_mid_epi.h"
#include <stdlib.h>
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
lo... |
5cedab589ea0b10477be84f80f843b6df1db6f3a61879fc4f084d4f68680e7a6 | C | 26,916 | 832 | /*
Copyright (c) 2015, 2018-2020, 2022-2023 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright... |
5d501e870260cfe0ff3426837abab0ff6c26f4cea3f76f0c629d9a6496c5caeb | C | 26,947 | 798 | //========================================================================
// GLFW 3.4 WGL - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'a... |
bb06c7f13c13888d4033182e93955f6c31b31594de5b7f0fadb93e32bdb0b17d | C | 27,141 | 846 | //========================================================================
// GLFW 3.4 EGL - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'a... |
428eca03df80e00ddec9f1265a4784120ea2344a6b49eb1b25e21c215d6d68c0 | C | 27,638 | 791 | #include "ToRORd_fkatp_mixed_endo_mid_epi.h"
#include <stdlib.h>
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
lo... |
3035722ffe76d796f4041774170a5bb21894047fa11965dddc48696ed15a6114 | C | 27,699 | 830 | // Avoid NaN errors
//if (v >= 100.0) v = 100.0;
//if (v <= -100.0) v = -100.0;
//real aux, aux2, aux3;
// Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Additiona... |
51da3481295ab1eddbc0f0962dc677cf27c0ddccde397906c0b86557838fa422 | C | 27,956 | 721 | //
// Created by sachetto on 13/10/17.
//
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
#include "../alg/grid/grid.h"
#include "../config/restore_state_config.h"
#include "../save_mesh_library/save_mesh_helper.h"
#include "../3dparty/stb_ds.h"
#ifdef COMPILE_CUDA
#include "../gpu_utils/gpu_utils.h"
... |
7cae89d10b30b38cb32b70a18c7c29e1e2aa3620fb522ae701a6f5f87d0a452d | C | 28,126 | 1,051 | /*
* bw_mem64.c - simple memory write bandwidth benchmark
*
* Usage: bw_mem64 [-P <parallelism>] [-W <warmup>] [-N <repetitions>] size what
* what: rd wr rdwr cp fwr frd fcp bzero bcopy
*
* Copyright (c) 1994-1996 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may p... |
8a6abd48412e7ecd4e573a2820f4d3c8f242dbebe19d06f44a13616750227a57 | C | 28,386 | 921 | /* hts_expr.c -- filter expression parsing and processing.
Copyright (C) 2020-2022 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the ... |
10a57972982af211cc7c84c2f6973412820fd7e3cc7d168df18b3fd493d025c5 | C | 28,748 | 782 | #include "trovato_2020.h"
#include <stdlib.h>
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
log_info("Using Trova... |
2153208f4f4f48ffc24ed52149094f43e68fc0df659665d9fdb55b8931b3222a | C | 28,752 | 1,113 | /* ==============================================================================
Binaries and/or source for the following packages or projects are presented under one or more of the following open
source licenses:
cJSON.c The OpenLane Dataset Authors Apache License, Version 2.0
See:
https://githu... |
62d0d56693ac52e17482323d88cc7d90581a5c4442fb6e6d672e571c9545c0e6 | C | 28,795 | 1,007 | /* faidx.c -- FASTA and FASTQ random access.
Copyright (C) 2008, 2009, 2013-2020, 2022 Genome Research Ltd.
Portions copyright (C) 2011 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documen... |
6d5bbcd80995d18b1b06c8f5efd2554eb8edb441b1fe221306db9b9c553e0e71 | C | 28,966 | 886 | // Avoid NaN errors
//if (v >= 100.0) v = 100.0;
//if (v <= -100.0) v = -100.0;
//real aux, aux2, aux3;
// Changeable parameters
real nao = 140.0;
real cao = 1.8;
real ko = 5.0;
// Localization of ICaL and NCX: the fraction in junctional subspace
real ICaL_fractionSS = 0.8;
real INaCa_fractionSS = 0.35;
// Additiona... |
ca67aa465bd14e1a0ff691760c3ce92ffa359c673feb4b7fb30515dc39247ebe | C | 29,241 | 1,029 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <assert.h>
#include <ctype.h>
#include <limits.h>
#ifdef HAVE_MALLOC_H
#include <malloc.h>
#endif
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#inc... |
240645a2b0a48eaaed47234d473ca2867b36d202c9c8b2aa09e859fa648cb510 | C | 29,261 | 566 | //
// Created by sachetto on 21/08/2020.
//
struct gpu_persistent_data {
int *d_col, *d_row;
float *d_val, *d_x;
float *d_r, *d_p, *d_Ax, *d_rw, *d_v, *d_t, *d_omega;
int N, nz;
/* Get handle to the CUBLAS context */
cublasHandle_t cublasHandle;
/* Get handle to the CUSPARSE context */
... |
e86014fdb4c8443f0c73ab1e81f8d71e25b94878de5ecbc436865c315362b6e5 | C | 29,440 | 736 | #include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <errno.h>
#include "kthread.h"
#include "kvec.h"
#include "kalloc.h"
#include "sdust.h"
#include "mmpriv.h"
#include "bseq.h"
#include "khash.h"
mm_tbuf_t *mm_tbuf_init(void)
{
mm_tbuf_t *b;
b = (mm_tbuf_t*)calloc(1, sizeof(mm_tbuf_t));
if (!(mm_d... |
d14827a38e2f3538c874f666d47c96bbaecaa2269c5d4437f9680b02d8dce7d5 | C | 29,797 | 683 | //
// Created by sachetto on 04/10/17.
//
#include "../3dparty/stb_ds.h"
#include "../config/linear_system_solver_config.h"
#include "../config_helpers/config_helpers.h"
#include "../libraries_common/common_data_structures.h"
#include "../logger/logger.h"
//TODO: remove these global variables
bool jacobi_initialized =... |
af17606b83bbb3dae3c77eaa4ea6d44df1c40d0aa6b261c502e0a11108f75577 | C | 29,811 | 917 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
a2a836206ff3707f419f6d23fd376dd56310ff2a0d7a3c1d5044d024ebc5bb31 | C | 29,817 | 922 | /***************************************************************************/
/* */
/* Program: arteries.C */
/* Version: 2.0 */
/* By: ... |
c0f4ee4480867a9ab6760a2cadfaa5926b9d089767795552a1365c15b6680fa2 | C | 30,022 | 880 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
b4b00a78a75bbaaf54192e15c29a3b40dced8d2103dd928fcff81e2cd976f7e7 | C | 30,056 | 527 | #include "build.h"
void currentPMCA() {
I_PMCA_blk = f_PMCA_blk * Amp_PMCA * pow(Ca_2_blk[indx], 1.6) / (pow(K_m, 1.6) + pow(Ca_2_blk[indx], 1.6));
I_PMCA_iz = f_PMCA_iz * Amp_PMCA * pow(Ca_2_iz[indx], 1.6) / (pow(K_m, 1.6) + pow(Ca_2_iz[indx], 1.6));
I_PMCA = I_PMCA_iz + I_PMCA_blk;
}
void currentNCX() {
f_Caina_... |
ec37b45e8cc4c92bfd48b647c69377322a5aa19952caaed6733d52ca9170ca6f | C | 30,174 | 1,074 | #include <stdlib.h>
#include <assert.h>
#if defined(WIN32) || defined(_WIN32)
#include <io.h> // for open(2)
#else
#include <unistd.h>
#endif
#include <fcntl.h>
#include <stdio.h>
#define __STDC_LIMIT_MACROS
#include "kthread.h"
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
#include "kvec... |
a549454bc88f30ef51880a6b911189d00811c23a05fa4a0c45947b3d7e16e9df | C | 30,216 | 558 | #include "build.h"
void currentPMCA() {
I_PMCA_blk = f_PMCA_blk * Amp_PMCA * pow(Ca_2_blk[ii], 1.6) / (pow(K_m, 1.6) + pow(Ca_2_blk[ii], 1.6));
I_PMCA_iz = f_PMCA_iz * Amp_PMCA * pow(Ca_2_iz[ii], 1.6) / (pow(K_m, 1.6) + pow(Ca_2_iz[ii], 1.6));
I_PMCA = I_PMCA_iz + I_PMCA_blk;
}
void currentNCX() {
f_Caina_blk = Ca... |
2e07f4403e4ec18f1810e298c46471d5cabf7de7c87fc780780e5d343326e768 | C | 30,283 | 991 | /* THIS FILE IS AUTOMATICALLY GENERATED, DO NOT EDIT! */
/* Copyright (c) 2013-2014 Yoran Heling
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without lim... |
85793016ef95b6b51da2e4f5be873d70a5a5fb0663ce06d1242bc01e418131a8 | C | 30,331 | 895 | // GetMD5.c
// GetMD5 - 128 bit MD5 checksum: file, string, array, byte stream
// This function calculates a 128 bit checksum for arrays or files.
// Digest = GetMD5(Data, Mode, Format)
// INPUT:
// Data: File name or array.
// Mode: String to declare the type of the 1st input. Not case-sensitive.
// ... |
a92142465144cf6df8ca804ec2223b2b30a1b94c6fa982e02af76511cf78b846 | C | 30,673 | 1,028 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
778b2079250f51136c6f432d7429d084622297af55472a07e32a6e57b837e1fa | C | 30,709 | 755 | #include "gui_mesh_helpers.h"
#include "gui.h"
#include "gui_colors.h"
#include "raylib_ext.h"
#include <float.h>
struct mesh_info *new_mesh_info() {
struct mesh_info *mesh_info = (struct mesh_info *)calloc(1, sizeof(struct mesh_info));
return mesh_info;
}
#define SET_MAX(coord) ... |
5f06125807e32332650dc4391e248f02ff7dfafc8514d00fa99133a5f30e9e3c | C | 31,145 | 564 | #include "build.h"
void currentCaL() {
alpha_plus = 1 / (3.734 * exp(-Vm[ii] / 8.5) + 0.35 * exp(-Vm[ii] / 3500));
alpha_minus = 1 / (4.65 * exp(Vm[ii] / 15) + 1.363 * exp(Vm[ii] / 100));
epsilon_plus_iz = (Ca_2_iz[ii] * alpha_plus) / (T_L * K_L);
epsilon_plus_blk = (Ca_2_blk[ii] * alpha_plus) / (T_L * K_L);
Ca_... |
01f5ef248e841c51fcd04b63f4e3c539a1c6bb73d87436059bc6cad020728f8d | C | 32,270 | 565 | // this code for current is slightly different and corrected one.
// copy of the code 'currents_1d.c'
// in laptop code "asakura_modified/" contains version of this code
#include "build.h"
void currentCaL() {
alpha_plus = 1 / (3.734 * exp(-Vm[indx] / 8.5) + 0.35 * exp(-Vm[indx] / 3500));
alpha_minus = 1 / (4.65 * ... |
56fc5f801e9f861c963e1be63087b508a8eba5c61f867812884743fcf8b2c5cb | C | 32,488 | 1,084 | //
// Created by sachetto on 19/10/17.
//
#include "domain_helpers.h"
#include "../config_helpers/config_helpers.h"
#include "../libraries_common/common_data_structures.h"
#include "../logger/logger.h"
#include "../utils/stop_watch.h"
#include "../utils/utils.h"
#include "mesh_info_data.h"
#include <float.h>
#include... |
7f330bfe8978943cc819b0ae36241f7305553beba71d3fd489e18c260dfd40d5 | C | 33,125 | 996 | /*
COPYRIGHT
Copyright (C) 2015 Kyle Briggs (kbrig035<at>uottawa.ca)
This file is part of CUSUM.
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, ... |
3b5890bfb71b8aa283c4e9fd712440d6393ee52430965285ae323327b93ce01b | C | 33,127 | 998 | /*
COPYRIGHT
Copyright (C) 2015 Kyle Briggs (kbrig035<at>uottawa.ca)
This file is part of CUSUM.
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, ... |
72434e2ed5a7388b4590c436a512e76dc87634a8d571f746be27ec474da118cf | C | 33,568 | 1,114 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
// Copyright (c) 2012 Torsten Walluhn ... |
aebf113e414fa66a42724af0107202cddb680127702bcb8c7de1a610eb3970da | C | 33,867 | 975 |
/******************************************************************************
*
* This file is part of meryl-utility, a collection of miscellaneous code
* used by Meryl, Canu and others.
*
* This software is based on:
* 'Canu' v2.0 (https://github.com/marbl/canu)
* which is based on:
* ... |
4d36d3b5461ae3ed400b82477b550c0c36b7ebe988e4cb79377fca5a72d31d49 | C | 33,886 | 920 | #include <assert.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc_ambi)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
sc_ambi = sc_ambi > 0? -sc_ambi : sc_ambi... |
22a8ed759009ba022a8f0c07a991662785be0792cb9e05499db53b32d56ecab6 | C | 33,939 | 1,272 | /* lj92.c */
/* This file is a modified version of
https://bitbucket.org/baldand/mlrawviewer/src/master/liblj92/lj92.c
(c) Andrew Baldwin 2014
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software wi... |
2db2c9ef028571d7e7fef6f524e501f88c0038ecda9e944767b0379f438a14d2 | C | 33,952 | 1,052 | /*
File autogenerated by gengetopt version 2.22.6
generated with the following command:
gengetopt --input=q6q6.ggo --include-getopt --long-help --show-required --unamed-opts --file-name=q6q6_cmdline
The developers of gengetopt consider the fixed text that goes in all
gengetopt output files to be in the publ... |
ebe858ac0dc3dd1e38721077b394d58aa69b107ba6e7988b4ed12e68fd283587 | C | 34,268 | 970 | //
// Created by sachetto on 15/03/22.
//
#include "ecg.h"
#include "../3dparty/stb_ds.h"
#include "../config/ecg_config.h"
#include "../utils/file_utils.h"
#include "../utils/utils.h"
#include <float.h>
#ifdef COMPILE_CUDA
#include "../gpu_utils/gpu_utils.h"
// Precision to be used for the calculations on the GPU
... |
d823e0fce3523cc8a1173841cc761af07888fad0752806b0a25ae3214aeb9134 | C | 34,365 | 1,175 | /*
* The copyright in this software is being made available under the 2-clauses
* BSD License, included below. This software may be subject to other third
* party and contributor rights, including patent rights, and no such rights
* are granted under this license.
*
* Copyright (c) 2002-2014, Universite catholiqu... |
f1e14aa4add4ae8008a59a0418696ae8c93118ef509ca692cc6d0a95c305b0c9 | C | 34,468 | 1,274 | /* pixarlog.c */
/* SPDX-License-Identifier: HPND-sell-variant */
/* Adapted from libtiff's tif_pixarlog.c by Christoph Gohlke */
/*
* Original copyright and license from libtiff v4.7.1 tif_pixarlog.c:
*
* Copyright (c) 1996-1997 Sam Leffler
* Copyright (c) 1996 Pixar
*
* Permission to use, copy, modify, distr... |
9e57e57ce6d99dff62f97550fa5e803bf632c174311c00b7e4650d6524dfff00 | C | 34,906 | 854 | /* vcfutils.c -- allele-related utility functions.
Copyright (C) 2012-2018, 2020-2022 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the... |
4ec8921b299e15e3f62ca47c70ee13d03c181dc1b180a6854213364075bc5705 | C | 35,735 | 1,182 | /*
* Copyright (c) 2019-2022 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
740fc7ab6694040b63136b616d6a69ca33f76025aac4d7074885ce5eb0d8c37a | C | 35,846 | 1,058 | #include <stdio.h>
#include <math.h>
double R = 8.3143;
double T = 310;
double F = 96.4867;
double Vm = -91.4466885079348;
double dCaMCadt;
double k_on_CaM = 34;
double Ca_2_blk;
double B_tot_CaM = 0.024;
double CaMCa = 0.000228581865602447;
double k_off_CaM = 0.238;
double dTnChCadt;
double k_on_TnCh = ... |
5143a9e9eb392eac3e70f879266f3393a7c47ec73daec69c5ceeb4c667f0826f | C | 35,849 | 1,058 | #include <stdio.h>
#include <math.h>
double R = 8.3143;
double T = 310;
double F = 96.4867;
double Vm = -91.4466885079348;
double dCaMCadt;
double k_on_CaM = 34;
double Ca_2_blk;
double B_tot_CaM = 0.024;
double CaMCa = 0.000228581865602447;
double k_off_CaM = 0.238;
double dTnChCadt;
double k_on_TnCh = ... |
6a8472d1dd2fce00bac0938039811a747e6313164ab5348c51e38ee475e2ae90 | C | 36,256 | 1,109 | #define FORTRANOBJECT_C
#include "fortranobject.h"
#ifdef __cplusplus
extern "C" {
#endif
#include <stdlib.h>
#include <string.h>
/*
This file implements: FortranObject, array_from_pyobj, copy_ND_array
Author: Pearu Peterson <[email protected]>
$Revision: 1.52 $
$Date: 2005/07/11 07:44:20 $
*/
int
F2PyDict... |
568aef8e0de0506df89194a74ab891f48f65bfd462670a388d47ea9248b3228a | C | 36,647 | 316 | const real mScaleFactorGks=1.0;
const real mScaleFactorIto=1.0;
const real mScaleFactorGkr=1.0;
const real mScaleFactorGna=1.0;
const real mScaleFactorAch=1e-24;
const real mScaleFactorGNaK=1.0;
const real mScaleFactorGNaCa=1.0;
const real mScaleFactorGCaL=1.0;
const real mScaleFactorGKur=1.0;
const real mScaleFactorGK... |
8455b78727293314d6f99fb57b23dd8693ee7b18ba9e01a90d191a680b186aae | C | 37,298 | 593 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <glad/vulkan.h>
#ifndef GLAD_IMPL_UTIL_C_
#define GLAD_IMPL_UTIL_C_
#ifdef _MSC_VER
#define GLAD_IMPL_UTIL_SSCANF sscanf_s
#else
#define GLAD_IMPL_UTIL_SSCANF sscanf
#endif
#endif /* GLAD_IMPL_UTIL_C_ */
int GLAD_VK_VERSION_1_0 = 0;
int GLAD_VK_VE... |
a5e0af63edf4452b23162acfc73ecdff986e84ef1ad27298ca4d9f76cf254f6c | C | 37,431 | 1,064 | #include "lbfgsb.h"
static integer c__1 = 1;
/*
L-BFGS-B is released under the "New BSD License" (aka "Modified BSD License"
or "3-clause license")
Please read attached file License.txt
=========== L-BFGS-B (version 3.0. April 25, 2011 ===================
This is a modified version of L-BFGS-B. Minor... |
b0f3717efe054fdf5f114b6f27052634b72e57358004749ee1b953c87608cb42 | C | 37,756 | 1,105 | //
// Created by sachetto on 29/09/17.
//
#include <assert.h>
#include <inttypes.h>
#include "grid.h"
#include "../../3dparty/stb_ds.h"
#include "../../utils/file_utils.h"
#include "../../utils/utils.h"
struct grid *new_grid() {
struct grid *result = MALLOC_ONE_TYPE(struct grid);
result->first_cell = NULL;
... |
620abac683a08b4f9edebc4af56bf8de0b76948ff62c6c2b550efcf08d27d4f1 | C | 38,235 | 749 | #include "save_mesh_helper.h"
#include "../domains_library/mesh_info_data.h"
static void write_pvd_header(FILE *pvd_file) {
fprintf(pvd_file, "<VTKFile type=\"Collection\" version=\"0.1\" compressor=\"vtkZLibDataCompressor\">\n");
fprintf(pvd_file, "\t<Collection>\n");
fprintf(pvd_file, "\t</Collection>\n"... |
cdc8912a1dc84423e31771aacdd3b84e7ee7a34f6e54ad03fc80f2eb89655444 | C | 38,526 | 1,406 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is... |
78ed4e947d8768dd6836f72ed146dc6773e5500fffd1e7b0d9f502cab62ad205 | C | 38,565 | 1,611 | /* surface: This program is part of the HOLE suit of programs */
/* Copyright Guy M.P. Coates 1998-1999 */
/* Version 1.0 */
/* This program generates a solid triangular mesh surface of a hole surface
in various formats.
It uses a Step-by-step method of delaunay triangulation to calculate
the polygons:
Program re... |
4460cda67e4bfb461e31ffa5888e0d93dc1c3713616d9563abb7230d98e8ff4c | C | 38,929 | 1,126 | /*
COPYRIGHT
Copyright (C) 2015 Kyle Briggs (kbrig035<at>uottawa.ca)
This file is part of CUSUM.
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, ... |
1d773ebdf7f7a10c47841b2f3a757c148dda4846ace63497500188ef8bd54167 | C | 39,291 | 1,072 | /*
* Copyright (c) 2017-2023 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
052dcfcf1236e091402268382ff4e167e242cc32210aee613a95acf968ece074 | C | 39,755 | 1,405 | /* hfile.c -- buffered low-level input/output streams.
Copyright (C) 2013-2021 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Soft... |
78bc113ddde7ba3d4ed0bb82030a729da6cae4b689f76279d0f770ef4c25df26 | C | 39,895 | 1,408 | /* hfile_s3.c -- Amazon S3 backend for low-level file streams.
Copyright (C) 2015-2017, 2019-2022 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), ... |
5c218e81f38a15ec089d5ba56d905d7f88a6f14d516ecfcc3b565e4ddacaf5c0 | C | 39,973 | 1,079 | /***************************************************************************/
/* */
/* The junction.C main program */
/* Version: 1.0 */
/* Date... |
c6a96fbd038d47e5ce986c676c63de46855f2bdd5f535b403876eb2bcccfc51b | C | 40,196 | 1,293 | /* SDSLib 2.0 -- A C dynamic strings library
*
* Copyright (c) 2006-2015, Salvatore Sanfilippo <antirez at gmail dot com>
* Copyright (c) 2015, Oran Agra
* Copyright (c) 2015, Redis Labs, Inc
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permit... |
9baf9866fa01962aebb837c7e5c8de0d53a8fa76576e4cfaae0af2b7e0eb2d36 | C | 40,540 | 1,907 | /*
* a timing utilities library
*
* Requires 64bit integers to work.
*
* %W% %@%
*
* Copyright (c) 2000 Carl Staelin.
* Copyright (c) 1994-1998 Larry McVoy.
* Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the benchmark is unmodified, and
* (2) the versi... |
5d160a2c91edd2d1b91e36f157d8169aac27e93ed381c3c66e90920d3a061da4 | C | 41,236 | 1,222 | //
// Created by sachetto on 13/10/17.
//
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../alg/grid/grid.h"
#include "../config/assembly_matrix_config.h"
#include "../libraries_common/common_d... |
8abb12d446f372afe11a511bf0fc12da47ed077600543851d4b6ad6282a51389 | C | 42,485 | 1,120 | #include <assert.h>
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
#define MM_MAX_QLEN_FLANK 100
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc_ambi)
{
int i, j;
a = a < 0? -a : a;
b = b > 0? -b : b;
sc_ambi = ... |
c44641ae89b4a8410fd76c479928d884c7b01ab1b1e6af0199cd5896292ce655 | C | 42,520 | 948 | /* Copyright 2003-2018, University Corporation for Atmospheric
* Research. See COPYRIGHT file for copying and redistribution
* conditions.*/
/**
* @file
* @internal This file is part of netcdf-4, a netCDF-like interface
* for HDF5, or a HDF5 backend for netCDF, depending on your point of
* view. This file handles... |
fcdea2c87cad6b1c13b6c31f1155b008b81c50751e8248835f70dd29481f1b01 | C | 43,277 | 1,149 | /*
* Library: lmfit (Levenberg-Marquardt least squares fitting)
*
* File: lmmin_int64.c
*
* Contents: Levenberg-Marquardt minimization.
*
* Copyright: MINPACK authors, The University of Chikago (1980-1999)
* Joachim Wuttke, Forschungszentrum Juelich GmbH (2004-2013)
*
* License: FreeBSD
... |
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