if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
+if("${CMAKE_INSTALL_PREFIX}" STREQUAL "${CMAKE_BINARY_DIR}")
+ message(FATAL_ERROR "GROMACS cannot be installed into the build tree, choose a different location for CMAKE_INSTALL_PREFIX")
+endif()
include(gmxBuildTypeReference)
include(gmxBuildTypeProfile)
Bioinformatics 29 (2013) pp. 845-54
DOI: 10.1093/bioinformatics/btt055
+* Tackling Exascale Software Challenges in Molecular Dynamics Simulations
+ with GROMACS
+ Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
+ In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale,
+ 8759 (2015) pp. 3–27
+ DOI: 10.1007/978-3-319-15976-8_1
+
There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in
form of code, hardware and funding! Industrial users who choose to pay
* ``-DGMX_BUILD_MDRUN_ONLY=on`` for `building only mdrun`_, e.g. for compute cluster back-end nodes
* ``-DGMX_DOUBLE=on`` to run |Gromacs| in double precision (slower, and not normally useful)
* ``-DCMAKE_PREFIX_PATH=xxx`` to add a non-standard location for CMake to `search for libraries, headers or programs`_
-* ``-DCMAKE_INSTALL_PREFIX=xxx`` to install |Gromacs| to a non-standard location (default ``/usr/local/gromacs``)
+* ``-DCMAKE_INSTALL_PREFIX=xxx`` to install |Gromacs| to a `non-standard location`_ (default ``/usr/local/gromacs``)
* ``-DBUILD_SHARED_LIBS=off`` to turn off the building of shared libraries to help with `static linking`_
* ``-DGMX_FFT_LIBRARY=xxx`` to select whether to use ``fftw``, ``mkl`` or ``fftpack`` libraries for `FFT support`_
* ``-DCMAKE_BUILD_TYPE=Debug`` to build |Gromacs| in debug mode
You cannot attempt to change compilers after the initial run of
``cmake``. If you need to change, clean up, and start again.
+.. _non-standard location:
+
+Where to install GROMACS
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+A key thing to consider is the setting of
+``CMAKE_INSTALL_PREFIX``. You will need to be able to write to this
+directory in order to install GROMACS later, this directory cannot
+be the same as the build tree, and if you change your
+mind later, changing it in the cache triggers a full re-build,
+unfortunately. So if you do not have super-user privileges on your
+machine, then you will need to choose a sensible location within your
+home directory for your GROMACS installation. Even if you do have
+super-user privileges, you should use them only for the installation
+phase, and never for configuring, building, or running GROMACS!
+
.. _cmake options:
Using CMake command-line options
\eeq
where $m_i$ is the mass of atom $i$ and ${\bf r}_i$ the position of
atom $i$ with respect to the center of mass of the molecule. It is especially
-useful to characterize polymer solutions and proteins.
+useful to characterize polymer solutions and proteins. The program will also
+provide the radius of gyration around the coordinate axis (or, optionally, principal axes)
+by only summing the radii components orthogonal to each axis, for instance
+\beq
+R_{g,x} ~=~ \left({\frac{\sum_i \left( r_{i,y}^2 + r_{i,z}^2 \right) m_i}{\sum_i m_i}}\right)^{\half}
+\label{eqn:rg}
+\eeq
Sometimes it is interesting to plot the {\em distance} between two atoms,
or the {\em minimum} distance between two groups of atoms
when set to a floating-point value, overrides the default tolerance of
1e-5 for force-field floating-point parameters.
-``GMX_MAX_MPI_THREADS``
- sets the maximum number of MPI-threads that :ref:`gmx mdrun`
- can use.
-
``GMX_MAXCONSTRWARN``
if set to -1, :ref:`gmx mdrun` will
not exit if it produces too many LINCS warnings.
// directory.
#if (defined CMAKE_SOURCE_DIR && defined CMAKE_BINARY_DIR)
std::string buildBinPath;
-#ifdef CMAKE_INTDIR
+#ifdef CMAKE_INTDIR /*In multi-configuration build systems the output subdirectory*/
buildBinPath = Path::join(CMAKE_BINARY_DIR, "bin", CMAKE_INTDIR);
#else
buildBinPath = Path::join(CMAKE_BINARY_DIR, "bin");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014,2015, 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.
fprintf(debug, "Running on %d threads\n", nthreads);
}
-#ifdef GMX_FFT_FFTW3 /*if not FFTW - then we don't do a 3d plan but instead use only 1D plans */
+#ifdef GMX_FFT_FFTW3
+ /* Don't add more stuff here! We have already had at least one bug because we are reimplementing
+ * the low-level FFT interface instead of using the Gromacs FFT module. If we need more
+ * generic functionality it is far better to extend the interface so we can use it for
+ * all FFT libraries instead of writing FFTW-specific code here.
+ */
+
+ /*if not FFTW - then we don't do a 3d plan but instead use only 1D plans */
/* It is possible to use the 3d plan with OMP threads - but in that case it is not allowed to be called from
* within a parallel region. For now deactivated. If it should be supported it has to made sure that
* that the execute of the 3d plan is in a master/serial block (since it contains it own parallel region)
int inNG = NG, outMG = MG, outKG = KG;
FFTW_LOCK;
- if (!(flags&FFT5D_NOMEASURE))
- {
- fftwflags |= FFTW_MEASURE;
- }
+
+ fftwflags |= (flags & FFT5D_NOMEASURE) ? FFTW_ESTIMATE : FFTW_MEASURE;
+
if (flags&FFT5D_REALCOMPLEX)
{
if (!(flags&FFT5D_BACKWARD)) /*input pointer is not complex*/
*
* 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.
rvec x[], rvec *v, matrix box)
{
char name[6];
+ char resname[6], oldresname[6];
char line[STRLEN+1], *ptr;
char buf[256];
double x1, y1, z1, x2, y2, z2;
bVel = FALSE;
+ resname[0] = '\0';
+ oldresname[0] = '\0';
+
/* just pray the arrays are big enough */
for (i = 0; (i < natoms); i++)
{
memcpy(name, line, 5);
name[5] = '\0';
sscanf(name, "%d", &resnr);
- memcpy(name, line+5, 5);
- name[5] = '\0';
- if (resnr != oldres)
+ sscanf(line+5, "%5s", resname);
+
+ if (resnr != oldres || strncmp(resname, oldresname, sizeof(resname)))
{
oldres = resnr;
newres++;
infile, natoms);
}
atoms->atom[i].resind = newres;
- t_atoms_set_resinfo(atoms, i, symtab, name, resnr, ' ', 0, ' ');
+ t_atoms_set_resinfo(atoms, i, symtab, resname, resnr, ' ', 0, ' ');
}
else
{
memcpy(name, line+10, 5);
atoms->atomname[i] = put_symtab(symtab, name);
+ /* Copy resname to oldresname after we are done with the sanity check above */
+ strncpy(oldresname, resname, sizeof(oldresname));
+
/* eventueel controle atomnumber met i+1 */
/* coordinates (start after residue data) */
*
* 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.
int nxframe;
t_fileio *fio;
tng_trajectory_t tng;
- int NATOMS;
+ int natoms;
double DT, BOX[3];
gmx_bool bReadBox;
char *persistent_line; /* Persistent line for reading g96 trajectories */
lasttime =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
- status->xframe->natoms, &bOK);
+ status->natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
fr->t0 = fr->time;
+ /* We need the number of atoms for random-access XTC searching, even when
+ * we don't have access to the actual frame data.
+ */
+ (*status)->natoms = fr->natoms;
+
return (fr->natoms > 0);
}
}
static void luzar_correl(int nn, real *time, int nset, real **val, real temp,
- gmx_bool bError, real fit_start, real smooth_tail_start,
- const output_env_t oenv)
+ gmx_bool bError, real fit_start)
{
const real tol = 1e-8;
real *kt;
fprintf(debug, "RMS difference in derivatives is %g\n", sqrt(d2/nn));
}
analyse_corr(nn, time, val[0], val[2], kt, NULL, NULL, NULL, fit_start,
- temp, smooth_tail_start, oenv);
+ temp);
sfree(kt);
}
else if (nset == 6)
{
analyse_corr(nn, time, val[0], val[2], val[4],
- val[1], val[3], val[5], fit_start, temp, smooth_tail_start, oenv);
+ val[1], val[3], val[5], fit_start, temp);
}
else
{
static gmx_bool bEESEF = FALSE, bEENLC = FALSE, bEeFitAc = FALSE, bPower = FALSE;
static gmx_bool bIntegrate = FALSE, bRegression = FALSE, bLuzar = FALSE, bLuzarError = FALSE;
static int nsets_in = 1, d = 1, nb_min = 4, resol = 10, nBalExp = 4, nFitPoints = 100;
- static real temp = 298.15, fit_start = 1, fit_end = 60, smooth_tail_start = -1, balTime = 0.2, diffusion = 5e-5, rcut = 0.35;
+ static real temp = 298.15, fit_start = 1, fit_end = 60, balTime = 0.2, diffusion = 5e-5, rcut = 0.35;
/* must correspond to enum avbar* declared at beginning of file */
static const char *avbar_opt[avbarNR+1] = {
"Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation" },
{ "-fitend", FALSE, etREAL, {&fit_end},
"Time (ps) where to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation. Only with [TT]-gem[tt]" },
- { "-smooth", FALSE, etREAL, {&smooth_tail_start},
- "If this value is >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: [MATH]y = A [EXP]-x/[GRK]tau[grk][exp][math]" },
{ "-nbmin", FALSE, etINT, {&nb_min},
"HIDDENMinimum number of blocks for block averaging" },
{ "-resol", FALSE, etINT, {&resol},
if (bLuzar)
{
- luzar_correl(n, t, nset, val, temp, bXYdy, fit_start, smooth_tail_start, oenv);
+ luzar_correl(n, t, nset, val, temp, bXYdy, fit_start);
}
view_all(oenv, NFILE, fnm);
com[m] /= tmass;
}
calc_box_center(ecenterDEF, box, box_center);
- rvec_sub(box_center, com, shift);
+ rvec_sub(com, box_center, shift);
/* Important - while the center was calculated based on a group, we should move all atoms */
for (i = 0; (i < atoms->nr); i++)
fprintf(out, "\n");
}
+
int gmx_gyrate(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the radius of gyration of a molecule",
"and the radii of gyration about the [IT]x[it]-, [IT]y[it]- and [IT]z[it]-axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
+ "The axis components corresponds to the mass-weighted root-mean-square",
+ "of the radii components orthogonal to each axis, for example:[PAR]",
+ "Rg(x) = sqrt((sum_i m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
atom_id *index;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
- const char *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
+ const char *leg[] = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
const char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
if (bQ)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
- "Radius of Charge", "Time (ps)", "Rg (nm)", oenv);
+ "Radius of Charge (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
else if (bMOI)
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
- "Moments of inertia", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
+ "Moments of inertia (total and around axes)", "Time (ps)", "I (a.m.u. nm\\S2\\N)", oenv);
}
else
{
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
- "Radius of gyration", "Time (ps)", "Rg (nm)", oenv);
+ "Radius of gyration (total and around axes)", "Time (ps)", "Rg (nm)", oenv);
}
if (bMOI)
{
return chi2;
}
-static void smooth_tail(int n, real t[], real c[], real sigma_c[], real start,
- const output_env_t oenv)
-{
- FILE *fp;
- real e_1;
- double fitparm[4];
- int i;
-
- e_1 = exp(-1);
- for (i = 0; (i < n); i++)
- {
- if (c[i] < e_1)
- {
- break;
- }
- }
- if (i < n)
- {
- fitparm[0] = t[i];
- }
- else
- {
- fitparm[0] = 10;
- }
- fitparm[1] = 0.95;
- do_lmfit(n, c, sigma_c, 0, t, start, t[n-1], oenv, bDebugMode(),
- effnEXP2, fitparm, 0, NULL);
-}
-
void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
real sigma_ct[], real sigma_nt[], real sigma_kt[],
- real fit_start, real temp, real smooth_tail_start,
- const output_env_t oenv)
+ real fit_start, real temp)
{
int i0, i;
real k = 1, kp = 1, kow = 1;
double tmp, sn2 = 0, sc2 = 0, sk2 = 0, scn = 0, sck = 0, snk = 0;
gmx_bool bError = (sigma_ct != NULL) && (sigma_nt != NULL) && (sigma_kt != NULL);
- if (smooth_tail_start >= 0)
- {
- smooth_tail(n, t, ct, sigma_ct, smooth_tail_start, oenv);
- smooth_tail(n, t, nt, sigma_nt, smooth_tail_start, oenv);
- smooth_tail(n, t, kt, sigma_kt, smooth_tail_start, oenv);
- }
for (i0 = 0; (i0 < n-2) && ((t[i0]-t[0]) < fit_start); i0++)
{
;
*/
static void do_hbac(const char *fn, t_hbdata *hb,
int nDump, gmx_bool bMerge, gmx_bool bContact, real fit_start,
- real temp, gmx_bool R2, real smooth_tail_start, const output_env_t oenv,
+ real temp, gmx_bool R2, const output_env_t oenv,
const char *gemType, int nThreads,
const int NN, const gmx_bool bBallistic, const gmx_bool bGemFit)
{
xvgrclose(fp);
analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
- fit_start, temp, smooth_tail_start, oenv);
+ fit_start, temp);
do_view(oenv, fn, NULL);
sfree(rhbex);
};
static real acut = 30, abin = 1, rcut = 0.35, r2cut = 0, rbin = 0.005, rshell = -1;
- static real maxnhb = 0, fit_start = 1, fit_end = 60, temp = 298.15, smooth_tail_start = -1, D = -1;
+ static real maxnhb = 0, fit_start = 1, fit_end = 60, temp = 298.15, D = -1;
static gmx_bool bNitAcc = TRUE, bDA = TRUE, bMerge = TRUE;
static int nDump = 0, nFitPoints = 100;
static int nThreads = 0, nBalExp = 4;
"Time (ps) to which to stop fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation (only with [TT]-gemfit[tt])" },
{ "-temp", FALSE, etREAL, {&temp},
"Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming" },
- { "-smooth", FALSE, etREAL, {&smooth_tail_start},
- "If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/[GRK]tau[grk])" },
{ "-dump", FALSE, etINT, {&nDump},
"Dump the first N hydrogen bond ACFs in a single [REF].xvg[ref] file for debugging" },
{ "-max_hb", FALSE, etREAL, {&maxnhb},
}
gemstring = gmx_strdup(gemType[hb->per->gemtype]);
do_hbac(opt2fn("-ac", NFILE, fnm), hb, nDump,
- bMerge, bContact, fit_start, temp, r2cut > 0, smooth_tail_start, oenv,
+ bMerge, bContact, fit_start, temp, r2cut > 0, oenv,
gemstring, nThreads, NN, bBallistic, bGemFit);
}
if (opt2bSet("-life", NFILE, fnm))
close_trj(status);
- calc_rms(isize, teller, dtot, dtot2, mean, &meanmax, rms, &rmsmax, rmsc, &rmscmax);
+ calc_rms(isize, teller, dtot, dtot2, rms, &rmsmax, rmsc, &rmscmax, mean, &meanmax);
fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
if (bNMR)
"trajectories must be concatenated without having double frames.[PAR]",
"Option [TT]-dump[tt] can be used to extract a frame at or near",
- "one specific time from your trajectory.[PAR]",
+ "one specific time from your trajectory, but only works reliably",
+ "if the time interval between frames is uniform.[PAR]",
"Option [TT]-drop[tt] reads an [REF].xvg[ref] file with times and values.",
"When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
*
* 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.
/* Routines from g_hbond */
void analyse_corr(int n, real t[], real ct[], real nt[], real kt[],
real sigma_ct[], real sigma_nt[], real sigma_kt[],
- real fit_start, real temp, real smooth_tail_start,
- const output_env_t oenv);
+ real fit_start, real temp);
void compute_derivative(int nn, real x[], real y[], real dydx[]);
"N. Goga and A. J. Rzepiela and A. H. de Vries and S. J. Marrink and H. J. C. Berendsen",
"Efficient Algorithms for Langevin and DPD Dynamics",
"J. Chem. Theory Comput.",
- 8, 2012, "3637--3649"}
+ 8, 2012, "3637--3649"},
+ { "Pronk2013",
+ "S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl",
+ "GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit",
+ "Bioinformatics",
+ 29, 2013, "845-54"},
+ { "Pall2015",
+ "S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl",
+ "Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS",
+ "In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale",
+ 8759, 2015, "3–27" }
};
#define NSTR (int)asize(citedb)
{
int npppn;
char th_or_proc[STRLEN], th_or_proc_plural[STRLEN], pernode[STRLEN];
- gmx_bool btMPI, bMPI, bMaxMpiThreadsSet, bNthreadsAuto, bEmulateGPU;
+ gmx_bool btMPI, bMPI, bNthreadsAuto, bEmulateGPU;
assert(hwinfo);
assert(cr);
/* GPU emulation detection is done later, but we need here as well
* -- uncool, but there's no elegant workaround */
bEmulateGPU = (getenv("GMX_EMULATE_GPU") != NULL);
- bMaxMpiThreadsSet = (getenv("GMX_MAX_MPI_THREADS") != NULL);
if (hwinfo->gpu_info.n_dev_compatible > 0)
{
could automatically start. */
gmx_fatal(FARGS,
"%d GPU%s provided, but only %d PP thread-MPI thread%s coud be started.\n"
- "%s requires one PP tread-MPI thread per GPU; use fewer GPUs%s.",
+ "%s requires one PP tread-MPI thread per GPU; use fewer GPUs.",
ngpu_use, gpu_use_plural,
npppn, th_or_proc_plural,
- ShortProgram(), bMaxMpiThreadsSet ? "\nor allow more threads to be used" : "");
+ ShortProgram());
}
if (!hw_opt->gpu_opt.bUserSet && npppn < ngpu_comp)
limited the number GPUs used. */
md_print_warn(cr, fplog,
"NOTE: %d GPU%s were detected, but only %d PP thread-MPI thread%s can be started.\n"
- " %s can use one GPU per PP tread-MPI thread, so only %d GPU%s will be used.%s\n",
+ " %s can use one GPU per PP tread-MPI thread, so only %d GPU%s will be used.\n",
ngpu_comp, gpu_comp_plural,
npppn, th_or_proc_plural,
ShortProgram(), npppn,
- npppn > 1 ? "s" : "",
- bMaxMpiThreadsSet ? "\n Also, you can allow more threads to be used by increasing GMX_MAX_MPI_THREADS" : "");
+ npppn > 1 ? "s" : "");
}
}
*
* 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.
}
}
- /* The above approach is great in that we double-check that e.g. an angle
- * really corresponds to three atoms connected by bonds, but this is not
- * generally true. Go through the angle and dihedral hackblocks to add
- * entries that we have not yet marked as matched when going through bonds.
- */
- for (i = 0; i < atoms->nres; i++)
+ if (hb)
{
- /* Add remaining angles from hackblock */
- hbang = &hb[i].rb[ebtsANGLES];
- for (j = 0; j < hbang->nb; j++)
+ /* The above approach is great in that we double-check that e.g. an angle
+ * really corresponds to three atoms connected by bonds, but this is not
+ * generally true. Go through the angle and dihedral hackblocks to add
+ * entries that we have not yet marked as matched when going through bonds.
+ */
+ for (i = 0; i < atoms->nres; i++)
{
- if (hbang->b[j].match == TRUE)
- {
- /* We already used this entry, continue to the next */
- continue;
- }
- /* Hm - entry not used, let's see if we can find all atoms */
- if (nang == maxang)
- {
- maxang += ninc;
- srenew(ang, maxang);
- }
- bFound = TRUE;
- for (k = 0; k < 3 && bFound; k++)
+ /* Add remaining angles from hackblock */
+ hbang = &hb[i].rb[ebtsANGLES];
+ for (j = 0; j < hbang->nb; j++)
{
- p = hbang->b[j].a[k];
- res = i;
- if (p[0] == '-')
+ if (hbang->b[j].match == TRUE)
{
- p++;
- res--;
+ /* We already used this entry, continue to the next */
+ continue;
}
- else if (p[0] == '+')
+ /* Hm - entry not used, let's see if we can find all atoms */
+ if (nang == maxang)
{
- p++;
- res++;
+ maxang += ninc;
+ srenew(ang, maxang);
}
- ang[nang].a[k] = search_res_atom(p, res, atoms, "angle", TRUE);
- bFound = (ang[nang].a[k] != NO_ATID);
- }
- ang[nang].C0 = NOTSET;
- ang[nang].C1 = NOTSET;
+ bFound = TRUE;
+ for (k = 0; k < 3 && bFound; k++)
+ {
+ p = hbang->b[j].a[k];
+ res = i;
+ if (p[0] == '-')
+ {
+ p++;
+ res--;
+ }
+ else if (p[0] == '+')
+ {
+ p++;
+ res++;
+ }
+ ang[nang].a[k] = search_res_atom(p, res, atoms, "angle", TRUE);
+ bFound = (ang[nang].a[k] != NO_ATID);
+ }
+ ang[nang].C0 = NOTSET;
+ ang[nang].C1 = NOTSET;
- if (bFound)
- {
- set_p_string(&(ang[nang]), hbang->b[j].s);
- hbang->b[j].match = TRUE;
- /* Incrementing nang means we save this angle */
- nang++;
+ if (bFound)
+ {
+ set_p_string(&(ang[nang]), hbang->b[j].s);
+ hbang->b[j].match = TRUE;
+ /* Incrementing nang means we save this angle */
+ nang++;
+ }
}
- }
- /* Add remaining dihedrals from hackblock */
- hbdih = &hb[i].rb[ebtsPDIHS];
- for (j = 0; j < hbdih->nb; j++)
- {
- if (hbdih->b[j].match == TRUE)
- {
- /* We already used this entry, continue to the next */
- continue;
- }
- /* Hm - entry not used, let's see if we can find all atoms */
- if (ndih == maxdih)
- {
- maxdih += ninc;
- srenew(dih, maxdih);
- }
- bFound = TRUE;
- for (k = 0; k < 4 && bFound; k++)
+ /* Add remaining dihedrals from hackblock */
+ hbdih = &hb[i].rb[ebtsPDIHS];
+ for (j = 0; j < hbdih->nb; j++)
{
- p = hbdih->b[j].a[k];
- res = i;
- if (p[0] == '-')
+ if (hbdih->b[j].match == TRUE)
{
- p++;
- res--;
+ /* We already used this entry, continue to the next */
+ continue;
}
- else if (p[0] == '+')
+ /* Hm - entry not used, let's see if we can find all atoms */
+ if (ndih == maxdih)
{
- p++;
- res++;
+ maxdih += ninc;
+ srenew(dih, maxdih);
+ }
+ bFound = TRUE;
+ for (k = 0; k < 4 && bFound; k++)
+ {
+ p = hbdih->b[j].a[k];
+ res = i;
+ if (p[0] == '-')
+ {
+ p++;
+ res--;
+ }
+ else if (p[0] == '+')
+ {
+ p++;
+ res++;
+ }
+ dih[ndih].a[k] = search_res_atom(p, res, atoms, "dihedral", TRUE);
+ bFound = (dih[ndih].a[k] != NO_ATID);
+ }
+ for (m = 0; m < MAXFORCEPARAM; m++)
+ {
+ dih[ndih].c[m] = NOTSET;
}
- dih[ndih].a[k] = search_res_atom(p, res, atoms, "dihedral", TRUE);
- bFound = (dih[ndih].a[k] != NO_ATID);
- }
- for (m = 0; m < MAXFORCEPARAM; m++)
- {
- dih[ndih].c[m] = NOTSET;
- }
- if (bFound)
- {
- set_p_string(&(dih[ndih]), hbdih->b[j].s);
- hbdih->b[j].match = TRUE;
- /* Incrementing ndih means we save this dihedral */
- ndih++;
+ if (bFound)
+ {
+ set_p_string(&(dih[ndih]), hbdih->b[j].s);
+ hbdih->b[j].match = TRUE;
+ /* Incrementing ndih means we save this dihedral */
+ ndih++;
+ }
}
}
}
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#define RTP_MAXCHAR 5
typedef struct {
- char gmx[6];
- char main[6];
- char nter[6];
- char cter[6];
- char bter[6];
+ char gmx[RTP_MAXCHAR+2];
+ char main[RTP_MAXCHAR+2];
+ char nter[RTP_MAXCHAR+2];
+ char cter[RTP_MAXCHAR+2];
+ char bter[RTP_MAXCHAR+2];
} rtprename_t;
while (get_a_line(fp, line, STRLEN))
{
srenew(rr, n+1);
- nc = sscanf(line, "%s %s %s %s %s %s",
- rr[n].gmx, rr[n].main, rr[n].nter, rr[n].cter, rr[n].bter, buf);
+ /* line is NULL-terminated and length<STRLEN, so final arg cannot overflow.
+ * For other args, we read up to 6 chars (so we can detect if the length is > 5).
+ * Note that the buffer length has been increased to 7 to allow this,
+ * so we just need to make sure the strings have zero-length initially.
+ */
+ rr[n].gmx[0] = '\0';
+ rr[n].main[0] = '\0';
+ rr[n].nter[0] = '\0';
+ rr[n].cter[0] = '\0';
+ rr[n].bter[0] = '\0';
+ nc = sscanf(line, "%6s %6s %6s %6s %6s %s",
+ rr[n].gmx, rr[n].main, rr[n].nter, rr[n].cter, rr[n].bter, buf);
+ if (strlen(rr[n].gmx) > RTP_MAXCHAR || strlen(rr[n].main) > RTP_MAXCHAR ||
+ strlen(rr[n].nter) > RTP_MAXCHAR || strlen(rr[n].cter) > RTP_MAXCHAR || strlen(rr[n].bter) > RTP_MAXCHAR)
+ {
+ gmx_fatal(FARGS, "Residue renaming database '%s' has strings longer than %d chars in first 5 columns:\n%s",
+ fname, RTP_MAXCHAR, line);
+ }
+
if (ncol == 0)
{
if (nc != 2 && nc != 5)
ir->epsilon_r = 1.0;
}
+ if (ir->epsilon_r == 0)
+ {
+ sprintf(err_buf,
+ "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
+ "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
+ CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
+ }
+
if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
{
sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
*
* 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.
push_bond(d, plist, mi0->plist, &(mi0->atoms), atype, pline, FALSE,
bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
break;
+ case d_pairs_nb:
+ push_bond(d, plist, mi0->plist, &(mi0->atoms), atype, pline, FALSE,
+ FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
+ break;
case d_vsites2:
case d_vsites3:
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, 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.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * 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 "config.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#ifdef GMX_LIB_MPI
#include "gromacs/utility/gmxmpi.h"
else
{
#ifdef GMX_FAHCORE
- (void) fah_MPI_Init(argc, argv);
+ fah_MPI_Init(argc, argv);
#else
- (void) MPI_Init(argc, argv);
+# ifdef GMX_OPENMP
+ /* Formally we need to use MPI_Init_thread and ask for MPI_THREAD_FUNNELED
+ * level of thread support when using OpenMP. However, in practice we
+ * have never seen any problems with just using MPI_Init(), and some MPI
+ * versions that only return MPI_THREAD_SINGLE as their support level
+ * still return an OK initialization code when we request MPI_THREAD_FUNNELED.
+ *
+ * To avoid requiring users to recompile and install new libraries for something
+ * that probably isn't a problem, we don't make a fuss about it (no warning)
+ * if MPI_Init_thread() returns ok. If it does not return OK we
+ * call a second init call without thread support, but since the library
+ * apparently tried to prevent this we do issue a warning in this case.
+ *
+ * support, and if that doesn't work we simply use the simple MPI_Init().
+ * Note that MPICH does not allow us to call MPI_Query_thread() before
+ * we have initialized the library, and calling MPI_Init twice could
+ * be a bit fragile. However, some implementations also advice against
+ * doing anything else after calling MPI_Finalize, so at the end of the
+ * day we'll have to cross our fingers...
+ */
+ int provided, rc;
+ rc = MPI_Init_thread(argc, argv, MPI_THREAD_FUNNELED, &provided);
+ if (rc != 0 && provided < MPI_THREAD_FUNNELED)
+ {
+ gmx_warning("GROMACS was compiled with OpenMP support, but there is no thread support in the MPI library. Keep your fingers crossed.");
+ MPI_Init(argc, argv);
+ }
+# else
+ MPI_Init(argc, argv);
+# endif
#endif
}
// Bump the counter to record this initialization event
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015, 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.
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
- if (nmultisim > 1)
+ if (nmultisim >= 1)
{
#ifndef GMX_THREAD_MPI
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
- gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library. "
- "Please compile GROMACS with MPI support");
+ gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
+ "Please compile GROMACS with a proper external MPI library.");
#endif
}
if (fplog != NULL)
{
/* Print references after all software/hardware printing */
+ please_cite(fplog, "Pall2015");
+ please_cite(fplog, "Pronk2013");
please_cite(fplog, "Hess2008b");
please_cite(fplog, "Spoel2005a");
please_cite(fplog, "Lindahl2001a");
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff