sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
c96935507a3dc9bb75fff590bbd606f341a1ba721d7f08932749c3704eb8c95a | C | 7,740 | 219 | #include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#define __STDC_LIMIT_MACROS
#include "kvec.h"
#include "mmpriv.h"
#include <cmath>
#include <iostream>
#include <fstream>
/**
* option to dump minimizers to file
* use empty fasta/q read file when using this
* NOTE: writing done to file ... |
64da2b18fe6f589380dc1ab0568491e42abaa7b3a32557fbe60bf2ef870b8a8e | C | 7,747 | 371 | /*
* Does the lifting for determining focus lock offsets
* by maximizing the correlation of the image from the
* focus lock camera with a 2D Gaussian.
*
* Hazen 04/18
*
* gcc -fPIC -g -c -Wall multi_fit.c
* gcc -shared -Wl,-soname,multi_fit.so.1 -o multi_fit.so.1.0.1 multi_fit.o cubic_spline.o -lc -llapack
*... |
b274d0860889736be59e9e9813533759b351e7b013aa6ca569f57d3757ddc250 | C | 7,749 | 350 | /*
* lat_ctx.c - context switch timer
*
* usage: lat_ctx [-P parallelism] [-W <warmup>] [-N <repetitions>] [-s size] #procs [#procs....]
*
* Copyright (c) 1994 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the benchmark is unmodified, and
* (... |
91d9b026b79be14325eec1c26002eb22d772dd6cc79c40dfa1dfd29ab0b62180 | C | 7,759 | 276 | /* region.c -- Functions to create and free region lists
Copyright (C) 2019 Genome Research Ltd.
Author: Valeriu Ohan <[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 ... |
3b909e206cdd8728dec4a73850a04e9c540d7d3df05f7f5b177cf2c4430f5e18 | C | 7,760 | 276 |
/******************************************************************************
*
* 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:
* ... |
cdee8421631a2d9ce835db7c3f1a73caea501dea5e1d911a19299ca0598aa4b3 | C | 7,768 | 197 | /*%% --------------------------------------------------------------------------------------------------
% dcm_euler_integration - Integrates the DCM-fMRI dynamical system using
* Euler's method
% [x,s,f,v,q] = dcm_euler_integration(A,C,U,B,D,...
rho,alphainv,tau,gamma,kappa,paramList);
%---------... |
12bb4694ccf8b2715141ff4f9fb88603e31edb1a7866feaa03538a962c1d7c4e | C | 7,791 | 273 | /* [email protected] */
/* copyright (C) 2018 */
#include "mexutils.h"
int
seria_set_summary_fields(
const SERIA_SUMMARY *summary,
int index,
mxArray *mstruct)
{
mxArray *late_pro_prob = mxCreateDoubleScalar(summary->late_pro_prob);
mxSetField(mstruct, index, "late_pro_pro... |
ebe6a6aebc2946c056555217ad068683892ed984c5ba0f66b663f2c8aa26a4ab | C | 7,841 | 164 | #include "mpi.h"
#include <stdio.h>
FILE *fp_acidos;
FILE *Vout[200],*Tser[200],*F2; //,*obst[200] obstacle file pointer
char filename0[100];
char filename_acidos[50];
char filename_V[200],filename_Tser[200],filename_obst[200];
double i_K1 ; // inward_rectifier_potassium_current (picoA_per_picoF).
double i_to ; // ... |
68814f60ddcae0ee24f5b53453cee7826990c63d5d3574b7d2879afbbc05bd3a | C | 7,850 | 183 | #include"build.h"
void allocate_arrays()
{
DAD = (int*)malloc(((mypoints+2)*(y_space+2)*(z_space+2)*sizeof(int)));
work = (double*) malloc((mypoints*y_space*z_space*sizeof(double)));
data = (double*) malloc((mypoints*y_space*z_space*sizeof(double)));
I_app1 = (double*) malloc(((mypoints+2)*(y_space+2)*(z_space... |
ebf8fe7f6cc47dbb699e1f4217c24da5953830d45a26f33d08ea5382e5514544 | C | 7,857 | 190 | /*%% --------------------------------------------------------------------------------------------------
% dcm_euler_integration - Integrates the DCM-fMRI dynamical system using Euler's method
% [x,s,f,v,q] = dcm_euler_integration(A,C,U,B,D,...
rho,alphainv,tau,gamma,kappa,paramList);
%--------... |
fec72286a2d8a0c53fd56ea61b3766b87031f6f803f6de6c3c656e39bc85cdc2 | C | 7,882 | 303 | /* mmap.c -- Memory allocation with mmap.
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) Redistributions of source c... |
cf442bc65af8e940f09b8411c818b0bcb3c78acfc2d19fac9896cd2af85c637b | C | 7,883 | 257 |
/******************************************************************************
*
* 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://... |
903668eeecdaed89d5bf31d9bfbb5b1b0dab991d69403c46504591d7dffe0818 | C | 7,907 | 289 |
/******************************************************************************
*
* 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:
* ... |
edbdeeaa7a74dbd4831560274a094aeeed674c9424bc63b6fe4b562e5e3042b2 | C | 7,910 | 304 | /*
* 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... |
c075b174448cc1774e910ccbe7523ac786c33fe6d12da8e02045c6317b4163d8 | C | 7,917 | 239 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include "3dparty/stb_ds.h"
#include "common_types/common_types.h"
#include "utils/file_utils.h"
#include "config/config_common.h"
#include "config/domain_config.h"
#include "domains_library/mesh_info_data.h"
static const char *expansion_o... |
d26e19175311d92e89730b52587d946a78afb4138eb8d9fa5d97bdf1de55ac1f | C | 7,923 | 201 | #include <stdio.h>
#include "mmpriv.h"
#include "kalloc.h"
#define MM_MIN_EXON_LEN 20
static int32_t mm_jump_check(void *km, const mm_idx_t *mi, int32_t qlen, const uint8_t *qseq0, const mm_reg1_t *r, int32_t ext, int32_t is_left) // TODO: check close N
{
int32_t clip, clen, e = !r->rev ^ !is_left; // 0 for left of ... |
290fe6457626906c0d477872c86533f3078f72883625888db5f65d7068a0b35c | C | 7,924 | 194 | //
// Created by sachetto on 13/10/17.
//
#include <stdbool.h>
#include <stdint.h>
#include <stdlib.h>
#include "../alg/grid/grid.h"
#include "../config/update_monodomain_config.h"
#include "../utils/utils.h"
#include "../3dparty/stb_ds.h"
#ifdef COMPILE_CUDA
#include "../gpu_utils/gpu_utils.h"
#endif
UPDATE_MONOD... |
e39b3e13a616050bb3e0af32df358fccc72d9040afe2bdea1f42f21e61bc9812 | C | 7,934 | 228 | // CStrAinBP.c
// Cell strings: Find positions of strings of A in B [MEX]
//
// [AI, BI] = CStrAinBP(A, B, CaseSensitive)
// INPUT:
// A, B: Cell strings of any size.
// CaseSensitive: If this string starts with 'i', the upper/lower case of the
// strings is ignored. Optional, default: 'sensitive'.
// OUTPU... |
ea39ce197505bfbbc00b9a60d4f5f57a51b72ad45add10d30a4f68dbf81257d1 | C | 7,935 | 367 |
/******************************************************************************
*
* 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:
* ... |
8f4b1799e75fdb7b0e541e57680273f7901c294f0793699f280f01e873bf923b | C | 7,956 | 233 | #include "3dparty/ini_parser/ini.h"
#include "3dparty/sds/sds.h"
#include "alg/grid/grid.h"
#include "config_helpers/config_helpers.h"
#include "logger/logger.h"
#include "monodomain/monodomain_solver.h"
#include "ode_solver/ode_solver.h"
#include "utils/file_utils.h"
#include <stdlib.h>
#include <string.h>
#ifdef COM... |
547f78c6f151052d5dea2847ef89f384eb26acdecbed0204439138fff8e91328 | C | 7,960 | 289 |
/******************************************************************************
*
* 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://... |
f4585534c6f2247b7ec7dc6984a2993d74c431e56dd069b703cbfd13935a9a0a | C | 7,971 | 299 | /*
* 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... |
170fbc3e023f7a4499b3407c3633f8d4a2d8bcba9d8f3d90a44cc2316d75378d | C | 8,053 | 230 | /* Copyright (c) 2012, Kim Gräsman
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* * Redistributions of source code must retain the above copyright notice,
* this list of conditions an... |
095b07825c42436673deb1d287e9f0b9c8ab9db7abbe8b913c1ac6e79187505d | C | 8,054 | 224 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "kalloc.h"
/* In kalloc, a *core* is a large chunk of contiguous memory. Each core is
* associated with a master header, which keeps the size of the current core
* and the pointer to next core. Kalloc allocates small *blocks* of memory from
* the c... |
f251ed73ad57197c55336559bf72329292a8da9acccf498cb5ec00ead3bf51e8 | C | 8,077 | 273 | /*
* 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... |
921ad36601ecd6660095f02177d86ef70d0eaa1d6c46a07cf998f4cc9b3ebe5b | C | 8,110 | 267 | /*
Kanwei Li, 2009
Inspired by previous ClusterTree
This clustering algorithm uses a binary tree structure. Nodes correspond to
non-overlapping intervals, where overlapping means that the distance between
two intervals is less or equal to max_dist, which is the max separation.
The tre... |
2297b3b5b5b62d93370690fa40621efcebf6d54feb73eba96c7044f81668c02e | C | 8,158 | 398 | /*
* http_srv.c - simple HTTP "server"
*
* Only implements the simplest GET operation.
*
* usage: http_srv [-f#] [-l] [-d] [port]
*
* Copyright (c) 1994-6 Larry McVoy. Distributed under the FSF GPL with
* additional restriction that results may published only if
* (1) the benchmark is unmodified, and
* (2) t... |
35b3bd990c7524912345d0813698f1014e2dd8f5b5d94d8482b1b199e11ec9c7 | C | 8,161 | 322 | /*
* 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... |
30d52db94e019d04799c7729a3c6c81fd18386d83811e55effdd31b6e5d21377 | C | 8,193 | 230 | #include"variables.h"
#include"constants.h"
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
void I_currents()
{
/* INa: Fast Na+ current (inward) */
I_Na[i][j]=G_Na*pow(m[i][j],3)*h[i][j]*j_1[i][j]*(V[i][j]-E_Na);
m_inf=1/pow((1+exp((-56.86-V[i][j])/9.03)),2);
alpha_m=1/(1+exp((... |
338182f8c0f1e7fab6e856a4705c208990cdfa2e721c9ea9074ded3d3e343576 | C | 8,239 | 260 | /*
* Bitshuffle HDF5 filter
*
* This file is part of Bitshuffle
* Author: Kiyoshi Masui <[email protected]>
* Website: https://www.github.com/kiyo-masui/bitshuffle
* Created: 2014
*
* See LICENSE file for details about copyright and rights to use.
*
*/
#include "bitshuffle.h"
#include "bshuf_h5filter.h"
... |
6f23f7017356d1fd4e98e48e22b4eaa79c7aacef8582fc0e7803349201015a17 | C | 8,242 | 184 |
/******************************************************************************
*
* 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:
* ... |
fa06a9f92189f793f6c5b8a6765ab0c620b2b81ac862b4f0d8e9c81d81b97ef8 | C | 8,247 | 331 | /*
* 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... |
06d0b1c668a4e6e37e43140e2dfe6a98ba4d15b07ecfda50f05a07a5dbff8126 | C | 8,263 | 193 | if (layer == ENDO)
{
sv[0] = -87.0332008799399000; // membrane_v
sv[1] = 8.9547882348124400; // ions_na_junc
sv[2] = 8.9538419549615500; // ions_na_sl
sv[3] = 8.9540793850280800; // ions_na_i
sv[4] = 134.1526087617420000; // ions_k_i
sv[5] = 0.0000861759484523; // ions_ca_junc
sv[6] = 0.0000947028878157;... |
8b2c542a942ce4c9345a5b58b1bb076e11254d1a0585bfb27a035c827ada1961 | C | 8,320 | 289 | /* Performs fast detrended fluctuation analysis on a nonstationary input signal.
Useage:
Inputs
x - input signal: must be a row vector
Optional inputs:
intervals - List of sample interval widths at each scale
(If not specified, then a binary subdivision is constructed)
O... |
5cd1b2d584431dc3ff944b0488914378d122f27d8115da7b9d98bea9bf4f4e50 | C | 8,338 | 253 |
/******************************************************************************
*
* 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://... |
4455434ef660a66fd93ef0b8cee34375defac6742a7f7c8037f906593e7e486c | C | 8,354 | 200 | #include "build.h"
void initial_cond()
{
// Global variables to be updated in euler();
// euler variables initialization
I_Kto_Na = 0;
I_f = 0;
I_gap = 0;
E_f = -69.6;//-69.6;
//if (SWITCH == 0) {
if(DAD_flag == 1) {
//sprintf(filename_acidos,"obstacle/acidos_at_rank_%d.dat",rank);
sp... |
b4f86c15fe9cdcf5ce6ba5992f49e6aa522a83754fcd4dd304b805f8c88e8854 | C | 8,367 | 316 | /* sspmv.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... |
a78e17ee302bd809248856eec374722edb88861c2a9b1211f417d2e1480ed6e1 | C | 8,375 | 329 | /*
* 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... |
98184b7548129f9715cc99c3c70773d1555357bf36f147fade07c8885453623e | C | 8,391 | 316 | /* dspmv.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... |
167bc1f65d64245251456520fa92333257ec6b25d4df01727bcc75c6e94e69bb | C | 8,465 | 308 | /* program to produce vrml output from HOLE .sph
format input file written by
Xiaonan Wang and Oliver Smart from July 1996 */
/* standard headers */
# include <stdio.h>
# include <stdlib.h>
# include <math.h>
# include <string.h>
/* file pointers */
FILE *input_sphfile;
FILE *output_wrl_file;
void main()
{
in... |
c1ad7900788315cf0c8e8db452008686e540eea594578554de9efba2542011c7 | C | 8,491 | 277 | #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#define PY_SSIZE_T_CLEAN /* Make "s#" use Py_ssize_t rather than int. */
#include <Python.h>
#include <float.h>
#include "numpy/arrayobject.h"
#include "numpy/npy_math.h"
static PyObject *stack_windows(PyObject *self, PyObject *args, PyObject *kwds) {
PyObject *off... |
133e9723eb6f672616fb6b0066c4d83dc07af3b7e65e672901f94841180f51f8 | C | 8,506 | 284 | /*
* Bitshuffle - Filter for improving compression of typed binary data.
*
* Author: Kiyoshi Masui <[email protected]>
* Website: https://www.github.com/kiyo-masui/bitshuffle
* Created: 2014
*
* See LICENSE file for details about copyright and rights to use.
*
*/
#include "bitshuffle.h"
#include "bitshuffle... |
82829dbe94f263118c56f095bfdbefb871fee0e675dcbe2a46b8f09f7fde9c38 | C | 8,521 | 267 | /* multipart.c -- GA4GH redirection and multipart backend for file streams.
Copyright (C) 2016-2017 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")... |
79fac7af0af0fa4633d5501e23dc3ebb337bf7bbb8302da4ce64bffd797d5733 | C | 8,543 | 336 | /*
* Copyright 1993-2003 The MathWorks, Inc.
* $Revision: 1.5.4.3 $ $Date: 2004/02/01 21:44:32 $
*/
/*
* EUCDIST2 MEX-file
*
* Distance transform, Euclidean version
*
* D = EUCDIST2(BW) computes the Euclidean distance transform on the input
* binary image BW. Specifically, it computes the distance to the n... |
69742c43f018fdd8a9a91025dbd1c93cdf121efebbc79c56a95ab2768da75989 | C | 8,594 | 382 | /* Downloaded from http://www.netlib.org/clapack/cblas/
* This is a merger of the 4 following cblas files:
* daxpy.c dcopy.c ddot.c dscal.c
* These files were long ago taken from the fortran source
* using f2c.
* Use this file for the simple, unoptimized implementation
* of these basic BLAS functions. These ... |
98c759d74eef7a5277dfa61fc40e3d4a52951c859140d23133e5e1b8c17fa36f | C | 8,605 | 297 | #include "build.h"
void main(int argc,char *argv[]){
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&numProcs);
MPI_Comm_rank(MPI_COMM_WORLD,&myrank);
// starttime = MPI_Wtime();
/*********** NUMBER OF INTERIOR GRID POINTS ALLOCATED TO EACH PROCESSOR ************/
mypoints = x_sp... |
b1ce0d49fc16d5715564bd673001e0dd3cdd17d13a3ea78e203b44b46e5a5b1e | C | 8,611 | 293 | /*
* 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... |
77ca0a2d9bf0eaa16f2b49d7f8baf79fd5534dffe20dbd0e36ba61a88a022b76 | C | 8,621 | 262 |
/******************************************************************************
*
* 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://... |
6d4dd11c997f14ce8bd7ef5e5c4a87f0fdfe2be2650c5b959f7214b559f40e18 | C | 8,685 | 326 | // ==================================================
// straightforward implementations of matrix multiply
// ==================================================
void multAB(double* C, double* A, double* B, const int a1, const int a2, const int b2) {
int i, j, k;
double *a, *c, tmp;
for( i=0; i<b2; i++ ){
... |
6f24fc97dbb28852681567dd307bf34ad8bbbc54b992bb89dd97d4406095912f | C | 8,761 | 287 |
/******************************************************************************
*
* 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:
* ... |
95ea084c741011f3734b91faf4d028b722139f1a3e243553f089447f962d0c73 | C | 8,788 | 334 |
/******************************************************************************
*
* 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:
* ... |
3683a50f4a3e3896435e4414f2d0581c551557f4622827f87c8dadaedd75e89a | C | 8,797 | 151 | #include "luo_rudy_1991.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) {
uint32_t num_cells = solver->original_nu... |
9030f8ae7202b700eb16bc95cd2bcaebb1b2e18ade8e80f4230d23f410674543 | C | 8,810 | 283 |
/******************************************************************************
*
* 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:
* ... |
69caf992a7a3fbb3151519b31de770076b3cbe6e1734af6ae6f80325a43e6d8a | C | 8,819 | 261 |
/******************************************************************************
*
* 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://... |
a523df18b49606752072aa8897ba949e7a397b646ef56e287766deab641d2170 | C | 8,842 | 336 | /*
Copyright (c) 2010 Serge A. Zaitsev
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 limitation the rights
to use, copy, modify, merge, publish, distribute... |
80838d23eda9aaa792d5e3349d3a872e91da2de920dfc7dc2e7c64c6db343393 | C | 8,863 | 296 | //Feichen Shen
//Float/half conversion
//avx/f16c CPU support
#include <cstdio>
#include <x86intrin.h>
#include <malloc.h>
#include <stdint.h>
unsigned int buffer_size = 1024*1024;
char mode = 0;
void cpuid(unsigned info, unsigned *eax, unsigned *ebx, unsigned *ecx, unsigned *edx)
{
*eax = info;
__asm volatile
("... |
3a49fa846861b24b595854dfcfd8889ddf9c6927f3b28ae55484766205841781 | C | 8,906 | 257 |
/******************************************************************************
*
* 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://... |
9e80aa36161cd8953b0785fc9df5ee1f05c5c2805ee2a0f584911bb8d60257b8 | C | 8,907 | 353 | //External concentrations
real Ko=5.4;
real Cao=2.0;
real Nao=140.0;
//Intracellular volumes
real Vc=0.016404;
real Vsr=0.001094;
//Calcium dynamics
real Bufc=0.15f;
real Kbufc=0.001f;
real Bufsr=10.f;
real Kbufsr=0.3f;
real taufca=2.f;
real taug=2.f;
real V... |
0ebf78660c1d9209ca003d01e182a4d185018e283aa1efccee02469d6a0a9e1c | C | 8,971 | 248 | //
// Created by sachetto on 07/04/2020.
//
#include "../3dparty/ini_parser/ini.h"
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../alg/grid/grid.h"
#include "../config/domain_config.h"
#include "../config/save_mesh_config.h"
#include "../utils/stop_watch.h"
#include <gdbm.h>
struct elapse... |
dda9a46aba45b2cdc3564a67f3b42563b2a56e21d57cd4f8ff0fc07d768554e2 | C | 8,986 | 244 | #include"variables.h"
#include"constants.h"
#include <stdio.h>
/*void Open_files()
{
sprintf(filename_V,"V_%d.dat",rank);
Vout[rank]=fopen(filename_V,"w");
//sprintf(filename_Tser,"Tser_%d.dat",rank);
//Tser[rank]=fopen(filename_Tser,"w");
}*/
/*void Open_snaps()
{
sprintf(filename_V,"output/procesor... |
b0b37d1be02449d5415196031b9d75c1d7549cd1cd68b058984bfe5d566e9128 | C | 9,013 | 365 | /* 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 ... |
abefa3cebbf78b8c98f424af069610b59d91720a385852babf08a44e17bbf4f0 | C | 9,036 | 248 | /* ==============================================================================
Binaries and/or source for the following packages or projects are presented under one or more of the following open
source licenses:
maskApi.c The OpenLane Dataset Authors Apache License, Version 2.0
See:
https://github.co... |
05f3b5cc0b1975888ad9f661e638efefde19e9fc0cd6ffa47ac743adf4c525a9 | C | 9,041 | 178 | #include "gui_window_helpers.h"
#include <float.h>
static inline void move_rect(Vector2 new_pos, Rectangle *rect) {
float new_x = new_pos.x;
float new_y = new_pos.y;
if(new_x > 1 && new_x + rect->width < (float)GetScreenWidth()) {
rect->x = new_x;
}
if(new_y > 1 && new_y + rect->height < ... |
980d81c5233816edbcac00289c100ece8cfefbcd4f42edc04243f8e18e188f76 | C | 9,052 | 193 | #include "constants.h"
#include "variable.c"
void currents()
{
indx = i*(space_y+2)*(space_z+2)+j*(space_z+2)+k;
/*if(myrank == 32 && i_Stim[indx] != 0) {
printf("%d\t %d\t indx=%d\n",i,j,indx);
}*/
f_inf = 1.00000/(1.00000+exp((V[indx]+20.0000)/7.00000));
tau_f = 1102.50*exp(- pow(V[indx]+27.0000, 2.00000... |
c16a234c640d845d884f30886c597f76bad40dc7f524cf4528ff2c6a68e96809 | C | 9,063 | 281 | #include "courtemanche_ramirez_nattel_1998_RL.h"
#include <stdlib.h>
SET_ODE_INITIAL_CONDITIONS_CPU(set_model_initial_conditions_cpu) {
log_info("Using courtemanche_ramirez_nattel_1998_RL CPU model\n");
uint32_t num_cells = solver->original_num_cells;
solver->sv = (real*)malloc(NEQ*num_cells*sizeof(real)... |
963e7a4f5123410033c970d2b4e7e236216110db24647d908038d8e72e4423f8 | C | 9,077 | 295 | /*
* Copyright (c) 2000-2010 Marc Alexander Lehmann <[email protected]>
*
* Redistribution and use in source and binary forms, with or without modifica-
* tion, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
6ee9f779bd8cb860c11dc261424a6ef15f83c0ea589f58743a00d6f3c68c5a2f | C | 9,126 | 426 | /* [email protected] */
/* copyright (C) 2015 */
#include "antisaccades.h"
#include <stdlib.h>
#include <string.h>
/* Compares between trials */
int cmpfunc(const void *a, const void *b)
{
// Get the values from the pointers
double *da = ((MODEL_INPUTS *) a)->t;
double *db = ((MODEL_INPUTS *) b)->t... |
0c297bee0d51f61f99ff00dc802914eff8edc41983fe6fc3b57d7949788a2cdc | C | 9,128 | 383 |
/******************************************************************************
*
* 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://... |
1601b1aaa7fde74d3a40fadee3ef75a6c8279cfc74febc700b7eba504639136b | C | 9,128 | 383 |
/******************************************************************************
*
* 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://... |
508ca755cf2f3971100d4554844e96e6444caf999b4f2c0ec5fb7b76ae755892 | C | 9,130 | 358 |
/******************************************************************************
*
* 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:
* ... |
effd4efe9540beb4d4fc4e4afa908e0f64c341c4e09f1bb7597d4bd91eac98b0 | C | 9,136 | 245 | #include "../3dparty/sds/sds.h"
#include "../config/postprocessor_config.h"
#include "../config_helpers/config_helpers.h"
#include "../utils/file_utils.h"
#include "../vtk_utils/vtk_unstructured_grid.h"
#include <stdio.h>
POSTPROCESS(calculate_all_cells_activation_time) {
char *input_dir = NULL;
GET_PARAMETE... |
c88420e976ba0b7260e2400f0f98e273a2d23ecd5e2f661aa6ee37fb7fac6d0d | C | 9,170 | 291 |
/******************************************************************************
*
* 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:
* ... |
983f7a14e63e126010236bbbef7f72dacbcd9b473cd346985b2b8798785667c7 | C | 9,220 | 234 | #include "lbfgsb.h"
/*
L-BFGS-B is released under the "New BSD License" (aka “Modified BSD License”
or "3-clause license")
Please read attached file License.txt
DRIVER 2 in Fortran 77
(Convert to C with f2c and hand-coding)
---------------------------... |
701ae58ea7d1110b4893e4052b57f7568f081327e203b22432c157ddb5be33b6 | C | 9,395 | 370 | /**
* @file
*
* @author [email protected]
*
* Copyright (c) 2015 Battelle Memorial Institute.
*
* These functions borrow heavily, if not verbatim, from the files in
* the parsail contrib directory. Please see contrib for details and
* copyrights of the respective authors/sources.
*/
#include "config.h"
... |
0aca1a4f787e0b8af68ddbc231188f508238c5ea1ed24bd6ce9c91e172035198 | C | 9,410 | 310 |
/******************************************************************************
*
* 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:
* ... |
1280b7841c9ba1a6d919de3a901e6f2b1dfb4a8dbb7f72312e133bc7cc01be8e | C | 9,416 | 321 | const real natp = 0.24; // K dependence of ATP-sensitive K current
const real nicholsarea = 0.00005; // Nichol's areas (cm^2)
const real hatp = 2; // Hill coefficient
//Linear changing of atpi depending on the fibrosis and distance from the center of the scar (only for border zone ... |
cede09823e1ddaf6147dbd98957ef549e57f2d77084836eec4774118498f8b5a | C | 9,438 | 369 | /*
* 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... |
6d4038df95ac984f557b49fa3c9e122018fc8e0ac9e635ea0b17ba169b2997d4 | C | 9,439 | 341 | /*
* 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... |
2acee76027809d08aabec3559de44eabf2d0f261438778881b2a29f597ae2771 | C | 9,475 | 326 |
/******************************************************************************
*
* 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:
* ... |
afab5660d8b7391e4131adba337c387ecbf7fda0f6a3970e467d5d2254868d18 | C | 9,582 | 263 | //
// Created by sachetto on 07/04/2020.
//
#include "../alg/grid/grid.h"
#include "../config/domain_config.h"
#include "../config/save_mesh_config.h"
#include "../3dparty/ini_parser/ini.h"
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../utils/stop_watch.h"
#include "../vtk_utils/vtk_unstru... |
5f216fede797c4afc34ccba192a0a93df15b6754148aec793abf48af14285680 | C | 9,601 | 342 | /*
* 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... |
70d1901afc4fcfc5e54b5668b83076be1ed8c5ce3761936f7e10fa4f2bdf1e48 | C | 9,671 | 355 | /*
* 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... |
b8f3ff34ca2bc122bfc9e0f345058573749f9fe38a873d63c1d3107d1128ce8d | C | 9,707 | 346 | //Feichen Shen
//Float/half conversion
//avx/f16c CPU support
#include "malloc.h"
#include "stdint.h"
#include "stdio.h"
#include "string.h"
#include "x86intrin.h"
#define buffer_size 1024*1024
typedef FILE* file_handle;
file_handle binary_input_handles[256];
FILE * output_file;
int input_count = 0;
void cpuid(u... |
96aacd2a55a86ca1e6e94e11201f1d1cd2ec831748b7a02408ebc9c05e243406 | C | 9,880 | 265 | /*
bessel.c is a C port of select functions from the
python library bessel filter implementation, scipy.signal.bessel.
Copyright (c) 2001, 2002 Enthought, Inc.
All rights reserved.
Copyright (c) 2003-2016 SciPy Developers.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modifi... |
0697445eefe63998a222d4dd150aec9d965262da58fbcf0997eea5678f68d851 | C | 9,916 | 345 | /*
* 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... |
8ffd0235798712c87c8126f54503a75066153d37691cc48f9cd6ec618920bd9e | C | 9,943 | 277 | #include <stdio.h>
#include <limits.h>
#include "mmpriv.h"
void mm_idxopt_init(mm_idxopt_t *opt)
{
memset(opt, 0, sizeof(mm_idxopt_t));
opt->k = 15, opt->w = 10, opt->flag = 0;
opt->bucket_bits = 14;
opt->mini_batch_size = 50000000;
opt->batch_size = 8000000000ULL;
}
void mm_mapopt_init(mm_mapopt_t *opt)
{
mems... |
d00d20c7c49ea7abe588acade478871a9d0edf5a0e02393b914655fcf0fde733 | C | 9,981 | 319 |
/******************************************************************************
*
* 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:
* ... |
002a74caa725cdf34deb78cfe05751c7a857ecb9e6855ffe1d7e5b369faaad2b | C | 10,077 | 357 | //========================================================================
// GLFW 3.4 - www.glfw.org
//------------------------------------------------------------------------
// Copyright (c) 2002-2006 Marcus Geelnard
// Copyright (c) 2006-2018 Camilla Löwy <[email protected]>
//
// This software is provided 'as-is... |
691110e219672ebf30f7b7e3d40f12ef128a0be40847b6785337c24824b7224a | C | 10,166 | 383 | /*
* 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... |
ddb98b8cb8cd4389ea8bbee171c0da772a93a03ff8c37c688dc556faa1206117 | C | 10,331 | 395 | /*
* 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... |
f1c432eb8145755d613cf27fd7c19f1605b728a994307a6057668c8ea883d39e | C | 10,378 | 362 |
/******************************************************************************
*
* 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://... |
263c8b8bb4a62ab49364976546a229c8b91d431d07600c80ff2afdff4469f01b | C | 10,390 | 393 |
/******************************************************************************
*
* 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:
* ... |
a9422b0a36b60fadb3ad4edd8649b3625be9de794d0b25ce31385814776afd99 | C | 10,418 | 356 | #include <stdio.h>
#include "CRN2017_TASK1_IKACh.h"
real max_step;
real min_step;
real abstol;
real reltol;
bool adpt;
real *ode_dt, *ode_previous_dt, *ode_time_new;
GET_CELL_MODEL_DATA(init_cell_model_data)
{
if(get_initial_v)
cell_model->initial_v = INITIAL_V;
if(get_neq)
cell_model->numbe... |
95a35a14e8505e4cd7e8e956b68ba74e94c9f5f9eb9e6b4f5b2756f21c8c24a7 | C | 10,421 | 339 | #include "lbfgsb.h"
int prn1lb(integer *n, integer *m, double *l,
double *u, double *x, integer *iprint, fileType itfile,
double *epsmch)
{
/*
************
Subroutine prn1lb
This subroutine prints the input data, initial point, upper and
lower bounds of each variable, machine precision, ... |
d6a740f8634e46c5dac779ae6f82896f7ba11c4d9f513a0403009e757bc36ad0 | C | 10,470 | 383 | /*
* 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... |
366d19f23a76f640761df3ad626d1f44b25971f4b81d908eb02325b726a01f1a | C | 10,495 | 300 | #include "../3dparty/ini_parser/ini_file_sections.h"
#include "../3dparty/sds/sds.h"
#include "../3dparty/stb_ds.h"
#include "../config/config_parser.h"
#include "batch_utils.h"
#include <stdio.h>
#include <string.h>
void configure_new_parameters(struct changed_parameters *changed, struct user_options *options) {
... |
8e1a8b33c68dcccec202926fe52b91d79b2767a0a3b277b367598c74aee31b64 | C | 10,495 | 310 |
/******************************************************************************
*
* 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:
* ... |
8852c6aa641f3af107f835ae2b9d56012e5eb660d07feec94e7a13c4426595bf | C | 10,554 | 366 | /* dsbmv.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... |
ac5c54214bcb84cd28d5a625db1ec73b7a99c0348f60197ce94931c514375302 | C | 10,568 | 388 |
/******************************************************************************
*
* 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:
* ... |
2c83fcf758fdd8a842c1e8e3123af48a4a40c8560e89e190c5fabec0cce87ed9 | C | 10,578 | 368 | /* ssbmv.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... |
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