set(HAVE_RDTSCP 1)
endif()
-include(gmxTestFloatFormat)
-gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
- GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
- GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
-
include(gmxTestLargeFiles)
gmx_test_large_files(GMX_LARGEFILES)
include(gmxTestPipes)
gmx_test_pipes(HAVE_PIPES)
-include(gmxTestIsfinite)
-gmx_test_isfinite(HAVE_ISFINITE)
-gmx_test__isfinite(HAVE__ISFINITE)
-gmx_test__finite(HAVE__FINITE)
-
include(gmxTestCXX11)
gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
if(NOT GMX_CXX11_SUPPORTED)
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include <stdio.h>
-
-volatile const double abc [10] = {
- /* Zero-terminated strings encoded as floating-point numbers */
- /* "GROMACSX" in ascii */
- (double) 3.80279098314984902657e+35, (double) 0.0,
- /* "GROMACSX" in ebcdic */
- (double) -1.37384666579378297437e+38, (double) 0.0,
- /* "D__float" (vax) */
- (double) 3.53802595280598432000e+18, (double) 0.0,
- /* "IBMHEXFP" s390/ascii */
- (double) 1.77977764695171661377e+10, (double) 0.0,
- /* "IBMHEXFP" s390/ebcdic */
- (double) -5.22995989424860458374e+10, (double) 0.0,
-};
-
-/* Check that a double is 8 bytes - compilation dies if it isnt */
-extern char xyz [sizeof(double) == 8 ? 1 : -1];
-
-int
-main()
-{
- int i;
- double d;
-
- /* Make sure some compilers do not optimize away the entire structure
- * with floating-point data by using it to produce a return value.
- */
- for (i = 0, d = 0; i < 10; i++)
- {
- d += abc[i];
- }
- return (d == 12345.0);
-}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# warnings about harmless things in src/gromacs/utility/cstringutil.h.
set(HAVE_PWD_H OFF)
-# The automatic testing for endianness does not work for the BlueGene cross-compiler
-set(GMX_FLOAT_FORMAT_IEEE754 1 CACHE INTERNAL "" FORCE)
-set(GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER 1 CACHE INTERNAL "BlueGene has big-endian floating-point byte order (by default)" FORCE)
-set(GMX_IEEE754_BIG_ENDIAN_WORD_ORDER 1 CACHE INTERNAL "BlueGene has big-endian floating-point word order (by default)" FORCE)
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2009,2014, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-# - Define macro to determine floating point format properties
-#
-# GMX_TEST_FLOAT_FORMAT(FP_IEEE754 FP_BIG_ENDIAN_BYTE FP_BIG_ENDIAN_WORD)
-#
-# The thee variables are set to true when:
-# FP_IEEE754 Floating-point numbers are stored in IEEE754 format
-# FP_BIG_ENDIAN_BYTE The order of bytes in each FP word (4 bytes) is big endian
-# FP_BIG_ENDIAN_WORD The order of FP words in double precision dwords (2 words) is big endian
-#
-# On *most* platforms the two last tests will be the same as the integer endian,
-# big e.g. ARM processors have different byte/word order for floating-point storage,
-# so we figured it is a good idea to test both before relying on the format.
-
-MACRO(GMX_TEST_FLOAT_FORMAT FP_IEEE754 FP_BIG_ENDIAN_BYTE FP_BIG_ENDIAN_WORD)
- IF(NOT DEFINED HAVE_${FP_IEEE754})
- MESSAGE(STATUS "Checking floating point format")
-
- TRY_COMPILE(HAVE_${FP_IEEE754} "${CMAKE_BINARY_DIR}"
- "${CMAKE_SOURCE_DIR}/cmake/TestFloatFormat.cpp"
- COPY_FILE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin")
-
- if(HAVE_${FP_IEEE754})
-
- # dont match first/last letter because of string rounding errors :-)
- FILE(STRINGS "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin"
- GMX_IEEE754_BB_BW LIMIT_COUNT 1 REGEX "ROMACS")
- FILE(STRINGS "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin"
- GMX_IEEE754_BB_LW LIMIT_COUNT 1 REGEX "CSXGRO")
- FILE(STRINGS "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin"
- GMX_IEEE754_LB_BW LIMIT_COUNT 1 REGEX "ORGXSC")
- FILE(STRINGS "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin"
- GMX_IEEE754_LB_LW REGEX "SCAMOR")
- FILE(STRINGS "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/TestFloatFormat.bin"
- GMX_IEEE754 REGEX "GROMACS|CSXGRO|ORGXSC|SCAMOR")
-
- # OS X Universal binaries will contain both strings, set it to the host
- IF(GMX_IEEE754_BB_BW AND GMX_IEEE754_LB_LW)
- IF(CMAKE_SYSTEM_PROCESSOR MATCHES powerpc)
- SET(GMX_IEEE754_BB_BW TRUE)
- SET(GMX_IEEE754_LB_LW FALSE)
- ELSE()
- SET(GMX_IEEE754_BB_BW FALSE)
- SET(GMX_IEEE754_LB_LW TRUE)
- ENDIF()
- MESSAGE(STATUS "GMX_TEST_IEEE754_FORMAT found different results, consider setting CMAKE_OSX_ARCHITECTURES or CMAKE_TRY_COMPILE_OSX_ARCHITECTURES to one or no architecture !")
- ENDIF()
-
- IF(GMX_IEEE754)
- SET(${FP_IEEE754} 1 CACHE INTERNAL "Result of test for IEEE754 FP format" FORCE)
- ENDIF()
-
- IF(GMX_IEEE754_BB_BW OR GMX_IEEE754_BB_LW)
- SET(${FP_BIG_ENDIAN_BYTE} 1 CACHE INTERNAL "Result of test for big endian FP byte order" FORCE)
- ENDIF()
-
- IF(GMX_IEEE754_BB_BW OR GMX_IEEE754_LB_BW)
- SET(${FP_BIG_ENDIAN_WORD} 1 CACHE INTERNAL "Result of test for big endian FP word order" FORCE)
- ENDIF()
-
- endif()
-
- # just some informational output for the user
- if(GMX_IEEE754_BB_BW)
- MESSAGE(STATUS "Checking floating point format - IEEE754 (BE byte, BE word)")
- elseif(GMX_IEEE754_BB_LW)
- MESSAGE(STATUS "Checking floating point format - IEEE754 (BE byte, LE word)")
- elseif(GMX_IEEE754_LB_BW)
- MESSAGE(STATUS "Checking floating point format - IEEE754 (LE byte, BE word)")
- elseif(GMX_IEEE754_LB_LW)
- MESSAGE(STATUS "Checking floating point format - IEEE754 (LE byte, LE word)")
- else()
- MESSAGE(STATUS "Checking floating point format - unknown")
- MESSAGE(WARNING "Cannot detect your floating-point format. It is extremely unlikely to be anything else than IEEE754, but if we do not know the endian we need to rely on your OS providing the math functions erfd() and erfcd() rather than using our built-in ones.")
- endif()
- ENDIF()
-ENDMACRO(GMX_TEST_FLOAT_FORMAT FP_IEEE754 FP_BIG_ENDIAN_BYTE FP_BIG_ENDIAN_WORD)
-
-
-
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-# - Define macro to check if isfinite or _isfinite exists
-#
-# gmx_test_isfinite(VARIABLE)
-#
-# VARIABLE will be set to true if isfinite exists
-#
-# gmx_test__isfinite(VARIABLE)
-#
-# VARIABLE will be set to true if _isfinite exists
-#
-# gmx_test__finite(VARIABLE) - disabled since it doesn't seem to work the way the MSVC docs suggest
-#
-# VARIABLE will be set to true if _finite exists
-#
-
-MACRO(gmx_test_isfinite VARIABLE)
-
- if(NOT DEFINED isfinite_compile_ok)
- MESSAGE(STATUS "Checking for isfinite")
-
- set(CMAKE_REQUIRED_INCLUDES "math.h")
- if (HAVE_LIBM)
- set(CMAKE_REQUIRED_LIBRARIES "m")
- endif()
- check_c_source_compiles(
- "#include <math.h>
-int main(void) {
- float f;
- isfinite(f);
- return 0;
-}" isfinite_compile_ok)
-
- if(isfinite_compile_ok)
- MESSAGE(STATUS "Checking for isfinite - yes")
- else()
- MESSAGE(STATUS "Checking for isfinite - no")
- endif()
- set(isfinite_compile_ok "${isfinite_compile_ok}" CACHE INTERNAL "Result of isfinite check")
- set(CMAKE_REQUIRED_INCLUDES)
- set(CMAKE_REQUIRED_LIBRARIES)
- endif()
-
- if(isfinite_compile_ok)
- set(${VARIABLE} ${isfinite_compile_ok}
- "Result of test for isfinite")
- endif()
-
-ENDMACRO(gmx_test_isfinite VARIABLE)
-
-MACRO(gmx_test__isfinite VARIABLE)
-
- if(NOT DEFINED _isfinite_compile_ok)
- MESSAGE(STATUS "Checking for _isfinite")
-
- set(CMAKE_REQUIRED_INCLUDES "math.h")
- if (HAVE_LIBM)
- set(CMAKE_REQUIRED_LIBRARIES "m")
- endif()
- check_c_source_compiles(
- "#include <math.h>
-int main(void) {
- float f;
- _isfinite(f);
-}" _isfinite_compile_ok)
-
- if(_isfinite_compile_ok)
- MESSAGE(STATUS "Checking for _isfinite - yes")
- else()
- MESSAGE(STATUS "Checking for _isfinite - no")
- endif()
- set(_isfinite_compile_ok "${_isfinite_compile_ok}" CACHE INTERNAL "Result of _isfinite check")
- set(CMAKE_REQUIRED_INCLUDES)
- set(CMAKE_REQUIRED_LIBRARIES)
- endif()
-
- if(_isfinite_compile_ok)
- set(${VARIABLE} ${_isfinite_compile_ok}
- "Result of test for _isfinite")
- endif()
-
-ENDMACRO(gmx_test__isfinite VARIABLE)
-
-# Necessary for MSVC
-MACRO(gmx_test__finite VARIABLE)
-
- if(NOT DEFINED _finite_compile_ok)
- MESSAGE(STATUS "Checking for _finite")
-
- set(CMAKE_REQUIRED_INCLUDES "float.h")
- check_c_source_compiles(
- "#include <float.h>
-int main(void) {
- float f;
- _finite(f);
-}" _finite_compile_ok)
-
- if(_finite_compile_ok)
- MESSAGE(STATUS "Checking for _finite - yes")
- else()
- MESSAGE(STATUS "Checking for _finite - no")
- endif()
- set(_finite_compile_ok "${_finite_compile_ok}" CACHE INTERNAL "Result of _finite check")
- set(CMAKE_REQUIRED_INCLUDES)
- endif()
-
- if(_finite_compile_ok)
- set(${VARIABLE} ${_finite_compile_ok}
- "Result of test for _finite")
- endif()
-
-ENDMACRO(gmx_test__finite VARIABLE)
/* TODO: For now, disable Doxygen warnings from here */
/*! \cond */
-/* IEEE754 floating-point format. Memory layout is defined by macros
- * GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER and GMX_IEEE754_BIG_ENDIAN_WORD_ORDER.
- */
-#cmakedefine01 GMX_FLOAT_FORMAT_IEEE754
-
/* Work around broken calloc() */
#cmakedefine GMX_BROKEN_CALLOC
/* Define to 1 if you have the all the affinity functions in sched.h */
#cmakedefine HAVE_SCHED_AFFINITY
-/* Bytes in IEEE fp word are in big-endian order if set, little-endian if not.
- Only relevant when FLOAT_FORMAT_IEEE754 is defined. */
-#cmakedefine01 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
-
-/* The two words in a double precision variable are in b ig-endian order if
- set, little-endian if not. Do NOT assume this is the same as the byte
- order! Only relevant when FLOAT_FORMAT_IEEE754 is defined. */
-#cmakedefine01 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
-
/* Define if SIGUSR1 is present */
#cmakedefine01 HAVE_SIGUSR1
#include "expfit.h"
-#include <math.h>
#include <string.h>
+#include <cmath>
+
#include <algorithm>
#include "external/lmfit/lmcurve.h"
if (a[3] != 0)
{
erfarg = (x-a[2])/(a[3]*a[3]);
- myerf = gmx_erfd(erfarg);
+ myerf = std::erf(erfarg);
}
else
{
}
else
{
- return gmx_expm1(x);
+ return std::expm1(x);
}
}
#include "long-range-correction.h"
-#include <math.h>
+#include <cmath>
#include "gromacs/legacyheaders/names.h"
#include "gromacs/legacyheaders/types/commrec.h"
dr = 1.0/rinv;
ewcdr = ewc_q*dr;
- vc = qqA*gmx_erf(ewcdr)*rinv;
+ vc = qqA*std::erf(ewcdr)*rinv;
Vexcl_q += vc;
#ifdef GMX_DOUBLE
/* Relative accuracy at R_ERF_R_INACC of 3e-10 */
real dr;
dr = 1.0/rinv;
- v = gmx_erf(ewc_q*dr)*rinv;
+ v = std::erf(ewc_q*dr)*rinv;
vc = qqL*v;
Vexcl_q += vc;
/* fscal is the scalar force pre-multiplied by rinv,
/* TODO: centralize the code that sets the potentials shifts */
if (ic->coulomb_modifier == eintmodPOTSHIFT)
{
- ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb);
}
if (EVDW_PME(ic->vdwtype))
{
#include "pme-solve.h"
-#include <math.h>
+#include <cmath>
#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/math/vec.h"
for (kx = start; kx < end; kx++)
{
mk = tmp2[kx];
- tmp2[kx] = sqrt(M_PI)*mk*gmx_erfc(mk);
+ tmp2[kx] = sqrt(M_PI)*mk*std::erfc(mk);
}
}
#endif
#include "matio.h"
#include <cctype>
+#include <cmath>
#include <cstdio>
#include <cstring>
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
-#define round(a) (int)(a+0.5)
-
static const char mapper[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*()-_=+{}|;:',<.>/?";
#define NMAP (long int)strlen(mapper)
fprintf(out, "\"");
for (i = 0; (i < n_x); i++)
{
- c = gmx_nint((mat[i][j]-lo)*invlevel);
+ c = std::round((mat[i][j]-lo)*invlevel);
if (c < 0)
{
c = 0;
{
if (mat[i][j] >= mid)
{
- c = nmid+gmx_nint((mat[i][j]-mid)*invlev_hi);
+ c = nmid+std::round((mat[i][j]-mid)*invlev_hi);
}
else if (mat[i][j] >= lo)
{
- c = gmx_nint((mat[i][j]-lo)*invlev_lo);
+ c = std::round((mat[i][j]-lo)*invlev_lo);
}
else
{
anm_copy[2] = nc;
if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
{
- atomnumber = gmx_nint(eval);
+ atomnumber = std::round(eval);
}
else
{
anm_copy[1] = nc;
if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
{
- atomnumber = gmx_nint(eval);
+ atomnumber = std::round(eval);
}
}
}
anm_copy[1] = nc;
if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
{
- atomnumber = gmx_nint(eval);
+ atomnumber = std::round(eval);
}
}
atoms->atom[i].atomnumber = atomnumber;
lambda = eigval[i]*AMU;
w = std::sqrt(BOLTZMANN*temp/lambda)/NANO;
hwkT = (hbar*w)/(BOLTZMANN*temp);
- dS = (hwkT/gmx_expm1(hwkT) - gmx_log1p(-std::exp(-hwkT)));
+ dS = (hwkT/std::expm1(hwkT) - std::log1p(-std::exp(-hwkT)));
S += dS;
if (debug)
{
fprintf(stdout, "First time is not larger than 0, using index number as time for power fit\n");
for (i = 0; i < n; i++)
{
- x[i] = gmx_log1p(static_cast<real>(i));
+ x[i] = std::log1p(static_cast<real>(i));
}
}
static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi)
{
- int cy, index = gmx_nint(r/gb->spacing);
+ int cy, index = std::round(r/gb->spacing);
real alpha;
if (index < gb->nelem)
cosa = cos_angle(mu[gi], mu[gj]);
phi = 0;
}
- if (debug || gmx_isnan(cosa))
+ if (debug || std::isnan(cosa))
{
fprintf(debug ? debug : stderr,
"mu[%d] = %5.2f %5.2f %5.2f |mi| = %5.2f, mu[%d] = %5.2f %5.2f %5.2f |mj| = %5.2f rr = %5.2f cosa = %5.2f\n",
}
else
{
- return bhn/gmx_expm1(bhn) - gmx_log1p(-std::exp(-bhn));
+ return bhn/std::expm1(bhn) - std::log1p(-std::exp(-bhn));
}
}
}
else
{
- return bhn/2 + bhn/gmx_expm1(bhn)-1;
+ return bhn/2 + bhn/std::expm1(bhn)-1;
}
}
#include "gmxpre.h"
#include <cctype>
+#include <cmath>
#include <cstdlib>
#include <cstring>
{
qtot += atoms.atom[i].q;
}
- iqtot = gmx_nint(qtot);
+ iqtot = std::round(qtot);
if (conc > 0)
{
/* Compute number of ions to be added */
vol = det(box);
- nsalt = gmx_nint(conc*vol*AVOGADRO/1e24);
+ nsalt = std::round(conc*vol*AVOGADRO/1e24);
p_num = abs(nsalt*n_q);
n_num = abs(nsalt*p_q);
}
*skmean += skmol[i];
/* Compute sliced stuff in x y z*/
- slindex_x = gmx_nint((1+x[i][XX]/box[XX][XX])*nslicex) % nslicex;
- slindex_y = gmx_nint((1+x[i][YY]/box[YY][YY])*nslicey) % nslicey;
- slindex_z = gmx_nint((1+x[i][ZZ]/box[ZZ][ZZ])*nslicez) % nslicez;
+ slindex_x = static_cast<int>(std::round((1+x[i][XX]/box[XX][XX])*nslicex)) % nslicex;
+ slindex_y = static_cast<int>(std::round((1+x[i][YY]/box[YY][YY])*nslicey)) % nslicey;
+ slindex_z = static_cast<int>(std::round((1+x[i][ZZ]/box[ZZ][ZZ])*nslicez)) % nslicez;
sggrid[slindex_x][slindex_y][slindex_z] += sgmol[i];
skgrid[slindex_x][slindex_y][slindex_z] += skmol[i];
(sl_count[slindex_x][slindex_y][slindex_z])++;
*skmean += skmol[i];
/* Compute sliced stuff */
- sl_index = gmx_nint((1+x[i][slice_dim]/box[slice_dim][slice_dim])*nslice) % nslice;
+ sl_index = static_cast<int>(std::round((1+x[i][slice_dim]/box[slice_dim][slice_dim])*nslice)) % nslice;
sgslice[sl_index] += sgmol[i];
skslice[sl_index] += skmol[i];
sl_count[sl_index]++;
if (MASTER(cr))
{
calc_q2all(mtop, &(info->q2all), &(info->q2allnr));
- info->ewald_rtol[0] = gmx_erfc(info->rcoulomb[0]*info->ewald_beta[0]);
+ info->ewald_rtol[0] = std::erfc(info->rcoulomb[0]*info->ewald_beta[0]);
/* Write some info to log file */
fprintf(fp_out, "Box volume : %g nm^3\n", info->volume);
fprintf(fp_out, "Number of charged atoms : %d (total atoms %d)\n", ncharges, info->natoms);
}
}
- info->ewald_rtol[0] = gmx_erfc(info->rcoulomb[0]*info->ewald_beta[0]);
+ info->ewald_rtol[0] = std::erfc(info->rcoulomb[0]*info->ewald_beta[0]);
if (MASTER(cr))
{
fp_out[i] = open_trx(fnms_out[i], "w");
}
k = 0;
- if (gmx_nint(time[k] - t) != 0)
+ if (std::round(time[k] - t) != 0)
{
gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
}
for (i = 0; (i < nset); i++)
{
- j = gmx_nint(value[i][k]);
+ j = std::round(value[i][k]);
range_check(j, 0, nset);
if (bSet[j])
{
fprintf(debug, "%10g", t[i]);
for (j = 0; (j < nset); j++)
{
- fprintf(debug, " %3d", gmx_nint(val[j][i]));
+ fprintf(debug, " %3d", static_cast<int>(std::round(val[j][i])));
}
fprintf(debug, "\n");
}
/* get flat distribution in [0,1] using cumulative distribution function of Gauusian
Note: CDF(Gaussian) = 0.5*{1+erf[x/sqrt(2)]}
*/
- r = 0.5*(1+gmx_erf(x*invsqrt2));
+ r = 0.5*(1+std::erf(x*invsqrt2));
searchCumulative(thisWindow->cum[pullid], nbins+1, r, &r_index);
synthWindow->Histo[0][r_index] += 1.;
}
{
x = -x;
}
- ix = gmx_nint(x);
+ ix = std::round(x);
return (fabs(x-ix) < tol);
}
}
else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
{
- simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
+ simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(std::expm1(temperature_lambdas[i])/std::expm1(1.0));
}
else
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
i++;
beta *= 2;
}
- while (gmx_erfc(beta*rc) > rtol);
+ while (std::erfc(beta*rc) > rtol);
/* Do a binary search with tolerance 2^-60 */
n = i+60;
for (i = 0; i < n; i++)
{
beta = (low+high)/2;
- if (gmx_erfc(beta*rc) > rtol)
+ if (std::erfc(beta*rc) > rtol)
{
low = beta;
}
#include <cmath>
#ifdef GMX_NATIVE_WINDOWS
+// for _BitScanReverse()
#include <intrin.h>
#endif
-#ifdef HAVE__FINITE
-#include <float.h>
-#endif
#ifndef GMX_NATIVE_WINDOWS
+// for fp exception control stuff
#include <fenv.h>
#endif
-int gmx_nint(real a)
-{
- const real half = .5;
- int result;
-
- result = (a < 0.) ? ((int)(a - half)) : ((int)(a + half));
- return result;
-}
-
-real cuberoot(real x)
-{
- if (x < 0)
- {
- return (-std::pow(-x, 1.0/3.0));
- }
- else
- {
- return (std::pow(x, 1.0/3.0));
- }
-}
-
-real sign(real x, real y)
-{
- if (y < 0)
- {
- return -fabs(x);
- }
- else
- {
- return +fabs(x);
- }
-}
-
-/* Double and single precision erf() and erfc() from
- * the Sun Freely Distributable Math Library FDLIBM.
- * See http://www.netlib.org/fdlibm
- * Specific file used: s_erf.c, version 1.3 95/01/18
- */
-/*
- * ====================================================
- * Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved.
- *
- * Developed at SunSoft, a Sun Microsystems, Inc. business.
- * Permission to use, copy, modify, and distribute this
- * software is freely granted, provided that this notice
- * is preserved.
- * ====================================================
- */
-
-static const double
- tiny = 1e-300,
- half = 5.00000000000000000000e-01, /* 0x3FE00000, 0x00000000 */
- one = 1.00000000000000000000e+00, /* 0x3FF00000, 0x00000000 */
- two = 2.00000000000000000000e+00, /* 0x40000000, 0x00000000 */
-/* c = (float)0.84506291151 */
- erx = 8.45062911510467529297e-01, /* 0x3FEB0AC1, 0x60000000 */
-/*
- * Coefficients for approximation to erf on [0,0.84375]
- */
- efx = 1.28379167095512586316e-01, /* 0x3FC06EBA, 0x8214DB69 */
- efx8 = 1.02703333676410069053e+00, /* 0x3FF06EBA, 0x8214DB69 */
- pp0 = 1.28379167095512558561e-01, /* 0x3FC06EBA, 0x8214DB68 */
- pp1 = -3.25042107247001499370e-01, /* 0xBFD4CD7D, 0x691CB913 */
- pp2 = -2.84817495755985104766e-02, /* 0xBF9D2A51, 0xDBD7194F */
- pp3 = -5.77027029648944159157e-03, /* 0xBF77A291, 0x236668E4 */
- pp4 = -2.37630166566501626084e-05, /* 0xBEF8EAD6, 0x120016AC */
- qq1 = 3.97917223959155352819e-01, /* 0x3FD97779, 0xCDDADC09 */
- qq2 = 6.50222499887672944485e-02, /* 0x3FB0A54C, 0x5536CEBA */
- qq3 = 5.08130628187576562776e-03, /* 0x3F74D022, 0xC4D36B0F */
- qq4 = 1.32494738004321644526e-04, /* 0x3F215DC9, 0x221C1A10 */
- qq5 = -3.96022827877536812320e-06, /* 0xBED09C43, 0x42A26120 */
-/*
- * Coefficients for approximation to erf in [0.84375,1.25]
- */
- pa0 = -2.36211856075265944077e-03, /* 0xBF6359B8, 0xBEF77538 */
- pa1 = 4.14856118683748331666e-01, /* 0x3FDA8D00, 0xAD92B34D */
- pa2 = -3.72207876035701323847e-01, /* 0xBFD7D240, 0xFBB8C3F1 */
- pa3 = 3.18346619901161753674e-01, /* 0x3FD45FCA, 0x805120E4 */
- pa4 = -1.10894694282396677476e-01, /* 0xBFBC6398, 0x3D3E28EC */
- pa5 = 3.54783043256182359371e-02, /* 0x3FA22A36, 0x599795EB */
- pa6 = -2.16637559486879084300e-03, /* 0xBF61BF38, 0x0A96073F */
- qa1 = 1.06420880400844228286e-01, /* 0x3FBB3E66, 0x18EEE323 */
- qa2 = 5.40397917702171048937e-01, /* 0x3FE14AF0, 0x92EB6F33 */
- qa3 = 7.18286544141962662868e-02, /* 0x3FB2635C, 0xD99FE9A7 */
- qa4 = 1.26171219808761642112e-01, /* 0x3FC02660, 0xE763351F */
- qa5 = 1.36370839120290507362e-02, /* 0x3F8BEDC2, 0x6B51DD1C */
- qa6 = 1.19844998467991074170e-02, /* 0x3F888B54, 0x5735151D */
-/*
- * Coefficients for approximation to erfc in [1.25,1/0.35]
- */
- ra0 = -9.86494403484714822705e-03, /* 0xBF843412, 0x600D6435 */
- ra1 = -6.93858572707181764372e-01, /* 0xBFE63416, 0xE4BA7360 */
- ra2 = -1.05586262253232909814e+01, /* 0xC0251E04, 0x41B0E726 */
- ra3 = -6.23753324503260060396e+01, /* 0xC04F300A, 0xE4CBA38D */
- ra4 = -1.62396669462573470355e+02, /* 0xC0644CB1, 0x84282266 */
- ra5 = -1.84605092906711035994e+02, /* 0xC067135C, 0xEBCCABB2 */
- ra6 = -8.12874355063065934246e+01, /* 0xC0545265, 0x57E4D2F2 */
- ra7 = -9.81432934416914548592e+00, /* 0xC023A0EF, 0xC69AC25C */
- sa1 = 1.96512716674392571292e+01, /* 0x4033A6B9, 0xBD707687 */
- sa2 = 1.37657754143519042600e+02, /* 0x4061350C, 0x526AE721 */
- sa3 = 4.34565877475229228821e+02, /* 0x407B290D, 0xD58A1A71 */
- sa4 = 6.45387271733267880336e+02, /* 0x40842B19, 0x21EC2868 */
- sa5 = 4.29008140027567833386e+02, /* 0x407AD021, 0x57700314 */
- sa6 = 1.08635005541779435134e+02, /* 0x405B28A3, 0xEE48AE2C */
- sa7 = 6.57024977031928170135e+00, /* 0x401A47EF, 0x8E484A93 */
- sa8 = -6.04244152148580987438e-02, /* 0xBFAEEFF2, 0xEE749A62 */
-/*
- * Coefficients for approximation to erfc in [1/.35,28]
- */
- rb0 = -9.86494292470009928597e-03, /* 0xBF843412, 0x39E86F4A */
- rb1 = -7.99283237680523006574e-01, /* 0xBFE993BA, 0x70C285DE */
- rb2 = -1.77579549177547519889e+01, /* 0xC031C209, 0x555F995A */
- rb3 = -1.60636384855821916062e+02, /* 0xC064145D, 0x43C5ED98 */
- rb4 = -6.37566443368389627722e+02, /* 0xC083EC88, 0x1375F228 */
- rb5 = -1.02509513161107724954e+03, /* 0xC0900461, 0x6A2E5992 */
- rb6 = -4.83519191608651397019e+02, /* 0xC07E384E, 0x9BDC383F */
- sb1 = 3.03380607434824582924e+01, /* 0x403E568B, 0x261D5190 */
- sb2 = 3.25792512996573918826e+02, /* 0x40745CAE, 0x221B9F0A */
- sb3 = 1.53672958608443695994e+03, /* 0x409802EB, 0x189D5118 */
- sb4 = 3.19985821950859553908e+03, /* 0x40A8FFB7, 0x688C246A */
- sb5 = 2.55305040643316442583e+03, /* 0x40A3F219, 0xCEDF3BE6 */
- sb6 = 4.74528541206955367215e+02, /* 0x407DA874, 0xE79FE763 */
- sb7 = -2.24409524465858183362e+01; /* 0xC03670E2, 0x42712D62 */
-
-double gmx_erfd(double x)
-{
-#if GMX_FLOAT_FORMAT_IEEE754
- gmx_int32_t hx, ix, i;
- double R, S, P, Q, s, y, z, r;
-
- union
- {
- double d;
- int i[2];
- }
- conv;
-
- conv.d = x;
-
-#if GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
- hx = conv.i[0];
-#else
- hx = conv.i[1];
-#endif
-
- ix = hx&0x7fffffff;
- if (ix >= 0x7ff00000)
- {
- /* erf(nan)=nan */
- i = ((gmx_uint32_t)hx>>31)<<1;
- return (double)(1-i)+one/x; /* erf(+-inf)=+-1 */
- }
-
- if (ix < 0x3feb0000)
- {
- /* |x|<0.84375 */
- if (ix < 0x3e300000)
- {
- /* |x|<2**-28 */
- if (ix < 0x00800000)
- {
- return 0.125*(8.0*x+efx8*x); /*avoid underflow */
- }
- return x + efx*x;
- }
- z = x*x;
- r = pp0+z*(pp1+z*(pp2+z*(pp3+z*pp4)));
- s = one+z*(qq1+z*(qq2+z*(qq3+z*(qq4+z*qq5))));
- y = r/s;
- return x + x*y;
- }
- if (ix < 0x3ff40000)
- {
- /* 0.84375 <= |x| < 1.25 */
- s = fabs(x)-one;
- P = pa0+s*(pa1+s*(pa2+s*(pa3+s*(pa4+s*(pa5+s*pa6)))));
- Q = one+s*(qa1+s*(qa2+s*(qa3+s*(qa4+s*(qa5+s*qa6)))));
- if (hx >= 0)
- {
- return erx + P/Q;
- }
- else
- {
- return -erx - P/Q;
- }
- }
- if (ix >= 0x40180000)
- {
- /* inf>|x|>=6 */
- if (hx >= 0)
- {
- return one-tiny;
- }
- else
- {
- return tiny-one;
- }
- }
- x = fabs(x);
- s = one/(x*x);
- if (ix < 0x4006DB6E)
- {
- /* |x| < 1/0.35 */
- R = ra0+s*(ra1+s*(ra2+s*(ra3+s*(ra4+s*(ra5+s*(ra6+s*ra7))))));
- S = one+s*(sa1+s*(sa2+s*(sa3+s*(sa4+s*(sa5+s*(sa6+s*(sa7+s*sa8)))))));
- }
- else
- {
- /* |x| >= 1/0.35 */
- R = rb0+s*(rb1+s*(rb2+s*(rb3+s*(rb4+s*(rb5+s*rb6)))));
- S = one+s*(sb1+s*(sb2+s*(sb3+s*(sb4+s*(sb5+s*(sb6+s*sb7))))));
- }
-
- conv.d = x;
-
-#if GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
- conv.i[1] = 0;
-#else
- conv.i[0] = 0;
-#endif
-
- z = conv.d;
-
- r = exp(-z*z-0.5625)*exp((z-x)*(z+x)+R/S);
- if (hx >= 0)
- {
- return one-r/x;
- }
- else
- {
- return r/x-one;
- }
-#else
- /* No IEEE754 information. We need to trust that the OS provides erf(). */
- return erf(x);
-#endif
-}
-
-
-double gmx_erfcd(double x)
-{
-#if GMX_FLOAT_FORMAT_IEEE754
- gmx_int32_t hx, ix;
- double R, S, P, Q, s, y, z, r;
-
- union
- {
- double d;
- int i[2];
- }
- conv;
-
- conv.d = x;
-
-#if GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
- hx = conv.i[0];
-#else
- hx = conv.i[1];
-#endif
-
- ix = hx&0x7fffffff;
- if (ix >= 0x7ff00000)
- {
- /* erfc(nan)=nan */
- /* erfc(+-inf)=0,2 */
- return (double)(((gmx_uint32_t)hx>>31)<<1)+one/x;
- }
-
- if (ix < 0x3feb0000)
- {
- /* |x|<0.84375 */
- if (ix < 0x3c700000) /* |x|<2**-56 */
- {
- return one-x;
- }
- z = x*x;
- r = pp0+z*(pp1+z*(pp2+z*(pp3+z*pp4)));
- s = one+z*(qq1+z*(qq2+z*(qq3+z*(qq4+z*qq5))));
- y = r/s;
- if (hx < 0x3fd00000)
- {
- /* x<1/4 */
- return one-(x+x*y);
- }
- else
- {
- r = x*y;
- r += (x-half);
- return half - r;
- }
- }
-
- if (ix < 0x3ff40000)
- {
- /* 0.84375 <= |x| < 1.25 */
- s = fabs(x)-one;
- P = pa0+s*(pa1+s*(pa2+s*(pa3+s*(pa4+s*(pa5+s*pa6)))));
- Q = one+s*(qa1+s*(qa2+s*(qa3+s*(qa4+s*(qa5+s*qa6)))));
- if (hx >= 0)
- {
- z = one-erx; return z - P/Q;
- }
- else
- {
- z = erx+P/Q; return one+z;
- }
- }
- if (ix < 0x403c0000)
- {
- /* |x|<28 */
- x = fabs(x);
- s = one/(x*x);
- if (ix < 0x4006DB6D)
- {
- /* |x| < 1/.35 ~ 2.857143*/
- R = ra0+s*(ra1+s*(ra2+s*(ra3+s*(ra4+s*(ra5+s*(ra6+s*ra7))))));
- S = one+s*(sa1+s*(sa2+s*(sa3+s*(sa4+s*(sa5+s*(sa6+s*(sa7+s*sa8)))))));
- }
- else
- {
- /* |x| >= 1/.35 ~ 2.857143 */
- if (hx < 0 && ix >= 0x40180000)
- {
- return two-tiny; /* x < -6 */
- }
- R = rb0+s*(rb1+s*(rb2+s*(rb3+s*(rb4+s*(rb5+s*rb6)))));
- S = one+s*(sb1+s*(sb2+s*(sb3+s*(sb4+s*(sb5+s*(sb6+s*sb7))))));
- }
-
- conv.d = x;
-
-#if GMX_IEEE754_BIG_ENDIAN_WORD_ORDER
- conv.i[1] = 0;
-#else
- conv.i[0] = 0;
-#endif
-
- z = conv.d;
-
- r = exp(-z*z-0.5625)*exp((z-x)*(z+x)+R/S);
-
- if (hx > 0)
- {
- return r/x;
- }
- else
- {
- return two-r/x;
- }
- }
- else
- {
- if (hx > 0)
- {
- return tiny*tiny;
- }
- else
- {
- return two-tiny;
- }
- }
-#else
- /* No IEEE754 information. We need to trust that the OS provides erfc(). */
- return erfc(x);
-#endif
-}
-
-
-static const float
- tinyf = 1e-30,
- halff = 5.0000000000e-01, /* 0x3F000000 */
- onef = 1.0000000000e+00, /* 0x3F800000 */
- twof = 2.0000000000e+00, /* 0x40000000 */
-/* c = (subfloat)0.84506291151 */
- erxf = 8.4506291151e-01, /* 0x3f58560b */
-/*
- * Coefficients for approximation to erf on [0,0.84375]
- */
- efxf = 1.2837916613e-01, /* 0x3e0375d4 */
- efx8f = 1.0270333290e+00, /* 0x3f8375d4 */
- pp0f = 1.2837916613e-01, /* 0x3e0375d4 */
- pp1f = -3.2504209876e-01, /* 0xbea66beb */
- pp2f = -2.8481749818e-02, /* 0xbce9528f */
- pp3f = -5.7702702470e-03, /* 0xbbbd1489 */
- pp4f = -2.3763017452e-05, /* 0xb7c756b1 */
- qq1f = 3.9791721106e-01, /* 0x3ecbbbce */
- qq2f = 6.5022252500e-02, /* 0x3d852a63 */
- qq3f = 5.0813062117e-03, /* 0x3ba68116 */
- qq4f = 1.3249473704e-04, /* 0x390aee49 */
- qq5f = -3.9602282413e-06, /* 0xb684e21a */
-/*
- * Coefficients for approximation to erf in [0.84375,1.25]
- */
- pa0f = -2.3621185683e-03, /* 0xbb1acdc6 */
- pa1f = 4.1485610604e-01, /* 0x3ed46805 */
- pa2f = -3.7220788002e-01, /* 0xbebe9208 */
- pa3f = 3.1834661961e-01, /* 0x3ea2fe54 */
- pa4f = -1.1089469492e-01, /* 0xbde31cc2 */
- pa5f = 3.5478305072e-02, /* 0x3d1151b3 */
- pa6f = -2.1663755178e-03, /* 0xbb0df9c0 */
- qa1f = 1.0642088205e-01, /* 0x3dd9f331 */
- qa2f = 5.4039794207e-01, /* 0x3f0a5785 */
- qa3f = 7.1828655899e-02, /* 0x3d931ae7 */
- qa4f = 1.2617121637e-01, /* 0x3e013307 */
- qa5f = 1.3637083583e-02, /* 0x3c5f6e13 */
- qa6f = 1.1984500103e-02, /* 0x3c445aa3 */
-/*
- * Coefficients for approximation to erfc in [1.25,1/0.35]
- */
- ra0f = -9.8649440333e-03, /* 0xbc21a093 */
- ra1f = -6.9385856390e-01, /* 0xbf31a0b7 */
- ra2f = -1.0558626175e+01, /* 0xc128f022 */
- ra3f = -6.2375331879e+01, /* 0xc2798057 */
- ra4f = -1.6239666748e+02, /* 0xc322658c */
- ra5f = -1.8460508728e+02, /* 0xc3389ae7 */
- ra6f = -8.1287437439e+01, /* 0xc2a2932b */
- ra7f = -9.8143291473e+00, /* 0xc11d077e */
- sa1f = 1.9651271820e+01, /* 0x419d35ce */
- sa2f = 1.3765776062e+02, /* 0x4309a863 */
- sa3f = 4.3456588745e+02, /* 0x43d9486f */
- sa4f = 6.4538726807e+02, /* 0x442158c9 */
- sa5f = 4.2900814819e+02, /* 0x43d6810b */
- sa6f = 1.0863500214e+02, /* 0x42d9451f */
- sa7f = 6.5702495575e+00, /* 0x40d23f7c */
- sa8f = -6.0424413532e-02, /* 0xbd777f97 */
-/*
- * Coefficients for approximation to erfc in [1/.35,28]
- */
- rb0f = -9.8649431020e-03, /* 0xbc21a092 */
- rb1f = -7.9928326607e-01, /* 0xbf4c9dd4 */
- rb2f = -1.7757955551e+01, /* 0xc18e104b */
- rb3f = -1.6063638306e+02, /* 0xc320a2ea */
- rb4f = -6.3756646729e+02, /* 0xc41f6441 */
- rb5f = -1.0250950928e+03, /* 0xc480230b */
- rb6f = -4.8351919556e+02, /* 0xc3f1c275 */
- sb1f = 3.0338060379e+01, /* 0x41f2b459 */
- sb2f = 3.2579251099e+02, /* 0x43a2e571 */
- sb3f = 1.5367296143e+03, /* 0x44c01759 */
- sb4f = 3.1998581543e+03, /* 0x4547fdbb */
- sb5f = 2.5530502930e+03, /* 0x451f90ce */
- sb6f = 4.7452853394e+02, /* 0x43ed43a7 */
- sb7f = -2.2440952301e+01; /* 0xc1b38712 */
-
-
-float gmx_erff(float x)
-{
- gmx_int32_t hx, ix, i;
- float R, S, P, Q, s, y, z, r;
-
- union
- {
- float f;
- int i;
- }
- conv;
-
- conv.f = x;
- hx = conv.i;
-
- ix = hx&0x7fffffff;
- if (ix >= 0x7f800000)
- {
- /* erf(nan)=nan */
- i = ((gmx_uint32_t)hx>>31)<<1;
- return (float)(1-i)+onef/x; /* erf(+-inf)=+-1 */
- }
-
- if (ix < 0x3f580000)
- {
- /* |x|<0.84375 */
- if (ix < 0x31800000)
- {
- /* |x|<2**-28 */
- if (ix < 0x04000000)
- {
- return (float)0.125*((float)8.0*x+efx8f*x); /*avoid underflow */
- }
- return x + efxf*x;
- }
- z = x*x;
- r = pp0f+z*(pp1f+z*(pp2f+z*(pp3f+z*pp4f)));
- s = onef+z*(qq1f+z*(qq2f+z*(qq3f+z*(qq4f+z*qq5f))));
- y = r/s;
- return x + x*y;
- }
- if (ix < 0x3fa00000)
- {
- /* 0.84375 <= |x| < 1.25 */
- s = fabs(x)-onef;
- P = pa0f+s*(pa1f+s*(pa2f+s*(pa3f+s*(pa4f+s*(pa5f+s*pa6f)))));
- Q = onef+s*(qa1f+s*(qa2f+s*(qa3f+s*(qa4f+s*(qa5f+s*qa6f)))));
- if (hx >= 0)
- {
- return erxf + P/Q;
- }
- else
- {
- return -erxf - P/Q;
- }
- }
- if (ix >= 0x40c00000)
- {
- /* inf>|x|>=6 */
- if (hx >= 0)
- {
- return onef-tinyf;
- }
- else
- {
- return tinyf-onef;
- }
- }
- x = fabs(x);
- s = onef/(x*x);
- if (ix < 0x4036DB6E)
- {
- /* |x| < 1/0.35 */
- R = ra0f+s*(ra1f+s*(ra2f+s*(ra3f+s*(ra4f+s*(ra5f+s*(ra6f+s*ra7f))))));
- S = onef+s*(sa1f+s*(sa2f+s*(sa3f+s*(sa4f+s*(sa5f+s*(sa6f+s*(sa7f+s*sa8f)))))));
- }
- else
- {
- /* |x| >= 1/0.35 */
- R = rb0f+s*(rb1f+s*(rb2f+s*(rb3f+s*(rb4f+s*(rb5f+s*rb6f)))));
- S = onef+s*(sb1f+s*(sb2f+s*(sb3f+s*(sb4f+s*(sb5f+s*(sb6f+s*sb7f))))));
- }
-
- conv.f = x;
- conv.i = conv.i & 0xfffff000;
- z = conv.f;
-
- r = exp(-z*z-(float)0.5625)*exp((z-x)*(z+x)+R/S);
- if (hx >= 0)
- {
- return onef-r/x;
- }
- else
- {
- return r/x-onef;
- }
-}
-
-float gmx_erfcf(float x)
-{
- gmx_int32_t hx, ix;
- float R, S, P, Q, s, y, z, r;
-
- union
- {
- float f;
- int i;
- }
- conv;
-
- conv.f = x;
- hx = conv.i;
-
- ix = hx&0x7fffffff;
- if (ix >= 0x7f800000)
- {
- /* erfc(nan)=nan */
- /* erfc(+-inf)=0,2 */
- return (float)(((gmx_uint32_t)hx>>31)<<1)+onef/x;
- }
-
- if (ix < 0x3f580000)
- {
- /* |x|<0.84375 */
- if (ix < 0x23800000)
- {
- return onef-x; /* |x|<2**-56 */
- }
- z = x*x;
- r = pp0f+z*(pp1f+z*(pp2f+z*(pp3f+z*pp4f)));
- s = onef+z*(qq1f+z*(qq2f+z*(qq3f+z*(qq4f+z*qq5f))));
- y = r/s;
- if (hx < 0x3e800000)
- {
- /* x<1/4 */
- return onef-(x+x*y);
- }
- else
- {
- r = x*y;
- r += (x-halff);
- return halff - r;
- }
- }
- if (ix < 0x3fa00000)
- {
- /* 0.84375 <= |x| < 1.25 */
- s = fabs(x)-onef;
- P = pa0f+s*(pa1f+s*(pa2f+s*(pa3f+s*(pa4f+s*(pa5f+s*pa6f)))));
- Q = onef+s*(qa1f+s*(qa2f+s*(qa3f+s*(qa4f+s*(qa5f+s*qa6f)))));
- if (hx >= 0)
- {
- z = onef-erxf; return z - P/Q;
- }
- else
- {
- z = erxf+P/Q; return onef+z;
- }
- }
- if (ix < 0x41e00000)
- {
- /* |x|<28 */
- x = fabs(x);
- s = onef/(x*x);
- if (ix < 0x4036DB6D)
- {
- /* |x| < 1/.35 ~ 2.857143*/
- R = ra0f+s*(ra1f+s*(ra2f+s*(ra3f+s*(ra4f+s*(ra5f+s*(ra6f+s*ra7f))))));
- S = onef+s*(sa1f+s*(sa2f+s*(sa3f+s*(sa4f+s*(sa5f+s*(sa6f+s*(sa7f+s*sa8f)))))));
- }
- else
- {
- /* |x| >= 1/.35 ~ 2.857143 */
- if (hx < 0 && ix >= 0x40c00000)
- {
- return twof-tinyf; /* x < -6 */
- }
- R = rb0f+s*(rb1f+s*(rb2f+s*(rb3f+s*(rb4f+s*(rb5f+s*rb6f)))));
- S = onef+s*(sb1f+s*(sb2f+s*(sb3f+s*(sb4f+s*(sb5f+s*(sb6f+s*sb7f))))));
- }
-
- conv.f = x;
- conv.i = conv.i & 0xfffff000;
- z = conv.f;
-
- r = exp(-z*z-(float)0.5625)*exp((z-x)*(z+x)+R/S);
- if (hx > 0)
- {
- return r/x;
- }
- else
- {
- return twof-r/x;
- }
- }
- else
- {
- if (hx > 0)
- {
- return tinyf*tinyf;
- }
- else
- {
- return twof-tinyf;
- }
- }
-}
-
-
-gmx_bool gmx_isfinite(real gmx_unused x)
-{
- gmx_bool returnval;
-
-#ifdef HAVE__FINITE
- returnval = _finite(x);
-#elif defined HAVE_ISFINITE
- returnval = std::isfinite(x);
-#elif defined HAVE__ISFINITE
- returnval = _isfinite(x);
-#else
- /* If no suitable function was found, assume the value is
- * finite. */
- returnval = TRUE;
-#endif
- return returnval;
-}
-
-gmx_bool gmx_isnan(real x)
-{
- return x != x;
-}
-
int
gmx_within_tol(double f1,
double f2,
#define M_2_SQRTPI 1.128379167095513
#endif
-int gmx_nint(real a);
-real sign(real x, real y);
-
-real cuberoot (real a);
-double gmx_erfd(double x);
-double gmx_erfcd(double x);
-float gmx_erff(float x);
-float gmx_erfcf(float x);
-#ifdef GMX_DOUBLE
-#define gmx_erf(x) gmx_erfd(x)
-#define gmx_erfc(x) gmx_erfcd(x)
-#else
-#define gmx_erf(x) gmx_erff(x)
-#define gmx_erfc(x) gmx_erfcf(x)
-#endif
-
-#if defined(_MSC_VER) && _MSC_VER < 1800
-#define gmx_expm1(x) (exp(x)-1)
-#define gmx_log1p(x) log(1+x)
-#else
-#define gmx_expm1 expm1
-#define gmx_log1p log1p
-#endif
-
-gmx_bool gmx_isfinite(real x);
-gmx_bool gmx_isnan(real x);
-
/*! \brief Check if two numbers are within a tolerance
*
* This routine checks if the relative difference between two numbers is
#include "calc_verletbuf.h"
#include <assert.h>
-#include <math.h>
#include <stdlib.h>
+#include <cmath>
+
#include <algorithm>
#include "gromacs/legacyheaders/typedefs.h"
real ex, er;
ex = exp(-x*x/(2*s2));
- er = gmx_erfc(x/sqrt(2*s2));
+ er = std::erfc(x/sqrt(2*s2));
*shift = -x + sqrt(2*s2/M_PI)*ex/er;
*scale = 0.5*M_PI*exp(ex*ex/(M_PI*er*er))*er;
* atom density still needs to be put in.
*/
c_exp = exp(-rsh*rsh/(2*s2))/sqrt(2*M_PI);
- c_erfc = 0.5*gmx_erfc(rsh/(sqrt(2*s2)));
+ c_erfc = 0.5*std::erfc(rsh/(sqrt(2*s2)));
}
s = sqrt(s2);
rsh2 = rsh*rsh;
b = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
rc = ir->rcoulomb;
br = b*rc;
- md1_el = elfac*(b*exp(-br*br)*M_2_SQRTPI/rc + gmx_erfc(br)/(rc*rc));
- d2_el = elfac/(rc*rc)*(2*b*(1 + br*br)*exp(-br*br)*M_2_SQRTPI + 2*gmx_erfc(br)/rc);
+ md1_el = elfac*(b*exp(-br*br)*M_2_SQRTPI/rc + std::erfc(br)/(rc*rc));
+ d2_el = elfac/(rc*rc)*(2*b*(1 + br*br)*exp(-br*br)*M_2_SQRTPI + 2*std::erfc(br)/rc);
}
else
{
#include "config.h"
#include <assert.h>
-#include <math.h>
#include <stdlib.h>
+#include <cmath>
+
#include <algorithm>
#include "gromacs/domdec/domdec.h"
{
fprintf(fplog, "%s", buf);
}
- if (!gmx_isfinite(d1))
+ if (!std::isfinite(d1))
{
gmx_fatal(FARGS, "Bond length not finite.");
}
#include "config.h"
#include <assert.h>
-#include <math.h>
#include <stdlib.h>
#include <string.h>
+#include <cmath>
+
#include <algorithm>
#include "gromacs/domdec/domdec.h"
if (fr->coulomb_modifier == eintmodPOTSHIFT)
{
- ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb);
}
else
{
if (bEner)
{
- vcoul = qq*((int_bit - gmx_erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
+ vcoul = qq*((int_bit - std::erf(iconst->ewaldcoeff_q*r))*rinv - int_bit*iconst->sh_ewald);
}
}
#include "config.h"
+#include <cmath>
+
#include <vector>
-#include "gromacs/math/utilities.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/simd/simd.h"
GMX_EXPECT_SIMD_FUNC_NEAR(ref_log, gmx_simd_log_r);
}
-// MSVC does not support exp2(), so we have no reference to test against
-#ifndef _MSC_VER
-/*! \brief Function wrapper for exp2(x), with argument/return in default Gromacs precision */
-real ref_exp2(real x)
-{
- return exp2(x);
-}
-
TEST_F(SimdMathTest, gmxSimdExp2R)
{
setRange(-100, 100);
- GMX_EXPECT_SIMD_FUNC_NEAR(ref_exp2, gmx_simd_exp2_r);
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, gmx_simd_exp2_r);
// We do not care about the SIMD implementation getting denormal values right,
// but they must be clamped to zero rather than producing garbage.
setAbsTol(GMX_REAL_EPS);
// First two values will have denormal results in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(ref_exp2(-150.0), ref_exp2(-300.0), ref_exp2(-1050.0)),
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-150.0), std::exp2(-300.0), std::exp2(-1050.0)),
gmx_simd_exp2_r(setSimdRealFrom3R(-150.0, -300.0, -1050.0)));
// Reset absolute tolerance to enforce ULP checking
// Make sure that underflowing values are set to zero.
// First two values underflow in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(ref_exp2(-200.0), ref_exp2(-600.0), ref_exp2(-1500.0)),
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-200.0), std::exp2(-600.0), std::exp2(-1500.0)),
gmx_simd_exp2_r(setSimdRealFrom3R(-200.0, -600.0, -1500.0)));
}
-#endif
/*! \brief Function wrapper for exp(x), with argument/return in default Gromacs precision */
real ref_exp(real x)
/*! \brief Function wrapper for erf(x), with argument/return in default Gromacs precision.
*
- * \note The single-precision gmx_erff() in gmxlib is slightly lower precision
- * than the SIMD flavor, so we use double for reference.
+ * \note Single-precision erf() in some libraries can be slightly lower precision
+ * than the SIMD flavor, so we use a cast to force double precision for reference.
*/
real ref_erf(real x)
{
- return gmx_erfd(x);
+ return std::erf(static_cast<double>(x));
}
TEST_F(SimdMathTest, gmxSimdErfR)
/*! \brief Function wrapper for erfc(x), with argument/return in default Gromacs precision.
*
- * \note The single-precision gmx_erfcf() in gmxlib is slightly lower precision
- * than the SIMD flavor, so we use double for reference.
+ * \note Single-precision erfc() in some libraries can be slightly lower precision
+ * than the SIMD flavor, so we use a cast to force double precision for reference.
*/
real ref_erfc(real x)
{
- return gmx_erfcd(x);
+ return std::erfc(static_cast<double>(x));
}
TEST_F(SimdMathTest, gmxSimdErfcR)
if (x != 0)
{
real y = sqrt(x);
- return 2*exp(-x)/(sqrt(M_PI)*x) - gmx_erfd(y)/(x*y);
+ return 2*exp(-x)/(sqrt(M_PI)*x) - std::erf(static_cast<double>(y))/(x*y);
}
else
{
real ref_pmecorrV(real x)
{
real y = sqrt(x);
- return gmx_erfd(y)/y;
+ return std::erf(static_cast<double>(y))/y;
}
// The PME corrections will be added to ~1/r, so absolute tolerance of EPS is fine.
GMX_EXPECT_SIMD_FUNC_NEAR(ref_log, gmx_simd_log_singleaccuracy_r);
}
-// MSVC does not support exp2(), so we have no reference to test against
-#ifndef _MSC_VER
TEST_F(SimdMathTest, gmxSimdExp2SingleaccuracyR)
{
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
setRange(-100, 100);
- GMX_EXPECT_SIMD_FUNC_NEAR(ref_exp2, gmx_simd_exp2_singleaccuracy_r);
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, gmx_simd_exp2_singleaccuracy_r);
}
-#endif
TEST_F(SimdMathTest, gmxSimdExpSingleaccuracyR)
{
}
else
{
- return gmx_erfd(beta*r)/r;
+ return std::erf(beta*r)/r;
}
}
real sc_q;
/* Energy tolerance: 0.1 times the cut-off jump */
- etol = 0.1*gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
+ etol = 0.1*std::erfc(ic->ewaldcoeff_q*ic->rcoulomb);
sc_q = spline3_table_scale(erf_x_d3, ic->ewaldcoeff_q, etol);
break;
case etabEwald:
case etabEwaldSwitch:
- Vcut = gmx_erfc(ewc*rc)/rc;
+ Vcut = std::erfc(ewc*rc)/rc;
break;
case etabEwaldUser:
/* Only calculate minus the reciprocal space contribution */
- Vcut = -gmx_erf(ewc*rc)/rc;
+ Vcut = -std::erf(ewc*rc)/rc;
break;
case etabRF:
case etabRF_ZERO:
break;
case etabEwald:
case etabEwaldSwitch:
- Vtab = gmx_erfc(ewc*r)/r;
- Ftab = gmx_erfc(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
+ Vtab = std::erfc(ewc*r)/r;
+ Ftab = std::erfc(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
break;
case etabEwaldUser:
case etabEwaldUserSwitch:
/* Only calculate the negative of the reciprocal space contribution */
- Vtab = -gmx_erf(ewc*r)/r;
- Ftab = -gmx_erf(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
+ Vtab = -std::erf(ewc*r)/r;
+ Ftab = -std::erf(ewc*r)/r2+exp(-(ewc*ewc*r2))*ewc*M_2_SQRTPI/r;
break;
case etabLJ6Ewald:
Vtab = -r6*exp(-ewclj*ewclj*r2)*(1 + ewclj*ewclj*r2 + pow4(ewclj)*r2*r2/2);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include <string.h>
+#include <cmath>
+
#include "gromacs/fileio/strdb.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/math/utilities.h"
set_prop(aps, epropElement);
for (i = 0; (i < ap->prop[epropElement].nprop); i++)
{
- if (gmx_nint(ap->prop[epropElement].value[i]) == atomnumber)
+ if (std::round(ap->prop[epropElement].value[i]) == atomnumber)
{
return ap->prop[epropElement].atomnm[i];
}
{
if (gmx_strcasecmp(ap->prop[epropElement].atomnm[i], elem) == 0)
{
- return gmx_nint(ap->prop[epropElement].value[i]);
+ return std::round(ap->prop[epropElement].value[i]);
}
}
return -1;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff