sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
dfaae50051e7892ef1f09b390148641c85c6946c9207a57b2e5574e2fd689424 | C | 15,013 | 468 | #include "Tworld.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_msg("Using Tworld CPU model\n")... |
856366c6d1a7f8dc36144c12e1319e26f654a1a89996a9b5469879b48620a025 | C | 15,052 | 359 | //Drug
real ACh = 0.0;
real IK1_Block = 0.0;
real IKr_Block = 0.0;
real IKs_Block = 0.0;
real IKur_Block = 0.0;
real INa_Block = 0.0;
real INaK_Block = 0.0;
real INCX_Block = 0.0;
real Ito_Block = 0.0;
real ICaL_Block = 0.0;
real IK2P_Block = 0.0;
real IKACH_Block = 0.0;
// POM-specific
real GNa... |
f17c004aaf87ac39282c4d96d5e95461a9869bd1a9fa486549f086e504549ce8 | C | 15,138 | 587 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 2 of the Li... |
09f4715bd7a35f0f958175059463f51ffa193c93cd7abfdf4598b1de2382cc9a | C | 15,139 | 394 |
/******************************************************************************
*
* 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://... |
6c7890ba277c014d0f916ddf639c03160a17de13744b42c061a628cd6df2b073 | C | 15,342 | 474 |
/******************************************************************************
*
* 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://... |
825cf96b8acaa309bb3bdefeac8445f2b581265b9ca13c52800f71177527ea28 | C | 15,559 | 837 | /* [email protected] */
/* copyright (C) 2015 */
#include "antisaccades.h"
#define INTSTEPS 8000
// Log of cosh
double
lcosh(double x)
{
return gsl_sf_lncosh(x);
}
double
wald_pdf(double x, double mu, double lambda)
{
return sqrt(lambda / (2.0 * M_PI * x * x * x)) *
exp(- 0.5 * lambda... |
002d6dbc050357a0637869d3000191d54a60cb6bc26a6f55a3e581be0e1488da | C | 15,595 | 487 | /* chbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
2f4ee9f8c978be4e4323836e158797ac768ab995337c10afd5c6b5c8f5b9df48 | C | 15,632 | 488 | /* zhbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
cf5e2baade0f2261c15575f220b68e3efb0cff508da334c95077685e1f17de22 | C | 15,832 | 433 | /**********************************************************************************************
*
* raylib.utils - Some common utility functions
*
* CONFIGURATION:
*
* #define SUPPORT_TRACELOG
* Show TraceLog() output messages
* NOTE: By default LOG_DEBUG traces not shown
*
*
* LICENSE: zlib/libpng
... |
157c06aa2c40c1684985465bac64f57b2da5c84657d12483bc77ee5a35279fac | C | 15,879 | 485 | #include <string.h>
#include <stdlib.h>
#include <math.h>
#include "mmpriv.h"
#include "kalloc.h"
#include "khash.h"
static inline void mm_cal_fuzzy_len(mm_reg1_t *r, const mm128_t *a)
{
int i;
r->mlen = r->blen = 0;
if (r->cnt <= 0) return;
r->mlen = r->blen = a[r->as].y>>32&0xff;
for (i = r->as + 1; i < r->as +... |
534827867077387391f95b9c72847c58743630113b147fb0e91f95b115f26452 | C | 15,905 | 351 | #include <assert.h>
#include <stdlib.h>
#include "ten_tusscher_2006.h"
GET_CELL_MODEL_DATA(init_cell_model_data) {
assert(cell_model);
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->number_of_ode_equations = NEQ;
}
//TODO: this should be called only once fo... |
56e8433c3e59956f4b287a21a9ed11caf9497bcc2def7f84bc01136480b2c7bc | C | 15,962 | 510 |
/******************************************************************************
*
* 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:
* ... |
39c9810f1fd44b1e2613f6c158ad4e9e4b4b682579d9521bd32510af8450a8ad | C | 16,019 | 488 | /* tbx.c -- tabix API functions.
Copyright (C) 2009, 2010, 2012-2015, 2017-2020, 2022 Genome Research Ltd.
Copyright (C) 2010-2012 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 documentatio... |
b6dbfaaf5c4b6272b60a006c30280900a2d87f5eb95ae811993c36974db384c7 | C | 16,027 | 465 | //
// Created by sachetto on 01/10/17.
//
#include "domain_helpers.h"
#include "../3dparty/stb_ds.h"
#include "../config_helpers/config_helpers.h"
#include "../libraries_common/common_data_structures.h"
#include "../logger/logger.h"
#include "../utils/utils.h"
#include <time.h>
#include <unistd.h>
SET_SPATIAL_DOMAI... |
2de3bd58c711438542b4211d2eb4a97587bd02a8a658b6a2555ef53571b95b5e | C | 16,061 | 440 | // peaks. Copyright (c) 2020. Winfield Chen.
#define _GNU_SOURCE
#include <stdio.h>
#include <stddef.h>
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <errno.h>
#include <alloca.h>
#include <sys/types.h>
#include <sys/wait.h>
#include "maps.h"
#include "hea... |
13cfd7c2a2a824170949fc42003499fb14c70690c93344828bf181d793fb3eec | C | 16,109 | 486 |
/******************************************************************************
*
* 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://... |
e91547ab1af8872766020a495fe049ff6d551598cb552f92241d2888f731d967 | C | 16,118 | 448 | /* The MIT License
Copyright (C) 2003-2006, 2008-2010 by Heng Li <[email protected]>
Copyright (C) 2016-2017, 2020 Genome Research Ltd.
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 Softw... |
8aeacef5da1d52d30b40891d004fd0c8336fc9f135a6031bd79da7073e91570f | C | 16,357 | 537 | //========================================================================
// 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 ... |
b9589d007efa81bec19ccd4c831d66400f786646dd04e8387c76e40f608ea2a1 | C | 16,390 | 600 |
/******************************************************************************
*
* 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:
* ... |
6f96282d4508204a8b5bcf3a8bb7b6054f1b84fc310ff10c9eb99891f88cffc9 | C | 16,414 | 591 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 2 of the Li... |
19a791ecc3ec21222e96ce49d5cb5b52712e257476da0cd9d800f0f6f78b512a | C | 16,552 | 414 | //
// Created by sachetto on 06/06/24.
// Based on https://github.com/SCIInstitute/StructuredEikonal
#include <assert.h>
#include <cuda_runtime.h>
#include "eikonal_solver.h"
#include "../gpu_utils/gpu_utils.h"
#include "../logger/logger.h"
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include "../3dparty/... |
ddd18a008a9d067459f9b795789c23d568366533887547c67c0fba565f58c174 | C | 16,617 | 612 | /* 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 ... |
edbd126427fc709320cf78108fb9a0a2151bfb20934341831de6cefa3a0c181a | C | 16,671 | 165 |
#define IFNUMBER_1(name)if((V_old_==(-4.713000000000000e+01))) { (name) = 3.200000000000000e+00; } else{ (name) = ((3.200000000000000e-01*(V_old_+4.713000000000000e+01))/(1.000000000000000e+00-exp(((-1.000000000000000e-01)*(V_old_+4.713000000000000e+01))))); }
#define IFNUMBER_2(name)if((V_old_<(-4.000000000000... |
099db2fc662cdd82545913e4df80992ca503cce0e2ddfd7a64d138c7627faaad | C | 16,846 | 660 | /*
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, ... |
6dd2ced01c99e463a89310bc973f4203621e4844b545bc5ed2138307f07a3421 | C | 16,898 | 770 | /*
* bw_mem64a.c - simple memory write bandwidth benchmark
*
* Usage: bw_mem64a [-P <parallelism>] [-W <warmup>] [-N <repetitions>] size what
* what: frd fwr rd16 wr16 rd32 wr32 rd64 wr64 frd_sse fwr_sse frd_avx fwr_avx
*
* Copyright (c) 2026 Huang Ying
*
* Distributed under the FSF GPL with additional r... |
c6e92177eadf4a5505675b5d0a76be7ac64535701e5d125dfd4ab88932e44884 | C | 16,906 | 613 | /* 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 ... |
7c1814cc98055c1800a16e1bfa8aa9169df9930a18a7d19e667ce2abd0827297 | C | 16,955 | 492 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_ALTIVEC
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#include "internal_altivec.h"
#define SG_TRACE
#define SG_SUFFIX _striped_altivec_128_... |
a9b0151a5a6980c7fc24e21d2440922a2d24278db1e5a4b8fa0a3a5282cd0fb9 | C | 16,973 | 492 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_ALTIVEC
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#include "internal_altivec.h"
#define SG_TRACE
#define SG_SUFFIX _striped_altivec_128_... |
6407c64d4b6526be806302587123e27c070dde65de17a26993d696bb85b5f33c | C | 17,035 | 497 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#if defined(_MSC_VER)
#include <intrin.h>
#else
#include <emmintrin.h>
#include <smmintrin.h>
#endif
#include "parasail.h"
#include ... |
3f881945344a5bd9715fb41844a3bd355b627729837e40a45c9e633b7350df96 | C | 17,039 | 396 | // Avoid NaN errors
if (V >= 200.0) V = 200.0;
// Constants
real nao = 140;
real cao = 1.8;
real ko = 5.4;
real R = 8314;
real T = 310;
real F = 96485;
real zna = 1;
real zca = 2;
real zk = 1;
real L = 0.0164;
real rad = 0.00175;
real greekpi = 3.14159265;
real KmCaMK = 0.15;
real aCaMK = 0.05;
real bCaMK = 0.00068;
r... |
03c44e0476ed7703d46de78ecb21ca67bcd40ebc3cc617884bb7b2a41254a006 | C | 17,053 | 497 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#if defined(_MSC_VER)
#include <intrin.h>
#else
#include <emmintrin.h>
#include <smmintrin.h>
#endif
#include "parasail.h"
#include ... |
aa73ad5a29a2da45258d1e26c0fe0f1aee41b6f19b491821bcd2431395579bbd | C | 17,085 | 508 | #include <string.h>
#include <stdlib.h>
#include <math.h>
#include "mmpriv.h"
#include "kalloc.h"
#include "khash.h"
static inline void mm_cal_fuzzy_len(mm_reg1_t *r, const mm128_t *a)
{
int i;
r->mlen = r->blen = 0;
if (r->cnt <= 0) return;
r->mlen = r->blen = a[r->as].y>>32&0xff;
for (i = r->as + 1; i < r->as +... |
fb749a98db7db6f69c45f52756a85824be3b8cfd84404c2868366b8527abb8ea | C | 17,147 | 666 | /*
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, ... |
9b9d829ddb14ad2cd85f9bf09a9b5b94728ca967812df9ea9a7b684142806191 | C | 17,164 | 570 | /*
* $Id: jsonread.c 7257 2018-02-12 15:51:12Z guillaume $
* Guillaume Flandin
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "jsmn.h"
#include "mex.h"
/* for MATLAB <= R2008a or GNU Octave */
/*
#if defined(mxSetLogical) || !defined(MATLAB_MEX_FILE)
mxArray *mexCallMATLABWithTrap(int nlhs,... |
9f480a2265346f411e647717072f1a2e2ff13ebea04e2456cf751c599264dba8 | C | 17,166 | 622 |
/******************************************************************************
*
* 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:
* ... |
14dba1709f128eb7ae0c34826c7f8d619a614090f6127e5ff2685b4555fe6f39 | C | 17,180 | 514 | /* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* T... |
f64ca53df736df19642fc320fb5e7bcd1fced9507318f6c91f42a1e7f0aaf99f | C | 17,235 | 502 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#if defined(_MSC_VER)
#include <intrin.h>
#else
#include <emmintrin.h>
#endif
#include "parasail.h"
#include "memory.h"
#include "in... |
176d11dcda70c0674d0f002f777a70660e3aad48e45b244ec5ea0386c9c6caab | C | 17,265 | 668 | /*
Copyright (c) 2005-2006, 2008-2009, 2013, 2015, 2017-2019 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 th... |
02d11b3015a527a10d3c7b64fb7a785a7d2bc47ae5d9810760fd858f6c8b4953 | C | 17,425 | 457 |
/******************************************************************************
*
* 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://... |
4aa461fb05874d9d7df39e0292a7e9beaf37a4ce7111f03251cd135d37c0d5c9 | C | 17,464 | 394 | #include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
#endif
#ifdef KSW_CPU_DISPATCH
#ifdef __SSE4_1__
void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, i... |
e493be7dadc195912d4640992e754006d516277ad8290168a29e82b8fa1dd88a | C | 17,530 | 670 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2016 Google Inc.
// Copyright (c) 2016-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is', withou... |
46911ad50e3b03e02354371bb756f6c0ce30d0f22feb87c30822874abe7452f1 | C | 17,583 | 402 | #include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#ifdef USE_SIMDE
#include <simde/x86/sse2.h>
#else
#include <emmintrin.h>
#endif
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#ifdef USE_SIMDE
#include <simde/x86/sse4.1.h>
#else
#include <smmintrin.h>
#en... |
477f2b3ac4f0ebf633be00e0b915923a49b0439e106c3d14df3816e72515d70c | C | 17,624 | 523 |
/******************************************************************************
*
* 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://... |
e41148ed5f28c6eece5a8411e3731d179936b9bd6cc263f121cd16965481c07c | C | 17,625 | 752 | /* certain changes (mainly global names) by Andreas Schmitz (1997) */
/* certain changes (mainly cleanup) by Thomas Schreiber (1998) */
/**************************************************************************
Javier Soley, Ph. D, FJSOLEY @UCRVM2.BITNET
Escuela de Física y Centro de Investigaciones Geofísic... |
b95173ebf8e035a7f7f630b7655e9f5ce8e03c30f0d3851e158239a4831e938b | C | 17,759 | 675 | /* 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 ... |
86584e20c7b44f3b300178a4beb1fc24fa2a476a1fce8b030a5d6ea6c12c1536 | C | 17,766 | 496 | #include <math.h>
#include <stdio.h>
#include <stdarg.h>
#include <gsl/gsl_cdf.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_statistics_double.h>
#include "../include/type.h"
#include "../include/util.h"
#include "../include/myfunc.h"
#include "../include/global... |
330cf2077f99f179ea2a3c9952634f46452193b233f140fa8820557d71c14be3 | C | 17,821 | 667 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.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 !NRNGPU
#undef exp
#d... |
07a95a330066fbee1259f689bbe54c1a3bb550105b934485cc8f5478958ccd26 | C | 17,830 | 462 | /*******************************************************************
Copyright (C) 2001-9 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;... |
7e14cbee83da4b59e392c35e58143e2ff002ba4e91aac7693b4cbe79c36401c4 | C | 17,848 | 490 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#include "internal_neon.h"
#define SG_TRACE
#define SG_SUFFIX _striped_neon_128_32
#define SG_SUFFIX_PRO... |
03db0c0419a3ae2d787fee99e3340803d07341fa671c37d27c504816fb9b1c8f | C | 17,853 | 566 | // Avoid NaN errors
if (v >= 100.0) v = 100.0;
if (v <= -100.0) v = -100.0;
real INaCa_fractionSS = 0.2;
// Constants
real pi = 3.14;
real cao = 1.8; //[Ca]o mM
real nao = 140.0; //[Na]o mM
real ko = 5.4; //[K]o mM
// Physical Constants:
real R = 8314.0; // J/kmol/K
real T = 310.0; // K
real F = 96485.0; /... |
5b1729b8613f499c96a51624d759c342e442939a99a01b6860de9573d9e10857 | C | 17,866 | 490 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <stdint.h>
#include <stdlib.h>
#include "parasail.h"
#include "memory.h"
#include "internal_neon.h"
#define SG_TRACE
#define SG_SUFFIX _striped_neon_128_16
#define SG_SUFFIX_PRO... |
19670b2d7f1f346fed7affe7b0839a1f705f6f07bf5ec9684fac87eb420e18d4 | C | 17,920 | 559 | //
// Created by sachetto on 29/09/17.
//
#include "cell.h"
#include <math.h>
#include "../../3dparty/stb_ds.h"
struct cell_node *new_cell_node() {
struct cell_node *result = (struct cell_node *)malloc(sizeof(struct cell_node));
init_cell_node(result);
return result;
}
void init_cell_node(struct cell_no... |
166cfe2993d3350264e513069b04c1a81f5c93c566dbf5d26359be6fd01c8e98 | C | 17,942 | 191 |
#define IFNUMBER_1(name)if((V_old_==(-4.713000000000000e+01))) { (name) = 3.200000000000000e+00; } else{ (name) = ((3.200000000000000e-01*(V_old_+4.713000000000000e+01))/(1.000000000000000e+00-exp(((-1.000000000000000e-01)*(V_old_+4.713000000000000e+01))))); }
#define IFNUMBER_2(name)if((V_old_<(-4.000000000000... |
d5f519d1a6e57c9c324f05ec68e45e16f869a0686ed6f59d9d65a50c42b73724 | C | 18,012 | 529 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#if defined(_MSC_VER)
#include <intrin.h>
#else
#include <emmintrin.h>
#endif
#include "parasail.h"
#include "memory.h"
#include "in... |
f60720b79c0da6871e8a0cdce7b375e6966d8259fba6c5a3534d593fc79a1ce6 | C | 18,049 | 517 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#include <immintrin.h>
#include "parasail.h"
#include "memory.h"
#include "internal_avx.h"
#define SG_TRACE
#define SG_SUFFIX _stri... |
071e55eb0eca190d1a6e495f917b98afb047c1e664c51de225fd2582e4a7072b | C | 18,080 | 696 | //
// Created by sachetto on 13/10/17.
//
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
#include "../alg/grid/grid.h"
#include "../config/stim_config.h"
#include "../config_helpers/config_helpers.h"
#include "../utils/utils.h"
SET_SPATIAL_STIM(stim_if_point_equal) {
uint32_t n_active = the_grid->... |
945bfe676340304ab095f8e04733aa240fde90da7a3001273d922679cb1b65eb | C | 18,085 | 517 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <stdint.h>
#include <stdlib.h>
#include <immintrin.h>
#include "parasail.h"
#include "memory.h"
#include "internal_avx.h"
#define SG_TRACE
#define SG_SUFFIX _stri... |
4f676362f746ac03d9154dd989e8240ae067759165c10257eb4fdb22081d6945 | C | 18,220 | 409 | #include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
#endif
#ifdef KSW_CPU_DISPATCH
#ifdef __SSE4_1__
void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, i... |
12543d685adae64fe26d05b69fe86dc80406fc5d09a948f1e2b25328028fb715 | C | 18,293 | 533 | #include <ctype.h>
#include <float.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "3dparty/sds/sds.h"
#include "3dparty/stb_ds.h"
#include "config/config_parser.h"
#include "gui/gui.h"
#include "logger/logger.h"
#include "utils/file_utils.h"
#include "vtk_utils/pvd_utils.h"
#include "vtk_utils/... |
82dbc25dc43a820e88673b050ce34dc3001f8ca81b7dc982524b174e02f4a161 | C | 18,371 | 456 | // Avoid NaN errors
if (V >= 200.0) V = 200.0;
// Constants
real nao = 140;
real cao = 1.8;
real ko = 5.4;
real R = 8314;
real T = 310;
real F = 96485;
real zna = 1;
real zca = 2;
real zk = 1;
real L = 0.0164;
real rad = 0.00175;
real greekpi = 3.14159265;
real KmCaMK = 0.15;
real aCaMK = 0.05;
real bCaMK = 0.00068;
r... |
b03dada8c9c289e08ac8980b6a250bd916b8719bd609384e994d38ce594204a7 | C | 18,447 | 705 | /*
* lib_mem.c - library of routines used to analyze the memory hierarchy
*
* @(#)lib_mem.c 1.15 [email protected]
*
* Copyright (c) 2000 Carl Staelin.
* Copyright (c) 1994 Larry McVoy.
* Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the b... |
426c35e0735321d7cf388a53e49ff7b4524b6d11c53982a8d8a82f39e9e213ac | C | 18,462 | 537 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <emmintrin.h>
#include "memory.h"
#include "internal_sse.h"
__m128i * parasail_memalign___m128i(size_t alignment, size_t size)
{
return (__m128i *) parasail_me... |
e7b86894b19f03b5e02949108987e466fb18b7e94deef71845d4e785dd0bc7ab | C | 18,515 | 537 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_INTEL
#include <immintrin.h>
#include "memory.h"
#include "internal_avx.h"
__m256i * parasail_memalign___m256i(size_t alignment, size_t size)
{
return (__m256i *) parasail_me... |
71a76ee0f13faa2539347c0328170025f8b56ead1fd1254a85fb3abf1afa5030 | C | 18,554 | 538 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#if HAVE_ALTIVEC
#include <stdint.h>
#include <stdlib.h>
#include "memory.h"
#include "internal_altivec.h"
vec128i * parasail_memalign_vec128i(size_t alignment, size_t size)
{
return ... |
705dc85cb64b961bf153f8690515241c563997dadae4fdb9c9c529799aad4b74 | C | 18,568 | 492 |
// EIF_common.c
#include "EIF_common.h"
#include <stdlib.h>
#include <time.h>
#ifndef M_PI
#define M_PI 3.14159265358979323846
#endif
static inline double fast_exp(double x) {
if (x > 700.0) return INFINITY;
if (x < -700.0) return 0.0;
return exp(x);
}
// --- helpers
static const mxArray* get_field2(con... |
a5c468fa0a8b12f62d3df3c5dddcd950333ba2aa0758729625fe0d2805abffce | C | 18,726 | 698 | /* Created by Language version: 6.2.0 */
/* VECTORIZED */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "scoplib_ansi.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 !NRNGPU
#undef exp
#d... |
8d0ff6e307f86e36ef1b6aaee2f1311393f479f4b014fccb6869faa77093140b | C | 18,798 | 561 | #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->... |
b8268033b01e3804f94e3baea9ebf5727129f692522d7ddf8910246f9fb34e2f | C | 18,808 | 535 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*/
#include "config.h"
#include <stdint.h>
#include <stdlib.h>
#include "memory.h"
#include "internal_neon.h"
simde__m128i * parasail_memalign_simde__m128i(size_t alignment, size_t size)
{
return (simde__m12... |
bbee4c1532444f6e564e8a98d597e5038c54cd8bcde8aa9c542cdaaddf30fc3a | C | 18,828 | 721 | /*
* This file is part of TISEAN
*
* Copyright (c) 1998-2007 Rainer Hegger, Holger Kantz, Thomas Schreiber
*
* TISEAN 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 2 of the Li... |
d8b145fe3be8f2ab02a387a74a09427acee26ef3dc17645a02889a0d6476d458 | C | 18,927 | 579 | //
// Created by bergolho on 29/09/20.
//
#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... |
34b8c28c4c093a59a4d1c89914bbb670cbcb99451d623c256532768f9a126bb9 | C | 18,941 | 639 | /* THIS CODE CARRIES NO GUARANTEE OF USABILITY OR FITNESS FOR ANY PURPOSE.
* WHILE THE AUTHORS HAVE TRIED TO ENSURE THE PROGRAM WORKS CORRECTLY,
* IT IS STRICTLY USE AT YOUR OWN RISK. */
#include "rgbe.h"
#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include <stdarg.h>
#include <string.h>
#include <ctyp... |
1344b8a7a9ca747caf92a88b9d3caef9cc43ece4525df894725bd1229d93f7ed | C | 18,970 | 750 | /*
* cache.c - guess the cache size(s)
*
* usage: cache [-c] [-L <line size>] [-M len[K|M]] [-W <warmup>] [-N <repetitions>]
*
* Copyright (c) 2000 Carl Staelin.
* Copyright (c) 1994 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the benchmark ... |
0f56c49b3bc5f5132bf0350fd9a547415184682044a905e8bb481100ce36dee9 | C | 18,988 | 693 | /* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
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 li... |
1821ae7ef56cfcab3e9084595a3e63cacb63dfef1c64ce9e793c64d8848bb17a | C | 19,002 | 536 | #include "ToRORd_fkatp_mixed_endo_mid_epi_GKsGKrtjca_adjustments.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_co... |
837c587a7c320047befe520261e080cafb1267da2c2bc7b260fac883f56d9ea3 | C | 19,030 | 570 | #include <math.h>
#include <time.h>
#include <string.h>
#include <stdarg.h>
#include <stdio.h>
#include <gsl/gsl_vector.h>
#include <omp.h>
#include "../include/type.h"
#include "../include/util.h"
#include "../include/global.h"
extern clock_t dur;
extern char *optarg;
extern int optind;
/**
* @brief initiator of ... |
4b0915fabd87972b42875ba18f590883bb9b2da84812fde96f035af3d6bddeb9 | C | 19,091 | 894 | char *id = "$Id: lmdd.c,v 1.23 1997/12/01 23:47:59 lm Exp $\n";
/*
* defaults:
* bs=8k
* count=forever
* if=internal
* of=internal
* ipat=0
* opat=0
* mismatch=0
* rusage=0
* flush=0
* rand=0
* print=0
* direct=0
* rt=0
* rtmax=0
* wtmax=0
* rtmin=0
* wtmin=0
* label=""
* shorthands:
* k, m, g are ... |
7063210bdcf07c8542f8bbbde67128cd3bfaa85ba461fb8ffe99ff29eed355c2 | C | 19,172 | 625 | // Avoid NaN errors
if (v >= 100.0) v = 100.0;
if (v <= -100.0) v = -100.0;
real INaCa_fractionSS = 0.2;
// Constants
real pi = 3.14;
real cao = 1.8; //[Ca]o mM
real nao = 140.0; //[Na]o mM
real ko = 5.4; //[K]o mM
// Physical Constants:
real R = 8314.0; // J/kmol/K
real T = 310.0; // K
real F = 96485.0; /... |
e1170a0c180c01426a40d6caa76e9f93f4d4989f1fe78ded387a60090231975b | C | 19,174 | 629 | //
// Created by sachetto on 01/10/17.
//
#include <unistd.h>
#include "../config/extra_data_config.h"
#include "../config_helpers/config_helpers.h"
#include "../libraries_common/common_data_structures.h"
#include "../domains_library/mesh_info_data.h"
#include "helper_functions.h"
struct uv {
real_cpu u;
rea... |
48eb7ef351efc4c887df78388d6b8c5f3de93c3e352e6952a11caf11acc7a3d3 | C | 19,282 | 832 | //
// Created by sachetto on 18/10/17.
//
#include "file_utils.h"
#include <time.h>
#define STB_DS_IMPLEMENTATION
#include "../3dparty/stb_ds.h"
#include "../3dparty/sds/sds.h"
#include <ctype.h>
#include <dirent.h>
#include <errno.h>
#include <fcntl.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#incl... |
f86379d3b1e98685a52cac9d6fb48ad9a464bc83107bfaee59ed0ad4a587ed18 | C | 19,443 | 683 |
/******************************************************************************
*
* 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://... |
b07485f2dc4df89370ff5cddf70b74712f2ada1fa5a2d2093c48f07c6fa5c2a1 | C | 19,592 | 647 | /* ctbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
d018e3f49aa1b4b92fbcd11a44d7be7f858e4163d4485d794f2ab0f4422191e8 | C | 19,620 | 647 | /* ztbmv.f -- translated by f2c (version 20100827).
You must link the resulting object file with libf2c:
on Microsoft Windows system, link with libf2c.lib;
on Linux or Unix systems, link with .../path/to/libf2c.a -lm
or, if you install libf2c.a in a standard place, with -lf2c -lm
-- in that order, at the en... |
08158668ec025c2aac5b26f1fad08b6e1c7984c2618738965c0c90bcb2e661c4 | C | 19,712 | 614 | //========================================================================
// GLFW 3.4 X11 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2019 Camilla Löwy <[email protected]>
//
// This software is provided 'a... |
138fa41f8f69477606963db4464591f99d22079b47babaf66f59cb2ac615125a | C | 19,921 | 686 | /*
Copyright (C) 2014-2019 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 ... |
c7966e06ab7162a2e6cf4c8a5d01c9480c306e6ebcd14e16407f37edb192d539 | C | 20,031 | 446 | //
// 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 */
... |
7fff4834a011265b0e0cc4dc43141fbaf114860a116ce24710330e8a67b0fadf | C | 20,132 | 691 | #include <stdlib.h>
#include "Ohara_Rudy_2011.h"
int celltype = 0;
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) {
... |
09bec41a2cf1ee6fb87e5d987bb895df09d48044810a5c78a86d5459d37026c7 | C | 20,351 | 523 |
/******************************************************************************
*
* 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://... |
6fab461239435f3a538a069942625a3c98351d3a98e76025135231c1be9cd74d | C | 20,464 | 302 | const real mScaleFactorGks = 1.0;
const real mScaleFactorIto = 1.0;
const real mScaleFactorGkr = 1.0;const real var_Environment__R = 8.314472;
const real var_Environment__T = 308.0;
const real var_Environment__F = 96.4853415;
const real var_Environment__K_o = 5.4;
const real var_Environment__Ca_o = 1.8;
const real var_... |
4133da83cb1938bdca50120dcdd3860267e87e81e78ae350c38ce70aecb68a26 | C | 20,520 | 673 | //
// Created by sachetto on 30/10/18.
//
#include "ensight_grid.h"
#include "../3dparty/stb_ds.h"
#include "../domains_library/mesh_info_data.h"
#include "../logger/logger.h"
#include <math.h>
#include <stdint.h>
#include <sys/mman.h>
#include <float.h>
static inline void new_line(FILE *f, bool binary) {
if(!bin... |
5b3bc72b9ca28282800e37f5bc9822d251bbcd7a67733742a9899f7830a63af7 | C | 20,585 | 706 |
/******************************************************************************
*
* 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://... |
29c0788db5f7827b03118b443a7e13a56766b0885e63a7c1c00cd75e0eb3a2e4 | C | 20,627 | 419 | // A Model of Cardiac Electrical Activity Incorporating Ionic Pumps and Concentration Changes
// Reference: https://models.physiomeproject.org/exposure/91d93b61d7da56b6baf1f0c4d88ecd77/difrancesco_noble_1985.cellml
#include "difrancesco.h"
real CONSTANTS[50];
GET_CELL_MODEL_DATA(init_cell_model_data) {
if(get_i... |
3c273cef98590b5dd9dad0a2186445801d4c845348841e7a03b1ed34bc36e789 | C | 20,767 | 487 | //
// Created by sachetto on 30/09/17.
//
#include <assert.h>
#include "cell.h"
#include "../../3dparty/stb_ds.h"
/**
* Decides if the bunch should be derefined. A bunch will not be derefined if
* the highest of all directional fluxes coming into its six directions is
* greater than derefinement_bound.
*
* @param... |
05f5fb72aec7ac78aae6e80d92e434fe1a959f8eccd5b8430af32840c26a12e6 | C | 20,807 | 466 | #include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#ifdef __SSE2__
#ifdef USE_SIMDE
#include <simde/x86/sse2.h>
#else
#include <emmintrin.h>
#endif
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#ifdef USE_SIMDE
#include <simde/x86/sse4.1.h>
#else
#include <smmintrin.h>
#end... |
c463c38db6c91a77242856347ebcc42b02995a8112360e3912c0e87d56608cfa | C | 20,968 | 908 | /*
* C library for the autofocus lock.
*
* So named because this lock works on the same principle as
* the autofocus system in a SLR camera. The primary difference
* is the use of an IR laser to create the object to focus on.
*
* Hazen 9/19
*/
/* Include */
#include <stdlib.h>
#include <stdio.h>
#include <s... |
2c46beacf250f9ff357d847305c2ed7a8a26a1781371249dc13822fca2973efd | C | 21,059 | 880 |
/******************************************************************************
*
* 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://... |
85318aa8f5e5271c3010e135736517971ed266b424fa971519cd48439d2ca577 | C | 21,182 | 653 | /*
* TINYEXPR - Tiny recursive descent parser and evaluation engine in C
*
* Copyright (c) 2015-2018 Lewis Van Winkle
*
* http://CodePlea.com
*
* This software is provided 'as-is', without any express or implied
* warranty. In no event will the authors be held liable for any damages
* arising from the use of t... |
d0906fa8768957905a3081c5a5a317cfe3817f21c391b475e8a118e05657ba8d | C | 21,730 | 444 | #include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <errno.h>
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "ketopt.h"
#include <thread>
#define MM_VERSION "2.03"
#ifdef __linux__
#include <sys/resource.h>
#include <sys/time.h>
#include <sched.h>
void liftrli... |
fe56de5f351b2324234d8124cd79517b93b3613ed4b639247fdd1edc864d6f24 | C | 21,752 | 890 |
/******************************************************************************
*
* 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://... |
e2be6dc141384d686eafdd8507a782cb266c0c97d272d16cb26a4d95aa28c51e | C | 22,069 | 563 | /******************************************************************************
*
* 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:
* ... |
fd527f6af9cc46476dc109f17af2e4fd5dc4abd99e70b74fb573e4cc9ea7741e | C | 22,131 | 484 | //
// Created by sachetto on 13/10/17.
//
#include <stdlib.h>
#include <string.h>
#include "../alg/grid/grid.h"
#include "../config/save_state_config.h"
#include "../save_mesh_library/save_mesh_helper.h"
#ifdef COMPILE_CUDA
#include "../gpu_utils/gpu_utils.h"
#endif
SAVE_STATE(save_simulation_state) {
//Here we... |
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