#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 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.
.. |Gromacs| replace:: GROMACS
.. _gmx-manual: manual-{gmx_version_string}.pdf
.. _gmx-manual-parent-dir: ../manual-{gmx_version_string}.pdf
-.. |gmx-source-package| replace:: ftp://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
+.. |gmx-source-package-ftp| replace:: As ftp ftp://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
+.. |gmx-source-package-http| replace:: As http http://ftp.gromacs.org/pub/gromacs/gromacs-{gmx_version_string}.tar.gz
.. |gmx-regressiontests-package| replace:: http://gerrit.gromacs.org/download/regressiontests-{regressiontest_version}.tar.gz
.. _up-to-date installation instructions: http://www.gromacs.org/Documentation/Installation_Instructions
.. _CUDA: http://www.nvidia.com/object/cuda_home_new.html
Source code
-----------
-* |gmx-source-package|
+* |gmx-source-package-ftp|
+* |gmx-source-package-http|
* (md5sum |SOURCE_MD5SUM|)
Other source code versions may be found at the
force constants in kJ/mol/rad$^2$.
\begin{figure}
-\centerline{\includegraphics[width=8cm]{plots/f-imps}}
+\centerline{\includegraphics[width=10cm]{plots/f-imps.pdf}}
\caption{Improper dihedral potential.}
\label{fig:imps}
\end{figure}
statistically noisy in most cases. This behavior can be overwritten
by using the mdp option {\tt sc-coul} to {\tt yes}. Note that the {\tt sc-coul}
is only taken into account when lambda states are used, not with
-{\tt couple-lambda0/couple-lambda1}, and you can still turn off soft-core
+{\tt couple-lambda0}~/ {\tt couple-lambda1}, and you can still turn off soft-core
interactions by setting {\tt sc-alpha=0}. Additionally, the soft-core
interaction potential is only applied when either the A or B
state has zero interaction potential. If both A and B states have
electrostatic interaction such as PME grid dimensions and cut-off radii.
This is particularly relevant to do before launching long production runs.
-{\gromacs} includes a special tool, {\tt g_tune_pme}, which automates the
-process of selecting the optimal size of the grid and number of PME-only
-notes.
-
-%
-% Temporarily removed since I am not sure about the state of the testlr
-% program...
-%
-%It is possible to test the accuracy of your settings using the program
-%{\tt\normindex{testlr}} in the {\tt src/gmxlib} dir. This program computes
-%forces and potentials using PPPM and an Ewald implementation and gives the
-%absolute and RMS errors in both:
-%\begin{verbatim}
-%ERROR ANALYSIS
-%Error: Max Abs RMS
-%Force 1.132 0.251
-%Potential 0.113 0.035
-%\end{verbatim}
-%{\bf Note:} these numbers were generated using a grid spacing of
-%0.058 nm and $r_c$ = 1.0 nm.
-%
-%You can see what the accuracy is without optimizing the
-%$\hat{G}(k)$ function, if you pass the {\tt -ghat} option to {\tt
-%testlr}. Try it if you think the {\tt mk_ghat} procedure is a waste
-%of time.
-%} % Brace matches ifthenelse test for gmxlite
-
+{\tt gmx mdrun} will automatically do a lot of PME optimization, and
+{\gromacs} also includes a special tool, {\tt gmx tune_pme}, which
+automates the process of selecting the optimal number of PME-only ranks.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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t_bond_atomtype bat, char *line,
warninp_t wi)
{
- const char *formal = "%s%s%s%s%s%s%s%s";
+ const char *formal = "%s%s%s%s%s%s%s%s%n";
int i, ft, ftype, nn, nrfp, nrfpA, nrfpB;
- int start;
+ int start, nchar_consumed;
int nxcmap, nycmap, ncmap, read_cmap, sl, nct;
char s[20], alc[MAXATOMLIST+2][20];
t_param p;
read_cmap = 0;
start = 0;
- if ((nn = sscanf(line, formal, alc[0], alc[1], alc[2], alc[3], alc[4], alc[5], alc[6], alc[7])) != nral+3)
+ GMX_ASSERT(nral == 5, "CMAP requires 5 atoms per interaction");
+
+ /* Here we can only check for < 8 */
+ if ((nn = sscanf(line, formal, alc[0], alc[1], alc[2], alc[3], alc[4], alc[5], alc[6], alc[7], &nchar_consumed)) < nral+3)
{
sprintf(errbuf, "Incorrect number of atomtypes for cmap (%d instead of 5)", nn-1);
warning_error(wi, errbuf);
return;
}
-
- /* Compute an offset for each line where the cmap parameters start
- * ie. where the atom types and grid spacing information ends
- */
- for (i = 0; i < nn; i++)
- {
- start += (int)strlen(alc[i]);
- }
-
- /* There are nn-1 spaces between the atom types and the grid spacing info in the cmap.itp file */
- /* start is the position on the line where we start to read the actual cmap grid data from the itp file */
- start = start + nn -1;
+ start += nchar_consumed;
ft = strtol(alc[nral], NULL, 10);
nxcmap = strtol(alc[nral+1], NULL, 10);
return FALSE;
}
- if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
- {
- /* LJ PME with LB combination rule does 7 mesh operations.
- * This so slow that we don't compile GPU non-bonded kernels for that.
- */
- md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with GPUs, falling back to CPU only\n");
- return FALSE;
- }
-
return TRUE;
}
*/
static void split_sci_entry(nbnxn_pairlist_t *nbl,
int nsp_target_av,
- gmx_bool progBal, int nsp_tot_est,
+ gmx_bool progBal, float nsp_tot_est,
int thread, int nthread)
{
- int nsp_est;
int nsp_max;
int cj4_start, cj4_end, j4len;
int sci;
if (progBal)
{
+ float nsp_est;
+
/* Estimate the total numbers of ci's of the nblist combined
* over all threads using the target number of ci's.
*/
* The last ci blocks should be smaller, to improve load balancing.
* The factor 3/2 makes the first block 3/2 times the target average
* and ensures that the total number of blocks end up equal to
- * that with of equally sized blocks of size nsp_target_av.
+ * that of equally sized blocks of size nsp_target_av.
*/
- nsp_max = nsp_target_av*nsp_tot_est*3/(2*(nsp_est + nsp_tot_est));
+ nsp_max = static_cast<int>(nsp_target_av*(nsp_tot_est*1.5/(nsp_est + nsp_tot_est)));
}
else
{
/* Clost this super/sub list i entry */
static void close_ci_entry_supersub(nbnxn_pairlist_t *nbl,
int nsp_max_av,
- gmx_bool progBal, int nsp_tot_est,
+ gmx_bool progBal, float nsp_tot_est,
int thread, int nthread)
{
/* All content of the new ci entry have already been filled correctly,
real rlist,
int min_ci_balanced,
int *nsubpair_target,
- int *nsubpair_tot_est)
+ float *nsubpair_tot_est)
{
/* The target value of 36 seems to be the optimum for Kepler.
* Maxwell is less sensitive to the exact value.
grid = &nbs->grid[0];
+ /* We don't need to balance list sizes if:
+ * - We didn't request balancing.
+ * - The number of grid cells >= the number of lists requested,
+ * since we will always generate at least #cells lists.
+ * - We don't have any cells, since then there won't be any lists.
+ */
if (min_ci_balanced <= 0 || grid->nc >= min_ci_balanced || grid->nc == 0)
{
- /* We don't need to balance the list sizes */
+ /* nsubpair_target==0 signals no balancing */
*nsubpair_target = 0;
*nsubpair_tot_est = 0;
gmx_bool bFBufferFlag,
int nsubpair_max,
gmx_bool progBal,
- int nsubpair_tot_est,
+ float nsubpair_tot_est,
int th, int nth,
nbnxn_pairlist_t *nbl,
t_nblist *nbl_fep)
nbnxn_grid_t *gridi, *gridj;
gmx_bool bGPUCPU;
int nzi, zj0, zj1;
- int nsubpair_target, nsubpair_tot_est;
+ int nsubpair_target;
+ float nsubpair_tot_est;
int nnbl;
nbnxn_pairlist_t **nbl;
int ci_block;
*
* 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.
* Turn this on when we have multiple acceleration groups
* or one accelerated group.
*/
- ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
+ ekind->bNEMD = (opts->ngacc > 1 || norm2(opts->acc[0]) > 0);
ekind->ngtc = opts->ngtc;
snew(ekind->tcstat, opts->ngtc);
}
}
+static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real ftol, real abstol)
+{
+ cmp_int(fp, "cmap ngrid", -1, cmap1->ngrid, cmap2->ngrid);
+ cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
+ if (cmap1->ngrid == cmap2->ngrid &&
+ cmap1->grid_spacing == cmap2->grid_spacing)
+ {
+ int g;
+
+ for (g = 0; g < cmap1->ngrid; g++)
+ {
+ int i;
+
+ fprintf(fp, "comparing cmap %d\n", g);
+
+ for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
+ {
+ cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], ftol, abstol);
+ }
+ }
+ }
+}
+
static void cmp_idef(FILE *fp, t_idef *id1, t_idef *id2, real ftol, real abstol)
{
int i;
id1->iparams[i], id2->iparams[i], ftol, abstol);
}
cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol);
+ cmp_cmap(fp, &id1->cmap_grid, &id2->cmap_grid, ftol, abstol);
for (i = 0; (i < F_NRE); i++)
{
cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i]));
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff