#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, 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.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
#!/usr/bin/perl -w
+use strict;
#
# This script reads an XPLOR input file with distance restraint data
# as sometimes is found in the pdb database (http://www.pdb.org).
#
# Turn debugging off (0), or on ( > 0).
-$debug = 1;
+my $debug = 1;
# Turn atom name translation on and off
-$trans = 1;
+my $trans = 1;
-#$res0 = shift;# || die "I need the residue offset\n";
-$pdb = shift || die "I need the name of the pdb file with correct atom numbers\n";
-$core = shift || "core.ndx";
-$tbl = "$ENV{GMXDATA}/top/atom_nom.tbl";
+my $pdb = shift || die "I need the name of the pdb file with correct atom numbers\n";
+my $core = shift || "core.ndx";
+my $tbl = "$ENV{GMXDATA}/top/atom_nom.tbl";
printf "[ distance_restraints ]\n";
printf "; Read an xplor distance restraint file, and output GROMACS distance restraints.\n";
printf "; This also needs a pdb file with correct GROMACS atom numbering.\n";
printf "; I used $pdb for the atom numbers\n";
printf "; This also needs the offset in residues.\n";
-#printf "; I used $res0 for the residue offset\n";
# Read the pdb file
# If things go wrong, check whether your pdb file is read correctly.
-$natom = 0;
-$nres = 0;
-@resname = ();
+my $natom = 0;
+my $nres = 0;
+my @resname;
+my @aname;
+my @resnr;
open(PDB,$pdb) || die "Can not open file $pdb\n";
-while ($line = <PDB>) {
+while (
my $line = <PDB>) {
if (index($line,"ATOM") >= 0) {
- @tmp = split(' ',$line);
+ my @tmp = split(' ',$line);
$aname[$natom] = $tmp[2];
$resnr[$natom] = $tmp[4];
if (!defined $resname[$tmp[4]]) {
printf "; I found $natom atoms in the pdb file $pdb\n";
printf "; I found $nres residues in the pdb file $pdb\n";
if ($debug > 1) {
- for ($i = 0; ($i < $natom); $i ++) {
+ for (my $i = 0; ($i < $natom); $i ++) {
printf("; %5d %5s %5s %5d\n",$i+1,$aname[$i],
$resname[$resnr[$i]],$resnr[$i]);
}
# not for content
#
open(TBL,$tbl) || die "Can not open atom-name translation table $tbl\n";
-$ntbl=0;
-while ($line = <TBL>) {
- @ttt = split('#',$line);
- @tmp = split(' ',$ttt[0]);
+my $ntbl=0;
+my @tblxplor;
+my @tblgmx;
+my @tblres;
+while (my $line = <TBL>) {
+ my @ttt = split('#',$line);
+ my @tmp = split(' ',$ttt[0]);
if ($#tmp == 3) {
# New table entry
$tblres[$ntbl] = $tmp[0];
close TBL;
printf "; Read $ntbl entries from $tbl\n";
-@templates = (
- [ "HA#", "HA1", "HA2" ],
- [ "HA*", "HA1", "HA2" ],
- [ "HB#", "HB", "HB1", "HB2" ],
- [ "HB*", "HB", "HB1", "HB2" ],
- [ "HG#", "HG", "HG1", "HG2", "HG11", "HG12", "HG13", "HG21", "HG22", "HG23" ],
- [ "HG*", "HG", "HG1", "HG2", "HG11", "HG12", "HG13", "HG21", "HG22", "HG23" ],
- [ "HG1#", "HG11", "HG12", "HG13" ],
- [ "HG1*", "HG11", "HG12", "HG13" ],
- [ "HG2#", "HG21", "HG22", "HG23" ],
- [ "HG2*", "HG21", "HG22", "HG23" ],
- [ "HD#", "HD1", "HD2", "HD11", "HD12", "HD13", "HD21", "HD22", "HD23" ],
- [ "HD*", "HD1", "HD2", "HD11", "HD12", "HD13", "HD21", "HD22", "HD23" ],
- [ "HD1#", "HD11", "HD12" ],
- [ "HD1*", "HD11", "HD12" ],
- [ "HD2#", "HD21", "HD22" ],
- [ "HD2*", "HD21", "HD22" ],
- [ "HE#", "HE", "HE1", "HE2" ],
- [ "HE*", "HE", "HE1", "HE2" ],
- [ "HH#", "HH11", "HH12", "HH21", "HH22" ],
- [ "HH*", "HH11", "HH12", "HH21", "HH22" ],
- [ "HZ#", "HZ", "HZ1", "HZ2", "HZ3" ],
- [ "HZ*", "HZ", "HZ1", "HZ2", "HZ3" ],
- [ "HN", "H" ]
+my $default = "XXX";
+
+my @templates = (
+ [ $default, "HA#", "HA1", "HA2" ],
+ [ $default, "HA*", "HA1", "HA2" ],
+ [ $default, "HB#", "HB", "HB1", "HB2" ],
+ [ $default, "HB*", "HB", "HB1", "HB2" ],
+ [ $default, "HG#", "HG", "HG1", "HG2", "HG11", "HG12", "HG13", "HG21", "HG22", "HG23" ],
+ [ $default, "HG*", "HG", "HG1", "HG2", "HG11", "HG12", "HG13", "HG21", "HG22", "HG23" ],
+ [ $default, "HG1#", "HG11", "HG12", "HG13" ],
+ [ $default, "HG1*", "HG11", "HG12", "HG13" ],
+ [ $default, "HG2#", "HG21", "HG22", "HG23" ],
+ [ $default, "HG2*", "HG21", "HG22", "HG23" ],
+ [ $default, "HD#", "HD1", "HD2", "HD11", "HD12", "HD13", "HD21", "HD22", "HD23" ],
+ [ $default, "HD*", "HD1", "HD2", "HD11", "HD12", "HD13", "HD21", "HD22", "HD23" ],
+ [ $default, "HD1#", "HD11", "HD12" ],
+ [ "ILE", "HD1*", "HD1", "HD2", "HD3" ],
+ [ $default, "HD1*", "HD11", "HD12" ],
+ [ $default, "HD2#", "HD21", "HD22" ],
+ [ $default, "HD2*", "HD21", "HD22" ],
+ [ $default, "HE#", "HE", "HE1", "HE2" ],
+ [ "GLN", "HE*", "HE21", "HE22" ],
+ [ $default, "HE*", "HE", "HE1", "HE2" ],
+ [ $default, "HE2*", "HE2", "HE21", "HE22" ],
+ [ $default, "HH#", "HH11", "HH12", "HH21", "HH22" ],
+ [ $default, "HH*", "HH11", "HH12", "HH21", "HH22" ],
+ [ $default, "HZ#", "HZ", "HZ1", "HZ2", "HZ3" ],
+ [ $default, "HZ*", "HZ", "HZ1", "HZ2", "HZ3" ],
+ [ $default, "HN", "H" ]
);
-$ntranslated = 0;
-$nuntransltd = 0;
+my $ntranslated = 0;
+my $nuntransltd = 0;
sub transl_aname {
my $resnm = shift;
my $atom = shift;
}
$nuntransltd++;
if ($debug > 1) {
- printf "; No name change for $resname[$resnr] $atom\n";
+ printf "; No name change for $resnm $atom\n";
}
return $atom;
}
die("No residue name for residue $rnum") if (!defined ($resname[$rnum]));
for (my $tt=0; (($tt <= $#templates) && ($bdone == 0)); $tt++) {
- $templ = $templates[$tt];
- if ($atom eq $templ->[0]) {
- for ($jj = 1; ($jj <= $#{$templ}); $jj++) {
+ my $templ = $templates[$tt];
+ if (($resname[$rnum] eq $templ->[0] ||
+ $default eq $templ->[0]) &&
+ ($atom eq $templ->[1])) {
+ for ($jj = 2; ($jj <= $#{$templ}); $jj++) {
push @atoms, transl_aname($resname[$rnum],$templ->[$jj]);
}
$bdone = 1;
if ($debug > 0) {
my $natom = $#atoms+1;
printf("; Found $natom elements for atom $resname[$rnum] %d $atom:",
- $rnum+1);
- for $aa ( @atoms ) {
+ $rnum);
+ for my $aa ( @atoms ) {
printf " $aa";
}
printf "\n";
if ($debug > 1) {
printf "; There are $#templates template entries\n";
- for ($tt=0; ($tt <= $#templates); $tt++) {
- $templ = $templates[$tt];
- $ntempl = $#{$templ};
- printf "; Item $tt ($templates[$tt][0]) has $ntempl entries\n";
+ for (my $tt=0; ($tt <= $#templates); $tt++) {
+ my $templ = $templates[$tt];
+ my $ntempl = $#{$templ};
+ printf "; Item $tt ($templates[$tt][0] $templates[$tt][1]) has $ntempl entries\n";
}
}
# This index file holds numbers of restraints involving core atoms
-@protcore = ( "H", "HN", "HA", "HA1", "HA2", "HB", "HB1", "HB2", "HB3", "HG", "HG1", "HG2", "HG3", "N", "O" );
+my @protcore = ( "H", "HN", "HA", "HA1", "HA2", "HB", "HB1", "HB2", "HB3", "HG", "HG1", "HG2", "HG3", "N", "O" );
open(CORE,">$core") || die "Can not open $core\n";
print CORE "[ core-restraints ]\n";
-$ncore = 0;
+my $ncore = 0;
-$myindex = 0;
-$linec = 0;
-$npair = 0;
-$nunresolved = 0;
-while ($line = <STDIN>) {
- @ttt = split('!',$line);
- if ((index($ttt[0],"assign") >= 0) && (index($ttt[0],"!assign") < 0)) {
- @tmp = split('\(',$ttt[0]);
+my $myindex = 0;
+my $linec = 0;
+my $npair = 0;
+my $nunresolved = 0;
+while (my $line = <STDIN>) {
+ my @ttt = split('!',$line);
+ if (index($ttt[0], "dihedral") >= 0) {
+ last;
+ }
+ elsif ((index($ttt[0],"assign") >= 0) && (index($ttt[0],"!assign") < 0)) {
+ my @tmp = split('\(',$ttt[0]);
# Find first argument
+ my $rhaak = undef;
if (($rhaak = index($tmp[1],')')) < 0) {
printf "No ) in '$tmp[1]'\n";
}
- $atres1 = substr($tmp[1],0,$rhaak);
- @at1 = split('or',$atres1);
+ my $atres1 = substr($tmp[1],0,$rhaak);
+ my @at1 = split('or',$atres1);
# Find second argument
if (($rhaak = index($tmp[2],')')) < 0) {
printf "No ) in '$tmp[2]'\n";
}
- $atres2 = substr($tmp[2],0,$rhaak);
- @at2 = split('or',$atres2);
+ my $atres2 = substr($tmp[2],0,$rhaak);
+ my @at2 = split('or',$atres2);
- @expdata = split('\)',$tmp[2]);
- @dist = split(' ',$expdata[1]);
+ my @expdata = split('\)',$tmp[2]);
+ my @dist = split(' ',$expdata[1]);
- $bOK = 0;
- $bCore = 1;
- foreach $a1 ( @at1 ) {
- @info1 = split(' ',$a1);
- $r1 = $info1[1];
- @atoms1 = expand_template($info1[4],$r1);
+ my $bOK = 0;
+ my $bCore = 1;
+ foreach my $a1 ( @at1 ) {
+ my @info1 = split(' ',$a1);
+ my $r1 = $info1[1];
+ my @atoms1 = expand_template($info1[4],$r1);
- foreach $a2 ( @at2 ) {
- @info2 = split(' ',$a2);
- $r2 = $info2[1];
- @atoms2 = expand_template($info2[4],$r2);
+ foreach my $a2 ( @at2 ) {
+ my @info2 = split(' ',$a2);
+ my $r2 = $info2[1];
+ my @atoms2 = expand_template($info2[4],$r2);
+ my $i = undef;
for ($i = 0; ($i < $natom) && ($resnr[$i] < $r1); $i++) { ; }
for ( ; ($i < $natom) && ($resnr[$i] == $r1); $i++) {
- foreach $ii ( @atoms1 ) {
+ foreach my $ii ( @atoms1 ) {
if ($ii eq $aname[$i]) {
- $bCoreI = 0;
- for $pp ( @protcore ) {
+ my $bCoreI = 0;
+ for my $pp ( @protcore ) {
if ($ii eq $pp) {
$bCoreI = 1;
}
}
-
+ my $j = undef;
for ($j = 0; ($j < $natom) && ($resnr[$j] < $r2); $j++) { ; }
for ( ; ($j < $natom) && ($resnr[$j] == $r2); $j++) {
- foreach $jj ( @atoms2 ) {
+ foreach my $jj ( @atoms2 ) {
if ($jj eq $aname[$j]) {
- $dd = 0.1*$dist[0];
- $dminus = 0.1*$dist[1];
- $dplus = 0.1*$dist[2];
- $low = $dd-$dminus;
- $up1 = $dd+$dplus;
- $up2 = $up1+1;
+ my $dd = 0.1*$dist[0];
+ my $dminus = 0.1*$dist[1];
+ my $dplus = 0.1*$dist[2];
+ my $low = $dd-$dminus;
+ my $up1 = $dd+$dplus;
+ my $up2 = $up1+1;
printf("%5d %5d %5d %5d %5d %7.3f %7.3f %7.3f 1.0; res $r1 $ii - res $r2 $jj\n",$i+1,$j+1,1,$myindex,1,$low,$up1,$up2);
# Do some checks
$bOK = 1;
- $bCoreJ = 0;
- for $pp ( @protcore ) {
+ my $bCoreJ = 0;
+ for my $pp ( @protcore ) {
if ($jj eq $pp) {
$bCoreJ = 1;
}
ILE HG21 HG21 1HG2
ILE HG22 HG22 2HG2
ILE HG23 HG23 3HG2
-ILE HD11 HD11 1HD1
-ILE HD12 HD12 2HD1
-ILE HD13 HD13 3HD1
+ILE HD1 HD1 HD1
+ILE HD2 HD2 HD2
+ILE HD3 HD3 HD3
ILE C C C
ILE CA CA CA
ILE CB CB CB
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
};
static gmx_bool bSum = FALSE, bFee = FALSE, bPrAll = FALSE, bFluct = FALSE, bDriftCorr = FALSE;
static gmx_bool bDp = FALSE, bMutot = FALSE, bOrinst = FALSE, bOvec = FALSE, bFluctProps = FALSE;
- static int skip = 0, nmol = 1, nbmin = 5, nbmax = 5;
+ static int nmol = 1, nbmin = 5, nbmax = 5;
static real reftemp = 300.0, ezero = 0;
t_pargs pa[] = {
{ "-fee", FALSE, etBOOL, {&bFee},
"Maximum number of blocks for error estimate" },
{ "-mutot", FALSE, etBOOL, {&bMutot},
"Compute the total dipole moment from the components" },
- { "-skip", FALSE, etINT, {&skip},
- "Skip number of frames between data points" },
{ "-aver", FALSE, etBOOL, {&bPrAll},
"Also print the exact average and rmsd stored in the energy frames (only when 1 term is requested)" },
{ "-nmol", FALSE, etINT, {&nmol},
t_enxframe *frame, *fr = nullptr;
int cur = 0;
#define NEXT (1-cur)
- int nre, teller, nfr;
+ int nre, nfr;
gmx_int64_t start_step;
real start_t;
gmx_bool bDHDL;
snew(edat.s, nset);
/* Initiate counters */
- teller = 0;
bFoundStart = FALSE;
start_step = 0;
start_t = 0;
time[edat.nframes] = fr->t;
edat.nframes++;
}
- /*
- * Printing time, only when we do not want to skip frames
- */
- if (!skip || teller % skip == 0)
+ if (bDHDL)
{
- if (bDHDL)
- {
- do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
- }
+ do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
+ }
- /*******************************************
- * E N E R G I E S
- *******************************************/
- else
+ /*******************************************
+ * E N E R G I E S
+ *******************************************/
+ else
+ {
+ if (fr->nre > 0)
{
- if (fr->nre > 0)
+ if (bPrAll)
+ {
+ /* We skip frames with single points (usually only the first frame),
+ * since they would result in an average plot with outliers.
+ */
+ if (fr->nsum > 1)
+ {
+ print_time(out, fr->t);
+ print1(out, bDp, fr->ener[set[0]].e);
+ print1(out, bDp, fr->ener[set[0]].esum/fr->nsum);
+ print1(out, bDp, std::sqrt(fr->ener[set[0]].eav/fr->nsum));
+ fprintf(out, "\n");
+ }
+ }
+ else
{
- if (bPrAll)
+ print_time(out, fr->t);
+ if (bSum)
{
- /* We skip frames with single points (usually only the first frame),
- * since they would result in an average plot with outliers.
- */
- if (fr->nsum > 1)
+ sum = 0;
+ for (i = 0; i < nset; i++)
{
- print_time(out, fr->t);
- print1(out, bDp, fr->ener[set[0]].e);
- print1(out, bDp, fr->ener[set[0]].esum/fr->nsum);
- print1(out, bDp, std::sqrt(fr->ener[set[0]].eav/fr->nsum));
- fprintf(out, "\n");
+ sum += fr->ener[set[i]].e;
}
+ print1(out, bDp, sum/nmol-ezero);
}
else
{
- print_time(out, fr->t);
- if (bSum)
+ for (i = 0; (i < nset); i++)
{
- sum = 0;
- for (i = 0; i < nset; i++)
+ if (bIsEner[i])
{
- sum += fr->ener[set[i]].e;
+ print1(out, bDp, (fr->ener[set[i]].e)/nmol-ezero);
}
- print1(out, bDp, sum/nmol-ezero);
- }
- else
- {
- for (i = 0; (i < nset); i++)
+ else
{
- if (bIsEner[i])
- {
- print1(out, bDp, (fr->ener[set[i]].e)/nmol-ezero);
- }
- else
- {
- print1(out, bDp, fr->ener[set[i]].e);
- }
+ print1(out, bDp, fr->ener[set[i]].e);
}
}
- fprintf(out, "\n");
}
+ fprintf(out, "\n");
}
}
}
- teller++;
}
}
while (bCont && (timecheck == 0));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2010, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2017, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, 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.
using Base = internal::SimdArrayRef<const SimdFloat>;
using Base::Base;
};
-template<>
-class ArrayRef<SimdFInt32> : public internal::SimdArrayRef<SimdFInt32>
-{
- using Base = internal::SimdArrayRef<SimdFInt32>;
- using Base::Base;
-};
-template<>
-class ArrayRef<const SimdFInt32> : public internal::SimdArrayRef<const SimdFInt32>
-{
- using Base = internal::SimdArrayRef<const SimdFInt32>;
- using Base::Base;
-};
#endif
#if GMX_SIMD_HAVE_DOUBLE
template<>
using Base = internal::SimdArrayRef<const SimdDouble>;
using Base::Base;
};
-template<>
-class ArrayRef<SimdDInt32> : public internal::SimdArrayRef<SimdDInt32>
-{
- using Base = internal::SimdArrayRef<SimdDInt32>;
- using Base::Base;
-};
-template<>
-class ArrayRef<const SimdDInt32> : public internal::SimdArrayRef<const SimdDInt32>
-{
- using Base = internal::SimdArrayRef<const SimdDInt32>;
- using Base::Base;
-};
#endif
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017,2018, 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.
namespace gmx
{
-namespace
+#if GMX_SIMD_HAVE_REAL
+
+/* SimdInt32 is a strange type which would never belong in an interface,
+ * because its properties are peculiar to int-to-float conversions within
+ * SIMD types, so there is no need to support it as a specialization of
+ * SimdArrayRef. But it is useful here for better test coverage of
+ * SimdArrayRef. */
+
+template<>
+class ArrayRef<SimdInt32> : public internal::SimdArrayRef<SimdInt32>
{
+ using Base = internal::SimdArrayRef<SimdInt32>;
+ using Base::Base;
+};
+template<>
+class ArrayRef<const SimdInt32> : public internal::SimdArrayRef<const SimdInt32>
+{
+ using Base = internal::SimdArrayRef<const SimdInt32>;
+ using Base::Base;
+};
-#if GMX_SIMD_HAVE_REAL
+namespace
+{
TEST(EmptyArrayRefTest, IsEmpty)
{
#endif // GTEST_HAS_TYPED_TEST
-#endif // GMX_HAVE_SIMD_REAL
-
} // namespace
-} // namespace
+#endif // GMX_HAVE_SIMD_REAL
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017,2018, 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.
{ "A computer once beat me at chess, but it was no match for me at kick boxing.", "Emo Philips" },
{ "Home computers are being called upon to perform many new functions, including the consumption of homework formerly eaten by the dog.", "Doug Larson" },
{ "Forcefields are like dating; things go fine for a while and then sometimes it goes really bad.", "Alex MacKerell" },
- { "This type of advanced sampling techniques... which are not so advanced, really.", "Viveca Lindahl, on AWH, at her thesis defense." }
+ { "This type of advanced sampling techniques... which are not so advanced, really.", "Viveca Lindahl, on AWH, at her thesis defense." },
+ { "C++ is tricky. You can do everything. You can even make every mistake.", "Nicolai Josuttis, CppCon2017" },
};
if (beCool())
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, 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.
/* CAUTION: threads may be started later on in this function, so
cr doesn't reflect the final parallel state right now */
- gmx::MDModules mdModules;
- t_inputrec inputrecInstance;
- t_inputrec *inputrec = &inputrecInstance;
+ std::unique_ptr<gmx::MDModules> mdModules(new gmx::MDModules);
+ t_inputrec inputrecInstance;
+ t_inputrec *inputrec = &inputrecInstance;
snew(mtop, 1);
if (mdrunOptions.continuationOptions.appendFiles)
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
// TODO: Error handling
- mdModules.assignOptionsToModules(*inputrec->params, nullptr);
+ mdModules->assignOptionsToModules(*inputrec->params, nullptr);
if (fplog != nullptr)
{
{
/* Initiate forcerecord */
fr = mk_forcerec();
- fr->forceProviders = mdModules.initForceProviders();
+ fr->forceProviders = mdModules->initForceProviders();
init_forcerec(fplog, mdlog, fr, fcd,
inputrec, mtop, cr, box,
opt2fn("-table", nfile, fnm),
oenv,
mdrunOptions,
vsite, constr,
- mdModules.outputProvider(),
+ mdModules->outputProvider(),
inputrec, mtop,
fcd,
globalState.get(),
// As soon as we destroy GPU contexts after mdrunner() exits, these lines should go.
mdAtoms.reset(nullptr);
globalState.reset(nullptr);
+ mdModules.reset(nullptr); // destruct force providers here as they might also use the GPU
/* Free GPU memory and set a physical node tMPI barrier (which should eventually go away) */
free_gpu_resources(fr, cr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2017,2018, 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.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, 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.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2014,2016,2017,2018, 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.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016,2017,2018, 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.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff