For details see \tabref{topfile2}.
The table files are supplied to the {\tt mdrun} program.
After the table file name an underscore, the letter ``b'' for bonds,
-``a'' for angles or ``d'' for dihedrals and the table number are appended.
-For example, for a bond with $n=0$ (and using the default table file name)
-the table is read from the file {\tt table_b0.xvg}. Multiple tables can be
-supplied simply by using different values of $n$, and are applied to the appropriate
+``a'' for angles or ``d'' for dihedrals and the table number must be appended.
+For example, a tabulated bond with $n=0$ can be read from the file {\tt table_b0.xvg}.
+Multiple tables can be
+supplied simply by adding files with different values of $n$, and are applied to the appropriate
bonds, as specified in the topology (\tabref{topfile2}).
-The format for the table files is three columns with $x$, $f(x)$, $-f'(x)$,
-where $x$ should be uniformly-spaced. Requirements for entries in the topology
+The format for the table files is three fixed-format columns of any suitable width. These columns must contain $x$, $f(x)$, $-f'(x)$,
+and the values of $x$ should be uniformly spaced. Requirements for entries in the topology
are given in~\tabref{topfile2}.
The setup of the tables is as follows:
\\{\bf bonds}:
*
* 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) 2013,2014,2016, 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.
return i;
}
-const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
+const t_filenm *getFilenm(const char *opt, int nfile, const t_filenm fnm[])
{
int i;
{
if (strcmp(opt, fnm[i].opt) == 0)
{
- return fnm[i].fns[0];
+ return &fnm[i];
}
}
+ return NULL;
+}
+
+const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
+{
+ const t_filenm *f = getFilenm(opt, nfile, fnm);
+ if (f != NULL)
+ {
+ return f->fns[0];
+ }
+
fprintf(stderr, "No option %s\n", opt);
return NULL;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
/* Return the filenames belonging to cmd-line option opt, or NULL when
* no such option. */
+/*! \brief
+ * Return a pointer to the t_filenm data structure of filenames belonging to
+ * command-line option opt, or NULL when no such option was used.
+ */
+const t_filenm *getFilenm(const char *opt, int nfile, const t_filenm fnm[]);
+
#define opt2FILE(opt, nfile, fnm, mode) gmx_ffopen(opt2fn(opt, nfile, fnm), mode)
/* Return a file pointer from the filename (see above) */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
#define _force_h
+#include "gromacs/fileio/filenm.h"
#include "gromacs/legacyheaders/genborn.h"
#include "gromacs/legacyheaders/network.h"
#include "gromacs/legacyheaders/tgroup.h"
* to .xvg files
*/
-bondedtable_t make_bonded_table(FILE *fplog, char *fn, int angle);
+bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle);
/* Return a table for bonded interactions,
* angle should be: bonds 0, angles 1, dihedrals 2
*/
const char *tabfn,
const char *tabafn,
const char *tabpfn,
- const char *tabbfn,
+ const t_filenm *tabbfnm,
const char *nbpu_opt,
gmx_bool bNoSolvOpt,
real print_force);
#include "gromacs/domdec/domdec.h"
#include "gromacs/ewald/ewald.h"
+#include "gromacs/fileio/filenm.h"
#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
#include "gromacs/legacyheaders/copyrite.h"
#include "gromacs/legacyheaders/force.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/simd/simd.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "nbnxn_gpu_jit_support.h"
}
}
+/*!\brief If there's bonded interactions of type \c ftype1 or \c
+ * ftype2 present in the topology, build an array of the number of
+ * interactions present for each bonded interaction index found in the
+ * topology.
+ *
+ * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
+ * valid type with that parameter.
+ *
+ * \c count will be reallocated as necessary to fit the largest bonded
+ * interaction index found, and its current size will be returned in
+ * \c ncount. It will contain zero for every bonded interaction index
+ * for which no interactions are present in the topology.
+ */
static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
int *ncount, int **count)
{
const t_ilist *il;
int mt, ftype, stride, i, j, tabnr;
+ // Loop over all moleculetypes
for (mt = 0; mt < mtop->nmoltype; mt++)
{
molt = &mtop->moltype[mt];
+ // Loop over all interaction types
for (ftype = 0; ftype < F_NRE; ftype++)
{
+ // If the current interaction type is one of the types whose tables we're trying to count...
if (ftype == ftype1 || ftype == ftype2)
{
il = &molt->ilist[ftype];
stride = 1 + NRAL(ftype);
+ // ... and there are actually some interactions for this type
for (i = 0; i < il->nr; i += stride)
{
+ // Find out which table index the user wanted
tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
if (tabnr < 0)
{
gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
}
+ // Make room for this index in the data structure
if (tabnr >= *ncount)
{
srenew(*count, tabnr+1);
}
*ncount = tabnr+1;
}
+ // Record that this table index is used and must have a valid file
(*count)[tabnr]++;
}
}
}
}
+/*!\brief If there's bonded interactions of flavour \c tabext and type
+ * \c ftype1 or \c ftype2 present in the topology, seek them in the
+ * list of filenames passed to mdrun, and make bonded tables from
+ * those files.
+ *
+ * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
+ * valid type with that parameter.
+ *
+ * A fatal error occurs if no matching filename is found.
+ */
static bondedtable_t *make_bonded_tables(FILE *fplog,
int ftype1, int ftype2,
const gmx_mtop_t *mtop,
- const char *basefn, const char *tabext)
+ const t_filenm *tabbfnm,
+ const char *tabext)
{
- int i, ncount, *count;
- char tabfn[STRLEN];
+ int ncount, *count;
bondedtable_t *tab;
tab = NULL;
count = NULL;
count_tables(ftype1, ftype2, mtop, &ncount, &count);
+ // Are there any relevant tabulated bond interactions?
if (ncount > 0)
{
snew(tab, ncount);
- for (i = 0; i < ncount; i++)
+ for (int i = 0; i < ncount; i++)
{
+ // Do any interactions exist that requires this table?
if (count[i] > 0)
{
- sprintf(tabfn, "%s", basefn);
- sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
- tabext, i, ftp2ext(efXVG));
- tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
+ // This pattern enforces the current requirement that
+ // table filenames end in a characteristic sequence
+ // before the file type extension, and avoids table 13
+ // being recognized and used for table 1.
+ std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
+ bool madeTable = false;
+ for (int j = 0; j < tabbfnm->nfiles && !madeTable; ++j)
+ {
+ std::string filename(tabbfnm->fns[j]);
+ if (gmx::endsWith(filename, patternToFind))
+ {
+ // Finally read the table from the file found
+ tab[i] = make_bonded_table(fplog, tabbfnm->fns[j], NRAL(ftype1)-2);
+ madeTable = true;
+ }
+ }
+ if (!madeTable)
+ {
+ bool isPlural = (ftype2 != -1);
+ gmx_fatal(FARGS, "Tabulated interaction of type '%s%s%s' with index %d cannot be used because no table file whose name matched '%s' was passed via the gmx mdrun -tableb command-line option.",
+ interaction_function[ftype1].longname,
+ isPlural ? "' or '" : "",
+ isPlural ? interaction_function[ftype2].longname : "",
+ i,
+ patternToFind.c_str());
+ }
}
}
sfree(count);
const char *tabfn,
const char *tabafn,
const char *tabpfn,
- const char *tabbfn,
+ const t_filenm *tabbfnm,
const char *nbpu_opt,
gmx_bool bNoSolvOpt,
real print_force)
make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
}
- if (fcd && tabbfn)
+ if (fcd && tabbfnm)
{
- fcd->bondtab = make_bonded_tables(fp,
- F_TABBONDS, F_TABBONDSNC,
- mtop, tabbfn, "b");
- fcd->angletab = make_bonded_tables(fp,
- F_TABANGLES, -1,
- mtop, tabbfn, "a");
- fcd->dihtab = make_bonded_tables(fp,
- F_TABDIHS, -1,
- mtop, tabbfn, "d");
+ // Need to catch std::bad_alloc
+ // TODO Don't need to catch this here, when merging with master branch
+ try
+ {
+ fcd->bondtab = make_bonded_tables(fp,
+ F_TABBONDS, F_TABBONDSNC,
+ mtop, tabbfnm, "b");
+ fcd->angletab = make_bonded_tables(fp,
+ F_TABANGLES, -1,
+ mtop, tabbfnm, "a");
+ fcd->dihtab = make_bonded_tables(fp,
+ F_TABDIHS, -1,
+ mtop, tabbfnm, "d");
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
else
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, 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.
{
/* Take the centered difference */
numf = -(vp - vm)*0.5*tabscale;
- ssd += fabs(2*(f - numf)/(f + numf));
+ if (f + numf != 0)
+ {
+ ssd += fabs(2*(f - numf)/(f + numf));
+ }
ns++;
}
}
if (ns > 0)
{
ssd /= ns;
- sprintf(buf, "For the %d non-zero entries for table %d in %s the forces deviate on average %d%% from minus the numerical derivative of the potential\n", ns, k, libfn, (int)(100*ssd+0.5));
+ sprintf(buf, "For the %d non-zero entries for table %d in %s the forces deviate on average %lld%% from minus the numerical derivative of the potential\n", ns, k, libfn, (long long int)(100*ssd+0.5));
if (debug)
{
fprintf(debug, "%s", buf);
return table;
}
-bondedtable_t make_bonded_table(FILE *fplog, char *fn, int angle)
+bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle)
{
t_tabledata td;
double start;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016, 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.
*/
bool endsWith(const std::string &str, const char *suffix);
+//! \copydoc endsWith(const std::string &str, const char *suffix)
+static inline bool endsWith(const std::string &str, const std::string &suffix)
+{
+ return endsWith(str, suffix.c_str());
+}
+
+/*! \brief
+ * Tests whether a string contains another as a substring.
+ *
+ * \param[in] str String to process.
+ * \param[in] substr Substring to find.
+ * \returns true if \p str contains \p substr.
+ *
+ * Does not throw.
+ */
+static inline bool contains(const std::string &str, const char *substr)
+{
+ return str.find(substr) != std::string::npos;
+}
+//! \copydoc contains(const std::string &str, const char *substr)
+static inline bool contains(const std::string &str, const std::string &substr)
+{
+ return str.find(substr) != std::string::npos;
+}
+
/*! \brief
* Removes a suffix from a string.
*
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
- "For each different tabulated interaction type the table file name is",
- "modified in a different way: before the file extension an underscore is",
- "appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
- "and finally the table number of the interaction type.[PAR]",
+ "For each different tabulated interaction type used, a table file name must",
+ "be given. For the topology to work, a file name given here must match a",
+ "character sequence before the file extension. That sequence is: an underscore,",
+ "then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
+ "and finally the matching table number index used in the topology.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [REF].mdp[ref] file.[PAR]",
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRDMULT },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
opt2fn("-table", nfile, fnm),
opt2fn("-tabletf", nfile, fnm),
opt2fn("-tablep", nfile, fnm),
- opt2fn("-tableb", nfile, fnm),
+ getFilenm("-tableb", nfile, fnm),
nbpu_opt,
FALSE,
pforce);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016, 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.
${testname}
${exename}
# files with code for tests
+ tabulated_bonded_interactions.cpp
grompp.cpp
rerun.cpp
trajectory_writing.cpp
--- /dev/null
+A single butane
+ 4
+ 1BUT C1 1 1.382 1.573 1.482
+ 1BUT C2 2 1.281 1.559 1.596
+ 1BUT C3 3 1.292 1.422 1.663
+ 1BUT C4 4 1.189 1.407 1.775
+ 2.46298 2.46298 2.46298
--- /dev/null
+[ System ]
+ 1 2 3 4
--- /dev/null
+# Table was made with:
+#
+# seq 0 1 180 | awk '{print $1" "$1*3.14159265358979323846/180}' | awk '{printf "%20g %20g %20g\n", $1,
+# 0.5*460.2 *($1-111)^2,
+# -1*0.5*406.2*2*($1-111)}'
+ 0 2.83506e+06 45088.2
+ 1 2.78421e+06 44682
+ 2 2.73382e+06 44275.8
+ 3 2.68389e+06 43869.6
+ 4 2.63441e+06 43463.4
+ 5 2.5854e+06 43057.2
+ 6 2.53685e+06 42651
+ 7 2.48876e+06 42244.8
+ 8 2.44113e+06 41838.6
+ 9 2.39396e+06 41432.4
+ 10 2.34725e+06 41026.2
+ 11 2.301e+06 40620
+ 12 2.25521e+06 40213.8
+ 13 2.20988e+06 39807.6
+ 14 2.16501e+06 39401.4
+ 15 2.1206e+06 38995.2
+ 16 2.07665e+06 38589
+ 17 2.03316e+06 38182.8
+ 18 1.99013e+06 37776.6
+ 19 1.94757e+06 37370.4
+ 20 1.90546e+06 36964.2
+ 21 1.86381e+06 36558
+ 22 1.82262e+06 36151.8
+ 23 1.78189e+06 35745.6
+ 24 1.74163e+06 35339.4
+ 25 1.70182e+06 34933.2
+ 26 1.66247e+06 34527
+ 27 1.62359e+06 34120.8
+ 28 1.58516e+06 33714.6
+ 29 1.54719e+06 33308.4
+ 30 1.50969e+06 32902.2
+ 31 1.47264e+06 32496
+ 32 1.43605e+06 32089.8
+ 33 1.39993e+06 31683.6
+ 34 1.36426e+06 31277.4
+ 35 1.32906e+06 30871.2
+ 36 1.29431e+06 30465
+ 37 1.26003e+06 30058.8
+ 38 1.2262e+06 29652.6
+ 39 1.19284e+06 29246.4
+ 40 1.15993e+06 28840.2
+ 41 1.12749e+06 28434
+ 42 1.09551e+06 28027.8
+ 43 1.06398e+06 27621.6
+ 44 1.03292e+06 27215.4
+ 45 1.00232e+06 26809.2
+ 46 972172 26403
+ 47 942490 25996.8
+ 48 913267 25590.6
+ 49 884504 25184.4
+ 50 856202 24778.2
+ 51 828360 24372
+ 52 800978 23965.8
+ 53 774056 23559.6
+ 54 747595 23153.4
+ 55 721594 22747.2
+ 56 696052 22341
+ 57 670972 21934.8
+ 58 646351 21528.6
+ 59 622190 21122.4
+ 60 598490 20716.2
+ 61 575250 20310
+ 62 552470 19903.8
+ 63 530150 19497.6
+ 64 508291 19091.4
+ 65 486892 18685.2
+ 66 465952 18279
+ 67 445474 17872.8
+ 68 425455 17466.6
+ 69 405896 17060.4
+ 70 386798 16654.2
+ 71 368160 16248
+ 72 349982 15841.8
+ 73 332264 15435.6
+ 74 315007 15029.4
+ 75 298210 14623.2
+ 76 281872 14217
+ 77 265996 13810.8
+ 78 250579 13404.6
+ 79 235622 12998.4
+ 80 221126 12592.2
+ 81 207090 12186
+ 82 193514 11779.8
+ 83 180398 11373.6
+ 84 167743 10967.4
+ 85 155548 10561.2
+ 86 143812 10155
+ 87 132538 9748.8
+ 88 121723 9342.6
+ 89 111368 8936.4
+ 90 101474 8530.2
+ 91 92040 8124
+ 92 83066.1 7717.8
+ 93 74552.4 7311.6
+ 94 66498.9 6905.4
+ 95 58905.6 6499.2
+ 96 51772.5 6093
+ 97 45099.6 5686.8
+ 98 38886.9 5280.6
+ 99 33134.4 4874.4
+ 100 27842.1 4468.2
+ 101 23010 4062
+ 102 18638.1 3655.8
+ 103 14726.4 3249.6
+ 104 11274.9 2843.4
+ 105 8283.6 2437.2
+ 106 5752.5 2031
+ 107 3681.6 1624.8
+ 108 2070.9 1218.6
+ 109 920.4 812.4
+ 110 230.1 406.2
+ 111 0 -0
+ 112 230.1 -406.2
+ 113 920.4 -812.4
+ 114 2070.9 -1218.6
+ 115 3681.6 -1624.8
+ 116 5752.5 -2031
+ 117 8283.6 -2437.2
+ 118 11274.9 -2843.4
+ 119 14726.4 -3249.6
+ 120 18638.1 -3655.8
+ 121 23010 -4062
+ 122 27842.1 -4468.2
+ 123 33134.4 -4874.4
+ 124 38886.9 -5280.6
+ 125 45099.6 -5686.8
+ 126 51772.5 -6093
+ 127 58905.6 -6499.2
+ 128 66498.9 -6905.4
+ 129 74552.4 -7311.6
+ 130 83066.1 -7717.8
+ 131 92040 -8124
+ 132 101474 -8530.2
+ 133 111368 -8936.4
+ 134 121723 -9342.6
+ 135 132538 -9748.8
+ 136 143812 -10155
+ 137 155548 -10561.2
+ 138 167743 -10967.4
+ 139 180398 -11373.6
+ 140 193514 -11779.8
+ 141 207090 -12186
+ 142 221126 -12592.2
+ 143 235622 -12998.4
+ 144 250579 -13404.6
+ 145 265996 -13810.8
+ 146 281872 -14217
+ 147 298210 -14623.2
+ 148 315007 -15029.4
+ 149 332264 -15435.6
+ 150 349982 -15841.8
+ 151 368160 -16248
+ 152 386798 -16654.2
+ 153 405896 -17060.4
+ 154 425455 -17466.6
+ 155 445474 -17872.8
+ 156 465952 -18279
+ 157 486892 -18685.2
+ 158 508291 -19091.4
+ 159 530150 -19497.6
+ 160 552470 -19903.8
+ 161 575250 -20310
+ 162 598490 -20716.2
+ 163 622190 -21122.4
+ 164 646351 -21528.6
+ 165 670972 -21934.8
+ 166 696052 -22341
+ 167 721594 -22747.2
+ 168 747595 -23153.4
+ 169 774056 -23559.6
+ 170 800978 -23965.8
+ 171 828360 -24372
+ 172 856202 -24778.2
+ 173 884504 -25184.4
+ 174 913267 -25590.6
+ 175 942490 -25996.8
+ 176 972172 -26403
+ 177 1.00232e+06 -26809.2
+ 178 1.03292e+06 -27215.4
+ 179 1.06398e+06 -27621.6
+ 180 1.09551e+06 -28027.8
--- /dev/null
+# Table was made with:
+#
+# seq 0 0.001 0.3 | awk '{print $1" "$1*atan2(0,-1)/180}' | awk '{printf "%20g %20g %20g\n", $1,
+# 0.5*334700 *($1-0.153)^2,
+#-1*(0.5*334700*2*($1-0.153))}'
+ 0 3917.5 51209.1
+ 0.001 3866.45 50874.4
+ 0.002 3815.75 50539.7
+ 0.003 3765.38 50205
+ 0.004 3715.34 49870.3
+ 0.005 3665.63 49535.6
+ 0.006 3616.27 49200.9
+ 0.007 3567.23 48866.2
+ 0.008 3518.53 48531.5
+ 0.009 3470.17 48196.8
+ 0.01 3422.14 47862.1
+ 0.011 3374.45 47527.4
+ 0.012 3327.09 47192.7
+ 0.013 3280.06 46858
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--- /dev/null
+# Table was made with:
+#
+# seq -180 1 180 | awk '{print $1" "$1*3.14159265358979323846/180}' | awk '{printf "%20g %20g %20g\n", $1,
+# 9.2789 -12.156*cos($2) -13.12 *cos($2)^2 +3.0597 *cos($2)^3 +26.24 *cos($2)^4 +31.495 *cos($2)^5,
+# -1*(0.0 +12.156*sin($2) +13.12*2*sin($2)*cos($2) -3.0597*3*sin($2)*cos($2)^2 -26.24*4*sin($2)*cos($2)^3 -31.495*5*sin($2)*cos($2)^4)*3.14159265358979323846/180}'
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--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, 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.
+ */
+
+/*! \internal \file
+ * \brief
+ * Tests for tabulated bonded interactions
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_mdrun_integration_tests
+ */
+#include "gmxpre.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/file.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/cmdlinetest.h"
+
+#include "moduletest.h"
+
+namespace gmx
+{
+namespace test
+{
+
+//! Format string for building a configurable .top file
+const char *g_butaneTopFileFormatString = "\
+[ defaults ]\n\
+; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ\n\
+ 1 1 no 1.0 1.0\n\
+\n\
+[ atomtypes ]\n\
+;name mass charge ptype c6 c12\n\
+ CH2 14.02700 0.000 A 0.90975E-02 0.35333E-04\n\
+ CH3 15.03500 0.000 A 0.88765E-02 0.26150E-04\n\
+\n\
+[ moleculetype ]\n\
+; name nrexcl\n\
+ butane 3\n\
+\n\
+[ atoms ]\n\
+; nr type resnr residu atom cgnr\n\
+ 1 CH3 1 BUT C1 1\n\
+ 2 CH2 1 BUT C2 2\n\
+ 3 CH2 1 BUT C3 3\n\
+ 4 CH3 1 BUT C4 4\n\
+\n\
+%s\n\
+\n\
+[ system ]\n\
+; The name of the system to be simulated\n\
+A single butane\n\
+\n\
+[ molecules ]\n\
+; Molname Number\n\
+Butane 1\n\
+";
+
+//! Test fixture for bonded interactions
+class BondedInteractionsTest : public gmx::test::MdrunTestFixture
+{
+ public:
+ //! Execute the trajectory writing test
+ void setupGrompp(const char *interaction)
+ {
+ runner_.topFileName_ = fileManager_.getTemporaryFilePath("butane1.top");
+ File::writeFileFromString(runner_.topFileName_, formatString(g_butaneTopFileFormatString, interaction));
+ runner_.groFileName_ = fileManager_.getInputFilePath("butane1.gro");
+ runner_.ndxFileName_ = fileManager_.getInputFilePath("butane1.ndx");
+ /* TODO Now that Verlet is the default, change the implementation
+ of useEmptyMdpFile() to do that. */
+ runner_.useStringAsMdpFile("");
+ }
+ //! Prepare an mdrun caller
+ CommandLine setupMdrun()
+ {
+ CommandLine rerunCaller;
+ rerunCaller.append("mdrun");
+ rerunCaller.addOption("-rerun", runner_.groFileName_);
+ return rerunCaller;
+ }
+ //! Check the output of mdrun
+ void checkMdrun()
+ {
+ // TODO verifying some energies and forces would be good,
+ // once other code in gerrit is reviewed
+ }
+};
+
+// This test ensures that a normal non-tabulated bond interaction works
+TEST_F(BondedInteractionsTest, NormalBondWorks)
+{
+ setupGrompp("[ bonds ]\n\
+; ai aj funct c0 c1\n\
+ 1 2 1 1.530000e-01 3.347000e+05");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+// This test ensures that a normal abulated bond interaction works
+TEST_F(BondedInteractionsTest, TabulatedBondWorks)
+{
+ setupGrompp("[ bonds ]\n\
+; ai aj funct n k\n\
+ 1 2 8 0 1000");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ std::string tableFileName = fileManager_.getInputFilePath("butane_b0.xvg");
+ rerunCaller.addOption("-tableb", tableFileName);
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+// This test ensures that a normal non-tabulated angle interaction works
+TEST_F(BondedInteractionsTest, NormalAngleWorks)
+{
+ setupGrompp("[ angles ]\n\
+; ai aj ak funct c0 c1\n\
+ 1 2 3 1 1.110000e+02 4.602000e+02");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+// This test ensures that a tabulated angle interaction works
+TEST_F(BondedInteractionsTest, TabulatedAngleWorks)
+{
+ setupGrompp("[ angles ]\n\
+; ai aj ak funct n k\n\
+ 1 2 3 8 0 1000");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ std::string tableFileName = fileManager_.getInputFilePath("butane_a0.xvg");
+ rerunCaller.addOption("-tableb", tableFileName);
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+// This test ensures that a normal non-tabulated dihedral interaction works
+TEST_F(BondedInteractionsTest, NormalDihedralWorks)
+{
+ setupGrompp("[ dihedrals ]\n \
+; ai aj ak al funct c0 c1 c2 c3 c4 c5\n\
+ 1 2 3 4 3 9.2789 12.156 -13.12 -3.0597 26.24 -31.495");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+// This test ensures that a tabulated dihedral interaction works
+TEST_F(BondedInteractionsTest, TabulatedDihedralWorks)
+{
+ setupGrompp("[ dihedrals ]\n\
+; ai aj ak al funct n k\n\
+ 1 2 3 4 8 0 1000");
+ EXPECT_EQ(0, runner_.callGrompp());
+
+ test::CommandLine rerunCaller = setupMdrun();
+ std::string tableFileName = fileManager_.getInputFilePath("butane_d0.xvg");
+ rerunCaller.addOption("-tableb", tableFileName);
+ ASSERT_EQ(0, runner_.callMdrun(rerunCaller));
+ checkMdrun();
+}
+
+} // namespace
+
+} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff